The flight of white-collars: Civil conflict, availability of medical service providers and public health.

PubMed

Kıbrıs, Arzu; Metternich, Nils

2016-01-01

Civil conflicts devastate public health both in the short run and in the long run. Analyzing novel data sets that include yearly information on public health and the availability of health professionals across provinces in Turkey in the 1964-2010 period, we provide empirical evidence for our theoretical argument that a major mechanism through which civil conflicts exert their long term negative influences on public health is by discouraging medical personnel to practice in conflict regions. We also assess the effectiveness of certain policy measures that Turkish governments have tried out over the years to counteract this mechanism. Our results reveal that the long running civil conflict in Turkey has been driving away doctors and other highly trained medical personnel from conflict areas and that mandatory service requirements do help counteract this flight. Copyright © 2015 Elsevier Ltd. All rights reserved.

Interaction of arch type and footwear on running mechanics.

PubMed

Butler, Robert J; Davis, Irene S; Hamill, Joseph

2006-12-01

Running shoes are designed to accommodate various arch types to reduce the risk of lower extremity injuries sustained during running. Yet little is known about the biomechanical changes of running in the recommended footwear that may allow for a reduction in injuries. To evaluate the effects of motion control and cushion trainer shoes on running mechanics in low- and high-arched runners. Controlled laboratory study. Twenty high-arched and 20 low-arched recreational runners (>10 miles per week) were recruited for the study. Three-dimensional kinematic and kinetics were collected as subjects ran at 3.5 ms(-1) +/- 5% along a 25-m runway. The motion control shoe evaluated was the New Balance 1122, and the cushioning shoe evaluated was the New Balance 1022. Repeated-measures analyses of variance were used to determine if low- and high-arched runners responded differently to motion control and cushion trainer shoes. A significant interaction was observed in the instantaneous loading rate such that the low-arched runners had a lower instantaneous loading rate in the motion control condition, and the high-arched runners had a lower instantaneous loading rate in the cushion trainer condition. Significant main effects for shoe were observed for peak positive tibial acceleration, peak-to-peak tibial acceleration, mean loading rate, peak eversion, and eversion excursion. These results suggest that motion control shoes control rearfoot motion better than do cushion trainer shoes. In addition, cushion trainer shoes attenuate shock better than motion control shoes do. However, with the exception of instantaneous loading rate, these benefits do not differ between arch type. Running footwear recommendations should be based on an individual's running mechanics. If a mechanical analysis is not available, footwear recommendations can be based empirically on the individual's arch type.

Lg Attenuation Anisotropy Across the Western US

NASA Astrophysics Data System (ADS)

Phillips, W. S.; Rowe, C. A.; Stead, R. J.; Begnaud, M. L.

2017-12-01

The USArray has allowed us to map seismic attenuation of local and regional phases to unprecedented spatial extent and resolution. Following standard mantle Pn velocity anisotropy methods, we have incorporated azimuthal anisotropy into our tomographic inversion of high-frequency Lg amplitudes. The Lg is a crustal shear phase made up of many trapped modes, thus results can be considered to be crustal averages. Azimuthal anisotropy reduces residual variance by just over 10% for 1.5-3 Hz Lg. We observe a median anisotropic variation of 12%, and a high of 50% in the Salton Trough. Low attenuation (high-Q) directions run parallel to topographic fabric and major strike slip faults in tectonically active areas, and often run parallel to mantle shear wave splitting directions in stable regions. Tradeoffs are of concern, and synthetic tests show that elongated attenuation anomalies will produce anisotropy artifacts, but of factors 2-3 times lower than observations. In particular, the strength of a long, narrow high-Q anomaly will trade off with high-Q directions parallel to the long axis, while an elongated low-Q anomaly will trade off with high-Q directions perpendicular to the long axis. We observe an elongated low-Q anomaly associated with the Walker Lane; however, observed high-Q directions run parallel to the long axis of this anomaly, opposite to the tradeoff effect, supporting the anisotropic observation, and implying that the effect may be underestimated. Further, we observe an elongated high-Q anomaly associated with the Great Valley and Sierra Nevada that runs across the long axis, again opposite to the tradeoff effect. This study was performed using waveforms, event locations and phase picks made available by IRIS, NEIC and ANF, and processing was done using semi-automated means, thus this is a technique that can be applied quickly to study crustal anisotropy over large areas when appropriate station density is available.

Barefoot running: does it prevent injuries?

PubMed

Murphy, Kelly; Curry, Emily J; Matzkin, Elizabeth G

2013-11-01

Endurance running has evolved over the course of millions of years and it is now one of the most popular sports today. However, the risk of stress injury in distance runners is high because of the repetitive ground impact forces exerted. These injuries are not only detrimental to the runner, but also place a burden on the medical community. Preventative measures are essential to decrease the risk of injury within the sport. Common running injuries include patellofemoral pain syndrome, tibial stress fractures, plantar fasciitis, and Achilles tendonitis. Barefoot running, as opposed to shod running (with shoes), has recently received significant attention in both the media and the market place for the potential to promote the healing process, increase performance, and decrease injury rates. However, there is controversy over the use of barefoot running to decrease the overall risk of injury secondary to individual differences in lower extremity alignment, gait patterns, and running biomechanics. While barefoot running may benefit certain types of individuals, differences in running stance and individual biomechanics may actually increase injury risk when transitioning to barefoot running. The purpose of this article is to review the currently available clinical evidence on barefoot running and its effectiveness for preventing injury in the runner. Based on a review of current literature, barefoot running is not a substantiated preventative running measure to reduce injury rates in runners. However, barefoot running utility should be assessed on an athlete-specific basis to determine whether barefoot running will be beneficial.

How to keep the Grid full and working with ATLAS production and physics jobs

NASA Astrophysics Data System (ADS)

Pacheco Pagés, A.; Barreiro Megino, F. H.; Cameron, D.; Fassi, F.; Filipcic, A.; Di Girolamo, A.; González de la Hoz, S.; Glushkov, I.; Maeno, T.; Walker, R.; Yang, W.; ATLAS Collaboration

2017-10-01

The ATLAS production system provides the infrastructure to process millions of events collected during the LHC Run 1 and the first two years of Run 2 using grid, clouds and high performance computing. We address in this contribution the strategies and improvements that have been implemented to the production system for optimal performance and to achieve the highest efficiency of available resources from operational perspective. We focus on the recent developments.

Achieving behavioral control with millisecond resolution in a high-level programming environment.

PubMed

Asaad, Wael F; Eskandar, Emad N

2008-08-30

The creation of psychophysical tasks for the behavioral neurosciences has generally relied upon low-level software running on a limited range of hardware. Despite the availability of software that allows the coding of behavioral tasks in high-level programming environments, many researchers are still reluctant to trust the temporal accuracy and resolution of programs running in such environments, especially when they run atop non-real-time operating systems. Thus, the creation of behavioral paradigms has been slowed by the intricacy of the coding required and their dissemination across labs has been hampered by the various types of hardware needed. However, we demonstrate here that, when proper measures are taken to handle the various sources of temporal error, accuracy can be achieved at the 1 ms time-scale that is relevant for the alignment of behavioral and neural events.

Framework for architecture-independent run-time reconfigurable applications

NASA Astrophysics Data System (ADS)

Lehn, David I.; Hudson, Rhett D.; Athanas, Peter M.

2000-10-01

Configurable Computing Machines (CCMs) have emerged as a technology with the computational benefits of custom ASICs as well as the flexibility and reconfigurability of general-purpose microprocessors. Significant effort from the research community has focused on techniques to move this reconfigurability from a rapid application development tool to a run-time tool. This requires the ability to change the hardware design while the application is executing and is known as Run-Time Reconfiguration (RTR). Widespread acceptance of run-time reconfigurable custom computing depends upon the existence of high-level automated design tools. Such tools must reduce the designers effort to port applications between different platforms as the architecture, hardware, and software evolves. A Java implementation of a high-level application framework, called Janus, is presented here. In this environment, developers create Java classes that describe the structural behavior of an application. The framework allows hardware and software modules to be freely mixed and interchanged. A compilation phase of the development process analyzes the structure of the application and adapts it to the target platform. Janus is capable of structuring the run-time behavior of an application to take advantage of the memory and computational resources available.

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

Boyd, J.; Herner, K.; Jayatilaka, B.

The Fermilab Tevatron collider's data-taking run ended in September 2011, yielding a dataset with rich scientific potential. The CDF and DO experiments each have nearly 9 PB of collider and simulated data stored on tape. A large computing infrastructure consisting of tape storage, disk cache, and distributed grid computing for physics analysis with the Tevatron data is present at Fermilab. The Fermilab Run II data preservation project intends to keep this analysis capability sustained through the year 2020 or beyond. To achieve this, we are implementing a system that utilizes virtualization, automated validation, and migration to new standards in bothmore » software and data storage technology as well as leveraging resources available from currently-running experiments at Fermilab. Furthermore, these efforts will provide useful lessons in ensuring long-term data access for numerous experiments throughout high-energy physics, and provide a roadmap for high-quality scientific output for years to come.« less

Achieving behavioral control with millisecond resolution in a high-level programming environment

PubMed Central

Asaad, Wael F.; Eskandar, Emad N.

2008-01-01

The creation of psychophysical tasks for the behavioral neurosciences has generally relied upon low-level software running on a limited range of hardware. Despite the availability of software that allows the coding of behavioral tasks in high-level programming environments, many researchers are still reluctant to trust the temporal accuracy and resolution of programs running in such environments, especially when they run atop non-real-time operating systems. Thus, the creation of behavioral paradigms has been slowed by the intricacy of the coding required and their dissemination across labs has been hampered by the various types of hardware needed. However, we demonstrate here that, when proper measures are taken to handle the various sources of temporal error, accuracy can be achieved at the one millisecond time-scale that is relevant for the alignment of behavioral and neural events. PMID:18606188

Data preservation at the Fermilab Tevatron

DOE PAGES

Boyd, J.; Herner, K.; Jayatilaka, B.; ...

2015-12-23

The Fermilab Tevatron collider's data-taking run ended in September 2011, yielding a dataset with rich scientific potential. The CDF and DO experiments each have nearly 9 PB of collider and simulated data stored on tape. A large computing infrastructure consisting of tape storage, disk cache, and distributed grid computing for physics analysis with the Tevatron data is present at Fermilab. The Fermilab Run II data preservation project intends to keep this analysis capability sustained through the year 2020 or beyond. To achieve this, we are implementing a system that utilizes virtualization, automated validation, and migration to new standards in bothmore » software and data storage technology as well as leveraging resources available from currently-running experiments at Fermilab. Furthermore, these efforts will provide useful lessons in ensuring long-term data access for numerous experiments throughout high-energy physics, and provide a roadmap for high-quality scientific output for years to come.« less

Data preservation at the Fermilab Tevatron

NASA Astrophysics Data System (ADS)

Boyd, J.; Herner, K.; Jayatilaka, B.; Roser, R.; Sakumoto, W.

2015-12-01

The Fermilab Tevatron collider's data-taking run ended in September 2011, yielding a dataset with rich scientific potential. The CDF and DO experiments each have nearly 9 PB of collider and simulated data stored on tape. A large computing infrastructure consisting of tape storage, disk cache, and distributed grid computing for physics analysis with the Tevatron data is present at Fermilab. The Fermilab Run II data preservation project intends to keep this analysis capability sustained through the year 2020 or beyond. To achieve this, we are implementing a system that utilizes virtualization, automated validation, and migration to new standards in both software and data storage technology as well as leveraging resources available from currently-running experiments at Fermilab. These efforts will provide useful lessons in ensuring long-term data access for numerous experiments throughout high-energy physics, and provide a roadmap for high-quality scientific output for years to come.

A cross-sectional study of the effects of load carriage on running characteristics and tibial mechanical stress: implications for stress fracture injuries in women

DTIC Science & Technology

2017-03-23

performance computing resources made available by the US Department of Defense High Performance Computing Modernization Program at the Air Force...1Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, United...States Army Medical Research and Materiel Command, Fort Detrick, Maryland, USA Full list of author information is available at the end of the article

28 CFR 544.34 - Inmate running events.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 28 Judicial Administration 2 2010-07-01 2010-07-01 false Inmate running events. 544.34 Section 544... EDUCATION Inmate Recreation Programs § 544.34 Inmate running events. Running events will ordinarily not... available for all inmate running events. ...

28 CFR 544.34 - Inmate running events.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 28 Judicial Administration 2 2012-07-01 2012-07-01 false Inmate running events. 544.34 Section 544... EDUCATION Inmate Recreation Programs § 544.34 Inmate running events. Running events will ordinarily not... available for all inmate running events. ...

28 CFR 544.34 - Inmate running events.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 28 Judicial Administration 2 2013-07-01 2013-07-01 false Inmate running events. 544.34 Section 544... EDUCATION Inmate Recreation Programs § 544.34 Inmate running events. Running events will ordinarily not... available for all inmate running events. ...

28 CFR 544.34 - Inmate running events.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 28 Judicial Administration 2 2014-07-01 2014-07-01 false Inmate running events. 544.34 Section 544... EDUCATION Inmate Recreation Programs § 544.34 Inmate running events. Running events will ordinarily not... available for all inmate running events. ...

28 CFR 544.34 - Inmate running events.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 28 Judicial Administration 2 2011-07-01 2011-07-01 false Inmate running events. 544.34 Section 544... EDUCATION Inmate Recreation Programs § 544.34 Inmate running events. Running events will ordinarily not... available for all inmate running events. ...

ChronQC: a quality control monitoring system for clinical next generation sequencing.

PubMed

Tawari, Nilesh R; Seow, Justine Jia Wen; Perumal, Dharuman; Ow, Jack L; Ang, Shimin; Devasia, Arun George; Ng, Pauline C

2018-05-15

ChronQC is a quality control (QC) tracking system for clinical implementation of next-generation sequencing (NGS). ChronQC generates time series plots for various QC metrics to allow comparison of current runs to historical runs. ChronQC has multiple features for tracking QC data including Westgard rules for clinical validity, laboratory-defined thresholds and historical observations within a specified time period. Users can record their notes and corrective actions directly onto the plots for long-term recordkeeping. ChronQC facilitates regular monitoring of clinical NGS to enable adherence to high quality clinical standards. ChronQC is freely available on GitHub (https://github.com/nilesh-tawari/ChronQC), Docker (https://hub.docker.com/r/nileshtawari/chronqc/) and the Python Package Index. ChronQC is implemented in Python and runs on all common operating systems (Windows, Linux and Mac OS X). tawari.nilesh@gmail.com or pauline.c.ng@gmail.com. Supplementary data are available at Bioinformatics online.

PPC750 Performance Monitor

NASA Technical Reports Server (NTRS)

Meyer, Donald; Uchenik, Igor

2007-01-01

The PPC750 Performance Monitor (Perfmon) is a computer program that helps the user to assess the performance characteristics of application programs running under the Wind River VxWorks real-time operating system on a PPC750 computer. Perfmon generates a user-friendly interface and collects performance data by use of performance registers provided by the PPC750 architecture. It processes and presents run-time statistics on a per-task basis over a repeating time interval (typically, several seconds or minutes) specified by the user. When the Perfmon software module is loaded with the user s software modules, it is available for use through Perfmon commands, without any modification of the user s code and at negligible performance penalty. Per-task run-time performance data made available by Perfmon include percentage time, number of instructions executed per unit time, dispatch ratio, stack high water mark, and level-1 instruction and data cache miss rates. The performance data are written to a file specified by the user or to the serial port of the computer

Effects of acute voluntary loaded wheel running on BDNF expression in the rat hippocampus.

PubMed

Lee, Minchul; Soya, Hideaki

2017-12-31

Voluntary loaded wheel running involves the use of a load during a voluntary running activity. A muscle-strength or power-type activity performed at a relatively high intensity and a short duration may cause fewer apparent metabolic adaptations but may still elicit muscle fiber hypertrophy. This study aimed to determine the effects of acute voluntary wheel running with an additional load on brain-derived neurotrophic factor (BDNF) expression in the rat hippocampus. Ten-week old male Wistar rats were assigned randomly to a (1) sedentary (Control) group; (2) voluntary exercise with no load (No-load) group; or (3) voluntary exercise with an additional load (Load) group for 1-week (acute period). The expression of BDNF genes was quantified by real-time PCR. The average distance levels were not significantly different in the No-load and Load groups. However, the average work levels significantly increased in the Load group. The relative soleus weights were greater in the No-load group. Furthermore, loaded wheel running up-regulated the BDNF mRNA level compared with that in the Control group. The BDNF mRNA levels showed a positive correlation with workload levels (r=0.75), suggesting that the availability of multiple workload levels contributes to the BDNF-related benefits of loaded wheel running noted in this study. This novel approach yielded the first set of findings showing that acute voluntary loaded wheel running, which causes muscular adaptation, enhanced BDNF expression, suggesting a possible role of high-intensity short-term exercise in hippocampal BDNF activity. ©2017 The Korean Society for Exercise Nutrition

Measurements of rearfoot motion during running.

PubMed

Milani, T L; Hennig, E M

2000-09-01

Excessive rearfoot motion is an important factor that has been linked to the development of injuries in running. Therefore, extensive research has been performed that to investigate the movement of the foot and factors that influence the degree of rearfoot motion. Several methodological procedures are available that indirectly determine the degree of rearfoot movement. High-speed film, high-speed video and opto-electric techniques have been used to analyse the posterior aspect of the heel counter of the shoe in the frontal plane to determine rearfoot motion at ground contact on a treadmill or during overground running. Recent studies used invasive pin methods to determine rearfoot motion during running under different conditions. Using a non-invasive approach, electrogoniometers have been used to quantify rearfoot motion. The purpose of this study was to explore the use of an in-shoe electrogoniometric method to investigate rearfoot motion during running in different running shoes. The results showed that rearfoot motion variables were lower using the in-shoe goniometer compared to a heel counter method. This confirms previous bone pin studies where significant lower eversion and eversion velocity values were revealed by the bone pins compared to the shoe counter markers. Thus, external measurements seem to overestimate rearfoot motion significantly. On the other hand, the in-shoe measurements revealed slightly lower GRF related values. As with any other shoe insert, an in-shoe device elevates the foot slightly and thus may influence the mechanical behaviour of the shoe.

Cake: a bioinformatics pipeline for the integrated analysis of somatic variants in cancer genomes

PubMed Central

Rashid, Mamunur; Robles-Espinoza, Carla Daniela; Rust, Alistair G.; Adams, David J.

2013-01-01

Summary: We have developed Cake, a bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone. Cake can be run on a high-performance computer cluster or used as a stand-alone application. Availabilty: Cake is open-source and is available from http://cakesomatic.sourceforge.net/ Contact: da1@sanger.ac.uk Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:23803469

Developing an Integrated Model Framework for the Assessment of Sustainable Agricultural Residue Removal Limits for Bioenergy Systems

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

David Muth, Jr.; Jared Abodeely; Richard Nelson

Agricultural residues have significant potential as a feedstock for bioenergy production, but removing these residues can have negative impacts on soil health. Models and datasets that can support decisions about sustainable agricultural residue removal are available; however, no tools currently exist capable of simultaneously addressing all environmental factors that can limit availability of residue. The VE-Suite model integration framework has been used to couple a set of environmental process models to support agricultural residue removal decisions. The RUSLE2, WEPS, and Soil Conditioning Index models have been integrated. A disparate set of databases providing the soils, climate, and management practice datamore » required to run these models have also been integrated. The integrated system has been demonstrated for two example cases. First, an assessment using high spatial fidelity crop yield data has been run for a single farm. This analysis shows the significant variance in sustainably accessible residue across a single farm and crop year. A second example is an aggregate assessment of agricultural residues available in the state of Iowa. This implementation of the integrated systems model demonstrates the capability to run a vast range of scenarios required to represent a large geographic region.« less

An Innovative Running Wheel-based Mechanism for Improved Rat Training Performance.

PubMed

Chen, Chi-Chun; Yang, Chin-Lung; Chang, Ching-Ping

2016-09-19

This study presents an animal mobility system, equipped with a positioning running wheel (PRW), as a way to quantify the efficacy of an exercise activity for reducing the severity of the effects of the stroke in rats. This system provides more effective animal exercise training than commercially available systems such as treadmills and motorized running wheels (MRWs). In contrast to an MRW that can only achieve speeds below 20 m/min, rats are permitted to run at a stable speed of 30 m/min on a more spacious and high-density rubber running track supported by a 15 cm wide acrylic wheel with a diameter of 55 cm in this work. Using a predefined adaptive acceleration curve, the system not only reduces the operator error but also trains the rats to run persistently until a specified intensity is reached. As a way to evaluate the exercise effectiveness, real-time position of a rat is detected by four pairs of infrared sensors deployed on the running wheel. Once an adaptive acceleration curve is initiated using a microcontroller, the data obtained by the infrared sensors are automatically recorded and analyzed in a computer. For comparison purposes, 3 week training is conducted on rats using a treadmill, an MRW and a PRW. After surgically inducing middle cerebral artery occlusion (MCAo), modified neurological severity scores (mNSS) and an inclined plane test were conducted to assess the neurological damages to the rats. PRW is experimentally validated as the most effective among such animal mobility systems. Furthermore, an exercise effectiveness measure, based on rat position analysis, showed that there is a high negative correlation between the effective exercise and the infarct volume, and can be employed to quantify a rat training in any type of brain damage reduction experiments.

Considerations for initiating and progressing running programs in obese individuals.

PubMed

Vincent, Heather K; Vincent, Kevin R

2013-06-01

Running has rapidly increased in popularity and elicits numerous health benefits, including weight loss. At present, no practical guidelines are available for obese persons who wish to start a running program. This article is a narrative review of the emerging evidence of the musculoskeletal factors to consider in obese patients who wish to initiate a running program and increase its intensity. Main program goals should include gradual weight loss, avoidance of injury, and enjoyment of the exercise. Pre-emptive strengthening exercises can improve the strength of the foot and ankle, hip abductor, quadriceps, and trunk to help support the joints bearing the loads before starting a running program. Depending on the presence of comorbid joint pain, nonimpact exercise or walking (on a flat surface, on an incline, and at high intensity) can be used to initiate the program. For progression to running, intensity or mileage increases should be slow and consistent to prevent musculoskeletal injury. A stepwise transition to running at a rate not exceeding 5%-10% of weekly mileage or duration is reasonable for this population. Intermittent walk-jog programs are also attractive for persons who are not able to sustain running for a long period. Musculoskeletal pain should neither carry over to the next day nor be increased the day after exercising. Rest days in between running sessions may help prevent overuse injury. Patients who have undergone bariatric surgery and are now lean can also run, but special foci such as hydration and energy replacement must be considered. In summary, obese persons can run for exercise, provided they follow conservative transitions and progression, schedule rest days, and heed onset of pain symptoms. Copyright © 2013 American Academy of Physical Medicine and Rehabilitation. Published by Elsevier Inc. All rights reserved.

An approach to combining parallel and cross-over trials with and without run-in periods using individual patient data.

PubMed

Tvete, Ingunn F; Olsen, Inge C; Fagerland, Morten W; Meland, Nils; Aldrin, Magne; Smerud, Knut T; Holden, Lars

2012-04-01

In active run-in trials, where patients may be excluded after a run-in period based on their response to the treatment, it is implicitly assumed that patients have individual treatment effects. If individual patient data are available, active run-in trials can be modelled using patient-specific random effects. With more than one trial on the same medication available, one can obtain a more precise overall treatment effect estimate. We present a model for joint analysis of a two-sequence, four-period cross-over trial (AABB/BBAA) and a three-sequence, two-period active run-in trial (AB/AA/A), where the aim is to investigate the effect of a new treatment for patients with pain due to osteoarthritis. Our approach enables us to separately estimate the direct treatment effect for all patients, for the patients excluded after the active run-in trial prior to randomisation, and for the patients who completed the active run-in trial. A similar model approach can be used to analyse other types of run-in trials, but this depends on the data and type of other trials available. We assume equality of the various carry-over effects over time. The proposed approach is flexible and can be modified to handle other designs. Our results should be encouraging for those responsible for planning cost-efficient clinical development programmes.

The biomechanical differences between barefoot and shod distance running: a systematic review and preliminary meta-analysis.

PubMed

Hall, Jonathan P L; Barton, Christian; Jones, Paul Remy; Morrissey, Dylan

2013-12-01

Distance running continues to experience increased participation in the Western world, although it is associated with high injury rates. Barefoot running has been increasingly proposed as a means to prevent overuse injury due to various biomechanical differences, including reduced joint loading rates and altered kinematics and muscle activity patterns compared to shod running. The aim of this review was to systematically evaluate biomechanical differences between running barefoot and shod, including the quality of available evidence, in order to provide guidance on the phenomenon of barefoot running to the running and sports medicine communities. A comprehensive search of MEDLINE, Web of Knowledge and EMBASE from inception to January 2013 was performed. Trials evaluating injury-free recreational or competitive adults who participate in long-distance running (≥5 km), where a comparison of barefoot and shod running lower-limb kinetics, kinematics and/or electromyography were included. Studies examining sprinting and studies of single-subject design were excluded. Following initial searching, two reviewers identified a shortlist of relevant studies based on title and abstract, with the full text of these studies being tested against the inclusion criteria. References of included studies were examined and citation tracking was performed in Web of Knowledge. Two independent reviewers evaluated the methodological quality of each included study using a modified version of the Downs and Black quality index. Results of the quality assessment were used to identify high- and low-quality studies, data pooling was completed where possible and levels of evidence were determined based on the van Tulder criteria. Eighteen studies were identified, all of low methodological quality. Effect size (ES) calculation was possible for 12 studies. Pooled results indicate moderate evidence that barefoot running is associated with reduced peak ground reaction force (GRF), increased foot and ankle plantarflexion and increased knee flexion at ground contact compared with running in a neutral shoe. Limited evidence indicates barefoot running is associated with reduced impact GRF, reduced peak knee flexion and varus joint moments, and a higher stride frequency compared to a neutral shoe. Very limited to limited evidence also indicates power absorption at the knee is decreased while being increased at the ankle whilst barefoot running. Additionally, the effects of barefoot running on loading rate appear dependent on strike pattern adopted, with a forefoot strike pattern found to reduce loading rate, whilst a rearfoot strike pattern increases loading rate when running barefoot compared to shod. Key methodological weaknesses that must be addressed in future research were identified. Of particular note were absence of investigator blinding, infrequent intervention randomisation, small sample sizes and lack of evaluation following habituation. Two studies could not be retrieved because of publication in a non-English-language journal. Of particular note is that the validity of the body of work is compromised by the lack of evaluation after habituation, or re-training, of previously shod rearfoot-striking runners to barefoot forefoot-striking running styles. There has been a great deal of publicity for barefoot running, and many claims made about its effects and risks. Despite a large amount of biomechanical data available for meta-analysis, clear guidance for clinical practice is limited because of the low methodological quality of the associated studies. Preliminary biomechanical differences identified suggest barefoot running may be associated with positive biomechanical changes in regards to injury prevention, although this may be dependent on strike pattern adopted. Further research employing more robust methodology, which addresses weaknesses highlighted in this review, is needed to confirm current preliminary evidence. Additionally, prospective research would have higher validity were the biomechanical effects of habituating to barefoot running fully examined alongside an evaluation of prevention of repetitive use injury.

Surface effects on dynamic stability and loading during outdoor running using wireless trunk accelerometry.

PubMed

Schütte, Kurt H; Aeles, Jeroen; De Beéck, Tim Op; van der Zwaard, Babette C; Venter, Rachel; Vanwanseele, Benedicte

2016-07-01

Despite frequently declared benefits of using wireless accelerometers to assess running gait in real-world settings, available research is limited. The purpose of this study was to investigate outdoor surface effects on dynamic stability and dynamic loading during running using tri-axial trunk accelerometry. Twenty eight runners (11 highly-trained, 17 recreational) performed outdoor running on three outdoor training surfaces (concrete road, synthetic track and woodchip trail) at self-selected comfortable running speeds. Dynamic postural stability (tri-axial acceleration root mean square (RMS) ratio, step and stride regularity, sample entropy), dynamic loading (impact and breaking peak amplitudes and median frequencies), as well as spatio-temporal running gait measures (step frequency, stance time) were derived from trunk accelerations sampled at 1024Hz. Results from generalized estimating equations (GEE) analysis showed that compared to concrete road, woodchip trail had several significant effects on dynamic stability (higher AP ratio of acceleration RMS, lower ML inter-step and inter-stride regularity), on dynamic loading (downward shift in vertical and AP median frequency), and reduced step frequency (p<0.05). Surface effects were unaffected when both running level and running speed were added as potential confounders. Results suggest that woodchip trails disrupt aspects of dynamic stability and loading that are detectable using a single trunk accelerometer. These results provide further insight into how runners adapt their locomotor biomechanics on outdoor surfaces in situ. Copyright © 2016 Elsevier B.V. All rights reserved.

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

Amerio, S.; Behari, S.; Boyd, J.

The Fermilab Tevatron collider's data-taking run ended in September 2011, yielding a dataset with rich scientific potential. The CDF and D0 experiments each have approximately 9 PB of collider and simulated data stored on tape. A large computing infrastructure consisting of tape storage, disk cache, and distributed grid computing for physics analysis with the Tevatron data is present at Fermilab. The Fermilab Run II data preservation project intends to keep this analysis capability sustained through the year 2020 and beyond. To achieve this goal, we have implemented a system that utilizes virtualization, automated validation, and migration to new standards inmore » both software and data storage technology and leverages resources available from currently-running experiments at Fermilab. Lastly, these efforts have also provided useful lessons in ensuring long-term data access for numerous experiments, and enable high-quality scientific output for years to come.« less

Performance of the LHCb RICH detectors during the LHC Run II

NASA Astrophysics Data System (ADS)

Papanestis, A.; D'Ambrosio, C.; LHCb RICH Collaboration

2017-12-01

The LHCb RICH system provides hadron identification over a wide momentum range (2-100 GeV/c). This detector system is key to LHCb's precision flavour physics programme, which has unique sensitivity to physics beyond the standard model. This paper reports on the performance of the LHCb RICH in Run II, following significant changes in the detector and operating conditions. The changes include the refurbishment of significant number of photon detectors, assembled using new vacuum technologies, and the removal of the aerogel radiator. The start of Run II of the LHC saw the beam energy increase to 6.5 TeV per beam and a new trigger strategy for LHCb with full online detector calibration. The RICH information has also been made available for all trigger streams in the High Level Trigger for the first time.

Data preservation at the Fermilab Tevatron

NASA Astrophysics Data System (ADS)

Amerio, S.; Behari, S.; Boyd, J.; Brochmann, M.; Culbertson, R.; Diesburg, M.; Freeman, J.; Garren, L.; Greenlee, H.; Herner, K.; Illingworth, R.; Jayatilaka, B.; Jonckheere, A.; Li, Q.; Naymola, S.; Oleynik, G.; Sakumoto, W.; Varnes, E.; Vellidis, C.; Watts, G.; White, S.

2017-04-01

The Fermilab Tevatron collider's data-taking run ended in September 2011, yielding a dataset with rich scientific potential. The CDF and D0 experiments each have approximately 9 PB of collider and simulated data stored on tape. A large computing infrastructure consisting of tape storage, disk cache, and distributed grid computing for physics analysis with the Tevatron data is present at Fermilab. The Fermilab Run II data preservation project intends to keep this analysis capability sustained through the year 2020 and beyond. To achieve this goal, we have implemented a system that utilizes virtualization, automated validation, and migration to new standards in both software and data storage technology and leverages resources available from currently-running experiments at Fermilab. These efforts have also provided useful lessons in ensuring long-term data access for numerous experiments, and enable high-quality scientific output for years to come.

Voluntary running of defined distances reduces body adiposity and its associated inflammation in C57BL/6 mice fed a high-fat diet.

PubMed

Yan, Lin; Sundaram, Sneha; Nielsen, Forrest H

2017-11-01

This study investigated the effect of voluntary running of defined distances on body adiposity in male C57BL/6 mice fed a high-fat diet. Mice were assigned to 6 groups and fed a standard AIN93G diet (sedentary) or a modified high-fat AIN93G diet (sedentary; unrestricted running; or 75%, 50%, or 25% of unrestricted running) for 12 weeks. The average running distance was 8.3, 6.3, 4.2, and 2.1 km/day for the unrestricted, 75%, 50%, and 25% of unrestricted runners, respectively. Body adiposity was 46% higher in sedentary mice when fed the high-fat diet instead of the standard diet. Running decreased adiposity in mice fed the high-fat diet in a dose-dependent manner but with no significant difference between sedentary mice and those running 2.1 km/day. In sedentary mice, the high-fat instead of the standard diet increased insulin resistance, hepatic triacylglycerides, and adipose and plasma concentrations of leptin and monocyte chemotactic protein-1 (MCP-1). Running reduced these variables in a dose-dependent manner. Adipose adiponectin was lowest in sedentary mice fed the high-fat diet; running raised adiponectin in both adipose tissue and plasma. Running 8.3 and 6.3 km/day had the greatest, but similar, effects on the aforementioned variables. Running 2.1 km/day did not affect these variables except, when compared with sedentariness, it significantly decreased MCP-1. The findings showed that running 6.3 kg/day was optimal for reducing adiposity and associated inflammation that was increased in mice by feeding a high-fat diet. The findings suggest that voluntary running of defined distances may counteract the obesogenic effects of a high-fat diet.

Study on advanced life support devices in the ambulances for emergency cases in Klang Valley, Malaysia.

PubMed

Ismail, M S; Hasinah, A B; Syaiful, M N; Murshidah, H B; Thong, T J; Zairi, Z; Idzwan, Z; Herbosa, T J; Johar, M J; Ho, S E; Das, S

2012-01-01

In an effort to improve pre-hospital care, the authors assessed the availability and utility of ambulance devices. The study aimed to identify commonly used devices for managing emergency cases in Klang Valley of Malaysia. This was a prospective study comprising of 1075 emergency ambulances running on 30 days. The study analyzed the availability and utilization of life support equipment in nine ambulance providers of Klang Valley in Malaysia. The devices were classified into: (a) airway and ventilation, (b) immobilization and haemorrhage control and (c) communication. The percentage of device utilization was analysed using computerised software. Results showed only one ambulance service had complete equipment in accordance to international standards. In term of utilisation of life support equipment, oxygen delivery devices were used in 493 (45.86%) runs. The most used devices in immobilisation and haemorrhage control were:- (a) scoop stretcher in 321 (29.86%) runs, (b) wound dressings in 250 (23.26%) runs and (c) rigid spinal board in 206 (19.16%) runs. Two-way radios were used in 745 (69.30%) runs while mobile phones were used in 429 (39.91%) runs. In conclusion, ambulances in Klang Valley had a large variation in the availability of life support devices. This emphasizes a need for standardization of equipment.

A reversed-phase high-performance liquid chromatography method for bovine serum albumin assay in pharmaceutical dosage forms and protein/antigen delivery systems.

PubMed

Hamidi, Mehrdad; Zarei, Najmeh

2009-05-01

Bovine serum albumin (BSA) is among the most widely used proteins in protein formulations as well as in the development of novel delivery systems as a typical model for therapeutic/diagnostic proteins and the new versions of vaccines. The development of reliable and easily available assay methods for quantitation of this protein would therefore play a crucial role in these types of studies. A simple gradient reversed-phase high-performance liquid chromatography with ultra-violet detection (HPLC-UV) method has been developed for quantitation of BSA in dosage forms and protein delivery systems. The method produced linear responses throughout the wide BSA concentration range of 1 to 100 micro g/mL. The average within-run and between-run variations of the method within the linear concentration range of BSA were 2.46% and 2.20%, respectively, with accuracies of 104.49% and 104.58% for within-run and between-run samples, respectively. The limits of detection (LOD) and quantitation (LOQ) of the method were 0.5 and 1 microg/mL, respectively. The method showed acceptable system suitability indices, which enabled us to use it successfully during our particulate vaccine delivery research project. Copyright 2009 John Wiley & Sons, Ltd.

Adapting NBODY4 with a GRAPE-6a Supercomputer for Web Access, Using NBodyLab

NASA Astrophysics Data System (ADS)

Johnson, V.; Aarseth, S.

2006-07-01

A demonstration site has been developed by the authors that enables researchers and students to experiment with the capabilities and performance of NBODY4 running on a GRAPE-6a over the web. NBODY4 is a sophisticated open-source N-body code for high accuracy simulations of dense stellar systems (Aarseth 2003). In 2004, NBODY4 was successfully tested with a GRAPE-6a, yielding an unprecedented low-cost tool for astrophysical research. The GRAPE-6a is a supercomputer card developed by astrophysicists to accelerate high accuracy N-body simulations with a cluster or a desktop PC (Fukushige et al. 2005, Makino & Taiji 1998). The GRAPE-6a card became commercially available in 2004, runs at 125 Gflops peak, has a standard PCI interface and costs less than 10,000. Researchers running the widely used NBODY6 (which does not require GRAPE hardware) can compare their own PC or laptop performance with simulations run on http://www.NbodyLab.org. Such comparisons may help justify acquisition of a GRAPE-6a. For workgroups such as university physics or astronomy departments, the demonstration site may be replicated or serve as a model for a shared computing resource. The site was constructed using an NBodyLab server-side framework.

Moderate running and plyometric training during off-season did not show a significant difference on soccer-related high-intensity performances compared with no-training controls.

PubMed

Nakamura, Daisuke; Suzuki, Tomohiro; Yasumatsu, Mikinobu; Akimoto, Takayuki

2012-12-01

Several investigators have reported the effects of reduced training and interrupted training on athletic performance, but few reports are available for soccer players. The purpose of this study was to examine, using the Yo-Yo intermittent recovery level 2 (YoYoIR2) test and sprint performance, the effects on soccer players of a reduced training program consisting of either moderate running training, plyometric training. After the completion of a competitive season, 29 male soccer players were divided into 3 groups: the running group (n = 13), the plyometric group (n = 11), and the control group (n = 5). Both training groups completed either running or plyometric training sessions 2 d·wk(-1) for 3 weeks, whereas the control group was not allowed to perform any training. The subjects performed YoYoIR2 and 20-m sprint tests before (pre) and after (post) the experimental period. Neither training group showed any significant training effects on the YoYoIR2 performance or 20-m sprint times compared with the control group. This study suggests that neither endurance running nor plyometric training 2 d·wk(-1) for 3 weeks has a significant effect on high-intensity performance compared with a nontraining regimen. However, our results do not support complete inactivity. These results may have important implications for the management of training cessation for a few weeks.

A distributed infrastructure for publishing VO services: an implementation

NASA Astrophysics Data System (ADS)

Cepparo, Francesco; Scagnetto, Ivan; Molinaro, Marco; Smareglia, Riccardo

2016-07-01

This contribution describes both the design and the implementation details of a new solution for publishing VO services, enlightening its maintainable, distributed, modular and scalable architecture. Indeed, the new publisher is multithreaded and multiprocess. Multiple instances of the modules can run on different machines to ensure high performance and high availability, and this will be true both for the interface modules of the services and the back end data access ones. The system uses message passing to let its components communicate through an AMQP message broker that can itself be distributed to provide better scalability and availability.

AlgoRun: a Docker-based packaging system for platform-agnostic implemented algorithms.

PubMed

Hosny, Abdelrahman; Vera-Licona, Paola; Laubenbacher, Reinhard; Favre, Thibauld

2016-08-01

There is a growing need in bioinformatics for easy-to-use software implementations of algorithms that are usable across platforms. At the same time, reproducibility of computational results is critical and often a challenge due to source code changes over time and dependencies. The approach introduced in this paper addresses both of these needs with AlgoRun, a dedicated packaging system for implemented algorithms, using Docker technology. Implemented algorithms, packaged with AlgoRun, can be executed through a user-friendly interface directly from a web browser or via a standardized RESTful web API to allow easy integration into more complex workflows. The packaged algorithm includes the entire software execution environment, thereby eliminating the common problem of software dependencies and the irreproducibility of computations over time. AlgoRun-packaged algorithms can be published on http://algorun.org, a centralized searchable directory to find existing AlgoRun-packaged algorithms. AlgoRun is available at http://algorun.org and the source code under GPL license is available at https://github.com/algorun laubenbacher@uchc.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Using wheel availability to shape running behavior of the rat towards improved behavioral and neurobiological outcomes.

PubMed

Basso, Julia C; Morrell, Joan I

2017-10-01

Though voluntary wheel running (VWR) has been used extensively to induce changes in both behavior and biology, little attention has been given to the way in which different variables influence VWR. This lack of understanding has led to an inability to utilize this behavior to its full potential, possibly blunting its effects on the endpoints of interest. We tested how running experience, sex, gonadal hormones, and wheel apparatus influence VWR in a range of wheel access "doses". VWR increases over several weeks, with females eventually running 1.5 times farther and faster than males. Limiting wheel access can be used as a tool to motivate subjects to run but restricts maximal running speeds attained by the rodents. Additionally, circulating gonadal hormones regulate wheel running behavior, but are not the sole basis of sex differences in running. Limitations from previous studies include the predominate use of males, emphasis on distance run, variable amounts of wheel availability, variable light-dark cycles, and possible food and/or water deprivation. We designed a comprehensive set of experiments to address these inconsistencies, providing data regarding the "microfeatures" of running, including distance run, time spent running, running rate, bouting behavior, and daily running patterns. By systematically altering wheel access, VWR behavior can be finely tuned - a feature that we hypothesize is due to its positive incentive salience. We demonstrate how to maximize VWR, which will allow investigators to optimize exercise-induced changes in their behavioral and/or biological endpoints of interest. Published by Elsevier B.V.

Smoothed Particle Hydrodynamic Simulator

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

2016-10-05

This code is a highly modular framework for developing smoothed particle hydrodynamic (SPH) simulations running on parallel platforms. The compartmentalization of the code allows for rapid development of new SPH applications and modifications of existing algorithms. The compartmentalization also allows changes in one part of the code used by many applications to instantly be made available to all applications.

An overview of the DII-HEP OpenStack based CMS data analysis

NASA Astrophysics Data System (ADS)

Osmani, L.; Tarkoma, S.; Eerola, P.; Komu, M.; Kortelainen, M. J.; Kraemer, O.; Lindén, T.; Toor, S.; White, J.

2015-05-01

An OpenStack based private cloud with the Cluster File System has been built and used with both CMS analysis and Monte Carlo simulation jobs in the Datacenter Indirection Infrastructure for Secure High Energy Physics (DII-HEP) project. On the cloud we run the ARC middleware that allows running CMS applications without changes on the job submission side. Our test results indicate that the adopted approach provides a scalable and resilient solution for managing resources without compromising on performance and high availability. To manage the virtual machines (VM) dynamically in an elastic fasion, we are testing the EMI authorization service (Argus) and the Execution Environment Service (Argus-EES). An OpenStackplugin has been developed for Argus-EES. The Host Identity Protocol (HIP) has been designed for mobile networks and it provides a secure method for IP multihoming. HIP separates the end-point identifier and locator role for IP address which increases the network availability for the applications. Our solution leverages HIP for traffic management. This presentation gives an update on the status of the work and our lessons learned in creating an OpenStackbased cloud for HEP.

Role of natural gas in meeting an electric sector emissions ...

EPA Pesticide Factsheets

With advances in natural gas extraction technologies, there is an increase in availability of domestic natural gas, and natural gas is gaining a larger share of use as a fuel in electricity production. At the power plant, natural gas is a cleaner burning fuel than coal, but uncertainties exist in the amount of methane leakage occurring upstream in the extraction and production of natural gas. At high leakage levels, these methane emissions could outweigh the benefits of switching from coal to natural gas. This analysis uses the MARKAL linear optimization model to compare the carbon emissions profiles and system-wide global warming potential of the U.S. energy system over a series of model runs in which the power sector is asked to meet a specific CO2 reduction target and the availability of natural gas changes. Scenarios are run with a range of upstream methane emission leakage rates from natural gas production. While the total CO2 emissions are reduced in most scenarios, total greenhouse gas emissions show an increase or no change when both natural gas availability and methane emissions from natural gas production are high. Article presents summary of results from an analyses of natural gas resource availability and power sector emissions reduction strategies under different estimates of methane leakage rates during natural gas extraction and production. This was study was undertaken as part of the Energy Modeling Forum Study #31:

Wheel-running activity modulates circadian organization and the daily rhythm of eating behavior

PubMed Central

Pendergast, Julie S.; Branecky, Katrina L.; Huang, Roya; Niswender, Kevin D.; Yamazaki, Shin

2014-01-01

Consumption of high-fat diet acutely alters the daily rhythm of eating behavior and circadian organization (the phase relationship between oscillators in central and peripheral tissues) in mice. Voluntary wheel-running activity counteracts the obesogenic effects of high-fat diet and also modulates circadian rhythms in mice. In this study, we sought to determine whether voluntary wheel-running activity could prevent the proximate effects of high-fat diet consumption on circadian organization and behavioral rhythms in mice. Mice were housed with locked or freely rotating running wheels and fed chow or high-fat diet for 1 week and rhythms of locomotor activity, eating behavior, and molecular timekeeping (PERIOD2::LUCIFERASE luminescence rhythms) in ex vivo tissues were measured. Wheel-running activity delayed the phase of the liver rhythm by 4 h in both chow- and high-fat diet-fed mice. The delayed liver phase was specific to wheel-running activity since an enriched environment without the running wheel did not alter the phase of the liver rhythm. In addition, wheel-running activity modulated the effect of high-fat diet consumption on the daily rhythm of eating behavior. While high-fat diet consumption caused eating events to be more evenly dispersed across the 24 h-day in both locked-wheel and wheel-running mice, the effect of high-fat diet was much less pronounced in wheel-running mice. Together these data demonstrate that wheel-running activity is a salient factor that modulates liver phase and eating behavior rhythms in both chow- and high-fat-diet fed mice. Wheel-running activity in mice is both a source of exercise and a self-motivating, rewarding behavior. Understanding the putative reward-related mechanisms whereby wheel-running activity alters circadian rhythms could have implications for human obesity since palatable food and exercise may modulate similar reward circuits. PMID:24624109

Data preservation at the Fermilab Tevatron

DOE PAGES

Amerio, S.; Behari, S.; Boyd, J.; ...

2017-01-22

The Fermilab Tevatron collider's data-taking run ended in September 2011, yielding a dataset with rich scientific potential. The CDF and D0 experiments each have approximately 9 PB of collider and simulated data stored on tape. A large computing infrastructure consisting of tape storage, disk cache, and distributed grid computing for physics analysis with the Tevatron data is present at Fermilab. The Fermilab Run II data preservation project intends to keep this analysis capability sustained through the year 2020 and beyond. To achieve this goal, we have implemented a system that utilizes virtualization, automated validation, and migration to new standards inmore » both software and data storage technology and leverages resources available from currently-running experiments at Fermilab. Lastly, these efforts have also provided useful lessons in ensuring long-term data access for numerous experiments, and enable high-quality scientific output for years to come.« less

libRoadRunner: a high performance SBML simulation and analysis library

PubMed Central

Somogyi, Endre T.; Bouteiller, Jean-Marie; Glazier, James A.; König, Matthias; Medley, J. Kyle; Swat, Maciej H.; Sauro, Herbert M.

2015-01-01

Motivation: This article presents libRoadRunner, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using Systems Biology Markup Language (SBML). SBML is the most widely used standard for representing dynamic networks, especially biochemical networks. libRoadRunner is fast enough to support large-scale problems such as tissue models, studies that require large numbers of repeated runs and interactive simulations. Results: libRoadRunner is a self-contained library, able to run both as a component inside other tools via its C++ and C bindings, and interactively through its Python interface. Its Python Application Programming Interface (API) is similar to the APIs of MATLAB (www.mathworks.com) and SciPy (http://www.scipy.org/), making it fast and easy to learn. libRoadRunner uses a custom Just-In-Time (JIT) compiler built on the widely used LLVM JIT compiler framework. It compiles SBML-specified models directly into native machine code for a variety of processors, making it appropriate for solving extremely large models or repeated runs. libRoadRunner is flexible, supporting the bulk of the SBML specification (except for delay and non-linear algebraic equations) including several SBML extensions (composition and distributions). It offers multiple deterministic and stochastic integrators, as well as tools for steady-state analysis, stability analysis and structural analysis of the stoichiometric matrix. Availability and implementation: libRoadRunner binary distributions are available for Mac OS X, Linux and Windows. The library is licensed under Apache License Version 2.0. libRoadRunner is also available for ARM-based computers such as the Raspberry Pi. http://www.libroadrunner.org provides online documentation, full build instructions, binaries and a git source repository. Contacts: hsauro@u.washington.edu or somogyie@indiana.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26085503

Simulation of LHC events on a millions threads

NASA Astrophysics Data System (ADS)

Childers, J. T.; Uram, T. D.; LeCompte, T. J.; Papka, M. E.; Benjamin, D. P.

2015-12-01

Demand for Grid resources is expected to double during LHC Run II as compared to Run I; the capacity of the Grid, however, will not double. The HEP community must consider how to bridge this computing gap by targeting larger compute resources and using the available compute resources as efficiently as possible. Argonne's Mira, the fifth fastest supercomputer in the world, can run roughly five times the number of parallel processes that the ATLAS experiment typically uses on the Grid. We ported Alpgen, a serial x86 code, to run as a parallel application under MPI on the Blue Gene/Q architecture. By analysis of the Alpgen code, we reduced the memory footprint to allow running 64 threads per node, utilizing the four hardware threads available per core on the PowerPC A2 processor. Event generation and unweighting, typically run as independent serial phases, are coupled together in a single job in this scenario, reducing intermediate writes to the filesystem. By these optimizations, we have successfully run LHC proton-proton physics event generation at the scale of a million threads, filling two-thirds of Mira.

Running and osteoarthritis.

PubMed

Willick, Stuart E; Hansen, Pamela A

2010-07-01

The overall health benefits of cardiovascular exercise, such as running, are well established. However, it is also well established that in certain circumstances running can lead to overload injuries of muscle, tendon, and bone. In contrast, it has not been established that running leads to degeneration of articular cartilage, which is the hallmark of osteoarthritis. This article reviews the available literature on the association between running and osteoarthritis, with a focus on clinical epidemiologic studies. The preponderance of clinical reports refutes an association between running and osteoarthritis. Copyright 2010 Elsevier Inc. All rights reserved.

CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models.

PubMed

Haraldsdóttir, Hulda S; Cousins, Ben; Thiele, Ines; Fleming, Ronan M T; Vempala, Santosh

2017-06-01

In constraint-based metabolic modelling, physical and biochemical constraints define a polyhedral convex set of feasible flux vectors. Uniform sampling of this set provides an unbiased characterization of the metabolic capabilities of a biochemical network. However, reliable uniform sampling of genome-scale biochemical networks is challenging due to their high dimensionality and inherent anisotropy. Here, we present an implementation of a new sampling algorithm, coordinate hit-and-run with rounding (CHRR). This algorithm is based on the provably efficient hit-and-run random walk and crucially uses a preprocessing step to round the anisotropic flux set. CHRR provably converges to a uniform stationary sampling distribution. We apply it to metabolic networks of increasing dimensionality. We show that it converges several times faster than a popular artificial centering hit-and-run algorithm, enabling reliable and tractable sampling of genome-scale biochemical networks. https://github.com/opencobra/cobratoolbox . ronan.mt.fleming@gmail.com or vempala@cc.gatech.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

A public dataset of running biomechanics and the effects of running speed on lower extremity kinematics and kinetics

PubMed Central

Fukuchi, Claudiane A.; Duarte, Marcos

2017-01-01

Background The goals of this study were (1) to present the set of data evaluating running biomechanics (kinematics and kinetics), including data on running habits, demographics, and levels of muscle strength and flexibility made available at Figshare (DOI: 10.6084/m9.figshare.4543435); and (2) to examine the effect of running speed on selected gait-biomechanics variables related to both running injuries and running economy. Methods The lower-extremity kinematics and kinetics data of 28 regular runners were collected using a three-dimensional (3D) motion-capture system and an instrumented treadmill while the subjects ran at 2.5 m/s, 3.5 m/s, and 4.5 m/s wearing standard neutral shoes. Results A dataset comprising raw and processed kinematics and kinetics signals pertaining to this experiment is available in various file formats. In addition, a file of metadata, including demographics, running characteristics, foot-strike patterns, and muscle strength and flexibility measurements is provided. Overall, there was an effect of running speed on most of the gait-biomechanics variables selected for this study. However, the foot-strike patterns were not affected by running speed. Discussion Several applications of this dataset can be anticipated, including testing new methods of data reduction and variable selection; for educational purposes; and answering specific research questions. This last application was exemplified in the study’s second objective. PMID:28503379

A public dataset of running biomechanics and the effects of running speed on lower extremity kinematics and kinetics.

PubMed

Fukuchi, Reginaldo K; Fukuchi, Claudiane A; Duarte, Marcos

2017-01-01

The goals of this study were (1) to present the set of data evaluating running biomechanics (kinematics and kinetics), including data on running habits, demographics, and levels of muscle strength and flexibility made available at Figshare (DOI: 10.6084/m9.figshare.4543435); and (2) to examine the effect of running speed on selected gait-biomechanics variables related to both running injuries and running economy. The lower-extremity kinematics and kinetics data of 28 regular runners were collected using a three-dimensional (3D) motion-capture system and an instrumented treadmill while the subjects ran at 2.5 m/s, 3.5 m/s, and 4.5 m/s wearing standard neutral shoes. A dataset comprising raw and processed kinematics and kinetics signals pertaining to this experiment is available in various file formats. In addition, a file of metadata, including demographics, running characteristics, foot-strike patterns, and muscle strength and flexibility measurements is provided. Overall, there was an effect of running speed on most of the gait-biomechanics variables selected for this study. However, the foot-strike patterns were not affected by running speed. Several applications of this dataset can be anticipated, including testing new methods of data reduction and variable selection; for educational purposes; and answering specific research questions. This last application was exemplified in the study's second objective.

Prototype methodology for obtaining cloud seeding guidance from HRRR model data

NASA Astrophysics Data System (ADS)

Dawson, N.; Blestrud, D.; Kunkel, M. L.; Waller, B.; Ceratto, J.

2017-12-01

Weather model data, along with real time observations, are critical to determine whether atmospheric conditions are prime for super-cooled liquid water during cloud seeding operations. Cloud seeding groups can either use operational forecast models, or run their own model on a computer cluster. A custom weather model provides the most flexibility, but is also expensive. For programs with smaller budgets, openly-available operational forecasting models are the de facto method for obtaining forecast data. The new High-Resolution Rapid Refresh (HRRR) model (3 x 3 km grid size), developed by the Earth System Research Laboratory (ESRL), provides hourly model runs with 18 forecast hours per run. While the model cannot be fine-tuned for a specific area or edited to provide cloud-seeding-specific output, model output is openly available on a near-real-time basis. This presentation focuses on a prototype methodology for using HRRR model data to create maps which aid in near-real-time cloud seeding decision making. The R programming language is utilized to run a script on a Windows® desktop/laptop computer either on a schedule (such as every half hour) or manually. The latest HRRR model run is downloaded from NOAA's Operational Model Archive and Distribution System (NOMADS). A GRIB-filter service, provided by NOMADS, is used to obtain surface and mandatory pressure level data for a subset domain which greatly cuts down on the amount of data transfer. Then, a set of criteria, identified by the Idaho Power Atmospheric Science Group, is used to create guidance maps. These criteria include atmospheric stability (lapse rates), dew point depression, air temperature, and wet bulb temperature. The maps highlight potential areas where super-cooled liquid water may exist, reasons as to why cloud seeding should not be attempted, and wind speed at flight level.

Stretching Your Energetic Budget: How Tendon Compliance Affects the Metabolic Cost of Running

PubMed Central

Uchida, Thomas K.; Hicks, Jennifer L.; Dembia, Christopher L.; Delp, Scott L.

2016-01-01

Muscles attach to bones via tendons that stretch and recoil, affecting muscle force generation and metabolic energy consumption. In this study, we investigated the effect of tendon compliance on the metabolic cost of running using a full-body musculoskeletal model with a detailed model of muscle energetics. We performed muscle-driven simulations of running at 2–5 m/s with tendon force–strain curves that produced between 1 and 10% strain when the muscles were developing maximum isometric force. We computed the average metabolic power consumed by each muscle when running at each speed and with each tendon compliance. Average whole-body metabolic power consumption increased as running speed increased, regardless of tendon compliance, and was lowest at each speed when tendon strain reached 2–3% as muscles were developing maximum isometric force. When running at 2 m/s, the soleus muscle consumed less metabolic power at high tendon compliance because the strain of the tendon allowed the muscle fibers to operate nearly isometrically during stance. In contrast, the medial and lateral gastrocnemii consumed less metabolic power at low tendon compliance because less compliant tendons allowed the muscle fibers to operate closer to their optimal lengths during stance. The software and simulations used in this study are freely available at simtk.org and enable examination of muscle energetics with unprecedented detail. PMID:26930416

Taverna: a tool for building and running workflows of services

PubMed Central

Hull, Duncan; Wolstencroft, Katy; Stevens, Robert; Goble, Carole; Pocock, Mathew R.; Li, Peter; Oinn, Tom

2006-01-01

Taverna is an application that eases the use and integration of the growing number of molecular biology tools and databases available on the web, especially web services. It allows bioinformaticians to construct workflows or pipelines of services to perform a range of different analyses, such as sequence analysis and genome annotation. These high-level workflows can integrate many different resources into a single analysis. Taverna is available freely under the terms of the GNU Lesser General Public License (LGPL) from . PMID:16845108

Embedded Implementation of VHR Satellite Image Segmentation

PubMed Central

Li, Chao; Balla-Arabé, Souleymane; Ginhac, Dominique; Yang, Fan

2016-01-01

Processing and analysis of Very High Resolution (VHR) satellite images provide a mass of crucial information, which can be used for urban planning, security issues or environmental monitoring. However, they are computationally expensive and, thus, time consuming, while some of the applications, such as natural disaster monitoring and prevention, require high efficiency performance. Fortunately, parallel computing techniques and embedded systems have made great progress in recent years, and a series of massively parallel image processing devices, such as digital signal processors or Field Programmable Gate Arrays (FPGAs), have been made available to engineers at a very convenient price and demonstrate significant advantages in terms of running-cost, embeddability, power consumption flexibility, etc. In this work, we designed a texture region segmentation method for very high resolution satellite images by using the level set algorithm and the multi-kernel theory in a high-abstraction C environment and realize its register-transfer level implementation with the help of a new proposed high-level synthesis-based design flow. The evaluation experiments demonstrate that the proposed design can produce high quality image segmentation with a significant running-cost advantage. PMID:27240370

An integrated pipeline of open source software adapted for multi-CPU architectures: use in the large-scale identification of single nucleotide polymorphisms.

PubMed

Jayashree, B; Hanspal, Manindra S; Srinivasan, Rajgopal; Vigneshwaran, R; Varshney, Rajeev K; Spurthi, N; Eshwar, K; Ramesh, N; Chandra, S; Hoisington, David A

2007-01-01

The large amounts of EST sequence data available from a single species of an organism as well as for several species within a genus provide an easy source of identification of intra- and interspecies single nucleotide polymorphisms (SNPs). In the case of model organisms, the data available are numerous, given the degree of redundancy in the deposited EST data. There are several available bioinformatics tools that can be used to mine this data; however, using them requires a certain level of expertise: the tools have to be used sequentially with accompanying format conversion and steps like clustering and assembly of sequences become time-intensive jobs even for moderately sized datasets. We report here a pipeline of open source software extended to run on multiple CPU architectures that can be used to mine large EST datasets for SNPs and identify restriction sites for assaying the SNPs so that cost-effective CAPS assays can be developed for SNP genotyping in genetics and breeding applications. At the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), the pipeline has been implemented to run on a Paracel high-performance system consisting of four dual AMD Opteron processors running Linux with MPICH. The pipeline can be accessed through user-friendly web interfaces at http://hpc.icrisat.cgiar.org/PBSWeb and is available on request for academic use. We have validated the developed pipeline by mining chickpea ESTs for interspecies SNPs, development of CAPS assays for SNP genotyping, and confirmation of restriction digestion pattern at the sequence level.

Is There an Optimal Speed for Economical Running?

PubMed

Black, Matthew I; Handsaker, Joseph C; Allen, Sam J; Forrester, Stephanie E; Folland, Jonathan P

2018-01-01

The influence of running speed and sex on running economy is unclear and may have been confounded by measurements of oxygen cost that do not account for known differences in substrate metabolism, across a limited range of speeds, and differences in performance standard. Therefore, this study assessed the energy cost of running over a wide range of speeds in high-level and recreational runners to investigate the effect of speed (in absolute and relative terms) and sex (men vs women of equivalent performance standard) on running economy. To determine the energy cost (kcal · kg -1  · km -1 ) of submaximal running, speed at lactate turn point (sLTP), and maximal rate of oxygen uptake, 92 healthy runners (high-level men, n = 14; high-level women, n = 10; recreational men, n = 35; recreational women, n = 33) completed a discontinuous incremental treadmill test. There were no sex-specific differences in the energy cost of running for the recreational or high-level runners when compared at absolute or relative running speeds (P > .05). The absolute and relative speed-energy cost relationships for the high-level runners demonstrated a curvilinear U shape with a nadir reflecting the most economical speed at 13 km/h or 70% sLTP. The high-level runners were more economical than the recreational runners at all absolute and relative running speeds (P < .05). These findings demonstrate that there is an optimal speed for economical running, there is no sex-specific difference, and high-level endurance runners exhibit better running economy than recreational endurance runners.

Running Simulations without Ruining Your Life: Simple Ways to Incorporate Active Learning into Your Teaching

ERIC Educational Resources Information Center

Glazier, Rebecca A.

2011-01-01

Despite the growing availability and popularity of simulations and other active teaching techniques, many instructors may be deterred from using simulations because of the potentially high costs involved. Instructors could spend a preponderance of their time and resources developing and executing simulations, but such an approach is not necessary.…

Lawrence Livermore National Laboratories Perspective on Code Development and High Performance Computing Resources in Support of the National HED/ICF Effort

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

Clouse, C. J.; Edwards, M. J.; McCoy, M. G.

2015-07-07

Through its Advanced Scientific Computing (ASC) and Inertial Confinement Fusion (ICF) code development efforts, Lawrence Livermore National Laboratory (LLNL) provides a world leading numerical simulation capability for the National HED/ICF program in support of the Stockpile Stewardship Program (SSP). In addition the ASC effort provides high performance computing platform capabilities upon which these codes are run. LLNL remains committed to, and will work with, the national HED/ICF program community to help insure numerical simulation needs are met and to make those capabilities available, consistent with programmatic priorities and available resources.

The 2006 July 17 Java (Indonesia) tsunami from satellite imagery and numerical modelling: a single or complex source?

NASA Astrophysics Data System (ADS)

Hébert, H.; Burg, P.-E.; Binet, R.; Lavigne, F.; Allgeyer, S.; Schindelé, F.

2012-12-01

The Mw 7.8 2006 July 17 earthquake off the southern coast of Java, Indonesia, has been responsible for a very large tsunami causing more than 700 casualties. The tsunami has been observed on at least 200 km of coastline in the region of Pangandaran (West Java), with run-up heights from 5 to more than 20 m. Such a large tsunami, with respect to the source magnitude, has been attributed to the slow character of the seismic rupture, defining the event as a so-called tsunami earthquake, but it has also been suggested that the largest run-up heights are actually the result of a second local landslide source. Here we test whether a single slow earthquake source can explain the tsunami run-up, using a combination of new detailed data in the region of the largest run-ups and comparison with modelled run-ups for a range of plausible earthquake source models. Using high-resolution satellite imagery (SPOT 5 and Quickbird), the coastal impact of the tsunami is refined in the surroundings of the high-security Permisan prison on Nusa Kambangan island, where 20 m run-up had been recorded directly after the event. These data confirm the extreme inundation lengths close to the prison, and extend the area of maximum impact further along the Nusa Kambangan island (about 20 km of shoreline), where inundation lengths reach several hundreds of metres, suggesting run-up as high as 10-15 m. Tsunami modelling has been conducted in detail for the high run-up Permisan area (Nusa Kambangan) and the PLTU power plant about 25 km eastwards, where run-up reached only 4-6 m and a video recording of the tsunami arrival is available. For the Permisan prison a high-resolution DEM was built from stereoscopic satellite imagery. The regular basin of the PLTU plant was designed using photographs and direct observations. For the earthquake's mechanism, both static (infinite) and finite (kinematic) ruptures are investigated using two published source models. The models account rather well for the sea level variation at PLTU, showing a better agreement in arrival times with the finite rupture, and predict the Permisan area to be one of the regions where tsunami waves would have focussed. However, the earthquake models that match the data at PTLU do not predict that the wave heights at Permisan are an overall maximum, and do not predict there more than 10 m of the 21 observed. Hence, our results confirm that an additional localized tsunami source off Nusa Kambangan island, such as a submarine landslide, may have increased the tsunami impact for the Permisan site. This reinforces the importance for hazard assessment of further mapping and understanding local potential for submarine sliding, as a tsunami source added to usual earthquake sources.

76 FR 3524 - Final Flood Elevation Determinations

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-20

... proof Flood Insurance Study and FIRM available at the address cited below for each community. The BFEs...-Long Run Road. Duck Run (backwater effects from Scioto Approximately 547 feet +535 Unincorporated Areas of River). upstream of Duck Run- Scioto County. Otway Road. Just downstream of +535 McDermott Pond...

NONMEMory: a run management tool for NONMEM.

PubMed

Wilkins, Justin J

2005-06-01

NONMEM is an extremely powerful tool for nonlinear mixed-effect modelling and simulation of pharmacokinetic and pharmacodynamic data. However, it is a console-based application whose output does not lend itself to rapid interpretation or efficient management. NONMEMory has been created to be a comprehensive project manager for NONMEM, providing detailed summary, comparison and overview of the runs comprising a given project, including the display of output data, simple post-run processing, fast diagnostic plots and run output management, complementary to other available modelling aids. Analysis time ought not to be spent on trivial tasks, and NONMEMory's role is to eliminate these as far as possible by increasing the efficiency of the modelling process. NONMEMory is freely available from http://www.uct.ac.za/depts/pha/nonmemory.php.

Evaluation of quality of precipitation products: A case study using WRF and IMERG data over the central United States

NASA Astrophysics Data System (ADS)

Zhang, J.; Lin, L. F.; Bras, R. L.

2017-12-01

Hydrological applications rely on the availability and quality of precipitation products, specially model- and satellite-based products for use in areas without ground measurements. It is known that the quality of model- and satellite-based precipitation products are complementary—model-based products exhibiting high quality during winters while satellite-based products seem to be better during summers. To explore that behavior, this study uses 2-m air temperature as auxiliary information to evaluate high-resolution (0.1°×0.1° every hour) precipitation products from Weather Research and Forecasting (WRF) simulations and from version-4 Integrated Multi-satellite Retrievals for GPM (IMERG) early and final runs. The products are evaluated relative to the reference NCEP Stage IV precipitation estimates over the central United States in 2016. The results show that the WRF and IMERG final-run estimates are nearly unbiased while the IMERG early-run estimates positively biased. The results also show that the WRF estimates exhibit high correlations with the reference data when the temperature falls below 280°K and the IMERG estimates (i.e., both early and final runs) do so when the temperature exceeds 280°K. Moreover, the temperature threshold of 280°K, which distinguishes the quality of the WRF and the IMERG products, does not vary significantly with either season or location. This study not only adds insight into current precipitation research on the quality of precipitation products but also suggests a simple way for choosing either a model- or satellite-based product or a hybrid model/satellite product for applications.

Experiments with microcomputer-based artificial intelligence environments

USGS Publications Warehouse

Summers, E.G.; MacDonald, R.A.

1988-01-01

The U.S. Geological Survey (USGS) has been experimenting with the use of relatively inexpensive microcomputers as artificial intelligence (AI) development environments. Several AI languages are available that perform fairly well on desk-top personal computers, as are low-to-medium cost expert system packages. Although performance of these systems is respectable, their speed and capacity limitations are questionable for serious earth science applications foreseen by the USGS. The most capable artificial intelligence applications currently are concentrated on what is known as the "artificial intelligence computer," and include Xerox D-series, Tektronix 4400 series, Symbolics 3600, VAX, LMI, and Texas Instruments Explorer. The artificial intelligence computer runs expert system shells and Lisp, Prolog, and Smalltalk programming languages. However, these AI environments are expensive. Recently, inexpensive 32-bit hardware has become available for the IBM/AT microcomputer. USGS has acquired and recently completed Beta-testing of the Gold Hill Systems 80386 Hummingboard, which runs Common Lisp on an IBM/AT microcomputer. Hummingboard appears to have the potential to overcome many of the speed/capacity limitations observed with AI-applications on standard personal computers. USGS is a Beta-test site for the Gold Hill Systems GoldWorks expert system. GoldWorks combines some high-end expert system shell capabilities in a medium-cost package. This shell is developed in Common Lisp, runs on the 80386 Hummingboard, and provides some expert system features formerly available only on AI-computers including frame and rule-based reasoning, on-line tutorial, multiple inheritance, and object-programming. ?? 1988 International Association for Mathematical Geology.

High-throughput sequence alignment using Graphics Processing Units

PubMed Central

Schatz, Michael C; Trapnell, Cole; Delcher, Arthur L; Varshney, Amitabh

2007-01-01

Background The recent availability of new, less expensive high-throughput DNA sequencing technologies has yielded a dramatic increase in the volume of sequence data that must be analyzed. These data are being generated for several purposes, including genotyping, genome resequencing, metagenomics, and de novo genome assembly projects. Sequence alignment programs such as MUMmer have proven essential for analysis of these data, but researchers will need ever faster, high-throughput alignment tools running on inexpensive hardware to keep up with new sequence technologies. Results This paper describes MUMmerGPU, an open-source high-throughput parallel pairwise local sequence alignment program that runs on commodity Graphics Processing Units (GPUs) in common workstations. MUMmerGPU uses the new Compute Unified Device Architecture (CUDA) from nVidia to align multiple query sequences against a single reference sequence stored as a suffix tree. By processing the queries in parallel on the highly parallel graphics card, MUMmerGPU achieves more than a 10-fold speedup over a serial CPU version of the sequence alignment kernel, and outperforms the exact alignment component of MUMmer on a high end CPU by 3.5-fold in total application time when aligning reads from recent sequencing projects using Solexa/Illumina, 454, and Sanger sequencing technologies. Conclusion MUMmerGPU is a low cost, ultra-fast sequence alignment program designed to handle the increasing volume of data produced by new, high-throughput sequencing technologies. MUMmerGPU demonstrates that even memory-intensive applications can run significantly faster on the relatively low-cost GPU than on the CPU. PMID:18070356

Holistic Context-Sensitivity for Run-Time Optimization of Flexible Manufacturing Systems.

PubMed

Scholze, Sebastian; Barata, Jose; Stokic, Dragan

2017-02-24

Highly flexible manufacturing systems require continuous run-time (self-) optimization of processes with respect to diverse parameters, e.g., efficiency, availability, energy consumption etc. A promising approach for achieving (self-) optimization in manufacturing systems is the usage of the context sensitivity approach based on data streaming from high amount of sensors and other data sources. Cyber-physical systems play an important role as sources of information to achieve context sensitivity. Cyber-physical systems can be seen as complex intelligent sensors providing data needed to identify the current context under which the manufacturing system is operating. In this paper, it is demonstrated how context sensitivity can be used to realize a holistic solution for (self-) optimization of discrete flexible manufacturing systems, by making use of cyber-physical systems integrated in manufacturing systems/processes. A generic approach for context sensitivity, based on self-learning algorithms, is proposed aiming at a various manufacturing systems. The new solution encompasses run-time context extractor and optimizer. Based on the self-learning module both context extraction and optimizer are continuously learning and improving their performance. The solution is following Service Oriented Architecture principles. The generic solution is developed and then applied to two very different manufacturing processes.

Holistic Context-Sensitivity for Run-Time Optimization of Flexible Manufacturing Systems

PubMed Central

Scholze, Sebastian; Barata, Jose; Stokic, Dragan

2017-01-01

Highly flexible manufacturing systems require continuous run-time (self-) optimization of processes with respect to diverse parameters, e.g., efficiency, availability, energy consumption etc. A promising approach for achieving (self-) optimization in manufacturing systems is the usage of the context sensitivity approach based on data streaming from high amount of sensors and other data sources. Cyber-physical systems play an important role as sources of information to achieve context sensitivity. Cyber-physical systems can be seen as complex intelligent sensors providing data needed to identify the current context under which the manufacturing system is operating. In this paper, it is demonstrated how context sensitivity can be used to realize a holistic solution for (self-) optimization of discrete flexible manufacturing systems, by making use of cyber-physical systems integrated in manufacturing systems/processes. A generic approach for context sensitivity, based on self-learning algorithms, is proposed aiming at a various manufacturing systems. The new solution encompasses run-time context extractor and optimizer. Based on the self-learning module both context extraction and optimizer are continuously learning and improving their performance. The solution is following Service Oriented Architecture principles. The generic solution is developed and then applied to two very different manufacturing processes. PMID:28245564

A High Temperature Cyclic Oxidation Data Base for Selected Materials Tested at NASA Glenn Research Center

NASA Technical Reports Server (NTRS)

Barrett, Charles A.

2003-01-01

The cyclic oxidation test results for some 1000 high temperature commercial and experimental alloys have been collected in an EXCEL database. This database represents over thirty years of research at NASA Glenn Research Center in Cleveland, Ohio. The data is in the form of a series of runs of specific weight change versus time values for a set of samples tested at a given temperature, cycle time, and exposure time. Included on each run is a set of embedded plots of the critical data. The nature of the data is discussed along with analysis of the cyclic oxidation process. In addition examples are given as to how a set of results can be analyzed. The data is assembled on a read-only compact disk which is available on request from Materials Durability Branch, NASA Glenn Research Center, Cleveland, Ohio.

GPU Particle Tracking and MHD Simulations with Greatly Enhanced Computational Speed

NASA Astrophysics Data System (ADS)

Ziemba, T.; O'Donnell, D.; Carscadden, J.; Cash, M.; Winglee, R.; Harnett, E.

2008-12-01

GPUs are intrinsically highly parallelized systems that provide more than an order of magnitude computing speed over a CPU based systems, for less cost than a high end-workstation. Recent advancements in GPU technologies allow for full IEEE float specifications with performance up to several hundred GFLOPs per GPU, and new software architectures have recently become available to ease the transition from graphics based to scientific applications. This allows for a cheap alternative to standard supercomputing methods and should increase the time to discovery. 3-D particle tracking and MHD codes have been developed using NVIDIA's CUDA and have demonstrated speed up of nearly a factor of 20 over equivalent CPU versions of the codes. Such a speed up enables new applications to develop, including real time running of radiation belt simulations and real time running of global magnetospheric simulations, both of which could provide important space weather prediction tools.

SeWeR: a customizable and integrated dynamic HTML interface to bioinformatics services.

PubMed

Basu, M K

2001-06-01

Sequence analysis using Web Resources (SeWeR) is an integrated, Dynamic HTML (DHTML) interface to commonly used bioinformatics services available on the World Wide Web. It is highly customizable, extendable, platform neutral, completely server-independent and can be hosted as a web page as well as being used as stand-alone software running within a web browser.

Multipass reconfiguration of the HELEN Nd:glass laser at the Atomic Weapons Establishment.

PubMed

Norman, Michael J; Andrew, James E; Bett, Thomas H; Clifford, Roger K; England, John E; Hopps, Nicholas W; Parker, Kenneth W; Porter, Kenneth; Stevenson, Mark

2002-06-20

The HELEN high-power Nd:glass laser has been rebuilt in a new multipass configuration that requires fewer components to maintain existing performance. This is expected to lead to greater system availability and reduced running costs. We describe the new design, discuss some of the key issues that had to be addressed, and present operational results.

Impact of construction and remodeling markets on the U.S. secondary hardwood products industry

Treesearch

Matt Bumgardner; Urs Buehlmann; Al Schuler; Karen Koenig

2011-01-01

The housing correction that started in 2007 continues to run its course. Excessive inventory levels, limited credit availability, and record foreclosure rates continue to have an impact on U.S. housing markets. With inventories high and demand for new construction low, the U.S. hardwood industry's largest markets for appearance-grade products remain under pressure...

--No Title--

Science.gov Websites

CFS UPDATES NEW The CFS server has been upgraded. If you have been downloading data using anonymous data. Thank you for your cooperation. NEW CMIP2 Simulation Run extended CMIP126 Simulation Run has been extended from 100 to 225 years! Monthly data from this run is available! NEW CFS Retrospective Forecast

The ATLAS Software Installation System v2: a highly available system to install and validate Grid and Cloud sites via Panda

NASA Astrophysics Data System (ADS)

De Salvo, A.; Kataoka, M.; Sanchez Pineda, A.; Smirnov, Y.

2015-12-01

The ATLAS Installation System v2 is the evolution of the original system, used since 2003. The original tool has been completely re-designed in terms of database backend and components, adding support for submission to multiple backends, including the original Workload Management Service (WMS) and the new PanDA modules. The database engine has been changed from plain MySQL to Galera/Percona and the table structure has been optimized to allow a full High-Availability (HA) solution over Wide Area Network. The servlets, running on each frontend, have been also decoupled from local settings, to allow an easy scalability of the system, including the possibility of an HA system with multiple sites. The clients can also be run in multiple copies and in different geographical locations, and take care of sending the installation and validation jobs to the target Grid or Cloud sites. Moreover, the Installation Database is used as source of parameters by the automatic agents running in CVMFS, in order to install the software and distribute it to the sites. The system is in production for ATLAS since 2013, having as main sites in HA the INFN Roma Tier 2 and the CERN Agile Infrastructure. The Light Job Submission Framework for Installation (LJSFi) v2 engine is directly interfacing with PanDA for the Job Management, the Atlas Grid Information System (AGIS) for the site parameter configurations, and CVMFS for both core components and the installation of the software itself. LJSFi2 is also able to use other plugins, and is essentially Virtual Organization (VO) agnostic, so can be directly used and extended to cope with the requirements of any Grid or Cloud enabled VO. In this work we will present the architecture, performance, status and possible evolutions to the system for the LHC Run2 and beyond.

Photoionization and High Density Gas

NASA Technical Reports Server (NTRS)

Kallman, T.; Bautista, M.; White, Nicholas E. (Technical Monitor)

2002-01-01

We present results of calculations using the XSTAR version 2 computer code. This code is loosely based on the XSTAR v.1 code which has been available for public use for some time. However it represents an improvement and update in several major respects, including atomic data, code structure, user interface, and improved physical description of ionization/excitation. In particular, it now is applicable to high density situations in which significant excited atomic level populations are likely to occur. We describe the computational techniques and assumptions, and present sample runs with particular emphasis on high density situations.

A Brief Opportunity to Run Does Not Function as a Reinforcer for Mice Selected for High Daily Wheel-Running Rates

ERIC Educational Resources Information Center

Belke, Terry W.; Garland, Theodore, Jr.

2007-01-01

Mice from replicate lines, selectively bred based on high daily wheel-running rates, run more total revolutions and at higher average speeds than do mice from nonselected control lines. Based on this difference it was assumed that selected mice would find the opportunity to run in a wheel a more efficacious consequence. To assess this assumption…

Attacking 22 entries in rugby union: running demands and differences between successful and unsuccessful entries.

PubMed

Tierney, P; Tobin, D P; Blake, C; Delahunt, E

2017-12-01

Global Positioning System (GPS) technology is commonly utilized in team sports, including rugby union. It has been used to describe the average running demands of rugby union. This has afforded an enhanced understanding of the physical fitness requirements for players. However, research in team sports has suggested that training players relative to average demands may underprepare them for certain scenarios within the game. To date, no research has investigated the running demands of attacking 22 entries in rugby union. Additionally, no research has been undertaken to determine whether differences exist in the running intensity of successful and unsuccessful attacking 22 entries in rugby union. The first aim of this study was to describe the running intensity of attacking 22 entries. The second aim of this study was to investigate whether differences exist in the running intensity of successful and unsuccessful attacking 22 entries. Running intensity was measured using meters per minute (m min -1 ) for (a) total distance, (b) running distance, (c) high-speed running distance, and (d) very high-speed running distance. This study provides normative data for the running intensity of attacking 22 entries in rugby union. Forwards achieved greater high-speed running intensity in successful (3.6 m min -1 ) compared to unsuccessful (1.8 m min -1 ) attacking 22 entries. Forwards should try and achieve greater high-speed running intensity in attacking 22 entries to increase the likelihood of successful outcomes during this period of gameplay. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

First LHCb measurement with data from the LHC Run 2

NASA Astrophysics Data System (ADS)

Anderlini, L.; Amerio, S.

2017-01-01

LHCb has recently introduced a novel real-time detector alignment and calibration strategy for the Run 2. Data collected at the start of each LHC fill are processed in few minutes and used to update the alignment. On the other hand, the calibration constants will be evaluated for each run of data taking. An increase in the CPU and disk capacity of the event filter farm, combined with improvements to the reconstruction software, allow for efficient, exclusive selections already in the first stage of the High Level Trigger (HLT1), while the second stage, HLT2, performs complete, offline-quality, event reconstruction. In Run 2, LHCb will collect the largest data sample of charm mesons ever recorded. Novel data processing and analysis techniques are required to maximise the physics potential of this data sample with the available computing resources, taking into account data preservation constraints. In this write-up, we describe the full analysis chain used to obtain important results analysing the data collected in proton-proton collisions in 2015, such as the J/ψ and open charm production cross-sections, and consider the further steps required to obtain real-time results after the LHCb upgrade.

mr: A C++ library for the matching and running of the Standard Model parameters

NASA Astrophysics Data System (ADS)

Kniehl, Bernd A.; Pikelner, Andrey F.; Veretin, Oleg L.

2016-09-01

We present the C++ program library mr that allows us to reliably calculate the values of the running parameters in the Standard Model at high energy scales. The initial conditions are obtained by relating the running parameters in the MS bar renormalization scheme to observables at lower energies with full two-loop precision. The evolution is then performed in accordance with the renormalization group equations with full three-loop precision. Pure QCD corrections to the matching and running are included through four loops. We also provide a Mathematica interface for this program library. Catalogue identifier: AFAI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AFAI_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 517613 No. of bytes in distributed program, including test data, etc.: 2358729 Distribution format: tar.gz Programming language: C++. Computer: IBM PC. Operating system: Linux, Mac OS X. RAM: 1 GB Classification: 11.1. External routines: TSIL [1], OdeInt [2], boost [3] Nature of problem: The running parameters of the Standard Model renormalized in the MS bar scheme at some high renormalization scale, which is chosen by the user, are evaluated in perturbation theory as precisely as possible in two steps. First, the initial conditions at the electroweak energy scale are evaluated from the Fermi constant GF and the pole masses of the W, Z, and Higgs bosons and the bottom and top quarks including the full two-loop threshold corrections. Second, the evolution to the high energy scale is performed by numerically solving the renormalization group evolution equations through three loops. Pure QCD corrections to the matching and running are included through four loops. Solution method: Numerical integration of analytic expressions Additional comments: Available for download from URL: http://apik.github.io/mr/. The MathLink interface is tested to work with Mathematica 7-9 and, with an additional flag, also with Mathematica 10 under Linux and with Mathematica 10 under Mac OS X. Running time: less than 1 second References: [1] S. P. Martin and D. G. Robertson, Comput. Phys. Commun. 174 (2006) 133-151 [hep-ph/0501132]. [2] K. Ahnert and M. Mulansky, AIP Conf. Proc. 1389 (2011) 1586-1589 [arxiv:1110.3397 [cs.MS

eWaterCycle: A high resolution global hydrological model

NASA Astrophysics Data System (ADS)

van de Giesen, Nick; Bierkens, Marc; Drost, Niels; Hut, Rolf; Sutanudjaja, Edwin

2014-05-01

In 2013, the eWaterCycle project was started, which has the ambitious goal to run a high resolution global hydrological model. Starting point was the PCR-GLOBWB built by Utrecht University. The software behind this model will partially be re-engineered in order to enable to run it in a High Performance Computing (HPC) environment. The aim is to have a spatial resolution of 1km x 1km. The idea is also to run the model in real-time and forecasting mode, using data assimilation. An on-demand hydraulic model will be available for detailed flow and flood forecasting in support of navigation and disaster management. The project faces a set of scientific challenges. First, to enable the model to run in a HPC environment, model runs were analyzed to examine on which parts of the program most CPU time was spent. These parts were re-coded in Open MPI to allow for parallel processing. Different parallelization strategies are thinkable. In our case, it was decided to use watershed logic as a first step to distribute the analysis. There is rather limited recent experience with HPC in hydrology and there is much to be learned and adjusted, both on the hydrological modeling side and the computer science side. For example, an interesting early observation was that hydrological models are, due to their localized parameterization, much more memory intensive than models of sister-disciplines such as meteorology and oceanography. Because it would be deadly to have to swap information between CPU and hard drive, memory management becomes crucial. A standard Ensemble Kalman Filter (enKF) would, for example, have excessive memory demands. To circumvent these problems, an alternative to the enKF was developed that produces equivalent results. This presentation shows the most recent results from the model, including a 5km x 5km simulation and a proof of concept for the new data assimilation approach. Finally, some early ideas about financial sustainability of an operational global hydrological model are presented.

The diverse use of clouds by CMS

DOE PAGES

Andronis, Anastasios; Bauer, Daniela; Chaze, Olivier; ...

2015-12-23

The resources CMS is using are increasingly being offered as clouds. In Run 2 of the LHC the majority of CMS CERN resources, both in Meyrin and at the Wigner Computing Centre, will be presented as cloud resources on which CMS will have to build its own infrastructure. This infrastructure will need to run all of the CMS workflows including: Tier 0, production and user analysis. In addition, the CMS High Level Trigger will provide a compute resource comparable in scale to the total offered by the CMS Tier 1 sites, when it is not running as part of themore » trigger system. During these periods a cloud infrastructure will be overlaid on this resource, making it accessible for general CMS use. Finally, CMS is starting to utilise cloud resources being offered by individual institutes and is gaining experience to facilitate the use of opportunistically available cloud resources. Lastly, we present a snap shot of this infrastructure and its operation at the time of the CHEP2015 conference.« less

Walking, running, and resting under time, distance, and average speed constraints: optimality of walk-run-rest mixtures.

PubMed

Long, Leroy L; Srinivasan, Manoj

2013-04-06

On a treadmill, humans switch from walking to running beyond a characteristic transition speed. Here, we study human choice between walking and running in a more ecological (non-treadmill) setting. We asked subjects to travel a given distance overground in a given allowed time duration. During this task, the subjects carried, and could look at, a stopwatch that counted down to zero. As expected, if the total time available were large, humans walk the whole distance. If the time available were small, humans mostly run. For an intermediate total time, humans often use a mixture of walking at a slow speed and running at a higher speed. With analytical and computational optimization, we show that using a walk-run mixture at intermediate speeds and a walk-rest mixture at the lowest average speeds is predicted by metabolic energy minimization, even with costs for transients-a consequence of non-convex energy curves. Thus, sometimes, steady locomotion may not be energy optimal, and not preferred, even in the absence of fatigue. Assuming similar non-convex energy curves, we conjecture that similar walk-run mixtures may be energetically beneficial to children following a parent and animals on long leashes. Humans and other animals might also benefit energetically from alternating between moving forward and standing still on a slow and sufficiently long treadmill.

High-resolution quantification of atmospheric CO2 mixing ratios in the Greater Toronto Area, Canada

NASA Astrophysics Data System (ADS)

Pugliese, Stephanie C.; Murphy, Jennifer G.; Vogel, Felix R.; Moran, Michael D.; Zhang, Junhua; Zheng, Qiong; Stroud, Craig A.; Ren, Shuzhan; Worthy, Douglas; Broquet, Gregoire

2018-03-01

Many stakeholders are seeking methods to reduce carbon dioxide (CO2) emissions in urban areas, but reliable, high-resolution inventories are required to guide these efforts. We present the development of a high-resolution CO2 inventory available for the Greater Toronto Area and surrounding region in Southern Ontario, Canada (area of ˜ 2.8 × 105 km2, 26 % of the province of Ontario). The new SOCE (Southern Ontario CO2 Emissions) inventory is available at the 2.5 × 2.5 km spatial and hourly temporal resolution and characterizes emissions from seven sectors: area, residential natural-gas combustion, commercial natural-gas combustion, point, marine, on-road, and off-road. To assess the accuracy of the SOCE inventory, we developed an observation-model framework using the GEM-MACH chemistry-transport model run on a high-resolution grid with 2.5 km grid spacing coupled to the Fossil Fuel Data Assimilation System (FFDAS) v2 inventories for anthropogenic CO2 emissions and the European Centre for Medium-Range Weather Forecasts (ECMWF) land carbon model C-TESSEL for biogenic fluxes. A run using FFDAS for the Southern Ontario region was compared to a run in which its emissions were replaced by the SOCE inventory. Simulated CO2 mixing ratios were compared against in situ measurements made at four sites in Southern Ontario - Downsview, Hanlan's Point, Egbert and Turkey Point - in 3 winter months, January-March 2016. Model simulations had better agreement with measurements when using the SOCE inventory emissions versus other inventories, quantified using a variety of statistics such as correlation coefficient, root-mean-square error, and mean bias. Furthermore, when run with the SOCE inventory, the model had improved ability to capture the typical diurnal pattern of CO2 mixing ratios, particularly at the Downsview, Hanlan's Point, and Egbert sites. In addition to improved model-measurement agreement, the SOCE inventory offers a sectoral breakdown of emissions, allowing estimation of average time-of-day and day-of-week contributions of different sectors. Our results show that at night, emissions from residential and commercial natural-gas combustion and other area sources can contribute > 80 % of the CO2 enhancement, while during the day emissions from the on-road sector dominate, accounting for > 70 % of the enhancement.

77 FR 51993 - Western Technical College; Notice of Availability of Environmental Assessment

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-28

... hydroelectric generation at the dam. The dam is operated manually in a run-of-river mode (i.e., an operating...) distribution line; and (5) appurtenant facilities. The project would be operated in a run-of-river mode using... could otherwise enter project waters or adjacent non-project lands; Operating the project in a run-of...

76 FR 28505 - Okanogan Public Utility District No. 1 of Okanogan County, WA; Notice of Availability of Draft...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-17

....5 miles of new and upgraded access roads. The Enloe Project would operate automatically in a run-of... run-of-river and implementing agency-recommended ramping rates downstream of the project during... effects on geology and soils and water quality. Run-of-river operation would minimize effects on aquatic...

Using container orchestration to improve service management at the RAL Tier-1

NASA Astrophysics Data System (ADS)

Lahiff, Andrew; Collier, Ian

2017-10-01

In recent years container orchestration has been emerging as a means of gaining many potential benefits compared to a traditional static infrastructure, such as increased utilisation through multi-tenancy, improved availability due to self-healing, and the ability to handle changing loads due to elasticity and auto-scaling. To this end we have been investigating migrating services at the RAL Tier-1 to an Apache Mesos cluster. In this model the concept of individual machines is abstracted away and services are run in containers on a cluster of machines, managed by schedulers, enabling a high degree of automation. Here we describe Mesos, the infrastructure deployed at RAL, and describe in detail the explicit example of running a batch farm on Mesos.

Running climate model on a commercial cloud computing environment: A case study using Community Earth System Model (CESM) on Amazon AWS

NASA Astrophysics Data System (ADS)

Chen, Xiuhong; Huang, Xianglei; Jiao, Chaoyi; Flanner, Mark G.; Raeker, Todd; Palen, Brock

2017-01-01

The suites of numerical models used for simulating climate of our planet are usually run on dedicated high-performance computing (HPC) resources. This study investigates an alternative to the usual approach, i.e. carrying out climate model simulations on commercially available cloud computing environment. We test the performance and reliability of running the CESM (Community Earth System Model), a flagship climate model in the United States developed by the National Center for Atmospheric Research (NCAR), on Amazon Web Service (AWS) EC2, the cloud computing environment by Amazon.com, Inc. StarCluster is used to create virtual computing cluster on the AWS EC2 for the CESM simulations. The wall-clock time for one year of CESM simulation on the AWS EC2 virtual cluster is comparable to the time spent for the same simulation on a local dedicated high-performance computing cluster with InfiniBand connections. The CESM simulation can be efficiently scaled with the number of CPU cores on the AWS EC2 virtual cluster environment up to 64 cores. For the standard configuration of the CESM at a spatial resolution of 1.9° latitude by 2.5° longitude, increasing the number of cores from 16 to 64 reduces the wall-clock running time by more than 50% and the scaling is nearly linear. Beyond 64 cores, the communication latency starts to outweigh the benefit of distributed computing and the parallel speedup becomes nearly unchanged.

LHCb detector and trigger performance in Run II

NASA Astrophysics Data System (ADS)

Francesca, Dordei

2017-12-01

The LHCb detector is a forward spectrometer at the LHC, designed to perform high precision studies of b- and c- hadrons. In Run II of the LHC, a new scheme for the software trigger at LHCb allows splitting the triggering of events into two stages, giving room to perform the alignment and calibration in real time. In the novel detector alignment and calibration strategy for Run II, data collected at the start of the fill are processed in a few minutes and used to update the alignment, while the calibration constants are evaluated for each run. This allows identical constants to be used in the online and offline reconstruction, thus improving the correlation between triggered and offline selected events. The required computing time constraints are met thanks to a new dedicated framework using the multi-core farm infrastructure for the trigger. The larger timing budget, available in the trigger, allows to perform the same track reconstruction online and offline. This enables LHCb to achieve the best reconstruction performance already in the trigger, and allows physics analyses to be performed directly on the data produced by the trigger reconstruction. The novel real-time processing strategy at LHCb is discussed from both the technical and operational point of view. The overall performance of the LHCb detector on the data of Run II is presented as well.

Can High-resolution WRF Simulations Be Used for Short-term Forecasting of Lightning?

NASA Technical Reports Server (NTRS)

Goodman, S. J.; Lapenta, W.; McCaul, E. W., Jr.; LaCasse, K.; Petersen, W.

2006-01-01

A number of research teams have begun to make quasi-operational forecast simulations at high resolution with models such as the Weather Research and Forecast (WRF) model. These model runs have used horizontal meshes of 2-4 km grid spacing, and thus resolved convective storms explicitly. In the light of recent global satellite-based observational studies that reveal robust relationships between total lightning flash rates and integrated amounts of precipitation-size ice hydrometeors in storms, it is natural to inquire about the capabilities of these convection-resolving models in representing the ice hydrometeor fields faithfully. If they do, this might make operational short-term forecasts of lightning activity feasible. We examine high-resolution WRF simulations from several Southeastern cases for which either NLDN or LMA lightning data were available. All the WRF runs use a standard microphysics package that depicts only three ice species, cloud ice, snow and graupel. The realism of the WRF simulations is examined by comparisons with both lightning and radar observations and with additional even higher-resolution cloud-resolving model runs. Preliminary findings are encouraging in that they suggest that WRF often makes convective storms of the proper size in approximately the right location, but they also indicate that higher resolution and better hydrometeor microphysics would be helpful in improving the realism of the updraft strengths, reflectivity and ice hydrometeor fields.

A Registrar Administration System Requirements Analysis and Product Recommendation for Marine Corps University, Quantico, VA

DTIC Science & Technology

2011-09-01

rate Python’s maturity as “High.” Python is nine years old and has been continuously been developed and enhanced since then. During fiscal year 2010...We rate Python’s developer toolkit availability/extensibility as “Yes.” Python runs on a SQL database and is 64 compatible with Oracle database...MODEL...........................................................................11 D. GOAL DEVELOPMENT

Selecting a Benchmark Suite to Profile High-Performance Computing (HPC) Machines

DTIC Science & Technology

2014-11-01

architectures. Machines now contain central processing units (CPUs), graphics processing units (GPUs), and many integrated core ( MIC ) architecture all...evaluate the feasibility and applicability of a new architecture just released to the market . Researchers are often unsure how available resources will...architectures. Having a suite of programs running on different architectures, such as GPUs, MICs , and CPUs, adds complexity and technical challenges

libRoadRunner: a high performance SBML simulation and analysis library.

PubMed

Somogyi, Endre T; Bouteiller, Jean-Marie; Glazier, James A; König, Matthias; Medley, J Kyle; Swat, Maciej H; Sauro, Herbert M

2015-10-15

This article presents libRoadRunner, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using Systems Biology Markup Language (SBML). SBML is the most widely used standard for representing dynamic networks, especially biochemical networks. libRoadRunner is fast enough to support large-scale problems such as tissue models, studies that require large numbers of repeated runs and interactive simulations. libRoadRunner is a self-contained library, able to run both as a component inside other tools via its C++ and C bindings, and interactively through its Python interface. Its Python Application Programming Interface (API) is similar to the APIs of MATLAB ( WWWMATHWORKSCOM: ) and SciPy ( HTTP//WWWSCIPYORG/: ), making it fast and easy to learn. libRoadRunner uses a custom Just-In-Time (JIT) compiler built on the widely used LLVM JIT compiler framework. It compiles SBML-specified models directly into native machine code for a variety of processors, making it appropriate for solving extremely large models or repeated runs. libRoadRunner is flexible, supporting the bulk of the SBML specification (except for delay and non-linear algebraic equations) including several SBML extensions (composition and distributions). It offers multiple deterministic and stochastic integrators, as well as tools for steady-state analysis, stability analysis and structural analysis of the stoichiometric matrix. libRoadRunner binary distributions are available for Mac OS X, Linux and Windows. The library is licensed under Apache License Version 2.0. libRoadRunner is also available for ARM-based computers such as the Raspberry Pi. http://www.libroadrunner.org provides online documentation, full build instructions, binaries and a git source repository. hsauro@u.washington.edu or somogyie@indiana.edu Supplementary data are available at Bioinformatics online. Published by Oxford University Press 2015. This work is written by US Government employees and is in the public domain in the US.

Improving overlay control through proper use of multilevel query APC

NASA Astrophysics Data System (ADS)

Conway, Timothy H.; Carlson, Alan; Crow, David A.

2003-06-01

Many state-of-the-art fabs are operating with increasingly diversified product mixes. For example, at Cypress Semiconductor, it is not unusual to be concurrently running multiple technologies and many devices within each technology. This diverse product mix significantly increases the difficulty of manually controlling overlay process corrections. As a result, automated run-to-run feedforward-feedback control has become a necessary and vital component of manufacturing. However, traditional run-to-run controllers rely on highly correlated historical events to forecast process corrections. For example, the historical process events typically are constrained to match the current event for exposure tool, device, process level and reticle ID. This narrowly defined process stream can result in insufficient data when applied to lowvolume or new-release devices. The run-to-run controller implemented at Cypress utilizes a multi-level query (Level-N) correlation algorithm, where each subsequent level widens the search criteria for available historical data. The paper discusses how best to widen the search criteria and how to determine and apply a known bias to account for tool-to-tool and device-to-device differences. Specific applications include offloading lots from one tool to another when the first tool is down for preventive maintenance, utilizing related devices to determine a default feedback vector for new-release devices, and applying bias values to account for known reticle-to-reticle differences. In this study, we will show how historical data can be leveraged from related devices or tools to overcome the limitations of narrow process streams. In particular, this paper discusses how effectively handling narrow process streams allows Cypress to offload lots from a baseline tool to an alternate tool.

Bridge Crossing Simulator

DTIC Science & Technology

2014-10-07

is counted as. Per the TDTC, a test bridge with longitudinal and/or lateral symmetry under non- eccentric loading can be considered as 1, 2, or 4...Level Run036 3 MLC70T (tracked) BA Run046 6 AB Run055 9 AB Run060 9 BA Run064 12 BA Run071 15 AB Run155 3 MLC96W ( wheeled ) AB...Run331 9 AB Run359 15 AB Run430 12 MLC96W ( wheeled ) BA Run434 12 AB Run447 3 BA Bank Condition: Side Slope, Even Strain Channels High

Soy protein is beneficial but high-fat diet and voluntary running are detrimental to bone structure in mice.

PubMed

Yan, Lin; Graef, George L; Nielsen, Forrest H; Johnson, LuAnn K; Cao, Jay

2015-06-01

Physical activity and soy protein isolate (SPI) augmentation have been reported to be beneficial for bone health. We hypothesized that combining voluntary running and SPI intake would alleviate detrimental changes in bone induced by a high-fat diet. A 2 × 2 × 2 experiment was designed with diets containing 16% or 45% of energy as corn oil and 20% SPI or casein fed to sedentary or running male C57BL/6 mice for 14 weeks. Distal femurs were assessed for microstructural changes. The high-fat diet significantly decreased trabecular number (Tb.N) and bone mineral density (BMD) and increased trabecular separation (Tb.Sp). Soy protein instead of casein, regardless of fat content, in the diet significantly increased bone volume fraction, Tb.N, connectivity density, and BMD and decreased Tb.Sp. Voluntary running, regardless of fat content, significantly decreased bone volume fraction, Tb.N, connectivity density, and BMD and increased Tb.Sp. The high-fat diet significantly decreased osteocalcin and increased tartrate-resistant acid phosphatase 5b (TRAP 5b) concentrations in plasma. Plasma concentrations of osteocalcin were increased by both SPI and running. Running alleviated the increase in TRAP 5b induced by the high-fat diet. These findings demonstrate that a high-fat diet is deleterious, and SPI is beneficial to trabecular bone properties. The deleterious effect of voluntary running on trabecular structural characteristics indicates that there may be a maximal threshold of running beyond which beneficial effects cease and detrimental effects occur. Increases in plasma osteocalcin and decreases in plasma TRAP 5b in running mice suggest that a compensatory response occurs to counteract the detrimental effects of excessive running. Published by Elsevier Inc.

Lower limb mechanics during moderate high-heel jogging and running in different experienced wearers.

PubMed

Fu, Fengqin; Zhang, Yan; Shu, Yang; Ruan, Guoqing; Sun, Jianjun; Baker, Julien S; Gu, Yaodong

2016-08-01

The aim of this study is to investigate the differences in lower limb kinematics and kinetics between experienced (EW) and inexperienced (IEW) moderate high-heel wearers during jogging and running. Eleven experienced female wearers of moderate high-heel shoes and eleven matched controls participated in jogging and running tests. A Vicon motion analysis system was used to capture kinematic data and a Kistler force platform was used to collect ground reaction force (GRF). There were no significant differences in jogging and running speed respectively. Compared with IEW, EW adopted larger stride length (SL) with lower stride frequency (SF) at each corresponding speed. During running, EW enlarged SL significantly while IEW increased both SL and SF significantly. Kinematic data showed that IEW had generally larger joint range of motion (ROM) and peak angles during stance phase. Speed effect was not obvious within IEW. EW exhibited a significantly increased maximal vertical GRF (Fz2) and vertical average loading rate (VALR) during running, which was potentially caused by overlong stride. These suggest that both EW and IEW are at high risk of joint injuries when running on moderate high heels. For wearers who have to do some running on moderate high heels, it is crucial to control joint stability and balance SL and SF consciously. Copyright © 2016 Elsevier B.V. All rights reserved.

Running economy : the forgotten factor in elite performance.

PubMed

Foster, Carl; Lucia, Alejandro

2007-01-01

Running performance depends on maximal oxygen uptake (VO(2max)), the ability to sustain a high percentage of VO(2max) for an extended period of time and running economy. Running economy has been studied relatively less than the other factors. Running economy, measured as steady state oxygen uptake (VO(2)) at intensities below the ventilatory threshold is the standard method. Extrapolation to a common running speed (268 m/min) or as the VO(2) required to run a kilometer is the standard method of assessment. Individuals of East African origin may be systematically more economical, although a smaller body size and a thinner lower leg may be the primary factors. Strategies for improving running economy remain to be developed, although it appears that high intensity running may be a common element acting to improve economy.

CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment

PubMed Central

Manavski, Svetlin A; Valle, Giorgio

2008-01-01

Background Searching for similarities in protein and DNA databases has become a routine procedure in Molecular Biology. The Smith-Waterman algorithm has been available for more than 25 years. It is based on a dynamic programming approach that explores all the possible alignments between two sequences; as a result it returns the optimal local alignment. Unfortunately, the computational cost is very high, requiring a number of operations proportional to the product of the length of two sequences. Furthermore, the exponential growth of protein and DNA databases makes the Smith-Waterman algorithm unrealistic for searching similarities in large sets of sequences. For these reasons heuristic approaches such as those implemented in FASTA and BLAST tend to be preferred, allowing faster execution times at the cost of reduced sensitivity. The main motivation of our work is to exploit the huge computational power of commonly available graphic cards, to develop high performance solutions for sequence alignment. Results In this paper we present what we believe is the fastest solution of the exact Smith-Waterman algorithm running on commodity hardware. It is implemented in the recently released CUDA programming environment by NVidia. CUDA allows direct access to the hardware primitives of the last-generation Graphics Processing Units (GPU) G80. Speeds of more than 3.5 GCUPS (Giga Cell Updates Per Second) are achieved on a workstation running two GeForce 8800 GTX. Exhaustive tests have been done to compare our implementation to SSEARCH and BLAST, running on a 3 GHz Intel Pentium IV processor. Our solution was also compared to a recently published GPU implementation and to a Single Instruction Multiple Data (SIMD) solution. These tests show that our implementation performs from 2 to 30 times faster than any other previous attempt available on commodity hardware. Conclusions The results show that graphic cards are now sufficiently advanced to be used as efficient hardware accelerators for sequence alignment. Their performance is better than any alternative available on commodity hardware platforms. The solution presented in this paper allows large scale alignments to be performed at low cost, using the exact Smith-Waterman algorithm instead of the largely adopted heuristic approaches. PMID:18387198

SWATShare- A Platform for Collaborative Hydrology Research and Education with Cyber-enabled Sharing, Running and Visualization of SWAT Models

NASA Astrophysics Data System (ADS)

Rajib, M. A.; Merwade, V.; Song, C.; Zhao, L.; Kim, I. L.; Zhe, S.

2014-12-01

Setting up of any hydrologic model requires a large amount of efforts including compilation of all the data, creation of input files, calibration and validation. Given the amount of efforts involved, it is possible that models for a watershed get created multiple times by multiple groups or organizations to accomplish different research, educational or policy goals. To reduce the duplication of efforts and enable collaboration among different groups or organizations around an already existing hydrology model, a platform is needed where anyone can search for existing models, perform simple scenario analysis and visualize model results. The creator and users of a model on such a platform can then collaborate to accomplish new research or educational objectives. From this perspective, a prototype cyber-infrastructure (CI), called SWATShare, is developed for sharing, running and visualizing Soil Water Assessment Tool (SWAT) models in an interactive GIS-enabled web environment. Users can utilize SWATShare to publish or upload their own models, search and download existing SWAT models developed by others, run simulations including calibration using high performance resources provided by XSEDE and Cloud. Besides running and sharing, SWATShare hosts a novel spatio-temporal visualization system for SWAT model outputs. In temporal scale, the system creates time-series plots for all the hydrology and water quality variables available along the reach as well as in watershed-level. In spatial scale, the system can dynamically generate sub-basin level thematic maps for any variable at any user-defined date or date range; and thereby, allowing users to run animations or download the data for subsequent analyses. In addition to research, SWATShare can also be used within a classroom setting as an educational tool for modeling and comparing the hydrologic processes under different geographic and climatic settings. SWATShare is publicly available at https://www.water-hub.org/swatshare.

Dual design resistor for high voltage conditioning and transmission lines

DOEpatents

Siggins, Timothy Lynn [Newport News, VA; Murray, Charles W [Hayes, VA; Walker, Richard L [Norfolk, VA

2007-01-23

A dual resistor for eliminating the requirement for two different value resistors. The dual resistor includes a conditioning resistor at a high resistance value and a run resistor at a low resistance value. The run resistor can travel inside the conditioning resistor. The run resistor is capable of being advanced by a drive assembly until an electrical path is completed through the run resistor thereby shorting out the conditioning resistor and allowing the lower resistance run resistor to take over as the current carrier.

Enhanced Endurance Performance by Periodization of Carbohydrate Intake: "Sleep Low" Strategy.

PubMed

Marquet, Laurie-Anne; Brisswalter, Jeanick; Louis, Julien; Tiollier, Eve; Burke, Louise M; Hawley, John A; Hausswirth, Christophe

2016-04-01

We investigated the effect of a chronic dietary periodization strategy on endurance performance in trained athletes. Twenty-one triathletes (V˙O2max: 58.7 ± 5.7 mL·min(-1)·kg(-1)) were divided into two groups: a "sleep-low" (SL) (n = 11) and a control (CON) group (n = 10) consumed the same daily carbohydrate (CHO) intake (6 g·kg(-1)·d(-1)) but with different timing over the day to manipulate CHO availability before and after training sessions. The SL strategy consisted of a 3-wk training-diet intervention comprising three blocks of diet-exercise manipulations: 1) "train-high" interval training sessions in the evening with high-CHO availability, 2) overnight CHO restriction ("sleeping-low"), and 3) "train-low" sessions with low endogenous and exogenous CHO availability. The CON group followed the same training program but with high CHO availability throughout training sessions (no CHO restriction overnight, training sessions with exogenous CHO provision). There was a significant improvement in delta efficiency during submaximal cycling for SL versus CON (CON, +1.4% ± 9.3%; SL, +11% ± 15%, P < 0.05). SL also improved supramaximal cycling to exhaustion at 150% of peak aerobic power (CON, +1.63% ± 12.4%; SL, +12.5% ± 19.0%; P = 0.06) and 10-km running performance (CON, -0.10% ± 2.03%; SL, -2.9% ± 2.15%; P < 0.05). Fat mass was decreased in SL (CON, -2.6 ± 7.4; SL, -8.5% ± 7.4% before; P < 0.01), but not lean mass (CON, -0.22 ± 1.0; SL, -0.16% ± 1.7% PRE). Short-term periodization of dietary CHO availability around selected training sessions promoted significant improvements in submaximal cycling economy, as well as supramaximal cycling capacity and 10-km running time in trained endurance athletes.

Surrogate Reservoir Model

NASA Astrophysics Data System (ADS)

Mohaghegh, Shahab

2010-05-01

Surrogate Reservoir Model (SRM) is new solution for fast track, comprehensive reservoir analysis (solving both direct and inverse problems) using existing reservoir simulation models. SRM is defined as a replica of the full field reservoir simulation model that runs and provides accurate results in real-time (one simulation run takes only a fraction of a second). SRM mimics the capabilities of a full field model with high accuracy. Reservoir simulation is the industry standard for reservoir management. It is used in all phases of field development in the oil and gas industry. The routine of simulation studies calls for integration of static and dynamic measurements into the reservoir model. Full field reservoir simulation models have become the major source of information for analysis, prediction and decision making. Large prolific fields usually go through several versions (updates) of their model. Each new version usually is a major improvement over the previous version. The updated model includes the latest available information incorporated along with adjustments that usually are the result of single-well or multi-well history matching. As the number of reservoir layers (thickness of the formations) increases, the number of cells representing the model approaches several millions. As the reservoir models grow in size, so does the time that is required for each run. Schemes such as grid computing and parallel processing helps to a certain degree but do not provide the required speed for tasks such as: field development strategies using comprehensive reservoir analysis, solving the inverse problem for injection/production optimization, quantifying uncertainties associated with the geological model and real-time optimization and decision making. These types of analyses require hundreds or thousands of runs. Furthermore, with the new push for smart fields in the oil/gas industry that is a natural growth of smart completion and smart wells, the need for real time reservoir modeling becomes more pronounced. SRM is developed using the state of the art in neural computing and fuzzy pattern recognition to address the ever growing need in the oil and gas industry to perform accurate, but high speed simulation and modeling. Unlike conventional geo-statistical approaches (response surfaces, proxy models …) that require hundreds of simulation runs for development, SRM is developed only with a few (from 10 to 30 runs) simulation runs. SRM can be developed regularly (as new versions of the full field model become available) off-line and can be put online for real-time processing to guide important decisions. SRM has proven its value in the field. An SRM was developed for a giant oil field in the Middle East. The model included about one million grid blocks with more than 165 horizontal wells and took ten hours for a single run on 12 parallel CPUs. Using only 10 simulation runs, an SRM was developed that was able to accurately mimic the behavior of the reservoir simulation model. Performing a comprehensive reservoir analysis that included making millions of SRM runs, wells in the field were divided into five clusters. It was predicted that wells in cluster one & two are best candidates for rate relaxation with minimal, long term water production while wells in clusters four and five are susceptive to high water cuts. Two and a half years and 20 wells later, rate relaxation results from the field proved that all the predictions made by the SRM analysis were correct. While incremental oil production increased in all wells (wells in clusters 1 produced the most followed by wells in cluster 2, 3 …) the percent change in average monthly water cut for wells in each cluster clearly demonstrated the analytic power of SRM. As it was correctly predicted, wells in clusters 1 and 2 actually experience a reduction in water cut while a substantial increase in water cut was observed in wells classified into clusters 4 and 5. Performing these analyses would have been impossible using the original full field simulation model.

The influence of breast support on torso, pelvis and arm kinematics during a five kilometer treadmill run.

PubMed

Milligan, Alexandra; Mills, Chris; Corbett, Jo; Scurr, Joanna

2015-08-01

Many women wear sports bras due to positive benefits associated with these garments (i.e. reduction in breast movement and breast pain), however the effects these garments have on upper body running kinematics has not been investigated. Ten female participants (32 DD or 34 D) completed two five kilometer treadmill runs (9 km h(-1)), once in a low and once in a high breast support. The range of motion (ROM) and peak torso, pelvis, and upper arm Cardan joint angles were calculated over five gait cycles during a five kilometer run. Peak torso yaw, peak rotation of the pelvis, peak pelvis obliquity, ROM in rotation of the pelvis, and ROM in upper arm extension were significant, but marginally reduced when participants ran in the high breast support. The running kinematics reported in the high breast support condition more closely align with economical running kinematics previously defined in the literature, therefore, running in a high breast support may be more beneficial to female runners, with a high breast support advocated for middle distance runners. Copyright © 2015 Elsevier B.V. All rights reserved.

Clumpak: a program for identifying clustering modes and packaging population structure inferences across K.

PubMed

Kopelman, Naama M; Mayzel, Jonathan; Jakobsson, Mattias; Rosenberg, Noah A; Mayrose, Itay

2015-09-01

The identification of the genetic structure of populations from multilocus genotype data has become a central component of modern population-genetic data analysis. Application of model-based clustering programs often entails a number of steps, in which the user considers different modelling assumptions, compares results across different predetermined values of the number of assumed clusters (a parameter typically denoted K), examines multiple independent runs for each fixed value of K, and distinguishes among runs belonging to substantially distinct clustering solutions. Here, we present Clumpak (Cluster Markov Packager Across K), a method that automates the postprocessing of results of model-based population structure analyses. For analysing multiple independent runs at a single K value, Clumpak identifies sets of highly similar runs, separating distinct groups of runs that represent distinct modes in the space of possible solutions. This procedure, which generates a consensus solution for each distinct mode, is performed by the use of a Markov clustering algorithm that relies on a similarity matrix between replicate runs, as computed by the software Clumpp. Next, Clumpak identifies an optimal alignment of inferred clusters across different values of K, extending a similar approach implemented for a fixed K in Clumpp and simplifying the comparison of clustering results across different K values. Clumpak incorporates additional features, such as implementations of methods for choosing K and comparing solutions obtained by different programs, models, or data subsets. Clumpak, available at http://clumpak.tau.ac.il, simplifies the use of model-based analyses of population structure in population genetics and molecular ecology. © 2015 John Wiley & Sons Ltd.

Carbohydrate Nutrition and Team Sport Performance.

PubMed

Williams, Clyde; Rollo, Ian

2015-11-01

The common pattern of play in 'team sports' is 'stop and go', i.e. where players perform repeated bouts of brief high-intensity exercise punctuated by lower intensity activity. Sprints are generally 2-4 s long and recovery between sprints is of variable length. Energy production during brief sprints is derived from the degradation of intra-muscular phosphocreatine and glycogen (anaerobic metabolism). Prolonged periods of multiple sprints drain muscle glycogen stores, leading to a decrease in power output and a reduction in general work rate during training and competition. The impact of dietary carbohydrate interventions on team sport performance have been typically assessed using intermittent variable-speed shuttle running over a distance of 20 m. This method has evolved to include specific work to rest ratios and skills specific to team sports such as soccer, rugby and basketball. Increasing liver and muscle carbohydrate stores before sports helps delay the onset of fatigue during prolonged intermittent variable-speed running. Carbohydrate intake during exercise, typically ingested as carbohydrate-electrolyte solutions, is also associated with improved performance. The mechanisms responsible are likely to be the availability of carbohydrate as a substrate for central and peripheral functions. Variable-speed running in hot environments is limited by the degree of hyperthermia before muscle glycogen availability becomes a significant contributor to the onset of fatigue. Finally, ingesting carbohydrate immediately after training and competition will rapidly recover liver and muscle glycogen stores.

High-intensity interval running is perceived to be more enjoyable than moderate-intensity continuous exercise: implications for exercise adherence.

PubMed

Bartlett, Jonathan D; Close, Graeme L; MacLaren, Don P M; Gregson, Warren; Drust, Barry; Morton, James P

2011-03-01

The aim of this study was to objectively quantify ratings of perceived enjoyment using the Physical Activity Enjoyment Scale following high-intensity interval running versus moderate-intensity continuous running. Eight recreationally active men performed two running protocols consisting of high-intensity interval running (6 × 3 min at 90% VO(2max) interspersed with 6 × 3 min active recovery at 50% VO(2max) with a 7-min warm-up and cool down at 70% VO(2max)) or 50 min moderate-intensity continuous running at 70% VO(2max). Ratings of perceived enjoyment after exercise were higher (P < 0.05) following interval running compared with continuous running (88 ± 6 vs. 61 ± 12) despite higher (P < 0.05) ratings of perceived exertion (14 ± 1 vs. 13 ± 1). There was no difference (P < 0.05) in average heart rate (88 ± 3 vs. 87 ± 3% maximum heart rate), average VO(2) (71 ± 6 vs. 73 ± 4%VO(2max)), total VO(2) (162 ± 16 vs. 166 ± 27 L) or energy expenditure (811 ± 83 vs. 832 ± 136 kcal) between protocols. The greater enjoyment associated with high-intensity interval running may be relevant for improving exercise adherence, since running is a low-cost exercise intervention requiring no exercise equipment and similar relative exercise intensities have previously induced health benefits in patient populations.

Walking, running, and resting under time, distance, and average speed constraints: optimality of walk–run–rest mixtures

PubMed Central

Long, Leroy L.; Srinivasan, Manoj

2013-01-01

On a treadmill, humans switch from walking to running beyond a characteristic transition speed. Here, we study human choice between walking and running in a more ecological (non-treadmill) setting. We asked subjects to travel a given distance overground in a given allowed time duration. During this task, the subjects carried, and could look at, a stopwatch that counted down to zero. As expected, if the total time available were large, humans walk the whole distance. If the time available were small, humans mostly run. For an intermediate total time, humans often use a mixture of walking at a slow speed and running at a higher speed. With analytical and computational optimization, we show that using a walk–run mixture at intermediate speeds and a walk–rest mixture at the lowest average speeds is predicted by metabolic energy minimization, even with costs for transients—a consequence of non-convex energy curves. Thus, sometimes, steady locomotion may not be energy optimal, and not preferred, even in the absence of fatigue. Assuming similar non-convex energy curves, we conjecture that similar walk–run mixtures may be energetically beneficial to children following a parent and animals on long leashes. Humans and other animals might also benefit energetically from alternating between moving forward and standing still on a slow and sufficiently long treadmill. PMID:23365192

Anthropometric, Sprint, and High-Intensity Running Profiles of English Academy Rugby Union Players by Position.

PubMed

Darrall-Jones, Joshua D; Jones, Ben; Till, Kevin

2016-05-01

The purpose of this study was to evaluate the anthropometric, sprint, and high-intensity running profiles of English academy rugby union players by playing positions, and to investigate the relationships between anthropometric, sprint, and high-intensity running characteristics. Data were collected from 67 academy players after the off-season period and consisted of anthropometric (height, body mass, sum of 8 skinfolds [∑SF]), 40-m linear sprint (5-, 10-, 20-, and 40-m splits), the Yo-Yo intermittent recovery test level 1 (Yo-Yo IRTL-1), and the 30-15 intermittent fitness test (30-15 IFT). Forwards displayed greater stature, body mass, and ∑SF; sprint times and sprint momentum, with lower high-intensity running ability and sprint velocities than backs. Comparisons between age categories demonstrated body mass and sprint momentum to have the largest differences at consecutive age categories for forwards and backs; whereas 20-40-m sprint velocity was discriminate for forwards between under 16s, 18s, and 21s. Relationships between anthropometric, sprint velocity, momentum, and high-intensity running ability demonstrated body mass to negatively impact on sprint velocity (10 m; r = -0.34 to -0.46) and positively affect sprint momentum (e.g., 5 m; r = 0.85-0.93), with large to very large negative relationships with the Yo-Yo IRTL-1 (r = -0.65 to -0.74) and 30-15 IFT (r = -0.59 to -0.79). These findings suggest that there are distinct anthropometric, sprint, and high-intensity running ability differences between and within positions in junior rugby union players. The development of sprint and high-intensity running ability may be impacted by continued increases in body mass as there seems to be a trade-off between momentum, velocity, and the ability to complete high-intensity running.

Factors affecting running performance in 6-12-year-olds: The Health Oriented Pedagogical Project (HOPP).

PubMed

Fredriksen, Per Morten; Mamen, Asgeir; Gammelsrud, Heidi; Lindberg, Morten; Hjelle, Ole Petter

2018-05-01

The purpose of this study was to examine factors affecting running performance in children. A cross-sectional study exploring the relationships between height, weight, waist circumference, muscle mass, body fat percentage, relevant biomarkers, and the Andersen intermittent running test in 2272 children aged 6 to 12 years. Parental education level was used as a non-physiological explanatory variable. Mean values (SD) and percentiles are presented as reference values. Height (β = 6.4, p < .0001), high values of haemoglobin (β = 18, p = .013) and low percentage of body fat (β = -7.5, p < .0001) showed an association with results from the running test. In addition, high parental education level showed a positive association with the running test. Boys display better running performance than girls at all age ages, except 7 years old, probably because of additional muscle mass and less fatty tissue. Height and increased level of haemoglobin positively affected running performance. Lower body fat percentage and high parental education level correlated with better running performance.

Automated multi-dimensional purification of tagged proteins.

PubMed

Sigrell, Jill A; Eklund, Pär; Galin, Markus; Hedkvist, Lotta; Liljedahl, Pia; Johansson, Christine Markeland; Pless, Thomas; Torstenson, Karin

2003-01-01

The capacity for high throughput purification (HTP) is essential in fields such as structural genomics where large numbers of protein samples are routinely characterized in, for example, studies of structural determination, functionality and drug development. Proteins required for such analysis must be pure and homogenous and available in relatively large amounts. AKTA 3D system is a powerful automated protein purification system, which minimizes preparation, run-time and repetitive manual tasks. It has the capacity to purify up to 6 different His6- or GST-tagged proteins per day and can produce 1-50 mg protein per run at >90% purity. The success of automated protein purification increases with careful experimental planning. Protocol, columns and buffers need to be chosen with the final application area for the purified protein in mind.

The HEASARC graphical user interface

NASA Technical Reports Server (NTRS)

White, N.; Barrett, P.; Jacobs, P.; Oneel, B.

1992-01-01

An OSF/Motif-based graphical user interface has been developed to facilitate the use of the database and data analysis software packages available from the High Energy Astrophysics Science Archive Research Center (HEASARC). It can also be used as an interface to other, similar, routines. A small number of tables are constructed to specify the possible commands and command parameters for a given set of analysis routines. These tables can be modified by a designer to affect the appearance of the interface screens. They can also be dynamically changed in response to parameter adjustments made while the underlying program is running. Additionally, a communication protocol has been designed so that the interface can operate locally or across a network. It is intended that this software be able to run on a variety of workstations and X terminals.

Effect of sucrose availability and pre-running on the intrinsic value of wheel running as an operant and a reinforcing consequence.

PubMed

Belke, Terry W; Pierce, W David

2014-03-01

The current study investigated the effect of motivational manipulations on operant wheel running for sucrose reinforcement and on wheel running as a behavioral consequence for lever pressing, within the same experimental context. Specifically, rats responded on a two-component multiple schedule of reinforcement in which lever pressing produced the opportunity to run in a wheel in one component of the schedule (reinforcer component) and wheel running produced the opportunity to consume sucrose solution in the other component (operant component). Motivational manipulations involved removal of sucrose contingent on wheel running and providing 1h of pre-session wheel running. Results showed that, in opposition to a response strengthening view, sucrose did not maintain operant wheel running. The motivational operations of withdrawing sucrose or providing pre-session wheel running, however, resulted in different wheel-running rates in the operant and reinforcer components of the multiple schedule; this rate discrepancy revealed the extrinsic reinforcing effects of sucrose on operant wheel running, but also indicated the intrinsic reinforcement value of wheel running across components. Differences in wheel-running rates between components were discussed in terms of arousal, undermining of intrinsic motivation, and behavioral contrast. Copyright © 2013 Elsevier B.V. All rights reserved.

Capsule modeling of high foot implosion experiments on the National Ignition Facility

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

Clark, D. S.; Kritcher, A. L.; Milovich, J. L.

This study summarizes the results of detailed, capsule-only simulations of a set of high foot implosion experiments conducted on the National Ignition Facility (NIF). These experiments span a range of ablator thicknesses, laser powers, and laser energies, and modeling these experiments as a set is important to assess whether the simulation model can reproduce the trends seen experimentally as the implosion parameters were varied. Two-dimensional (2D) simulations have been run including a number of effects—both nominal and off-nominal—such as hohlraum radiation asymmetries, surface roughness, the capsule support tent, and hot electron pre-heat. Selected three-dimensional simulations have also been run tomore » assess the validity of the 2D axisymmetric approximation. As a composite, these simulations represent the current state of understanding of NIF high foot implosion performance using the best and most detailed computational model available. While the most detailed simulations show approximate agreement with the experimental data, it is evident that the model remains incomplete and further refinements are needed. Nevertheless, avenues for improved performance are clearly indicated.« less

Capsule modeling of high foot implosion experiments on the National Ignition Facility

DOE PAGES

Clark, D. S.; Kritcher, A. L.; Milovich, J. L.; ...

2017-03-21

This study summarizes the results of detailed, capsule-only simulations of a set of high foot implosion experiments conducted on the National Ignition Facility (NIF). These experiments span a range of ablator thicknesses, laser powers, and laser energies, and modeling these experiments as a set is important to assess whether the simulation model can reproduce the trends seen experimentally as the implosion parameters were varied. Two-dimensional (2D) simulations have been run including a number of effects—both nominal and off-nominal—such as hohlraum radiation asymmetries, surface roughness, the capsule support tent, and hot electron pre-heat. Selected three-dimensional simulations have also been run tomore » assess the validity of the 2D axisymmetric approximation. As a composite, these simulations represent the current state of understanding of NIF high foot implosion performance using the best and most detailed computational model available. While the most detailed simulations show approximate agreement with the experimental data, it is evident that the model remains incomplete and further refinements are needed. Nevertheless, avenues for improved performance are clearly indicated.« less

Development and Implementation of the DTOPLATS-MP land surface model over the Continental US at 30 meters

NASA Astrophysics Data System (ADS)

Chaney, N.; Wood, E. F.

2014-12-01

The increasing accessibility of high-resolution land data (< 100 m) and high performance computing allows improved parameterizations of subgrid hydrologic processes in macroscale land surface models. Continental scale fully distributed modeling at these spatial scales is possible; however, its practicality for operational use is still unknown due to uncertainties in input data, model parameters, and storage requirements. To address these concerns, we propose a modeling framework that provides the spatial detail of a fully distributed model yet maintains the benefits of a semi-distributed model. In this presentation we will introduce DTOPLATS-MP, a coupling between the NOAH-MP land surface model and the Dynamic TOPMODEL hydrologic model. This new model captures a catchment's spatial heterogeneity by clustering high-resolution land datasets (soil, topography, and land cover) into hundreds of hydrologic similar units (HSUs). A prior DEM analysis defines the connections between each HSU. At each time step, the 1D land surface model updates each HSU; the HSUs then interact laterally via the subsurface and surface. When compared to the fully distributed form of the model, this framework allows a significant decrease in computation and storage while providing most of the same information and enabling parameter transferability. As a proof of concept, we will show how this new modeling framework can be run over CONUS at a 30-meter spatial resolution. For each catchment in the WBD HUC-12 dataset, the model is run between 2002 and 2012 using available high-resolution continental scale land and meteorological datasets over CONUS (dSSURGO, NLCD, NED, and NCEP Stage IV). For each catchment, the model is run with 1000 model parameter sets obtained from a Latin hypercube sample. This exercise will illustrate the feasibility of running the model operationally at continental scales while accounting for model parameter uncertainty.

DeNovoGUI: An Open Source Graphical User Interface for de Novo Sequencing of Tandem Mass Spectra

PubMed Central

2013-01-01

De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on a protein sequence database. Despite the strong potential of de novo sequencing algorithms, their adoption threshold remains quite high. We here present a user-friendly and lightweight graphical user interface called DeNovoGUI for running parallelized versions of the freely available de novo sequencing software PepNovo+, greatly simplifying the use of de novo sequencing in proteomics. Our platform-independent software is freely available under the permissible Apache2 open source license. Source code, binaries, and additional documentation are available at http://denovogui.googlecode.com. PMID:24295440

DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra.

PubMed

Muth, Thilo; Weilnböck, Lisa; Rapp, Erdmann; Huber, Christian G; Martens, Lennart; Vaudel, Marc; Barsnes, Harald

2014-02-07

De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on a protein sequence database. Despite the strong potential of de novo sequencing algorithms, their adoption threshold remains quite high. We here present a user-friendly and lightweight graphical user interface called DeNovoGUI for running parallelized versions of the freely available de novo sequencing software PepNovo+, greatly simplifying the use of de novo sequencing in proteomics. Our platform-independent software is freely available under the permissible Apache2 open source license. Source code, binaries, and additional documentation are available at http://denovogui.googlecode.com .

The relationship between aerobic fitness and recovery from high-intensity exercise in infantry soldiers.

PubMed

Hoffman, J R

1997-07-01

The relationship between aerobic fitness and recovery from high-intensity exercise was examined in 197 infantry soldiers. Aerobic fitness was determined by a maximal-effort, 2,000-m run (RUN). High-intensity exercise consisted of three bouts of a continuous 140-m sprint with several changes of direction. A 2-minute passive rest separated each sprint. A fatigue index was developed by dividing the mean time of the three sprints by the fastest time. Times for the RUN were converted into standardized T scores and separated into five groups (group 1 had the slowest run time and group 5 had the fastest run time). Significant differences in the fatigue index were seen between group 1 (4.9 +/- 2.4%) and groups 3 (2.6 +/- 1.7%), 4 (2.3 +/- 1.6%), and 5 (2.3 +/- 1.3%). It appears that recovery from high-intensity exercise is improved at higher levels of aerobic fitness (faster time for the RUN). However, as the level of aerobic fitness improves above the population mean, no further benefit in the recovery rate from high-intensity exercise is apparent.

78 FR 76903 - Lockhart Power Company, Inc.; Notice of Availability of Draft Environmental Assessment

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-19

..., and enhancement measure Riverdale LLC Riverdale Development Venture, LLC ROR run-of-river ROW rights.... Lockhart Power would operate the project using a combination of run-of-river (ROR) and peaking modes...

Developments in the ATLAS Tracking Software ahead of LHC Run 2

NASA Astrophysics Data System (ADS)

Styles, Nicholas; Bellomo, Massimiliano; Salzburger, Andreas; ATLAS Collaboration

2015-05-01

After a hugely successful first run, the Large Hadron Collider (LHC) is currently in a shut-down period, during which essential maintenance and upgrades are being performed on the accelerator. The ATLAS experiment, one of the four large LHC experiments has also used this period for consolidation and further developments of the detector and of its software framework, ahead of the new challenges that will be brought by the increased centre-of-mass energy and instantaneous luminosity in the next run period. This is of particular relevance for the ATLAS Tracking software, responsible for reconstructing the trajectory of charged particles through the detector, which faces a steep increase in CPU consumption due to the additional combinatorics of the high-multiplicity environment. The steps taken to mitigate this increase and stay within the available computing resources while maintaining the excellent performance of the tracking software in terms of the information provided to the physics analyses will be presented. Particular focus will be given to changes to the Event Data Model, replacement of the maths library, and adoption of a new persistent output format. The resulting CPU profiling results will be discussed, as well as the performance of the algorithms for physics processes under the expected conditions for the next LHC run.

Deployable Aeroshell Flexible Thermal Protection System Testing

NASA Technical Reports Server (NTRS)

Hughes, Stephen J.; Ware, Joanne S.; DelCorso, Joseph A.; Lugo, Rafael A.

2009-01-01

Deployable aeroshells offer the promise of achieving larger aeroshell surface areas for entry vehicles than otherwise attainable without deployment. With the larger surface area comes the ability to decelerate high-mass entry vehicles at relatively low ballistic coefficients. However, for an aeroshell to perform even at the low ballistic coefficients attainable with deployable aeroshells, a flexible thermal protection system (TPS) is required that is capable of surviving reasonably high heat flux and durable enough to survive the rigors of construction handling, high density packing, deployment, aerodynamic loading and aerothermal heating. The Program for the Advancement of Inflatable Decelerators for Atmospheric Entry (PAIDAE) is tasked with developing the technologies required to increase the technology readiness level (TRL) of inflatable deployable aeroshells, and one of several of the technologies PAIDAE is developing for use on inflatable aeroshells is flexible TPS. Several flexible TPS layups were designed, based on commercially available materials, and tested in NASA Langley Research Center's 8 Foot High Temperature Tunnel (8ft HTT). The TPS layups were designed for, and tested at three different conditions that are representative of conditions seen in entry simulation analyses of inflatable aeroshell concepts. Two conditions were produced in a single run with a sting-mounted dual wedge test fixture. The dual wedge test fixture had one row of sample mounting locations (forward) at about half the running length of the top surface of the wedge. At about two thirds of the running length of the wedge, a second test surface drafted up at five degrees relative to the first test surface established the remaining running length of the wedge test fixture. A second row of sample mounting locations (aft) was positioned in the middle of the running length of the second test surface. Once the desired flow conditions were established in the test section the dual wedge test fixture, oriented at 5 degrees angle of attack down, was injected into the flow. In this configuration the aft sample mounting location was subjected to roughly twice the heat flux and surface pressure of the forward mounting location. The tunnel was run at two different conditions for the test series: 1) 'Low Pressure', and 2) 'High Pressure'. At 'Low Pressure' conditions the TPS layups were tested at 6W/cm2 and 11W/cm2 while at 'High Pressure' conditions the TPS layups were tested at 11W/cm2 and 20W/cm2. This paper details the test configuration of the TPS samples in the 8Ft HTT, the sample holder assembly, TPS sample layup construction, sample instrumentation, results from this testing, as well as lessons learned.

Very high-current-density Nb/AlN/Nb tunnel junctions for low-noise submillimeter mixers

NASA Astrophysics Data System (ADS)

Kawamura, Jonathan; Miller, David; Chen, Jian; Zmuidzinas, Jonas; Bumble, Bruce; LeDuc, Henry G.; Stern, Jeff A.

2000-04-01

We have fabricated and tested submillimeter-wave superconductor-insulator-superconductor (SIS) mixers using very high-current-density Nb/AlN/Nb tunnel junctions (Jc≈30 kA cm-2). The junctions have low-resistance-area products (RNA≈5.6 Ω μm2), good subgap-to-normal resistance ratios Rsg/RN≈10, and good run-to-run reproducibility. From Fourier transform spectrometer measurements, we infer that ωRNC=1 at 270 GHz. This is a factor of 2.5 improvement over what is generally available with Nb/AlOx/Nb junctions suitable for low-noise mixers. The AlN-barrier junctions are indeed capable of low-noise operation: we measure an uncorrected double-sideband receiver noise temperature of TRX=110 K at 533 GHz for an unoptimized device. In addition to providing wider bandwidth operation at lower frequencies, the AlN-barrier junctions will considerably improve the performance of THz SIS mixers by reducing rf loss in the tuning circuits.

A theoretical perspective on running-related injuries.

PubMed

Gallant, Jodi Lynn; Pierrynowski, Michael Raymond

2014-03-01

The etiology of running-related injuries remains unknown; however, an implicit theory underlies much of the conventional research and practice in the prevention of these injuries. This theory posits that the cause of running-related injuries lies in the high-impact forces experienced when the foot contacts the ground and the subsequent abnormal movement of the subtalar joint. The application of this theory is seen in the design of the modern running shoe, with cushioning, support, and motion control. However, a new theory is emerging that suggests that it is the use of these modern running shoes that has caused a maladaptive running style, which contributes to a high incidence of injury among runners. The suggested application of this theory is to cease use of the modern running shoe and transition to barefoot or minimalist running. This new running paradigm, which is at present inadequately defined, is proposed to avoid the adverse biomechanical effects of the modern running shoe. Future research should rigorously define and then test both theories regarding their ability to discover the etiology of running-related injury. Once discovered, the putative cause of running-related injury will then provide an evidence-based rationale for clinical prevention and treatment.

Scale-dependency of macroinvertebrate communities: responses to contaminated sediments within run-of-river dams.

PubMed

Colas, Fanny; Archaimbault, Virginie; Devin, Simon

2011-03-01

Due to their nutrient recycling function and their importance in food-webs, macroinvertebrates are essential for the functioning of aquatic ecosystems. These organisms also constitute an important component of biodiversity. Sediment evaluation and monitoring is an essential aspect of ecosystem monitoring since sediments represent an important component of aquatic habitats and are also a potential source of contamination. In this study, we focused on macroinvertebrate communities within run-of-river dams, that are prime areas for sediment and pollutant accumulation. Little is known about littoral macroinvertebrate communities within run-of-river dam or their response to sediment levels and pollution. We therefore aimed to evaluate the following aspects: the functional and structural composition of macroinvertebrate communities in run-of-river dams; the impact of pollutant accumulation on such communities, and the most efficient scales and tools needed for the biomonitoring of contaminated sediments in such environments. Two run-of-river dams located in the French alpine area were selected and three spatial scales were examined: transversal (banks and channel), transversal x longitudinal (banks/channel x tail/middle/dam) and patch scale (erosion, sedimentation and vegetation habitats). At the patch scale, we noted that the heterogeneity of littoral habitats provided many available niches that allow for the development of diversified macroinvertebrate communities. This implies highly variable responses to contamination. Once combined on a global 'banks' spatial scale, littoral habitats can highlight the effects of toxic disturbances. Copyright © 2011 Elsevier B.V. All rights reserved.

Automated system for smoke dispersion prediction due to wild fires in Alaska

NASA Astrophysics Data System (ADS)

Kulchitsky, A.; Stuefer, M.; Higbie, L.; Newby, G.

2007-12-01

Community climate models have enabled development of specific environmental forecast systems. The University of Alaska (UAF) smoke group was created to adapt a smoke forecast system to the Alaska region. The US Forest Service (USFS) Missoula Fire Science Lab had developed a smoke forecast system based on the Weather Research and Forecasting (WRF) Model including chemistry (WRF/Chem). Following the successful experience of USFS, which runs their model operationally for the contiguous U.S., we develop a similar system for Alaska in collaboration with scientists from the USFS Missoula Fire Science Lab. Wildfires are a significant source of air pollution in Alaska because the climate and vegetation favor annual summer fires that burn huge areas. Extreme cases occurred in 2004, when an area larger than Maryland (more than 25000~km2) burned. Small smoke particles with a diameter less than 10~μm can penetrate deep into lungs causing health problems. Smoke also creates a severe restriction to air transport and has tremendous economical effect. The smoke dispersion and forecast system for Alaska was developed at the Geophysical Institute (GI) and the Arctic Region Supercomputing Center (ARSC), both at University of Alaska Fairbanks (UAF). They will help the public and plan activities a few days in advance to avoid dangerous smoke exposure. The availability of modern high performance supercomputers at ARSC allows us to create and run high-resolution, WRF-based smoke dispersion forecast for the entire State of Alaska. The core of the system is a Python program that manages the independent pieces. Our adapted Alaska system performs the following steps \\begin{itemize} Calculate the medium-resolution weather forecast using WRF/Met. Adapt the near real-time satellite-derived wildfire location and extent data that are received via direct broadcast from UAF's "Geographic Information Network of Alaska" (GINA) Calculate fuel moisture using WRF forecasts and National Fire Danger Rating System (NFDRS) fuel maps Calculate smoke emission components using a first order fire emission model Model the smoke plume rise yielding a vertically distribution that accounts for one-dimensional (vertical) concentrations of smoke constituents in the atmosphere above the fire Run WRF/Chem at high resolution for the forecast Use standard graphical tools to provide accessible smoke dispersion The system run twice each day at ARSC. The results will be freely available from a dedicated wildfire smoke web portal at ARSC.

Access and Diversity in the Running Start Program: A Comparison of Washington's Running Start Program to Other State Level Dual Enrollment Programs Hosted on a College Campus

ERIC Educational Resources Information Center

Smith, Karl

2014-01-01

Since 1990, high school students in Washington have had the choice of earning college credit through the Running Start program. Running start is a dual enrollment and dual credit program that allows eleventh and twelfth grade high school students to take college courses at any of Washington's 34 community and technical colleges, Central Washington…

Compute Server Performance Results

NASA Technical Reports Server (NTRS)

Stockdale, I. E.; Barton, John; Woodrow, Thomas (Technical Monitor)

1994-01-01

Parallel-vector supercomputers have been the workhorses of high performance computing. As expectations of future computing needs have risen faster than projected vector supercomputer performance, much work has been done investigating the feasibility of using Massively Parallel Processor systems as supercomputers. An even more recent development is the availability of high performance workstations which have the potential, when clustered together, to replace parallel-vector systems. We present a systematic comparison of floating point performance and price-performance for various compute server systems. A suite of highly vectorized programs was run on systems including traditional vector systems such as the Cray C90, and RISC workstations such as the IBM RS/6000 590 and the SGI R8000. The C90 system delivers 460 million floating point operations per second (FLOPS), the highest single processor rate of any vendor. However, if the price-performance ration (PPR) is considered to be most important, then the IBM and SGI processors are superior to the C90 processors. Even without code tuning, the IBM and SGI PPR's of 260 and 220 FLOPS per dollar exceed the C90 PPR of 160 FLOPS per dollar when running our highly vectorized suite,

Runtime visualization of the human arterial tree.

PubMed

Insley, Joseph A; Papka, Michael E; Dong, Suchuan; Karniadakis, George; Karonis, Nicholas T

2007-01-01

Large-scale simulation codes typically execute for extended periods of time and often on distributed computational resources. Because these simulations can run for hours, or even days, scientists like to get feedback about the state of the computation and the validity of its results as it runs. It is also important that these capabilities be made available with little impact on the performance and stability of the simulation. Visualizing and exploring data in the early stages of the simulation can help scientists identify problems early, potentially avoiding a situation where a simulation runs for several days, only to discover that an error with an input parameter caused both time and resources to be wasted. We describe an application that aids in the monitoring and analysis of a simulation of the human arterial tree. The application provides researchers with high-level feedback about the state of the ongoing simulation and enables them to investigate particular areas of interest in greater detail. The application also offers monitoring information about the amount of data produced and data transfer performance among the various components of the application.

Development and performance of a new version of the OASIS coupler, OASIS3-MCT_3.0

NASA Astrophysics Data System (ADS)

Craig, Anthony; Valcke, Sophie; Coquart, Laure

2017-09-01

OASIS is coupling software developed primarily for use in the climate community. It provides the ability to couple different models with low implementation and performance overhead. OASIS3-MCT is the latest version of OASIS. It includes several improvements compared to OASIS3, including elimination of a separate hub coupler process, parallelization of the coupling communication and run-time grid interpolation, and the ability to easily reuse mapping weight files. OASIS3-MCT_3.0 is the latest release and includes the ability to couple between components running sequentially on the same set of tasks as well as to couple within a single component between different grids or decompositions such as physics, dynamics, and I/O. OASIS3-MCT has been tested with different configurations on up to 32 000 processes, with components running on high-resolution grids with up to 1.5 million grid cells, and with over 10 000 2-D coupling fields. Several new features will be available in OASIS3-MCT_4.0, and some of those are also described.

Comparison of Varying Heel to Toe Differences and Cushion to Barefoot Running in Novice Minimalist Runners

PubMed Central

MOODY, DANNY; HUNTER, IAIN; RIDGE, SARAH; MYRER, J. WILLIAM

2018-01-01

There are many different types of footwear available for runners in today’s market. Many of these shoes claim to help runners run more efficiently by altering an individual’s stride mechanics. Minimalist footwear claims to aid runners run more on their forefeet whereas more traditional footwear provides more cushioning specifically for a heel first landing. The purpose of this paper was to determine if runners, who were accustomed to running in traditional footwear would alter their running mechanics while running acutely in various types of minimalist footwear. Twelve subjects, accustomed to running in traditional 12 mm heel/toe differential footwear, ran in five footwear conditions on a treadmill at a controlled pace for two minutes after warming up in each condition for 5 minutes. While running in 12 mm heel/toe differential footwear compared to barefoot, subjects ran with a significantly longer ground time, a lower stride rate and greater vertical oscillation. There were not any differences in variables when running in the shod conditions despite the varying heel/toe differentials. Running barefoot proved to be different than running in traditional 12 mm drop cushioned footwear. PMID:29795721

Comparison of Varying Heel to Toe Differences and Cushion to Barefoot Running in Novice Minimalist Runners.

PubMed

Moody, Danny; Hunter, Iain; Ridge, Sarah; Myrer, J William

2018-01-01

There are many different types of footwear available for runners in today's market. Many of these shoes claim to help runners run more efficiently by altering an individual's stride mechanics. Minimalist footwear claims to aid runners run more on their forefeet whereas more traditional footwear provides more cushioning specifically for a heel first landing. The purpose of this paper was to determine if runners, who were accustomed to running in traditional footwear would alter their running mechanics while running acutely in various types of minimalist footwear. Twelve subjects, accustomed to running in traditional 12 mm heel/toe differential footwear, ran in five footwear conditions on a treadmill at a controlled pace for two minutes after warming up in each condition for 5 minutes. While running in 12 mm heel/toe differential footwear compared to barefoot, subjects ran with a significantly longer ground time, a lower stride rate and greater vertical oscillation. There were not any differences in variables when running in the shod conditions despite the varying heel/toe differentials. Running barefoot proved to be different than running in traditional 12 mm drop cushioned footwear.

fluff: exploratory analysis and visualization of high-throughput sequencing data

PubMed Central

Georgiou, Georgios

2016-01-01

Summary. In this article we describe fluff, a software package that allows for simple exploration, clustering and visualization of high-throughput sequencing data mapped to a reference genome. The package contains three command-line tools to generate publication-quality figures in an uncomplicated manner using sensible defaults. Genome-wide data can be aggregated, clustered and visualized in a heatmap, according to different clustering methods. This includes a predefined setting to identify dynamic clusters between different conditions or developmental stages. Alternatively, clustered data can be visualized in a bandplot. Finally, fluff includes a tool to generate genomic profiles. As command-line tools, the fluff programs can easily be integrated into standard analysis pipelines. The installation is straightforward and documentation is available at http://fluff.readthedocs.org. Availability. fluff is implemented in Python and runs on Linux. The source code is freely available for download at https://github.com/simonvh/fluff. PMID:27547532

The Robust Running Ape: Unraveling the Deep Underpinnings of Coordinated Human Running Proficiency

PubMed Central

Kiely, John

2017-01-01

In comparison to other mammals, humans are not especially strong, swift or supple. Nevertheless, despite these apparent physical limitations, we are among Natures most superbly well-adapted endurance runners. Paradoxically, however, notwithstanding this evolutionary-bestowed proficiency, running-related injuries, and Overuse syndromes in particular, are widely pervasive. The term ‘coordination’ is similarly ubiquitous within contemporary coaching, conditioning, and rehabilitation cultures. Various theoretical models of coordination exist within the academic literature. However, the specific neural and biological underpinnings of ‘running coordination,’ and the nature of their integration, remain poorly elaborated. Conventionally running is considered a mundane, readily mastered coordination skill. This illusion of coordinative simplicity, however, is founded upon a platform of immense neural and biological complexities. This extensive complexity presents extreme organizational difficulties yet, simultaneously, provides a multiplicity of viable pathways through which the computational and mechanical burden of running can be proficiently dispersed amongst expanded networks of conditioned neural and peripheral tissue collaborators. Learning to adequately harness this available complexity, however, is a painstakingly slowly emerging, practice-driven process, greatly facilitated by innate evolutionary organizing principles serving to constrain otherwise overwhelming complexity to manageable proportions. As we accumulate running experiences persistent plastic remodeling customizes networked neural connectivity and biological tissue properties to best fit our unique neural and architectural idiosyncrasies, and personal histories: thus neural and peripheral tissue plasticity embeds coordination habits. When, however, coordinative processes are compromised—under the integrated influence of fatigue and/or accumulative cycles of injury, overuse, misuse, and disuse—this spectrum of available ‘choice’ dysfunctionally contracts, and our capacity to safely disperse the mechanical ‘stress’ of running progressively diminishes. Now the running work burden falls increasingly on reduced populations of collaborating components. Accordingly our capacity to effectively manage, dissipate and accommodate running-imposed stress diminishes, and vulnerability to Overuse syndromes escalates. Awareness of the deep underpinnings of running coordination enhances conceptual clarity, thereby informing training and rehabilitation insights designed to offset the legacy of excessive or progressively accumulating exposure to running-imposed mechanical stress. PMID:28659838

Effect of match-run frequencies on the number of transplants and waiting times in kidney exchange.

PubMed

Ashlagi, Itai; Bingaman, Adam; Burq, Maximilien; Manshadi, Vahideh; Gamarnik, David; Murphey, Cathi; Roth, Alvin E; Melcher, Marc L; Rees, Michael A

2018-05-01

Numerous kidney exchange (kidney paired donation [KPD]) registries in the United States have gradually shifted to high-frequency match-runs, raising the question of whether this harms the number of transplants. We conducted simulations using clinical data from 2 KPD registries-the Alliance for Paired Donation, which runs multihospital exchanges, and Methodist San Antonio, which runs single-center exchanges-to study how the frequency of match-runs impacts the number of transplants and the average waiting times. We simulate the options facing each of the 2 registries by repeated resampling from their historical pools of patient-donor pairs and nondirected donors, with arrival and departure rates corresponding to the historical data. We find that longer intervals between match-runs do not increase the total number of transplants, and that prioritizing highly sensitized patients is more effective than waiting longer between match-runs for transplanting highly sensitized patients. While we do not find that frequent match-runs result in fewer transplanted pairs, we do find that increasing arrival rates of new pairs improves both the fraction of transplanted pairs and waiting times. © 2017 The American Society of Transplantation and the American Society of Transplant Surgeons.

Match-to-match variability in high-speed running activity in a professional soccer team.

PubMed

Carling, Christopher; Bradley, Paul; McCall, Alan; Dupont, Gregory

2016-12-01

This study investigated variability in competitive high-speed running performance in an elite soccer team. A semi-automated tracking system quantified running performance in 12 players over a season (median 17 matches per player, 207 observations). Variability [coefficient of variation (CV)] was compared for total sprint distance (TSD, >25.2 km/h), high-speed running (HSR, 19.8-25.2 km/h), total high-speed running (THSR, ≥19.8 km/h); THSR when the team was in and out of ball possession, in individual ball possession, in the peak 5 min activity period; and distance run according to individual maximal aerobic speed (MAS). Variability for % declines in THSR and distance covered at ≥80% MAS across halves, at the end of play (final 15 min vs. mean for all 15 min periods) and transiently (5 min period following peak 5 min activity period), was analysed. Collectively, variability was higher for TSD versus HSR and THSR and lowest for distance run at ≥80% MAS (CVs: 37.1%, 18.1%, 19.8% and 11.8%). THSR CVs when the team was in/out of ball possession, in individual ball possession and during the peak 5 min period were 31.5%, 26.1%, 60.1% and 23.9%. Variability in THSR declines across halves, at the end of play and transiently, ranged from 37.1% to 142.6%, while lower CVs were observed in these metrics for running at ≥80% MAS (20.9-53.3%).These results cast doubt on the appropriateness of general measures of high-speed activity for determining variability in an elite soccer team, although individualisation of HSR thresholds according to fitness characteristics might provide more stable indicators of running performance and fatigue occurrence.

Integrating a Trusted Computing Base Extension Server and Secure Session Server into the LINUX Operating System

DTIC Science & Technology

2001-09-01

Readily Available Linux has been copyrighted under the terms of the GNU General Public 5 License (GPL)1. This is a license written by the Free...GNOME and KDE . d. Portability Linux is highly compatible with many common operating systems. For...using suitable libraries, Linux is able to run programs written for other operating systems. [Ref. 8] 1 The GNU Project is coordinated by the

Influence of footwear designed to boost energy return on running economy in comparison to a conventional running shoe.

PubMed

Sinclair, J; Mcgrath, R; Brook, O; Taylor, P J; Dillon, S

2016-01-01

Running economy is a reflection of the amount of inspired oxygen required to maintain a given velocity and is considered a determining factor for running performance. Athletic footwear has been advocated as a mechanism by which running economy can be enhanced. New commercially available footwear has been developed in order to increase energy return, although their efficacy has not been investigated. This study aimed to examine the effects of energy return footwear on running economy in relation to conventional running shoes. Twelve male runners completed 6-min steady-state runs in conventional and energy return footwear. Overall, oxygen consumption (VO2), heart rate, respiratory exchange ratio, shoe comfort and rating of perceived exertion were assessed. Moreover, participants subjectively indicated which shoe condition they preferred for running. Differences in shoe comfort and physiological parameters were examined using Wilcoxon signed-rank tests, whilst shoe preferences were tested using a chi-square analysis. The results showed that VO2 and respiratory exchange ratio were significantly lower, and shoe comfort was significantly greater, in the energy return footwear. Given the relationship between running economy and running performance, these observations indicate that the energy return footwear may be associated with enhanced running performance in comparison to conventional shoes.

Effects of long-term voluntary exercise on learning and memory processes: dependency of the task and level of exercise.

PubMed

García-Capdevila, Sílvia; Portell-Cortés, Isabel; Torras-Garcia, Meritxell; Coll-Andreu, Margalida; Costa-Miserachs, David

2009-09-14

The effect of long-term voluntary exercise (running wheel) on anxiety-like behaviour (plus maze and open field) and learning and memory processes (object recognition and two-way active avoidance) was examined on Wistar rats. Because major individual differences in running wheel behaviour were observed, the data were analysed considering the exercising animals both as a whole and grouped according to the time spent in the running wheel (low, high, and very-high running). Although some variables related to anxiety-like behaviour seem to reflect an anxiogenic compatible effect, the view of the complete set of variables could be interpreted as an enhancement of defensive and risk assessment behaviours in exercised animals, without major differences depending on the exercise level. Effects on learning and memory processes were dependent on task and level of exercise. Two-way avoidance was not affected either in the acquisition or in the retention session, while the retention of object recognition task was affected. In this latter task, an enhancement in low running subjects and impairment in high and very-high running animals were observed.

Is there really an eccentric action of the hamstrings during the swing phase of high-speed running? Part II: Implications for exercise.

PubMed

Van Hooren, Bas; Bosch, Frans

2017-12-01

We have previously argued that there may actually be no significant eccentric, but rather predominantly an isometric action of the hamstring muscle fibres during the swing phase of high-speed running when the attachment points of the hamstrings are moving apart. Based on this we suggested that isometric rather than eccentric exercises are a more specific way of conditioning the hamstrings for high-speed running. In this review we argue that some of the presumed beneficial adaptations following eccentric training may actually not be related to the eccentric muscle fibre action, but to other factors such as exercise intensity. Furthermore, we discuss several disadvantages associated with commonly used eccentric hamstring exercises. Subsequently, we argue that high-intensity isometric exercises in which the series elastic element stretches and recoils may be equally or even more effective at conditioning the hamstrings for high-speed running, since they also avoid some of the negative side effects associated with eccentric training. We provide several criteria that exercises should fulfil to effectively condition the hamstrings for high-speed running. Adherence to these criteria will guarantee specificity with regards to hamstrings functioning during running. Practical examples of isometric exercises that likely meet several criteria are provided.

CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing.

PubMed

Tristão Ramos, Ravi José; de Azevedo Martins, Allan Cézar; da Silva Delgado, Gabrielle; Ionescu, Crina-Maria; Ürményi, Turán Peter; Silva, Rosane; Koca, Jaroslav

2017-11-15

CrocoBLAST is a tool for dramatically speeding up BLAST+ execution on any computer. Alignments that would take days or weeks with NCBI BLAST+ can be run overnight with CrocoBLAST. Additionally, CrocoBLAST provides features critical for NGS data analysis, including: results identical to those of BLAST+; compatibility with any BLAST+ version; real-time information regarding calculation progress and remaining run time; access to partial alignment results; queueing, pausing, and resuming BLAST+ calculations without information loss. CrocoBLAST is freely available online, with ample documentation (webchem.ncbr.muni.cz/Platform/App/CrocoBLAST). No installation or user registration is required. CrocoBLAST is implemented in C, while the graphical user interface is implemented in Java. CrocoBLAST is supported under Linux and Windows, and can be run under Mac OS X in a Linux virtual machine. jkoca@ceitec.cz. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Wheel running decreases palatable diet preference in Sprague-Dawley rats.

PubMed

Moody, Laura; Liang, Joy; Choi, Pique P; Moran, Timothy H; Liang, Nu-Chu

2015-10-15

Physical activity has beneficial effects on not only improving some disease conditions but also by preventing the development of multiple disorders. Experiments in this study examined the effects of wheel running on intakes of chow and palatable diet e.g. high fat (HF) or high sucrose (HS) diet in male and female Sprague-Dawley rats. Experiment 1 demonstrated that acute wheel running results in robust HF or HS diet avoidance in male rats. Although female rats with running wheel access initially showed complete avoidance of the two palatable diets, the avoidance of the HS diet was transient. Experiment 2 demonstrated that male rats developed decreased HF diet preferences regardless of the order of diet and wheel running access presentation. Running associated changes in HF diet preference in females, on the other hand, depended on the testing schedule. In female rats, simultaneous presentation of the HF diet and running access resulted in transient complete HF diet avoidance whereas running experience prior to HF diet access did not affect the high preference for the HF diet. Ovariectomy in females resulted in HF diet preference patterns that were similar to those in male rats during simultaneous exposure of HF and wheel running access but similar to intact females when running occurred before HF exposure. Overall, the results demonstrated wheel running associated changes in palatable diet preferences that were in part sex dependent. Furthermore, ovarian hormones play a role in some of the sex differences. These data reveal complexity in the mechanisms underlying exercise associated changes in palatable diet preference. Published by Elsevier Inc.

Wheel running decreases palatable diet preference in Sprague-Dawley rats

PubMed Central

Moody, Laura; Liang, Joy; Choi, Pique P.; Moran, Timothy H.; Liang, Nu-Chu

2015-01-01

Physical activity has beneficial effects on not only improving some disease conditions but also by preventing the development of multiple disorders. Experiments in this study examined the effects of wheel running on intakes of chow and palatable diet e.g. high fat (HF) or high sucrose (HS) diet in male and female Sprague Dawley rats. Experiment 1 demonstrated that acute wheel running results in robust HF or HS diet avoidance in male rats. Although female rats with running wheel access initially showed complete avoidance of the two palatable diets, the avoidance of the HS diet was transient. Experiment 2 demonstrated that male rats developed decreased HF diet preferences regardless of the order of diet and wheel running access presentation. Running associated changes in HF diet preference in females, on the other hand, depended on the testing schedule. In female rats, simultaneous presentation of the HF diet and running access resulted in transient complete HF diet avoidance whereas running experience prior to HF diet access did not affect the high preference for the HF diet. Ovariectomy in females resulted in HF diet preference patterns that were similar to those in male rats during simultaneous exposure of HF and wheel running access but similar to intact females when running occurred before HF exposure. Overall, the results demonstrated wheel running associated changes in palatable diet preferences that were in part sex dependent. Furthermore, ovarian hormones play a role in some of the sex differences. These data reveal complexity in the mechanisms underlying exercise associated changes in palatable diet preference. PMID:25791204

Accelerating Virtual High-Throughput Ligand Docking: current technology and case study on a petascale supercomputer.

PubMed

Ellingson, Sally R; Dakshanamurthy, Sivanesan; Brown, Milton; Smith, Jeremy C; Baudry, Jerome

2014-04-25

In this paper we give the current state of high-throughput virtual screening. We describe a case study of using a task-parallel MPI (Message Passing Interface) version of Autodock4 [1], [2] to run a virtual high-throughput screen of one-million compounds on the Jaguar Cray XK6 Supercomputer at Oak Ridge National Laboratory. We include a description of scripts developed to increase the efficiency of the predocking file preparation and postdocking analysis. A detailed tutorial, scripts, and source code for this MPI version of Autodock4 are available online at http://www.bio.utk.edu/baudrylab/autodockmpi.htm.

The relationship between gamma frequency and running speed differs for slow and fast gamma rhythms in freely behaving rats

PubMed Central

Zheng, Chenguang; Bieri, Kevin Wood; Trettel, Sean Gregory; Colgin, Laura Lee

2015-01-01

In hippocampal area CA1 of rats, the frequency of gamma activity has been shown to increase with running speed (Ahmed and Mehta, 2012). This finding suggests that different gamma frequencies simply allow for different timings of transitions across cell assemblies at varying running speeds, rather than serving unique functions. However, accumulating evidence supports the conclusion that slow (~25–55 Hz) and fast (~60–100 Hz) gamma are distinct network states with different functions. If slow and fast gamma constitute distinct network states, then it is possible that slow and fast gamma frequencies are differentially affected by running speed. In this study, we tested this hypothesis and found that slow and fast gamma frequencies change differently as a function of running speed in hippocampal areas CA1 and CA3, and in the superficial layers of the medial entorhinal cortex (MEC). Fast gamma frequencies increased with increasing running speed in all three areas. Slow gamma frequencies changed significantly less across different speeds. Furthermore, at high running speeds, CA3 firing rates were low, and MEC firing rates were high, suggesting that CA1 transitions from CA3 inputs to MEC inputs as running speed increases. These results support the hypothesis that slow and fast gamma reflect functionally distinct states in the hippocampal network, with fast gamma driven by MEC at high running speeds and slow gamma driven by CA3 at low running speeds. PMID:25601003

Effects of running-induced fatigue on plantar pressure distribution in novice runners with different foot types.

PubMed

Anbarian, Mehrdad; Esmaeili, Hamed

2016-07-01

This study aimed to assess the effects of running-induced fatigue on plantar pressure parameters in novice runners with low and high medial longitudinal arch. Plantar pressure data from 42 novice runners (21 with high, and 21 with low arch) were collected before and after running-induced fatigue protocol during running at 3.3m/s along the Footscan(®) platform. Peak plantar pressure, peak force and force-time integral (impulse) were measured in ten anatomical zones. Relative time for foot roll-over phases and medio-lateral force ratio were calculated before and after the fatigue protocol. After the fatigue protocol, increases in the peak pressure under the first-third metatarsal zones and reduction under the fourth-fifth metatarsal regions were observed in the low arch individuals. In the high arch group, increases in peak pressure under the fourth-fifth metatarsal zones after the running-induced fatigue was observed. It could be concluded that running-induced fatigue had different effects on plantar pressure distribution pattern among novice runners with low and high medial longitudinal foot arch. These findings could provide some information related to several running injuries among individuals with different foot types. Copyright © 2016 Elsevier B.V. All rights reserved.

The effect of breast support on upper body muscle activity during 5 km treadmill running.

PubMed

Milligan, Alexandra; Mills, Chris; Scurr, Joanna

2014-12-01

Breast support has previously been shown to influence surface EMG of the pectoralis major during running. Reductions in muscle activity have previously been associated with a reduction in energy cost, which may be advantageous for female runners. Ten female participants performed two self-paced (average pace 9 km h(-1)) 5 km treadmill runs under two breast support conditions (low and high); an additional bare-breasted 2 min run was also conducted. Surface EMG electrodes were positioned on the pectoralis major, anterior deltoid, medial deltoid, and upper trapezius, with data collected during the first 2 min of running and each kilometer interval thereafter. Reductions in peak EMG of the pectoralis major, anterior and medial deltoid were reported when participants ran in the high breast support during the initial intervals of the run (up to the second kilometer). The increased activation in the pectoralis major, anterior and medial deltoid in the low breast support may be due to increased tension within these muscles, induced by the greater breast pain experienced in the low breast support. This may be a strategy to reduce the independent breast movement causing the pain through increased muscular activation. This study further promotes the use of a high breast support during running with potential benefits for treadmill running associated with reductions in muscular demand during a 5 km run. Copyright © 2014 Elsevier B.V. All rights reserved.

Recent results of high p(T) physics at the CDF II

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

Tsuno, Soushi; /Okayama U.

2005-02-01

The Tevatron Run II program has been in progress since 2001. The CDF experiment has accumulated roughly five times as much data as did Run I, with much improved detectors. Preliminary results from the CDF experiment are presented. The authors focus on recent high p{sub T} physics results in the Tevatron Run II program.

How Much of a "Running Start" Do Dual Enrollment Programs Provide Students?

ERIC Educational Resources Information Center

Cowan, James; Goldhaber, Dan

2015-01-01

We study a popular dual enrollment program in Washington State, "Running Start" using a new administrative database that links high school and postsecondary data. Conditional on prior high school performance, we find that students participating in Running Start are more likely to attend any college but less likely to attend four-year…

RHIC Au beam in Run 2014

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

Zhang, S. Y.

Au beam at the RHIC ramp in run 2014 is reviewed together with the run 2011 and run 2012. Observed bunch length and longitudinal emittance are compared with the IBS simulations. The IBS growth rate of the longitudinal emittance in run 2014 is similar to run 2011, and both are larger than run 2012. This is explained by the large transverse emittance at high intensity observed in run 2012, but not in run 2014. The big improvement of the AGS ramping in run 2014 might be related to this change. The importance of the injector intensity improvement in run 2014more » is emphasized, which gives rise to the initial luminosity improvement of 50% in run 2014, compared with the previous Au-Au run 2011. In addition, a modified IBS model, which is calibrated using the RHIC Au runs from 9.8 GeV/n to 100 GeV/n, is presented and used in the study.« less

The ATLAS Production System Evolution: New Data Processing and Analysis Paradigm for the LHC Run2 and High-Luminosity

NASA Astrophysics Data System (ADS)

Barreiro, F. H.; Borodin, M.; De, K.; Golubkov, D.; Klimentov, A.; Maeno, T.; Mashinistov, R.; Padolski, S.; Wenaus, T.; ATLAS Collaboration

2017-10-01

The second generation of the ATLAS Production System called ProdSys2 is a distributed workload manager that runs daily hundreds of thousands of jobs, from dozens of different ATLAS specific workflows, across more than hundred heterogeneous sites. It achieves high utilization by combining dynamic job definition based on many criteria, such as input and output size, memory requirements and CPU consumption, with manageable scheduling policies and by supporting different kind of computational resources, such as GRID, clouds, supercomputers and volunteer-computers. The system dynamically assigns a group of jobs (task) to a group of geographically distributed computing resources. Dynamic assignment and resources utilization is one of the major features of the system, it didn’t exist in the earliest versions of the production system where Grid resources topology was predefined using national or/and geographical pattern. Production System has a sophisticated job fault-recovery mechanism, which efficiently allows to run multi-Terabyte tasks without human intervention. We have implemented “train” model and open-ended production which allow to submit tasks automatically as soon as new set of data is available and to chain physics groups data processing and analysis with central production by the experiment. We present an overview of the ATLAS Production System and its major components features and architecture: task definition, web user interface and monitoring. We describe the important design decisions and lessons learned from an operational experience during the first year of LHC Run2. We also report the performance of the designed system and how various workflows, such as data (re)processing, Monte-Carlo and physics group production, users analysis, are scheduled and executed within one production system on heterogeneous computing resources.

Fat intake and injury in female runners.

PubMed

Gerlach, Kristen E; Burton, Harold W; Dorn, Joan M; Leddy, John J; Horvath, Peter J

2008-01-03

Our purpose was to determine the relationship between energy intake, energy availability, dietary fat and lower extremity injury in adult female runners. We hypothesized that runners who develop overuse running-related injuries have lower energy intakes, lower energy availability and lower fat intake compared to non-injured runners. Eighty-six female subjects, running a minimum of 20 miles/week, completed a food frequency questionnaire and informed us about injury incidence over the next year. Injured runners had significantly lower intakes of total fat (63 +/- 20 vs. 80 +/- 50 g/d) and percentage of kilocalories from fat (27 +/- 5 vs. 30 +/- 8 %) compared with non-injured runners. A logistic regression analysis found that fat intake was the best dietary predictor, correctly identifying 64% of future injuries. Lower energy intake and lower energy availability approached, but did not reach, a significant association with overuse injury in this study. Fat intake is likely associated with injury risk in female runners. By documenting these associations, better strategies can be developed to reduce running injuries in women.

Taurine is absent from amino components in fruits of Opuntia ficus-indica.

PubMed

Ali, Hatem Salama Mohamed; Al-Khalifa, Abdulrahman Saleh; Brückner, Hans

2014-01-01

Juices of edible fruits from Opuntia ficus-indica (L.) Miller, commonly named prickly pears or Indian figs, were analysed for amino acids using an automated amino acid analyser run in the high-resolution physiological mode. Emphasis was put on the detection of free taurine (Tau), but Tau could be detected neither in different cultivars of prickly pears from Italy, South Africa and the Near East nor in commercially available prickly pear juices from the market.

Naval War College Review. Volume 66, Number 1, Winter 2013

DTIC Science & Technology

2013-01-01

planes to run experiments. The ships themselves had some new technology: four-channel very-high- frequency (VHF) radios for the fighter-direction teams...1 11 /6/12 8:31 AM Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for the collection of information is estimated to...SPONSORING/MONITORING AGENCY NAME(S) AND ADDRESS(ES) 10. SPONSOR/MONITOR’S ACRONYM(S) 11 . SPONSOR/MONITOR’S REPORT NUMBER(S) 12. DISTRIBUTION/AVAILABILITY

Energy system contributions in middle-distance running events.

PubMed

Hill, D W

1999-06-01

The aim of this study was to estimate the energy contributions in middle-distance running events for male and female university athletes. The oxygen uptake (VO2) response during high-speed running was measured directly during exhaustive treadmill tests. Muscle mass was estimated using anthropometry. Each athlete completed an average of three races over 400 m, 800 m or 1500 m. Five minutes after each race, they provided a blood sample for determination of blood lactate concentration. For each race, energy cost, which was expressed as oxygen equivalents, was calculated as the sum of the aerobic and anaerobic components. The aerobic contribution was calculated as the sum of oxygen stores (2.3 ml O2.kg body mass-1) and total VO2 (based on the VO2 response to treadmill running). The anaerobic contribution was calculated as the sum of the energy available from phosphocreatine stores (37 ml O2.kg muscle mass-1) and the energy from glycolysis (3.0 ml O2.kg body mass-1 per mmol.l-1 increase in blood lactate concentration). For the women, the anaerobic energy contributions for the 400 m, 800 m and 1500 m averaged 62%, 33% and 17%, respectively. For the men, the anaerobic contributions averaged 63%, 39% and 20%, respectively. This information will help coaches and sport scientists to design and implement individualized training programmes.

SARANA: language, compiler and run-time system support for spatially aware and resource-aware mobile computing.

PubMed

Hari, Pradip; Ko, Kevin; Koukoumidis, Emmanouil; Kremer, Ulrich; Martonosi, Margaret; Ottoni, Desiree; Peh, Li-Shiuan; Zhang, Pei

2008-10-28

Increasingly, spatial awareness plays a central role in many distributed and mobile computing applications. Spatially aware applications rely on information about the geographical position of compute devices and their supported services in order to support novel functionality. While many spatial application drivers already exist in mobile and distributed computing, very little systems research has explored how best to program these applications, to express their spatial and temporal constraints, and to allow efficient implementations on highly dynamic real-world platforms. This paper proposes the SARANA system architecture, which includes language and run-time system support for spatially aware and resource-aware applications. SARANA allows users to express spatial regions of interest, as well as trade-offs between quality of result (QoR), latency and cost. The goal is to produce applications that use resources efficiently and that can be run on diverse resource-constrained platforms ranging from laptops to personal digital assistants and to smart phones. SARANA's run-time system manages QoR and cost trade-offs dynamically by tracking resource availability and locations, brokering usage/pricing agreements and migrating programs to nodes accordingly. A resource cost model permeates the SARANA system layers, permitting users to express their resource needs and QoR expectations in units that make sense to them. Although we are still early in the system development, initial versions have been demonstrated on a nine-node system prototype.

40 CFR 86.134-96 - Running loss test.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 19 2012-07-01 2012-07-01 false Running loss test. 86.134-96 Section... Heavy-Duty Vehicles; Test Procedures § 86.134-96 Running loss test. (a) Overview. Gasoline- and methanol-fueled vehicles are to be tested for running loss emissions during simulated high-temperature urban...

40 CFR 86.134-96 - Running loss test.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 18 2011-07-01 2011-07-01 false Running loss test. 86.134-96 Section... Heavy-Duty Vehicles; Test Procedures § 86.134-96 Running loss test. (a) Overview. Gasoline- and methanol-fueled vehicles are to be tested for running loss emissions during simulated high-temperature urban...

40 CFR 86.134-96 - Running loss test.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 18 2010-07-01 2010-07-01 false Running loss test. 86.134-96 Section... Heavy-Duty Vehicles; Test Procedures § 86.134-96 Running loss test. (a) Overview. Gasoline- and methanol-fueled vehicles are to be tested for running loss emissions during simulated high-temperature urban...

40 CFR 86.134-96 - Running loss test.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 19 2013-07-01 2013-07-01 false Running loss test. 86.134-96 Section... Heavy-Duty Vehicles; Test Procedures § 86.134-96 Running loss test. (a) Overview. Gasoline- and methanol-fueled vehicles are to be tested for running loss emissions during simulated high-temperature urban...

What Research Tells the Coach About Distance Running.

ERIC Educational Resources Information Center

Costill, David L.

This booklet is designed to make available research findins concerning distance running with interpretations, for practical applications, and to point out areas of needed research. Chapter 1, "Describing the Distance Runner," considers the following aspects in relation to the distance runner: a) anatomical characteristics, b) aging, c) strength…

Effect of recording duration on the diagnostic performance of multifocal visual-evoked potentials in high-risk ocular hypertension and early glaucoma.

PubMed

Fortune, Brad; Zhang, Xian; Hood, Donald C; Demirel, Shaban; Patterson, Emily; Jamil, Annisa; Mansberger, Steven L; Cioffi, George A; Johnson, Chris A

2008-01-01

To evaluate the effect on diagnostic performance of reducing multifocal visual-evoked potential (mfVEP) recording duration from 16 to 8 minutes per eye. Both eyes of 185 individuals with high-risk ocular hypertension or early glaucoma were studied. Two 8-minute mfVEP recordings were obtained for each eye in an ABBA order using VERIS. The first recording for each eye was compared against single run (1-Run) mfVEP normative data; the average of both recordings for each eye was compared against 2-Run normative data. Visual fields (VFs) were obtained by standard automated perimetry (SAP) within 22.3+/-27.0 days of the mfVEP. Stereo disc photographs and Heidelberg Retina Tomograph images were obtained together, within 24.8+/-50.4 days of the mfVEP and 33.1+/-62.9 days of SAP. Masked experts graded disc photographs as either glaucomatous optic neuropathy or normal. The overall Moorfields Regression Analysis result from the Heidelberg Retina Tomograph was used as a separate diagnostic classification. Thus, 4 diagnostic standards were applied in total, 2 based on optic disc structure alone and 2 others based on disc structure and SAP. Agreement between the 1-Run and 2-Run mfVEP was 90%. Diagnostic performance of the 1-Run mfVEP was similar to that of the 2-Run mfVEP for all 4 diagnostic standards. Sensitivity was slightly higher for the 2-Run mfVEP, whereas specificity was slightly higher for the 1-Run mfVEP. If higher sensitivity is sought, the 2-Run mfVEP will provide better discrimination between groups of eyes with relatively high signal-to-noise ratio (eg, early glaucoma or high-risk suspects). But if higher specificity is a more important goal, the 1-Run mfVEP provides adequate sensitivity and requires only half the test time. Considered alongside prior studies, the present results suggest that the 1-Run mfVEP is an efficient way to confirm (or refute) the extent of VF loss in patients with moderate or advanced glaucoma, particularly in those with unreliable VFs, including malingering or other "functional" forms of VF loss.

Dopamine D1 receptor modulation in nucleus accumbens lowers voluntary wheel running in rats bred to run high distances.

PubMed

Roberts, Michael D; Gilpin, Leigh; Parker, Kyle E; Childs, Thomas E; Will, Matthew J; Booth, Frank W

2012-02-01

Dopamine signaling in the nucleus accumbens (NAc) has been postulated to influence reward development towards drugs of abuse and exercise. Herein, we used generation 4-5 rats that were selectively bred to voluntary run high (HVR) versus low (LVR) distances in order to examine if dopamine-like 1 (D1) receptor modulation in the NAc differentially affects nightly voluntary wheel running between these lines. A subset of generation 5-6 HVR and LVR rats were also used to study the mRNA expression of key genes related to reward and addiction in the NAc (i.e., DRD1, DRD5, DRD2, Nr4a2, FosB, and BDNF). In a crossover fashion, a D1-like agonist SKF 82958 (2 μg per side) or D1-like full antagonist SCH 23390 (4 μg per side) was bilaterally injected into the NAc of HVR and LVR female Wistar rats prior to their high running nights. Notably, during hours 2-4 (between 2000 and 2300) of the dark cycle there was a significant decrement in running distances in the HVR rats treated with the D1 agonist (p=0.025) and antagonist (p=0.017) whereas the running distances in LVR rats were not affected. Interestingly, HVR and LVR rats possessed similar NAc concentrations of the studied mRNAs. These data suggest that: a) animals predisposed to run high distances on a nightly basis may quickly develop a rewarding response to exercise due to an optimal D1-like receptor signaling pathway in the NAc that can be perturbed by either activation or blocking, b) D1-like agonist or antagonist injections do not increase running distances in rats that are bred to run low nightly distances, and c) running differences between HVR and LVR animals are seemingly not due to the expression of the studied mRNAs. Given the societal prevalence of obesity and extraneous physical inactivity, future studies should be performed in order to further determine the culprit for the low running phenotype observed in LVR animals. Copyright © 2011. Published by Elsevier Inc.

Voluntary wheel running in dystrophin-deficient (mdx) mice: Relationships between exercise parameters and exacerbation of the dystrophic phenotype.

PubMed

Smythe, Gayle M; White, Jason D

2011-12-18

Voluntary wheel running can potentially be used to exacerbate the disease phenotype in dystrophin-deficient mdx mice. While it has been established that voluntary wheel running is highly variable between individuals, the key parameters of wheel running that impact the most on muscle pathology have not been examined in detail. We conducted a 2-week test of voluntary wheel running by mdx mice and the impact of wheel running on disease pathology. There was significant individual variation in the average daily distance (ranging from 0.003 ± 0.005 km to 4.48 ± 0.96 km), culminating in a wide range (0.040 km to 67.24 km) of total cumulative distances run by individuals. There was also variation in the number and length of run/rest cycles per night, and the average running rate. Correlation analyses demonstrated that in the quadriceps muscle, a low number of high distance run/rest cycles was the most consistent indicator for increased tissue damage. The amount of rest time between running bouts was a key factor associated with gastrocnemius damage. These data emphasize the need for detailed analysis of individual running performance, consideration of the length of wheel exposure time, and the selection of appropriate muscle groups for analysis, when applying the use of voluntary wheel running to disease exacerbation and/or pre-clinical testing of the efficacy of therapeutic agents in the mdx mouse.

Lower-volume muscle-damaging exercise protects against high-volume muscle-damaging exercise and the detrimental effects on endurance performance.

PubMed

Burt, Dean; Lamb, Kevin; Nicholas, Ceri; Twist, Craig

2015-07-01

This study examined whether lower-volume exercise-induced muscle damage (EIMD) performed 2 weeks before high-volume muscle-damaging exercise protects against its detrimental effect on running performance. Sixteen male participants were randomly assigned to a lower-volume (five sets of ten squats, n = 8) or high-volume (ten sets of ten squats, n = 8) EIMD group and completed baseline measurements for muscle soreness, knee extensor torque, creatine kinase (CK), a 5-min fixed-intensity running bout and a 3-km running time-trial. Measurements were repeated 24 and 48 h after EIMD, and the running time-trial after 48 h. Two weeks later, both groups repeated the baseline measurements, ten sets of ten squats and the same follow-up testing (Bout 2). Data analysis revealed increases in muscle soreness and CK and decreases in knee extensor torque 24-48 h after the initial bouts of EIMD. Increases in oxygen uptake [Formula: see text], minute ventilation [Formula: see text] and rating of perceived exertion were observed during fixed-intensity running 24-48 h after EIMD Bout 1. Likewise, time increased and speed and [Formula: see text] decreased during a 3-km running time-trial 48 h after EIMD. Symptoms of EIMD, responses during fixed-intensity and running time-trial were attenuated in the days after the repeated bout of high-volume EIMD performed 2 weeks after the initial bout. This study demonstrates that the protective effect of lower-volume EIMD on subsequent high-volume EIMD is transferable to endurance running. Furthermore, time-trial performance was found to be preserved after a repeated bout of EIMD.

Endurance capacity of mice selectively bred for high voluntary wheel running.

PubMed

Meek, Thomas H; Lonquich, Brian P; Hannon, Robert M; Garland, Theodore

2009-09-15

Mice from four lines bred for high voluntary wheel activity run approximately 3-fold more revolutions per day and have elevated maximal oxygen consumption during forced treadmill exercise, as compared with four unselected control (C) lines. We hypothesized that these high runner (HR) lines would have greater treadmill endurance-running capacity. Ninety-six mice from generation 49 were familiarized with running on a motorized treadmill for 3 days. On days 4 and 5, mice were given an incremental speed test (starting at 20 m min(-1), increased 1.5 m min(-1) every 2 min) and endurance was measured as the total time or distance run to exhaustion. Blood samples were taken to measure glucose and lactate concentrations at rest during the photophase, during peak nightly wheel running, and immediately following the second endurance test. Individual differences in endurance time were highly repeatable between days (r=0.79), and mice tended to run longer on the second day (paired t-test, P<0.0001). Blood glucose following the treadmill test was low for all animals ( approximately 53 mg dl(-1)) and lactate was high ( approximately 6.5 mmol l(-1)), suggesting that exhaustion occurred. The HR lines had significantly higher endurance than the C lines (1-tailed P<0.05), whether or not body mass was used as a covariate in the analysis. The relationship between line means for wheel running and treadmill endurance differed between the sexes, reinforcing previous studies that indicate sex-specific responses to selective breeding. HR mice appear to have a higher endurance capacity than reported in the literature for inbred strains of mice or transgenics intended to enhance endurance.

High-intensity sprint fatigue does not alter constant-submaximal velocity running mechanics and spring-mass behavior.

PubMed

Morin, Jean-Benoit; Tomazin, Katja; Samozino, Pierre; Edouard, Pascal; Millet, Guillaume Y

2012-04-01

We investigated the changes in constant velocity spring-mass behavior after high intensity sprint fatigue in order to better interpret the results recently reported after ultra-long distance (ULD) exercises. Our hypothesis was that after repeated sprints (RS), subjects may likely experience losses of force such as after ULD, but the necessity to modify their running pattern to attenuate the overall impact at each step (such as after ULD) may not be present. Eleven male subjects performed four sets of five 6-s sprints with 24-s recovery between sprints and 3 min between sets, on a sprint treadmill and on a bicycle ergometer. For each session, their running mechanics and spring-mass characteristics were measured at 10 and 20 km h(-1) on an instrumented treadmill before and after RS. Two-way (period and velocity) ANOVAs showed that high-intensity fatigue did not induce any change in the constant velocity running pattern at low or high velocity, after both running and cycling RS, despite significant decreases (P < 0.001) in maximal power (-27.1 ± 8.2% after running RS and -15.4 ± 11.5 % after cycling RS) and knee extensors maximal voluntary force (-18.8 ± 6.7 % after running RS and -15.0 ± 7.6 % after cycling RS). These results bring indirect support to the hypothesis put forward in recent ULD studies that the changes in running mechanics observed after ULD are likely not related to the decrease in strength capabilities, but rather to the necessity for subjects to adopt a protective running pattern.

Job Priorities on Peregrine | High-Performance Computing | NREL

Science.gov Websites

allocation when run with qos=high. Requesting a Node Reservation If you are doing work that requires real scheduler more efficiently plan resources for larger jobs. When projects reach their allocation limit, jobs associated with those projects will run at very low priority, which will ensure that these jobs run only when

Running High-Throughput Jobs on Peregrine | High-Performance Computing |

Science.gov Websites

unique name (using "name=") and usse the task name to create a unique output file name. For runs on and how many tasks to give to each worker at a time using the NITRO_COORD_OPTIONS environment . Finally, you start Nitro by executing launch_nitro.sh. Sample Nitro job script To run a job using the

How Much of a "Running Start" Do Dual Enrollment Programs Provide Students? CEDR Working Paper. WP #2014-­7

ERIC Educational Resources Information Center

Cowan, James; Goldhaber, Dan

2014-01-01

We study a popular dual enrollment program in Washington State, "Running Start" using a new administrative database that links high school and postsecondary data. Conditional on prior high school performance, we find that students participating in Running Start are more likely to attend any college but less likely to attend four-year…

Neuromuscular fatigue and recovery dynamics following prolonged continuous run at anaerobic threshold.

PubMed

Skof, B; Strojnik, V

2006-03-01

The aim of this study was to determine the influence of intensive aerobic running on some muscle contractile characteristics and the dynamics of their recovery during a 2 hour period afterwards. Seven well trained runners performed a 6 km run at anaerobic threshold (V(OBLA)). Knee torque during single twitch, low and high frequency electrical stimulation (ES), maximum voluntary knee extension, and muscle activation level test of the quadriceps femoris muscles were measured before and immediately after the run, and at several time points during a 120 minute interval that followed the run. After exercise, the mean (SE) maximum twitch torque (T(TW)) and torque at ES with 20 Hz (low frequency ES; T(F20)) dropped by 14.1 (5.1)% (p<0.05) and 20.6 (7.9)% (p<0.05) respectively, while torque at stimulation with 100 Hz (high frequency ES; T(F100)), maximum isometric knee extension torque (maximum voluntary contraction torque; T(MVC)), and activation level did not change significantly. Twitch contraction time was shortened by 8 (2)% (p<0.05). Ten minutes after the run, T(TW) was 40% higher than immediately after the run and 10% (p<0.05) higher than before the run. T(F20), T(F100), and T(MVC) remained lower for 60 minutes (p<0.05) than before the run. A 6 km continuous run at V(OBLA) caused peripheral fatigue by impairing excitation-contraction coupling. Twitch torque recovered very quickly. However, the process of torque restoration at maximum isometric knee extension torque and at high and low frequency ES took much longer.

New laser materials for laser diode pumping

NASA Technical Reports Server (NTRS)

Jenssen, H. P.

1990-01-01

The potential advantages of laser diode pumped solid state lasers are many with high overall efficiency being the most important. In order to realize these advantages, the solid state laser material needs to be optimized for diode laser pumping and for the particular application. In the case of the Nd laser, materials with a longer upper level radiative lifetime are desirable. This is because the laser diode is fundamentally a cw source, and to obtain high energy storage, a long integration time is necessary. Fluoride crystals are investigated as host materials for the Nd laser and also for IR laser transitions in other rare earths, such as the 2 micron Ho laser and the 3 micron Er laser. The approach is to investigate both known crystals, such as BaY2F8, as well as new crystals such as NaYF8. Emphasis is on the growth and spectroscopy of BaY2F8. These two efforts are parallel efforts. The growth effort is aimed at establishing conditions for obtaining large, high quality boules for laser samples. This requires numerous experimental growth runs; however, from these runs, samples suitable for spectroscopy become available.

Working research codes into fluid dynamics education: a science gateway approach

NASA Astrophysics Data System (ADS)

Mason, Lachlan; Hetherington, James; O'Reilly, Martin; Yong, May; Jersakova, Radka; Grieve, Stuart; Perez-Suarez, David; Klapaukh, Roman; Craster, Richard V.; Matar, Omar K.

2017-11-01

Research codes are effective for illustrating complex concepts in educational fluid dynamics courses, compared to textbook examples, an interactive three-dimensional visualisation can bring a problem to life! Various barriers, however, prevent the adoption of research codes in teaching: codes are typically created for highly-specific `once-off' calculations and, as such, have no user interface and a steep learning curve. Moreover, a code may require access to high-performance computing resources that are not readily available in the classroom. This project allows academics to rapidly work research codes into their teaching via a minimalist `science gateway' framework. The gateway is a simple, yet flexible, web interface allowing students to construct and run simulations, as well as view and share their output. Behind the scenes, the common operations of job configuration, submission, monitoring and post-processing are customisable at the level of shell scripting. In this talk, we demonstrate the creation of an example teaching gateway connected to the Code BLUE fluid dynamics software. Student simulations can be run via a third-party cloud computing provider or a local high-performance cluster. EPSRC, UK, MEMPHIS program Grant (EP/K003976/1), RAEng Research Chair (OKM).

Next Generation MUT-MAP, a High-Sensitivity High-Throughput Microfluidics Chip-Based Mutation Analysis Panel

PubMed Central

Patel, Rajesh; Tsan, Alison; Sumiyoshi, Teiko; Fu, Ling; Desai, Rupal; Schoenbrunner, Nancy; Myers, Thomas W.; Bauer, Keith; Smith, Edward; Raja, Rajiv

2014-01-01

Molecular profiling of tumor tissue to detect alterations, such as oncogenic mutations, plays a vital role in determining treatment options in oncology. Hence, there is an increasing need for a robust and high-throughput technology to detect oncogenic hotspot mutations. Although commercial assays are available to detect genetic alterations in single genes, only a limited amount of tissue is often available from patients, requiring multiplexing to allow for simultaneous detection of mutations in many genes using low DNA input. Even though next-generation sequencing (NGS) platforms provide powerful tools for this purpose, they face challenges such as high cost, large DNA input requirement, complex data analysis, and long turnaround times, limiting their use in clinical settings. We report the development of the next generation mutation multi-analyte panel (MUT-MAP), a high-throughput microfluidic, panel for detecting 120 somatic mutations across eleven genes of therapeutic interest (AKT1, BRAF, EGFR, FGFR3, FLT3, HRAS, KIT, KRAS, MET, NRAS, and PIK3CA) using allele-specific PCR (AS-PCR) and Taqman technology. This mutation panel requires as little as 2 ng of high quality DNA from fresh frozen or 100 ng of DNA from formalin-fixed paraffin-embedded (FFPE) tissues. Mutation calls, including an automated data analysis process, have been implemented to run 88 samples per day. Validation of this platform using plasmids showed robust signal and low cross-reactivity in all of the newly added assays and mutation calls in cell line samples were found to be consistent with the Catalogue of Somatic Mutations in Cancer (COSMIC) database allowing for direct comparison of our platform to Sanger sequencing. High correlation with NGS when compared to the SuraSeq500 panel run on the Ion Torrent platform in a FFPE dilution experiment showed assay sensitivity down to 0.45%. This multiplexed mutation panel is a valuable tool for high-throughput biomarker discovery in personalized medicine and cancer drug development. PMID:24658394

The physiological basis of bird flight

PubMed Central

Butler, Patrick J.

2016-01-01

Flapping flight is energetically more costly than running, although it is less costly to fly a given body mass a given distance per unit time than it is for a similar mass to run the same distance per unit time. This is mainly because birds can fly faster than they can run. Oxygen transfer and transport are enhanced in migrating birds compared with those in non-migrators: at the gas-exchange regions of the lungs the effective area is greater and the diffusion distance smaller. Also, migrating birds have larger hearts and haemoglobin concentrations in the blood, and capillary density in the flight muscles tends to be higher. Species like bar-headed geese migrate at high altitudes, where the availability of oxygen is reduced and the energy cost of flapping flight increased compared with those at sea level. Physiological adaptations to these conditions include haemoglobin with a higher affinity for oxygen than that in lowland birds, a greater effective ventilation of the gas-exchange surface of the lungs and a greater capillary-to-muscle fibre ratio. Migrating birds use fatty acids as their source of energy, so they have to be transported at a sufficient rate to meet the high demand. Since fatty acids are insoluble in water, birds maintain high concentrations of fatty acid–binding proteins to transport fatty acids across the cell membrane and within the cytoplasm. The concentrations of these proteins, together with that of a key enzyme in the β-oxidation of fatty acids, increase before migration. This article is part of the themed issue ‘Moving in a moving medium: new perspectives on flight’. PMID:27528774

Cocaine self-administration and reinstatement in female rats selectively bred for high and low voluntary running.

PubMed

Smethells, J R; Zlebnik, N E; Miller, D K; Will, M J; Booth, F; Carroll, M E

2016-10-01

Previous research has found that rats behaviorally screened for high (vs. low) wheel running were more vulnerable to cocaine abuse. To assess the extent to which a genetic component is involved in this drug-abuse vulnerability, rats selectively bred for high or low voluntary running (HVR or LVR, respectively) were examined for differences in cocaine seeking in the present study. Female rats were trained to lever press for food and then were assessed for differences in acquisition of cocaine (0.4mg/kg; i.v.) self-administration across 10 sessions. Once acquired, rats self-administered cocaine for a 14-day maintenance phase, followed by a 14-day extinction phase when cocaine was no longer available. Subsequently, reinstatement of cocaine seeking was examined with priming injections of cocaine (5, 10 & 15mg/kg), caffeine (30mg/kg), yohimbine (2.5mg/kg) and cocaine-paired cues. A greater percentage of LVR rats met the acquisition criteria for cocaine self-administration and in fewer sessions than HVR rats. No differences in responding for cocaine were observed between phenotypes during maintenance. However, during extinction LVR rats initially responded at higher rates and persisted in cocaine seeking for a greater number of sessions. No phenotype differences were observed following drug and cue-primed reinstatement of cocaine seeking. In general, LVR rats were more sensitive to the reinforcing effects of cocaine than HVR rats during periods of transition into and out of cocaine self-administration. Thus, LVR rats sometimes showed a greater vulnerability cocaine seeking than HVR rats. Published by Elsevier Ireland Ltd.

Development of a timing detector for the TOTEM experiment at the LHC

NASA Astrophysics Data System (ADS)

Minafra, Nicola

2017-09-01

The upgrade program of the TOTEM experiment will include the installation of timing detectors inside vertical Roman Pots to allow the reconstruction of the longitudinal vertex position in the presence of event pile-up in high- β^{\\ast} dedicated runs. The small available space inside the Roman Pot, optimized for high-intensity LHC runs, and the required time precision led to the study of a solution using single crystal CVD diamonds. The sensors are read out using fast low-noise front-end electronics developed by the TOTEM Collaboration, achieving a signal-to-noise ratio larger than 20 for MIPs. A prototype was designed, manufactured and tested during a test beam campaign, proving a time precision below 100ps and an efficiency above 99%. The geometry of the detector has been designed to guarantee uniform occupancy in the expected running conditions keeping, at the same time, the number of channels below 12. The read-out electronics was developed during an extensive campaign of beam tests dedicated first to the characterization of existing solution and then to the optimization of the electronics designed within the Collaboration. The detectors were designed to be read out using the SAMPIC chip, a fast sampler designed specifically for picosecond timing measurements with high-rate capabilities; later, a modified version was realized using the HPTDC to achieve the higher trigger rates required for the CT-PPS experiment. The first set of prototypes was successfully installed and tested in the LHC in November 2015; moreover the detectors modified for CT-PPS are successfully part of the global CMS data taking since October 2016.

Influence of "J"-Curve Spring Stiffness on Running Speeds of Segmented Legs during High-Speed Locomotion.

PubMed

Wang, Runxiao; Zhao, Wentao; Li, Shujun; Zhang, Shunqi

2016-01-01

Both the linear leg spring model and the two-segment leg model with constant spring stiffness have been broadly used as template models to investigate bouncing gaits for legged robots with compliant legs. In addition to these two models, the other stiffness leg spring models developed using inspiration from biological characteristic have the potential to improve high-speed running capacity of spring-legged robots. In this paper, we investigate the effects of "J"-curve spring stiffness inspired by biological materials on running speeds of segmented legs during high-speed locomotion. Mathematical formulation of the relationship between the virtual leg force and the virtual leg compression is established. When the SLIP model and the two-segment leg model with constant spring stiffness and with "J"-curve spring stiffness have the same dimensionless reference stiffness, the two-segment leg model with "J"-curve spring stiffness reveals that (1) both the largest tolerated range of running speeds and the tolerated maximum running speed are found and (2) at fast running speed from 25 to 40/92 m s -1 both the tolerated range of landing angle and the stability region are the largest. It is suggested that the two-segment leg model with "J"-curve spring stiffness is more advantageous for high-speed running compared with the SLIP model and with constant spring stiffness.

Influence of “J”-Curve Spring Stiffness on Running Speeds of Segmented Legs during High-Speed Locomotion

PubMed Central

2016-01-01

Both the linear leg spring model and the two-segment leg model with constant spring stiffness have been broadly used as template models to investigate bouncing gaits for legged robots with compliant legs. In addition to these two models, the other stiffness leg spring models developed using inspiration from biological characteristic have the potential to improve high-speed running capacity of spring-legged robots. In this paper, we investigate the effects of “J”-curve spring stiffness inspired by biological materials on running speeds of segmented legs during high-speed locomotion. Mathematical formulation of the relationship between the virtual leg force and the virtual leg compression is established. When the SLIP model and the two-segment leg model with constant spring stiffness and with “J”-curve spring stiffness have the same dimensionless reference stiffness, the two-segment leg model with “J”-curve spring stiffness reveals that (1) both the largest tolerated range of running speeds and the tolerated maximum running speed are found and (2) at fast running speed from 25 to 40/92 m s−1 both the tolerated range of landing angle and the stability region are the largest. It is suggested that the two-segment leg model with “J”-curve spring stiffness is more advantageous for high-speed running compared with the SLIP model and with constant spring stiffness. PMID:28018127

Integrated starting and running amalgam assembly for an electrodeless fluorescent lamp

DOEpatents

Borowiec, Joseph Christopher; Cocoma, John Paul; Roberts, Victor David

1998-01-01

An integrated starting and running amalgam assembly for an electrodeless SEF fluorescent lamp includes a wire mesh amalgam support constructed to jointly optimize positions of a starting amalgam and a running amalgam in the lamp, thereby optimizing mercury vapor pressure in the lamp during both starting and steady-state operation in order to rapidly achieve and maintain high light output. The wire mesh amalgam support is constructed to support the starting amalgam toward one end thereof and the running amalgam toward the other end thereof, and the wire mesh is rolled for friction-fitting within the exhaust tube of the lamp. The positions of the starting and running amalgams on the wire mesh are jointly optimized such that high light output is achieved quickly and maintained, while avoiding any significant reduction in light output between starting and running operation.

Does “Live High-Train Low (and High)” Hypoxic Training Alter Running Mechanics In Elite Team-sport Players?

PubMed Central

Girard, Olivier; Millet, Grégoire P.; Morin, Jean-Benoit; Brocherie, Franck

2017-01-01

This study aimed to investigate if “Live High-Train Low (and High)” hypoxic training alters constant-velocity running mechanics. While residing under normobaric hypoxia (≥14 h·d-1; FiO2 14.5-14.2%) for 14 days, twenty field hockey players performed, in addition to their usual training in normoxia, six sessions (4 × 5 × 5-s maximal sprints; 25 s passive recovery; 5 min rest) under either normobaric hypoxia (FiO2 ~14.5%, n = 9) or normoxia (FiO2 20.9%, n = 11). Before and immediately after the intervention, their running pattern was assessed at 10 and 15 km·h-1 as well as during six 30-s runs at ~20 km·h-1 with 30-s passive recovery on an instrumented motorised treadmill. No clear changes in running kinematics and spring-mass parameters occurred globally either at 10, 15 or ~20 km·h-1, with also no significant time × condition interaction for any parameters (p > 0.14). Independently of the condition, heart rate (all p < 0.05) and ratings of perceived exertion decreased post-intervention (only at 15 km·h-1, p < 0.05). Despite indirect signs for improved psycho-physiological responses, no forthright change in stride mechanical pattern occurred after “Live High-Train Low (and High)” hypoxic training. Key points There are indirect signs for improved psycho-physiological responses in responses to “Live High-Train Low (and High)” hypoxic training. This hypoxic training regimen, however, does not modify the running mechanics of elite team-sport players at low and high velocities. Coaches can be confident that this intervention, known for inducing significant metabolic benefits, is appropriate for athletes since their running kinetics and kinematics are not negatively affected by chronic hypoxic exposure. PMID:28912649

Cloning and establishment of a line of rats for high levels of voluntary wheel running.

PubMed

Morishima-Yamato, Masaki; Hisaoka, Fumiko; Shinomiya, Sachiko; Harada, Nagakatsu; Matoba, Hideki; Takahashi, Akira; Nakaya, Yutaka

2005-06-17

We generated an original Wistar line of rats that displayed increased levels of wheel running, which we named SPORTS (Spontaneously-Running-Tokushima-Shikoku). Male SPORTS rats ran voluntarily in a running wheel almost six times longer than male control Wistar rats, established without selection for their running activity. The running phenotype of female SPORTS rats was the same as female control Wistar rats. However, male offspring from the cross-mating between a female SPORTS rat and a male control rat also showed a similar level of hyper-running activity as the original SPORTS line. Compared to control rats, male SPORTS rats had lower levels of mean body weight, abdominal fat and plasma insulin after 4 weeks of running. It is likely that all these beneficial changes observed in the SPORTS rats reflected the increases in glucose disposal we observed in oral glucose tolerance tests carried out on the animals. We also found hyper-running caused a significant increase in skeletal muscle oxidative capacity, measured as the ratio of malate dehydrogenase to phosphofructokinase activity, an index of aerobic metabolism. These results indicate that the SPORTS rat may be a good animal model for determining the mechanisms responsible for up-regulation of running motivation, in addition to investigating changes in nutrient metabolism induced by high intensity exercise.

Improvement in Running Economy after 6 Weeks of Plyometric Training.

ERIC Educational Resources Information Center

Turner, Amanda M.; Owings, Matt; Schwane, James A.

2003-01-01

Investigated whether a 6-week regimen of plyometric training would improve running economy. Data were collected on 18 regular but not highly trained distance runners who participated in either regular running training or plyometric training. Results indicated that 6 weeks of plyometric training improved running economy at selected speeds in this…

40 CFR 86.134-96 - Running loss test.

Code of Federal Regulations, 2014 CFR

2014-07-01

... running loss test procedure as approved for a specific vehicle. (4) High-altitude testing. For testing... 40 Protection of Environment 19 2014-07-01 2014-07-01 false Running loss test. 86.134-96 Section... Heavy-Duty Vehicles; Test Procedures § 86.134-96 Running loss test. (a) Overview. Gasoline- and methanol...

Metabolic power demands of rugby league match play.

PubMed

Kempton, Tom; Sirotic, Anita Claire; Rampinini, Ermanno; Coutts, Aaron James

2015-01-01

To describe the metabolic demands of rugby league match play for positional groups and compare match distances obtained from high-speed-running classifications with those derived from high metabolic power. Global positioning system (GPS) data were collected from 25 players from a team competing in the National Rugby League competition over 39 matches. Players were classified into positional groups (adjustables, outside backs, hit-up forwards, and wide-running forwards). The GPS devices provided instantaneous raw velocity data at 5 Hz, which were exported to a customized spreadsheet. The spreadsheet provided calculations for speed-based distances (eg, total distance; high-speed running, >14.4 km/h; and very-high-speed running, >18.1 km/h) and metabolic-power variables (eg, energy expenditure; average metabolic power; and high-power distance, >20 W/kg). The data show that speed-based distances and metabolic power varied between positional groups, although this was largely related to differences in time spent on field. The distance covered at high running speed was lower than that obtained from high-power thresholds for all positional groups; however, the difference between the 2 methods was greatest for hit-up forwards and adjustables. Positional differences existed for all metabolic parameters, although these are at least partially related to time spent on the field. Higher-speed running may underestimate the demands of match play when compared with high-power distance-although the degree of difference between the measures varied by position. The analysis of metabolic power may complement traditional speed-based classifications and improve our understanding of the demands of rugby league match play.

HipMCL: a high-performance parallel implementation of the Markov clustering algorithm for large-scale networks

PubMed Central

Azad, Ariful; Ouzounis, Christos A; Kyrpides, Nikos C; Buluç, Aydin

2018-01-01

Abstract Biological networks capture structural or functional properties of relevant entities such as molecules, proteins or genes. Characteristic examples are gene expression networks or protein–protein interaction networks, which hold information about functional affinities or structural similarities. Such networks have been expanding in size due to increasing scale and abundance of biological data. While various clustering algorithms have been proposed to find highly connected regions, Markov Clustering (MCL) has been one of the most successful approaches to cluster sequence similarity or expression networks. Despite its popularity, MCL’s scalability to cluster large datasets still remains a bottleneck due to high running times and memory demands. Here, we present High-performance MCL (HipMCL), a parallel implementation of the original MCL algorithm that can run on distributed-memory computers. We show that HipMCL can efficiently utilize 2000 compute nodes and cluster a network of ∼70 million nodes with ∼68 billion edges in ∼2.4 h. By exploiting distributed-memory environments, HipMCL clusters large-scale networks several orders of magnitude faster than MCL and enables clustering of even bigger networks. HipMCL is based on MPI and OpenMP and is freely available under a modified BSD license. PMID:29315405

HipMCL: a high-performance parallel implementation of the Markov clustering algorithm for large-scale networks

DOE PAGES

Azad, Ariful; Pavlopoulos, Georgios A.; Ouzounis, Christos A.; ...

2018-01-05

Biological networks capture structural or functional properties of relevant entities such as molecules, proteins or genes. Characteristic examples are gene expression networks or protein–protein interaction networks, which hold information about functional affinities or structural similarities. Such networks have been expanding in size due to increasing scale and abundance of biological data. While various clustering algorithms have been proposed to find highly connected regions, Markov Clustering (MCL) has been one of the most successful approaches to cluster sequence similarity or expression networks. Despite its popularity, MCL’s scalability to cluster large datasets still remains a bottleneck due to high running times andmore » memory demands. In this paper, we present High-performance MCL (HipMCL), a parallel implementation of the original MCL algorithm that can run on distributed-memory computers. We show that HipMCL can efficiently utilize 2000 compute nodes and cluster a network of ~70 million nodes with ~68 billion edges in ~2.4 h. By exploiting distributed-memory environments, HipMCL clusters large-scale networks several orders of magnitude faster than MCL and enables clustering of even bigger networks. Finally, HipMCL is based on MPI and OpenMP and is freely available under a modified BSD license.« less

HipMCL: a high-performance parallel implementation of the Markov clustering algorithm for large-scale networks

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

Azad, Ariful; Pavlopoulos, Georgios A.; Ouzounis, Christos A.

Biological networks capture structural or functional properties of relevant entities such as molecules, proteins or genes. Characteristic examples are gene expression networks or protein–protein interaction networks, which hold information about functional affinities or structural similarities. Such networks have been expanding in size due to increasing scale and abundance of biological data. While various clustering algorithms have been proposed to find highly connected regions, Markov Clustering (MCL) has been one of the most successful approaches to cluster sequence similarity or expression networks. Despite its popularity, MCL’s scalability to cluster large datasets still remains a bottleneck due to high running times andmore » memory demands. In this paper, we present High-performance MCL (HipMCL), a parallel implementation of the original MCL algorithm that can run on distributed-memory computers. We show that HipMCL can efficiently utilize 2000 compute nodes and cluster a network of ~70 million nodes with ~68 billion edges in ~2.4 h. By exploiting distributed-memory environments, HipMCL clusters large-scale networks several orders of magnitude faster than MCL and enables clustering of even bigger networks. Finally, HipMCL is based on MPI and OpenMP and is freely available under a modified BSD license.« less

ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq.

PubMed

Kucukural, Alper; Özadam, Hakan; Singh, Guramrit; Moore, Melissa J; Cenik, Can

2013-10-01

Unlike DNA, RNA abundances can vary over several orders of magnitude. Thus, identification of RNA-protein binding sites from high-throughput sequencing data presents unique challenges. Although peak identification in ChIP-Seq data has been extensively explored, there are few bioinformatics tools tailored for peak calling on analogous datasets for RNA-binding proteins. Here we describe ASPeak (abundance sensitive peak detection algorithm), an implementation of an algorithm that we previously applied to detect peaks in exon junction complex RNA immunoprecipitation in tandem experiments. Our peak detection algorithm yields stringent and robust target sets enabling sensitive motif finding and downstream functional analyses. ASPeak is implemented in Perl as a complete pipeline that takes bedGraph files as input. ASPeak implementation is freely available at https://sourceforge.net/projects/as-peak under the GNU General Public License. ASPeak can be run on a personal computer, yet is designed to be easily parallelizable. ASPeak can also run on high performance computing clusters providing efficient speedup. The documentation and user manual can be obtained from http://master.dl.sourceforge.net/project/as-peak/manual.pdf.

Very High Current Density Nb/AlN/Nb Tunnel Junctions for Low-Noise Submillimeter Mixers

NASA Technical Reports Server (NTRS)

Kawamura, Jonathan; Miller, David; Chen, Jian; Zmuidzinas, Jonas; Bumble, Bruce; LeDuc, Henry G.; Stern, Jeff A.

2000-01-01

We have fabricated and tested submillimeter-wave superconductor-insulator-superconductor (SIS) mixers using very high current density Nb/AlN/Nb tunnel junctions (J(sub c) approximately equal 30 kA/sq cm) . The junctions have low resistance-area products (R(sub N)A approximately 5.6 Omega.sq micron), good subgap to normal resistance ratios R(sub sg)/R(sub N) approximately equal 10, and good run-to-run reproducibility. From Fourier transform spectrometer measurements, we infer that omega.R(sub N)C = 1 at 270 GHz. This is a factor of 2.5 improvement over what is generally available with Nb/AlO(x)/Nb junctions suitable for low-noise mixers. The AlN-barrier junctions are indeed capable of low-noise operation: we measure an uncorrected receiver noise temperature of T(sub RX) = 110 K (DSB) at 533 GHz for an unoptimized device. In addition to providing wider bandwidth operation at lower frequencies, the AlN-barrier junctions will considerably improve the performance of THz SIS mixers by reducing RF loss in the tuning circuits.

Achieving High Throughput for Data Transfer over ATM Networks

NASA Technical Reports Server (NTRS)

Johnson, Marjory J.; Townsend, Jeffrey N.

1996-01-01

File-transfer rates for ftp are often reported to be relatively slow, compared to the raw bandwidth available in emerging gigabit networks. While a major bottleneck is disk I/O, protocol issues impact performance as well. Ftp was developed and optimized for use over the TCP/IP protocol stack of the Internet. However, TCP has been shown to run inefficiently over ATM. In an effort to maximize network throughput, data-transfer protocols can be developed to run over UDP or directly over IP, rather than over TCP. If error-free transmission is required, techniques for achieving reliable transmission can be included as part of the transfer protocol. However, selected image-processing applications can tolerate a low level of errors in images that are transmitted over a network. In this paper we report on experimental work to develop a high-throughput protocol for unreliable data transfer over ATM networks. We attempt to maximize throughput by keeping the communications pipe full, but still keep packet loss under five percent. We use the Bay Area Gigabit Network Testbed as our experimental platform.

Physiological and Biomechanical Mechanisms of Distance Specific Human Running Performance.

PubMed

Thompson, M A

2017-08-01

Running events range from 60-m sprints to ultra-marathons covering 100 miles or more, which presents an interesting diversity in terms of the parameters for successful performance. Here, we review the physiological and biomechanical variations underlying elite human running performance in sprint to ultramarathon distances. Maximal running speeds observed in sprint disciplines are achieved by high vertical ground reaction forces applied over short contact times. To create this high force output, sprint events rely heavily on anaerobic metabolism, as well as a high number and large cross-sectional area of type II fibers in the leg muscles. Middle distance running performance is characterized by intermediates of biomechanical and physiological parameters, with the possibility of unique combinations of each leading to high-level performance. The relatively fast velocities in mid-distance events require a high mechanical power output, though ground reaction forces are less than in sprinting. Elite mid-distance runners exhibit local muscle adaptations that, along with a large anaerobic capacity, provide the ability to generate a high power output. Aerobic capacity starts to become an important aspect of performance in middle distance events, especially as distance increases. In distance running events, V˙O2max is an important determinant of performance, but is relatively homogeneous in elite runners. V˙O2 and velocity at lactate threshold have been shown to be superior predictors of elite distance running performance. Ultramarathons are relatively new running events, as such, less is known about physiological and biomechanical parameters that underlie ultra-marathon performance. However, it is clear that performance in these events is related to aerobic capacity, fuel utilization, and fatigue resistance. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology 2017. This work is written by US Government employees and is in the public domain in the US.

Exercise-induced muscle damage and running economy in humans.

PubMed

Assumpção, Cláudio de Oliveira; Lima, Leonardo Coelho Rabello; Oliveira, Felipe Bruno Dias; Greco, Camila Coelho; Denadai, Benedito Sérgio

2013-01-01

Running economy (RE), defined as the energy demand for a given velocity of submaximal running, has been identified as a critical factor of overall distance running performance. Plyometric and resistance trainings, performed during a relatively short period of time (~15-30 days), have been successfully used to improve RE in trained athletes. However, these exercise types, particularly when they are unaccustomed activities for the individuals, may cause delayed onset muscle soreness, swelling, and reduced muscle strength. Some studies have demonstrated that exercise-induced muscle damage has a negative impact on endurance running performance. Specifically, the muscular damage induced by an acute bout of downhill running has been shown to reduce RE during subsequent moderate and high-intensity exercise (>65% VO₂max). However, strength exercise (i.e., jumps, isoinertial and isokinetic eccentric exercises) seems to impair RE only for subsequent high-intensity exercise (~90% VO₂max). Finally, a single session of resistance exercise or downhill running (i.e., repeated bout effect) attenuates changes in indirect markers of muscle damage and blunts changes in RE.

Running as an Adjunct to Psychotherapy.

ERIC Educational Resources Information Center

Leer, Frederic

1980-01-01

Physical benefits of running have been highly publicized. Explores the equally valuable psychological benefits to be derived from running and examines how mastering a physical skill can be generalized to mastery in other areas of life. (Author)

Experimental Evaluation of Cermet Turbine Stator Blades for Use at Elevated Gas Temperatures

NASA Technical Reports Server (NTRS)

Chiarito, Patrick T.; Johnston, James R.

1959-01-01

The suitability of cermets for turbine stator blades of a modified turbojet engine was determined at an average turbine-inlet-gas temperature of 2000 F. Such an increase in temperature would yield a premium in thrust from a service engine. Because the cermet blades require no cooling, all the available compressor bleed air could be used to cool a turbine made from conventional ductile alloys. Cermet blades were first run in 100-hour endurance tests at normal gas temperatures in order to evaluate two methods for mounting them. The elevated gas-temperature test was then run using the method of support considered best for high-temperature operation. After 52 hours at 2000 F, one of the group of four cermet blades fractured probably because of end loads resulting from thermal distortion of the spacer band of the nozzle diaphragm. Improved design of a service engine would preclude this cause of premature failure.

Jflow: a workflow management system for web applications.

PubMed

Mariette, Jérôme; Escudié, Frédéric; Bardou, Philippe; Nabihoudine, Ibouniyamine; Noirot, Céline; Trotard, Marie-Stéphane; Gaspin, Christine; Klopp, Christophe

2016-02-01

Biologists produce large data sets and are in demand of rich and simple web portals in which they can upload and analyze their files. Providing such tools requires to mask the complexity induced by the needed High Performance Computing (HPC) environment. The connection between interface and computing infrastructure is usually specific to each portal. With Jflow, we introduce a Workflow Management System (WMS), composed of jQuery plug-ins which can easily be embedded in any web application and a Python library providing all requested features to setup, run and monitor workflows. Jflow is available under the GNU General Public License (GPL) at http://bioinfo.genotoul.fr/jflow. The package is coming with full documentation, quick start and a running test portal. Jerome.Mariette@toulouse.inra.fr. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A ChIP-Seq Data Analysis Pipeline Based on Bioconductor Packages.

PubMed

Park, Seung-Jin; Kim, Jong-Hwan; Yoon, Byung-Ha; Kim, Seon-Young

2017-03-01

Nowadays, huge volumes of chromatin immunoprecipitation-sequencing (ChIP-Seq) data are generated to increase the knowledge on DNA-protein interactions in the cell, and accordingly, many tools have been developed for ChIP-Seq analysis. Here, we provide an example of a streamlined workflow for ChIP-Seq data analysis composed of only four packages in Bioconductor: dada2, QuasR, mosaics, and ChIPseeker. 'dada2' performs trimming of the high-throughput sequencing data. 'QuasR' and 'mosaics' perform quality control and mapping of the input reads to the reference genome and peak calling, respectively. Finally, 'ChIPseeker' performs annotation and visualization of the called peaks. This workflow runs well independently of operating systems (e.g., Windows, Mac, or Linux) and processes the input fastq files into various results in one run. R code is available at github: https://github.com/ddhb/Workflow_of_Chipseq.git.

A ChIP-Seq Data Analysis Pipeline Based on Bioconductor Packages

PubMed Central

Park, Seung-Jin; Kim, Jong-Hwan; Yoon, Byung-Ha; Kim, Seon-Young

2017-01-01

Nowadays, huge volumes of chromatin immunoprecipitation-sequencing (ChIP-Seq) data are generated to increase the knowledge on DNA-protein interactions in the cell, and accordingly, many tools have been developed for ChIP-Seq analysis. Here, we provide an example of a streamlined workflow for ChIP-Seq data analysis composed of only four packages in Bioconductor: dada2, QuasR, mosaics, and ChIPseeker. ‘dada2’ performs trimming of the high-throughput sequencing data. ‘QuasR’ and ‘mosaics’ perform quality control and mapping of the input reads to the reference genome and peak calling, respectively. Finally, ‘ChIPseeker’ performs annotation and visualization of the called peaks. This workflow runs well independently of operating systems (e.g., Windows, Mac, or Linux) and processes the input fastq files into various results in one run. R code is available at github: https://github.com/ddhb/Workflow_of_Chipseq.git. PMID:28416945

The Q continuum simulation: Harnessing the power of GPU accelerated supercomputers

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

Heitmann, Katrin; Frontiere, Nicholas; Sewell, Chris

2015-08-01

Modeling large-scale sky survey observations is a key driver for the continuing development of high-resolution, large-volume, cosmological simulations. We report the first results from the "Q Continuum" cosmological N-body simulation run carried out on the GPU-accelerated supercomputer Titan. The simulation encompasses a volume of (1300 Mpc)(3) and evolves more than half a trillion particles, leading to a particle mass resolution of m(p) similar or equal to 1.5 . 10(8) M-circle dot. At thismass resolution, the Q Continuum run is currently the largest cosmology simulation available. It enables the construction of detailed synthetic sky catalogs, encompassing different modeling methodologies, including semi-analyticmore » modeling and sub-halo abundance matching in a large, cosmological volume. Here we describe the simulation and outputs in detail and present first results for a range of cosmological statistics, such as mass power spectra, halo mass functions, and halo mass-concentration relations for different epochs. We also provide details on challenges connected to running a simulation on almost 90% of Titan, one of the fastest supercomputers in the world, including our usage of Titan's GPU accelerators.« less

Snowmelt runoff modeling in simulation and forecasting modes with the Martinec-Mango model

NASA Technical Reports Server (NTRS)

Shafer, B.; Jones, E. B.; Frick, D. M. (Principal Investigator)

1982-01-01

The Martinec-Rango snowmelt runoff model was applied to two watersheds in the Rio Grande basin, Colorado-the South Fork Rio Grande, a drainage encompassing 216 sq mi without reservoirs or diversions and the Rio Grande above Del Norte, a drainage encompassing 1,320 sq mi without major reservoirs. The model was successfully applied to both watersheds when run in a simulation mode for the period 1973-79. This period included both high and low runoff seasons. Central to the adaptation of the model to run in a forecast mode was the need to develop a technique to forecast the shape of the snow cover depletion curves between satellite data points. Four separate approaches were investigated-simple linear estimation, multiple regression, parabolic exponential, and type curve. Only the parabolic exponential and type curve methods were run on the South Fork and Rio Grande watersheds for the 1980 runoff season using satellite snow cover updates when available. Although reasonable forecasts were obtained in certain situations, neither method seemed ready for truly operational forecasts, possibly due to a large amount of estimated climatic data for one or two primary base stations during the 1980 season.

Pipettor Version 5.x

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

Thorn, David L.

Code is written in Basic to run using web-available Basic assembler, available at justbasic.com. It drives a set of stepper motors to mechanize the operation of pipetting radioactive solutions within a hot cell, and it communicates via serial port with the C4 stepper controller sold by Arrick, see http://www.arrickrobotics.com/c4md2.html. It is intended to operate stand-alone, that is, the justbasic assembler/application is downloaded onto a PC, the application runs the software program Pipettor, and the instructions are included as comments within the software.

Voluntary wheel-running attenuates insulin and weight gain and affects anxiety-like behaviors in C57BL6/J mice exposed to a high-fat diet.

PubMed

Hicks, Jasmin A; Hatzidis, Aikaterini; Arruda, Nicole L; Gelineau, Rachel R; De Pina, Isabella Monteiro; Adams, Kenneth W; Seggio, Joseph A

2016-09-01

It is widely accepted that lifestyle plays a crucial role on the quality of life in individuals, particularly in western societies where poor diet is correlated to alterations in behavior and the increased possibility of developing type-2 diabetes. While exercising is known to produce improvements to overall health, there is conflicting evidence on how much of an effect exercise has staving off the development of type-2 diabetes or counteracting the effects of diet on anxiety. Thus, this study investigated the effects of voluntary wheel-running access on the progression of diabetes-like symptoms and open field and light-dark box behaviors in C57BL/6J mice fed a high-fat diet. C57BL/6J mice were placed into either running-wheel cages or cages without a running-wheel, given either regular chow or a high-fat diet, and their body mass, food consumption, glucose tolerance, insulin and c-peptide levels were measured. Mice were also exposed to the open field and light-dark box tests for anxiety-like behaviors. Access to a running-wheel partially attenuated the obesity and hyperinsulinemia associated with high-fat diet consumption in these mice, but did not affect glucose tolerance or c-peptide levels. Wheel-running strongly increased anxiety-like and decreased explorative-like behaviors in the open field and light-dark box, while high-fat diet consumption produced smaller increases in anxiety. These results suggest that voluntary wheel-running can assuage some, but not all, of the physiological problems associated with high-fat diet consumption, and can modify anxiety-like behaviors regardless of diet consumed. Copyright © 2016 Elsevier B.V. All rights reserved.

Analysis of stratospheric ozone, temperature, and minor constituent data

NASA Technical Reports Server (NTRS)

Stolarski, Richard S.; Douglass, Anne R.; Jackman, Charles H.; Kaye, Jack A.; Rood, Richard B.

1990-01-01

The objective of this research is to use available satellite measurements of temperature and constituent concentrations to test the conceptual picture of stratospheric chemistry and transport. This was originally broken down into two sub-goals: first, to use the constituent data to search for critical tests of our understanding of stratospheric chemistry and second, to examine constituent transport processes emphasizing interactions with chemistry on various time scales. A third important goal which has evolved is to use the available solar backscattered ultraviolet (SBUV) and Total Ozone Mapping Spectrometer (TOMS) data from Nimbus 7 to describe the morphology of recent changes in Antarctic and global ozone with emphasis on searching for constraints to theories. The major effort now being pursued relative to the two original goals is our effort as a theoretical team for the Arctic Airborne Stratospheric Expedition (AASE). Our effort for the AASE is based on the 3D transport and chemistry model at Goddard. Our goal is to use this model to place the results from the mission data in a regional and global context. Specifically, we set out to make model runs starting in late December and running through March of 1989, both with and without heterogeneous chemistry. The transport is to be carried out using dynamical fields from a 4D data assimilation model being developed under separate funding from this task. We have successfully carried out a series of single constituent transport experiments. One of the things demonstrated by these runs was the difficulty in obtaining observed low N2O abundances in the vortex without simultaneously obtaining very high ozone values. Because the runs start in late December, this difficulty arises in the attempt to define consistent initial conditions for the 3D model. To accomplish a consistent set of initial conditions, we are using the 2D photochemistry-transport model of Jackman and Douglass and mapping in potential temperature, potential vorticity space as developed by Schoeberl and coworkers.

Rational Temporal Predictions Can Underlie Apparent Failures to Delay Gratification

ERIC Educational Resources Information Center

McGuire, Joseph T.; Kable, Joseph W.

2013-01-01

An important category of seemingly maladaptive decisions involves failure to postpone gratification. A person pursuing a desirable long-run outcome may abandon it in favor of a short-run alternative that has been available all along. Here we present a theoretical framework in which this seemingly irrational behavior emerges from stable preferences…

MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems.

PubMed

González-Domínguez, Jorge; Liu, Yongchao; Touriño, Juan; Schmidt, Bertil

2016-12-15

MSAProbs is a state-of-the-art protein multiple sequence alignment tool based on hidden Markov models. It can achieve high alignment accuracy at the expense of relatively long runtimes for large-scale input datasets. In this work we present MSAProbs-MPI, a distributed-memory parallel version of the multithreaded MSAProbs tool that is able to reduce runtimes by exploiting the compute capabilities of common multicore CPU clusters. Our performance evaluation on a cluster with 32 nodes (each containing two Intel Haswell processors) shows reductions in execution time of over one order of magnitude for typical input datasets. Furthermore, MSAProbs-MPI using eight nodes is faster than the GPU-accelerated QuickProbs running on a Tesla K20. Another strong point is that MSAProbs-MPI can deal with large datasets for which MSAProbs and QuickProbs might fail due to time and memory constraints, respectively. Source code in C ++ and MPI running on Linux systems as well as a reference manual are available at http://msaprobs.sourceforge.net CONTACT: jgonzalezd@udc.esSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Falco: a quick and flexible single-cell RNA-seq processing framework on the cloud.

PubMed

Yang, Andrian; Troup, Michael; Lin, Peijie; Ho, Joshua W K

2017-03-01

Single-cell RNA-seq (scRNA-seq) is increasingly used in a range of biomedical studies. Nonetheless, current RNA-seq analysis tools are not specifically designed to efficiently process scRNA-seq data due to their limited scalability. Here we introduce Falco, a cloud-based framework to enable paralellization of existing RNA-seq processing pipelines using big data technologies of Apache Hadoop and Apache Spark for performing massively parallel analysis of large scale transcriptomic data. Using two public scRNA-seq datasets and two popular RNA-seq alignment/feature quantification pipelines, we show that the same processing pipeline runs 2.6-145.4 times faster using Falco than running on a highly optimized standalone computer. Falco also allows users to utilize low-cost spot instances of Amazon Web Services, providing a ∼65% reduction in cost of analysis. Falco is available via a GNU General Public License at https://github.com/VCCRI/Falco/. j.ho@victorchang.edu.au. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Metabolic rate and environmental productivity: Well-provisioned animals evolved to run and idle fast

PubMed Central

Mueller, Pamela; Diamond, Jared

2001-01-01

Even among vertebrate species of the same body mass and higher-level taxonomic group, metabolic rates exhibit substantial differences, for which diverse explanatory factors—such as dietary energy content, latitude, altitude, temperature, and rainfall—have been postulated. A unifying underlying factor could be food availability, in turn controlled by net primary productivity (NPP) of the animal's natural environment. We tested this possibility by studying five North American species of Peromyscus mice, all of them similar in diet (generalist omnivores) and in gut morphology but differing by factors of up to 13 in NPP of their habitat of origin. We maintained breeding colonies of all five species in the laboratory under identical conditions and consuming identical diets. Basal metabolic rate (BMR) and daily ad libitum food intake both increased with NPP, which explained 88% and 90% of their variances, respectively. High-metabolism mouse species from high-NPP environments were behaviorally more active than were low-metabolism species from low-NPP environments. Intestinal glucose uptake capacity also increased with NPP (and with BMR and food intake), because species of high-NPP environments had larger small intestines and higher uptake rates. For metabolic rates of our five species, the driving environmental variable is environmental productivity itself (and hence food availability), rather than temporal variability of productivity. Thus, species that have evolved in the presence of abundant food run their metabolism “fast,” both while active and while idling, as compared with species of less productive environments, even when all species are given access to unlimited food. PMID:11606744

Physical Performance Tasks Required of U.S. Marines Operating in a High Altitude Cold Weather Environment.

DTIC Science & Technology

1982-07-23

readiness has not been scientifically valiated. The test batter c ists of pll-upe, sit-ups and a three-mile run e as Scoring of the PIT is arbitrary... cognitive tasks, with little information available on physical tasks cc the environmental conditions under which these tasks are to be performed. A well...environment can drastically distort operational requirements. It is difficult to convey all the encumbrances associated with maintenance of basal tasks in

[Do Multiplex PCR techniques displace classical cultures in microbiology?].

PubMed

Auckenthaler, Raymond; Risch, Martin

2015-02-01

Multiplex PCR technologies progressively find their way in clinical microbiology. This technique allows the simultaneous amplification of multiple DNA targets in a single test run for the identification of pathogens up to the species level. Various pathogens of infectious diseases can be detected by a symptom-oriented approach clearly and quickly with high reliability. Essentially multiplex PCR panels are available for clarification of gastrointestinal, respiratory, sexually transmitted infections and meningitis. Today's offer from industry, university hospitals and large private laboratories of Switzerland is tabulated and commented.

Bridging the scales in atmospheric composition simulations using a nudging technique

NASA Astrophysics Data System (ADS)

D'Isidoro, Massimo; Maurizi, Alberto; Russo, Felicita; Tampieri, Francesco

2010-05-01

Studying the interaction between climate and anthropogenic activities, specifically those concentrated in megacities/hot spots, requires the description of processes in a very wide range of scales from local, where anthropogenic emissions are concentrated to global where we are interested to study the impact of these sources. The description of all the processes at all scales within the same numerical implementation is not feasible because of limited computer resources. Therefore, different phenomena are studied by means of different numerical models that can cover different range of scales. The exchange of information from small to large scale is highly non-trivial though of high interest. In fact uncertainties in large scale simulations are expected to receive large contribution from the most polluted areas where the highly inhomogeneous distribution of sources connected to the intrinsic non-linearity of the processes involved can generate non negligible departures between coarse and fine scale simulations. In this work a new method is proposed and investigated in a case study (August 2009) using the BOLCHEM model. Monthly simulations at coarse (0.5° European domain, run A) and fine (0.1° Central Mediterranean domain, run B) horizontal resolution are performed using the coarse resolution as boundary condition for the fine one. Then another coarse resolution run (run C) is performed, in which the high resolution fields remapped on to the coarse grid are used to nudge the concentrations on the Po Valley area. The nudging is applied to all gas and aerosol species of BOLCHEM. Averaged concentrations and variances over Po Valley and other selected areas for O3 and PM are computed. It is observed that although the variance of run B is markedly larger than that of run A, the variance of run C is smaller because the remapping procedure removes large portion of variance from run B fields. Mean concentrations show some differences depending on species: in general mean values of run C lie between run A and run B. A propagation of the signal outside the nudging region is observed, and is evaluated in terms of differences between coarse resolution (with and without nudging) and fine resolution simulations.

Molgenis-impute: imputation pipeline in a box.

PubMed

Kanterakis, Alexandros; Deelen, Patrick; van Dijk, Freerk; Byelas, Heorhiy; Dijkstra, Martijn; Swertz, Morris A

2015-08-19

Genotype imputation is an important procedure in current genomic analysis such as genome-wide association studies, meta-analyses and fine mapping. Although high quality tools are available that perform the steps of this process, considerable effort and expertise is required to set up and run a best practice imputation pipeline, particularly for larger genotype datasets, where imputation has to scale out in parallel on computer clusters. Here we present MOLGENIS-impute, an 'imputation in a box' solution that seamlessly and transparently automates the set up and running of all the steps of the imputation process. These steps include genome build liftover (liftovering), genotype phasing with SHAPEIT2, quality control, sample and chromosomal chunking/merging, and imputation with IMPUTE2. MOLGENIS-impute builds on MOLGENIS-compute, a simple pipeline management platform for submission and monitoring of bioinformatics tasks in High Performance Computing (HPC) environments like local/cloud servers, clusters and grids. All the required tools, data and scripts are downloaded and installed in a single step. Researchers with diverse backgrounds and expertise have tested MOLGENIS-impute on different locations and imputed over 30,000 samples so far using the 1,000 Genomes Project and new Genome of the Netherlands data as the imputation reference. The tests have been performed on PBS/SGE clusters, cloud VMs and in a grid HPC environment. MOLGENIS-impute gives priority to the ease of setting up, configuring and running an imputation. It has minimal dependencies and wraps the pipeline in a simple command line interface, without sacrificing flexibility to adapt or limiting the options of underlying imputation tools. It does not require knowledge of a workflow system or programming, and is targeted at researchers who just want to apply best practices in imputation via simple commands. It is built on the MOLGENIS compute workflow framework to enable customization with additional computational steps or it can be included in other bioinformatics pipelines. It is available as open source from: https://github.com/molgenis/molgenis-imputation.

MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics.

PubMed

Helaers, Raphaël; Milinkovitch, Michel C

2010-07-15

The development, in the last decade, of stochastic heuristics implemented in robust application softwares has made large phylogeny inference a key step in most comparative studies involving molecular sequences. Still, the choice of a phylogeny inference software is often dictated by a combination of parameters not related to the raw performance of the implemented algorithm(s) but rather by practical issues such as ergonomics and/or the availability of specific functionalities. Here, we present MetaPIGA v2.0, a robust implementation of several stochastic heuristics for large phylogeny inference (under maximum likelihood), including a Simulated Annealing algorithm, a classical Genetic Algorithm, and the Metapopulation Genetic Algorithm (metaGA) together with complex substitution models, discrete Gamma rate heterogeneity, and the possibility to partition data. MetaPIGA v2.0 also implements the Likelihood Ratio Test, the Akaike Information Criterion, and the Bayesian Information Criterion for automated selection of substitution models that best fit the data. Heuristics and substitution models are highly customizable through manual batch files and command line processing. However, MetaPIGA v2.0 also offers an extensive graphical user interface for parameters setting, generating and running batch files, following run progress, and manipulating result trees. MetaPIGA v2.0 uses standard formats for data sets and trees, is platform independent, runs in 32 and 64-bits systems, and takes advantage of multiprocessor and multicore computers. The metaGA resolves the major problem inherent to classical Genetic Algorithms by maintaining high inter-population variation even under strong intra-population selection. Implementation of the metaGA together with additional stochastic heuristics into a single software will allow rigorous optimization of each heuristic as well as a meaningful comparison of performances among these algorithms. MetaPIGA v2.0 gives access both to high customization for the phylogeneticist, as well as to an ergonomic interface and functionalities assisting the non-specialist for sound inference of large phylogenetic trees using nucleotide sequences. MetaPIGA v2.0 and its extensive user-manual are freely available to academics at http://www.metapiga.org.

MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics

PubMed Central

2010-01-01

Background The development, in the last decade, of stochastic heuristics implemented in robust application softwares has made large phylogeny inference a key step in most comparative studies involving molecular sequences. Still, the choice of a phylogeny inference software is often dictated by a combination of parameters not related to the raw performance of the implemented algorithm(s) but rather by practical issues such as ergonomics and/or the availability of specific functionalities. Results Here, we present MetaPIGA v2.0, a robust implementation of several stochastic heuristics for large phylogeny inference (under maximum likelihood), including a Simulated Annealing algorithm, a classical Genetic Algorithm, and the Metapopulation Genetic Algorithm (metaGA) together with complex substitution models, discrete Gamma rate heterogeneity, and the possibility to partition data. MetaPIGA v2.0 also implements the Likelihood Ratio Test, the Akaike Information Criterion, and the Bayesian Information Criterion for automated selection of substitution models that best fit the data. Heuristics and substitution models are highly customizable through manual batch files and command line processing. However, MetaPIGA v2.0 also offers an extensive graphical user interface for parameters setting, generating and running batch files, following run progress, and manipulating result trees. MetaPIGA v2.0 uses standard formats for data sets and trees, is platform independent, runs in 32 and 64-bits systems, and takes advantage of multiprocessor and multicore computers. Conclusions The metaGA resolves the major problem inherent to classical Genetic Algorithms by maintaining high inter-population variation even under strong intra-population selection. Implementation of the metaGA together with additional stochastic heuristics into a single software will allow rigorous optimization of each heuristic as well as a meaningful comparison of performances among these algorithms. MetaPIGA v2.0 gives access both to high customization for the phylogeneticist, as well as to an ergonomic interface and functionalities assisting the non-specialist for sound inference of large phylogenetic trees using nucleotide sequences. MetaPIGA v2.0 and its extensive user-manual are freely available to academics at http://www.metapiga.org. PMID:20633263

Higher Precision of Heart Rate Compared with VO2 to Predict Exercise Intensity in Endurance-Trained Runners.

PubMed

Reis, Victor M; den Tillaar, Roland Van; Marques, Mario C

2011-01-01

The aim of the present study was to assess the precision of oxygen uptake with heart rate regression during track running in highly-trained runners. Twelve national and international level male long-distance road runners (age 30.7 ± 5.5 yrs, height 1.71 ± 0.04 m and mass 61.2 ± 5.8 kg) with a personal best on the half marathon of 62 min 37 s ± 1 min 22 s participated in the study. Each participant performed, in an all-weather synthetic track five, six min bouts at constant velocity with each bout at an increased running velocity. The starting velocity was 3.33 m·s(-1) with a 0.56 m·s(-1) increase on each subsequent bout. VO2 and heart rate were measured during the runs and blood lactate was assessed immediately after each run. Mean peak VO2 and mean peak heart rate were, respectively, 76.2 ± 9.7 mL·kg(-1)·min(-1) and 181 ± 13 beats·min(-1). The linearity of the regressions between heart rate, running velocity and VO2 were all very high (r > 0.99) with small standard errors of regression (i.e. Sy.x < 5% at the velocity associated with the 2 and 4 mmol·L(-1) lactate thresholds). The strong relationships between heart rate, running velocity and VO2 found in this study show that, in highly trained runners, it is possible to have heart rate as an accurate indicator of energy demand and of the running speed. Therefore, in this subject cohort it may be unnecessary to use VO2 to track changes in the subjects' running economy during training periods. Key pointsHeart rate is used in the control of exercise intensity in endurance sports.However, few studies have quantified the precision of its relationship with oxygen uptake in highly trained runners.We evaluated twelve elite half-marathon runners during track running at various intensities and established three regressions: oxygen uptake / heart rate; heart rate / running velocity and oxygen uptake / running velocity.The three regressions presented, respectively, imprecision of 4,2%, 2,75% and 4,5% at the velocity associated with the 4 mmol·L(-1) threshold.The results of the present study show that, in highly trained runners, it is possible to use heart rate as an accurate index of the external work rate during sub maximal running speeds.

NASADIG - NASA DEVICE INDEPENDENT GRAPHICS LIBRARY (AMDAHL VERSION)

NASA Technical Reports Server (NTRS)

Rogers, J. E.

1994-01-01

The NASA Device Independent Graphics Library, NASADIG, can be used with many computer-based engineering and management applications. The library gives the user the opportunity to translate data into effective graphic displays for presentation. The software offers many features which allow the user flexibility in creating graphics. These include two-dimensional plots, subplot projections in 3D-space, surface contour line plots, and surface contour color-shaded plots. Routines for three-dimensional plotting, wireframe surface plots, surface plots with hidden line removal, and surface contour line plots are provided. Other features include polar and spherical coordinate plotting, world map plotting utilizing either cylindrical equidistant or Lambert equal area projection, plot translation, plot rotation, plot blowup, splines and polynomial interpolation, area blanking control, multiple log/linear axes, legends and text control, curve thickness control, and multiple text fonts (18 regular, 4 bold). NASADIG contains several groups of subroutines. Included are subroutines for plot area and axis definition; text set-up and display; area blanking; line style set-up, interpolation, and plotting; color shading and pattern control; legend, text block, and character control; device initialization; mixed alphabets setting; and other useful functions. The usefulness of many routines is dependent on the prior definition of basic parameters. The program's control structure uses a serial-level construct with each routine restricted for activation at some prescribed level(s) of problem definition. NASADIG provides the following output device drivers: Selanar 100XL, VECTOR Move/Draw ASCII and PostScript files, Tektronix 40xx, 41xx, and 4510 Rasterizer, DEC VT-240 (4014 mode), IBM AT/PC compatible with SmartTerm 240 emulator, HP Lasergrafix Film Recorder, QMS 800/1200, DEC LN03+ Laserprinters, and HP LaserJet (Series III). NASADIG is written in FORTRAN and is available for several platforms. NASADIG 5.7 is available for DEC VAX series computers running VMS 5.0 or later (MSC-21801), Cray X-MP and Y-MP series computers running UNICOS (COS-10049), and Amdahl 5990 mainframe computers running UTS (COS-10050). NASADIG 5.1 is available for UNIX-based operating systems (MSC-22001). The UNIX version has been successfully implemented on Sun4 series computers running SunOS, SGI IRIS computers running IRIX, Hewlett Packard 9000 computers running HP-UX, and Convex computers running Convex OS (MSC-22001). The standard distribution medium for MSC-21801 is a set of two 6250 BPI 9-track magnetic tapes in DEC VAX BACKUP format. It is also available on a set of two TK50 tape cartridges in DEC VAX BACKUP format. The standard distribution medium for COS-10049 and COS-10050 is a 6250 BPI 9-track magnetic tape in UNIX tar format. Other distribution media and formats may be available upon request. The standard distribution medium for MSC-22001 is a .25 inch streaming magnetic tape cartridge (Sun QIC-24) in UNIX tar format. Alternate distribution media and formats are available upon request. With minor modification, the UNIX source code can be ported to other platforms including IBM PC/AT series computers and compatibles. NASADIG is also available bundled with TRASYS, the Thermal Radiation Analysis System (COS-10026, DEC VAX version; COS-10040, CRAY version).

NASADIG - NASA DEVICE INDEPENDENT GRAPHICS LIBRARY (UNIX VERSION)

NASA Technical Reports Server (NTRS)

Rogers, J. E.

1994-01-01

The NASA Device Independent Graphics Library, NASADIG, can be used with many computer-based engineering and management applications. The library gives the user the opportunity to translate data into effective graphic displays for presentation. The software offers many features which allow the user flexibility in creating graphics. These include two-dimensional plots, subplot projections in 3D-space, surface contour line plots, and surface contour color-shaded plots. Routines for three-dimensional plotting, wireframe surface plots, surface plots with hidden line removal, and surface contour line plots are provided. Other features include polar and spherical coordinate plotting, world map plotting utilizing either cylindrical equidistant or Lambert equal area projection, plot translation, plot rotation, plot blowup, splines and polynomial interpolation, area blanking control, multiple log/linear axes, legends and text control, curve thickness control, and multiple text fonts (18 regular, 4 bold). NASADIG contains several groups of subroutines. Included are subroutines for plot area and axis definition; text set-up and display; area blanking; line style set-up, interpolation, and plotting; color shading and pattern control; legend, text block, and character control; device initialization; mixed alphabets setting; and other useful functions. The usefulness of many routines is dependent on the prior definition of basic parameters. The program's control structure uses a serial-level construct with each routine restricted for activation at some prescribed level(s) of problem definition. NASADIG provides the following output device drivers: Selanar 100XL, VECTOR Move/Draw ASCII and PostScript files, Tektronix 40xx, 41xx, and 4510 Rasterizer, DEC VT-240 (4014 mode), IBM AT/PC compatible with SmartTerm 240 emulator, HP Lasergrafix Film Recorder, QMS 800/1200, DEC LN03+ Laserprinters, and HP LaserJet (Series III). NASADIG is written in FORTRAN and is available for several platforms. NASADIG 5.7 is available for DEC VAX series computers running VMS 5.0 or later (MSC-21801), Cray X-MP and Y-MP series computers running UNICOS (COS-10049), and Amdahl 5990 mainframe computers running UTS (COS-10050). NASADIG 5.1 is available for UNIX-based operating systems (MSC-22001). The UNIX version has been successfully implemented on Sun4 series computers running SunOS, SGI IRIS computers running IRIX, Hewlett Packard 9000 computers running HP-UX, and Convex computers running Convex OS (MSC-22001). The standard distribution medium for MSC-21801 is a set of two 6250 BPI 9-track magnetic tapes in DEC VAX BACKUP format. It is also available on a set of two TK50 tape cartridges in DEC VAX BACKUP format. The standard distribution medium for COS-10049 and COS-10050 is a 6250 BPI 9-track magnetic tape in UNIX tar format. Other distribution media and formats may be available upon request. The standard distribution medium for MSC-22001 is a .25 inch streaming magnetic tape cartridge (Sun QIC-24) in UNIX tar format. Alternate distribution media and formats are available upon request. With minor modification, the UNIX source code can be ported to other platforms including IBM PC/AT series computers and compatibles. NASADIG is also available bundled with TRASYS, the Thermal Radiation Analysis System (COS-10026, DEC VAX version; COS-10040, CRAY version).

Another Program For Generating Interactive Graphics

NASA Technical Reports Server (NTRS)

Costenbader, Jay; Moleski, Walt; Szczur, Martha; Howell, David; Engelberg, Norm; Li, Tin P.; Misra, Dharitri; Miller, Philip; Neve, Leif; Wolf, Karl;

Regulation of substrate use during the marathon.

PubMed

Spriet, Lawrence L

2007-01-01

The energy required to run a marathon is mainly provided through oxidative phosphorylation in the mitochondria of the active muscles. Small amounts of energy from substrate phosphorylation are also required during transitions and short periods when running speed is increased. The three inputs for adenosine triphosphate production in the mitochondria include oxygen, free adenosine diphosphate and inorganic phosphate, and reducing equivalents. The reducing equivalents are derived from the metabolism of fat and carbohydrate (CHO), which are mobilised from intramuscular stores and also delivered from adipose tissue and liver, respectively. The metabolism of fat and CHO is tightly controlled at several regulatory sites during marathon running. Slower, recreational runners run at 60-65% maximal oxygen uptake (VO(2max)) for approximately 3:45:00 and faster athletes run at 70-75% for approximately 2:45:00. Both groups rely heavily on fat and CHO fuels. However, elite athletes run marathons at speeds requiring between 80% and 90% VO(2max), and finish in times between 2:05:00 and 2:20:00. They are highly adapted to oxidise fat and must do so during training. However, they compete at such high running speeds, that CHO oxidation (also highly adapted) may be the exclusive source of energy while racing. Further work with elite athletes is needed to examine this possibility.

A New Code SORD for Simulation of Polarized Light Scattering in the Earth Atmosphere

NASA Technical Reports Server (NTRS)

Korkin, Sergey; Lyapustin, Alexei; Sinyuk, Aliaksandr; Holben, Brent

2016-01-01

We report a new publicly available radiative transfer (RT) code for numerical simulation of polarized light scattering in plane-parallel atmosphere of the Earth. Using 44 benchmark tests, we prove high accuracy of the new RT code, SORD (Successive ORDers of scattering). We describe capabilities of SORD and show run time for each test on two different machines. At present, SORD is supposed to work as part of the Aerosol Robotic NETwork (AERONET) inversion algorithm. For natural integration with the AERONET software, SORD is coded in Fortran 90/95. The code is available by email request from the corresponding (first) author or from ftp://climate1.gsfc.nasa.gov/skorkin/SORD/.

Comparison of live high: train low altitude and intermittent hypoxic exposure.

PubMed

Humberstone-Gough, Clare E; Saunders, Philo U; Bonetti, Darrell L; Stephens, Shaun; Bullock, Nicola; Anson, Judith M; Gore, Christopher J

2013-01-01

Live High:Train Low (LHTL) altitude training is a popular ergogenic aid amongst athletes. An alternative hypoxia protocol, acute (60-90 min daily) Intermittent Hypoxic Exposure (IHE), has shown potential for improving athletic performance. The aim of this study was to compare directly the effects of LHTL and IHE on the running and blood characteristics of elite triathletes. Changes in total haemoglobin mass (Hbmass), maximal oxygen consumption (VO2max), velocity at VO2max (vVO2max), time to exhaustion (TTE), running economy, maximal blood lactate concentration ([La]) and 3 mM [La] running speed were compared following 17 days of LHTL (240 h of hypoxia), IHE (10.2 h of hypoxia) or Placebo treatment in 24 Australian National Team triathletes (7 female, 17 male). There was a clear 3.2 ± 4.8% (mean ± 90% confidence limits) increase in Hbmass following LHTL compared with Placebo, whereas the corresponding change of -1.4 ± 4.5% in IHE was unclear. Following LHTL, running economy was 2.8 ± 4.4% improved compared to IHE and 3mM [La] running speed was 4.4 ± 4.5% improved compared to Placebo. After IHE, there were no beneficial changes in running economy or 3mM [La] running speed compared to Placebo. There were no clear changes in VO2max, vVO2max and TTE following either method of hypoxia. The clear difference in Hbmass response between LHTL and IHE indicated that the dose of hypoxia in IHE was insufficient to induce accelerated erythropoiesis. Improved running economy and 3mM [La] running speed following LHTL suggested that this method of hypoxic exposure may enhance performance at submaximal running speeds. Overall, there was no evidence to support the use of IHE in elite triathletes. Key PointsDespite a clear 3.2% increase in haemoglobin mass following 17 days of Live High: Train Low altitude training, no change in maximal aerobic capacity was observed.There were positive changes in running economy and the lactate-speed relationship at submaximal running speeds following Live High: Train Low altitude training.There was no evidence to support the use of daily 60-90 minute Intermittent Hypoxic Exposure in elite triathletes.

Effect of Recording Duration on the Diagnostic Performance of Multifocal Visual-evoked Potentials in High-risk Ocular Hypertension and Early Glaucoma

PubMed Central

Fortune, Brad; Zhang, Xian; Hood, Donald C.; Demirel, Shaban; Patterson, Emily; Jamil, Annisa; Mansberger, Steven L.; Cioffi, George A.; Johnson, Chris A.

2010-01-01

Purpose To evaluate the effect on diagnostic performance of reducing multifocal visual-evoked potential (mfVEP) recording duration from 16 to 8 minutes per eye. Methods Both eyes of 185 individuals with high-risk ocular hypertension or early glaucoma were studied. Two 8-minute mfVEP recordings were obtained for each eye in an ABBA order using VERIS. The first recording for each eye was compared against single run (1-Run) mfVEP normative data; the average of both recordings for each eye was compared against 2-Run normative data. Visual fields (VFs) were obtained by standard automated perimetry (SAP) within 22.3±27.0 days of the mfVEP. Stereo disc photographs and Heidelberg Retina Tomograph images were obtained together, within 24.8±50.4 days of the mfVEP and 33.1±62.9 days of SAP. Masked experts graded disc photographs as either glaucomatous optic neuropathy or normal. The overall Moorfields Regression Analysis result from the Heidelberg Retina Tomograph was used as a separate diagnostic classification. Thus, 4 diagnostic standards were applied in total, 2 based on optic disc structure alone and 2 others based on disc structure and SAP. Results Agreement between the 1-Run and 2-Run mfVEP was 90%. Diagnostic performance of the 1-Run mfVEP was similar to that of the 2-Run mfVEP for all 4 diagnostic standards. Sensitivity was slightly higher for the 2-Run mfVEP, whereas specificity was slightly higher for the 1-Run mfVEP. Conclusions If higher sensitivity is sought, the 2-Run mfVEP will provide better discrimination between groups of eyes with relatively high signal-to-noise ratio (eg, early glaucoma or high-risk suspects). But if higher specificity is a more important goal, the 1-Run mfVEP provides adequate sensitivity and requires only half the test time. Considered alongside prior studies, the present results suggest that the 1-Run mfVEP is an efficient way to confirm (or refute) the extent of VF loss in patients with moderate or advanced glaucoma, particularly in those with unreliable VFs, including malingering or other “functional” forms of VF loss. PMID:18414101

Running Jobs on the Peregrine System | High-Performance Computing | NREL

Science.gov Websites

on the Peregrine high-performance computing (HPC) system. Running Different Types of Jobs Batch jobs scheduling policies - queue names, limits, etc. Requesting different node types Sample batch scripts

A new climate modeling framework for convection-resolving simulation at continental scale

NASA Astrophysics Data System (ADS)

Charpilloz, Christophe; di Girolamo, Salvatore; Arteaga, Andrea; Fuhrer, Oliver; Hoefler, Torsten; Schulthess, Thomas; Schär, Christoph

2017-04-01

Major uncertainties remain in our understanding of the processes that govern the water cycle in a changing climate and their representation in weather and climate models. Of particular concern are heavy precipitation events of convective origin (thunderstorms and rain showers). The aim of the crCLIM project [1] is to propose a new climate modeling framework that alleviates the I/O-bottleneck in large-scale, convection-resolving climate simulations and thus to enable new analysis techniques for climate scientists. Due to the large computational costs, convection-resolving simulations are currently restricted to small computational domains or very short time scales, unless the largest available supercomputers system such as hybrid CPU-GPU architectures are used [3]. Hence, the COSMO model has been adapted to run on these architectures for research and production purposes [2]. However, the amount of generated data also increases and storing this data becomes infeasible making the analysis of simulations results impractical. To circumvent this problem and enable high-resolution models in climate we propose a data-virtualization layer (DVL) that re-runs simulations on demand and transparently manages the data for the analysis, that means we trade off computational effort (time) for storage (space). This approach also requires a bit-reproducible version of the COSMO model that produces identical results on different architectures (CPUs and GPUs) [4] that will be coupled with a performance model in order enable optimal re-runs depending on requirements of the re-run and available resources. In this contribution, we discuss the strategy to develop the DVL, a first performance model, the challenge of bit-reproducibility and the first results of the crCLIM project. [1] http://www.c2sm.ethz.ch/research/crCLIM.html [2] O. Fuhrer, C. Osuna, X. Lapillonne, T. Gysi, M. Bianco, and T. Schulthess. "Towards gpu-accelerated operational weather forecasting." In The GPU Technology Conference, GTC. 2013. [3] D. Leutwyler, O. Fuhrer, X. Lapillonne, D. Lüthi, and C. Schär. "Towards European-scale convection-resolving climate simulations with GPUs: a study with COSMO 4.19." Geoscientific Model Development 9, no. 9 (2016): 3393. [4] A. Arteaga, O. Fuhrer, and T. Hoefler. "Designing bit-reproducible portable high-performance applications." In Parallel and Distributed Processing Symposium, 2014 IEEE 28th International, pp. 1235-1244. IEEE, 2014.

Nucleus accumbens neuronal maturation differences in young rats bred for low versus high voluntary running behaviour

PubMed Central

Roberts, Michael D; Toedebusch, Ryan G; Wells, Kevin D; Company, Joseph M; Brown, Jacob D; Cruthirds, Clayton L; Heese, Alexander J; Zhu, Conan; Rottinghaus, George E; Childs, Thomas E; Booth, Frank W

2014-01-01

We compared the nucleus accumbens (NAc) transcriptomes of generation 8 (G8), 34-day-old rats selectively bred for low (LVR) versus high voluntary running (HVR) behaviours in rats that never ran (LVRnon-run and HVRnon-run), as well as in rats after 6 days of voluntary wheel running (LVRrun and HVRrun). In addition, the NAc transcriptome of wild-type Wistar rats was compared. The purpose of this transcriptomics approach was to generate testable hypotheses as to possible NAc features that may be contributing to running motivation differences between lines. Ingenuity Pathway Analysis and Gene Ontology analyses suggested that ‘cell cycle’-related transcripts and the running-induced plasticity of dopamine-related transcripts were lower in LVR versus HVR rats. From these data, a hypothesis was generated that LVR rats might have less NAc neuron maturation than HVR rats. Follow-up immunohistochemistry in G9–10 LVRnon-run rats suggested that the LVR line inherently possessed fewer mature medium spiny (Darpp-32-positive) neurons (P < 0.001) and fewer immature (Dcx-positive) neurons (P < 0.001) than their G9–10 HVR counterparts. However, voluntary running wheel access in our G9–10 LVRs uniquely increased their Darpp-32-positive and Dcx-positive neuron densities. In summary, NAc cellularity differences and/or the lack of running-induced plasticity in dopamine signalling-related transcripts may contribute to low voluntary running motivation in LVR rats. PMID:24665095

Running in a minimalist and lightweight shoe is not the same as running barefoot: a biomechanical study.

PubMed

Bonacci, Jason; Saunders, Philo U; Hicks, Amy; Rantalainen, Timo; Vicenzino, Bill Guglielmo T; Spratford, Wayne

2013-04-01

The purpose of this study was to determine the changes in running mechanics that occur when highly trained runners run barefoot and in a minimalist shoe, and specifically if running in a minimalist shoe replicates barefoot running. Ground reaction force data and kinematics were collected from 22 highly trained runners during overground running while barefoot and in three shod conditions (minimalist shoe, racing flat and the athlete's regular shoe). Three-dimensional net joint moments and subsequent net powers and work were computed using Newton-Euler inverse dynamics. Joint kinematic and kinetic variables were statistically compared between barefoot and shod conditions using a multivariate analysis of variance for repeated measures and standardised mean differences calculated. There were significant differences between barefoot and shod conditions for kinematic and kinetic variables at the knee and ankle, with no differences between shod conditions. Barefoot running demonstrated less knee flexion during midstance, an 11% decrease in the peak internal knee extension and abduction moments and a 24% decrease in negative work done at the knee compared with shod conditions. The ankle demonstrated less dorsiflexion at initial contact, a 14% increase in peak power generation and a 19% increase in the positive work done during barefoot running compared with shod conditions. Barefoot running was different to all shod conditions. Barefoot running changes the amount of work done at the knee and ankle joints and this may have therapeutic and performance implications for runners.

COMPPAP - COMPOSITE PLATE BUCKLING ANALYSIS PROGRAM (IBM PC VERSION)

NASA Technical Reports Server (NTRS)

Smith, J. P.

1994-01-01

The Composite Plate Buckling Analysis Program (COMPPAP) was written to help engineers determine buckling loads of orthotropic (or isotropic) irregularly shaped plates without requiring hand calculations from design curves or extensive finite element modeling. COMPPAP is a one element finite element program that utilizes high-order displacement functions. The high order of the displacement functions enables the user to produce results more accurate than traditional h-finite elements. This program uses these high-order displacement functions to perform a plane stress analysis of a general plate followed by a buckling calculation based on the stresses found in the plane stress solution. The current version assumes a flat plate (constant thickness) subject to a constant edge load (normal or shear) on one or more edges. COMPPAP uses the power method to find the eigenvalues of the buckling problem. The power method provides an efficient solution when only one eigenvalue is desired. Once the eigenvalue is found, the eigenvector, which corresponds to the plate buckling mode shape, results as a by-product. A positive feature of the power method is that the dominant eigenvalue is the first found, which is this case is the plate buckling load. The reported eigenvalue expresses a load factor to induce plate buckling. COMPPAP is written in ANSI FORTRAN 77. Two machine versions are available from COSMIC: a PC version (MSC-22428), which is for IBM PC 386 series and higher computers and compatibles running MS-DOS; and a UNIX version (MSC-22286). The distribution medium for both machine versions includes source code for both single and double precision versions of COMPPAP. The PC version includes source code which has been optimized for implementation within DOS memory constraints as well as sample executables for both the single and double precision versions of COMPPAP. The double precision versions of COMPPAP have been successfully implemented on an IBM PC 386 compatible running MS-DOS, a Sun4 series computer running SunOS, an HP-9000 series computer running HP-UX, and a CRAY X-MP series computer running UNICOS. COMPPAP requires 1Mb of RAM and the BLAS and LINPACK math libraries, which are included on the distribution medium. The COMPPAP documentation provides instructions for using the commercial post-processing package PATRAN for graphical interpretation of COMPPAP output. The UNIX version includes two electronic versions of the documentation: one in LaTex format and one in PostScript format. The standard distribution medium for the PC version (MSC-22428) is a 5.25 inch 1.2Mb MS-DOS format diskette. The standard distribution medium for the UNIX version (MSC-22286) is a .25 inch streaming magnetic tape cartridge (Sun QIC-24) in UNIX tar format. For the UNIX version, alternate distribution media and formats are available upon request. COMPPAP was developed in 1992.

COMPPAP - COMPOSITE PLATE BUCKLING ANALYSIS PROGRAM (UNIX VERSION)

NASA Technical Reports Server (NTRS)

Smith, J. P.

1994-01-01

The Composite Plate Buckling Analysis Program (COMPPAP) was written to help engineers determine buckling loads of orthotropic (or isotropic) irregularly shaped plates without requiring hand calculations from design curves or extensive finite element modeling. COMPPAP is a one element finite element program that utilizes high-order displacement functions. The high order of the displacement functions enables the user to produce results more accurate than traditional h-finite elements. This program uses these high-order displacement functions to perform a plane stress analysis of a general plate followed by a buckling calculation based on the stresses found in the plane stress solution. The current version assumes a flat plate (constant thickness) subject to a constant edge load (normal or shear) on one or more edges. COMPPAP uses the power method to find the eigenvalues of the buckling problem. The power method provides an efficient solution when only one eigenvalue is desired. Once the eigenvalue is found, the eigenvector, which corresponds to the plate buckling mode shape, results as a by-product. A positive feature of the power method is that the dominant eigenvalue is the first found, which is this case is the plate buckling load. The reported eigenvalue expresses a load factor to induce plate buckling. COMPPAP is written in ANSI FORTRAN 77. Two machine versions are available from COSMIC: a PC version (MSC-22428), which is for IBM PC 386 series and higher computers and compatibles running MS-DOS; and a UNIX version (MSC-22286). The distribution medium for both machine versions includes source code for both single and double precision versions of COMPPAP. The PC version includes source code which has been optimized for implementation within DOS memory constraints as well as sample executables for both the single and double precision versions of COMPPAP. The double precision versions of COMPPAP have been successfully implemented on an IBM PC 386 compatible running MS-DOS, a Sun4 series computer running SunOS, an HP-9000 series computer running HP-UX, and a CRAY X-MP series computer running UNICOS. COMPPAP requires 1Mb of RAM and the BLAS and LINPACK math libraries, which are included on the distribution medium. The COMPPAP documentation provides instructions for using the commercial post-processing package PATRAN for graphical interpretation of COMPPAP output. The UNIX version includes two electronic versions of the documentation: one in LaTex format and one in PostScript format. The standard distribution medium for the PC version (MSC-22428) is a 5.25 inch 1.2Mb MS-DOS format diskette. The standard distribution medium for the UNIX version (MSC-22286) is a .25 inch streaming magnetic tape cartridge (Sun QIC-24) in UNIX tar format. For the UNIX version, alternate distribution media and formats are available upon request. COMPPAP was developed in 1992.

Direct liquefaction proof-of-concept program. Finaltopical report, Bench Run 4 (227-95)

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

Comolli, A.G.; Pradhan, V.R.; Lee, T.L.K.

This report presents the results of bench-scale work, Bench Run PB-04, conducted under the DOE Proof of Concept-Bench Option Program in direct coal liquefaction at Hydrocarbon Technologies, Inc. in Lawrenceville, New Jersey. The Bench Run PB-04 was the fifth of the nine runs planned in the POC Bench Option Contract between the U.S. DOE and Hydrocarbon Technologies, Inc. Bench Run PB-04 had multiple goals. These included the evaluation of the effects of dispersed slurry catalyst system on the performance of direct liquefaction of a subbituminous Wyoming Black Thunder mine coal under extinction recycle (454{degrees}C+ recycle) condition; another goal was tomore » investigate the effects of the combined processing of automobile shredder residue (auto-fluff) with coal and other organic waste materials. PB-04 employed a two-stage, back-mixed, slurry reactor system with an interstage V/L separator and an in-line fixed-bed hydrotreater. The HTI`s newly modified P/Fe catalyst was very effective for direct liquefaction and coprocessing of Black Thunder mine subbituminous coal with Hondo resid and auto-fluff; during `coal-only` liquefaction mode, over 93% maf coal conversion was obtained with about 90% residuum conversion and as high as 67% light distillate (C{sub 4}-975 F) yield, while during `coprocessing` mode of operation, distillate yields varied between 58 and 69%; the residuum conversions varied between 74 and 89% maf. Overall, it is concluded, based upon the yield data available from PB-04, that auto-effective as MSW plastics in improving coal hydroconversion process performance. Auto-fluff did not increase light distillate yields nor decrease light gas make and chemical hydrogen consumption in coal liquefaction, as was observed to occur with MSW plastics.« less

Investigation on the Practicality of Developing Reduced Thermal Models

NASA Technical Reports Server (NTRS)

Lombardi, Giancarlo; Yang, Kan

2015-01-01

Throughout the spacecraft design and development process, detailed instrument thermal models are created to simulate their on-orbit behavior and to ensure that they do not exceed any thermal limits. These detailed models, while generating highly accurate predictions, can sometimes lead to long simulation run times, especially when integrated with a spacecraft observatory model. Therefore, reduced models containing less detail are typically produced in tandem with the detailed models so that results may be more readily available, albeit less accurate. In the current study, both reduced and detailed instrument models are integrated with their associated spacecraft bus models to examine the impact of instrument model reduction on run time and accuracy. Preexisting instrument bus thermal model pairs from several projects were used to determine trends between detailed and reduced thermal models; namely, the Mirror Optical Bench (MOB) on the Gravity and Extreme Magnetism Small Explorer (GEMS) spacecraft, Advanced Topography Laser Altimeter System (ATLAS) on the Ice, Cloud, and Elevation Satellite 2 (ICESat-2), and the Neutral Mass Spectrometer (NMS) on the Lunar Atmosphere and Dust Environment Explorer (LADEE). Hot and cold cases were run for each model to capture the behavior of the models at both thermal extremes. It was found that, though decreasing the number of nodes from a detailed to reduced model brought about a reduction in the run-time, a large time savings was not observed, nor was it a linear relationship between the percentage of nodes reduced and time saved. However, significant losses in accuracy were observed with greater model reduction. It was found that while reduced models are useful in decreasing run time, there exists a threshold of reduction where, once exceeded, the loss in accuracy outweighs the benefit from reduced model runtime.

Relationships between triathlon performance and pacing strategy during the run in an international competition.

PubMed

Le Meur, Yann; Bernard, Thierry; Dorel, Sylvain; Abbiss, Chris R; Honnorat, Gérard; Brisswalter, Jeanick; Hausswirth, Christophe

2011-06-01

The purpose of the present study was to examine relationships between athlete's pacing strategies and running performance during an international triathlon competition. Running split times for each of the 107 finishers of the 2009 European Triathlon Championships (42 females and 65 males) were determined with the use of a digital synchronized video analysis system. Five cameras were placed at various positions of the running circuit (4 laps of 2.42 km). Running speed and an index of running speed variability (IRSVrace) were subsequently calculated over each section or running split. Mean running speed over the first 1272 m of lap 1 was 0.76 km·h-1 (+4.4%) and 1.00 km·h-1 (+5.6%) faster than the mean running speed over the same section during the three last laps, for females and males, respectively (P < .001). A significant inverse correlation was observed between RSrace and IRSVrace for all triathletes (females r = -0.41, P = .009; males r = -0.65, P = .002; and whole population -0.76, P = .001). Females demonstrated higher IRSVrace compared with men (6.1 ± 0.5 km·h-1 and 4.0 ± 1.4 km·h-1, for females and males, respectively, P = .001) due to greater decrease in running speed over uphill sections. Pacing during the run appears to play a key role in high-level triathlon performance. Elite triathletes should reduce their initial running speed during international competitions, even if high levels of motivation and direct opponents lead them to adopt an aggressive strategy.

A Portable Regional Weather and Climate Downscaling System Using GEOS-5, LIS-6, WRF, and the NASA Workflow Tool

NASA Astrophysics Data System (ADS)

Kemp, E. M.; Putman, W. M.; Gurganus, J.; Burns, R. W.; Damon, M. R.; McConaughy, G. R.; Seablom, M. S.; Wojcik, G. S.

2009-12-01

We present a regional downscaling system (RDS) suitable for high-resolution weather and climate simulations in multiple supercomputing environments. The RDS is built on the NASA Workflow Tool, a software framework for configuring, running, and managing computer models on multiple platforms with a graphical user interface. The Workflow Tool is used to run the NASA Goddard Earth Observing System Model Version 5 (GEOS-5), a global atmospheric-ocean model for weather and climate simulations down to 1/4 degree resolution; the NASA Land Information System Version 6 (LIS-6), a land surface modeling system that can simulate soil temperature and moisture profiles; and the Weather Research and Forecasting (WRF) community model, a limited-area atmospheric model for weather and climate simulations down to 1-km resolution. The Workflow Tool allows users to customize model settings to user needs; saves and organizes simulation experiments; distributes model runs across different computer clusters (e.g., the DISCOVER cluster at Goddard Space Flight Center, the Cray CX-1 Desktop Supercomputer, etc.); and handles all file transfers and network communications (e.g., scp connections). Together, the RDS is intended to aid researchers by making simulations as easy as possible to generate on the computer resources available. Initial conditions for LIS-6 and GEOS-5 are provided by Modern Era Retrospective-Analysis for Research and Applications (MERRA) reanalysis data stored on DISCOVER. The LIS-6 is first run for 2-4 years forced by MERRA atmospheric analyses, generating initial conditions for the WRF soil physics. GEOS-5 is then initialized from MERRA data and run for the period of interest. Large-scale atmospheric data, sea-surface temperatures, and sea ice coverage from GEOS-5 are used as boundary conditions for WRF, which is run for the same period of interest. Multiply nested grids are used for both LIS-6 and WRF, with the innermost grid run at a resolution sufficient for typical local weather features (terrain, convection, etc.) All model runs, restarts, and file transfers are coordinated by the Workflow Tool. Two use cases are being pursued. First, the RDS generates regional climate simulations down to 4-km for the Chesapeake Bay region, with WRF output provided as input to more specialized models (e.g., ocean/lake, hydrological, marine biology, and air pollution). This will allow assessment of climate impact on local interests (e.g., changes in Bay water levels and temperatures, innundation, fish kills, etc.) Second, the RDS generates high-resolution hurricane simulations in the tropical North Atlantic. This use case will support Observing System Simulation Experiments (OSSEs) of dynamically-targeted lidar observations as part of the NASA Sensor Web Simulator project. Sample results will be presented at the AGU Fall Meeting.

SBSI: an extensible distributed software infrastructure for parameter estimation in systems biology

PubMed Central

Adams, Richard; Clark, Allan; Yamaguchi, Azusa; Hanlon, Neil; Tsorman, Nikos; Ali, Shakir; Lebedeva, Galina; Goltsov, Alexey; Sorokin, Anatoly; Akman, Ozgur E.; Troein, Carl; Millar, Andrew J.; Goryanin, Igor; Gilmore, Stephen

2013-01-01

Summary: Complex computational experiments in Systems Biology, such as fitting model parameters to experimental data, can be challenging to perform. Not only do they frequently require a high level of computational power, but the software needed to run the experiment needs to be usable by scientists with varying levels of computational expertise, and modellers need to be able to obtain up-to-date experimental data resources easily. We have developed a software suite, the Systems Biology Software Infrastructure (SBSI), to facilitate the parameter-fitting process. SBSI is a modular software suite composed of three major components: SBSINumerics, a high-performance library containing parallelized algorithms for performing parameter fitting; SBSIDispatcher, a middleware application to track experiments and submit jobs to back-end servers; and SBSIVisual, an extensible client application used to configure optimization experiments and view results. Furthermore, we have created a plugin infrastructure to enable project-specific modules to be easily installed. Plugin developers can take advantage of the existing user-interface and application framework to customize SBSI for their own uses, facilitated by SBSI’s use of standard data formats. Availability and implementation: All SBSI binaries and source-code are freely available from http://sourceforge.net/projects/sbsi under an Apache 2 open-source license. The server-side SBSINumerics runs on any Unix-based operating system; both SBSIVisual and SBSIDispatcher are written in Java and are platform independent, allowing use on Windows, Linux and Mac OS X. The SBSI project website at http://www.sbsi.ed.ac.uk provides documentation and tutorials. Contact: stg@inf.ed.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23329415

Sphagnum-dominated bog systems are highly effective yet variable sources of bio-available iron to marine waters.

PubMed

Krachler, Regina; Krachler, Rudolf F; Wallner, Gabriele; Steier, Peter; El Abiead, Yasin; Wiesinger, Hubert; Jirsa, Franz; Keppler, Bernhard K

2016-06-15

Iron is a micronutrient of particular interest as low levels of iron limit primary production of phytoplankton and carbon fluxes in extended regions of the world's oceans. Sphagnum-peatland runoff is extraordinarily rich in dissolved humic-bound iron. Given that several of the world's largest wetlands are Sphagnum-dominated peatlands, this ecosystem type may serve as one of the major sources of iron to the ocean. Here, we studied five near-coastal creeks in North Scotland using freshwater/seawater mixing experiments of natural creek water and synthetic seawater based on a (59)Fe radiotracer technique combined with isotopic characterization of dissolved organic carbon by Accelerator Mass Spectrometry. Three of the creeks meander through healthy Sphagnum-dominated peat bogs and the two others through modified peatlands which have been subject to artificial drainage for centuries. The results revealed that, at the time of sampling (August 16-24, 2014), the creeks that run through modified peatlands delivered 11-15μg iron per liter creek water to seawater, whereas the creeks that run through intact peatlands delivered 350-470μg iron per liter creek water to seawater. To find out whether this humic-bound iron is bio-available to marine algae, we performed algal growth tests using the unicellular flagellated marine prymnesiophyte Diacronema lutheri and the unicellular marine green alga Chlorella salina, respectively. In both cases, the riverine humic material provided a highly bio-available source of iron to the marine algae. These results add a new item to the list of ecosystem services of Sphagnum-peatlands. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Evaluation Metrics for the Paragon XP/S-15

NASA Technical Reports Server (NTRS)

Traversat, Bernard; McNab, David; Nitzberg, Bill; Fineberg, Sam; Blaylock, Bruce T. (Technical Monitor)

1993-01-01

On February 17th 1993, the Numerical Aerodynamic Simulation (NAS) facility located at the NASA Ames Research Center installed a 224 node Intel Paragon XP/S-15 system. After its installation, the Paragon was found to be in a very immature state and was unable to support a NAS users' workload, composed of a wide range of development and production activities. As a first step towards addressing this problem, we implemented a set of metrics to objectively monitor the system as operating system and hardware upgrades were installed. The metrics were designed to measure four aspects of the system that we consider essential to support our workload: availability, utilization, functionality, and performance. This report presents the metrics collected from February 1993 to August 1993. Since its installation, the Paragon availability has improved from a low of 15% uptime to a high of 80%, while its utilization has remained low. Functionality and performance have improved from merely running one of the NAS Parallel Benchmarks to running all of them faster (between 1 and 2 times) than on the iPSC/860. In spite of the progress accomplished, fundamental limitations of the Paragon operating system are restricting the Paragon from supporting the NAS workload. The maximum operating system message passing (NORMA IPC) bandwidth was measured at 11 Mbytes/s, well below the peak hardware bandwidth (175 Mbytes/s), limiting overall virtual memory and Unix services (i.e. Disk and HiPPI I/O) performance. The high NX application message passing latency (184 microns), three times than on the iPSC/860, was found to significantly degrade performance of applications relying on small message sizes. The amount of memory available for an application was found to be approximately 10 Mbytes per node, indicating that the OS is taking more space than anticipated (6 Mbytes per node).

Nesting behavior of house mice (Mus domesticus) selected for increased wheel-running activity.

PubMed

Carter, P A; Swallow, J G; Davis, S J; Garland, T

2000-03-01

Nest building was measured in "active" (housed with access to running wheels) and "sedentary" (without wheel access) mice (Mus domesticus) from four replicate lines selected for 10 generations for high voluntary wheel-running behavior, and from four randombred control lines. Based on previous studies of mice bidirectionally selected for thermoregulatory nest building, it was hypothesized that nest building would show a negative correlated response to selection on wheel-running. Such a response could constrain the evolution of high voluntary activity because nesting has also been shown to be positively genetically correlated with successful production of weaned pups. With wheel access, selected mice of both sexes built significantly smaller nests than did control mice. Without wheel access, selected females also built significantly smaller nests than did control females, but only when body mass was excluded from the statistical model, suggesting that body mass mediated this correlated response to selection. Total distance run and mean running speed on wheels was significantly higher in selected mice than in controls, but no differences in amount of time spent running were measured, indicating a complex cause of the response of nesting to selection for voluntary wheel running.

The correlation between running economy and maximal oxygen uptake: cross-sectional and longitudinal relationships in highly trained distance runners.

PubMed

Shaw, Andrew J; Ingham, Stephen A; Atkinson, Greg; Folland, Jonathan P

2015-01-01

A positive relationship between running economy and maximal oxygen uptake (V̇O2max) has been postulated in trained athletes, but previous evidence is equivocal and could have been confounded by statistical artefacts. Whether this relationship is preserved in response to running training (changes in running economy and V̇O2max) has yet to be explored. This study examined the relationships of (i) running economy and V̇O2max between runners, and (ii) the changes in running economy and V̇O2max that occur within runners in response to habitual training. 168 trained distance runners (males, n = 98, V̇O2max 73.0 ± 6.3 mL∙kg-1∙min-1; females, n = 70, V̇O2max 65.2 ± 5.9 mL kg-1∙min-1) performed a discontinuous submaximal running test to determine running economy (kcal∙km-1). A continuous incremental treadmill running test to volitional exhaustion was used to determine V̇O2max 54 participants (males, n = 27; females, n = 27) also completed at least one follow up assessment. Partial correlation analysis revealed small positive relationships between running economy and V̇O2max (males r = 0.26, females r = 0.25; P<0.006), in addition to moderate positive relationships between the changes in running economy and V̇O2max in response to habitual training (r = 0.35; P<0.001). In conclusion, the current investigation demonstrates that only a small to moderate relationship exists between running economy and V̇O2max in highly trained distance runners. With >85% of the variance in these parameters unexplained by this relationship, these findings reaffirm that running economy and V̇O2max are primarily determined independently.

Inverse and Forward Modeling of The 2014 Iquique Earthquake with Run-up Data

NASA Astrophysics Data System (ADS)

Fuentes, M.

2015-12-01

The April 1, 2014 Mw 8.2 Iquique earthquake excited a moderate tsunami which turned on the national alert of tsunami threat. This earthquake was located in the well-known seismic gap in northern Chile which had a high seismic potential (~ Mw 9.0) after the two main large historic events of 1868 and 1877. Nonetheless, studies of the seismic source performed with seismic data inversions suggest that the event exhibited a main patch located around 19.8° S at 40 km of depth with a seismic moment equivalent to Mw = 8.2. Thus, a large seismic deficit remains in the gap being capable to release an event of Mw = 8.8-8.9. To understand the importance of the tsunami threat in this zone, a seismic source modeling of the Iquique Earthquake is performed. A new approach based on stochastic k2 seismic sources is presented. A set of those sources is generated and for each one, a full numerical tsunami model is performed in order to obtain the run-up heights along the coastline. The results are compared with the available field run-up measurements and with the tide gauges that registered the signal. The comparison is not uniform; it penalizes more when the discrepancies are larger close to the peak run-up location. This criterion allows to identify the best seismic source from the set of scenarios that explains better the observations from a statistical point of view. By the other hand, a L2 norm minimization is used to invert the seismic source by comparing the peak nearshore tsunami amplitude (PNTA) with the run-up observations. This method searches in a space of solutions the best seismic configuration by retrieving the Green's function coefficients in order to explain the field measurements. The results obtained confirm that a concentrated down-dip patch slip adequately models the run-up data.

Circadian Activity Rhythms and Voluntary Ethanol Intake in Male and Female Ethanol-Preferring Rats: Effects of Long-Term Ethanol Access

PubMed Central

Rosenwasser, Alan M.; McCulley, Walter D.; Fecteau, Matthew

2014-01-01

Chronic alcohol (ethanol) intake alters fundamental properties of the circadian clock. While previous studies have reported significant alterations in free-running circadian period during chronic ethanol access, these effects are typically subtle and appear to require high levels of intake. In the present study we examined the effects of long-term voluntary ethanol intake on ethanol consumption and free-running circadian period in male and female, selectively bred ethanol-preferring P and HAD2 rats. In light of previous reports that intermittent access can result in escalated ethanol intake, an initial 2-week water-only baseline was followed by either continuous or intermittent ethanol access (i.e., alternating 15-day epochs of ethanol access and ethanol deprivation) in separate groups of rats. Thus, animals were exposed to either 135 days of continuous ethanol access or to five 15-day access periods alternating with four 15-day periods of ethanol deprivation. Animals were maintained individually in running-wheel cages under continuous darkness throughout the experiment to allow monitoring of free-running activity and drinking rhythms, and 10% (v/v) ethanol and plain water were available continuously via separate drinking tubes during ethanol access. While there were no initial sex differences in ethanol drinking, ethanol preference increased progressively in male P and HAD2 rats under both continuous and intermittent-access conditions, and eventually exceeded that seen in females. Free-running period shortened during the initial ethanol-access epoch in all groups, but the persistence of this effect showed complex dependence on sex, breeding line, and ethanol-access schedule. Finally, while females of both breeding lines displayed higher levels of locomotor activity than males, there was little evidence for modulation of activity level by ethanol access. These results are consistent with previous findings that chronic ethanol intake alters free-running circadian period, and show further that the development of chronobiological tolerance to ethanol may vary by sex and genotype. PMID:25281289

Assessing Stride Variables and Vertical Stiffness with GPS-Embedded Accelerometers: Preliminary Insights for the Monitoring of Neuromuscular Fatigue on the Field

PubMed Central

Buchheit, Martin; Gray, Andrew; Morin, Jean-Benoit

2015-01-01

The aim of the present study was to examine the ability of a GPS-imbedded accelerometer to assess stride variables and vertical stiffness (K), which are directly related to neuromuscular fatigue during field-based high-intensity runs. The ability to detect stride imbalances was also examined. A team sport player performed a series of 30-s runs on an instrumented treadmill (6 runs at 10, 17 and 24 km·h-1) with or without his right ankle taped (aimed at creating a stride imbalance), while wearing on his back a commercially-available GPS unit with an embedded 100-Hz tri-axial accelerometer. Contact (CT) and flying (FT) time, and K were computed from both treadmill and accelerometers (Athletic Data Innovations) data. The agreement between treadmill (criterion measure) and accelerometer-derived data was examined. We also compared the ability of the different systems to detect the stride imbalance. Biases were small (CT and K) and moderate (FT). The typical error of the estimate was trivial (CT), small (K) and moderate (FT), with nearly perfect (CT and K) and large (FT) correlations for treadmill vs. accelerometer. The tape induced very large increase in the right - left foot ∆ in CT, FT and K measured by the treadmill. The tape effect on CT and K ∆ measured with the accelerometers were also very large, but of lower magnitude than with the treadmill. The tape effect on accelerometer-derived ∆ FT was unclear. Present data highlight the potential of a GPS-embedded accelerometer to assess CT and K during ground running. Key points GPS-embedded tri-axial accelerometers may be used to assess contact time and vertical stiffness during ground running. These preliminary results open new perspective for the field monitoring of neuromuscular fatigue and performance in run-based sports PMID:26664264

Mean platelet volume (MPV) predicts middle distance running performance.

PubMed

Lippi, Giuseppe; Salvagno, Gian Luca; Danese, Elisa; Skafidas, Spyros; Tarperi, Cantor; Guidi, Gian Cesare; Schena, Federico

2014-01-01

Running economy and performance in middle distance running depend on several physiological factors, which include anthropometric variables, functional characteristics, training volume and intensity. Since little information is available about hematological predictors of middle distance running time, we investigated whether some hematological parameters may be associated with middle distance running performance in a large sample of recreational runners. The study population consisted in 43 amateur runners (15 females, 28 males; median age 47 years), who successfully concluded a 21.1 km half-marathon at 75-85% of their maximal aerobic power (VO2max). Whole blood was collected 10 min before the run started and immediately thereafter, and hematological testing was completed within 2 hours after sample collection. The values of lymphocytes and eosinophils exhibited a significant decrease compared to pre-run values, whereas those of mean corpuscular volume (MCV), platelets, mean platelet volume (MPV), white blood cells (WBCs), neutrophils and monocytes were significantly increased after the run. In univariate analysis, significant associations with running time were found for pre-run values of hematocrit, hemoglobin, mean corpuscular hemoglobin (MCH), red blood cell distribution width (RDW), MPV, reticulocyte hemoglobin concentration (RetCHR), and post-run values of MCH, RDW, MPV, monocytes and RetCHR. In multivariate analysis, in which running time was entered as dependent variable whereas age, sex, blood lactate, body mass index, VO2max, mean training regimen and the hematological parameters significantly associated with running performance in univariate analysis were entered as independent variables, only MPV values before and after the trial remained significantly associated with running time. After adjustment for platelet count, the MPV value before the run (p = 0.042), but not thereafter (p = 0.247), remained significantly associated with running performance. The significant association between baseline MPV and running time suggest that hyperactive platelets may exert some pleiotropic effects on endurance performance.

On the Lifetime Prevalence of Running Away from Home

ERIC Educational Resources Information Center

Pergamit, Michael R.

2010-01-01

Nearly one in five U.S. youths will run away from home before age 18. Almost 30 percent of these youth will do so three or more times, greatly increasing their risk of violence, crime, drugs, prostitution, STDs, and many other problems. Employing new methodology to yield estimates not available elsewhere, this paper follows a nationally…

Global Reference Atmosphere Model (GRAM)

NASA Technical Reports Server (NTRS)

Woodrum, A. W.

1989-01-01

GRAM series of four-dimensional atmospheric model validated by years of data. GRAM program, still available. More current are Gram 86, which includes atmospheric data from 1986 and runs on DEC VAX, and GRAM 88, which runs on IBM 3084. Program generates altitude profiles of atmospheric parameters along any simulated trajectory through atmosphere, and also useful for global circulation and diffusion studies.

Running Wheel for Earthworms

PubMed Central

Wilson, W. Jeffrey; Johnson, Brandon A.

2016-01-01

We describe the construction and use of a running wheel responsive to the movement of the earthworm. The wheel employs readily available, inexpensive components and is easily constructed. Movement of the wheel can be monitored visually or via standard behavioral laboratory computer interfaces. Examples of data are presented, and possibilities for use in the teaching classroom are discussed. PMID:27385934

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

Thorson, L.D.

A description is given of a new version of the TRUMP (UCRL-14754) computer code, NOTRUMP, which runs on both the CDC-7600 and CRAY-1. There are slight differences in the input and major changes in output capability. A postprocessor, AFTER, is available to manipulate some of the new output features. Old data decks for TRUMP will normally run with only minor changes.

The barefoot debate: can minimalist shoes reduce running-related injuries?

PubMed

Rixe, Jeffrey A; Gallo, Robert A; Silvis, Matthew L

2012-01-01

Running has evolved throughout history from a necessary form of locomotion to an athletic and recreational pursuit. During this transition, our barefoot ancestors developed footwear. By the late 1970s, running popularity surged, and footwear manufacturers developed the running shoe. Despite new shoe technology and expert advice, runners still face high injury rates, which have yet to decline. Recently, "minimalist" running, marked by a soft forefoot strike and shorter, quicker strides, has become increasingly popular within the running community. Biomechanical studies have suggested that these features of barefoot-style running may lead to a reduction in injury rates. After conducting more outcomes-based research, minimalist footwear and gait retraining may serve as new methods to reduce injuries within the running population.

Voluntary wheel running is beneficial to the amino acid profile of lysine-deficient rats.

PubMed

Nagao, Kenji; Bannai, Makoto; Seki, Shinobu; Kawai, Nobuhiro; Mori, Masato; Takahashi, Michio

2010-06-01

Rats voluntarily run up to a dozen kilometers per night when their cages are equipped with a running wheel. Daily voluntary running is generally thought to enhance protein turnover. Thus, we sought to determine whether running worsens or improves protein degradation caused by a lysine-deficient diet and whether it changes the utilization of free amino acids released by proteolysis. Rats were fed a lysine-deficient diet and were given free access to a running wheel or remained sedentary (control) for 4 wk. Amino acid levels in plasma, muscle, and liver were measured together with plasma insulin levels and tissue weight. The lysine-deficient diet induced anorexia, skeletal muscle loss, and serine and threonine aminoacidemia, and it depleted plasma insulin and essential amino acids in skeletal muscle. Allowing rats to run voluntarily improved these symptoms; thus, voluntary wheel running made the rats less susceptible to dietary lysine deficiency. Amelioration of the declines in muscular leucine and plasma insulin observed in running rats could contribute to protein synthesis together with the enhanced availability of lysine and other essential amino acids in skeletal muscle. These results indicate that voluntary wheel running under lysine-deficient conditions does not enhance protein catabolism; on the contrary, it accelerates protein synthesis and contributes to the maintenance of muscle mass. The intense nocturnal voluntary running that characterizes rodents might be an adaptation of lysine-deficient grain eaters that allows them to maximize opportunities for food acquisition.

Robotic thoracic surgery: technical considerations and learning curve for pulmonary resection.

PubMed

Veronesi, Giulia

2014-05-01

Retrospective series indicate that robot-assisted approaches to lung cancer resection offer comparable radicality and safety to video-assisted thoracic surgery or open surgery. More intuitive movements, greater flexibility, and high-definition three-dimensional vision overcome limitations of video-assisted thoracic surgery and may encourage wider adoption of robotic surgery for lung cancer, particularly as more early stage cases are diagnosed by screening. High capital and running costs, limited instrument availability, and long operating times are important disadvantages. Entry of competitor companies should drive down costs. Studies are required to assess quality of life, morbidity, oncologic radicality, and cost effectiveness. Copyright © 2014 Elsevier Inc. All rights reserved.

ProjectQ: Compiling quantum programs for various backends

NASA Astrophysics Data System (ADS)

Haener, Thomas; Steiger, Damian S.; Troyer, Matthias

In order to control quantum computers beyond the current generation, a high level quantum programming language and optimizing compilers will be essential. Therefore, we have developed ProjectQ - an open source software framework to facilitate implementing and running quantum algorithms both in software and on actual quantum hardware. Here, we introduce the backends available in ProjectQ. This includes a high-performance simulator and emulator to test and debug quantum algorithms, tools for resource estimation, and interfaces to several small-scale quantum devices. We demonstrate the workings of the framework and show how easily it can be further extended to control upcoming quantum hardware.

Evolution of CMS workload management towards multicore job support

NASA Astrophysics Data System (ADS)

Pérez-Calero Yzquierdo, A.; Hernández, J. M.; Khan, F. A.; Letts, J.; Majewski, K.; Rodrigues, A. M.; McCrea, A.; Vaandering, E.

2015-12-01

The successful exploitation of multicore processor architectures is a key element of the LHC distributed computing system in the coming era of the LHC Run 2. High-pileup complex-collision events represent a challenge for the traditional sequential programming in terms of memory and processing time budget. The CMS data production and processing framework is introducing the parallel execution of the reconstruction and simulation algorithms to overcome these limitations. CMS plans to execute multicore jobs while still supporting singlecore processing for other tasks difficult to parallelize, such as user analysis. The CMS strategy for job management thus aims at integrating single and multicore job scheduling across the Grid. This is accomplished by employing multicore pilots with internal dynamic partitioning of the allocated resources, capable of running payloads of various core counts simultaneously. An extensive test programme has been conducted to enable multicore scheduling with the various local batch systems available at CMS sites, with the focus on the Tier-0 and Tier-1s, responsible during 2015 of the prompt data reconstruction. Scale tests have been run to analyse the performance of this scheduling strategy and ensure an efficient use of the distributed resources. This paper presents the evolution of the CMS job management and resource provisioning systems in order to support this hybrid scheduling model, as well as its deployment and performance tests, which will enable CMS to transition to a multicore production model for the second LHC run.

Evolution of CMS Workload Management Towards Multicore Job Support

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

Perez-Calero Yzquierdo, A.; Hernández, J. M.; Khan, F. A.

The successful exploitation of multicore processor architectures is a key element of the LHC distributed computing system in the coming era of the LHC Run 2. High-pileup complex-collision events represent a challenge for the traditional sequential programming in terms of memory and processing time budget. The CMS data production and processing framework is introducing the parallel execution of the reconstruction and simulation algorithms to overcome these limitations. CMS plans to execute multicore jobs while still supporting singlecore processing for other tasks difficult to parallelize, such as user analysis. The CMS strategy for job management thus aims at integrating single andmore » multicore job scheduling across the Grid. This is accomplished by employing multicore pilots with internal dynamic partitioning of the allocated resources, capable of running payloads of various core counts simultaneously. An extensive test programme has been conducted to enable multicore scheduling with the various local batch systems available at CMS sites, with the focus on the Tier-0 and Tier-1s, responsible during 2015 of the prompt data reconstruction. Scale tests have been run to analyse the performance of this scheduling strategy and ensure an efficient use of the distributed resources. This paper presents the evolution of the CMS job management and resource provisioning systems in order to support this hybrid scheduling model, as well as its deployment and performance tests, which will enable CMS to transition to a multicore production model for the second LHC run.« less

Running Performance of a Pinning-Type Superconducting Magnetic Levitation Guide

NASA Astrophysics Data System (ADS)

Okano, M.; Iwamoto, T.; Furuse, M.; Fuchino, S.; Ishii, I.

2006-06-01

A pinning-type superconducting magnetic levitation guide with bulk high-Tc superconductors was studied for use as a goods transportation system, an energy storage system, etc. A superconducting magnetic levitation running test apparatus with a circular track of ca. 38 m length, 12 m diameter, which comprises the magnetic rail constituted by Nd-B-Fe rare-earth permanent magnets and steel plates, was manufactured to examine loss and high-speed performance of the magnetic levitation guide. Running tests were conducted in air. These tests clarify that a vehicle supported by a superconducting magnetic levitation guide runs stably at speeds greater than 42 km/h above the circular track.

Evaluation of newly synthesized and commercially available charged cyclomaltooligosaccharides (cyclodextrins) for capillary electrokinetic chromatography.

PubMed

Culha, Mustafa; Schell, Fred M; Fox, Shannon; Green, Thomas; Betts, Thomas; Sepaniak, Michael J

2004-01-22

A highly new charged cyclodextrin (CD) derivatives, (6-O-carboxymethyl-2,3-di-O-methyl)cyclomaltoheptaoses (CDM-beta-CDs), was synthesized and characterized as anionic reagents for capillary electrophoresis (CE) in an electrokinetic chromatography mode of separation. Substitution with dimethyl groups at the secondary hydroxyl sites of the CD is aimed at influencing the magnitude and selectivity of analyte-CD interactions, while substitution by carboxymethyl groups at the primary hydroxyl sites provides for high charge and electrophoretic mobility. Full regioselective methylation at the secondary hydroxyl sites was achieved in this work, while substitution at the primary hydroxyl sites generated a mixture of multiply charged products. The separation performance of CDM-beta-CD was evaluated using a variety of analyte mixtures. The results obtained from commercially available negatively charged cyclodextrins, heptakis(2,3-di-O-methyl-6-O-sulfo)cyclomaltoheptaose (HDMS-beta-CD) and O-(carboxymethyl)cyclomaltoheptaose (CM-beta-CD) with an average degree of substitution one (DS 1), were compared to CDM-beta-CD using a sample composed of eight positional isomers of dihydroxynaphthalene. Four hydroxylated polychlorobiphenyl derivatives, a group of chiral and isomeric catchecins, and chiral binaphthyl compounds were also separated with CDM-beta-CD. The effect of adding neutral beta-cyclodextrin (beta-CD) into the running buffer containing charged cyclodextrins was investigated and provided evidence of significant inter-CD interactions. Under certain running buffer conditions, the charged cyclodextrins also appear to adsorb to the capillary walls to various degrees.

Acute administration of high doses of taurine does not substantially improve high-intensity running performance and the effect on maximal accumulated oxygen deficit is unclear.

PubMed

Milioni, Fabio; Malta, Elvis de Souza; Rocha, Leandro George Spinola do Amaral; Mesquita, Camila Angélica Asahi; de Freitas, Ellen Cristini; Zagatto, Alessandro Moura

2016-05-01

The aim of the present study was to investigate the effects of acute administration of taurine overload on time to exhaustion (TTE) of high-intensity running performance and alternative maximal accumulated oxygen deficit (MAODALT). The study design was a randomized, placebo-controlled, crossover design. Seventeen healthy male volunteers (age: 25 ± 6 years; maximal oxygen uptake: 50.5 ± 7.6 mL·kg(-1)·min(-1)) performed an incremental treadmill-running test until voluntary exhaustion to determine maximal oxygen uptake and exercise intensity at maximal oxygen uptake. Subsequently, participants completed randomly 2 bouts of supramaximal treadmill-running at 110% exercise intensity at maximal oxygen uptake until exhaustion (placebo (6 g dextrose) or taurine (6 g) supplementation), separated by 1 week. MAODALT was determined using a single supramaximal effort by summating the contribution of the phosphagen and glycolytic pathways. When comparing the results of the supramaximal trials (i.e., placebo and taurine conditions) no differences were observed for high-intensity running TTE (237.70 ± 66.00 and 277.30 ± 40.64 s; p = 0.44) and MAODALT (55.77 ± 8.22 and 55.06 ± 7.89 mL·kg(-1); p = 0.61), which seem to indicate trivial and unclear differences using the magnitude-based inferences approach, respectively. In conclusion, acute 6 g taurine supplementation before exercise did not substantially improve high-intensity running performance and showed an unclear effect on MAODALT.

The effects of food presentation at regular or irregular times on the development of activity-based anorexia in rats.

PubMed

Pérez-Padilla, Angeles; Magalhães, Paula; Pellón, Ricardo

2010-05-01

Activity-based anorexia occurs when food availability is restricted to 1h of the day and a wheel is freely available to the rest of the time. Under such conditions rats run excessively and stop eating even during periods in which food is available. A defining characteristic of the excessive activity is that there is a peak of running in the anticipation of food availability. The present study was designed to test whether the occurrence of the food period at different times of the light phase of the light-dark cycle (from 08:00 to 20:00h) could impede or postpone the normal development of activity anorexia. We compared the effect of presenting the food at a fixed time of the light period with presenting it on a variable schedule. Far from impeding or postponing the development of activity-based anorexia, presenting food at irregular times resulted in a pronounced body-weight loss, a low food intake and an increase in locomotor activity. Animals ran excessively, with a peak at the start of the dark period, and again when lights were turned on in the experimental room (running in the anticipation of food). Both fixed and variable schedules of food availability resulted in the development of activity-based anorexia in rats. Copyright (c) 2009 Elsevier B.V. All rights reserved.

42 CFR 401.621 - Termination of collection action.

Code of Federal Regulations, 2010 CFR

2010-10-01

... available; (ii) The debtor's future financial prospects; and (iii) Exemptions available to the debtor under... statute of limitations has run; or (iii) The prospects of collecting by offset, whether or not an...

CIVET: Continuous Integration, Verification, Enhancement, and Testing

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

Alger, Brian; Gaston, Derek R.; Permann, Cody J

A Git server (GitHub, GitLab, BitBucket) sends event notifications to the Civet server. These are either a " Pull Request" or a "Push" notification. Civet then checks the database to determine what tests need to be run and marks them as ready to run. Civet clients, running on dedicated machines, query the server for available jobs that are ready to run. When a client gets a job it executes the scripts attached to the job and report back to the server the output and exit status. When the client updates the server, the server will also update the Git servermore » with the result of the job, as well as updating the main web page.« less

Adjustments with running speed reveal neuromuscular adaptations during landing associated with high mileage running training.

PubMed

Verheul, Jasper; Clansey, Adam C; Lake, Mark J

2017-03-01

It remains to be determined whether running training influences the amplitude of lower limb muscle activations before and during the first half of stance and whether such changes are associated with joint stiffness regulation and usage of stored energy from tendons. Therefore, the aim of this study was to investigate neuromuscular and movement adaptations before and during landing in response to running training across a range of speeds. Two groups of high mileage (HM; >45 km/wk, n = 13) and low mileage (LM; <15 km/wk, n = 13) runners ran at four speeds (2.5-5.5 m/s) while lower limb mechanics and electromyography of the thigh muscles were collected. There were few differences in prelanding activation levels, but HM runners displayed lower activations of the rectus femoris, vastus medialis, and semitendinosus muscles postlanding, and these differences increased with running speed. HM runners also demonstrated higher initial knee stiffness during the impact phase compared with LM runners, which was associated with an earlier peak knee flexion velocity, and both were relatively unchanged by running speed. In contrast, LM runners had higher knee stiffness during the slightly later weight acceptance phase and the disparity was amplified with increases in speed. It was concluded that initial knee joint stiffness might predominantly be governed by tendon stiffness rather than muscular activations before landing. Estimated elastic work about the ankle was found to be higher in the HM runners, which might play a role in reducing weight acceptance phase muscle activation levels and improve muscle activation efficiency with running training. NEW & NOTEWORTHY Although neuromuscular factors play a key role during running, the influence of high mileage training on neuromuscular function has been poorly studied, especially in relation to running speed. This study is the first to demonstrate changes in neuromuscular conditioning with high mileage training, mainly characterized by lower thigh muscle activation after touch down, higher initial knee stiffness, and greater estimates of energy return, with adaptations being increasingly evident at faster running speeds. Copyright © 2017 the American Physiological Society.

Monitoring of the data processing and simulated production at CMS with a web-based service: the Production Monitoring Platform (pMp)

NASA Astrophysics Data System (ADS)

Franzoni, G.; Norkus, A.; Pol, A. A.; Srimanobhas, N.; Walker, J.

2017-10-01

Physics analysis at the Compact Muon Solenoid requires both the production of simulated events and processing of the data collected by the experiment. Since the end of the LHC Run-I in 2012, CMS has produced over 20 billion simulated events, from 75 thousand processing requests organised in one hundred different campaigns. These campaigns emulate different configurations of collision events, the detector, and LHC running conditions. In the same time span, sixteen data processing campaigns have taken place to reconstruct different portions of the Run-I and Run-II data with ever improving algorithms and calibrations. The scale and complexity of the events simulation and processing, and the requirement that multiple campaigns must proceed in parallel, demand that a comprehensive, frequently updated and easily accessible monitoring be made available. The monitoring must serve both the analysts, who want to know which and when datasets will become available, and the central production teams in charge of submitting, prioritizing, and running the requests across the distributed computing infrastructure. The Production Monitoring Platform (pMp) web-based service, has been developed in 2015 to address those needs. It aggregates information from multiple services used to define, organize, and run the processing requests. Information is updated hourly using a dedicated elastic database and the monitoring provides multiple configurable views to assess the status of single datasets as well as entire production campaigns. This contribution will describe the pMp development, the evolution of its functionalities, and one and half year of operational experience.

Running and Osteoarthritis: Does Recreational or Competitive Running Increase the Risk?

PubMed

2017-06-01

Exercise, like running, is good for overall health and, specifically, our hearts, lungs, muscles, bones, and brains. However, some people are concerned about the impact of running on longterm joint health. Does running lead to higher rates of arthritis in knees and hips? While many researchers find that running protects bone health, others are concerned that this exercise poses a high risk for age-related changes to hips and knees. A study published in the June 2017 issue of JOSPT suggests that the difference in these outcomes depends on the frequency and intensity of running. J Orthop Sports Phys Ther 2017;47(6):391. doi:10.2519/jospt.2017.0505.

Muons in the CMS High Level Trigger System

NASA Astrophysics Data System (ADS)

Verwilligen, Piet; CMS Collaboration

2016-04-01

The trigger systems of LHC detectors play a fundamental role in defining the physics capabilities of the experiments. A reduction of several orders of magnitude in the rate of collected events, with respect to the proton-proton bunch crossing rate generated by the LHC, is mandatory to cope with the limits imposed by the readout and storage system. An accurate and efficient online selection mechanism is thus required to fulfill the task keeping maximal the acceptance to physics signals. The CMS experiment operates using a two-level trigger system. Firstly a Level-1 Trigger (L1T) system, implemented using custom-designed electronics, is designed to reduce the event rate to a limit compatible to the CMS Data Acquisition (DAQ) capabilities. A High Level Trigger System (HLT) follows, aimed at further reducing the rate of collected events finally stored for analysis purposes. The latter consists of a streamlined version of the CMS offline reconstruction software and operates on a computer farm. It runs algorithms optimized to make a trade-off between computational complexity, rate reduction and high selection efficiency. With the computing power available in 2012 the maximum reconstruction time at HLT was about 200 ms per event, at the nominal L1T rate of 100 kHz. An efficient selection of muons at HLT, as well as an accurate measurement of their properties, such as transverse momentum and isolation, is fundamental for the CMS physics programme. The performance of the muon HLT for single and double muon triggers achieved in Run I will be presented. Results from new developments, aimed at improving the performance of the algorithms for the harsher scenarios of collisions per event (pile-up) and luminosity expected for Run II will also be discussed.

High-fat foods overcome the energy expenditure induced by high-intensity cycling or running.

PubMed

King, N A; Blundell, J E

1995-02-01

To examine the effects of two types of vigorous exercise [cycling (CYC) and running (RUN)] and diet composition on appetite control. Two studies using separate groups of subjects were used for the two forms of exercise. The studies used a 2 x 2 design with the factors being exercise and diet composition. Therefore both studies had four treatment conditions and used a repeated measures design. Both studies took place in the Human Appetite Research Unit at Leeds University. Twenty-four lean, healthy males were recruited from the student staff population of Leeds University. For both studies a control (no-exercise) and a vigorous exercise session (70% VO2 max) was followed by a free-selection lunch comprising high-fat/low-carbohydrate foods or low-fat/high-carbohydrate foods, during which energy and macronutrient intake was monitored. Motivation to eat was measured by visual analogue scales and by the latency to volitional onset of eating. Energy intake for the remainder of the day (outside of laboratory) was monitored by providing the subjects with airline-style food boxes. Both CYC and RUN produced similar effects on appetite responses. Both CYC and RUN induced a transitory suppression of hunger (P < 0.01 and P < 0.05) and a delay to the onset of eating (P < 0.001). Exercise (whether CYC or RUN) had no significant effect on the total amount of food eaten, but there was a significant effect of lunch type. When provided with the high-fat/low-carbohydrate foods energy intake was significantly elevated (CYC: P < 0.001; and RUN: P < 0.0001). Both types of exercise induced a short-term negative energy balance when followed by the low-fat/high-carbohydrate foods (P < 0.001), which was completely reversed (positive energy balance) when subjects ate from the high-fat/low carbohydrate foods. These results indicate that eating high-fat foods can prevent exercise inducing any (short-term) negative energy balance. Therefore, in order for exercise to have a significant impact on weight control, it is important to consider the energy density of the accompanying diet. Despite the different physiological aspects of cycling and running, they did not display different effects on appetite.

Hydrogeology and groundwater availability in Clarke County, Virginia

USGS Publications Warehouse

Nelms, David L.; Moberg, Roger M.

2010-01-01

The prolonged drought between 1999 and 2002 drew attention in Clarke County, Virginia, to the quantity and sustainability of its groundwater resources. The groundwater flow systems of the county are complex and are controlled by the extremely folded and faulted geology that underlies the county. A study was conducted between October 2002 and October 2008 by the U.S. Geological Survey, in cooperation with Clarke County, Virginia, to describe the hydrogeology and groundwater availability in the county and to establish a long-term water monitoring network. The study area encompasses approximately 177 square miles and includes the carbonate and siliciclastic rocks of the Great Valley section of the Valley and Ridge Physiographic Province and the metamorphic rocks of the Blue Ridge Physiographic Province (Blue Ridge). High-yielding wells generally tend to cluster along faults, within lineament zones, and in areas of tight folding throughout the county. Water-bearing zones are generally within 250 feet (ft) of land surface; however, median depths are slightly deeper for the hydrogeologic units of the Blue Ridge than for those of the Great Valley section of the county. Total water-level fluctuations between October 2002 and October 2008 ranged from 2.86 to 87.84 ft across the study area, with an average of 24.15 ft. Generally, water-level fluctuations were greatest near hydrologic divides, in isolated elevated areas, and in the Opequon Creek Basin. Seasonally, water-level highs occur in the early spring at the end of the major groundwater recharge period and lows occur in late autumn when evapotranspiration rates begin to decrease. An overall downward trend in water levels between 2003 and 2008, which closely follows a downward trend in annual precipitation over the same period, was observed in a majority of wells in the Great Valley and in some of the wells in the Blue Ridge. Water-level fluctuations in the Blue Ridge tend to follow current meteorological conditions, and seasonal highs and lows tend to shift in response to the current conditions. Springs generally are present along faults and fold axes, and discharges for the study period ranged from dry to 10 cubic feet per second. A similar downward trend in discharges correlates with the trend in water levels and is indicative of an aquifer system that, over time, drains to a base level controlled by springs and streams. Point discharge from springs can occur as the start of flows of streams and creeks, along banks, and as discrete discharge through streambeds in the Great Valley. For the most part, streams, creeks, and rivers in the Great Valley function as aqueducts. Springs in the Blue Ridge have relatively low discharge rates, have small drainage areas, and are susceptible to current meteorological conditions. Estimates of effective groundwater recharge from 2001 to 2007 ranged from 6.4 to 23.0 inches per year (in/yr) in the Dry Marsh Run and Spout Run Basins with averages of 11.6 and 11.9 in/yr, respectively. Base flow accounted for between 80 and 97 percent of mean streamflow and averaged about 90 percent in these basins. The high base-flow index values (percent of streamflow from base flow) in the Dry Marsh Run and Spout Run Basins indicate that groundwater is the dominant source of streamflow during both wet and drought conditions. Between 46 and 82 percent of the precipitation that fell on the Dry Marsh Run and Spout Run Basins from 2001 to 2007 was removed by evapotranspiration, and an average of approximately 30 percent of the precipitation reached the water table as effective recharge. The high permeability of the rocks and low relief in these basins are not conducive for runoff; therefore, on average, only about 3 to 4 percent of the precipitation becomes runoff. Groundwater flow systems in the county are extremely vulnerable to current climatic conditions. Successive years of below-average effective recharge cause declines in water levels, spring discha

The Influence of Rotations on Match Running Performance in Female Australian Football Midfielders.

PubMed

Black, Georgia M; Gabbett, Tim J; Johnston, Richard D; Naughton, Geraldine; Cole, Michael H; Dawson, Brian

2018-04-01

With female Australian football (AF) gaining popularity, understanding match demands is becoming increasingly important. The aim of this study was to compare running performances of rotated and whole-quarter state-level female AF players during match quarters. Twenty-two state-level female AF midfielders wore Global Positioning System units during 14 games to evaluate activity profiles. The Yo-Yo Intermittent Recovery Test Level 1 (Yo-Yo IR1) was used as a measure of high-intensity running ability. Data were categorized into whole quarter, rotation bout 1, and rotation bout 2 before being further divided into quartiles. Players were separated into high- or low-Yo-Yo IR1 groups using a median split based on their Yo-Yo IR1 performance. Short (4-6 min), moderate (6-12 min), and long (12-18 min) on-field bout activity profiles were compared with whole-quarter players. High Yo-Yo IR1 performance allowed players to cover greater relative distances (ES = 0.57-0.88) and high-speed distances (ES = 0.57-0.86) during rotations. No differences were reported between Yo-Yo IR1 groups when players were required to play whole quarters (ES ≤ 0.26, likelihood ≤64%). Players who were on field for short to moderate durations exhibited greater activity profiles than whole-quarter players. Superior high-speed running ability results in a greater activity profile than for players who possess lower high-speed running ability. The findings also highlight the importance of short to moderate (4-12 min) rotation periods and may be used to increase high-intensity running performance within quarters in female AF players.

Impact of high-fat diet and voluntary running on body weight and endothelial function in LDL receptor knockout mice.

PubMed

Langbein, Heike; Hofmann, Anja; Brunssen, Coy; Goettsch, Winfried; Morawietz, Henning

2015-05-01

Obesity and physical inactivity are important cardiovascular risk factors. Regular physical exercise has been shown to mediate beneficial effects in the prevention of cardiovascular diseases. However, the impact of physical exercise on endothelial function in proatherosclerotic low-density lipoprotein receptor deficient (LDLR(-/-)) mice has not been studied so far. Six-week-old male LDLR(-/-) mice were fed a standard diet or a high-fat diet (39 kcal% fat diet) for 20 weeks. The impact of high-fat diet and voluntary running on body weight and amount of white adipose tissue was monitored. Basal tone and endothelial function was investigated in aortic rings using a Mulvany myograph. LDLR(-/-) mice on high-fat diet had increased cumulative food energy intake, but also higher physical activity compared to mice on control diet. Body weight and amount of visceral and retroperitoneal white adipose tissue of LDLR(-/-) mice were significantly increased by high-fat diet and partially reduced by voluntary running. Endothelial function in aortae of LDLR(-/-) mice was impaired after 20 weeks on standard and high-fat diet and could not be improved by voluntary running. Basal tone showed a trend to be increased by high-fat diet. Voluntary running reduced body weight and amount of white adipose tissue in LDLR(-/-) mice. Endothelial dysfunction in LDLR(-/-) mice could not be improved by voluntary running. In a clinical context, physical exercise alone might not have an influence on functional parameters and LDL-C levels in patients with familial hypercholesterolemia. However, physical activity in these patients may be in general beneficial and should be performed. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Running as Interoceptive Exposure for Decreasing Anxiety Sensitivity: Replication and Extension.

PubMed

Sabourin, Brigitte C; Stewart, Sherry H; Watt, Margo C; Krigolson, Olav E

2015-01-01

A brief, group cognitive behavioural therapy with running as the interoceptive exposure (IE; exposure to physiological sensations) component was effective in decreasing anxiety sensitivity (AS; fear of arousal sensations) levels in female undergraduates (Watt et al., Anxiety and Substance Use Disorders: The Vicious Cycle of Comorbidity, 201-219, 2008). Additionally, repeated exposure to running resulted in decreases in cognitive (i.e., catastrophic thoughts) and affective (i.e., feelings of anxiety) reactions to running over time for high AS, but not low AS, participants (Sabourin et al., "Physical exercise as interoceptive exposure within a brief cognitive-behavioral treatment for anxiety-sensitive women", Journal of Cognitive Psychotherapy, 22:302-320, 2008). A follow-up study including the above-mentioned intervention with an expanded IE component also resulted in decreases in AS levels (Sabourin et al., under review). The goals of the present process study were (1) to replicate the original process study, with the expanded IE component, and (2) to determine whether decreases in cognitive, affective, and/or somatic (physiological sensations) reactions to running would be related to decreases in AS. Eighteen high AS and 10 low AS participants completed 20 IE running trials following the 3-day group intervention. As predicted, high AS participants, but not low AS participants, experienced decreases in cognitive, affective, and somatic reactions to running over time. Furthermore, decreases in cognitive and affective, but not in somatic, reactions to running were related to decreases in AS levels. These results suggest that the therapeutic effects of repeated exposure to running in decreasing sensitivity to anxiety-related sensations are not related to decreasing the experience of somatic sensations themselves. Rather, they are related to altering the cognitive and affective reactions to these sensations.

Bringing ocean observations to the classroom - integrating research infrastructure into education

NASA Astrophysics Data System (ADS)

Proctor, R.; Hoenner, X.; Mancini, S.; Tattersall, K.; Everett, J. D.; Suthers, I. M.; Steinberg, P.; Doblin, M.; Moltmann, T.

2016-02-01

For the past 4 years the Sydney Institute of Marine Science, a partnership of four Australian Universities (Macquarie University, the University of NSW, the University of Sydney and the University of Technology Sydney) has been running a Master's degree course called Topics in Australian Marine Science (TAMS). This course is unique in that the core of the course is built around research infrastructure - the Integrated Marine Observing System (IMOS). IMOS, established in 2007, is collecting unprecedented volumes of multi-disciplinary oceanographic data in the ocean and on the continental shelf which is made freely available across the web; IMOS frequently runs `data user workshops' throughout Australia to introduce scientists and managers to the wealth of observations available at their fingertips. The Masters course gives students an understanding of how different measurement platforms work and they explore the data that these platforms collect. Students combine attending seminars and lectures with hands on practicals and personal assignments, all built around access to IMOS data and the many tools available to visualise and analyse. The course attracts a diverse class with many mature students (i.e. > 25 years old) from a range of backgrounds who find that the ease of discovering and accessing data, coupled with the available tools, enables them to easily study the marine environment without the need for high level computational skills. Since its inception the popularity of the course has increased with 38 students undertaking the subject in 2014. The consensus from students and lecturers is that integrating `real' observations into the classroom is beneficial to all, and IMOS is seeking to extend this approach to other university campuses. The talk will describe the experiences from the TAMS course and highlight the IMOS approach to data discovery, availability and access through course examples.

GIF Animation of Mode Shapes and Other Data on the Internet

NASA Technical Reports Server (NTRS)

Pappa, Richard S.

1998-01-01

The World Wide Web abounds with animated cartoons and advertisements competing for our attention. Most of these figures are animated Graphics Interchange Format (GIF) files. These files contain a series of ordinary GIF images plus control information, and they provide an exceptionally simple, effective way to animate on the Internet. To date, however, this format has rarely been used for technical data, although there is no inherent reason not to do so. This paper describes a procedure for creating high-resolution animated GIFs of mode shapes and other types of structural dynamics data with readily available software. The paper shows three example applications using recent modal test data and video footage of a high-speed sled run. A fairly detailed summary of the GIF file format is provided in the appendix. All of the animations discussed in the paper are posted on the Internet available through the following address: http://sdb-www.larc.nasa.gov/.

Is there really an eccentric action of the hamstrings during the swing phase of high-speed running? part I: A critical review of the literature.

PubMed

Van Hooren, Bas; Bosch, Frans

2017-12-01

It is widely assumed that there is an eccentric hamstring muscle fibre action during the swing phase of high-speed running. However, animal and modelling studies in humans show that the increasing distance between musculotendinous attachment points during forward swing is primarily due to passive lengthening associated with the take-up of muscle slack. Later in the swing phase, the contractile element (CE) maintains a near isometric action while the series elastic (tendinous) element first stretches as the knee extends, and then recoils causing the swing leg to forcefully retract prior to ground contact. Although modelling studies showed some active lengthening of the contractile (muscular) element during the mid-swing phase of high-speed running, we argue that the increasing distance between the attachment points should not be interpreted as an eccentric action of the CE due to the effects of muscle slack. Therefore, there may actually be no significant eccentric, but rather predominantly an isometric action of the hamstrings CE during the swing phase of high-speed running when the attachment points of the hamstrings are moving apart. Based on this, we propose that isometric rather than eccentric exercises are a more specific way of conditioning the hamstrings for high-speed running.

Neuromuscular Risk Factors for Knee and Ankle Ligament Injuries in Male Youth Soccer Players.

PubMed

Read, Paul J; Oliver, Jon L; De Ste Croix, Mark B A; Myer, Gregory D; Lloyd, Rhodri S

2016-08-01

Injuries reported in male youth soccer players most commonly occur in the lower extremities, and include a high proportion of ligament sprains at the ankle and knee with a lower proportion of overuse injuries. There is currently a paucity of available literature that examines age- and sex-specific injury risk factors for such injuries within youth soccer players. Epidemiological data have reported movements that lead to non-contact ligament injury include running, twisting and turning, over-reaching and landing. Altered neuromuscular control during these actions has been suggested as a key mechanism in females and adult populations; however, data available in male soccer players is sparse. The focus of this article is to review the available literature and elucidate prevalent risk factors pertaining to male youth soccer players which may contribute to their relative risk of injury.

SSL - THE SIMPLE SOCKETS LIBRARY

NASA Technical Reports Server (NTRS)

Campbell, C. E.

1994-01-01

The Simple Sockets Library (SSL) allows C programmers to develop systems of cooperating programs using Berkeley streaming Sockets running under the TCP/IP protocol over Ethernet. The SSL provides a simple way to move information between programs running on the same or different machines and does so with little overhead. The SSL can create three types of Sockets: namely a server, a client, and an accept Socket. The SSL's Sockets are designed to be used in a fashion reminiscent of the use of FILE pointers so that a C programmer who is familiar with reading and writing files will immediately feel comfortable with reading and writing with Sockets. The SSL consists of three parts: the library, PortMaster, and utilities. The user of the SSL accesses it by linking programs to the SSL library. The PortMaster initializes connections between clients and servers. The PortMaster also supports a "firewall" facility to keep out socket requests from unapproved machines. The "firewall" is a file which contains Internet addresses for all approved machines. There are three utilities provided with the SSL. SKTDBG can be used to debug programs that make use of the SSL. SPMTABLE lists the servers and port numbers on requested machine(s). SRMSRVR tells the PortMaster to forcibly remove a server name from its list. The package also includes two example programs: multiskt.c, which makes multiple accepts on one server, and sktpoll.c, which repeatedly attempts to connect a client to some server at one second intervals. SSL is a machine independent library written in the C-language for computers connected via Ethernet using the TCP/IP protocol. It has been successfully compiled and implemented on a variety of platforms, including Sun series computers running SunOS, DEC VAX series computers running VMS, SGI computers running IRIX, DECstations running ULTRIX, DEC alpha AXPs running OSF/1, IBM RS/6000 computers running AIX, IBM PC and compatibles running BSD/386 UNIX and HP Apollo 3000/4000/9000/400T computers running HP-UX. SSL requires 45K of RAM to run under SunOS and 80K of RAM to run under VMS. For use on IBM PC series computers and compatibles running DOS, SSL requires Microsoft C 6.0 and the Wollongong TCP/IP package. Source code for sample programs and debugging tools are provided. The documentation is available on the distribution medium in TeX and PostScript formats. The standard distribution medium for SSL is a .25 inch streaming magnetic tape cartridge (QIC-24) in UNIX tar format. It is also available on a 3.5 inch diskette in UNIX tar format and a 5.25 inch 360K MS-DOS format diskette. The SSL was developed in 1992 and was updated in 1993.

How do prosthetic stiffness, height and running speed affect the biomechanics of athletes with bilateral transtibial amputations?

PubMed Central

Taboga, Paolo; Grabowski, Alena M.

2017-01-01

Limited available information describes how running-specific prostheses and running speed affect the biomechanics of athletes with bilateral transtibial amputations. Accordingly, we quantified the effects of prosthetic stiffness, height and speed on the biomechanics of five athletes with bilateral transtibial amputations during treadmill running. Each athlete performed a set of running trials with 15 different prosthetic model, stiffness and height combinations. Each set of trials began with the athlete running on a force-measuring treadmill at 3 m s−1, subsequent trials incremented by 1 m s−1 until they achieved their fastest attainable speed. We collected ground reaction forces (GRFs) during each trial. Prosthetic stiffness, height and running speed each affected biomechanics. Specifically, with stiffer prostheses, athletes exhibited greater peak and stance average vertical GRFs (β = 0.03; p < 0.001), increased overall leg stiffness (β = 0.21; p < 0.001), decreased ground contact time (β = −0.07; p < 0.001) and increased step frequency (β = 0.042; p < 0.001). Prosthetic height inversely associated with step frequency (β = −0.021; p < 0.001). Running speed inversely associated with leg stiffness (β = −0.58; p < 0.001). Moreover, at faster running speeds, the effect of prosthetic stiffness and height on biomechanics was mitigated and unchanged, respectively. Thus, prosthetic stiffness, but not height, likely influences distance running performance more than sprinting performance for athletes with bilateral transtibial amputations. PMID:28659414

How do prosthetic stiffness, height and running speed affect the biomechanics of athletes with bilateral transtibial amputations?

PubMed

Beck, Owen N; Taboga, Paolo; Grabowski, Alena M

2017-06-01

Limited available information describes how running-specific prostheses and running speed affect the biomechanics of athletes with bilateral transtibial amputations. Accordingly, we quantified the effects of prosthetic stiffness, height and speed on the biomechanics of five athletes with bilateral transtibial amputations during treadmill running. Each athlete performed a set of running trials with 15 different prosthetic model, stiffness and height combinations. Each set of trials began with the athlete running on a force-measuring treadmill at 3 m s -1 , subsequent trials incremented by 1 m s -1 until they achieved their fastest attainable speed. We collected ground reaction forces (GRFs) during each trial. Prosthetic stiffness, height and running speed each affected biomechanics. Specifically, with stiffer prostheses, athletes exhibited greater peak and stance average vertical GRFs ( β = 0.03; p < 0.001), increased overall leg stiffness ( β = 0.21; p < 0.001), decreased ground contact time ( β = -0.07; p < 0.001) and increased step frequency ( β = 0.042; p < 0.001). Prosthetic height inversely associated with step frequency ( β = -0.021; p < 0.001). Running speed inversely associated with leg stiffness ( β = -0.58; p < 0.001). Moreover, at faster running speeds, the effect of prosthetic stiffness and height on biomechanics was mitigated and unchanged, respectively. Thus, prosthetic stiffness, but not height, likely influences distance running performance more than sprinting performance for athletes with bilateral transtibial amputations. © 2017 The Author(s).

Influence of Number of Contact Efforts on Running Performance During Game-Based Activities.

PubMed

Johnston, Rich D; Gabbett, Tim J; Jenkins, David G

2015-09-01

To determine the influence the number of contact efforts during a single bout has on running intensity during game-based activities and assess relationships between physical qualities and distances covered in each game. Eighteen semiprofessional rugby league players (age 23.6 ± 2.8 y) competed in 3 off-side small-sided games (2 × 10-min halves) with a contact bout performed every 2 min. The rules of each game were identical except for the number of contact efforts performed in each bout. Players performed 1, 2, or 3 × 5-s wrestles in the single-, double-, and triple-contact game, respectively. The movement demands (including distance covered and intensity of exercise) in each game were monitored using global positioning system units. Bench-press and back-squat 1-repetition maximum and the 30-15 Intermittent Fitness Test (30-15IFT) assessed muscle strength and high-intensity-running ability, respectively. There was little change in distance covered during the single-contact game (ES = -0.16 to -0.61), whereas there were larger reductions in the double- (ES = -0.52 to -0.81) and triple-contact (ES = -0.50 to -1.15) games. Significant relationships (P < .05) were observed between 30-15IFT and high-speed running during the single- (r = .72) and double- (r = .75), but not triple-contact (r = .20) game. There is little change in running intensity when only single contacts are performed each bout; however, when multiple contacts are performed, greater reductions in running intensity result. In addition, high-intensity-running ability is only associated with running performance when contact demands are low.

Corticosterone administration in drinking water decreases high-fat diet intake but not preference in male rats

PubMed Central

Boersma, Gretha J.; Tamashiro, Kellie L.; Moran, Timothy H.

2016-01-01

One of the mechanisms through which regular exercise contributes to weight maintenance could be by reducing intake and preference for high-fat (HF) diets. Indeed, we previously demonstrated that wheel-running rats robustly reduced HF diet intake and preference. The reduced HF diet preference by wheel running can be so profound that the rats consumed only the chow diet and completely avoided the HF diet. Because previous research indicates that exercise activates the hypothalamic-pituitary-adrenal axis and increases circulating levels of corticosterone, this study tested the hypothesis that elevation of circulating corticosterone is involved in wheel running-induced reduction in HF diet preference in rats. Experiment 1 measured plasma corticosterone levels under sedentary and wheel-running conditions in the two-diet-choice (high-carbohydrate chow vs. HF) feeding regimen. The results revealed that plasma corticosterone is significantly increased and positively correlated with the levels of running in wheel-running rats with two-diet choice. Experiments 2 and 3 determined whether elevated corticosterone without wheel running is sufficient to reduce HF diet intake and preference. Corticosterone was elevated by adding it to the drinking water. Compared with controls, corticosterone-drinking rats had reduced HF diet intake and body weight, but the HF diet preference between groups did not differ. The results of this study support a role for elevated corticosterone on the reduced HF diet intake during wheel running. The elevation of corticosterone alone, however, is not sufficient to produce a robust reduction in HF diet preference. PMID:26818055

Corticosterone administration in drinking water decreases high-fat diet intake but not preference in male rats.

PubMed

Boersma, Gretha J; Tamashiro, Kellie L; Moran, Timothy H; Liang, Nu-Chu

2016-04-15

One of the mechanisms through which regular exercise contributes to weight maintenance could be by reducing intake and preference for high-fat (HF) diets. Indeed, we previously demonstrated that wheel-running rats robustly reduced HF diet intake and preference. The reduced HF diet preference by wheel running can be so profound that the rats consumed only the chow diet and completely avoided the HF diet. Because previous research indicates that exercise activates the hypothalamic-pituitary-adrenal axis and increases circulating levels of corticosterone, this study tested the hypothesis that elevation of circulating corticosterone is involved in wheel running-induced reduction in HF diet preference in rats.Experiment 1 measured plasma corticosterone levels under sedentary and wheel-running conditions in the two-diet-choice (high-carbohydrate chow vs. HF) feeding regimen. The results revealed that plasma corticosterone is significantly increased and positively correlated with the levels of running in wheel-running rats with two-diet choice.Experiments 2 and 3 determined whether elevated corticosterone without wheel running is sufficient to reduce HF diet intake and preference. Corticosterone was elevated by adding it to the drinking water. Compared with controls, corticosterone-drinking rats had reduced HF diet intake and body weight, but the HF diet preference between groups did not differ. The results of this study support a role for elevated corticosterone on the reduced HF diet intake during wheel running. The elevation of corticosterone alone, however, is not sufficient to produce a robust reduction in HF diet preference. Copyright © 2016 the American Physiological Society.

Water availability in +2°C and +4°C worlds.

PubMed

Fung, Fai; Lopez, Ana; New, Mark

2011-01-13

While the parties to the UNFCCC agreed in the December 2009 Copenhagen Accord that a 2°C global warming over pre-industrial levels should be avoided, current commitments on greenhouse gas emissions reductions from these same parties will lead to a 50 : 50 chance of warming greater than 3.5°C. Here, we evaluate the differences in impacts and adaptation issues for water resources in worlds corresponding to the policy objective (+2°C) and possible reality (+4°C). We simulate the differences in impacts on surface run-off and water resource availability using a global hydrological model driven by ensembles of climate models with global temperature increases of 2°C and 4°C. We combine these with UN-based population growth scenarios to explore the relative importance of population change and climate change for water availability. We find that the projected changes in global surface run-off from the ensemble show an increase in spatial coherence and magnitude for a +4°C world compared with a +2°C one. In a +2°C world, population growth in most large river basins tends to override climate change as a driver of water stress, while in a +4°C world, climate change becomes more dominant, even compensating for population effects where climate change increases run-off. However, in some basins where climate change has positive effects, the seasonality of surface run-off becomes increasingly amplified in a +4°C climate.

Computational Approaches to Simulation and Optimization of Global Aircraft Trajectories

NASA Technical Reports Server (NTRS)

Ng, Hok Kwan; Sridhar, Banavar

2016-01-01

This study examines three possible approaches to improving the speed in generating wind-optimal routes for air traffic at the national or global level. They are: (a) using the resources of a supercomputer, (b) running the computations on multiple commercially available computers and (c) implementing those same algorithms into NASAs Future ATM Concepts Evaluation Tool (FACET) and compares those to a standard implementation run on a single CPU. Wind-optimal aircraft trajectories are computed using global air traffic schedules. The run time and wait time on the supercomputer for trajectory optimization using various numbers of CPUs ranging from 80 to 10,240 units are compared with the total computational time for running the same computation on a single desktop computer and on multiple commercially available computers for potential computational enhancement through parallel processing on the computer clusters. This study also re-implements the trajectory optimization algorithm for further reduction of computational time through algorithm modifications and integrates that with FACET to facilitate the use of the new features which calculate time-optimal routes between worldwide airport pairs in a wind field for use with existing FACET applications. The implementations of trajectory optimization algorithms use MATLAB, Python, and Java programming languages. The performance evaluations are done by comparing their computational efficiencies and based on the potential application of optimized trajectories. The paper shows that in the absence of special privileges on a supercomputer, a cluster of commercially available computers provides a feasible approach for national and global air traffic system studies.

[Facts and fiction about running shoes].

PubMed

Schelde, Jacob

2012-11-26

Running as a means of exercise is becoming increasingly popular, but the rate of injury is very high among runners. To prevent running-related injuries much attention has been given the running shoe and its construction, particular its shock-absorbing capabilities and motion control features. It is recommended that running shoes should be purchased based on the runner's medial arch height and degree of pronation, and that the shoes should be changed frequently as their shock-absorbing capabilities decrease with usage. Randomized controlled trials and other studies in the scientific literature do not support these recommendations.

runDM: Running couplings of Dark Matter to the Standard Model

NASA Astrophysics Data System (ADS)

D'Eramo, Francesco; Kavanagh, Bradley J.; Panci, Paolo

2018-02-01

runDM calculates the running of the couplings of Dark Matter (DM) to the Standard Model (SM) in simplified models with vector mediators. By specifying the mass of the mediator and the couplings of the mediator to SM fields at high energy, the code can calculate the couplings at low energy, taking into account the mixing of all dimension-6 operators. runDM can also extract the operator coefficients relevant for direct detection, namely low energy couplings to up, down and strange quarks and to protons and neutrons.

The seasonal-cycle climate model

NASA Technical Reports Server (NTRS)

Marx, L.; Randall, D. A.

1981-01-01

The seasonal cycle run which will become the control run for the comparison with runs utilizing codes and parameterizations developed by outside investigators is discussed. The climate model currently exists in two parallel versions: one running on the Amdahl and the other running on the CYBER 203. These two versions are as nearly identical as machine capability and the requirement for high speed performance will allow. Developmental changes are made on the Amdahl/CMS version for ease of testing and rapidity of turnaround. The changes are subsequently incorporated into the CYBER 203 version using vectorization techniques where speed improvement can be realized. The 400 day seasonal cycle run serves as a control run for both medium and long range climate forecasts alsensitivity studies.

Fermilab DART run control

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

Oleynik, G.; Engelfried, J.; Mengel, L.

1996-02-01

DART is the high speed, Unix based data acquisition system being developed by Fermilab in collaboration with seven High Energy Physics Experiments. This paper describes DART run control, which has been developed over the past year and is a flexible, distributed, extensible system for the control and monitoring of the data acquisition systems. The authors discuss the unique and interesting concepts of the run control and some of the experiences in developing it. They also give a brief update and status of the whole DART system.

Fermilab DART run control

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

Oleynik, G.; Engelfried, J.; Mengel, L.

1995-05-01

DART is the high speed, Unix based data acquisition system being developed by Fermilab in collaboration with seven High Energy Physics Experiments. This paper describes DART run control, which has been developed over the past year and is a flexible, distributed, extensible system for the, control and monitoring of the data acquisition systems. We discuss the unique and interesting concepts of the run control and some of our experiences in developing it. We also give a brief update and status of the whole DART system.

Match-to-match variation in physical activity and technical skill measures in professional Australian Football.

PubMed

Kempton, Thomas; Sullivan, Courtney; Bilsborough, Johann C; Cordy, Justin; Coutts, Aaron J

2015-01-01

To determine the match-to-match variability in physical activity and technical performance measures in Australian Football, and examine the influence of playing position, time of season, and different seasons on these measures of variability. Longitudinal observational study. Global positioning system, accelerometer and technical performance measures (total kicks, handballs, possessions and Champion Data rank) were collected from 33 players competing in the Australian Football League over 31 matches during 2011-2012 (N=511 observations). The global positioning system data were categorised into total distance, mean speed (mmin(-1)), high-speed running (>14.4 kmh(-1)), very high-speed running (>19.9 kmh(-1)), and sprint (>23.0 kmh(-1)) distance while player load was collected from the accelerometer. The data were log transformed to provide coefficient of variation and the between subject standard deviation (expressed as percentages). Match-to-match variability was increased for higher speed activities (high-speed running, very high-speed running, sprint distance, coefficient of variation %: 13.3-28.6%) compared to global measures (speed, total distance, player load, coefficient of variation %: 5.3-9.2%). The between-match variability was relativity stable for all measures between and within AFL seasons, with only few differences between positions. Higher speed activities (high-speed running, very high-speed running, sprint distance), but excluding mean speed, total distance and player load, were all higher in the final third phase of the season compared to the start of the season. While global measures of physical performance are relatively stable, higher-speed activities and technical measures exhibit a large degree of between-match variability in Australian Football. However, these measures remain relatively stable between positions, and within and between Australian Football League seasons. Copyright © 2013 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

Lipid droplet-associated proteins in high-fat fed mice with the effects of voluntary running and diet change.

PubMed

Rinnankoski-Tuikka, Rita; Hulmi, Juha J; Torvinen, Sira; Silvennoinen, Mika; Lehti, Maarit; Kivelä, Riikka; Reunanen, Hilkka; Kujala, Urho M; Kainulainen, Heikki

2014-08-01

The relation between lipid accumulation and influence of exercise on insulin sensitivity is not straightforward. A proper balance between lipid droplet synthesis, lipolysis, and oxidative metabolism would ensure low local intramyocellular fatty acid levels, thereby possibly protecting against lipotoxicity-associated insulin resistance. This study investigated whether the accumulation of triglycerides and lipid droplets in response to high availability of fatty acids after high-fat feeding would parallel the abundance of intramyocellular perilipin proteins, especially PLIN5. The effects on these variables after diet change or voluntary running exercise intervention in skeletal muscle were also investigated. During a 19-week experiment, C57BL/6J mice were studied in six different groups: low-fat diet sedentary, low-fat diet active, high-fat diet sedentary, high-fat diet active and two groups which were high-fat sedentary for nine weeks, after which divided into low-fat sedentary or low-fat active groups. Myocellular triglyceride concentration and perilipin protein expression levels were assessed. We show that, concurrently with impaired insulin sensitivity, the expression level of PLIN5 and muscular triglyceride concentration increased dramatically after high-fat diet. These adaptations were reversible after the diet change intervention with no additional effect of exercise. After high-fat diet, lipid droplets become larger providing more surface area for PLIN5. We suggest that PLIN5 is an important regulator of lipid droplet turnover in altered conditions of fatty acid supply and consumption. Imbalances in lipid droplet metabolism and turnover might lead to lipotoxicity-related insulin resistance. Copyright © 2014 Elsevier Inc. All rights reserved.

Spontaneous running activity in male rats - Effect of age

NASA Technical Reports Server (NTRS)

Mondon, C. E.; Dolkas, C. B.; Sims, C.; Reaven, G. M.

1985-01-01

Variations in the intensity and the patterns of spontaneous running activity in wheel cages were studied in male rats aged 7 weeks to one year. Daily running records were obtained for periods of 12 mo, and 24-hour recordings were made for selected runners in order to study variations in running activity during the day. The data indicate that for rats running over two miles/day, the maximum running intensity can be divided into two groups: a group of high achievers running 8 miles/day; and a group of moderate achievers running 4.8 miles/day. For both groups spontaneous activity reached a maximum after 4-5 weeks. An hourly pattern of running activity during the day was identified in rats of increasing age who averaged 9.0, 4.5, 2.6, and 1.2 miles/day, respectively. Progressive losses were observed in both the speed and the duration of spontaneous running as the rats increased in age, with the intensity of exercise falling below 2 miles/day after 7-8 months of age.

WinHPC System Programming | High-Performance Computing | NREL

Science.gov Websites

Programming WinHPC System Programming Learn how to build and run an MPI (message passing interface (mpi.h) and library (msmpi.lib) are. To build from the command line, run... Start > Intel Software Development Tools > Intel C++ Compiler Professional... > C++ Build Environment for applications running

Simulated single molecule microscopy with SMeagol.

PubMed

Lindén, Martin; Ćurić, Vladimir; Boucharin, Alexis; Fange, David; Elf, Johan

2016-08-01

SMeagol is a software tool to simulate highly realistic microscopy data based on spatial systems biology models, in order to facilitate development, validation and optimization of advanced analysis methods for live cell single molecule microscopy data. SMeagol runs on Matlab R2014 and later, and uses compiled binaries in C for reaction-diffusion simulations. Documentation, source code and binaries for Mac OS, Windows and Ubuntu Linux can be downloaded from http://smeagol.sourceforge.net johan.elf@icm.uu.se Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Continuous flow room temperature reductive aqueous homo-coupling of aryl halides using supported Pd catalysts

PubMed Central

Feiz, Afsaneh; Bazgir, Ayoob; Balu, Alina M.; Luque, Rafael

2016-01-01

A convenient and environmentally friendly protocol for the preparation of biaryls at room temperature under continuous flow conditions is reported. A simple reductive homo-coupling Ullmann-type reaction was performed in an H-Cube mini using commercially available supported Pd catalysts under mild reaction conditions, with quantitative conversion to target products. Commercial Pd catalysts were found to be highly stable under the investigated reaction conditions, with a minimum Pd leaching into solution after several reaction runs (ca. 20 h on stream). PMID:27600989

Automatic Between-Pulse Analysis of DIII-D Experimental Data Performed Remotely on a Supercomputer at Argonne Leadership Computing Facility

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

Kostuk, M.; Uram, T. D.; Evans, T.

For the first time, an automatically triggered, between-pulse fusion science analysis code was run on-demand at a remotely located supercomputer at Argonne Leadership Computing Facility (ALCF, Lemont, IL) in support of in-process experiments being performed at DIII-D (San Diego, CA). This represents a new paradigm for combining geographically distant experimental and high performance computing (HPC) facilities to provide enhanced data analysis that is quickly available to researchers. Enhanced analysis improves the understanding of the current pulse, translating into a more efficient use of experimental resources, and to the quality of the resultant science. The analysis code used here, called SURFMN,more » calculates the magnetic structure of the plasma using Fourier transform. Increasing the number of Fourier components provides a more accurate determination of the stochastic boundary layer near the plasma edge by better resolving magnetic islands, but requires 26 minutes to complete using local DIII-D resources, putting it well outside the useful time range for between pulse analysis. These islands relate to confinement and edge localized mode (ELM) suppression, and may be controlled by adjusting coil currents for the next pulse. Argonne has ensured on-demand execution of SURFMN by providing a reserved queue, a specialized service that launches the code after receiving an automatic trigger, and with network access from the worker nodes for data transfer. Runs are executed on 252 cores of ALCF’s Cooley cluster and the data is available locally at DIII-D within three minutes of triggering. The original SURFMN design limits additional improvements with more cores, however our work shows a path forward where codes that benefit from thousands of processors can run between pulses.« less

Automatic Between-Pulse Analysis of DIII-D Experimental Data Performed Remotely on a Supercomputer at Argonne Leadership Computing Facility

DOE PAGES

Kostuk, M.; Uram, T. D.; Evans, T.; ...

2018-02-01

For the first time, an automatically triggered, between-pulse fusion science analysis code was run on-demand at a remotely located supercomputer at Argonne Leadership Computing Facility (ALCF, Lemont, IL) in support of in-process experiments being performed at DIII-D (San Diego, CA). This represents a new paradigm for combining geographically distant experimental and high performance computing (HPC) facilities to provide enhanced data analysis that is quickly available to researchers. Enhanced analysis improves the understanding of the current pulse, translating into a more efficient use of experimental resources, and to the quality of the resultant science. The analysis code used here, called SURFMN,more » calculates the magnetic structure of the plasma using Fourier transform. Increasing the number of Fourier components provides a more accurate determination of the stochastic boundary layer near the plasma edge by better resolving magnetic islands, but requires 26 minutes to complete using local DIII-D resources, putting it well outside the useful time range for between pulse analysis. These islands relate to confinement and edge localized mode (ELM) suppression, and may be controlled by adjusting coil currents for the next pulse. Argonne has ensured on-demand execution of SURFMN by providing a reserved queue, a specialized service that launches the code after receiving an automatic trigger, and with network access from the worker nodes for data transfer. Runs are executed on 252 cores of ALCF’s Cooley cluster and the data is available locally at DIII-D within three minutes of triggering. The original SURFMN design limits additional improvements with more cores, however our work shows a path forward where codes that benefit from thousands of processors can run between pulses.« less

Strain screen and haplotype association mapping of wheel running in inbred mouse strains.

PubMed

Lightfoot, J Timothy; Leamy, Larry; Pomp, Daniel; Turner, Michael J; Fodor, Anthony A; Knab, Amy; Bowen, Robert S; Ferguson, David; Moore-Harrison, Trudy; Hamilton, Alicia

2010-09-01

Previous genetic association studies of physical activity, in both animal and human models, have been limited in number of subjects and genetically homozygous strains used as well as number of genomic markers available for analysis. Expansion of the available mouse physical activity strain screens and the recently published dense single-nucleotide polymorphism (SNP) map of the mouse genome (approximately 8.3 million SNPs) and associated statistical methods allowed us to construct a more generalizable map of the quantitative trait loci (QTL) associated with physical activity. Specifically, we measured wheel running activity in male and female mice (average age 9 wk) in 41 inbred strains and used activity data from 38 of these strains in a haplotype association mapping analysis to determine QTL associated with activity. As seen previously, there was a large range of activity patterns among the strains, with the highest and lowest strains differing significantly in daily distance run (27.4-fold), duration of activity (23.6-fold), and speed (2.9-fold). On a daily basis, female mice ran further (24%), longer (13%), and faster (11%). Twelve QTL were identified, with three (on Chr. 12, 18, and 19) in both male and female mice, five specific to males, and four specific to females. Eight of the 12 QTL, including the 3 general QTL found for both sexes, fell into intergenic areas. The results of this study further support the findings of a moderate to high heritability of physical activity and add general genomic areas applicable to a large number of mouse strains that can be further mined for candidate genes associated with regulation of physical activity. Additionally, results suggest that potential genetic mechanisms arising from traditional noncoding regions of the genome may be involved in regulation of physical activity.

AWIPS II in the University Community: Unidata's efforts and capabilities of the software

NASA Astrophysics Data System (ADS)

Ramamurthy, Mohan; James, Michael

2015-04-01

The Advanced Weather Interactive Processing System, version II (AWIPS II) is a weather forecasting, display and analysis tool that is used by the National Oceanic and Atmospheric Administration/National Weather Service (NOAA/NWS) and the National Centers for Environmental Prediction (NCEP) to ingest analyze and disseminate operational weather data. The AWIPS II software is built on a Service Oriented Architecture, takes advantage of open source software, and its design affords expandability, flexibility, and portability. Since many university meteorology programs are eager to use the same tools used by NWS forecasters, Unidata community interest in AWIPS II is high. The Unidata Program Center (UPC) has worked closely with NCEP staff during AWIPS II development in order to devise a way to make it available to the university. The Unidata AWIPS II software was released in beta form in 2014, and it incorporates a number of key changes to the baseline U. S. National Weather Service release to process and display additional data formats and run all components in a single-server standalone configuration. In addition to making available open-source instances of the software libraries that can be downloaded and run at any university, Unidata has also deployed the data-server side of AWIPS II, known as EDEX, in the Amazon Web Service and Microsoft Azure cloud environments. In this set up, universities receive all of the data from remote cloud instances, while they only have to run the AWIPS II client, known as CAVE, to analyze and visualize the data. In this presentation, we will describe Unidata's AWIPS II efforts, including the capabilities of the software in visualizing many different types of real-time meteorological data and its myriad uses in university and other settings.

A high-resolution global-scale groundwater model

NASA Astrophysics Data System (ADS)

de Graaf, I. E. M.; Sutanudjaja, E. H.; van Beek, L. P. H.; Bierkens, M. F. P.

2015-02-01

Groundwater is the world's largest accessible source of fresh water. It plays a vital role in satisfying basic needs for drinking water, agriculture and industrial activities. During times of drought groundwater sustains baseflow to rivers and wetlands, thereby supporting ecosystems. Most global-scale hydrological models (GHMs) do not include a groundwater flow component, mainly due to lack of geohydrological data at the global scale. For the simulation of lateral flow and groundwater head dynamics, a realistic physical representation of the groundwater system is needed, especially for GHMs that run at finer resolutions. In this study we present a global-scale groundwater model (run at 6' resolution) using MODFLOW to construct an equilibrium water table at its natural state as the result of long-term climatic forcing. The used aquifer schematization and properties are based on available global data sets of lithology and transmissivities combined with the estimated thickness of an upper, unconfined aquifer. This model is forced with outputs from the land-surface PCRaster Global Water Balance (PCR-GLOBWB) model, specifically net recharge and surface water levels. A sensitivity analysis, in which the model was run with various parameter settings, showed that variation in saturated conductivity has the largest impact on the groundwater levels simulated. Validation with observed groundwater heads showed that groundwater heads are reasonably well simulated for many regions of the world, especially for sediment basins (R2 = 0.95). The simulated regional-scale groundwater patterns and flow paths demonstrate the relevance of lateral groundwater flow in GHMs. Inter-basin groundwater flows can be a significant part of a basin's water budget and help to sustain river baseflows, especially during droughts. Also, water availability of larger aquifer systems can be positively affected by additional recharge from inter-basin groundwater flows.

Evaluation of a handheld point-of-care analyser for measurement of creatinine in cats.

PubMed

Reeve, Jenny; Warman, Sheena; Lewis, Daniel; Watson, Natalie; Papasouliotis, Kostas

2017-02-01

Objectives The aim of the study was to evaluate whether a handheld creatinine analyser (StatSensor Xpress; SSXp), available for human patients, can be used to measure creatinine reliably in cats. Methods Analytical performance was evaluated by determining within- and between-run coefficient of variation (CV, %), total error observed (TE obs , %) and sigma metrics. Fifty client-owned cats presenting for investigation of clinical disease had creatinine measured simultaneously, using SSXp (whole blood and plasma) and a reference instrument (Konelab, serum); 48 paired samples were included in the study. Creatinine correlation between methodologies (SSXp vs Konelab) and sample types (SSXp whole blood vs SSXp plasma ) was assessed by Spearman's correlation coefficient and agreement was determined using Bland-Altman difference plots. Each creatinine value was assigned an IRIS stage (1-4); correlation and agreement between Konelab and SSXp IRIS stages were evaluated. Results Within-run CV (4.23-8.85%), between-run CV (8.95-11.72%), TE obs (22.15-34.92%) and sigma metrics (⩽3) did not meet desired analytical requirements. Correlation between sample types was high (SSXp whole blood vs SSXp plasma ; r = 0.89), and between instruments was high (SSXp whole blood vs Konelab serum ; r = 0.85) to very high (SSXp plasma vs Konelab serum ; r = 0.91). Konelab and SSXp whole blood IRIS scores exhibited high correlation ( r = 0.76). Packed cell volume did not significantly affect SSXp determination of creatinine. Bland-Altman difference plots identified a positive bias for the SSXp (7.13 μmol/l SSXp whole blood ; 20.23 μmol/l SSXp plasma ) compared with the Konelab. Outliers (1/48 whole blood; 2/48 plasma) occurred exclusively at very high creatinine concentrations. The SSXp failed to identify 2/21 azotaemic cats. Conclusions and relevance Analytical performance of the SSXp in feline patients is not considered acceptable. The SSXp exhibited a high to very high correlation compared with the reference methodology but the two instruments cannot be used interchangeably. Improvements in the SSXp analytical performance are needed before its use can be recommended in feline clinical practice.

A new code SORD for simulation of polarized light scattering in the Earth atmosphere

NASA Astrophysics Data System (ADS)

Korkin, Sergey; Lyapustin, Alexei; Sinyuk, Aliaksandr; Holben, Brent

2016-05-01

We report a new publicly available radiative transfer (RT) code for numerical simulation of polarized light scattering in plane-parallel Earth atmosphere. Using 44 benchmark tests, we prove high accuracy of the new RT code, SORD (Successive ORDers of scattering1, 2). We describe capabilities of SORD and show run time for each test on two different machines. At present, SORD is supposed to work as part of the Aerosol Robotic NETwork3 (AERONET) inversion algorithm. For natural integration with the AERONET software, SORD is coded in Fortran 90/95. The code is available by email request from the corresponding (first) author or from ftp://climate1.gsfc.nasa.gov/skorkin/SORD/ or ftp://maiac.gsfc.nasa.gov/pub/SORD.zip

Text mining meets workflow: linking U-Compare with Taverna

PubMed Central

Kano, Yoshinobu; Dobson, Paul; Nakanishi, Mio; Tsujii, Jun'ichi; Ananiadou, Sophia

2010-01-01

Summary: Text mining from the biomedical literature is of increasing importance, yet it is not easy for the bioinformatics community to create and run text mining workflows due to the lack of accessibility and interoperability of the text mining resources. The U-Compare system provides a wide range of bio text mining resources in a highly interoperable workflow environment where workflows can very easily be created, executed, evaluated and visualized without coding. We have linked U-Compare to Taverna, a generic workflow system, to expose text mining functionality to the bioinformatics community. Availability: http://u-compare.org/taverna.html, http://u-compare.org Contact: kano@is.s.u-tokyo.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20709690

Commercial-scale utilization of greenhouse residues.

PubMed

Maroušek, Josef; Kondo, Yoshikazu; Ueno, Masami; Kawamitsu, Yoshinobu

2013-01-01

Development of techniques utilizing waste without any additional energy or rare catalysts is a starting point for becoming sustainable. In the present work, the complex utilization of greenhouse residues was studied on a commercial scale. Only the energy produced by the process (8%) was used to run the technology, thanks to multilevel heat recuperation and high methane yields (over 340 m(3) volatile solid t(-1) ). Manifestations of labile carbon in relation to available nitrogen, methane yields, and the formation of inhibitors were investigated in detail. The results sweep away many false beliefs about the ratios of carbon to nitrogen and highlight the role of the availability of carbon in phytomass utilization. © 2013 International Union of Biochemistry and Molecular Biology, Inc.

Salinity changes and anoxia resulting from enhanced run-off during the late Permian global warming and mass extinction event

NASA Astrophysics Data System (ADS)

van Soelen, Elsbeth E.; Twitchett, Richard J.; Kürschner, Wolfram M.

2018-04-01

The late Permian biotic crisis had a major impact on marine and terrestrial environments. Rising CO2 levels following Siberian Trap volcanic activity were likely responsible for expanding marine anoxia and elevated water temperatures. This study focuses on one of the stratigraphically most expanded Permian-Triassic records known, from Jameson Land, East Greenland. High-resolution sampling allows for a detailed reconstruction of the changing environmental conditions during the extinction event and the development of anoxic water conditions. Since very little is known about how salinity was affected during the extinction event, we especially focus on the aquatic palynomorphs and infer changes in salinity from changes in the assemblage and morphology. The start of the extinction event, here defined by a peak in spore : pollen, indicating disturbance and vegetation destruction in the terrestrial environment, postdates a negative excursion in the total organic carbon, but predates the development of anoxia in the basin. Based on the newest estimations for sedimentation rates, the marine and terrestrial ecosystem collapse took between 1.6 and 8 kyr, a much shorter interval than previously estimated. The palynofacies and palynomorph records show that the environmental changes can be explained by enhanced run-off and increased primary productivity and water column stratification. A lowering in salinity is supported by changes in the acritarch morphology. The length of the processes of the acritarchs becomes shorter during the extinction event and we propose that these changes are evidence for a reduction in salinity in the shallow marine setting of the study site. This inference is supported by changes in acritarch distribution, which suggest a change in palaeoenvironment from open marine conditions before the start of the extinction event to more nearshore conditions during and after the crisis. In a period of sea-level rise, such a reduction in salinity can only be explained by increased run-off. High amounts of both terrestrial and marine organic fragments in the first anoxic layers suggest that high run-off, increased nutrient availability, possibly in combination with soil erosion, are responsible for the development of anoxia in the basin. Enhanced run-off could result from changes in the hydrological cycle during the late Permian extinction event, which is a likely consequence of global warming. In addition, vegetation destruction and soil erosion may also have resulted in enhanced run-off. Salinity stratification could potentially explain the development of anoxia in other shallow marine sites. The input of freshwater and related changes in coastal salinity could also have implications for the interpretation of oxygen isotope records and seawater temperature reconstructions at some sites.

RHIC Prefire Protection Masks

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

Drees, A.; Biscardi, C.; Curcio, T.

2015-01-07

The protection of the RHIC experimental detectors from damage due to beam hitting close upstream elements in cases of abort kicker prefires requires some dedicated precautionary measures with two general options: to bring the beam close to a limiting aperture (i.e. the beam pipe wall), as far upstream of the detector components as possible or, alternatively, to bring a limiting aperture close to the circulating beam. During the FY 2014 RHIC Heavy Ion run the first option was chosen because of the limited time available for preparation before the start of the run. For future runs the second option, inmore » this case the installation of dual-sided movable masks, is preferred. The installation of the masks, one per ring, is planned before the start of the FY 2015 run.« less

Development and Implementation of Dynamic Scripts to Support Local Model Verification at National Weather Service Weather Forecast Offices

NASA Technical Reports Server (NTRS)

Zavordsky, Bradley; Case, Jonathan L.; Gotway, John H.; White, Kristopher; Medlin, Jeffrey; Wood, Lance; Radell, Dave

2014-01-01

Local modeling with a customized configuration is conducted at National Weather Service (NWS) Weather Forecast Offices (WFOs) to produce high-resolution numerical forecasts that can better simulate local weather phenomena and complement larger scale global and regional models. The advent of the Environmental Modeling System (EMS), which provides a pre-compiled version of the Weather Research and Forecasting (WRF) model and wrapper Perl scripts, has enabled forecasters to easily configure and execute the WRF model on local workstations. NWS WFOs often use EMS output to help in forecasting highly localized, mesoscale features such as convective initiation, the timing and inland extent of lake effect snow bands, lake and sea breezes, and topographically-modified winds. However, quantitatively evaluating model performance to determine errors and biases still proves to be one of the challenges in running a local model. Developed at the National Center for Atmospheric Research (NCAR), the Model Evaluation Tools (MET) verification software makes performing these types of quantitative analyses easier, but operational forecasters do not generally have time to familiarize themselves with navigating the sometimes complex configurations associated with the MET tools. To assist forecasters in running a subset of MET programs and capabilities, the Short-term Prediction Research and Transition (SPoRT) Center has developed and transitioned a set of dynamic, easily configurable Perl scripts to collaborating NWS WFOs. The objective of these scripts is to provide SPoRT collaborating partners in the NWS with the ability to evaluate the skill of their local EMS model runs in near real time with little prior knowledge of the MET package. The ultimate goal is to make these verification scripts available to the broader NWS community in a future version of the EMS software. This paper provides an overview of the SPoRT MET scripts, instructions for how the scripts are run, and example use cases.

Regional sea level variability in a high-resolution global coupled climate model

NASA Astrophysics Data System (ADS)

Palko, D.; Kirtman, B. P.

2016-12-01

The prediction of trends at regional scales is essential in order to adapt to and prepare for the effects of climate change. However, GCMs are unable to make reliable predictions at regional scales. The prediction of local sea level trends is particularly critical. The main goal of this research is to utilize high-resolution (HR) (0.1° resolution in the ocean) coupled model runs of CCSM4 to analyze regional sea surface height (SSH) trends. Unlike typical, lower resolution (1.0°) GCM runs these HR runs resolve features in the ocean, like the Gulf Stream, which may have a large effect on regional sea level. We characterize the variability of regional SSH along the Atlantic coast of the US using tide gauge observations along with fixed radiative forcing runs of CCSM4 and HR interactive ensemble runs. The interactive ensemble couples an ensemble mean atmosphere with a single ocean realization. This coupling results in a 30% decrease in the strength of the Atlantic meridional overturning circulation; therefore, the HR interactive ensemble is analogous to a HR hosing experiment. By characterizing the variability in these high-resolution GCM runs and observations we seek to understand what processes influence coastal SSH along the Eastern Coast of the United States and better predict future SLR.

Overview of Proposal on High Resolution Climate Model Simulations of Recent Hurricane and Typhoon Activity: The Impact of SSTs and the Madden Julian Oscillation

NASA Technical Reports Server (NTRS)

Schubert, Siegfried; Kang, In-Sik; Reale, Oreste

2009-01-01

This talk gives an update on the progress and further plans for a coordinated project to carry out and analyze high-resolution simulations of tropical storm activity with a number of state-of-the-art global climate models. Issues addressed include, the mechanisms by which SSTs control tropical storm. activity on inter-annual and longer time scales, the modulation of that activity by the Madden Julian Oscillation on sub-seasonal time scales, as well as the sensitivity of the results to model formulation. The project also encourages companion coarser resolution runs to help assess resolution dependence, and. the ability of the models to capture the large-scale and long-terra changes in the parameters important for hurricane development. Addressing the above science questions is critical to understanding the nature of the variability of the Asian-Australian monsoon and its regional impacts, and thus CLIVAR RAMP fully endorses the proposed tropical storm simulation activity. The project is open to all interested organizations and investigators, and the results from the runs will be shared among the participants, as well as made available to the broader scientific community for analysis.

Preparation time influences ankle and knee joint control during dynamic change of direction movements.

PubMed

Fuerst, Patrick; Gollhofer, Albert; Gehring, Dominic

2017-04-01

The influence of preparation time on ankle joint biomechanics during highly dynamic movements is largely unknown. The aim of this study was to evaluate the impact of limited preparation time on ankle joint loading during highly dynamic run-and-cut movements. Thirteen male basketball players performed 45°-sidestep-cutting and 180°-turning manoeuvres in reaction to light signals which appeared during the approach run. Both movements were executed under (1) an easy condition, in which the light signal appeared very early, (2) a medium condition and (3) a hard condition with very little time to prepare the movements. Maximum ankle inversion angles, moments and velocities during ground contact, as well as EMG signals of three lower extremity muscles, were analysed. In 180°-turning movements, reduced preparation time led to significantly increased maximum ankle inversion velocities. Muscular activation levels, however, did not change. Increased inversion velocities, without accompanying changes in muscular activation, may have the potential to destabilise the ankle joint when less preparation time is available. This may result in a higher injury risk during turning movements and should therefore be considered in ankle injury research and the aetiology of ankle sprains.

THE MIRA–TITAN UNIVERSE: PRECISION PREDICTIONS FOR DARK ENERGY SURVEYS

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

Heitmann, Katrin; Habib, Salman; Biswas, Rahul

2016-04-01

Large-scale simulations of cosmic structure formation play an important role in interpreting cosmological observations at high precision. The simulations must cover a parameter range beyond the standard six cosmological parameters and need to be run at high mass and force resolution. A key simulation-based task is the generation of accurate theoretical predictions for observables using a finite number of simulation runs, via the method of emulation. Using a new sampling technique, we explore an eight-dimensional parameter space including massive neutrinos and a variable equation of state of dark energy. We construct trial emulators using two surrogate models (the linear powermore » spectrum and an approximate halo mass function). The new sampling method allows us to build precision emulators from just 26 cosmological models and to systematically increase the emulator accuracy by adding new sets of simulations in a prescribed way. Emulator fidelity can now be continuously improved as new observational data sets become available and higher accuracy is required. Finally, using one ΛCDM cosmology as an example, we study the demands imposed on a simulation campaign to achieve the required statistics and accuracy when building emulators for investigations of dark energy.« less

The mira-titan universe. Precision predictions for dark energy surveys

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

Heitmann, Katrin; Bingham, Derek; Lawrence, Earl

2016-03-28

Large-scale simulations of cosmic structure formation play an important role in interpreting cosmological observations at high precision. The simulations must cover a parameter range beyond the standard six cosmological parameters and need to be run at high mass and force resolution. A key simulation-based task is the generation of accurate theoretical predictions for observables using a finite number of simulation runs, via the method of emulation. Using a new sampling technique, we explore an eight-dimensional parameter space including massive neutrinos and a variable equation of state of dark energy. We construct trial emulators using two surrogate models (the linear powermore » spectrum and an approximate halo mass function). The new sampling method allows us to build precision emulators from just 26 cosmological models and to systematically increase the emulator accuracy by adding new sets of simulations in a prescribed way. Emulator fidelity can now be continuously improved as new observational data sets become available and higher accuracy is required. Finally, using one ΛCDM cosmology as an example, we study the demands imposed on a simulation campaign to achieve the required statistics and accuracy when building emulators for investigations of dark energy.« less

The Effects of Runaway-Homeless Episodes on High School Dropout

ERIC Educational Resources Information Center

Aratani, Yumiko; Cooper, Janice L.

2015-01-01

This article uses data from the National Longitudinal Survey of Youth 1997 to examine the relationship between running away from home between the ages of 12 and 14 and dropping from high school among youth. Propensity score matching was conducted in estimating the effect of running away on high school dropout while controlling for confounding…

The effect of footwear on running performance and running economy in distance runners.

PubMed

Fuller, Joel T; Bellenger, Clint R; Thewlis, Dominic; Tsiros, Margarita D; Buckley, Jonathan D

2015-03-01

The effect of footwear on running economy has been investigated in numerous studies. However, no systematic review and meta-analysis has synthesised the available literature and the effect of footwear on running performance is not known. The aim of this systematic review and meta-analysis was to investigate the effect of footwear on running performance and running economy in distance runners, by reviewing controlled trials that compare different footwear conditions or compare footwear with barefoot. The Web of Science, Scopus, MEDLINE, CENTRAL (Cochrane Central Register of Controlled Trials), EMBASE, AMED (Allied and Complementary Medicine), CINAHL and SPORTDiscus databases were searched from inception up until April 2014. Included articles reported on controlled trials that examined the effects of footwear or footwear characteristics (including shoe mass, cushioning, motion control, longitudinal bending stiffness, midsole viscoelasticity, drop height and comfort) on running performance or running economy and were published in a peer-reviewed journal. Of the 1,044 records retrieved, 19 studies were included in the systematic review and 14 studies were included in the meta-analysis. No studies were identified that reported effects on running performance. Individual studies reported significant, but trivial, beneficial effects on running economy for comfortable and stiff-soled shoes [standardised mean difference (SMD) <0.12; P < 0.05), a significant small beneficial effect on running economy for cushioned shoes (SMD = 0.37; P < 0.05) and a significant moderate beneficial effect on running economy for training in minimalist shoes (SMD = 0.79; P < 0.05). Meta-analysis found significant small beneficial effects on running economy for light shoes and barefoot compared with heavy shoes (SMD < 0.34; P < 0.01) and for minimalist shoes compared with conventional shoes (SMD = 0.29; P < 0.01). A significant positive association between shoe mass and metabolic cost of running was identified (P < 0.01). Footwear with a combined shoe mass less than 440 g per pair had no detrimental effect on running economy. Certain models of footwear and footwear characteristics can improve running economy. Future research in footwear performance should include measures of running performance.

A Comparison of the Energetic Cost of Running in Marathon Racing Shoes.

PubMed

Hoogkamer, Wouter; Kipp, Shalaya; Frank, Jesse H; Farina, Emily M; Luo, Geng; Kram, Rodger

2018-04-01

Reducing the energetic cost of running seems the most feasible path to a sub-2-hour marathon. Footwear mass, cushioning, and bending stiffness each affect the energetic cost of running. Recently, prototype running shoes were developed that combine a new highly compliant and resilient midsole material with a stiff embedded plate. The aim of this study was to determine if, and to what extent, these newly developed running shoes reduce the energetic cost of running compared with established marathon racing shoes. 18 high-caliber athletes ran six 5-min trials (three shoes × two replicates) in prototype shoes (NP), and two established marathon shoes (NS and AB) during three separate sessions: 14, 16, and 18 km/h. We measured submaximal oxygen uptake and carbon dioxide production during minutes 3-5 and averaged energetic cost (W/kg) for the two trials in each shoe model. Compared with the established racing shoes, the new shoes reduced the energetic cost of running in all 18 subjects tested. Averaged across all three velocities, the energetic cost for running in the NP shoes (16.45 ± 0.89 W/kg; mean ± SD) was 4.16 and 4.01% lower than in the NS and AB shoes, when shoe mass was matched (17.16 ± 0.92 and 17.14 ± 0.97 W/kg, respectively, both p < 0.001). The observed percent changes were independent of running velocity (14-18 km/h). The prototype shoes lowered the energetic cost of running by 4% on average. We predict that with these shoes, top athletes could run substantially faster and achieve the first sub-2-hour marathon.

A Highly Scalable Data Service (HSDS) using Cloud-based Storage Technologies for Earth Science Data

NASA Astrophysics Data System (ADS)

Michaelis, A.; Readey, J.; Votava, P.; Henderson, J.; Willmore, F.

2017-12-01

Cloud based infrastructure may offer several key benefits of scalability, built in redundancy, security mechanisms and reduced total cost of ownership as compared with a traditional data center approach. However, most of the tools and legacy software systems developed for online data repositories within the federal government were not developed with a cloud based infrastructure in mind and do not fully take advantage of commonly available cloud-based technologies. Moreover, services bases on object storage are well established and provided through all the leading cloud service providers (Amazon Web Service, Microsoft Azure, Google Cloud, etc…) of which can often provide unmatched "scale-out" capabilities and data availability to a large and growing consumer base at a price point unachievable from in-house solutions. We describe a system that utilizes object storage rather than traditional file system based storage to vend earth science data. The system described is not only cost effective, but shows a performance advantage for running many different analytics tasks in the cloud. To enable compatibility with existing tools and applications, we outline client libraries that are API compatible with existing libraries for HDF5 and NetCDF4. Performance of the system is demonstrated using clouds services running on Amazon Web Services.

Running Speed Can Be Predicted from Foot Contact Time during Outdoor over Ground Running.

PubMed

de Ruiter, Cornelis J; van Oeveren, Ben; Francke, Agnieta; Zijlstra, Patrick; van Dieen, Jaap H

2016-01-01

The number of validation studies of commercially available foot pods that provide estimates of running speed is limited and these studies have been conducted under laboratory conditions. Moreover, internal data handling and algorithms used to derive speed from these pods are proprietary and thereby unclear. The present study investigates the use of foot contact time (CT) for running speed estimations, which potentially can be used in addition to the global positioning system (GPS) in situations where GPS performance is limited. CT was measured with tri axial inertial sensors attached to the feet of 14 runners, during natural over ground outdoor running, under optimized conditions for GPS. The individual relationships between running speed and CT were established during short runs at different speeds on two days. These relations were subsequently used to predict instantaneous speed during a straight line 4 km run with a single turning point halfway. Stopwatch derived speed, measured for each of 32 consecutive 125m intervals during the 4 km runs, was used as reference. Individual speed-CT relations were strong (r2 >0.96 for all trials) and consistent between days. During the 4km runs, median error (ranges) in predicted speed from CT 2.5% (5.2) was higher (P<0.05) than for GPS 1.6% (0.8). However, around the turning point and during the first and last 125m interval, error for GPS-speed increased to 5.0% (4.5) and became greater (P<0.05) than the error predicted from CT: 2.7% (4.4). Small speed fluctuations during 4km runs were adequately monitored with both methods: CT and GPS respectively explained 85% and 73% of the total speed variance during 4km runs. In conclusion, running speed estimates bases on speed-CT relations, have acceptable accuracy and could serve to backup or substitute for GPS during tarmac running on flat terrain whenever GPS performance is limited.

Reinventing the wheel: comparison of two wheel cage styles for assessing mouse voluntary running activity.

PubMed

Seward, T; Harfmann, B D; Esser, K A; Schroder, E A

2018-04-01

Voluntary wheel cage assessment of mouse activity is commonly employed in exercise and behavioral research. Currently, no standardization for wheel cages exists resulting in an inability to compare results among data from different laboratories. The purpose of this study was to determine whether the distance run or average speed data differ depending on the use of two commonly used commercially available wheel cage systems. Two different wheel cages with structurally similar but functionally different wheels (electromechanical switch vs. magnetic switch) were compared side-by-side to measure wheel running data differences. Other variables, including enrichment and cage location, were also tested to assess potential impacts on the running wheel data. We found that cages with the electromechanical switch had greater inherent wheel resistance and consistently led to greater running distance per day and higher average running speed. Mice rapidly, within 1-2 days, adapted their running behavior to the type of experimental switch used, suggesting these running differences are more behavioral than due to intrinsic musculoskeletal, cardiovascular, or metabolic limits. The presence of enrichment or location of the cage had no detectable impact on voluntary wheel running. These results demonstrate that mice run differing amounts depending on the type of cage and switch mechanism used and thus investigators need to report wheel cage type/wheel resistance and use caution when interpreting distance/speed run across studies. NEW & NOTEWORTHY The results of this study highlight that mice will run different distances per day and average speed based on the inherent resistance present in the switch mechanism used to record data. Rapid changes in running behavior for the same mouse in the different cages demonstrate that a strong behavioral factor contributes to classic exercise outcomes in mice. Caution needs to be taken when interpreting mouse voluntary wheel running activity to include potential behavioral input and physiological parameters.

Effects of leptin treatment and Western diet on wheel running in selectively bred high runner mice.

PubMed

Meek, Thomas H; Dlugosz, Elizabeth M; Vu, Kim T; Garland, Theodore

2012-05-15

The role of leptin in regulating physical activity is varied. The behavioral effects of leptin signaling depend on the type of activity and the animal's physiological state. We used mice from lines selectively bred for high voluntary wheel running to further study how leptin regulates volitional exercise. Mice from four replicate high runner (HR) lines typically run ~3-fold more revolutions per day than those from four non-selected control (C) lines. HR mice have altered dopamine function and differences from C in brain regions known to be important in leptin-mediated behavior. Furthermore, male HR mice have been found to dramatically increase running when administered Western diet, an effect possibly mediated through leptin signaling. Male mice from generation 61 (representing three HR lines and one C line) were allowed wheel access at 24 days of age and given either Western diet (high in fat and with added sucrose) or standard chow. After four weeks, Western diet significantly increased circulating leptin, insulin, C-peptide, gastric inhibitory polypeptide, and inflammatory hormone resistin concentrations in HR mice (C mice not measured). Western diet increased running in HR mice, but did not significantly affect running in C mice. During the fifth week, all mice received two days of intra-peritoneal sham injections (physiological saline) followed by three days of murine recombinant leptin injections, and then another six days of sham injections. Leptin treatment significantly decreased caloric intake (adjusted for body mass) and body mass in all groups. Wheel running significantly increased with leptin injections in HR mice (fed Western or standard diet), but was unaffected in C mice. Whether Western diet and leptin treatment stimulate wheel running in HR mice through the same physiological pathways awaits future study. These results have implications for understanding the neural and endocrine systems that control locomotor activity, food consumption, and body weight, and how they may vary with genetic background. Copyright © 2012 Elsevier Inc. All rights reserved.

Changes in mRNA levels for brain-derived neurotrophic factor after wheel running in rats selectively bred for high- and low-aerobic capacity

PubMed Central

Groves-Chapman, Jessica L.; Murray, Patrick S.; Stevens, Kristin L.; Monroe, Derek; Koch, Lauren G.; Britton, Steven L.; Holmes, Philip V.

2012-01-01

We evaluated levels of exercise-induced brain-derived neurotrophic factor (BDNF) messenger RNA (mRNA) within the hippocampal formation in rats selectively bred for 1) high intrinsic (i.e., untrained) aerobic capacity (High Capacity Runners, HCR), 2) low intrinsic aerobic capacity (Low Capacity Runners, LCR), and 3) unselected Sprague-Dawley (SD) rats with or without free access to running wheels for three weeks. The specific aim of the study was to determine whether a dose-response relationship exists between cumulative running distance and levels of BDNF mRNA. No additional treatments or behavioral manipulations were used. HCR, LCR, and SD rats were grouped by strain and randomly assigned to sedentary or activity (voluntary access to activity wheel) conditions. Animals were killed after 21 days of exposure to the assigned conditions. Daily running distances (mean ± standard deviation meters/d) during week three were: HCR (4726 ± 3220), SD (2293 ± 3461), LCR (672 ± 323). Regardless of strain, levels of BDNF mRNA in CA1 were elevated in wheel runners compared to sedentary rats and this difference persisted after adjustment for age (p=0.040). BDNF mRNA was not affected by intrinsic aerobic capacity and was not related to total running distance. The results support that BDNF mRNA expression is increased by unlimited access to activity wheel running for 3 weeks but is not dependent upon accumulated running distance. PMID:22024546

Exercise training effects on hypoxic and hypercapnic ventilatory responses in mice selected for increased voluntary wheel running.

PubMed

Kelly, Scott A; Rezende, Enrico L; Chappell, Mark A; Gomes, Fernando R; Kolb, Erik M; Malisch, Jessica L; Rhodes, Justin S; Mitchell, Gordon S; Garland, Theodore

2014-02-01

What is the central question of this study? We used experimental evolution to determine how selective breeding for high voluntary wheel running and exercise training (7-11 weeks) affect ventilatory chemoreflexes of laboratory mice at rest. What is the main finding and its importance? Selective breeding, although significantly affecting some traits, did not systematically alter ventilation across gas concentrations. As with most human studies, our findings support the idea that endurance training attenuates resting ventilation. However, little evidence was found for a correlation between ventilatory chemoreflexes and the amount of individual voluntary wheel running. We conclude that exercise 'training' alters respiratory behaviours, but these changes may not be necessary to achieve high levels of wheel running. Ventilatory control is affected by genetics, the environment and gene-environment and gene-gene interactions. Here, we used an experimental evolution approach to test whether 37 generations of selective breeding for high voluntary wheel running (genetic effects) and/or long-term (7-11 weeks) wheel access (training effects) alter acute respiratory behaviour of mice resting in normoxic, hypoxic and hypercapnic conditions. As the four replicate high-runner (HR) lines run much more than the four non-selected control (C) lines, we also examined whether the amount of exercise among individual mice was a quantitative predictor of ventilatory chemoreflexes at rest. Selective breeding and/or wheel access significantly affected several traits. In normoxia, HR mice tended to have lower mass-adjusted rates of oxygen consumption and carbon dioxide production. Chronic wheel access increased oxygen consumption and carbon dioxide production in both HR and C mice during hypercapnia. Breathing frequency and minute ventilation were significantly reduced by chronic wheel access in both HR and C mice during hypoxia. Selection history, while significantly affecting some traits, did not systematically alter ventilation across all gas concentrations. As with most human studies, our findings support the idea that endurance training (access to wheel running) attenuates resting ventilation. However, little evidence was found for a correlation at the level of the individual variation between ventilatory chemoreflexes and performance (amount of individual voluntary wheel running). We tentatively conclude that exercise 'training' alters respiratory behaviours, but these changes may not be necessary to achieve high levels of wheel running.

Effects of age and spa treatment on match running performance over two consecutive games in highly trained young soccer players.

PubMed

Buchheit, Martin; Horobeanu, Cosmin; Mendez-Villanueva, Alberto; Simpson, Ben M; Bourdon, Pitre C

2011-03-01

The aim of this study was to examine the effect of age and spa treatment (i.e. combined sauna, cold water immersion, and jacuzzi) on match running performance over two consecutive matches in highly trained young soccer players. Fifteen pre- (age 12.8 ± 0.6 years) and 13 post- (15.9 ± 1 y) peak height velocity (PHV) players played two matches (Matches 1 and 2) within 48 h against the same opposition, with no specific between-match recovery intervention (control). Five post-PHV players also completed another set of two consecutive matches, with spa treatment implemented after the first match. Match running performance was assessed using a global positioning system with very-high-intensity running (> 16.1-19.0 km · h(-1)), sprinting distance (>19 km · h(-1)), and peak match speed determined. Match 2 very-high-intensity running was "possibly" impaired in post-PHV players (-9 ± 33%; ± 90% confidence limits), whereas it was "very likely" improved for the pre-PHV players (+27 ± 22%). The spa treatment had a beneficial impact on Match 2 running performance, with a "likely" rating for sprinting distance (+30 ± 67%) and "almost certain" for peak match speed (+6.4 ± 3%). The results suggest that spa treatment is an effective recovery intervention for post-PHV players, while its value in pre-PHV players is questionable.

Cerebellum Transcriptome of Mice Bred for High Voluntary Activity Offers Insights into Locomotor Control and Reward-Dependent Behaviors.

PubMed

Caetano-Anollés, Kelsey; Rhodes, Justin S; Garland, Theodore; Perez, Sam D; Hernandez, Alvaro G; Southey, Bruce R; Rodriguez-Zas, Sandra L

2016-01-01

The role of the cerebellum in motivation and addictive behaviors is less understood than that in control and coordination of movements. High running can be a self-rewarding behavior exhibiting addictive properties. Changes in the cerebellum transcriptional networks of mice from a line selectively bred for High voluntary running (H) were profiled relative to an unselected Control (C) line. The environmental modulation of these changes was assessed both in activity environments corresponding to 7 days of Free (F) access to running wheel and to Blocked (B) access on day 7. Overall, 457 genes exhibited a significant (FDR-adjusted P-value < 0.05) genotype-by-environment interaction effect, indicating that activity genotype differences in gene expression depend on environmental access to running. Among these genes, network analysis highlighted 6 genes (Nrgn, Drd2, Rxrg, Gda, Adora2a, and Rab40b) connected by their products that displayed opposite expression patterns in the activity genotype contrast within the B and F environments. The comparison of network expression topologies suggests that selection for high voluntary running is linked to a predominant dysregulation of hub genes in the F environment that enables running whereas a dysregulation of ancillary genes is favored in the B environment that blocks running. Genes associated with locomotor regulation, signaling pathways, reward-processing, goal-focused, and reward-dependent behaviors exhibited significant genotype-by-environment interaction (e.g. Pak6, Adora2a, Drd2, and Arhgap8). Neuropeptide genes including Adcyap1, Cck, Sst, Vgf, Npy, Nts, Penk, and Tac2 and related receptor genes also exhibited significant genotype-by-environment interaction. The majority of the 183 differentially expressed genes between activity genotypes (e.g. Drd1) were under-expressed in C relative to H genotypes and were also under-expressed in B relative to F environments. Our findings indicate that the high voluntary running mouse line studied is a helpful model for understanding the molecular mechanisms in the cerebellum that influence locomotor control and reward-dependent behaviors.

Cerebellum Transcriptome of Mice Bred for High Voluntary Activity Offers Insights into Locomotor Control and Reward-Dependent Behaviors

PubMed Central

Caetano-Anollés, Kelsey; Rhodes, Justin S.; Garland, Theodore; Perez, Sam D.; Hernandez, Alvaro G.; Southey, Bruce R.; Rodriguez-Zas, Sandra L.

2016-01-01

The role of the cerebellum in motivation and addictive behaviors is less understood than that in control and coordination of movements. High running can be a self-rewarding behavior exhibiting addictive properties. Changes in the cerebellum transcriptional networks of mice from a line selectively bred for High voluntary running (H) were profiled relative to an unselected Control (C) line. The environmental modulation of these changes was assessed both in activity environments corresponding to 7 days of Free (F) access to running wheel and to Blocked (B) access on day 7. Overall, 457 genes exhibited a significant (FDR-adjusted P-value < 0.05) genotype-by-environment interaction effect, indicating that activity genotype differences in gene expression depend on environmental access to running. Among these genes, network analysis highlighted 6 genes (Nrgn, Drd2, Rxrg, Gda, Adora2a, and Rab40b) connected by their products that displayed opposite expression patterns in the activity genotype contrast within the B and F environments. The comparison of network expression topologies suggests that selection for high voluntary running is linked to a predominant dysregulation of hub genes in the F environment that enables running whereas a dysregulation of ancillary genes is favored in the B environment that blocks running. Genes associated with locomotor regulation, signaling pathways, reward-processing, goal-focused, and reward-dependent behaviors exhibited significant genotype-by-environment interaction (e.g. Pak6, Adora2a, Drd2, and Arhgap8). Neuropeptide genes including Adcyap1, Cck, Sst, Vgf, Npy, Nts, Penk, and Tac2 and related receptor genes also exhibited significant genotype-by-environment interaction. The majority of the 183 differentially expressed genes between activity genotypes (e.g. Drd1) were under-expressed in C relative to H genotypes and were also under-expressed in B relative to F environments. Our findings indicate that the high voluntary running mouse line studied is a helpful model for understanding the molecular mechanisms in the cerebellum that influence locomotor control and reward-dependent behaviors. PMID:27893846

RAPPORT: running scientific high-performance computing applications on the cloud.

PubMed

Cohen, Jeremy; Filippis, Ioannis; Woodbridge, Mark; Bauer, Daniela; Hong, Neil Chue; Jackson, Mike; Butcher, Sarah; Colling, David; Darlington, John; Fuchs, Brian; Harvey, Matt

2013-01-28

Cloud computing infrastructure is now widely used in many domains, but one area where there has been more limited adoption is research computing, in particular for running scientific high-performance computing (HPC) software. The Robust Application Porting for HPC in the Cloud (RAPPORT) project took advantage of existing links between computing researchers and application scientists in the fields of bioinformatics, high-energy physics (HEP) and digital humanities, to investigate running a set of scientific HPC applications from these domains on cloud infrastructure. In this paper, we focus on the bioinformatics and HEP domains, describing the applications and target cloud platforms. We conclude that, while there are many factors that need consideration, there is no fundamental impediment to the use of cloud infrastructure for running many types of HPC applications and, in some cases, there is potential for researchers to benefit significantly from the flexibility offered by cloud platforms.

The Preventive Effect of Calcium Supplementation on Weak Bones Caused by the Interaction of Exercise and Food Restriction in Young Female Rats During the Period from Acquiring Bone Mass to Maintaining Bone Mass.

PubMed

Aikawa, Yuki; Agata, Umon; Kakutani, Yuya; Kato, Shoyo; Noma, Yuichi; Hattori, Satoshi; Ogata, Hitomi; Ezawa, Ikuko; Omi, Naomi

2016-01-01

Increasing calcium (Ca) intake is important for female athletes with a risk of weak bone caused by inadequate food intake. The aim of the present study was to examine the preventive effect of Ca supplementation on low bone strength in young female athletes with inadequate food intake, using the rats as an experimental model. Seven-week-old female Sprague-Dawley rats were divided into four groups: the sedentary and ad libitum feeding group (SED), voluntary running exercise and ad libitum feeding group (EX), voluntary running exercise and 30% food restriction group (EX-FR), and a voluntary running exercise, 30% food-restricted and high-Ca diet group (EX-FR+Ca). To Ca supplementation, we used 1.2% Ca diet as "high-Ca diet" that contains two-fold Ca of normal Ca diet. The experiment lasted for 12 weeks. As a result, the energy availability, internal organ weight, bone strength, bone mineral density, and Ca absorption in the EX-FR group were significantly lower than those in the EX group. The bone strength and Ca absorption in the EX-FR+Ca group were significantly higher than those in the EX-FR group. However, the bone strength in the EX-FR+Ca group did not reach that in the EX group. These results suggested that Ca supplementation had a positive effect on bone strength, but the effect was not sufficient to prevent lower bone strength caused by food restriction in young female athletes.

Collagen production of osteoblasts revealed by ultra-high voltage electron microscopy.

PubMed

Hosaki-Takamiya, Rumiko; Hashimoto, Mana; Imai, Yuichi; Nishida, Tomoki; Yamada, Naoko; Mori, Hirotaro; Tanaka, Tomoyo; Kawanabe, Noriaki; Yamashiro, Takashi; Kamioka, Hiroshi

2016-09-01

In the bone, collagen fibrils form a lamellar structure called the "twisted plywood-like model." Because of this unique structure, bone can withstand various mechanical stresses. However, the formation of this structure has not been elucidated because of the difficulty of observing the collagen fibril production of the osteoblasts via currently available methods. This is because the formation occurs in the very limited space between the osteoblast layer and bone matrix. In this study, we used ultra-high-voltage electron microscopy (UHVEM) to observe collagen fibril production three-dimensionally. UHVEM has 3-MV acceleration voltage and enables us to use thicker sections. We observed collagen fibrils that were beneath the cell membrane of osteoblasts elongated to the outside of the cell. We also observed that osteoblasts produced collagen fibrils with polarity. By using AVIZO software, we observed collagen fibrils produced by osteoblasts along the contour of the osteoblasts toward the bone matrix area. Immediately after being released from the cell, the fibrils run randomly and sparsely. But as they recede from the osteoblast, the fibrils began to run parallel to the definite direction and became thick, and we observed a periodical stripe at that area. Furthermore, we also observed membrane structures wrapped around filamentous structures inside the osteoblasts. The filamentous structures had densities similar to the collagen fibrils and a columnar form and diameter. Our results suggested that collagen fibrils run parallel and thickly, which may be related to the lateral movement of the osteoblasts. UHVEM is a powerful tool for observing collagen fibril production.

Running from Paris to Beijing: biomechanical and physiological consequences.

PubMed

Millet, Guillaume Y; Morin, Jean-Benoît; Degache, Francis; Edouard, Pascal; Feasson, Léonard; Verney, Julien; Oullion, Roger

2009-12-01

The purpose of this study was to examine the physiological and biomechanical changes occurring in a subject after running 8,500 km in 161 days (i.e. 52.8 km daily). Three weeks before, 3 weeks after (POST) and 5 months after (POST+5) running from Paris to Beijing, energy cost of running (Cr), knee flexor and extensor isokinetic strength and biomechanical parameters (using a treadmill dynamometer) at different velocities were assessed in an experienced ultra-runner. At POST, there was a tendency toward a 'smoother' running pattern, as shown by (a) a higher stride frequency and duty factor, and a reduced aerial time without a change in contact time, (b) a lower maximal vertical force and loading rate at impact and (c) a decrease in both potential and kinetic energy changes at each step. This was associated with a detrimental effect on Cr (+6.2%) and a loss of strength at all angular velocities for both knee flexors and extensors. At POST+5, the subject returned to his original running patterns at low but not at high speeds and maximal strength remained reduced at low angular velocities (i.e. at high levels of force). It is suggested that the running pattern changes observed in the present study were a strategy adopted by the subject to reduce the deleterious effects of long distance running. However, the running pattern changes could partly be linked to the decrease in maximal strength.

Wheel-running attenuates intravenous cocaine self-administration in rats: sex differences.

PubMed

Cosgrove, Kelly P; Hunter, Robb G; Carroll, Marilyn E

2002-10-01

This experiment examines the effect of access to a running-wheel on intravenous cocaine self-administration in male and female rats. Rats maintained at 85% of their free-feeding body weight were first exposed to the running-wheel alone during the 6-h sessions until behavior stabilized for 14 days. Intravenous cannulae were then implanted, and the rats were trained to self-administer a low dose of cocaine (0.2 mg/kg) under a fixed-ratio (FR 1) schedule during the 6-h sessions, while the wheel remained inactive and cocaine self-administration stabilized (cocaine-only condition). Next, the wheel access and cocaine self-administration were concurrently available followed by a period of cocaine-only. Behavior was allowed to stabilize for 10 days at each phase. During wheel access, cocaine infusions decreased by 21.9% in males and 70.6% in females compared to the cocaine-only condition; the effect was statistically significant in females. Infusions increased to baseline levels when wheel access was terminated. When cocaine infusions were concurrently available, wheel revolutions were reduced by 63.7% and 61.5% in males and females, respectively, compared to the wheel-only condition. This result did not differ due to sex, but it was statistically significant when data from males and females were combined. These results indicate that wheel-running activity had a greater suppressant effect on cocaine self-administration in females than in males, and in females, wheel-running and cocaine self-administration are substitutable as reinforcers.

Factors influencing equipment selection in electron beam processing

NASA Astrophysics Data System (ADS)

Barnard, J. W.

2003-08-01

During the eighties and nineties accelerator manufacturers dramatically increased the beam power available for high-energy equipment. This effort was directed primarily at meeting the demands of the sterilization industry. During this era, the perception that bigger (higher power, higher energy) was always better prevailed since the operating and capital costs of accelerators did not increase with power and energy as fast as the throughput. High power was needed to maintain per unit costs low for treatment. This philosophy runs counter to certain present-day realities of the sterilization business as well as conditions influencing accelerator selection in other electron beam applications. Recent experience in machine selection is described and factors affecting choice are presented.

Performance Studies on Distributed Virtual Screening

PubMed Central

Krüger, Jens; de la Garza, Luis; Kohlbacher, Oliver; Nagel, Wolfgang E.

2014-01-01

Virtual high-throughput screening (vHTS) is an invaluable method in modern drug discovery. It permits screening large datasets or databases of chemical structures for those structures binding possibly to a drug target. Virtual screening is typically performed by docking code, which often runs sequentially. Processing of huge vHTS datasets can be parallelized by chunking the data because individual docking runs are independent of each other. The goal of this work is to find an optimal splitting maximizing the speedup while considering overhead and available cores on Distributed Computing Infrastructures (DCIs). We have conducted thorough performance studies accounting not only for the runtime of the docking itself, but also for structure preparation. Performance studies were conducted via the workflow-enabled science gateway MoSGrid (Molecular Simulation Grid). As input we used benchmark datasets for protein kinases. Our performance studies show that docking workflows can be made to scale almost linearly up to 500 concurrent processes distributed even over large DCIs, thus accelerating vHTS campaigns significantly. PMID:25032219

Voluntary wheel running improves adipose tissue immunometabolism in ovariectomized low-fit rats.

PubMed

Zidon, Terese M; Park, Young-Min; Welly, Rebecca J; Woodford, Makenzie L; Scroggins, Rebecca J; Britton, Steven L; Koch, Lauren G; Booth, Frank W; Padilla, Jaume; Kanaley, Jill A; Vieira-Potter, Victoria J

2018-01-02

Loss of ovarian hormones is associated with increased adiposity, white adipose tissue (WAT) inflammation, and insulin resistance (IR). Previous work demonstrated ovariectomized (OVX) rats bred for high aerobic fitness (HCR) are protected against weight gain and IR compared to rats bred for low aerobic fitness (LCR) yet wheel running prevents OVX-induced IR in LCR rats. The purpose of this study was to determine whether adipose tissue immunometabolic characteristics from female HCR and LCR rats differs before or after OVX, and whether wheel running mitigates OVX-induced adipose tissue immunometabolic changes in LCR rats. Female OVX HCR and LCR rats were all fed a high fat diet (HFD) (n = 7-8/group) and randomized to either a running wheel or remain sedentary for 11 weeks. Ovary-intact rats (n = 7-12/group) were fed a standard chow diet with no wheel. Ovary-intact LCR rats had a greater visceral WAT inflammatory profile compared to HCR. Following OVX, sedentary LCR rats had greater serum leptin (p<0.001) and WAT inflammation (p<0.05) than sedentary HCR. Wheel running normalized the elevated serum leptin and reduced both visceral (p<0.05) and subcutaneous (p<0.03) WAT inflammatory markers in the LCR rats. Paradoxically, wheel running increased some markers of WAT inflammation in OVX HCR rats (p<0.05), which correlated with observed weight gain. Taken together, HCR rats appear to have a healthier WAT immune and metabolic profile compared to LCR, even following OVX. Wheel running improves WAT health in previously sedentary LCR rats. On the other hand, increased WAT inflammation is associated with adiposity gain despite a high volume of wheel running in HCR rats.

VisIVO: A Library and Integrated Tools for Large Astrophysical Dataset Exploration

NASA Astrophysics Data System (ADS)

Becciani, U.; Costa, A.; Ersotelos, N.; Krokos, M.; Massimino, P.; Petta, C.; Vitello, F.

2012-09-01

VisIVO provides an integrated suite of tools and services that can be used in many scientific fields. VisIVO development starts in the Virtual Observatory framework. VisIVO allows users to visualize meaningfully highly-complex, large-scale datasets and create movies of these visualizations based on distributed infrastructures. VisIVO supports high-performance, multi-dimensional visualization of large-scale astrophysical datasets. Users can rapidly obtain meaningful visualizations while preserving full and intuitive control of the relevant parameters. VisIVO consists of VisIVO Desktop - a stand-alone application for interactive visualization on standard PCs, VisIVO Server - a platform for high performance visualization, VisIVO Web - a custom designed web portal, VisIVOSmartphone - an application to exploit the VisIVO Server functionality and the latest VisIVO features: VisIVO Library allows a job running on a computational system (grid, HPC, etc.) to produce movies directly with the code internal data arrays without the need to produce intermediate files. This is particularly important when running on large computational facilities, where the user wants to have a look at the results during the data production phase. For example, in grid computing facilities, images can be produced directly in the grid catalogue while the user code is running in a system that cannot be directly accessed by the user (a worker node). The deployment of VisIVO on the DG and gLite is carried out with the support of EDGI and EGI-Inspire projects. Depending on the structure and size of datasets under consideration, the data exploration process could take several hours of CPU for creating customized views and the production of movies could potentially last several days. For this reason an MPI parallel version of VisIVO could play a fundamental role in increasing performance, e.g. it could be automatically deployed on nodes that are MPI aware. A central concept in our development is thus to produce unified code that can run either on serial nodes or in parallel by using HPC oriented grid nodes. Another important aspect, to obtain as high performance as possible, is the integration of VisIVO processes with grid nodes where GPUs are available. We have selected CUDA for implementing a range of computationally heavy modules. VisIVO is supported by EGI-Inspire, EDGI and SCI-BUS projects.

Hadoop-GIS: A High Performance Spatial Data Warehousing System over MapReduce.

PubMed

Aji, Ablimit; Wang, Fusheng; Vo, Hoang; Lee, Rubao; Liu, Qiaoling; Zhang, Xiaodong; Saltz, Joel

2013-08-01

Support of high performance queries on large volumes of spatial data becomes increasingly important in many application domains, including geospatial problems in numerous fields, location based services, and emerging scientific applications that are increasingly data- and compute-intensive. The emergence of massive scale spatial data is due to the proliferation of cost effective and ubiquitous positioning technologies, development of high resolution imaging technologies, and contribution from a large number of community users. There are two major challenges for managing and querying massive spatial data to support spatial queries: the explosion of spatial data, and the high computational complexity of spatial queries. In this paper, we present Hadoop-GIS - a scalable and high performance spatial data warehousing system for running large scale spatial queries on Hadoop. Hadoop-GIS supports multiple types of spatial queries on MapReduce through spatial partitioning, customizable spatial query engine RESQUE, implicit parallel spatial query execution on MapReduce, and effective methods for amending query results through handling boundary objects. Hadoop-GIS utilizes global partition indexing and customizable on demand local spatial indexing to achieve efficient query processing. Hadoop-GIS is integrated into Hive to support declarative spatial queries with an integrated architecture. Our experiments have demonstrated the high efficiency of Hadoop-GIS on query response and high scalability to run on commodity clusters. Our comparative experiments have showed that performance of Hadoop-GIS is on par with parallel SDBMS and outperforms SDBMS for compute-intensive queries. Hadoop-GIS is available as a set of library for processing spatial queries, and as an integrated software package in Hive.

Hadoop-GIS: A High Performance Spatial Data Warehousing System over MapReduce

PubMed Central

Aji, Ablimit; Wang, Fusheng; Vo, Hoang; Lee, Rubao; Liu, Qiaoling; Zhang, Xiaodong; Saltz, Joel

2013-01-01

Support of high performance queries on large volumes of spatial data becomes increasingly important in many application domains, including geospatial problems in numerous fields, location based services, and emerging scientific applications that are increasingly data- and compute-intensive. The emergence of massive scale spatial data is due to the proliferation of cost effective and ubiquitous positioning technologies, development of high resolution imaging technologies, and contribution from a large number of community users. There are two major challenges for managing and querying massive spatial data to support spatial queries: the explosion of spatial data, and the high computational complexity of spatial queries. In this paper, we present Hadoop-GIS – a scalable and high performance spatial data warehousing system for running large scale spatial queries on Hadoop. Hadoop-GIS supports multiple types of spatial queries on MapReduce through spatial partitioning, customizable spatial query engine RESQUE, implicit parallel spatial query execution on MapReduce, and effective methods for amending query results through handling boundary objects. Hadoop-GIS utilizes global partition indexing and customizable on demand local spatial indexing to achieve efficient query processing. Hadoop-GIS is integrated into Hive to support declarative spatial queries with an integrated architecture. Our experiments have demonstrated the high efficiency of Hadoop-GIS on query response and high scalability to run on commodity clusters. Our comparative experiments have showed that performance of Hadoop-GIS is on par with parallel SDBMS and outperforms SDBMS for compute-intensive queries. Hadoop-GIS is available as a set of library for processing spatial queries, and as an integrated software package in Hive. PMID:24187650

The influence of the magnetic field on running penumbral waves in the solar chromosphere

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

Jess, D. B.; Reznikova, V. E.; Van Doorsselaere, T.

2013-12-20

We use images of high spatial and temporal resolution, obtained using both ground- and space-based instrumentation, to investigate the role magnetic field inclination angles play in the propagation characteristics of running penumbral waves in the solar chromosphere. Analysis of a near-circular sunspot, close to the center of the solar disk, reveals a smooth rise in oscillatory period as a function of distance from the umbral barycenter. However, in one directional quadrant, corresponding to the north direction, a pronounced kink in the period-distance diagram is found. Utilizing a combination of the inversion of magnetic Stokes vectors and force-free field extrapolations, wemore » attribute this behavior to the cut-off frequency imposed by the magnetic field geometry in this location. A rapid, localized inclination of the magnetic field lines in the north direction results in a faster increase in the dominant periodicity due to an accelerated reduction in the cut-off frequency. For the first time, we reveal how the spatial distribution of dominant wave periods, obtained with one of the highest resolution solar instruments currently available, directly reflects the magnetic geometry of the underlying sunspot, thus opening up a wealth of possibilities in future magnetohydrodynamic seismology studies. In addition, the intrinsic relationships we find between the underlying magnetic field geometries connecting the photosphere to the chromosphere, and the characteristics of running penumbral waves observed in the upper chromosphere, directly supports the interpretation that running penumbral wave phenomena are the chromospheric signature of upwardly propagating magneto-acoustic waves generated in the photosphere.« less

Jobs masonry in LHCb with elastic Grid Jobs

NASA Astrophysics Data System (ADS)

Stagni, F.; Charpentier, Ph

2015-12-01

In any distributed computing infrastructure, a job is normally forbidden to run for an indefinite amount of time. This limitation is implemented using different technologies, the most common one being the CPU time limit implemented by batch queues. It is therefore important to have a good estimate of how much CPU work a job will require: otherwise, it might be killed by the batch system, or by whatever system is controlling the jobs’ execution. In many modern interwares, the jobs are actually executed by pilot jobs, that can use the whole available time in running multiple consecutive jobs. If at some point the available time in a pilot is too short for the execution of any job, it should be released, while it could have been used efficiently by a shorter job. Within LHCbDIRAC, the LHCb extension of the DIRAC interware, we developed a simple way to fully exploit computing capabilities available to a pilot, even for resources with limited time capabilities, by adding elasticity to production MonteCarlo (MC) simulation jobs. With our approach, independently of the time available, LHCbDIRAC will always have the possibility to execute a MC job, whose length will be adapted to the available amount of time: therefore the same job, running on different computing resources with different time limits, will produce different amounts of events. The decision on the number of events to be produced is made just in time at the start of the job, when the capabilities of the resource are known. In order to know how many events a MC job will be instructed to produce, LHCbDIRAC simply requires three values: the CPU-work per event for that type of job, the power of the machine it is running on, and the time left for the job before being killed. Knowing these values, we can estimate the number of events the job will be able to simulate with the available CPU time. This paper will demonstrate that, using this simple but effective solution, LHCb manages to make a more efficient use of the available resources, and that it can easily use new types of resources. An example is represented by resources provided by batch queues, where low-priority MC jobs can be used as "masonry" jobs in multi-jobs pilots. A second example is represented by opportunistic resources with limited available time.

Strategies for RUN1 Deployment Using RUN2 and REN2 to Manage Grapevine Powdery Mildew Informed by Studies of Race Specificity.

PubMed

Feechan, Angela; Kocsis, Marianna; Riaz, Summaira; Zhang, Wei; Gadoury, David M; Walker, M Andrew; Dry, Ian B; Reisch, Bruce; Cadle-Davidson, Lance

2015-08-01

The Toll/interleukin-1 receptor nucleotide-binding site leucine-rich repeat gene, "resistance to Uncinula necator 1" (RUN1), from Vitis rotundifolia was recently identified and confirmed to confer resistance to the grapevine powdery mildew fungus Erysiphe necator (syn. U. necator) in transgenic V. vinifera cultivars. However, sporulating powdery mildew colonies and cleistothecia of the heterothallic pathogen have been found on introgression lines containing the RUN1 locus growing in New York (NY). Two E. necator isolates collected from RUN1 vines were designated NY1-131 and NY1-137 and were used in this study to inform a strategy for durable RUN1 deployment. In order to achieve this, fitness parameters of NY1-131 and NY1-137 were quantified relative to powdery mildew isolates collected from V. rotundifolia and V. vinifera on vines containing alleles of the powdery mildew resistance genes RUN1, RUN2, or REN2. The results clearly demonstrate the race specificity of RUN1, RUN2, and REN2 resistance alleles, all of which exhibit programmed cell death (PCD)-mediated resistance. The NY1 isolates investigated were found to have an intermediate virulence on RUN1 vines, although this may be allele specific, while the Musc4 isolate collected from V. rotundifolia was virulent on all RUN1 vines. Another powdery mildew resistance locus, RUN2, was previously mapped in different V. rotundifolia genotypes, and two alleles (RUN2.1 and RUN2.2) were identified. The RUN2.1 allele was found to provide PCD-mediated resistance to both an NY1 isolate and Musc4. Importantly, REN2 vines were resistant to the NY1 isolates and RUN1REN2 vines combining both genes displayed additional resistance. Based on these results, RUN1-mediated resistance in grapevine may be enhanced by pyramiding with RUN2.1 or REN2; however, naturally occurring isolates in North America display some virulence on vines with these resistance genes. The characterization of additional resistance sources is needed to identify resistance gene combinations that will further enhance durability. For the resistance gene combinations currently available, we recommend using complementary management strategies, including fungicide application, to reduce populations of virulent isolates.

Defensive Swarm: An Agent Based Modeling Analysis

DTIC Science & Technology

2017-12-01

INITIAL ALGORITHM (SINGLE- RUN ) TESTING .........................43  1.  Patrol Algorithm—Passive...scalability are therefore quite important to modeling in this highly variable domain. One can force the software to run the gamut of options to see...changes in operating constructs or procedures. Additionally, modelers can run thousands of iterations testing the model under different circumstances

75 FR 54771 - Drawbridge Operation Regulation; Trent River, New Bern, NC

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-09

... New Bern, NC, to accommodate a Bridge Run. This deviation allows the drawbridge to be maintained in... approximately 14 feet above mean high water. On behalf of the Neuse River Bridge Run Organization and the City... Bridge Run schedule for Saturday, October 16, 2010. Under this deviation, the drawbridge would be allowed...

Maximizing Safety, Social Support, and Participation in Walking/Jogging/Running Classes

ERIC Educational Resources Information Center

Consolo, Kitty A.

2007-01-01

Physical education instructors who teach high school or college walking/jogging/running classes, or who include walking or running as a segment of a wellness class, face a particular challenge in trying to meet each student's individual fitness needs while ensuring safety. This article provides strategies for effectively meeting individual needs…

The NEST Dry-Run Mode: Efficient Dynamic Analysis of Neuronal Network Simulation Code.

PubMed

Kunkel, Susanne; Schenck, Wolfram

2017-01-01

NEST is a simulator for spiking neuronal networks that commits to a general purpose approach: It allows for high flexibility in the design of network models, and its applications range from small-scale simulations on laptops to brain-scale simulations on supercomputers. Hence, developers need to test their code for various use cases and ensure that changes to code do not impair scalability. However, running a full set of benchmarks on a supercomputer takes up precious compute-time resources and can entail long queuing times. Here, we present the NEST dry-run mode, which enables comprehensive dynamic code analysis without requiring access to high-performance computing facilities. A dry-run simulation is carried out by a single process, which performs all simulation steps except communication as if it was part of a parallel environment with many processes. We show that measurements of memory usage and runtime of neuronal network simulations closely match the corresponding dry-run data. Furthermore, we demonstrate the successful application of the dry-run mode in the areas of profiling and performance modeling.

The NEST Dry-Run Mode: Efficient Dynamic Analysis of Neuronal Network Simulation Code

PubMed Central

Kunkel, Susanne; Schenck, Wolfram

2017-01-01

NEST is a simulator for spiking neuronal networks that commits to a general purpose approach: It allows for high flexibility in the design of network models, and its applications range from small-scale simulations on laptops to brain-scale simulations on supercomputers. Hence, developers need to test their code for various use cases and ensure that changes to code do not impair scalability. However, running a full set of benchmarks on a supercomputer takes up precious compute-time resources and can entail long queuing times. Here, we present the NEST dry-run mode, which enables comprehensive dynamic code analysis without requiring access to high-performance computing facilities. A dry-run simulation is carried out by a single process, which performs all simulation steps except communication as if it was part of a parallel environment with many processes. We show that measurements of memory usage and runtime of neuronal network simulations closely match the corresponding dry-run data. Furthermore, we demonstrate the successful application of the dry-run mode in the areas of profiling and performance modeling. PMID:28701946

Preinjury and postinjury running analysis along with measurements of strength and tendon length in a patient with a surgically repaired Achilles tendon rupture.

PubMed

Silbernagel, Karin Grävare; Willy, Richard; Davis, Irene

2012-06-01

Case report. The Achilles tendon is the most frequently ruptured tendon, and the incidence of Achilles tendon rupture has increased in the last decade. The rupture generally occurs without any preceding warning signs, and therefore preinjury data are seldom available. This case represents a unique opportunity to compare preinjury running mechanics with postinjury evaluation in a patient with an Achilles tendon rupture. A 23-year-old female sustained a right complete Achilles tendon rupture while playing soccer. Running mechanics data were collected preinjury, as she was a healthy participant in a study on running analysis. In addition, patient-reported symptoms, physical activity level, strength, ankle range of motion, heel-rise ability, Achilles tendon length, and running kinetics were evaluated 1 year after surgical repair. During running, greater ankle dorsiflexion and eversion and rearfoot abduction were noted on the involved side postinjury when compared to preinjury data. In addition, postinjury, the magnitude of all kinetics data was lower on the involved limb when compared to the uninvolved limb. The involved side displayed differences in strength, ankle range of motion, heel rise, and tendon length when compared to the uninvolved side 1 year after injury. Despite a return to normal running routine and reports of only minor limitations with running, considerable changes were noted in running biomechanics 1 year after injury. Calf muscle weakness and Achilles tendon elongation were also found when comparing the involved and uninvolved sides.

Fatigue associated with prolonged graded running.

PubMed

Giandolini, Marlene; Vernillo, Gianluca; Samozino, Pierre; Horvais, Nicolas; Edwards, W Brent; Morin, Jean-Benoît; Millet, Guillaume Y

2016-10-01

Scientific experiments on running mainly consider level running. However, the magnitude and etiology of fatigue depend on the exercise under consideration, particularly the predominant type of contraction, which differs between level, uphill, and downhill running. The purpose of this review is to comprehensively summarize the neurophysiological and biomechanical changes due to fatigue in graded running. When comparing prolonged hilly running (i.e., a combination of uphill and downhill running) to level running, it is found that (1) the general shape of the neuromuscular fatigue-exercise duration curve as well as the etiology of fatigue in knee extensor and plantar flexor muscles are similar and (2) the biomechanical consequences are also relatively comparable, suggesting that duration rather than elevation changes affects neuromuscular function and running patterns. However, 'pure' uphill or downhill running has several fatigue-related intrinsic features compared with the level running. Downhill running induces severe lower limb tissue damage, indirectly evidenced by massive increases in plasma creatine kinase/myoglobin concentration or inflammatory markers. In addition, low-frequency fatigue (i.e., excitation-contraction coupling failure) is systematically observed after downhill running, although it has also been found in high-intensity uphill running for different reasons. Indeed, low-frequency fatigue in downhill running is attributed to mechanical stress at the interface sarcoplasmic reticulum/T-tubule, while the inorganic phosphate accumulation probably plays a central role in intense uphill running. Other fatigue-related specificities of graded running such as strategies to minimize the deleterious effects of downhill running on muscle function, the difference of energy cost versus heat storage or muscle activity changes in downhill, level, and uphill running are also discussed.

The use of a running wheel to measure activity in rodents: relationship to energy balance, general activity, and reward.

PubMed

Novak, Colleen M; Burghardt, Paul R; Levine, James A

2012-03-01

Running wheels are commonly employed to measure rodent physical activity in a variety of contexts, including studies of energy balance and obesity. There is no consensus on the nature of wheel-running activity or its underlying causes, however. Here, we will begin by systematically reviewing how running wheel availability affects physical activity and other aspects of energy balance in laboratory rodents. While wheel running and physical activity in the absence of a wheel commonly correlate in a general sense, in many specific aspects the two do not correspond. In fact, the presence of running wheels alters several aspects of energy balance, including body weight and composition, food intake, and energy expenditure of activity. We contend that wheel-running activity should be considered a behavior in and of itself, reflecting several underlying behavioral processes in addition to a rodent's general, spontaneous activity. These behavioral processes include defensive behavior, predatory aggression, and depression- and anxiety-like behaviors. As it relates to energy balance, wheel running engages several brain systems-including those related to the stress response, mood, and reward, and those responsive to growth factors-that influence energy balance indirectly. We contend that wheel-running behavior represents factors in addition to rodents' tendency to be physically active, engaging additional neural and physiological mechanisms which can then independently alter energy balance and behavior. Given the impact of wheel-running behavior on numerous overlapping systems that influence behavior and physiology, this review outlines the need for careful design and interpretation of studies that utilize running wheels as a means for exercise or as a measurement of general physical activity. Copyright © 2012 Elsevier Ltd. All rights reserved.

The use of a running wheel to measure activity in rodents: Relationship to energy balance, general activity, and reward

PubMed Central

Levine, James A.

2015-01-01

Running wheels are commonly employed to measure rodent physical activity in a variety of contexts, including studies of energy balance and obesity. There is no consensus on the nature of wheel-running activity or its underlying causes, however. Here, we will begin by systematically reviewing how running wheel availability affects physical activity and other aspects of energy balance in laboratory rodents. While wheel running and physical activity in the absence of a wheel commonly correlate in a general sense, in many specific aspects the two do not correspond. In fact, the presence of running wheels alters several aspects of energy balance, including body weight and composition, food intake, and energy expenditure of activity. We contend that wheel-running activity should be considered a behavior in and of itself, reflecting several underlying behavioral processes in addition to a rodent's general, spontaneous activity. These behavioral processes include defensive behavior, predatory aggression, and depression- and anxiety-like behaviors. As it relates to energy balance, wheel running engages several brain systems—including those related to the stress response, mood, and reward, and those responsive to growth factors—that influence energy balance indirectly. We contend that wheel-running behavior represents factors in addition to rodents' tendency to be physically active, engaging additional neural and physiological mechanisms which can then independently alter energy balance and behavior. Given the impact of wheel-running behavior on numerous overlapping systems that influence behavior and physiology, this review outlines the need for careful design and interpretation of studies that utilize running wheels as a means for exercise or as a measurement of general physical activity. PMID:22230703

Voluntary wheel running augments aortic l-arginine transport and endothelial function in rats with chronic kidney disease.

PubMed

Martens, Christopher R; Kuczmarski, James M; Kim, Jahyun; Guers, John J; Harris, M Brennan; Lennon-Edwards, Shannon; Edwards, David G

2014-08-15

Reduced nitric oxide (NO) synthesis contributes to risk for cardiovascular disease in chronic kidney disease (CKD). Vascular uptake of the NO precursor l-arginine (ARG) is attenuated in rodents with CKD, resulting in reduced substrate availability for NO synthesis and impaired vascular function. We tested the effect of 4 wk of voluntary wheel running (RUN) and/or ARG supplementation on endothelium-dependent relaxation (EDR) in rats with CKD. Twelve-week-old male Sprague-Dawley rats underwent ⅚ ablation infarction surgery to induce CKD, or SHAM surgery as a control. Beginning 4 wk following surgery, CKD animals either remained sedentary (SED) or received one of the following interventions: supplemental ARG, RUN, or combined RUN+ARG. Animals were euthanized 8 wk after surgery, and EDR was assessed. EDR was significantly impaired in SED vs. SHAM animals after 8 wk, in response to ACh (10(-9)-10(-5) M) as indicated by a reduced area under the curve (AUC; 44.56 ± 9.01 vs 100 ± 4.58, P < 0.05) and reduced maximal response (Emax; 59.9 ± 9.67 vs. 94.31 ± 1.27%, P < 0.05). AUC was not improved by ARG treatment but was significantly improved above SED animals in both RUN and RUN+ARG-treated animals. Maximal relaxation was elevated above SED in RUN+ARG animals only. l-[(3)H]arginine uptake was impaired in both SED and ARG animals and was improved in RUN and RUN+ARG animals. The results suggest that voluntary wheel running is an effective therapy to improve vascular function in CKD and may be more beneficial when combined with l-arginine. Copyright © 2014 the American Physiological Society.

Physiological and Biomechanical Responses of Highly Trained Distance Runners to Lower-Body Positive Pressure Treadmill Running.

PubMed

Barnes, Kyle R; Janecke, Jessica N

2017-11-21

As a way to train at faster running speeds, add training volume, prevent injury, or rehabilitate after an injury, lower-body positive pressure treadmills (LBPPT) have become increasingly commonplace among athletes. However, there are conflicting evidence and a paucity of data describing the physiological and biomechanical responses to LBPPT running in highly trained or elite caliber runners at the running speeds they habitually train at, which are considerably faster than those of recreational runners. Furthermore, data is lacking regarding female runners' responses to LBPPT running. Therefore, this study was designed to evaluate the physiological and biomechanical responses to LBPPT running in highly trained male and female distance runners. Fifteen highly trained distance runners (seven male; eight female) completed a single running test composed of 4 × 9-min interval series at fixed percentages of body weight ranging from 0 to 30% body weight support (BWS) in 10% increments on LBPPT. The first interval was always conducted at 0% BWS; thereafter, intervals at 10, 20, and 30% BWS were conducted in random order. Each interval consisted of three stages of 3 min each, at velocities of 14.5, 16.1, and 17.7 km·h -1 for men and 12.9, 14.5, and 16.1 km·h -1 for women. Expired gases, ventilation, breathing frequency, heart rate (HR), rating of perceived exertion (RPE), and stride characteristics were measured during each running speed and BWS. Male and female runners had similar physiological and biomechanical responses to running on LBPPT. Increasing BWS increased stride length (p < 0.02) and flight duration (p < 0.01) and decreased stride rate (p < 0.01) and contact time (p < 0.01) in small-large magnitudes. There was a large attenuation of oxygen consumption (VO 2 ) relative to BWS (p < 0.001), while there were trivial-moderate reductions in respiratory exchange ratio, minute ventilation, and respiratory frequency (p > 0.05), and small-large effects on HR and RPE (p < 0.01). There were trivial-small differences in V E , respiratory frequency, HR, and RPE for a given VO 2 across various BWS (p > 0.05). The results indicate the male and female distance runners have similar physiological and biomechanical responses to LBPPT running. Overall, the biomechanical changes during LBPPT running all contributed to less metabolic cost and corresponding physiological changes.

Effects of age, maturity and body dimensions on match running performance in highly trained under-15 soccer players.

PubMed

Buchheit, Martin; Mendez-Villanueva, Alberto

2014-01-01

The aim of the present study was to compare, in 36 highly trained under-15 soccer players, the respective effects of age, maturity and body dimensions on match running performance. Maximal sprinting (MSS) and aerobic speeds were estimated. Match running performance was analysed with GPS (GPSport, 1 Hz) during 19 international friendly games (n = 115 player-files). Total distance and distance covered >16 km h(-1) (D > 16 km h(-1)) were collected. Players advanced in age and/or maturation, or having larger body dimensions presented greater locomotor (Cohen's d for MSS: 0.5-1.0, likely to almost certain) and match running performances (D > 16 km h(-1): 0.2-0.5, possibly to likely) than their younger, less mature and/or smaller teammates. These age-, maturation- and body size-related differences were of larger magnitude for field test measures versus match running performance. Compared with age and body size (unclear to likely), maturation (likely to almost certainly for all match variables) had the greatest impact on match running performance. The magnitude of the relationships between age, maturation and body dimensions and match running performance were position-dependent. Within a single age-group in the present player sample, maturation had a substantial impact on match running performance, especially in attacking players. Coaches may need to consider players' maturity status when assessing their on-field playing performance.

Reliability of Leg and Vertical Stiffness During High Speed Treadmill Running.

PubMed

Pappas, Panagiotis; Dallas, Giorgos; Paradisis, Giorgos

2017-04-01

In research, the accurate and reliable measurement of leg and vertical stiffness could contribute to valid interpretations. The current study aimed at determining the intraparticipant variability (ie, intraday and interday reliabilities) of leg and vertical stiffness, as well as related parameters, during high speed treadmill running, using the "sine-wave" method. Thirty-one males ran on a treadmill at 6.67 m∙s -1 , and the contact and flight times were measured. To determine the intraday reliability, three 10-s running bouts with 10-min recovery were performed. In addition, to examine the interday reliability, three 10-s running bouts on 3 separate days with 48-h interbout intervals were performed. The reliability statistics included repeated-measure analysis of variance, average intertrial correlations, intraclass correlation coefficients (ICCs), Cronbach's α reliability coefficient, and the coefficient of variation (CV%). Both intraday and interday reliabilities were high for leg and vertical stiffness (ICC > 0.939 and CV < 4.3%), as well as related variables (ICC > 0.934 and CV < 3.9%). It was thus inferred that the measurements of leg and vertical stiffness, as well as the related parameters obtained using the "sine-wave" method during treadmill running at 6.67 m∙s -1 , were highly reliable, both within and across days.

Selecting and implementing the PBS scheduler on an SGI Onyx 2/Orgin 2000.

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

Bittner, S.

1999-06-28

In the Mathematics and Computer Science Division at Argonne, the demand for resources on the Onyx 2 exceeds the resources available for consumption. To distribute these scarce resources effectively, we need a scheduling and resource management package with multiple capabilities. In particular, it must accept standard interactive user logins, allow batch jobs, backfill the system based on available resources, and permit system activities such as accounting to proceed without interruption. The package must include a mechanism to treat the graphic pipes as a schedulable resource. Also required is the ability to create advance reservations, offer dedicated system modes for largemore » resource runs and benchmarking, and track the resources consumed for each job run. Furthermore, our users want to be able to obtain repeatable timing results on job runs. And, of course, package costs must be carefully considered. We explored several options, including NQE and various third-party products, before settling on the PBS scheduler.« less

SCALCE: boosting sequence compression algorithms using locally consistent encoding

PubMed Central

Hach, Faraz; Numanagić, Ibrahim; Sahinalp, S Cenk

2012-01-01

Motivation: The high throughput sequencing (HTS) platforms generate unprecedented amounts of data that introduce challenges for the computational infrastructure. Data management, storage and analysis have become major logistical obstacles for those adopting the new platforms. The requirement for large investment for this purpose almost signalled the end of the Sequence Read Archive hosted at the National Center for Biotechnology Information (NCBI), which holds most of the sequence data generated world wide. Currently, most HTS data are compressed through general purpose algorithms such as gzip. These algorithms are not designed for compressing data generated by the HTS platforms; for example, they do not take advantage of the specific nature of genomic sequence data, that is, limited alphabet size and high similarity among reads. Fast and efficient compression algorithms designed specifically for HTS data should be able to address some of the issues in data management, storage and communication. Such algorithms would also help with analysis provided they offer additional capabilities such as random access to any read and indexing for efficient sequence similarity search. Here we present SCALCE, a ‘boosting’ scheme based on Locally Consistent Parsing technique, which reorganizes the reads in a way that results in a higher compression speed and compression rate, independent of the compression algorithm in use and without using a reference genome. Results: Our tests indicate that SCALCE can improve the compression rate achieved through gzip by a factor of 4.19—when the goal is to compress the reads alone. In fact, on SCALCE reordered reads, gzip running time can improve by a factor of 15.06 on a standard PC with a single core and 6 GB memory. Interestingly even the running time of SCALCE + gzip improves that of gzip alone by a factor of 2.09. When compared with the recently published BEETL, which aims to sort the (inverted) reads in lexicographic order for improving bzip2, SCALCE + gzip provides up to 2.01 times better compression while improving the running time by a factor of 5.17. SCALCE also provides the option to compress the quality scores as well as the read names, in addition to the reads themselves. This is achieved by compressing the quality scores through order-3 Arithmetic Coding (AC) and the read names through gzip through the reordering SCALCE provides on the reads. This way, in comparison with gzip compression of the unordered FASTQ files (including reads, read names and quality scores), SCALCE (together with gzip and arithmetic encoding) can provide up to 3.34 improvement in the compression rate and 1.26 improvement in running time. Availability: Our algorithm, SCALCE (Sequence Compression Algorithm using Locally Consistent Encoding), is implemented in C++ with both gzip and bzip2 compression options. It also supports multithreading when gzip option is selected, and the pigz binary is available. It is available at http://scalce.sourceforge.net. Contact: fhach@cs.sfu.ca or cenk@cs.sfu.ca Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23047557

Shallow-Water Nitrox Diving, the NASA Experience

NASA Technical Reports Server (NTRS)

Fitzpatrick, Daniel T.

2009-01-01

NASA s Neutral Buoyancy Laboratory (NBL) contains a 6.2 million gallon, 12-meter deep pool where astronauts prepare for space missions involving space walks (extravehicular activity EVA). Training is conducted in a space suit (extravehicular mobility unit EMU) pressurized to 4.0 - 4.3 PSI for up to 6.5 hours while breathing a 46% NITROX mix. Since the facility opened in 1997, over 30,000 hours of suited training has been completed with no occurrence of decompression sickness (DCS) or oxygen toxicity. This study examines the last 5 years of astronaut suited training runs. All suited runs are computer monitored and data is recorded in the Environmental Control System (ECS) database. Astronaut training runs from 2004 - 2008 were reviewed and specific data including total run time, maximum depth and average depth were analyzed. One hundred twenty seven astronauts and cosmonauts completed 2,231 training runs totaling 12,880 exposure hours. Data was available for 96% of the runs. It was revealed that the suit configuration produces a maximum equivalent air depth of 7 meters, essentially eliminating the risk of DCS. Based on average run depth and time, approximately 17% of the training runs exceeded the NOAA oxygen maximum single exposure limits, with no resulting oxygen toxicity. The NBL suited training protocols are safe and time tested. Consideration should be given to reevaluate the NOAA oxygen exposure limits for PO2 levels at or below 1 ATA.

Questions and Answers in Extreme Energy Cosmic Rays - a guide to explore the data set of the Pierre Auger Observatory

NASA Astrophysics Data System (ADS)

Abreu, P.; Andringa, S.; Diogo, F.; Espírito Santo, M. C.; Pierre Auger Collaboration

2016-04-01

The Pierre Auger Observatory is the largest extensive air shower detector, covering 3000 km2 in Argentina. The Observatory makes available, for educational and outreach purposes, 1% of its cosmic ray data set, corresponding after 10 years of running to more than 35 000 cosmic ray events. Several different proposals of educational activities have been developed within the collaboration and are available. We will focus on the activity guide we developed with the aim of exploring the rich education and outreach potential of cosmic rays with Portuguese high school students. In this guide we use the Auger public data set as a starting point to introduce open questions on the origin, nature and spectrum of high energy cosmic rays. To address them, the students learn about the air-shower cascade development, data reconstruction and its statistical analysis. The guide has been used both in the context of student summer internships at research labs and directly in schools, under the supervision of trained teachers and in close collaboration with Auger researchers. It is now available in Portuguese, English and Spanish.

Running-related injuries in school-age children and adolescents treated in emergency departments from 1994 through 2007.

PubMed

Mehl, Ann J; Nelson, Nicolas G; McKenzie, Lara B

2011-02-01

Running for exercise is a popular way to motivate children to be physically active. Running-related injuries are well studied in adults but little information exists for children and adolescents. Through use of the National Electronic Injury Surveillance System database, cases of running-related injuries were selected by using activity codes for exercise (which included running and jogging). Sample weights were used to calculate national estimates. An estimated 225 344 children and adolescents 6 to 18 years old were treated in US emergency departments for running-related injuries. The annual number of cases increased by 34.0% over the study period. One third of the injuries involved a running-related fall and more than one half of the injuries occurred at school. The majority of injuries occurred to the lower extremities and resulted in a sprain or strain. These findings emphasize the need for scientific evidence-based guidelines for pediatric running. The high proportion of running-related falls warrants further research.

Predicting running away in girls who are victims of commercial sexual exploitation.

PubMed

Hershberger, Alexandra R; Sanders, Jasmyn; Chick, Crisanna; Jessup, Megan; Hanlin, Hugh; Cyders, Melissa A

2018-05-01

Youth that are victims of commercial sexual exploitation of children (CSEC) have a host of clinical problems and often run away from home, residential care, and treatment, which complicates and limits treatment effectiveness. No research to date has attempted to predict running away in CSEC victims. The present study aimed to 1) characterize a clinically referred sample of girls who were victims of CSEC and compare them to other high-risk girls (i.e., girls who also have a history of trauma and running away, but deny CSEC); and 2) examine the utility of using the Youth Level of Service/Case Management Inventory (YLS/CMI) to predict future running away. Data were collected from de-identified charts of 80 girls (mean age = 15.38, SD = 1.3, 37.9% White, 52.5% CSEC victims) who were referred for psychological assessment by the Department of Child Services. Girls in the CSEC group were more likely to have experienced sexual abuse (χ 2  = 6.85, p = .009), an STI (χ 2  = 6.45, p = .01), a post-traumatic stress disorder diagnosis (χ 2  = 11.84, p = .001), and a substance use disorder diagnosis (χ 2  = 11.32, p = .001) than high-risk girls. Moderated regression results indicated that YLS/CMI scores significantly predicted future running away among the CSEC group (β = 0.23, SE = .06, p = .02), but not the high-risk group (β = -.008, SE = .11, p =.90). The YLS/CMI shows initial promise for predicting future running away in girls who are CSEC victims. Predicting running away can help identify those at risk for and prevent running away and improve treatment outcomes. We hope current findings stimulate future work in this area. Copyright © 2018 Elsevier Ltd. All rights reserved.

Physiological Profiles of High School Female Cross Country Runners.

ERIC Educational Resources Information Center

Butts, Nancy Kay

1982-01-01

Percentage of body fat, ratings of perceived exertion, and maximal oxygen consumption were obtained during a continuous running treadmill test on 127 high school female cross country runners. The relatively low relationships between the variables tested and running performance indicated that other factors may be more important determinants of…

Sex determines effect of physical activity on diet preference: Association of striatal opioids and gut microbiota composition.

PubMed

Lee, Jenna R; Muckerman, Julie E; Wright, Anna M; Davis, Daniel J; Childs, Tom E; Gillespie, Catherine E; Vieira-Potter, Victoria J; Booth, Frank W; Ericsson, Aaron C; Will, Matthew J

2017-09-15

Previous studies suggest an interaction between the level of physical activity and diet preference. However, this relationship has not been well characterized for sex differences that may exist. The present study examined the influence of sex on diet preference in male and female Wistar rats that were housed under either sedentary (no wheel access) (SED) or voluntary wheel running access (RUN) conditions. Following a 1 week acclimation period to these conditions, standard chow was replaced with concurrent ad libitum access to a choice of 3 pelleted diets (high-fat, high-sucrose, and high-corn starch) in the home cage. SED and RUN conditions remained throughout the next 4 week diet preference assessment period. Body weight, running distance, and intake of each diet were measured daily. At the conclusion of the 4 week diet preference test, animals were sacrificed and brains were collected for mRNA analysis. Fecal samples were also collected before and after the 4 week diet preference phase to characterize microbiota composition. Results indicate sex dependent interactions between physical activity and both behavioral and physiological measures. Females in both RUN and SED conditions preferred the high-fat diet, consuming significantly more high-fat diet than either of the other two diets. While male SED rats also preferred the high-fat diet, male RUN rats consumed significantly less high-fat diet than the other groups, instead preferring all three diets equally. There was also a sex dependent influence of physical activity on both reward related opioid mRNA expression in the ventral striatum and the characterization of gut microbiota. The significant sex differences in response to physical activity observed through both behavioral and physiological measures suggest potential motivational or metabolic difference between males and females. The findings highlight the necessity for further exploration between male and female response to physical activity and feeding behavior. Copyright © 2017 Elsevier B.V. All rights reserved.

Neuromuscular Risk Factors for Knee and Ankle Ligament Injuries in Male Youth Soccer Players

PubMed Central

Read, Paul J.; Oliver, Jon L.; De Ste Croix, Mark B. A.; Myer, Gregory D.; Lloyd, Rhodri S.

2017-01-01

Injuries reported in male youth soccer players most commonly occur in the lower extremities, and include a high proportion of ligament sprains at the ankle and knee with a lower proportion of overuse injuries. There is currently a paucity of available literature that examines age- and sex-specific injury risk factors for such injuries within youth soccer players. Epidemiological data have reported movements that lead to non-contact ligament injury include running, twisting and turning, over-reaching and landing. Altered neuromuscular control during these actions has been suggested as a key mechanism in females and adult populations; however, data available in male soccer players is sparse. The focus of this article is to review the available literature and elucidate prevalent risk factors pertaining to male youth soccer players which may contribute to their relative risk of injury. PMID:26856339

Improving overly manufacturing metrics through application of feedforward mask-bias

NASA Astrophysics Data System (ADS)

Joubert, Etienne; Pellegrini, Joseph C.; Misra, Manish; Sturtevant, John L.; Bernhard, John M.; Ong, Phu; Crawshaw, Nathan K.; Puchalski, Vern

2003-06-01

Traditional run-to-run controllers that rely on highly correlated historical events to forecast process corrections have been shown to provide substantial benefit over manual control in the case of a fab that is primarily manufacturing high volume, frequent running parts (i.e., DRAM, MPU, and similar operations). However, a limitation of the traditional controller emerges when it is applied to a fab whose work in process (WIP) is composed of primarily short-running, high part count products (typical of foundries and ASIC fabs). This limitation exists because there is a strong likelihood that each reticle has a unique set of process corrections different from other reticles at the same process layer. Further limitations exist when it is realized that each reticle is loaded and aligned differently on multiple exposure tools.A structural change in how the run-to-run controller manages the frequent reticle changes associated with the high part count environment has allowed for breakthrough performance to be achieved. This breakthrough was mad possible by the realization that; 1. Reticle sourced errors were highly stable over long periods of time, thus allowing them to be deconvolved from the day to day tool and process drifts. 2. Reticle sourced errors can be modeled as a feedforward disturbance rather than as discriminates in defining and dividing process streams. In this paper, we show how to deconvolve the static (reticle) and dynamic (day to day tool and process) components from the overall error vector to better forecast feedback for existing products as well as how to compute or learn these values for new product introductions - or new tool startups. Manufacturing data will presented to support this discussion with some real world success stories.

Effect of Minimalist Footwear on Running Efficiency: A Randomized Crossover Trial.

PubMed

Gillinov, Stephen M; Laux, Sara; Kuivila, Thomas; Hass, Daniel; Joy, Susan M

2015-05-01

Although minimalist footwear is increasingly popular among runners, claims that minimalist footwear enhances running biomechanics and efficiency are controversial. Minimalist and barefoot conditions improve running efficiency when compared with traditional running shoes. Randomized crossover trial. Level 3. Fifteen experienced runners each completed three 90-second running trials on a treadmill, each trial performed in a different type of footwear: traditional running shoes with a heavily cushioned heel, minimalist running shoes with minimal heel cushioning, and barefoot (socked). High-speed photography was used to determine foot strike, ground contact time, knee angle, and stride cadence with each footwear type. Runners had more rearfoot strikes in traditional shoes (87%) compared with minimalist shoes (67%) and socked (40%) (P = 0.03). Ground contact time was longest in traditional shoes (265.9 ± 10.9 ms) when compared with minimalist shoes (253.4 ± 11.2 ms) and socked (250.6 ± 16.2 ms) (P = 0.005). There was no difference between groups with respect to knee angle (P = 0.37) or stride cadence (P = 0.20). When comparing running socked to running with minimalist running shoes, there were no differences in measures of running efficiency. When compared with running in traditional, cushioned shoes, both barefoot (socked) running and minimalist running shoes produce greater running efficiency in some experienced runners, with a greater tendency toward a midfoot or forefoot strike and a shorter ground contact time. Minimalist shoes closely approximate socked running in the 4 measurements performed. With regard to running efficiency and biomechanics, in some runners, barefoot (socked) and minimalist footwear are preferable to traditional running shoes.

The ATLAS Data Acquisition System: from Run 1 to Run 2

NASA Astrophysics Data System (ADS)

Panduro Vazquez, William; ATLAS Collaboration

2016-04-01

The experience gained during the first period of very successful data taking of the ATLAS experiment (Run 1) has inspired a number of ideas for improvement of the Data Acquisition (DAQ) system that are being put in place during the so-called Long Shutdown 1 of the Large Hadron Collider (LHC), in 2013/14. We have updated the data-flow architecture, rewritten an important fraction of the software and replaced hardware, profiting from state of the art technologies. This paper summarizes the main changes that have been applied to the ATLAS DAQ system and highlights the expected performance and functional improvements that will be available for the LHC Run 2. Particular emphasis will be put on explaining the reasons for our architectural and technical choices, as well as on the simulation and testing approach used to validate this system.

ACON: a multipurpose production controller for plasma physics codes

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

Snell, C.

1983-01-01

ACON is a BCON controller designed to run large production codes on the CTSS Cray-1 or the LTSS 7600 computers. ACON can also be operated interactively, with input from the user's terminal. The controller can run one code or a sequence of up to ten codes during the same job. Options are available to get and save Mass storage files, to perform Historian file updating operations, to compile and load source files, and to send out print and film files. Special features include ability to retry after Mass failures, backup options for saving files, startup messages for the various codes,more » and ability to reserve specified amounts of computer time after successive code runs. ACON's flexibility and power make it useful for running a number of different production codes.« less

Program For Generating Interactive Displays

NASA Technical Reports Server (NTRS)

Costenbader, Jay; Moleski, Walt; Szczur, Martha; Howell, David; Engelberg, Norm; Li, Tin P.; Misra, Dharitri; Miller, Philip; Neve, Leif; Wolf, Karl;

Locomotion characteristics and match-induced impairments in physical performance in male elite team handball players.

PubMed

Michalsik, L B; Aagaard, P; Madsen, K

2013-07-01

The purpose of this study was to determine the physical demands and match-induced impairments in physical performance in male elite Team Handball (TH) players in relation to playing position. Male elite TH field players were closely observed during 6 competitive seasons. Each player (wing players: WP, pivots: PV, backcourt players: BP) was evaluated during match-play using video recording and subsequently performing locomotion match analysis. A total distance of 3 627±568 m (group means±SD) was covered per match with a total effective playing time (TPT) of 53:51±5:52 min:s, while full-time players covered 3 945±538 m. The mean speed was 6.40±1.01 km · h - 1. High-intensity running constituted only 1.7±0.9% of TPT per match corresponding to 7.9±4.9% of the total distance covered. An average of 1 482.4±312.6 activity changes per player (n=82) with 53.2±14.1 high-intensity runs were observed per match. Total distance covered was greater in BP (3 765±532 m) and WP (3 641±501 m) than PV (3 295±495 m) (p<0.05), and WP performed more high-intensity running (10.9±5.7% of total distance covered) than PV (8.5±4.3%, p<0.05) and BP (6.2±3.2%, p<0.01). The amount of high-intensity running was lower (p<0.05) in the second (130.4±38.4 m) than in the first half (155.3±47.6 m) corresponding to a decrease of 16.2%.In conclusion, modern male elite TH is a complex team sport that comprises several types of movement categories, which during match-play place moderate-to-high demands on intermittent endurance running capacity and where the amount of high-intensity running may be high during brief periods of the match. Signs of fatigue-related changes were observed in terms of temporary impaired physical performance, since the amount of high-intensity running was reduced in the second half. Notably, physical demands differed between playing positions, with WP demonstrating a more intensive activity pattern than BP and PV, respectively. © Georg Thieme Verlag KG Stuttgart · New York.

Gut-training: the impact of two weeks repetitive gut-challenge during exercise on gastrointestinal status, glucose availability, fuel kinetics, and running performance.

PubMed

Costa, Ricardo J S; Miall, Atlanta; Khoo, Anthony; Rauch, Christopher; Snipe, Rhiannon; Camões-Costa, Vera; Gibson, Peter

2017-05-01

Due to gastrointestinal tract adaptability, the study aimed to determine the impact of gut-training protocol over 2 weeks on gastrointestinal status, blood glucose availability, fuel kinetics, and running performance. Endurance runners (n = 25) performed a gut-challenge trial (GC1), consisting of 2 h running exercise at 60% V̇O 2max whilst consuming gel-discs containing 30 g carbohydrates (2:1 glucose/fructose, 10% w/v) every 20 min and a 1 h distance test. Participants were then randomly assigned to a carbohydrate gel-disc (CHO-S), carbohydrate food (CHO-F), or placebo (PLA) gut-training group for 2 weeks of repetitive gut-challenge intervention. Participants then repeated a second gut-challenge trial (GC2). Gastrointestinal symptoms reduced in GC2 on CHO-S (60%; p = 0.008) and CHO-F (63%; p = 0.046); reductions were greater than PLA (p < 0.05). H 2 peak was lower in GC2 on CHO-S (mean (CI): 6 (4-8) ppm) compared with CHO-F (9 (6-12) ppm) and PLA (12 (2-21) ppm) (trial × time: p < 0.001). Blood glucose concentration was higher in GC2 on CHO-S (7.2 (6.3-8.1) mmol·L -1 ) compared with CHO-F (6.1 (5.7-6.5) mmol·L -1 ) and PLA (6.2 (4.9-7.5) mmol·L -1 ) (trial × time: p = 0.015). No difference in oxidation rates, plasma I-FABP, and cortisol concentrations were observed between groups and trials. Distance test improved on CHO-S (5.2%) and CHO-F (4.3%) in GC2, but not on PLA (-2.1%) (trial × time: p = 0.009). Two weeks of gut-training with CHO-S and CHO-F improved gastrointestinal symptoms and running performance compared with PLA. CHO-S also reduced malabsorption and increased blood glucose availability during endurance running compared with PLA.

The role of the cold Okhotsk Sea in strengthening of the Pacific subtropical high and Baiu precipitation

NASA Astrophysics Data System (ADS)

Kawasaki, K.; Tachibana, Y.; Nakamura, T.; Yamazaki, K.; Kodera, K.

2016-12-01

It is commonly known that the formation of a stationery precipitation zone in association with the Baiu front is influenced by the existence of the warm Tibetan Plateau. Some GCM studies in which the Tibetan Plateau is removed pointed out that without the Tibetan Plateau, the Baiu front wound not appear. The cold Okhotsk Sea, which is located to the north of Japan, is also important in forming cold air for the Bai front. This study focused on the role of the Okhotsk Sea in the formation of the Baiu front by using an atmospheric GCM. One GCM is executed without the Okhotsk Sea, in which was changed to an eastern part of the Eurasian continent as if the Okhotsk Sea was totally landfilled (land run). The other (sea run) is a control run under the boundary condition of climatic seasonal changes of the SST over the globe. The comparison of the land run with the sea run showed that precipitation over Japan would weaken in the Baiu season without the Okhotsk Sea, indicating that the existence of the Okhotsk Sea has an impact on the increase in precipitation. The precipitation increase in the sea run is directly accounted by the strengthening of southeast wind in association with the strengthening of the subtropical high located over the Pacific Ocean (Fig. 1). The westerly jet, which is located at the northern part of the subtropical high, was also accelerated in the sea run. The subtropical high in association with the accelerated jet was strengthened by meridional atmospheric thermal gradient caused by underlying cold Okhotsk Sea and the warm Pacific Ocean. The strengthened thermal gradient also activated the storm track that extends zonally over the Okhotsk Sea, and the activated storm track further strengthened the jet and subtropical high by wave-mean flow feedback. This feedback loop could further strengthen the Baiu precipitation. In consequence, the Okhotsk plays a significant role in the strengthening the subtropical high and its associated Baiu precipitation.

Fatty acid kinetic responses to running above or below lactate threshold.

PubMed

Kanaley, J A; Mottram, C D; Scanlon, P D; Jensen, M D

1995-08-01

During running exercise above the lactate threshold (LT), it is unknown whether free fatty acid (FFA) mobilization can meet the energy demands for fatty acid oxidation. This study was performed to determine whether FFA availability is reduced during running exercise above compared with below the LT and to assess whether the level of endurance training influences FFA mobilization. Twelve marathon runners and 12 moderately trained runners ran at a workload that was either above or below their individual LT. Fatty acid oxidation (indirect calorimetry) and FFA release ([1-14C]palmitate) were measured at baseline, throughout exercise, and at recovery. The plasma FFA rate of appearance increased during exercise in both groups; running above or below the LT, but the total FFA availability for 30 min of exercise was greater (P < 0.01) in the below LT group (marathon, 23 +/- 2 mmol; moderate, 21 +/- 2 mmol) than in the above LT group (18 +/- 3 and 13 +/- 3 mmol, respectively). Total fatty acid oxidation (indirect calorimetry) greatly exceeded circulating FFA availability, regardless of training or exercise group (P < 0.01). No statistically significant exercise intensity or training differences in fatty acid oxidation were found (above LT: marathon, 71 +/- 12, moderate, 64 +/- 17 mmol/30 min; below LT: marathon 91 +/- 12, moderate, 60 +/- 5 mmol/30 min). In conclusion, during exercise above or below LT, circulating FFA cannot meet the oxidative needs and intramuscular triglyceride stores must be utilized. Further marathon training does not enhance effective adipose tissue lipolysis during exercise compared with moderate endurance training.

Fatigue limit and Hysteresis Behavior of Type 304L Stainless Steel in Air and PWR Water, at 150°C and 300°C

NASA Astrophysics Data System (ADS)

Solomon, H. D.; Amzallag, C.; Vallee, A. J.; DeLair, R. E.

This is a study of the 107 cycle fatigue limit of Type 304L Stainless Steel, as measured in fully reversed (R=-1) load-controlled tests, at 150°C and 300°C, in air and PWR water. The staircase method was used to determine the fatigue limit. The tests run here utilized a cycle frequency of 1.818Hz and are compared to other tests from the literature that were run at 30Hz. The fatigue limit measured in the tests run at the high frequency was higher than that measured here. This is explained by measurements of the strain developed during cycling, using the different cycle frequencies. The tests run at the higher frequencies yielded lower strains for a given stress and, as expected, this resulted in higher fatigue limits. Using 107 cycles to define a run-out also led to a lower fatigue limit. These results are important as most previous fatigue limit measurements utilized 106 cycles or less to define a run-out, and when lives as long as 107 cycles are used the tests are generally run at high cycle frequencies, thus leading to higher fatigue limits than those measured here.

Flow Asymmetric Propargylation: Development of Continuous Processes for the Preparation of a Chiral β-Amino Alcohol.

PubMed

Li, Hui; Sheeran, Jillian W; Clausen, Andrew M; Fang, Yuan-Qing; Bio, Matthew M; Bader, Scott

2017-08-01

The development of a flow chemistry process for asymmetric propargylation using allene gas as a reagent is reported. The connected continuous process of allene dissolution, lithiation, Li-Zn transmetallation, and asymmetric propargylation provides homopropargyl β-amino alcohol 1 with high regio- and diastereoselectivity in high yield. This flow process enables practical use of an unstable allenyllithium intermediate. The process uses the commercially available and recyclable (1S,2R)-N-pyrrolidinyl norephedrine as a ligand to promote the highly diastereoselective (32:1) propargylation. Judicious selection of mixers based on the chemistry requirement and real-time monitoring of the process using process analytical technology (PAT) enabled stable and scalable flow chemistry runs. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Exercise economy in skiing and running

PubMed Central

Losnegard, Thomas; Schäfer, Daniela; Hallén, Jostein

2014-01-01

Substantial inter-individual variations in exercise economy exist even in highly trained endurance athletes. The variation is believed to be determined partly by intrinsic factors. Therefore, in the present study, we compared exercise economy in V2-skating, double poling, and uphill running. Ten highly trained male cross-country skiers (23 ± 3 years, 180 ± 6 cm, 75 ± 8 kg, VO2peak running: 76.3 ± 5.6 mL·kg−1·min−1) participated in the study. Exercise economy and VO2peak during treadmill running, ski skating (V2 technique) and double poling were compared based on correlation analysis. There was a very large correlation in exercise economy between V2-skating and double poling (r = 0.81) and large correlations between V2-skating and running (r = 0.53) and double poling and running (r = 0.58). There were trivial to moderate correlations between exercise economy and the intrinsic factors VO2peak (r = 0.00–0.23), cycle rate (r = 0.03–0.46), body mass (r = −0.09–0.46) and body height (r = 0.11–0.36). In conclusion, the inter-individual variation in exercise economy could be explained only moderately by differences in VO2peak, body mass and body height. Apparently other intrinsic factors contribute to the variation in exercise economy between highly trained subjects. PMID:24478718

Long-Term Marathon Running Is Associated with Low Coronary Plaque Formation in Women.

PubMed

Roberts, William O; Schwartz, Robert S; Kraus, Stacia Merkel; Schwartz, Jonathan G; Peichel, Gretchen; Garberich, Ross F; Lesser, John R; Oesterle, Stephen N; Wickstrom, Kelly K; Knickelbine, Thomas; Harris, Kevin M

2017-04-01

Marathon running is presumed to improve cardiovascular risk, but health benefits of high volume running are unknown. High-resolution coronary computed tomography angiography and cardiac risk factor assessment were completed in women with long-term marathon running histories to compare to sedentary women with similar risk factors. Women who had run at least one marathon per year for 10-25 yr underwent coronary computed tomography angiography, 12-lead ECG, blood pressure and heart rate measurement, lipid panel, and a demographic/health risk factor survey. Sedentary matched controls were derived from a contemporaneous clinical study database. CT scans were analyzed for calcified and noncalcified plaque prevalence, volume, stenosis severity, and calcium score. Women marathon runners (n = 26), age 42-82 yr, with combined 1217 marathons (average 47) exhibited significantly lower coronary plaque prevalence and less calcific plaque volume. The marathon runners also had less risk factors (smoking, hypertension, and hyperlipidemia); significantly lower resting heart rate, body weight, body mass index, and triglyceride levels; and higher high-density lipoprotein cholesterol levels compared with controls (n = 28). The five women runners with coronary plaque had run marathons for more years and were on average 12 yr older (65 vs 53) than the runners without plaque. Women marathon runners had minimal coronary artery calcium counts, lower coronary artery plaque prevalence, and less calcified plaque volume compared with sedentary women. Developing coronary artery plaque in long-term women marathon runners appears related to older age and more cardiac risk factors, although the runners with coronary artery plaque had accumulated significantly more years running marathons.

The Influence Of Team Rating On Running Performance In Elite Gaelic Football.

PubMed

Mangan, Shane; Malone, Shane; Ryan, Martin; Gahan, Jason Mc; Warne, Joe; Martin, Denise; O'Neill, Cian; Burns, Con; Collins, Kieran

2017-11-06

It is currently unknown how team rating influences running performance in Gaelic football. GPS technologies were used to quantify match-running performance within 5 elite Gaelic football teams over a period of 5 years (2012-2016). In total 780 player data sets were collected over 95 matches. Running performance variables included total distance, high-speed distance (≥17 km h) and the percentage of high-speed distance. Team ratings were determined objectively using the Elo Ratings System for Gaelic football. Reference team rating had trivial effects on total distance (p = 0.011, partial η2 = 0.008) and high-speed distance (p = 0.011, partial η2 = 0.008). Opposition team rating had small effects on total distance (p = 0.005, partial η2 = 0.016) and high-speed distance (p = 0.001, partial η2 = 0.020). Top tier teams cover greater total distances and high-speed distance than lower tier teams. Players cover considerably less total distance and high-speed distance against tier 3 and tier 4 teams. Tier 1 players ran a significantly higher percentage of distance at high-speed, than players who played for tier 2 teams (p = 0.020). The competitive advantage of top tier Gaelic football teams is closely linked with their ability to demonstrate a higher physical intensity than lower tier teams.

Effects of voluntary running with defined distances on body adiposity and its associated inflammation in mice fed a high-fat diet

USDA-ARS?s Scientific Manuscript database

Sedentary lifestyle contributes to obesity. This study examined the effect of quantitative voluntary running on body adiposity and its associated inflammation in mice fed a high-fat diet. Male C57BL/6 mice were assigned into six groups and fed the AIN93G (sedentary) or a high-fat diet (sedentary, ...

Circadian activity rhythms and voluntary ethanol intake in male and female ethanol-preferring rats: effects of long-term ethanol access.

PubMed

Rosenwasser, Alan M; McCulley, Walter D; Fecteau, Matthew

2014-11-01

Chronic alcohol (ethanol) intake alters fundamental properties of the circadian clock. While previous studies have reported significant alterations in free-running circadian period during chronic ethanol access, these effects are typically subtle and appear to require high levels of intake. In the present study we examined the effects of long-term voluntary ethanol intake on ethanol consumption and free-running circadian period in male and female, selectively bred ethanol-preferring P and HAD2 rats. In light of previous reports that intermittent access can result in escalated ethanol intake, an initial 2-week water-only baseline was followed by either continuous or intermittent ethanol access (i.e., alternating 15-day epochs of ethanol access and ethanol deprivation) in separate groups of rats. Thus, animals were exposed to either 135 days of continuous ethanol access or to five 15-day access periods alternating with four 15-day periods of ethanol deprivation. Animals were maintained individually in running-wheel cages under continuous darkness throughout the experiment to allow monitoring of free-running activity and drinking rhythms, and 10% (v/v) ethanol and plain water were available continuously via separate drinking tubes during ethanol access. While there were no initial sex differences in ethanol drinking, ethanol preference increased progressively in male P and HAD2 rats under both continuous and intermittent-access conditions, and eventually exceeded that seen in females. Free-running period shortened during the initial ethanol-access epoch in all groups, but the persistence of this effect showed complex dependence on sex, breeding line, and ethanol-access schedule. Finally, while females of both breeding lines displayed higher levels of locomotor activity than males, there was little evidence for modulation of activity level by ethanol access. These results are consistent with previous findings that chronic ethanol intake alters free-running circadian period, and show further that the development of chronobiological tolerance to ethanol may vary by sex and genotype. Copyright © 2014 Elsevier Inc. All rights reserved.

Fingerprinting Communication and Computation on HPC Machines

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

Peisert, Sean

2010-06-02

How do we identify what is actually running on high-performance computing systems? Names of binaries, dynamic libraries loaded, or other elements in a submission to a batch queue can give clues, but binary names can be changed, and libraries provide limited insight and resolution on the code being run. In this paper, we present a method for"fingerprinting" code running on HPC machines using elements of communication and computation. We then discuss how that fingerprint can be used to determine if the code is consistent with certain other types of codes, what a user usually runs, or what the user requestedmore » an allocation to do. In some cases, our techniques enable us to fingerprint HPC codes using runtime MPI data with a high degree of accuracy.« less

District-Run Public Charter High Schools: What Do We Know? Research Brief

ERIC Educational Resources Information Center

Bleyaert, Barbara

2010-01-01

Successful district-run charter high schools, ones where there is a higher than expected achievement and graduation rate, share three characteristics: (1) a clearly articulated focus or mission for the school; (2) a rigorous academic curriculum for all students that emphasizes relevance, critical thinking, and problem-solving; (3) an emphasis on…

A metabolomic study of the PPARδ agonist GW501516 for enhancing running endurance in Kunming mice.

PubMed

Chen, Wei; Gao, Rong; Xie, Xinni; Zheng, Zhibing; Li, Haijing; Li, Song; Dong, Fangting; Wang, Lili

2015-05-06

Exercise can increase peroxisome proliferator-activated receptor-δ (PPARδ) expression in skeletal muscle. PPARδ regulates muscle metabolism and reprograms muscle fibre types to enhance running endurance. This study utilized metabolomic profiling to examine the effects of GW501516, a PPARδ agonist, on running endurance in mice. While training alone increased the exhaustive running performance, GW501516 treatment enhanced running endurance and the proportion of succinate dehydrogenase (SDH)-positive muscle fibres in both trained and untrained mice. Furthermore, increased levels of intermediate metabolites and key enzymes in fatty acid oxidation pathways were observed following training and/or treatment. Training alone increased serum inositol, glucogenic amino acids, and branch chain amino acids. However, GW501516 increased serum galactose and β-hydroxybutyrate, independent of training. Additionally, GW501516 alone raised serum unsaturated fatty acid levels, especially polyunsaturated fatty acids, but levels increased even more when combined with training. These findings suggest that mechanisms behind enhanced running capacity are not identical for GW501516 and training. Training increases energy availability by promoting catabolism of proteins, and gluconeogenesis, whereas GW501516 enhances specific consumption of fatty acids and reducing glucose utilization.

A metabolomic study of the PPARδ agonist GW501516 for enhancing running endurance in Kunming mice

PubMed Central

Chen, Wei; Gao, Rong; Xie, Xinni; Zheng, Zhibing; Li, Haijing; Li, Song; Dong, Fangting; Wang, Lili

2015-01-01

Exercise can increase peroxisome proliferator-activated receptor-δ (PPARδ) expression in skeletal muscle. PPARδ regulates muscle metabolism and reprograms muscle fibre types to enhance running endurance. This study utilized metabolomic profiling to examine the effects of GW501516, a PPARδ agonist, on running endurance in mice. While training alone increased the exhaustive running performance, GW501516 treatment enhanced running endurance and the proportion of succinate dehydrogenase (SDH)-positive muscle fibres in both trained and untrained mice. Furthermore, increased levels of intermediate metabolites and key enzymes in fatty acid oxidation pathways were observed following training and/or treatment. Training alone increased serum inositol, glucogenic amino acids, and branch chain amino acids. However, GW501516 increased serum galactose and β-hydroxybutyrate, independent of training. Additionally, GW501516 alone raised serum unsaturated fatty acid levels, especially polyunsaturated fatty acids, but levels increased even more when combined with training. These findings suggest that mechanisms behind enhanced running capacity are not identical for GW501516 and training. Training increases energy availability by promoting catabolism of proteins, and gluconeogenesis, whereas GW501516 enhances specific consumption of fatty acids and reducing glucose utilization. PMID:25943561

Porting and refurbishment of the WSS TNG control software

NASA Astrophysics Data System (ADS)

Caproni, Alessandro; Zacchei, Andrea; Vuerli, Claudio; Pucillo, Mauro

2004-09-01

The Workstation Software Sytem (WSS) is the high level control software of the Italian Galileo Galilei Telescope settled in La Palma Canary Island developed at the beginning of '90 for HP-UX workstations. WSS may be seen as a middle layer software system that manages the communications between the real time systems (VME), different workstations and high level applications providing a uniform distributed environment. The project to port the control software from the HP workstation to Linux environment started at the end of 2001. It is aimed to refurbish the control software introducing some of the new software technologies and languages, available for free in the Linux operating system. The project was realized by gradually substituting each HP workstation with a Linux PC with the goal to avoid main changes in the original software running under HP-UX. Three main phases characterized the project: creation of a simulated control room with several Linux PCs running WSS (to check all the functionality); insertion in the simulated control room of some HPs (to check the mixed environment); substitution of HP workstation in the real control room. From a software point of view, the project introduces some new technologies, like multi-threading, and the possibility to develop high level WSS applications with almost every programming language that implements the Berkley sockets. A library to develop java applications has also been created and tested.

Climate SPHINX: High-resolution present-day and future climate simulations with an improved representation of small-scale variability

NASA Astrophysics Data System (ADS)

Davini, Paolo; von Hardenberg, Jost; Corti, Susanna; Subramanian, Aneesh; Weisheimer, Antje; Christensen, Hannah; Juricke, Stephan; Palmer, Tim

2016-04-01

The PRACE Climate SPHINX project investigates the sensitivity of climate simulations to model resolution and stochastic parameterization. The EC-Earth Earth-System Model is used to explore the impact of stochastic physics in 30-years climate integrations as a function of model resolution (from 80km up to 16km for the atmosphere). The experiments include more than 70 simulations in both a historical scenario (1979-2008) and a climate change projection (2039-2068), using RCP8.5 CMIP5 forcing. A total amount of 20 million core hours will be used at end of the project (March 2016) and about 150 TBytes of post-processed data will be available to the climate community. Preliminary results show a clear improvement in the representation of climate variability over the Euro-Atlantic following resolution increase. More specifically, the well-known atmospheric blocking negative bias over Europe is definitely resolved. High resolution runs also show improved fidelity in representation of tropical variability - such as the MJO and its propagation - over the low resolution simulations. It is shown that including stochastic parameterization in the low resolution runs help to improve some of the aspects of the MJO propagation further. These findings show the importance of representing the impact of small scale processes on the large scale climate variability either explicitly (with high resolution simulations) or stochastically (in low resolution simulations).

Effect of sucrose availability on wheel-running as an operant and as a reinforcing consequence on a multiple schedule: Additive effects of extrinsic and automatic reinforcement.

PubMed

Belke, Terry W; Pierce, W David

2015-07-01

As a follow up to Belke and Pierce's (2014) study, we assessed the effects of repeated presentation and removal of sucrose solution on the behavior of rats responding on a two-component multiple schedule. Rats completed 15 wheel turns (FR 15) for either 15% or 0% sucrose solution in the manipulated component and lever pressed 10 times on average (VR 10) for an opportunity to complete 15 wheel turns (FR 15) in the other component. In contrast to our earlier study, the components advanced based on time (every 8min) rather than completed responses. Results showed that in the manipulated component wheel-running rates were higher and the latency to initiate running longer when sucrose was present (15%) compared to absent (0% or water); the number of obtained outcomes (sucrose/water), however, did not differ with the presentation and withdrawal of sucrose. For the wheel-running as reinforcement component, rates of wheel turns, overall lever-pressing rates, and obtained wheel-running reinforcements were higher, and postreinforcement pauses shorter, when sucrose was present (15%) than absent (0%) in manipulated component. Overall, our findings suggest that wheel-running rate regardless of its function (operant or reinforcement) is maintained by automatically generated consequences (automatic reinforcement) and is increased as an operant by adding experimentally arranged sucrose reinforcement (extrinsic reinforcement). This additive effect on operant wheel-running generalizes through induction or arousal to the wheel-running as reinforcement component, increasing the rate of responding for opportunities to run and the rate of wheel-running per opportunity. Copyright © 2015 Elsevier B.V. All rights reserved.

SCALCE: boosting sequence compression algorithms using locally consistent encoding.

PubMed

Hach, Faraz; Numanagic, Ibrahim; Alkan, Can; Sahinalp, S Cenk

2012-12-01

The high throughput sequencing (HTS) platforms generate unprecedented amounts of data that introduce challenges for the computational infrastructure. Data management, storage and analysis have become major logistical obstacles for those adopting the new platforms. The requirement for large investment for this purpose almost signalled the end of the Sequence Read Archive hosted at the National Center for Biotechnology Information (NCBI), which holds most of the sequence data generated world wide. Currently, most HTS data are compressed through general purpose algorithms such as gzip. These algorithms are not designed for compressing data generated by the HTS platforms; for example, they do not take advantage of the specific nature of genomic sequence data, that is, limited alphabet size and high similarity among reads. Fast and efficient compression algorithms designed specifically for HTS data should be able to address some of the issues in data management, storage and communication. Such algorithms would also help with analysis provided they offer additional capabilities such as random access to any read and indexing for efficient sequence similarity search. Here we present SCALCE, a 'boosting' scheme based on Locally Consistent Parsing technique, which reorganizes the reads in a way that results in a higher compression speed and compression rate, independent of the compression algorithm in use and without using a reference genome. Our tests indicate that SCALCE can improve the compression rate achieved through gzip by a factor of 4.19-when the goal is to compress the reads alone. In fact, on SCALCE reordered reads, gzip running time can improve by a factor of 15.06 on a standard PC with a single core and 6 GB memory. Interestingly even the running time of SCALCE + gzip improves that of gzip alone by a factor of 2.09. When compared with the recently published BEETL, which aims to sort the (inverted) reads in lexicographic order for improving bzip2, SCALCE + gzip provides up to 2.01 times better compression while improving the running time by a factor of 5.17. SCALCE also provides the option to compress the quality scores as well as the read names, in addition to the reads themselves. This is achieved by compressing the quality scores through order-3 Arithmetic Coding (AC) and the read names through gzip through the reordering SCALCE provides on the reads. This way, in comparison with gzip compression of the unordered FASTQ files (including reads, read names and quality scores), SCALCE (together with gzip and arithmetic encoding) can provide up to 3.34 improvement in the compression rate and 1.26 improvement in running time. Our algorithm, SCALCE (Sequence Compression Algorithm using Locally Consistent Encoding), is implemented in C++ with both gzip and bzip2 compression options. It also supports multithreading when gzip option is selected, and the pigz binary is available. It is available at http://scalce.sourceforge.net. fhach@cs.sfu.ca or cenk@cs.sfu.ca Supplementary data are available at Bioinformatics online.

WIWS: a protein structure bioinformatics Web service collection.

PubMed

Hekkelman, M L; Te Beek, T A H; Pettifer, S R; Thorne, D; Attwood, T K; Vriend, G

2010-07-01

The WHAT IF molecular-modelling and drug design program is widely distributed in the world of protein structure bioinformatics. Although originally designed as an interactive application, its highly modular design and inbuilt control language have recently enabled its deployment as a collection of programmatically accessible web services. We report here a collection of WHAT IF-based protein structure bioinformatics web services: these relate to structure quality, the use of symmetry in crystal structures, structure correction and optimization, adding hydrogens and optimizing hydrogen bonds and a series of geometric calculations. The freely accessible web services are based on the industry standard WS-I profile and the EMBRACE technical guidelines, and are available via both REST and SOAP paradigms. The web services run on a dedicated computational cluster; their function and availability is monitored daily.

Mendel-GPU: haplotyping and genotype imputation on graphics processing units

PubMed Central

Chen, Gary K.; Wang, Kai; Stram, Alex H.; Sobel, Eric M.; Lange, Kenneth

2012-01-01

Motivation: In modern sequencing studies, one can improve the confidence of genotype calls by phasing haplotypes using information from an external reference panel of fully typed unrelated individuals. However, the computational demands are so high that they prohibit researchers with limited computational resources from haplotyping large-scale sequence data. Results: Our graphics processing unit based software delivers haplotyping and imputation accuracies comparable to competing programs at a fraction of the computational cost and peak memory demand. Availability: Mendel-GPU, our OpenCL software, runs on Linux platforms and is portable across AMD and nVidia GPUs. Users can download both code and documentation at http://code.google.com/p/mendel-gpu/. Contact: gary.k.chen@usc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22954633

A High-Throughput Biological Calorimetry Core: Steps to Startup, Run, and Maintain a Multiuser Facility.

PubMed

Yennawar, Neela H; Fecko, Julia A; Showalter, Scott A; Bevilacqua, Philip C

2016-01-01

Many labs have conventional calorimeters where denaturation and binding experiments are setup and run one at a time. While these systems are highly informative to biopolymer folding and ligand interaction, they require considerable manual intervention for cleaning and setup. As such, the throughput for such setups is limited typically to a few runs a day. With a large number of experimental parameters to explore including different buffers, macromolecule concentrations, temperatures, ligands, mutants, controls, replicates, and instrument tests, the need for high-throughput automated calorimeters is on the rise. Lower sample volume requirements and reduced user intervention time compared to the manual instruments have improved turnover of calorimetry experiments in a high-throughput format where 25 or more runs can be conducted per day. The cost and efforts to maintain high-throughput equipment typically demands that these instruments be housed in a multiuser core facility. We describe here the steps taken to successfully start and run an automated biological calorimetry facility at Pennsylvania State University. Scientists from various departments at Penn State including Chemistry, Biochemistry and Molecular Biology, Bioengineering, Biology, Food Science, and Chemical Engineering are benefiting from this core facility. Samples studied include proteins, nucleic acids, sugars, lipids, synthetic polymers, small molecules, natural products, and virus capsids. This facility has led to higher throughput of data, which has been leveraged into grant support, attracting new faculty hire and has led to some exciting publications. © 2016 Elsevier Inc. All rights reserved.

Effect of Minimalist Footwear on Running Efficiency

PubMed Central

Gillinov, Stephen M.; Laux, Sara; Kuivila, Thomas; Hass, Daniel; Joy, Susan M.

2015-01-01

Background: Although minimalist footwear is increasingly popular among runners, claims that minimalist footwear enhances running biomechanics and efficiency are controversial. Hypothesis: Minimalist and barefoot conditions improve running efficiency when compared with traditional running shoes. Study Design: Randomized crossover trial. Level of Evidence: Level 3. Methods: Fifteen experienced runners each completed three 90-second running trials on a treadmill, each trial performed in a different type of footwear: traditional running shoes with a heavily cushioned heel, minimalist running shoes with minimal heel cushioning, and barefoot (socked). High-speed photography was used to determine foot strike, ground contact time, knee angle, and stride cadence with each footwear type. Results: Runners had more rearfoot strikes in traditional shoes (87%) compared with minimalist shoes (67%) and socked (40%) (P = 0.03). Ground contact time was longest in traditional shoes (265.9 ± 10.9 ms) when compared with minimalist shoes (253.4 ± 11.2 ms) and socked (250.6 ± 16.2 ms) (P = 0.005). There was no difference between groups with respect to knee angle (P = 0.37) or stride cadence (P = 0.20). When comparing running socked to running with minimalist running shoes, there were no differences in measures of running efficiency. Conclusion: When compared with running in traditional, cushioned shoes, both barefoot (socked) running and minimalist running shoes produce greater running efficiency in some experienced runners, with a greater tendency toward a midfoot or forefoot strike and a shorter ground contact time. Minimalist shoes closely approximate socked running in the 4 measurements performed. Clinical Relevance: With regard to running efficiency and biomechanics, in some runners, barefoot (socked) and minimalist footwear are preferable to traditional running shoes. PMID:26131304

Research on natural frequency based on modal test for high speed vehicles

NASA Astrophysics Data System (ADS)

Ma, Guangsong; He, Guanglin; Guo, Yachao

2018-04-01

High speed vehicle as a vibration system, resonance generated in flight may be harmful to high speed vehicles. It is possible to solve the resonance problem by acquiring the natural frequency of the high-speed aircraft and then taking some measures to avoid the natural frequency of the high speed vehicle. Therefore, In this paper, the modal test of the high speed vehicle was carried out by using the running hammer method and the PolyMAX modal parameter identification method. Firstly, the total frequency response function, coherence function of the high speed vehicle are obtained by the running hammer stimulation test, and through the modal assurance criterion (MAC) to determine the accuracy of the estimated parameters. Secondly, the first three order frequencies, the pole steady state diagram of the high speed vehicles is obtained by the PolyMAX modal parameter identification method. At last, the natural frequency of the vibration system was accurately obtained by the running hammer method.

Wheel running reduces high-fat diet intake, preference and mu-opioid agonist stimulated intake

PubMed Central

Liang, Nu-Chu; Bello, Nicholas T.; Moran, Timothy H.

2015-01-01

The ranges of mechanisms by which exercise affects energy balance remain unclear. One potential mechanism may be that exercise reduces intake and preference for highly palatable, energy dense fatty foods. The current study used a rodent wheel running model to determine whether and how physical activity affects HF diet intake/preference and reward signaling. Experiment 1 examined whether wheel running affected the ability of intracerebroventricular (ICV) µ opioid receptor agonist D-Ala2, NMe-Phe4, Glyol5-enkephalin (DAMGO) to increase HF diet intake. Experiment 2 examined the effects of wheel running on the intake of and preference for a previously preferred HF diet. We also assessed the effects of wheel running and diet choice on mesolimbic dopaminergic and opioidergic gene expression. Experiment 1 revealed that wheel running decreased the ability of ICV DAMGO administration to stimulate HF diet intake. Experiment 2 showed that wheel running suppressed weight gain and reduced intake and preference for a previously preferred HF diet. Furthermore, the mesolimbic gene expression profile of wheel running rats was different from that of their sedentary paired-fed controls but similar to that of sedentary rats with large HF diet consumption. These data suggest that alterations in preference for palatable, energy dense foods play a role in the effects of exercise on energy homeostasis. The gene expression results also suggest that the hedonic effects of exercise may substitute for food reward to limit food intake and suppress weight gain. PMID:25668514

Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform

PubMed Central

2013-01-01

Background Immunoassays that employ multiplexed bead arrays produce high information content per sample. Such assays are now frequently used to evaluate humoral responses in clinical trials. Integrated software is needed for the analysis, quality control, and secure sharing of the high volume of data produced by such multiplexed assays. Software that facilitates data exchange and provides flexibility to perform customized analyses (including multiple curve fits and visualizations of assay performance over time) could increase scientists’ capacity to use these immunoassays to evaluate human clinical trials. Results The HIV Vaccine Trials Network and the Statistical Center for HIV/AIDS Research and Prevention collaborated with LabKey Software to enhance the open source LabKey Server platform to facilitate workflows for multiplexed bead assays. This system now supports the management, analysis, quality control, and secure sharing of data from multiplexed immunoassays that leverage Luminex xMAP® technology. These assays may be custom or kit-based. Newly added features enable labs to: (i) import run data from spreadsheets output by Bio-Plex Manager™ software; (ii) customize data processing, curve fits, and algorithms through scripts written in common languages, such as R; (iii) select script-defined calculation options through a graphical user interface; (iv) collect custom metadata for each titration, analyte, run and batch of runs; (v) calculate dose–response curves for titrations; (vi) interpolate unknown concentrations from curves for titrated standards; (vii) flag run data for exclusion from analysis; (viii) track quality control metrics across runs using Levey-Jennings plots; and (ix) automatically flag outliers based on expected values. Existing system features allow researchers to analyze, integrate, visualize, export and securely share their data, as well as to construct custom user interfaces and workflows. Conclusions Unlike other tools tailored for Luminex immunoassays, LabKey Server allows labs to customize their Luminex analyses using scripting while still presenting users with a single, graphical interface for processing and analyzing data. The LabKey Server system also stands out among Luminex tools for enabling smooth, secure transfer of data, quality control information, and analyses between collaborators. LabKey Server and its Luminex features are freely available as open source software at http://www.labkey.com under the Apache 2.0 license. PMID:23631706

Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform.

PubMed

Eckels, Josh; Nathe, Cory; Nelson, Elizabeth K; Shoemaker, Sara G; Nostrand, Elizabeth Van; Yates, Nicole L; Ashley, Vicki C; Harris, Linda J; Bollenbeck, Mark; Fong, Youyi; Tomaras, Georgia D; Piehler, Britt

2013-04-30

Immunoassays that employ multiplexed bead arrays produce high information content per sample. Such assays are now frequently used to evaluate humoral responses in clinical trials. Integrated software is needed for the analysis, quality control, and secure sharing of the high volume of data produced by such multiplexed assays. Software that facilitates data exchange and provides flexibility to perform customized analyses (including multiple curve fits and visualizations of assay performance over time) could increase scientists' capacity to use these immunoassays to evaluate human clinical trials. The HIV Vaccine Trials Network and the Statistical Center for HIV/AIDS Research and Prevention collaborated with LabKey Software to enhance the open source LabKey Server platform to facilitate workflows for multiplexed bead assays. This system now supports the management, analysis, quality control, and secure sharing of data from multiplexed immunoassays that leverage Luminex xMAP® technology. These assays may be custom or kit-based. Newly added features enable labs to: (i) import run data from spreadsheets output by Bio-Plex Manager™ software; (ii) customize data processing, curve fits, and algorithms through scripts written in common languages, such as R; (iii) select script-defined calculation options through a graphical user interface; (iv) collect custom metadata for each titration, analyte, run and batch of runs; (v) calculate dose-response curves for titrations; (vi) interpolate unknown concentrations from curves for titrated standards; (vii) flag run data for exclusion from analysis; (viii) track quality control metrics across runs using Levey-Jennings plots; and (ix) automatically flag outliers based on expected values. Existing system features allow researchers to analyze, integrate, visualize, export and securely share their data, as well as to construct custom user interfaces and workflows. Unlike other tools tailored for Luminex immunoassays, LabKey Server allows labs to customize their Luminex analyses using scripting while still presenting users with a single, graphical interface for processing and analyzing data. The LabKey Server system also stands out among Luminex tools for enabling smooth, secure transfer of data, quality control information, and analyses between collaborators. LabKey Server and its Luminex features are freely available as open source software at http://www.labkey.com under the Apache 2.0 license.

Burrowing as a novel voluntary strength training method for mice: A comparison of various voluntary strength or resistance exercise methods.

PubMed

Roemers, P; Mazzola, P N; De Deyn, P P; Bossers, W J; van Heuvelen, M J G; van der Zee, E A

2018-04-15

Voluntary strength training methods for rodents are necessary to investigate the effects of strength training on cognition and the brain. However, few voluntary methods are available. The current study tested functional and muscular effects of two novel voluntary strength training methods, burrowing (digging a substrate out of a tube) and unloaded tower climbing, in male C57Bl6 mice. To compare these two novel methods with existing exercise methods, resistance running and (non-resistance) running were included. Motor coordination, grip strength and muscle fatigue were measured at baseline, halfway through and near the end of a fourteen week exercise intervention. Endurance was measured by an incremental treadmill test after twelve weeks. Both burrowing and resistance running improved forelimb grip strength as compared to controls. Running and resistance running increased endurance in the treadmill test and improved motor skills as measured by the balance beam test. Post-mortem tissue analyses revealed that running and resistance running induced Soleus muscle hypertrophy and reduced epididymal fat mass. Tower climbing elicited no functional or muscular changes. As a voluntary strength exercise method, burrowing avoids the confounding effects of stress and positive reinforcers elicited in forced strength exercise methods. Compared to voluntary resistance running, burrowing likely reduces the contribution of aerobic exercise components. Burrowing qualifies as a suitable voluntary strength training method in mice. Furthermore, resistance running shares features of strength training and endurance (aerobic) exercise and should be considered a multi-modal aerobic-strength exercise method in mice. Copyright © 2017 Elsevier B.V. All rights reserved.

The NLstart2run study: Incidence and risk factors of running-related injuries in novice runners.

PubMed

Kluitenberg, B; van Middelkoop, M; Smits, D W; Verhagen, E; Hartgens, F; Diercks, R; van der Worp, H

2015-10-01

Running is a popular form of physical activity, despite of the high incidence of running-related injuries (RRIs). Because of methodological issues, the etiology of RRIs remains unclear. Therefore, the purposes of the study were to assess the incidence of RRIs and to identify risk factors for RRIs in a large group of novice runners. In total, 1696 runners of a 6-week supervised "Start to Run" program were included in the NLstart2run study. All participants were aged between 18 and 65, completed a baseline questionnaire that covered potential risk factors, and completed at least one running diary. RRIs were registered during the program with a weekly running log. An RRI was defined as a musculo-skeletal complaint of the lower extremity or back attributed to running and hampering running ability for three consecutive training sessions. During the running program, 10.9% of the runners sustained an RRI. The multivariable Cox regression analysis showed that a higher age, higher BMI, previous musculo-skeletal complaints not attributed to sports and no previous running experience were related to RRI. These findings indicate that many novice runners participating in a short-term running program suffer from RRIs. Therefore, the identified risk factors should be considered for screening and prevention purposes. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Main improvements of LHC Cryogenics Operation during Run 2 (2015-2018)

NASA Astrophysics Data System (ADS)

Delprat, L.; Bradu, B.; Brodzinski, K.; Ferlin, G.; Hafi, K.; Herblin, L.; Rogez, E.; Suraci, A.

2017-12-01

After the successful Run 1 (2010-2012), the LHC entered its first Long Shutdown period (LS1, 2013-2014). During LS1 the LHC cryogenic system went under a complete maintenance and consolidation program. The LHC resumed operation in 2015 with an increased beam energy from 4 TeV to 6.5 TeV. Prior to the new physics Run 2 (2015-2018), the LHC was progressively cooled down from ambient to the 1.9 K operation temperature. The LHC has resumed operation with beams in April 2015. Operational margins on the cryogenic capacity were reduced compared to Run 1, mainly due to the observed higher than expected electron-cloud heat load coming from increased beam energy and intensity. Maintaining and improving the cryogenic availability level required the implementation of a series of actions in order to deal with the observed heat loads. This paper describes the results from the process optimization and update of the control system, thus allowing the adjustment of the non-isothermal heat load at 4.5 - 20 K and the optimized dynamic behaviour of the cryogenic system versus the electron-cloud thermal load. Effects from the new regulation settings applied for operation on the electrical distribution feed-boxes and inner triplets will be discussed. The efficiency of the preventive and corrective maintenance, as well as the benefits and issues of the present cryogenic system configuration for Run 2 operational scenario will be described. Finally, the overall availability results and helium management of the LHC cryogenic system during the 2015-2016 operational period will be presented.

Data Triage

DTIC Science & Technology

2007-06-01

particle accelerators cannot run unless enough network band- width is available to absorb their data streams. DOE scientists running simulations routinely...send tuples to TelegraphCQ. To simulate a less-powerful machine, I increased the playback rate of the trace by a factor of 10 and reduced the query...III CPUs and 1.5 GB of main memory. To simulate using a less powerful embedded CPU, I wrote a program that would “play back” the trace at a multiple

46 CFR 169.680 - Installation of wiring for power and lighting circuits.

Code of Federal Regulations, 2010 CFR

2010-10-01

... and lighting circuits. (a) Wiring must be run as high as practicable above the bilges. (b) Each cable...; and (2) Grounded at each end of the run to— (i) The metal hull; or (ii) The common ground required by paragraph (e) of this section on nonmetallic vessels. (h) In lieu of being grounded at each end of the run...

46 CFR 169.680 - Installation of wiring for power and lighting circuits.

Code of Federal Regulations, 2011 CFR

2011-10-01

... and lighting circuits. (a) Wiring must be run as high as practicable above the bilges. (b) Each cable...; and (2) Grounded at each end of the run to— (i) The metal hull; or (ii) The common ground required by paragraph (e) of this section on nonmetallic vessels. (h) In lieu of being grounded at each end of the run...

46 CFR 169.680 - Installation of wiring for power and lighting circuits.

Code of Federal Regulations, 2014 CFR

2014-10-01

... and lighting circuits. (a) Wiring must be run as high as practicable above the bilges. (b) Each cable...; and (2) Grounded at each end of the run to— (i) The metal hull; or (ii) The common ground required by paragraph (e) of this section on nonmetallic vessels. (h) In lieu of being grounded at each end of the run...

46 CFR 169.680 - Installation of wiring for power and lighting circuits.

Code of Federal Regulations, 2013 CFR

2013-10-01

... and lighting circuits. (a) Wiring must be run as high as practicable above the bilges. (b) Each cable...; and (2) Grounded at each end of the run to— (i) The metal hull; or (ii) The common ground required by paragraph (e) of this section on nonmetallic vessels. (h) In lieu of being grounded at each end of the run...

46 CFR 169.680 - Installation of wiring for power and lighting circuits.

Code of Federal Regulations, 2012 CFR

2012-10-01

... and lighting circuits. (a) Wiring must be run as high as practicable above the bilges. (b) Each cable...; and (2) Grounded at each end of the run to— (i) The metal hull; or (ii) The common ground required by paragraph (e) of this section on nonmetallic vessels. (h) In lieu of being grounded at each end of the run...

NGEE Arctic Tram: Photographs over Low- and High-Centered Polygon Vegetation Communities, Barrow, Alaska, 2014-2017

DOE Data Explorer

J. Bryan Curtis; Margaret Torn

2017-10-05

This dataset provides a digital image of each measurement position stop for every run of the Tram. There are 137 stops per run and there were sometimes multiple runs per day. This first version provides 12,714 images (*.jpg) collected over 28 days in 2015. Images for the other years will be added.

Advanced overlay: sampling and modeling for optimized run-to-run control

NASA Astrophysics Data System (ADS)

Subramany, Lokesh; Chung, WoongJae; Samudrala, Pavan; Gao, Haiyong; Aung, Nyan; Gomez, Juan Manuel; Gutjahr, Karsten; Park, DongSuk; Snow, Patrick; Garcia-Medina, Miguel; Yap, Lipkong; Demirer, Onur Nihat; Pierson, Bill; Robinson, John C.

2016-03-01

In recent years overlay (OVL) control schemes have become more complicated in order to meet the ever shrinking margins of advanced technology nodes. As a result, this brings up new challenges to be addressed for effective run-to- run OVL control. This work addresses two of these challenges by new advanced analysis techniques: (1) sampling optimization for run-to-run control and (2) bias-variance tradeoff in modeling. The first challenge in a high order OVL control strategy is to optimize the number of measurements and the locations on the wafer, so that the "sample plan" of measurements provides high quality information about the OVL signature on the wafer with acceptable metrology throughput. We solve this tradeoff between accuracy and throughput by using a smart sampling scheme which utilizes various design-based and data-based metrics to increase model accuracy and reduce model uncertainty while avoiding wafer to wafer and within wafer measurement noise caused by metrology, scanner or process. This sort of sampling scheme, combined with an advanced field by field extrapolated modeling algorithm helps to maximize model stability and minimize on product overlay (OPO). Second, the use of higher order overlay models means more degrees of freedom, which enables increased capability to correct for complicated overlay signatures, but also increases sensitivity to process or metrology induced noise. This is also known as the bias-variance trade-off. A high order model that minimizes the bias between the modeled and raw overlay signature on a single wafer will also have a higher variation from wafer to wafer or lot to lot, that is unless an advanced modeling approach is used. In this paper, we characterize the bias-variance trade off to find the optimal scheme. The sampling and modeling solutions proposed in this study are validated by advanced process control (APC) simulations to estimate run-to-run performance, lot-to-lot and wafer-to- wafer model term monitoring to estimate stability and ultimately high volume manufacturing tests to monitor OPO by densely measured OVL data.

Analyzing large scale genomic data on the cloud with Sparkhit

PubMed Central

Huang, Liren; Krüger, Jan

2018-01-01

Abstract Motivation The increasing amount of next-generation sequencing data poses a fundamental challenge on large scale genomic analytics. Existing tools use different distributed computational platforms to scale-out bioinformatics workloads. However, the scalability of these tools is not efficient. Moreover, they have heavy run time overheads when pre-processing large amounts of data. To address these limitations, we have developed Sparkhit: a distributed bioinformatics framework built on top of the Apache Spark platform. Results Sparkhit integrates a variety of analytical methods. It is implemented in the Spark extended MapReduce model. It runs 92–157 times faster than MetaSpark on metagenomic fragment recruitment and 18–32 times faster than Crossbow on data pre-processing. We analyzed 100 terabytes of data across four genomic projects in the cloud in 21 h, which includes the run times of cluster deployment and data downloading. Furthermore, our application on the entire Human Microbiome Project shotgun sequencing data was completed in 2 h, presenting an approach to easily associate large amounts of public datasets with reference data. Availability and implementation Sparkhit is freely available at: https://rhinempi.github.io/sparkhit/. Contact asczyrba@cebitec.uni-bielefeld.de Supplementary information Supplementary data are available at Bioinformatics online. PMID:29253074

Positional Differences in External On-Field Load During Specific Drill Classifications Over a Professional Rugby League Preseason.

PubMed

Cummins, Cloe; McLean, Blake; Halaki, Mark; Orr, Rhonda

2017-07-01

To quantify the external training loads of positional groups in preseason training drills. Thirty-three elite rugby league players were categorized into 1 of 4 positional groups: outside backs (n = 9), adjustables (n = 9), wide-running forwards (n = 9), and hit-up forwards (n = 6). Data for 8 preseason weeks were collected using microtechnology devices. Training drills were classified based on drill focus: speed and agility, conditioning, and generic and positional skills. Total, high-speed, and very-high-speed distance decreased across the preseason in speed and agility (moderate, small, and small, respectively), conditioning (large, large, and small) and generic skills (large, large, and large). The duration of speed and generic skills also decreased (77% and 48%, respectively). This was matched by a concomitant increase in total distance (small), high-speed running (small), very-high-speed running (moderate), and 2-dimensional (2D) BodyLoad (small) demands in positional skills. In positional skills, hit-up forwards (1240 ± 386 m) completed less very-high-speed running than outside backs (2570 ± 1331 m) and adjustables (2121 ± 1163 m). Hit-up forwards (674 ± 253 AU) experienced greater 2D BodyLoad demands than outside backs (432 ± 230 AU, P = .034). In positional drills, hit-up forwards experienced greater relative 2D BodyLoad demands than outside backs (P = .015). Conversely, outside backs experienced greater relative high- (P = .007) and very-high-speed-running (P < .001) demands than hit-up forwards. Significant differences were observed in training loads between positional groups during positional skills but not in speed and agility, conditioning, and generic skills. This work also highlights the importance of different external-load parameters to adequately quantify workload across different positional groups.

Voluntary running of defined distances reduces body adiposity and its associated inflammation in C57BL/6 mice fed a high-fat diet

USDA-ARS?s Scientific Manuscript database

A sedentary lifestyle contributes to obesity. This study determined the effects of quantitative voluntary running on body adiposity and its associated inflammation in mice fed a high-fat diet. Male C57BL/6 mice were assigned to six groups and fed an AIN93G (sedentary) or a high-fat diet (sedentary...

Space shuttle main engine definition (phase B). Volume 2: Avionics. [for space shuttle

NASA Technical Reports Server (NTRS)

1971-01-01

The advent of the space shuttle engine with its requirements for high specific impulse, long life, and low cost have dictated a combustion cycle and a closed loop control system to allow the engine components to run close to operating limits. These performance requirements, combined with the necessity for low operational costs, have placed new demands on rocket engine control, system checkout, and diagnosis technology. Based on considerations of precision environment, and compatibility with vehicle interface commands, an electronic control, makes available many functions that logically provide the information required for engine system checkout and diagnosis.

Increasing the speed of medical image processing in MatLab®

PubMed Central

Bister, M; Yap, CS; Ng, KH; Tok, CH

2007-01-01

MatLab® has often been considered an excellent environment for fast algorithm development but is generally perceived as slow and hence not fit for routine medical image processing, where large data sets are now available e.g., high-resolution CT image sets with typically hundreds of 512x512 slices. Yet, with proper programming practices – vectorization, pre-allocation and specialization – applications in MatLab® can run as fast as in C language. In this article, this point is illustrated with fast implementations of bilinear interpolation, watershed segmentation and volume rendering. PMID:21614269

Running SINDA '85/FLUINT interactive on the VAX

NASA Technical Reports Server (NTRS)

Simmonds, Boris

1992-01-01

Computer software as engineering tools are typically run in three modes: Batch, Demand, and Interactive. The first two are the most popular in the SINDA world. The third one is not so popular, due probably to the users inaccessibility to the command procedure files for running SINDA '85, or lack of familiarity with the SINDA '85 execution processes (pre-processor, processor, compilation, linking, execution and all of the file assignment, creation, deletions and de-assignments). Interactive is the mode that makes thermal analysis with SINDA '85 a real-time design tool. This paper explains a command procedure sufficient (the minimum modifications required in an existing demand command procedure) to run SINDA '85 on the VAX in an interactive mode. To exercise the procedure a sample problem is presented exemplifying the mode, plus additional programming capabilities available in SINDA '85. Following the same guidelines the process can be extended to other SINDA '85 residence computer platforms.

Evaluation of the technical performance of novel holotranscobalamin (holoTC) assays in a multicenter European demonstration project.

PubMed

Morkbak, Anne L; Heimdal, Randi M; Emmens, Kathleen; Molloy, Anne; Hvas, Anne-Mette; Schneede, Joern; Clarke, Robert; Scott, John M; Ueland, Per M; Nexo, Ebba

2005-01-01

A commercially available holotranscobalamin (holo-TC) radioimmunoassay (RIA) (Axis-Shield, Dundee, Scotland) was evaluated in four laboratories and compared with a holoTC ELISA run in one laboratory. The performance of the holoTC RIA assay was comparable in three of the four participating laboratories. The results from these three laboratories, involving at least 20 initial runs of "low", "medium" and "high" serum-based controls (mean holoTC concentrations 34, 60 and 110 pmol/L, respectively) yielded an intra-laboratory imprecision of 6-10%. No systematic inter-laboratory deviations were observed on runs involving 72 patient samples (holoTC concentration range 10-160 pmol/L). A fourth laboratory demonstrated higher assay imprecision for control samples and systematic deviation of results for the patient samples. Measurement of holoTC by ELISA showed an imprecision of 4-5%, and slightly higher mean values for the controls (mean holoTC concentrations 40, 70 and 114 pmol/L, respectively). Comparable results were obtained for the patient samples. The long-term intra-laboratory imprecision was 12% for the holoTC RIA and 6% for the ELISA. In conclusion, it would be prudent to check the calibration and precision prior to starting to use these holoTC assays in research or clinical practice. The results obtained using the holoTC RIA were similar to those obtained using the holoTC ELISA assay.

AlexSys: a knowledge-based expert system for multiple sequence alignment construction and analysis

PubMed Central

Aniba, Mohamed Radhouene; Poch, Olivier; Marchler-Bauer, Aron; Thompson, Julie Dawn

2010-01-01

Multiple sequence alignment (MSA) is a cornerstone of modern molecular biology and represents a unique means of investigating the patterns of conservation and diversity in complex biological systems. Many different algorithms have been developed to construct MSAs, but previous studies have shown that no single aligner consistently outperforms the rest. This has led to the development of a number of ‘meta-methods’ that systematically run several aligners and merge the output into one single solution. Although these methods generally produce more accurate alignments, they are inefficient because all the aligners need to be run first and the choice of the best solution is made a posteriori. Here, we describe the development of a new expert system, AlexSys, for the multiple alignment of protein sequences. AlexSys incorporates an intelligent inference engine to automatically select an appropriate aligner a priori, depending only on the nature of the input sequences. The inference engine was trained on a large set of reference multiple alignments, using a novel machine learning approach. Applying AlexSys to a test set of 178 alignments, we show that the expert system represents a good compromise between alignment quality and running time, making it suitable for high throughput projects. AlexSys is freely available from http://alnitak.u-strasbg.fr/∼aniba/alexsys. PMID:20530533

LHCbDIRAC as Apache Mesos microservices

NASA Astrophysics Data System (ADS)

Haen, Christophe; Couturier, Benjamin

2017-10-01

The LHCb experiment relies on LHCbDIRAC, an extension of DIRAC, to drive its offline computing. This middleware provides a development framework and a complete set of components for building distributed computing systems. These components are currently installed and run on virtual machines (VM) or bare metal hardware. Due to the increased workload, high availability is becoming more and more important for the LHCbDIRAC services, and the current installation model is showing its limitations. Apache Mesos is a cluster manager which aims at abstracting heterogeneous physical resources on which various tasks can be distributed thanks to so called “frameworks” The Marathon framework is suitable for long running tasks such as the DIRAC services, while the Chronos framework meets the needs of cron-like tasks like the DIRAC agents. A combination of the service discovery tool Consul together with HAProxy allows to expose the running containers to the outside world while hiding their dynamic placements. Such an architecture brings a greater flexibility in the deployment of LHCbDirac services, allowing for easier deployment maintenance and scaling of services on demand (e..g LHCbDirac relies on 138 services and 116 agents). Higher reliability is also easier, as clustering is part of the toolset, which allows constraints on the location of the services. This paper describes the investigations carried out to package the LHCbDIRAC and DIRAC components into Docker containers and orchestrate them using the previously described set of tools.

The Challenge of Evaluating the Intensity of Short Actions in Soccer: A New Methodological Approach Using Percentage Acceleration.

PubMed

Sonderegger, Karin; Tschopp, Markus; Taube, Wolfgang

2016-01-01

There are several approaches to quantifying physical load in team sports using positional data. Distances in different speed zones are most commonly used. Recent studies have used acceleration data in addition in order to take short intense actions into account. However, the fact that acceleration decreases with increasing initial running speed is ignored and therefore introduces a bias. The aim of our study was to develop a new methodological approach that removes this bias. For this purpose, percentage acceleration was calculated as the ratio of the maximal acceleration of the action (amax,action) and the maximal voluntary acceleration (amax) that can be achieved for a particular initial running speed (percentage acceleration [%] = amax,action / amax * 100). To define amax, seventy-two highly trained junior male soccer players (17.1 ± 0.6 years) completed maximal sprints from standing and three different constant initial running speeds (vinit; trotting: ~6.0 km·h-1; jogging: ~10.8 km·h-1; running: ~15.0 km·h-1). The amax was 6.01 ± 0.55 from a standing start, 4.33 ± 0.40 from trotting, 3.20 ± 0.49 from jogging and 2.29 ± 0.34 m·s-2 from running. The amax correlated significantly with vinit (r = -0.98) and the linear regression equation of highly-trained junior soccer players was: amax = -0.23 * vinit + 5.99. Using linear regression analysis, we propose to classify high-intensity actions as accelerations >75% of the amax, corresponding to acceleration values for our population of >4.51 initiated from standing, >3.25 from trotting, >2.40 from jogging, and >1.72 m·s-2 from running. The use of percentage acceleration avoids the bias of underestimating actions with high and overestimating actions with low initial running speed. Furthermore, percentage acceleration allows determining individual intensity thresholds that are specific for one population or one single player.

Running increases ethanol preference.

PubMed

Werme, Martin; Lindholm, Sara; Thorén, Peter; Franck, Johan; Brené, Stefan

2002-07-18

Wheel running performed by rats is reinforcing, rewarding and possibly addictive. In this study we analyzed if wheel running could affect ethanol preference. Lewis rats, known to be both addiction-prone and to develop an excessive wheel running behavior, were given access to ethanol in a two-bottle free-choice paradigm. The animals reached a high and stable ethanol intake after 5 weeks. In the next phase, rats were subjected to ethanol withdrawal for 1, 2 or 4 weeks with or without access to running wheels. Finally animals were again given access to ethanol in the same two-bottle free-choice paradigm, combined with access to running wheels. The rats that ran in running wheels during 1 or 2, but not 4, weeks of ethanol withdrawal increased both ethanol intake and preference as compared with the control group that did not have access to the wheels. Previous studies have demonstrated that low doses of morphine increases ethanol preference. Here we show that also running potentiates ethanol intake and preference. Thus, running which shares many of the reinforcing properties with addictive drugs appears to potentiate rats to an increased preference for ethanol. Our results describe a behavioral interaction where running increases ethanol consumption.

Cumulative loads increase at the knee joint with slow-speed running compared to faster running: a biomechanical study.

PubMed

Petersen, Jesper; Sørensen, Henrik; Nielsen, Rasmus Østergaard

2015-04-01

Biomechanical cross-sectional study. To investigate the hypothesis that the cumulative load at the knee during running increases as running speed decreases. The knee joint load per stride decreases as running speed decreases. However, by decreasing running speed, the number of strides per given distance is increased. Running a given distance at a slower speed may increase the cumulative load at the knee joint compared with running the same distance at a higher speed, hence increasing the risk of running-related injuries in the knee. Kinematic and ground reaction force data were collected from 16 recreational runners, during steady-state running with a rearfoot strike pattern at 3 different speeds (mean ± SD): 8.02 ± 0.17 km/h, 11.79 ± 0.21 km/h, and 15.78 ± 0.22 km/h. The cumulative load (cumulative impulse) over a 1000-m distance was calculated at the knee joint on the basis of a standard 3-D inverse-dynamics approach. Based on a 1000-m running distance, the cumulative load at the knee was significantly higher at a slow running speed than at a high running speed (relative difference, 80%). The mean load per stride at the knee increased significantly across all biomechanical parameters, except impulse, following an increase in running speed. Slow-speed running decreases knee joint loads per stride and increases the cumulative load at the knee joint for a given running distance compared to faster running. The primary reason for the increase in cumulative load at slower speeds is an increase in number of strides needed to cover the same distance.

Changes in hippocampal theta rhythm and their correlations with speed during different phases of voluntary wheel running in rats.

PubMed

Li, J-Y; Kuo, T B J; Hsieh, I-T; Yang, C C H

2012-06-28

Hippocampal theta rhythm (4-12 Hz) can be observed during locomotor behavior, but findings on the relationship between locomotion speed and theta frequency are inconsistent if not contradictory. The inconsistency may be because of the difficulties that previous analyses and protocols have had excluding the effects of behavior training. We recorded the first or second voluntary wheel running each day, and assumed that theta frequency and activity are correlated with speed in different running phases. By simultaneously recording electroencephalography, physical activity, and wheel running speed, this experiment explored the theta oscillations during spontaneous running of the 12-h dark period. The recording was completely wireless and allowed the animal to run freely while being recorded in the wheel. Theta frequency and theta power of middle frequency were elevated before running and theta frequency, theta power of middle frequency, physical activity, and running speed maintained persistently high levels during running. The slopes of the theta frequency and theta activity (4-9.5 Hz) during the initial running were different compared to the same values during subsequent running. During the initial running, the running speed was positively correlated with theta frequency and with theta power of middle frequency. Over the 12-h dark period, the running speed did not positively correlate with theta frequency but was significantly correlated with theta power of middle frequency. Thus, theta frequency was associated with running speed only at the initiation of running. Furthermore, theta power of middle frequency was associated with speed and with physical activity during running when chronological order was not taken into consideration. Copyright © 2012 IBRO. Published by Elsevier Ltd. All rights reserved.

Research of x-ray nondestructive detector for high-speed running conveyor belt with steel wire ropes

NASA Astrophysics Data System (ADS)

Wang, Junfeng; Miao, Changyun; Wang, Wei; Lu, Xiaocui

2008-03-01

An X-ray nondestructive detector for high-speed running conveyor belt with steel wire ropes is researched in the paper. The principle of X-ray nondestructive testing (NDT) is analyzed, the general scheme of the X-ray nondestructive testing system is proposed, and the nondestructive detector for high-speed running conveyor belt with steel wire ropes is developed. The hardware of system is designed with Xilinx's VIRTEX-4 FPGA that embeds PowerPC and MAC IP core, and its network communication software based on TCP/IP protocol is programmed by loading LwIP to PowerPC. The nondestructive testing of high-speed conveyor belt with steel wire ropes and network transfer function are implemented. It is a strong real-time system with rapid scanning speed, high reliability and remotely nondestructive testing function. The nondestructive detector can be applied to the detection of product line in industry.

preAssemble: a tool for automatic sequencer trace data processing.

PubMed

Adzhubei, Alexei A; Laerdahl, Jon K; Vlasova, Anna V

2006-01-17

Trace or chromatogram files (raw data) are produced by automatic nucleic acid sequencing equipment or sequencers. Each file contains information which can be interpreted by specialised software to reveal the sequence (base calling). This is done by the sequencer proprietary software or publicly available programs. Depending on the size of a sequencing project the number of trace files can vary from just a few to thousands of files. Sequencing quality assessment on various criteria is important at the stage preceding clustering and contig assembly. Two major publicly available packages--Phred and Staden are used by preAssemble to perform sequence quality processing. The preAssemble pre-assembly sequence processing pipeline has been developed for small to large scale automatic processing of DNA sequencer chromatogram (trace) data. The Staden Package Pregap4 module and base-calling program Phred are utilized in the pipeline, which produces detailed and self-explanatory output that can be displayed with a web browser. preAssemble can be used successfully with very little previous experience, however options for parameter tuning are provided for advanced users. preAssemble runs under UNIX and LINUX operating systems. It is available for downloading and will run as stand-alone software. It can also be accessed on the Norwegian Salmon Genome Project web site where preAssemble jobs can be run on the project server. preAssemble is a tool allowing to perform quality assessment of sequences generated by automatic sequencing equipment. preAssemble is flexible since both interactive jobs on the preAssemble server and the stand alone downloadable version are available. Virtually no previous experience is necessary to run a default preAssemble job, on the other hand options for parameter tuning are provided. Consequently preAssemble can be used as efficiently for just several trace files as for large scale sequence processing.

Accelerating epistasis analysis in human genetics with consumer graphics hardware.

PubMed

Sinnott-Armstrong, Nicholas A; Greene, Casey S; Cancare, Fabio; Moore, Jason H

2009-07-24

Human geneticists are now capable of measuring more than one million DNA sequence variations from across the human genome. The new challenge is to develop computationally feasible methods capable of analyzing these data for associations with common human disease, particularly in the context of epistasis. Epistasis describes the situation where multiple genes interact in a complex non-linear manner to determine an individual's disease risk and is thought to be ubiquitous for common diseases. Multifactor Dimensionality Reduction (MDR) is an algorithm capable of detecting epistasis. An exhaustive analysis with MDR is often computationally expensive, particularly for high order interactions. This challenge has previously been met with parallel computation and expensive hardware. The option we examine here exploits commodity hardware designed for computer graphics. In modern computers Graphics Processing Units (GPUs) have more memory bandwidth and computational capability than Central Processing Units (CPUs) and are well suited to this problem. Advances in the video game industry have led to an economy of scale creating a situation where these powerful components are readily available at very low cost. Here we implement and evaluate the performance of the MDR algorithm on GPUs. Of primary interest are the time required for an epistasis analysis and the price to performance ratio of available solutions. We found that using MDR on GPUs consistently increased performance per machine over both a feature rich Java software package and a C++ cluster implementation. The performance of a GPU workstation running a GPU implementation reduces computation time by a factor of 160 compared to an 8-core workstation running the Java implementation on CPUs. This GPU workstation performs similarly to 150 cores running an optimized C++ implementation on a Beowulf cluster. Furthermore this GPU system provides extremely cost effective performance while leaving the CPU available for other tasks. The GPU workstation containing three GPUs costs $2000 while obtaining similar performance on a Beowulf cluster requires 150 CPU cores which, including the added infrastructure and support cost of the cluster system, cost approximately $82,500. Graphics hardware based computing provides a cost effective means to perform genetic analysis of epistasis using MDR on large datasets without the infrastructure of a computing cluster.

Towards future high performance computing: What will change? How can we be efficient?

NASA Astrophysics Data System (ADS)

Düben, Peter

2017-04-01

How can we make the most out of "exascale" supercomputers that will be available soon and enable us to calculate an amazing number of 1,000,000,000,000,000,000 real numbers operations within a single second? How do we need to design applications to use these machines efficiently? What are the limits? We will discuss opportunities and limits of the use of future high performance computers from the perspective of Earth System Modelling. We will provide an overview about future challenges and outline how numerical application will need to be changed to run efficiently on supercomputers in the future. We will also discuss how different disciplines can support each other and talk about data handling and numerical precision of data.

A meteorological distribution system for high-resolution terrestrial modeling (MicroMet)

Treesearch

Glen E. Liston; Kelly Elder

2006-01-01

An intermediate-complexity, quasi-physically based, meteorological model (MicroMet) has been developed to produce high-resolution (e.g., 30-m to 1-km horizontal grid increment) atmospheric forcings required to run spatially distributed terrestrial models over a wide variety of landscapes. The following eight variables, required to run most terrestrial models, are...

The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows

PubMed Central

O'Connor, Brian D.; Yuen, Denis; Chung, Vincent; Duncan, Andrew G.; Liu, Xiang Kun; Patricia, Janice; Paten, Benedict; Stein, Lincoln; Ferretti, Vincent

2017-01-01

As genomic datasets continue to grow, the feasibility of downloading data to a local organization and running analysis on a traditional compute environment is becoming increasingly problematic. Current large-scale projects, such as the ICGC PanCancer Analysis of Whole Genomes (PCAWG), the Data Platform for the U.S. Precision Medicine Initiative, and the NIH Big Data to Knowledge Center for Translational Genomics, are using cloud-based infrastructure to both host and perform analysis across large data sets. In PCAWG, over 5,800 whole human genomes were aligned and variant called across 14 cloud and HPC environments; the processed data was then made available on the cloud for further analysis and sharing. If run locally, an operation at this scale would have monopolized a typical academic data centre for many months, and would have presented major challenges for data storage and distribution. However, this scale is increasingly typical for genomics projects and necessitates a rethink of how analytical tools are packaged and moved to the data. For PCAWG, we embraced the use of highly portable Docker images for encapsulating and sharing complex alignment and variant calling workflows across highly variable environments. While successful, this endeavor revealed a limitation in Docker containers, namely the lack of a standardized way to describe and execute the tools encapsulated inside the container. As a result, we created the Dockstore ( https://dockstore.org), a project that brings together Docker images with standardized, machine-readable ways of describing and running the tools contained within. This service greatly improves the sharing and reuse of genomics tools and promotes interoperability with similar projects through emerging web service standards developed by the Global Alliance for Genomics and Health (GA4GH). PMID:28344774

The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows.

PubMed

O'Connor, Brian D; Yuen, Denis; Chung, Vincent; Duncan, Andrew G; Liu, Xiang Kun; Patricia, Janice; Paten, Benedict; Stein, Lincoln; Ferretti, Vincent

2017-01-01

As genomic datasets continue to grow, the feasibility of downloading data to a local organization and running analysis on a traditional compute environment is becoming increasingly problematic. Current large-scale projects, such as the ICGC PanCancer Analysis of Whole Genomes (PCAWG), the Data Platform for the U.S. Precision Medicine Initiative, and the NIH Big Data to Knowledge Center for Translational Genomics, are using cloud-based infrastructure to both host and perform analysis across large data sets. In PCAWG, over 5,800 whole human genomes were aligned and variant called across 14 cloud and HPC environments; the processed data was then made available on the cloud for further analysis and sharing. If run locally, an operation at this scale would have monopolized a typical academic data centre for many months, and would have presented major challenges for data storage and distribution. However, this scale is increasingly typical for genomics projects and necessitates a rethink of how analytical tools are packaged and moved to the data. For PCAWG, we embraced the use of highly portable Docker images for encapsulating and sharing complex alignment and variant calling workflows across highly variable environments. While successful, this endeavor revealed a limitation in Docker containers, namely the lack of a standardized way to describe and execute the tools encapsulated inside the container. As a result, we created the Dockstore ( https://dockstore.org), a project that brings together Docker images with standardized, machine-readable ways of describing and running the tools contained within. This service greatly improves the sharing and reuse of genomics tools and promotes interoperability with similar projects through emerging web service standards developed by the Global Alliance for Genomics and Health (GA4GH).

Limits to high-speed simulations of spiking neural networks using general-purpose computers.

PubMed

Zenke, Friedemann; Gerstner, Wulfram

2014-01-01

To understand how the central nervous system performs computations using recurrent neuronal circuitry, simulations have become an indispensable tool for theoretical neuroscience. To study neuronal circuits and their ability to self-organize, increasing attention has been directed toward synaptic plasticity. In particular spike-timing-dependent plasticity (STDP) creates specific demands for simulations of spiking neural networks. On the one hand a high temporal resolution is required to capture the millisecond timescale of typical STDP windows. On the other hand network simulations have to evolve over hours up to days, to capture the timescale of long-term plasticity. To do this efficiently, fast simulation speed is the crucial ingredient rather than large neuron numbers. Using different medium-sized network models consisting of several thousands of neurons and off-the-shelf hardware, we compare the simulation speed of the simulators: Brian, NEST and Neuron as well as our own simulator Auryn. Our results show that real-time simulations of different plastic network models are possible in parallel simulations in which numerical precision is not a primary concern. Even so, the speed-up margin of parallelism is limited and boosting simulation speeds beyond one tenth of real-time is difficult. By profiling simulation code we show that the run times of typical plastic network simulations encounter a hard boundary. This limit is partly due to latencies in the inter-process communications and thus cannot be overcome by increased parallelism. Overall, these results show that to study plasticity in medium-sized spiking neural networks, adequate simulation tools are readily available which run efficiently on small clusters. However, to run simulations substantially faster than real-time, special hardware is a prerequisite.

Variations in turbidity in streams of the Bull Run Watershed, Oregon 1989-90

USGS Publications Warehouse

LaHusen, Richard G.

1994-01-01

In this study, turbidity is used to help explain spatial and temporal patterns of erosion and sediment transport.Automated turbidity sampling in streams in the Bull Run watershed during water years 1989 and 1990, showed turbidity levels, in general, are remarkably low, with levels below 1 NTU (nephelometric turbidity unit) about 90 percent of the time. However, ephemeral increases in turbidity in streams of the Bull Run watershed occur in direct response to storms. Turbidity is caused by abundant organic particles as well as by materials eroded from unconsolidated geologic materials located along roads, stream channels, or stream banks. Seasonal and within-storm decreases in turbidity are attributed to depletion of accumulated particle supplies. During winter storms, erosion caused by rainfall intensities greater than 0.25 inches in 3 hours is sufficient to increase stream turbidities from less than 1 NTU to as much as 100 NTUs. Large-scale storms or floods cause persistent effects because mass erosion or scour of channel armor increases available sediment supply.Spatial variability in turbidity is evident only during storms when erosion and sediment-transport processes are active. Parts of the Rhododendron Formation are particularly prone to channel and mass erosion during large storms. Eroding glacial deposits in sections of Log Creek affected by a 1964 dam-break flood also cause high stream turbidity relative to other streams in the watershed.Analysis of characteristics of magnetic minerals in sediment sources and deposits was unproductive as a means to identify source areas of suspended sediment because high concentrations of magnetite in all samples of the volcanic rocks masked differences of less magnetic minerals in the samples.

The Validity and Reliability of an iPhone App for Measuring Running Mechanics.

PubMed

Balsalobre-Fernández, Carlos; Agopyan, Hovannes; Morin, Jean-Benoit

2017-07-01

The purpose of this investigation was to analyze the validity of an iPhone application (Runmatic) for measuring running mechanics. To do this, 96 steps from 12 different runs at speeds ranging from 2.77-5.55 m·s -1 were recorded simultaneously with Runmatic, as well as with an opto-electronic device installed on a motorized treadmill to measure the contact and aerial time of each step. Additionally, several running mechanics variables were calculated using the contact and aerial times measured, and previously validated equations. Several statistics were computed to test the validity and reliability of Runmatic in comparison with the opto-electronic device for the measurement of contact time, aerial time, vertical oscillation, leg stiffness, maximum relative force, and step frequency. The running mechanics values obtained with both the app and the opto-electronic device showed a high degree of correlation (r = .94-.99, p < .001). Moreover, there was very close agreement between instruments as revealed by the ICC (2,1) (ICC = 0.965-0.991). Finally, both Runmatic and the opto-electronic device showed almost identical reliability levels when measuring each set of 8 steps for every run recorded. In conclusion, Runmatic has been proven to be a highly reliable tool for measuring the running mechanics studied in this work.

Maximal metabolic rates during voluntary exercise, forced exercise, and cold exposure in house mice selectively bred for high wheel-running.

PubMed

Rezende, Enrico L; Chappell, Mark A; Gomes, Fernando R; Malisch, Jessica L; Garland, Theodore

2005-06-01

Selective breeding for high wheel-running activity has generated four lines of laboratory house mice (S lines) that run about 170% more than their control counterparts (C lines) on a daily basis, mostly because they run faster. We tested whether maximum aerobic metabolic rates (V(O2max)) have evolved in concert with wheel-running, using 48 females from generation 35. Voluntary activity and metabolic rates were measured on days 5+6 of wheel access (mimicking conditions during selection), using wheels enclosed in metabolic chambers. Following this, V(O2max) was measured twice on a motorized treadmill and twice during cold-exposure in a heliox atmosphere (HeO2). Almost all measurements, except heliox V(O2max), were significantly repeatable. After accounting for differences in body mass (S < C) and variation in age at testing, S and C did not differ in V(O2max) during forced exercise or in heliox, nor in maximal running speeds on the treadmill. However, running speeds and V(O2max) during voluntary exercise were significantly higher in S lines. Nevertheless, S mice never voluntarily achieved the V(O2max) elicited during their forced treadmill trials, suggesting that aerobic capacity per se is not limiting the evolution of even higher wheel-running speeds in these lines. Our results support the hypothesis that S mice have genetically higher motivation for wheel-running and they demonstrate that behavior can sometimes evolve independently of performance capacities. We also discuss the possible importance of domestication as a confounding factor to extrapolate results from this animal model to natural populations.

High Resolution Nature Runs and the Big Data Challenge

NASA Technical Reports Server (NTRS)

Webster, W. Phillip; Duffy, Daniel Q.

2015-01-01

NASA's Global Modeling and Assimilation Office at Goddard Space Flight Center is undertaking a series of very computationally intensive Nature Runs and a downscaled reanalysis. The nature runs use the GEOS-5 as an Atmospheric General Circulation Model (AGCM) while the reanalysis uses the GEOS-5 in Data Assimilation mode. This paper will present computational challenges from three runs, two of which are AGCM and one is downscaled reanalysis using the full DAS. The nature runs will be completed at two surface grid resolutions, 7 and 3 kilometers and 72 vertical levels. The 7 km run spanned 2 years (2005-2006) and produced 4 PB of data while the 3 km run will span one year and generate 4 BP of data. The downscaled reanalysis (MERRA-II Modern-Era Reanalysis for Research and Applications) will cover 15 years and generate 1 PB of data. Our efforts to address the big data challenges of climate science, we are moving toward a notion of Climate Analytics-as-a-Service (CAaaS), a specialization of the concept of business process-as-a-service that is an evolving extension of IaaS, PaaS, and SaaS enabled by cloud computing. In this presentation, we will describe two projects that demonstrate this shift. MERRA Analytic Services (MERRA/AS) is an example of cloud-enabled CAaaS. MERRA/AS enables MapReduce analytics over MERRA reanalysis data collection by bringing together the high-performance computing, scalable data management, and a domain-specific climate data services API. NASA's High-Performance Science Cloud (HPSC) is an example of the type of compute-storage fabric required to support CAaaS. The HPSC comprises a high speed Infinib and network, high performance file systems and object storage, and a virtual system environments specific for data intensive, science applications. These technologies are providing a new tier in the data and analytic services stack that helps connect earthbound, enterprise-level data and computational resources to new customers and new mobility-driven applications and modes of work. In our experience, CAaaS lowers the barriers and risk to organizational change, fosters innovation and experimentation, and provides the agility required to meet our customers' increasing and changing needs

The Automatic Neuroscientist: A framework for optimizing experimental design with closed-loop real-time fMRI

PubMed Central

Lorenz, Romy; Monti, Ricardo Pio; Violante, Inês R.; Anagnostopoulos, Christoforos; Faisal, Aldo A.; Montana, Giovanni; Leech, Robert

2016-01-01

Functional neuroimaging typically explores how a particular task activates a set of brain regions. Importantly though, the same neural system can be activated by inherently different tasks. To date, there is no approach available that systematically explores whether and how distinct tasks probe the same neural system. Here, we propose and validate an alternative framework, the Automatic Neuroscientist, which turns the standard fMRI approach on its head. We use real-time fMRI in combination with modern machine-learning techniques to automatically design the optimal experiment to evoke a desired target brain state. In this work, we present two proof-of-principle studies involving perceptual stimuli. In both studies optimization algorithms of varying complexity were employed; the first involved a stochastic approximation method while the second incorporated a more sophisticated Bayesian optimization technique. In the first study, we achieved convergence for the hypothesized optimum in 11 out of 14 runs in less than 10 min. Results of the second study showed how our closed-loop framework accurately and with high efficiency estimated the underlying relationship between stimuli and neural responses for each subject in one to two runs: with each run lasting 6.3 min. Moreover, we demonstrate that using only the first run produced a reliable solution at a group-level. Supporting simulation analyses provided evidence on the robustness of the Bayesian optimization approach for scenarios with low contrast-to-noise ratio. This framework is generalizable to numerous applications, ranging from optimizing stimuli in neuroimaging pilot studies to tailoring clinical rehabilitation therapy to patients and can be used with multiple imaging modalities in humans and animals. PMID:26804778

The Automatic Neuroscientist: A framework for optimizing experimental design with closed-loop real-time fMRI.

PubMed

Lorenz, Romy; Monti, Ricardo Pio; Violante, Inês R; Anagnostopoulos, Christoforos; Faisal, Aldo A; Montana, Giovanni; Leech, Robert

2016-04-01

Functional neuroimaging typically explores how a particular task activates a set of brain regions. Importantly though, the same neural system can be activated by inherently different tasks. To date, there is no approach available that systematically explores whether and how distinct tasks probe the same neural system. Here, we propose and validate an alternative framework, the Automatic Neuroscientist, which turns the standard fMRI approach on its head. We use real-time fMRI in combination with modern machine-learning techniques to automatically design the optimal experiment to evoke a desired target brain state. In this work, we present two proof-of-principle studies involving perceptual stimuli. In both studies optimization algorithms of varying complexity were employed; the first involved a stochastic approximation method while the second incorporated a more sophisticated Bayesian optimization technique. In the first study, we achieved convergence for the hypothesized optimum in 11 out of 14 runs in less than 10 min. Results of the second study showed how our closed-loop framework accurately and with high efficiency estimated the underlying relationship between stimuli and neural responses for each subject in one to two runs: with each run lasting 6.3 min. Moreover, we demonstrate that using only the first run produced a reliable solution at a group-level. Supporting simulation analyses provided evidence on the robustness of the Bayesian optimization approach for scenarios with low contrast-to-noise ratio. This framework is generalizable to numerous applications, ranging from optimizing stimuli in neuroimaging pilot studies to tailoring clinical rehabilitation therapy to patients and can be used with multiple imaging modalities in humans and animals. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Effects of Music Interventions on Emotional States and Running Performance

PubMed Central

Lane, Andrew M.; Davis, Paul A.; Devonport, Tracey J.

2011-01-01

The present study compared the effects of two different music interventions on changes in emotional states before and during running, and also explored effects of music interventions upon performance outcome. Volunteer participants (n = 65) who regularly listened to music when running registered online to participate in a three-stage study. Participants attempted to attain a personally important running goal to establish baseline performance. Thereafter, participants were randomly assigned to either a self-selected music group or an Audiofuel music group. Audiofuel produce pieces of music designed to assist synchronous running. The self-selected music group followed guidelines for selecting motivating playlists. In both experimental groups, participants used the Brunel Music Rating Inventory-2 (BMRI-2) to facilitate selection of motivational music. Participants again completed the BMRI-2 post- intervention to assess the motivational qualities of Audiofuel music or the music they selected for use during the study. Results revealed no significant differences between self-selected music and Audiofuel music on all variables analyzed. Participants in both music groups reported increased pleasant emotions and decreased unpleasant emotions following intervention. Significant performance improvements were demonstrated post-intervention with participants reporting a belief that emotional states related to performance. Further analysis indicated that enhanced performance was significantly greater among participants reporting music to be motivational as indicated by high scores on the BMRI-2. Findings suggest that both individual athletes and practitioners should consider using the BMRI-2 when selecting music for running. Key points Listening to music with a high motivational quotient as indicated by scores on the BMRI-2 was associated with enhanced running performance and meta-emotional beliefs that emotions experienced during running helped performance. Beliefs on the effectiveness of music intended to alter emotions were associated with high scores on the BMRI-2. Runners seeking to use music as an emotion regulating strategy should consider using the BMRI-2 as an effective means by which to identify potentially motivating tracks. PMID:24149889

High-Intensity Running and Plantar-Flexor Fatigability and Plantar-Pressure Distribution in Adolescent Runners

PubMed Central

Fourchet, François; Kelly, Luke; Horobeanu, Cosmin; Loepelt, Heiko; Taiar, Redha; Millet, Grégoire

2015-01-01

Context: Fatigue-induced alterations in foot mechanics may lead to structural overload and injury. Objectives: To investigate how a high-intensity running exercise to exhaustion modifies ankle plantar-flexor and dorsiflexor strength and fatigability, as well as plantar-pressure distribution in adolescent runners. Design: Controlled laboratory study. Setting: Academy research laboratory. Patients or Other Participants: Eleven male adolescent distance runners (age = 16.9 ± 2.0 years, height = 170.6 ± 10.9 cm, mass = 54.6 ± 8.6 kg) were tested. Intervention(s): All participants performed an exhausting run on a treadmill. An isokinetic plantar-flexor and dorsiflexor maximal-strength test and a fatigue test were performed before and after the exhausting run. Plantar-pressure distribution was assessed at the beginning and end of the exhausting run. Main Outcome Measure(s): We recorded plantar-flexor and dorsiflexor peak torques and calculated the fatigue index. Plantar-pressure measurements were recorded 1 minute after the start of the run and before exhaustion. Plantar variables (ie, mean area, contact time, mean pressure, relative load) were determined for 9 selected regions. Results: Isokinetic peak torques were similar before and after the run in both muscle groups, whereas the fatigue index increased in plantar flexion (28.1%; P = .01) but not in dorsiflexion. For the whole foot, mean pressure decreased from 1 minute to the end (−3.4%; P = .003); however, mean area (9.5%; P = .005) and relative load (7.2%; P = .009) increased under the medial midfoot, and contact time increased under the central forefoot (8.3%; P = .01) and the lesser toes (8.9%; P = .008). Conclusions: Fatigue resistance in the plantar flexors declined after a high-intensity running bout performed by adolescent male distance runners. This phenomenon was associated with increased loading under the medial arch in the fatigued state but without any excessive pronation. PMID:25531143

Effects of two neuromuscular training programs on running biomechanics with load carriage: a study protocol for a randomised controlled trial.

PubMed

Liew, Bernard X W; Morris, Susan; Keogh, Justin W L; Appleby, Brendyn; Netto, Kevin

2016-10-22

In recent years, athletes have ventured into ultra-endurance and adventure racing events, which tests their ability to race, navigate, and survive. These events often require race participants to carry some form of load, to bear equipment for navigation and survival purposes. Previous studies have reported specific alterations in biomechanics when running with load which potentially influence running performance and injury risk. We hypothesize that a biomechanically informed neuromuscular training program would optimize running mechanics during load carriage to a greater extent than a generic strength training program. This will be a two group, parallel randomized controlled trial design, with single assessor blinding. Thirty healthy runners will be recruited to participate in a six weeks neuromuscular training program. Participants will be randomized into either a generic training group, or a biomechanically informed training group. Primary outcomes include self-determined running velocity with a 20 % body weight load, jump power, hopping leg stiffness, knee extensor and triceps-surae strength. Secondary outcomes include running kinetics and kinematics. Assessments will occur at baseline and post-training. To our knowledge, no training programs are available that specifically targets a runner's ability to carry load while running. This will provide sport scientists and coaches with a foundation to base their exercise prescription on. ANZCTR ( ACTRN12616000023459 ) (14 Jan 2016).

A Multi-Season Study of the Effects of MODIS Sea-Surface Temperatures on Operational WRF Forecasts at NWS Miami, FL

NASA Technical Reports Server (NTRS)

Case, Jonathan L.; Santos, Pablo; Lazarus, Steven M.; Splitt, Michael E.; Haines, Stephanie L.; Dembek, Scott R.; Lapenta, William M.

2008-01-01

Studies at the Short-term Prediction Research and Transition (SPORT) Center have suggested that the use of Moderate Resolution Imaging Spectroradiometer (MODIS) sea-surface temperature (SST) composites in regional weather forecast models can have a significant positive impact on short-term numerical weather prediction in coastal regions. Recent work by LaCasse et al (2007, Monthly Weather Review) highlights lower atmospheric differences in regional numerical simulations over the Florida offshore waters using 2-km SST composites derived from the MODIS instrument aboard the polar-orbiting Aqua and Terra Earth Observing System satellites. To help quantify the value of this impact on NWS Weather Forecast Offices (WFOs), the SPORT Center and the NWS WFO at Miami, FL (MIA) are collaborating on a project to investigate the impact of using the high-resolution MODIS SST fields within the Weather Research and Forecasting (WRF) prediction system. The project's goal is to determine whether more accurate specification of the lower-boundary forcing within WRF will result in improved land/sea fluxes and hence, more accurate evolution of coastal mesoscale circulations and the associated sensible weather elements. The NWS MIA is currently running WRF in real-time to support daily forecast operations, using the National Centers for Environmental Prediction Nonhydrostatic Mesoscale Model dynamical core within the NWS Science and Training Resource Center's Environmental Modeling System (EMS) software. Twenty-seven hour forecasts are run dally initialized at 0300, 0900, 1500, and 2100 UTC on a domain with 4-km grid spacing covering the southern half of Florida and adjacent waters of the Gulf of Mexico and Atlantic Ocean. Each model run is initialized using the Local Analysis and Prediction System (LAPS) analyses available in AWIPS. The SSTs are initialized with the NCEP Real-Time Global (RTG) analyses at 1/12deg resolution (approx.9 km); however, the RTG product does not exhibit fine-scale details consistent with its grid resolution. SPORT is conducting parallel WRF EMS runs identical to the operational runs at NWS MIA except for the use of MODIS SST composites in place of the RTG product as the initial and boundary conditions over water, The MODIS SST composites for initializing the SPORT WRF runs are generated on a 2-km grid four times daily at 0400, 0700, 1600, and 1900 UTC, based on the times of the overhead passes of the Aqua and Terra satellites. The incorporation of the MODIS SST data into the SPORT WRF runs is staggered such that SSTs are updated with a new composite every six hours in each of the WRF runs. From mid-February to July 2007, over 500 parallel WRF simulations have been collected for analysis and verification. This paper will present verification results comparing the NWS MIA operational WRF runs to the SPORT experimental runs, and highlight any substantial differences noted in the predicted mesoscale phenomena for specific cases.

Land-use intensification impact on phosphorus fractions in highly weathered tropical soils

NASA Astrophysics Data System (ADS)

Maranguit, Deejay; Guillaume, Thomas; Kuzyakov, Yakov

2016-04-01

Deforestation and land-use intensification in tropics have increased over the past decades, driven by the demand for agricultural products. Despite the fact that phosphorus (P) is one of the main limiting nutrients for agricultural productivity in the tropics, the effect of land-use intensification on P availability remains unclear. The objective was to assess the impacts of land-use intensification on soil inorganic and organic P fractions of different availability (Hedley sequential fractionation) and P stocks in highly weathered tropical soils. We compared the P availability under extensive land-use (rubber agroforest) and intensive land-use with moderate fertilization (rubber monoculture plantations) or high fertilization (oil palm monoculture plantations) in Indonesia. The phosphorus stock was dominated by inorganic forms (60 to 85%) in all land-use types. Fertilizer application increased easily-available inorganic P (i.e., H2O-Pi, NaHCO3-Pi) in intensive rubber and oil palm plantations compared to agroforest. However, the easily-available organic P (NaHCO3-extractable Po) was reduced by half under oil palm and rubber. The decrease of moderately available and non-available P by land-use intensification means that fertilization maintains only short-term soil fertility that is not sustainable in the long run due to the depletion of P reserves. The mechanisms of this P reserve depletion are: soil erosion (here assessed by C/P ratio), mineralization of soil organic matter (SOM) and export of P with yield products. Easily-available P fractions (i.e., H2O-Pi, NaHCO3-Pi and Po) and total organic P were strongly positively correlated with carbon content suggesting that SOM plays a critical role in maintaining P availability. Therefore, the ecologically based management is necessary in mitigating SOM losses to increase the sustainability of agricultural production in P limited highly weathered tropical soils.

Effects of a 4-week high-intensity interval training on pacing during 5-km running trial

PubMed Central

Silva, R.; Damasceno, M.; Cruz, R.; Silva-Cavalcante, M.D.; Lima-Silva, A.E.; Bishop, D.J.; Bertuzzi, R.

2017-01-01

This study analyzed the influence of a 4-week high-intensity interval training on the pacing strategy adopted by runners during a 5-km running trial. Sixteen male recreational long-distance runners were randomly assigned to a control group (CON, n=8) or a high-intensity interval training group (HIIT, n=8). The HIIT group performed high-intensity interval-training twice per week, while the CON group maintained their regular training program. Before and after the training period, the runners performed an incremental exercise test to exhaustion to measure the onset of blood lactate accumulation, maximal oxygen uptake (VO2max), and peak treadmill speed (PTS). A submaximal constant-speed test to measure the running economy (RE) and a 5-km running trial on an outdoor track to establish pacing strategy and performance were also done. During the 5-km running trial, the rating of perceived exertion (RPE) and time to cover the 5-km trial (T5) were registered. After the training period, there were significant improvements in the HIIT group of ∼7 and 5% for RE (P=0.012) and PTS (P=0.019), respectively. There was no significant difference between the groups for VO2max (P=0.495) or onset of blood lactate accumulation (P=0.101). No difference was found in the parameters measured during the 5-km trial before the training period between HIIT and CON (P>0.05). These findings suggest that 4 weeks of HIIT can improve some traditional physiological variables related to endurance performance (RE and PTS), but it does not alter the perception of effort, pacing strategy, or overall performance during a 5-km running trial. PMID:29069224

Mechanical alterations during interval-training treadmill runs in high-level male team-sport players.

PubMed

Girard, Olivier; Brocherie, Franck; Morin, Jean-Benoit; Millet, Grégoire P

2017-01-01

To examine mechanical alterations during interval-training treadmill runs in high-level team-sport players. Within-participants repeated measures. Twenty high-level male field-hockey players performed six 30-s runs at 5.53±0.19ms -1 corresponding to 115% of their velocity associated with maximal oxygen uptake (vVO 2max ) with 30-s passive recovery on an instrumented treadmill. Continuous measurement of running kinetics/kinematics and spring-mass characteristics were performed and values were subsequently averaged over 20s (8th-28ths) for comparison. Contact time (+1.1±4.3%; p=0.044), aerial time (+4.1±5.3%; p=0.001), step length (+2.4±2.2%; p<0.001) along with mean loading rates (+7.1±10.6%; p=0.026) increased from the first to the last interval, whereas step frequency (-2.3±2.1%; p<0.001) decreased. Both centre of mass vertical displacement (+3.0±6.0%; p<0.001) and leg compression (+2.8±9.7%; p=0.036), but not peak vertical forces (0.0±4.1%; p=0.761), increased with fatigue. Vertical stiffness decreased (-2.8±6.9%; p=0.012), whereas leg stiffness did not change across intervals (p=0.149). During interval-training treadmill runs, high-level team-sport players modified their mechanical behaviour towards lower vertical stiffness while preserving a constant leg stiffness. Maintenance of running velocity induced longer step lengths and decreased step frequencies that were also accompanied by increased impact loading rates. These mechanical alterations occurred early during the set. Copyright © 2016 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

Accuracy and precision of loadsol® insole force-sensors for the quantification of ground reaction force-based biomechanical running parameters.

PubMed

Seiberl, Wolfgang; Jensen, Elisabeth; Merker, Josephine; Leitel, Marco; Schwirtz, Ansgar

2018-05-29

Force plates represent the "gold standard" in measuring running kinetics to predict performance or to identify the sources of running-related injuries. As these measurements are generally limited to laboratory analyses, wireless high-quality sensors for measuring in the field are needed. This work analysed the accuracy and precision of a new wireless insole forcesensor for quantifying running-related kinetic parameters. Vertical ground reaction force (GRF) was simultaneously measured with pit-mounted force plates (1 kHz) and loadsol ® sensors (100 Hz) under unshod forefoot and rearfoot running-step conditions. GRF data collections were repeated four times, each separated by 30 min treadmill running, to test influence of extended use. A repeated-measures ANOVA was used to identify differences between measurement devices. Additionally, mean bias and Bland-Altman limits of agreement (LoA) were calculated. We found a significant difference (p < .05) in ground contact time, peak force, and force rate, while there was no difference in parameters impulse, time to peak, and negative force rate. There was no influence of time point of measurement. The mean bias of ground contact time, impulse, peak force, and time to peak ranged between 0.6% and 3.4%, demonstrating high accuracy of loadsol ® devices for these parameters. For these same parameters, the LoA analysis showed that 95% of all measurement differences between insole and force plate measurements were less than 12%, demonstrating high precision of the sensors. However, highly dynamic behaviour of GRF, such as force rate, is not yet sufficiently resolved by the insole devices, which is likely explained by the low sampling rate.

Effects of a 4-week high-intensity interval training on pacing during 5-km running trial.

PubMed

Silva, R; Damasceno, M; Cruz, R; Silva-Cavalcante, M D; Lima-Silva, A E; Bishop, D J; Bertuzzi, R

2017-10-19

This study analyzed the influence of a 4-week high-intensity interval training on the pacing strategy adopted by runners during a 5-km running trial. Sixteen male recreational long-distance runners were randomly assigned to a control group (CON, n=8) or a high-intensity interval training group (HIIT, n=8). The HIIT group performed high-intensity interval-training twice per week, while the CON group maintained their regular training program. Before and after the training period, the runners performed an incremental exercise test to exhaustion to measure the onset of blood lactate accumulation, maximal oxygen uptake (VO2max), and peak treadmill speed (PTS). A submaximal constant-speed test to measure the running economy (RE) and a 5-km running trial on an outdoor track to establish pacing strategy and performance were also done. During the 5-km running trial, the rating of perceived exertion (RPE) and time to cover the 5-km trial (T5) were registered. After the training period, there were significant improvements in the HIIT group of ∼7 and 5% for RE (P=0.012) and PTS (P=0.019), respectively. There was no significant difference between the groups for VO2max (P=0.495) or onset of blood lactate accumulation (P=0.101). No difference was found in the parameters measured during the 5-km trial before the training period between HIIT and CON (P>0.05). These findings suggest that 4 weeks of HIIT can improve some traditional physiological variables related to endurance performance (RE and PTS), but it does not alter the perception of effort, pacing strategy, or overall performance during a 5-km running trial.

The match-to-match variation of match-running in elite female soccer.

PubMed

Trewin, Joshua; Meylan, César; Varley, Matthew C; Cronin, John

2018-02-01

The purpose of this study was to examine the match-to-match variation of match-running in elite female soccer players utilising GPS, using full-match and rolling period analyses. Longitudinal study. Elite female soccer players (n=45) from the same national team were observed during 55 international fixtures across 5 years (2012-2016). Data was analysed using a custom built MS Excel spreadsheet as full-matches and using a rolling 5-min analysis period, for all players who played 90-min matches (files=172). Variation was examined using co-efficient of variation and 90% confidence limits, calculated following log transformation. Total distance per minute exhibited the smallest variation when both the full-match and peak 5-min running periods were examined (CV=6.8-7.2%). Sprint-efforts were the most variable during a full-match (CV=53%), whilst high-speed running per minute exhibited the greatest variation in the post-peak 5-min period (CV=143%). Peak running periods were observed as slightly more variable than full-match analyses, with the post-peak period very-highly variable. Variability of accelerations (CV=17%) and Player Load (CV=14%) was lower than that of high-speed actions. Positional differences were also present, with centre backs exhibiting the greatest variation in high-speed movements (CV=41-65%). Practitioners and researchers should account for within player variability when examining match performances. Identification of peak running periods should be used to assist worst case scenarios. Whilst micro-sensor technology should be further examined as to its viable use within match-analyses. Copyright © 2017 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

On the potential of a chemical Bonds: Possible effects of steroids on home run production in baseball

NASA Astrophysics Data System (ADS)

Tobin, R. G.

2008-01-01

In recent years several baseball players have hit a remarkable number of home runs, and there has been speculation that their achievements were enhanced by the use of anabolic steroids. Basic mechanics and physiology, combined with simple but reasonable models, show that steroid use by a player who is already highly skilled could produce such dramatic increases in home run production. Because home runs are relatively rare events on the tail of a batter's range distribution, even modest changes in bat speed can increase the proportion of batted balls that result in home runs by 50-100%. The possible effect of steroid use by pitchers is briefly considered.

W Boson Mass Measurement at CDF

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

Kotwal, Ashutosh V.

2017-03-27

This is the closeout report for the grant for experimental research at the energy frontier in high energy physics. The report describes the precise measurement of the W boson mass at the CDF experiment at Fermilab, with an uncertainty of ≈ 12 MeV, using the full dataset of ≈ 9 fb -1 collected by the experiment up to the shutdown of the Tevatron in 2011. In this analysis, the statistical and most of the experimental systematic uncertainties have been reduced by a factor of two compared to the previous measurement with 2.2 fb -1 of CDF data. This research hasmore » been the culmination of the PI's track record of producing world-leading measurements of the W boson mass from the Tevatron. The PI performed the first and only measurement to date of the W boson mass using high-rapidity leptons using the D0 endcap calorimeters in Run 1. He has led this measurement in Run 2 at CDF, publishing two world-leading measurements in 2007 and 2012 with total uncertainties of 48 MeV and 19 MeV respectively. The analysis of the final dataset is currently under internal review in CDF. Upon approval of the internal review, the result will be available for public release.« less

High intensity interval training vs. high-volume running training during pre-season conditioning in high-level youth football: a cross-over trial.

PubMed

Faude, Oliver; Schnittker, Reinhard; Schulte-Zurhausen, Roman; Müller, Florian; Meyer, Tim

2013-01-01

We aimed at comparing the endurance effects of high-intensity interval training (HIIT) with high-volume running training (HVT) during pre-season conditioning in 20 high-level youth football players (15.9 (s 0.8) years). Players either conducted HVT or HIIT during the summer preparation period. During winter preparation they performed the other training programme. Before and after each training period several fitness tests were conducted: multi-stage running test (to assess the individual anaerobic threshold (IAT) and maximal running velocity (Vmax)), vertical jumping height, and straight sprinting. A significant increase from pre- to post-test was observed in IAT velocity (P < 0.001) with a greater increase after HVT (+0.8 km · h(-1) vs. +0.5 km · h(-1) after HIIT, P = 0.04). Maximal velocity during the incremental exercise test also slightly increased with time (P = 0.09). Forty per cent (HIIT) and 15% (HVT) of all players did not improve IAT beyond baseline variability. The players who did not respond to HIIT were significantly slower during 30 m sprinting than responders (P = 0.02). No further significant differences between responders and non-responders were observed. Jump heights deteriorated significantly after both training periods (P < 0.003). Both training programmes seem to be promising means to improve endurance capacity in high-level youth football players during pre-season conditioning.

The joy of interactive modeling

NASA Astrophysics Data System (ADS)

Donchyts, Gennadii; Baart, Fedor; van Dam, Arthur; Jagers, Bert

2013-04-01

The conventional way of working with hydrodynamical models usually consists of the following steps: 1) define a schematization (e.g., in a graphical user interface, or by editing input files) 2) run model from start to end 3) visualize results 4) repeat any of the previous steps. This cycle commonly takes up from hours to several days. What if we can make this happen instantly? As most of the research done using numerical models is in fact qualitative and exploratory (Oreskes et al., 1994), why not use these models as such? How can we adapt models so that we can edit model input, run and visualize results at the same time? More and more, interactive models become available as online apps, mainly for demonstration and educational purposes. These models often simplify the physics behind flows and run on simplified model geometries, particularly when compared with state-of-the-art scientific simulation packages. Here we show how the aforementioned conventional standalone models ("static, run once") can be transformed into interactive models. The basic concepts behind turning existing (conventional) model engines into interactive engines are the following. The engine does not run the model from start to end, but is always available in memory, and can be fed by new boundary conditions, or state changes at any time. The model can be run continuously, per step, or up to a specified time. The Hollywood principle dictates how the model engine is instructed from 'outside', instead of the model engine taking all necessary actions on its own initiative. The underlying techniques that facilitate these concepts are introspection of the computation engine, which exposes its state variables, and control functions, e.g. for time stepping, via a standardized interface, such as BMI (Peckam et. al., 2012). In this work we have used a shallow water flow model engine D-Flow Flexible Mesh. The model was converted from executable to a library, and coupled to the graphical modelling environment Delta Shell. Both the engine and the environment are open source tools under active development at Deltares. The combination provides direct interactive control over the time loop and model state, and offers live 3D visualization of the running model using VTK library.

Abusive User Policy | High-Performance Computing | NREL

Science.gov Websites

below. First Incident The user's ability to run new jobs or store new data will be suspended temporarily acknowledged and participated in a remedy, ability to run new jobs or store new data will be restored. Second Incident Suspend running new jobs or storing new data. Terminate jobs if necessary. The system and

Coho salmon spawner mortality in western US urban watersheds: bioinfiltration prevents lethal storm water impacts.

PubMed

Spromberg, Julann A; Baldwin, David H; Damm, Steven E; McIntyre, Jenifer K; Huff, Michael; Sloan, Catherine A; Anulacion, Bernadita F; Davis, Jay W; Scholz, Nathaniel L

2016-04-01

Adult coho salmon Oncorhynchus kisutch return each autumn to freshwater spawning habitats throughout western North America. The migration coincides with increasing seasonal rainfall, which in turn increases storm water run-off, particularly in urban watersheds with extensive impervious land cover. Previous field assessments in urban stream networks have shown that adult coho are dying prematurely at high rates (>50%). Despite significant management concerns for the long-term conservation of threatened wild coho populations, a causal role for toxic run-off in the mortality syndrome has not been demonstrated.We exposed otherwise healthy coho spawners to: (i) artificial storm water containing mixtures of metals and petroleum hydrocarbons, at or above concentrations previously measured in urban run-off; (ii) undiluted storm water collected from a high traffic volume urban arterial road (i.e. highway run-off); and (iii) highway run-off that was first pre-treated via bioinfiltration through experimental soil columns to remove pollutants.We find that mixtures of metals and petroleum hydrocarbons - conventional toxic constituents in urban storm water - are not sufficient to cause the spawner mortality syndrome. By contrast, untreated highway run-off collected during nine distinct storm events was universally lethal to adult coho relative to unexposed controls. Lastly, the mortality syndrome was prevented when highway run-off was pretreated by soil infiltration, a conventional green storm water infrastructure technology.Our results are the first direct evidence that: (i) toxic run-off is killing adult coho in urban watersheds, and (ii) inexpensive mitigation measures can improve water quality and promote salmon survival. Synthesis and applications . Coho salmon, an iconic species with exceptional economic and cultural significance, are an ecological sentinel for the harmful effects of untreated urban run-off. Wild coho populations cannot withstand the high rates of mortality that are now regularly occurring in urban spawning habitats. Green storm water infrastructure or similar pollution prevention methods should be incorporated to the maximal extent practicable, at the watershed scale, for all future development and redevelopment projects, particularly those involving transportation infrastructure.

10 CFR 2.1003 - Availability of material.

Code of Federal Regulations, 2013 CFR

2013-01-01

... its license application for a geologic repository, the NRC shall make available no later than thirty... privilege in § 2.1006, graphic-oriented documentary material that includes raw data, computer runs, computer... discrepancies; (ii) Gauge, meter and computer settings; (iii) Probe locations; (iv) Logging intervals and rates...

10 CFR 2.1003 - Availability of material.

Code of Federal Regulations, 2014 CFR

2014-01-01

... its license application for a geologic repository, the NRC shall make available no later than thirty... privilege in § 2.1006, graphic-oriented documentary material that includes raw data, computer runs, computer... discrepancies; (ii) Gauge, meter and computer settings; (iii) Probe locations; (iv) Logging intervals and rates...

Variation in annual run-off in the Rocky Mountain region: Chapter A in Contributions to the hydrology of the United States, 1923-1924

USGS Publications Warehouse

Follansbee, Robert

1925-01-01

Records of run-off in the Rocky Mountain States since the nineties and for a few stations since the eighties afford a means of studying the variation in the annual run-off in this region. The data presented in this report show that the variation in annual run-off differs in different areas in the Rocky Mountain region, owing to the differences in the sources of the precipitation in these areas. Except in the drainage basins of streams in northern Montana the year of lowest run-off shown by the records was 1902, when the run-ff at one station was only 36 per cent of the mean run-ff for the periods covered by the several records available. The percentage variation of run-ff for streams in different parts of Colorado is less for any one year than that for streams in the mountain region as a whole, and for streams in the same major drainage basin the annual variation is markedly similar. The influence of topography upon variation in annual run-ff for streams in Colorado is marked, the streams that rise in the central mountain region having a smaller range in variation than the streams that rise on the eastern or western edges of the central mountain mass. The streams that rise on the plains just east of the mountains have a greater variation than those of any of the mountain groups. The ratio of any 10-year mean to the mean for the entire period covered by the records ranges from 72 to 133 per cent. For the South Platte, Arkansas, and Rio Grande the run-off during the nineties was below the normal, but since about 1903 it has been above normal. For the Cache la Poudre low-water periods occurred during the eighties and from 1905 to 1922, but during the nineties the run-off was above the normal.

HZEFRG1 - SEMIEMPIRICAL NUCLEAR FRAGMENTATION MODEL

NASA Technical Reports Server (NTRS)

Townsend, L. W.

1994-01-01

The high charge and energy (HZE), Semiempirical Nuclear Fragmentation Model, HZEFRG1, was developed to provide a computationally efficient, user-friendly, physics-based program package for generating nuclear fragmentation databases. These databases can then be used in radiation transport applications such as space radiation shielding and dosimetry, cancer therapy with laboratory heavy ion beams, and simulation studies of detector design in nuclear physics experiments. The program provides individual element and isotope production cross sections for the breakup of high energy heavy ions by the combined nuclear and Coulomb fields of the interacting nuclei. The nuclear breakup contributions are estimated using an energy-dependent abrasion-ablation model of heavy ion fragmentation. The abrasion step involves removal of nucleons by direct knockout in the overlap region of the colliding nuclei. The abrasions are treated on a geometric basis and uniform spherical nuclear density distributions are assumed. Actual experimental nuclear radii obtained from tabulations of electron scattering data are incorporated. Nuclear transparency effects are included by using an energy-dependent, impact-parameter-dependent average transmission factor for the projectile and target nuclei, which accounts for the finite mean free path of nucleons in nuclear matter. The ablation step, as implemented by Bowman, Swiatecki, and Tsang (LBL report no. LBL-2908, July 1973), was treated as a single-nucleon emission for every 10 MeV of excitation energy. Fragmentation contributions from electromagnetic dissociation (EMD) processes, arising from the interacting Coulomb fields, are estimated by using the Weiszacker-Williams theory, extended to include electric dipole and electric quadrupole contributions to one-nucleon removal cross sections. HZEFRG1 consists of a main program, seven function subprograms, and thirteen subroutines. Each is fully commented and begins with a brief description of its functionality. The inputs, which are provided interactively by the user in response to on-screen questions, consist of the projectile kinetic energy in units of MeV/nucleon and the masses and charges of the projectile and target nuclei. With proper inputs, HZEFRG1 first calculates the EMD cross sections and then begins the calculations for nuclear fragmentation by searching through a specified number of isotopes for each charge number (Z) from Z=1 (hydrogen) to the charge of the incident fragmenting nucleus (Zp). After completing the nuclear fragmentation cross sections, HZEFRG1 sorts through the results and writes the sorted output to a file in descending order, based on the charge number of the fragmented nucleus. Details of the theory, extensive comparisons of its predictions with available experimental cross section data, and a complete description of the code implementing it are given in the program documentation. HZEFRG1 is written in ANSI FORTRAN 77 to be machine independent. It was originally developed on a DEC VAX series computer, and has been successfully implemented on a DECstation running RISC ULTRIX 4.3, a Sun4 series computer running SunOS 4.1, an HP 9000 series computer running HP-UX 8.0.1, a Cray Y-MP series computer running UNICOS, and IBM PC series computers running MS-DOS 3.3 and higher. HZEFRG1 requires 1Mb of RAM for execution. In addition, a FORTRAN 77 compiler is required to create an executable. A sample output run is included on the distribution medium for numerical comparison. The standard distribution medium for this program is a 3.5 inch 1.44Mb MS-DOS format diskette. Alternate distribution media and formats are available upon request. HZEFRG1 was completed in 1992.

Friction and Environmental Sensitivity of Molybdenum Disulfide: Effects of Microstructure

NASA Astrophysics Data System (ADS)

Curry, John F.

For nearly a century, molybdenum disulfide has been employed as a solid lubricant to reduce the friction and wear between surfaces. MoS2 is in a class of unique materials, transition metal dichalcogens (TMDC), that have a single crystal structure forming lamellae that interact via weak van der Waals forces. This dissertation focuses on the link between the microstructure of MoS2 and the energetics of running film formation to reduce friction, and effects of environmental sensitivities on performance. Nitrogen impinged MoS2 films are utilized as a comparator to amorphous PVD deposited MoS2 in many of the studies due to the highly ordered surface parallel basal texture of sprayed films. Comparisons showed that films with a highly ordered structure can reduce high friction behavior during run-in. It is thought that shear induced reorientation of amorphous films contributes to typically high initial friction during run-in. In addition to a reduction in initial friction, highly ordered MoS2 films are shown to be more resistant to penetration from oxidative aging processes. High sensitivity, low-energy ion scattering (HS-LEIS) enabled depth profiles that showed oxidation limited to the first monolayer for ordered films and throughout the depth (4-5 nm) for amorphous films. X-ray photoelectron spectroscopy supported these findings, showing far more oxidation in amorphous films than ordered films. Many of these results show the benefits of a well run-in coating, yet transient increases in initial friction can still be noticed after only 5 - 10 minutes. It was found that the transient return to high initial friction after dwell times past 5 - 10 minutes was not due to adsorbed species such as water, but possibly an effect of basal plane relaxation to a commensurate state. Additional techniques and methods were developed to study the effect of adsorbed water and load on running film formation via spiral orbit XRD studies. Spiral orbit experiments enabled large enough worn areas for study in the XRD. Diffraction patterns for sputtered coatings at high loads (1N) showed more intense signals for surface parallel basal plane representation than lower loads (100mN). Tests run in dry and humid nitrogen (20% RH), however, showed no differences in reorientation of basal planes. Microstructure was found to be an important factor in determining the tribological performance of MoS2 films in a variety of testing conditions and environments. These findings will be useful in developing a mechanistic framework that better understands the energetics of running film formation and how different environments play a role.

Django Remote Submission

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

Doucet, Mathieu; Hobson, Tanner C.; Ferraz Leal, Ricardo Miguel

The Django Remote Submission (DRS) is a Django (Django, n.d.) application to manage long running job submission, including starting the job, saving logs, and storing results. It is an independent project available as a standalone pypi package (PyPi, n.d.). It can be easily integrated in any Django project. The source code is freely available as a GitHub repository (django-remote-submission, n.d.). To run the jobs in background, DRS takes advantage of Celery (Celery, n.d.), a powerful asynchronous job queue used for running tasks in the background, and the Redis Server (Redis, n.d.), an in-memory data structure store. Celery uses brokers tomore » pass messages between a Django Project and the Celery workers. Redis is the message broker of DRS. In addition DRS provides real time monitoring of the progress of Jobs and associated logs. Through the Django Channels project (Channels, n.d.), and the usage of Web Sockets, it is possible to asynchronously display the Job Status and the live Job output (standard output and standard error) on a web page.« less

Mentat/A: Medium grain parallel processing

NASA Technical Reports Server (NTRS)

Grimshaw, Andrew S.

1992-01-01

The objective of this project is to test the Algorithm to Architecture Mapping Model (ATAMM) firing rules using the Mentat run-time system and the Mentat Programming Language (MPL). A special version of Mentat, Mentat/A (Mentat/ATAMM) was constructed. This required changes to: (1) modify the run-time system to control queue length and inhibit actor firing until required data tokens are available and space is available in the input queues of all of the direct descendent actors; (2) disallow the specification of persistent object classes in the MPL; and (3) permit only decision free graphs in the MPL. We were successful in implementing the spirit of the plan, although some goals changed as we came to better understand the problem. We report on what we accomplished and the lessons we learned. The Mentat/A run-time system is discussed, and we briefly present the compiler. We present results for three applications and conclude with a summary and some observations. Appendix A contains a list of technical reports and published papers partially supported by the grant. Appendix B contains listings for the three applications.

Django Remote Submission

DOE PAGES

Doucet, Mathieu; Hobson, Tanner C.; Ferraz Leal, Ricardo Miguel

2017-08-01

The Django Remote Submission (DRS) is a Django (Django, n.d.) application to manage long running job submission, including starting the job, saving logs, and storing results. It is an independent project available as a standalone pypi package (PyPi, n.d.). It can be easily integrated in any Django project. The source code is freely available as a GitHub repository (django-remote-submission, n.d.). To run the jobs in background, DRS takes advantage of Celery (Celery, n.d.), a powerful asynchronous job queue used for running tasks in the background, and the Redis Server (Redis, n.d.), an in-memory data structure store. Celery uses brokers tomore » pass messages between a Django Project and the Celery workers. Redis is the message broker of DRS. In addition DRS provides real time monitoring of the progress of Jobs and associated logs. Through the Django Channels project (Channels, n.d.), and the usage of Web Sockets, it is possible to asynchronously display the Job Status and the live Job output (standard output and standard error) on a web page.« less

Increased medial longitudinal arch mobility, lower extremity kinematics, and ground reaction forces in high-arched runners.

PubMed

Williams, D S Blaise; Tierney, Robin N; Butler, Robert J

2014-01-01

Runners with high medial longitudinal arch structure demonstrate unique kinematics and kinetics that may lead to running injuries. The mobility of the midfoot as measured by the change in arch height is also suspected to play a role in lower extremity function during running. The effect of arch mobility in high-arched runners is an important factor in prescribing footwear, training, and rehabilitating the running athlete after injury. To examine the effect of medial longitudinal arch mobility on running kinematics, ground reaction forces, and loading rates in high-arched runners. Cross-sectional study. Human movement research laboratory. A total of 104 runners were screened for arch height. Runners were then identified as having high arches if the arch height index was greater than 0.5 SD above the mean. Of the runners with high arches, 11 rigid runners with the lowest arch mobility (R) were compared with 8 mobile runners with the highest arch mobility (M). Arch mobility was determined by calculating the left arch height index in all runners. Three-dimensional motion analysis of running over ground. Rearfoot and tibial angular excursions, eversion-to-tibial internal-rotation ratio, vertical ground reaction forces, and the associated loading rates. Runners with mobile arches exhibited decreased tibial internal-rotation excursion (mobile: 5.6° ± 2.3° versus rigid: 8.0° ± 3.0°), greater eversion-to-tibial internal-rotation ratio (mobile: 2.1 ± 0.8 versus rigid: 1.5 ± 0.5), decreased second peak vertical ground reaction force values (mobile: 2.3 ± 0.2 × body weight versus rigid: 2.4 ± 0.1 × body weight), and decreased vertical loading rate values (mobile: 55.7 ± 14.1 × body weight/s versus rigid: 65.9 ± 11.4 × body weight/s). Based on the results of this study, it appears that runners with high arch structure but differing arch mobility exhibited differences in select lower extremity movement patterns and forces. Future authors should investigate the impact of arch mobility on running-related injuries.

FireMap: A Web Tool for Dynamic Data-Driven Predictive Wildfire Modeling Powered by the WIFIRE Cyberinfrastructure

NASA Astrophysics Data System (ADS)

Block, J.; Crawl, D.; Artes, T.; Cowart, C.; de Callafon, R.; DeFanti, T.; Graham, J.; Smarr, L.; Srivas, T.; Altintas, I.

2016-12-01

The NSF-funded WIFIRE project has designed a web-based wildfire modeling simulation and visualization tool called FireMap. The tool executes FARSITE to model fire propagation using dynamic weather and fire data, configuration settings provided by the user, and static topography and fuel datasets already built-in. Using GIS capabilities combined with scalable big data integration and processing, FireMap enables simple execution of the model with options for running ensembles by taking the information uncertainty into account. The results are easily viewable, sharable, repeatable, and can be animated as a time series. From these capabilities, users can model real-time fire behavior, analyze what-if scenarios, and keep a history of model runs over time for sharing with collaborators. Firemap runs FARSITE with national and local sensor networks for real-time weather data ingestion and High-Resolution Rapid Refresh (HRRR) weather for forecasted weather. The HRRR is a NOAA/NCEP operational weather prediction system comprised of a numerical forecast model and an analysis/assimilation system to initialize the model. It is run with a horizontal resolution of 3 km, has 50 vertical levels, and has a temporal resolution of 15 minutes. The HRRR requires an Environmental Data Exchange (EDEX) server to receive the feed and generate secondary products out of it for the modeling. UCSD's EDEX server, funded by NSF, makes high-resolution weather data available to researchers worldwide and enables visualization of weather systems and weather events lasting months or even years. The high-speed server aggregates weather data from the University Consortium for Atmospheric Research by way of a subscription service from the Consortium called the Internet Data Distribution system. These features are part of WIFIRE's long term goals to build an end-to-end cyberinfrastructure for real-time and data-driven simulation, prediction and visualization of wildfire behavior. Although Firemap is a research product of WIFIRE, developed in collaboration with a number of fire departments, the tool is operational in pilot form for providing big data-driven predictive fire spread modeling. Most recently, FireMap was used for situational awareness in the July 2016 Sand Fire by LA City and LA County Fire Departments.

Run-to-Run Optimization Control Within Exact Inverse Framework for Scan Tracking.

PubMed

Yeoh, Ivan L; Reinhall, Per G; Berg, Martin C; Chizeck, Howard J; Seibel, Eric J

2017-09-01

A run-to-run optimization controller uses a reduced set of measurement parameters, in comparison to more general feedback controllers, to converge to the best control point for a repetitive process. A new run-to-run optimization controller is presented for the scanning fiber device used for image acquisition and display. This controller utilizes very sparse measurements to estimate a system energy measure and updates the input parameterizations iteratively within a feedforward with exact-inversion framework. Analysis, simulation, and experimental investigations on the scanning fiber device demonstrate improved scan accuracy over previous methods and automatic controller adaptation to changing operating temperature. A specific application example and quantitative error analyses are provided of a scanning fiber endoscope that maintains high image quality continuously across a 20 °C temperature rise without interruption of the 56 Hz video.

State estimator for multisensor systems with irregular sampling and time-varying delays

NASA Astrophysics Data System (ADS)

Peñarrocha, I.; Sanchis, R.; Romero, J. A.

2012-08-01

This article addresses the state estimation in linear time-varying systems with several sensors with different availability, randomly sampled in time and whose measurements have a time-varying delay. The approach is based on a modification of the Kalman filter with the negative-time measurement update strategy, avoiding running back the full standard Kalman filter, the use of full augmented order models or the use of reorganisation techniques, leading to a lower implementation cost algorithm. The update equations are run every time a new measurement is available, independently of the time when it was taken. The approach is useful for networked control systems, systems with long delays and scarce measurements and for out-of-sequence measurements.

Characterisation of the responsive properties of two running-specific prosthetic models.

PubMed

Grobler, Lara; Ferreira, Suzanne; Vanwanseele, Benedicte; Terblanche, Elmarie E

2017-04-01

The need for information regarding running-specific prosthetic properties has previously been voiced. Such information is necessary to assist in athletes' prostheses selection. This study aimed to describe the characteristics of two commercially available running-specific prostheses. The running-specific prostheses were tested (in an experimental setup) without the external interference of athlete performance variations. Four stiffness categories of each running-specific prosthetic model (Xtend ™ and Xtreme ™ ) were tested at seven alignment setups and three drop masses (28, 38 and 48 kg). Results for peak ground reaction force (GRF peak ), contact time ( t c ), flight time ( t f ), reactive strength index (RSI) and maximal compression (Δ L) were determined during controlled dropping of running-specific prostheses onto a force platform with different masses attached to the experimental setup. No statistically significant differences were found between the different setups of the running-specific prostheses. Statistically significant differences were found between the two models for all outcome variables (GRF peak , Xtend > Xtreme; t c , Xtreme > Xtend; t f , Xtreme > Xtend; RSI, Xtend > Xtreme; Δ L, Xtreme > Xtend; p < 0.05). These findings suggest that the Xtreme stores more elastic energy than the Xtend, leading to a greater performance response. The specific responsive features of blades could guide sprint athletes in their choice of running-specific prostheses. Clinical relevance Insights into the running-specific prosthesis (RSP) properties and an understanding of its responsive characteristics have implications for athletes' prosthetic choice. Physiologically and metabolically, a short sprint event (i.e. 100 m) places different demands on the athlete than a long sprint event (i.e. 400 m), and the RSP should match these performance demands.

A brief opportunity to run does not function as a reinforcer for mice selected for high daily wheel-running rates.

PubMed

Belke, Terry W; Garland, Theodore

2007-09-01

Mice from replicate lines, selectively bred based on high daily wheel-running rates, run more total revolutions and at higher average speeds than do mice from nonselected control lines. Based on this difference it was assumed that selected mice would find the opportunity to run in a wheel a more efficacious consequence. To assess this assumption within an operant paradigm, mice must be trained to make a response to produce the opportunity to run as a consequence. In the present study an autoshaping procedure was used to compare the acquisition of lever pressing reinforced by the opportunity to run for a brief opportunity (i.e., 90 s) between selected and control mice and then, using an operant procedure, the effect of the duration of the opportunity to run on lever pressing was assessed by varying reinforcer duration over values of 90 s, 30 min, and 90 s. The reinforcement schedule was a ratio schedule (FR 1 or VR 3). Results from the autoshaping phase showed that more control mice met a criterion of responses on 50% of trials. During the operant phase, when reinforcer duration was 90 s, almost all control, but few selected mice completed a session of 20 reinforcers; however, when reinforcer duration was increased to 30 min almost all selected and control mice completed a session of 20 reinforcers. Taken together, these results suggest that selective breeding based on wheel-running rates over 24 hr may have altered the motivational system in a way that reduces the reinforcing value of shorter running durations. The implications of this finding for these mice as a model for attention deficit hyperactivity disorder (ADHD) are discussed. It also is proposed that there may be an inherent trade-off in the motivational system for activities of short versus long duration.

A Brief Opportunity to Run Does Not Function as a Reinforcer for Mice Selected for High Daily Wheel-running Rates

PubMed Central

Belke, Terry W; GarlandJr, Theodore

2007-01-01

Mice from replicate lines, selectively bred based on high daily wheel-running rates, run more total revolutions and at higher average speeds than do mice from nonselected control lines. Based on this difference it was assumed that selected mice would find the opportunity to run in a wheel a more efficacious consequence. To assess this assumption within an operant paradigm, mice must be trained to make a response to produce the opportunity to run as a consequence. In the present study an autoshaping procedure was used to compare the acquisition of lever pressing reinforced by the opportunity to run for a brief opportunity (i.e., 90 s) between selected and control mice and then, using an operant procedure, the effect of the duration of the opportunity to run on lever pressing was assessed by varying reinforcer duration over values of 90 s, 30 min, and 90 s. The reinforcement schedule was a ratio schedule (FR 1 or VR 3). Results from the autoshaping phase showed that more control mice met a criterion of responses on 50% of trials. During the operant phase, when reinforcer duration was 90 s, almost all control, but few selected mice completed a session of 20 reinforcers; however, when reinforcer duration was increased to 30 min almost all selected and control mice completed a session of 20 reinforcers. Taken together, these results suggest that selective breeding based on wheel-running rates over 24 hr may have altered the motivational system in a way that reduces the reinforcing value of shorter running durations. The implications of this finding for these mice as a model for attention deficit hyperactivity disorder (ADHD) are discussed. It also is proposed that there may be an inherent trade-off in the motivational system for activities of short versus long duration. PMID:17970415

Soy protein is beneficial but high-fat diet and voluntary running are detrimental to bone structure in mice

USDA-ARS?s Scientific Manuscript database

We investigated the effects of diet (AIN93G or high-fat), physical activity (sedentary or voluntary running) and protein source (casein or soy protein isolate) and their interactions on bone microstructural changes in distal femurs in male C57BL/6 mice by using micro-computed tomography. After 14 w...

Acute effects of high-intensity intermittent training on kinematics and foot strike patterns in endurance runners.

PubMed

Latorre-Román, P Á; García Pinillos, F; Bujalance-Moreno, P; Soto-Hermoso, V M

2017-07-01

The main purpose of this study was to evaluate running kinematic characteristics and foot strike patterns (FSP) during early and late stages of actual and common high-intensity intermittent training (HIIT): 5 × 2000 m with 120-s recovery between runs. Thirteen healthy, elite, highly trained male endurance runners participated in this study. They each had a personal record in the half-marathon of 70 ± 2.24 min, and each had a minimum experience of 4 years of training and competition. Heart rate (HR) and rate of perceived exertion (RPE) were monitored during HIIT. High levels of exhaustion were reached by the athletes during HIIT (HRpeak: 174.30 bpm; RPE: 17.23). There was a significant increase of HRpeak and RPE during HIIT; nevertheless, time for each run remained unchanged. A within-protocol paired t-test (first vs. last run) revealed no significant changes (P ≥ 0.05) in kinematics variables and FSP variables during HIIT. There were no substantial changes on kinematics and FSP characteristics in endurance runners after fatigue induced by a HIIT. Only the minimum ankle alignment showed a significant change. The author suggests that these results might be due to both the high athletic level of participants and their experience in HIIT.

The CMS muon system: status and upgrades for LHC Run-2 and performance of muon reconstruction with 13 TeV data

NASA Astrophysics Data System (ADS)

Battilana, C.

2017-01-01

The CMS muon system has played a key role for many physics results obtained from the LHC Run-1 and Run-2 data. During the Long Shutdown (2013-2014), as well as during the last year-end technical stop (2015-2016), significant consolidation and upgrades have been carried out on the muon detectors and on the L1 muon trigger. The algorithms for muon reconstruction and identification have also been improved for both the High-Level Trigger and the offline reconstruction. Results of the performance of muon detectors, reconstruction and trigger, obtained using data collected at 13 TeV centre-of-mass energy during the 2015 and 2016 LHC runs, will be presented. Comparison of simulation with experimental data will also be discussed where relevant. The system's state of the art performance will be shown, and the improvements foreseen to achieve excellent overall quality of muon reconstruction in CMS, in the conditions expected during the high-luminosity phase of Run-2, will be described.

Effects of restricted feeding schedules on circadian organization in squirrel monkeys

NASA Technical Reports Server (NTRS)

Boulos, Z.; Frim, D. M.; Dewey, L. K.; Moore-Ede, M. C.

1989-01-01

Free running circadian rhythms of motor activity, food-motivated lever-pressing, and either drinking (N = 7) or body temperature (N = 3) were recorded from 10 squirrel monkeys maintained in constant illumination with unlimited access to food. Food availability was then restricted to a single unsignaled 3-hour interval each day. The feeding schedule failed to entrain the activity rhythms of 8 monkeys, which continued to free-run. Drinking was almost completely synchronized by the schedule, while body temperature showed a feeding-induced rise superimposed on a free-running rhythm. Nonreinforced lever-pressing showed both a free-running component and a 24-hour component that anticipated the time of feeding. At the termination of the schedule, all recorded variables showed free-running rhythms, but in 3 animals the initial phase of the postschedule rhythms was advanced by several hours, suggesting relative coordination. Of the remaining 2 animals, one exhibited stable entrainment of all 3 recorded rhythms, while the other appeared to entrain temporarily to the feeding schedule. These results indicate that restricted feeding schedules are only a weak zeitgeber for the circadian pacemaker generating free-running rhythms in the squirrel monkey. Such schedules, however, may entrain a separate circadian system responsible for the timing of food-anticipatory changes in behavior and physiology.

Interfacing HTCondor-CE with OpenStack

NASA Astrophysics Data System (ADS)

Bockelman, B.; Caballero Bejar, J.; Hover, J.

2017-10-01

Over the past few years, Grid Computing technologies have reached a high level of maturity. One key aspect of this success has been the development and adoption of newer Compute Elements to interface the external Grid users with local batch systems. These new Compute Elements allow for better handling of jobs requirements and a more precise management of diverse local resources. However, despite this level of maturity, the Grid Computing world is lacking diversity in local execution platforms. As Grid Computing technologies have historically been driven by the needs of the High Energy Physics community, most resource providers run the platform (operating system version and architecture) that best suits the needs of their particular users. In parallel, the development of virtualization and cloud technologies has accelerated recently, making available a variety of solutions, both commercial and academic, proprietary and open source. Virtualization facilitates performing computational tasks on platforms not available at most computing sites. This work attempts to join the technologies, allowing users to interact with computing sites through one of the standard Computing Elements, HTCondor-CE, but running their jobs within VMs on a local cloud platform, OpenStack, when needed. The system will re-route, in a transparent way, end user jobs into dynamically-launched VM worker nodes when they have requirements that cannot be satisfied by the static local batch system nodes. Also, once the automated mechanisms are in place, it becomes straightforward to allow an end user to invoke a custom Virtual Machine at the site. This will allow cloud resources to be used without requiring the user to establish a separate account. Both scenarios are described in this work.

QuantWorm: a comprehensive software package for Caenorhabditis elegans phenotypic assays.

PubMed

Jung, Sang-Kyu; Aleman-Meza, Boanerges; Riepe, Celeste; Zhong, Weiwei

2014-01-01

Phenotypic assays are crucial in genetics; however, traditional methods that rely on human observation are unsuitable for quantitative, large-scale experiments. Furthermore, there is an increasing need for comprehensive analyses of multiple phenotypes to provide multidimensional information. Here we developed an automated, high-throughput computer imaging system for quantifying multiple Caenorhabditis elegans phenotypes. Our imaging system is composed of a microscope equipped with a digital camera and a motorized stage connected to a computer running the QuantWorm software package. Currently, the software package contains one data acquisition module and four image analysis programs: WormLifespan, WormLocomotion, WormLength, and WormEgg. The data acquisition module collects images and videos. The WormLifespan software counts the number of moving worms by using two time-lapse images; the WormLocomotion software computes the velocity of moving worms; the WormLength software measures worm body size; and the WormEgg software counts the number of eggs. To evaluate the performance of our software, we compared the results of our software with manual measurements. We then demonstrated the application of the QuantWorm software in a drug assay and a genetic assay. Overall, the QuantWorm software provided accurate measurements at a high speed. Software source code, executable programs, and sample images are available at www.quantworm.org. Our software package has several advantages over current imaging systems for C. elegans. It is an all-in-one package for quantifying multiple phenotypes. The QuantWorm software is written in Java and its source code is freely available, so it does not require use of commercial software or libraries. It can be run on multiple platforms and easily customized to cope with new methods and requirements.

RNA-Sequencing Reveals Unique Transcriptional Signatures of Running and Running-Independent Environmental Enrichment in the Adult Mouse Dentate Gyrus.

PubMed

Grégoire, Catherine-Alexandra; Tobin, Stephanie; Goldenstein, Brianna L; Samarut, Éric; Leclerc, Andréanne; Aumont, Anne; Drapeau, Pierre; Fulton, Stephanie; Fernandes, Karl J L

2018-01-01

Environmental enrichment (EE) is a powerful stimulus of brain plasticity and is among the most accessible treatment options for brain disease. In rodents, EE is modeled using multi-factorial environments that include running, social interactions, and/or complex surroundings. Here, we show that running and running-independent EE differentially affect the hippocampal dentate gyrus (DG), a brain region critical for learning and memory. Outbred male CD1 mice housed individually with a voluntary running disk showed improved spatial memory in the radial arm maze compared to individually- or socially-housed mice with a locked disk. We therefore used RNA sequencing to perform an unbiased interrogation of DG gene expression in mice exposed to either a voluntary running disk (RUN), a locked disk (LD), or a locked disk plus social enrichment and tunnels [i.e., a running-independent complex environment (CE)]. RNA sequencing revealed that RUN and CE mice showed distinct, non-overlapping patterns of transcriptomic changes versus the LD control. Bio-informatics uncovered that the RUN and CE environments modulate separate transcriptional networks, biological processes, cellular compartments and molecular pathways, with RUN preferentially regulating synaptic and growth-related pathways and CE altering extracellular matrix-related functions. Within the RUN group, high-distance runners also showed selective stress pathway alterations that correlated with a drastic decline in overall transcriptional changes, suggesting that excess running causes a stress-induced suppression of running's genetic effects. Our findings reveal stimulus-dependent transcriptional signatures of EE on the DG, and provide a resource for generating unbiased, data-driven hypotheses for novel mediators of EE-induced cognitive changes.

Biological and environmental determinants of 12-minute run performance in youth.

PubMed

Freitas, Duarte; Maia, José; Stasinopoulos, Mikis; Gouveia, Élvio Rúbio; Antunes, António M; Thomis, Martine; Lefevre, Johan; Claessens, Albrecht; Hedeker, Donald; Malina, Robert M

2017-11-01

The 12-minute run is a commonly used indicator of cardiorespiratory fitness in youth. Variation in growth and maturity status as potential correlates of test performance has not been systematically addressed. To evaluate biological and environmental determinants of 12-minute run performance in Portuguese youth aged 7-17 years. Mixed-longitudinal samples of 187 boys and 142 girls were surveyed in 1996, 1997 and 1998. The 12-minute run was the indicator of cardiorespiratory fitness. Height, body mass and five skinfolds were measured and skeletal maturity was assessed. Physical activity, socioeconomic status and area of residence were obtained with a questionnaire. Multi-level modelling was used for the analysis. Chronological age and sum of five skinfolds were significant predictors of 12-minute run performance. Older boys and girls ran longer distances than younger peers, while high levels of subcutaneous fat were associated with shorter running distances. Rural boys were more proficient in the 12-minute run than urban peers. Skeletal maturity, height, body mass index, physical activity and socioeconomic status were not significant predictors of 12-minute run performances. Age and sum of skinfolds in both sexes and rural residence in boys are significant predictors of 12-minute run performance in Portuguese youth.

Definition of run-off-road crash clusters-For safety benefit estimation and driver assistance development.

PubMed

Nilsson, Daniel; Lindman, Magdalena; Victor, Trent; Dozza, Marco

2018-04-01

Single-vehicle run-off-road crashes are a major traffic safety concern, as they are associated with a high proportion of fatal outcomes. In addressing run-off-road crashes, the development and evaluation of advanced driver assistance systems requires test scenarios that are representative of the variability found in real-world crashes. We apply hierarchical agglomerative cluster analysis to define similarities in a set of crash data variables, these clusters can then be used as the basis in test scenario development. Out of 13 clusters, nine test scenarios are derived, corresponding to crashes characterised by: drivers drifting off the road in daytime and night-time, high speed departures, high-angle departures on narrow roads, highways, snowy roads, loss-of-control on wet roadways, sharp curves, and high speeds on roads with severe road surface conditions. In addition, each cluster was analysed with respect to crash variables related to the crash cause and reason for the unintended lane departure. The study shows that cluster analysis of representative data provides a statistically based method to identify relevant properties for run-off-road test scenarios. This was done to support development of vehicle-based run-off-road countermeasures and driver behaviour models used in virtual testing. Future studies should use driver behaviour from naturalistic driving data to further define how test-scenarios and behavioural causation mechanisms should be included. Copyright © 2018 Elsevier Ltd. All rights reserved.

Development and testing of a new system for assessing wheel-running behaviour in rodents.

PubMed

Chomiak, Taylor; Block, Edward W; Brown, Andrew R; Teskey, G Campbell; Hu, Bin

2016-05-05

Wheel running is one of the most widely studied behaviours in laboratory rodents. As a result, improved approaches for the objective monitoring and gathering of more detailed information is increasingly becoming important for evaluating rodent wheel-running behaviour. Here our aim was to develop a new quantitative wheel-running system that can be used for most typical wheel-running experimental protocols. Here we devise a system that can provide a continuous waveform amenable to real-time integration with a high-speed video ideal for wheel-running experimental protocols. While quantification of wheel running behaviour has typically focused on the number of revolutions per unit time as an end point measure, the approach described here allows for more detailed information like wheel rotation fluidity, directionality, instantaneous velocity, and acceleration, in addition to total number of rotations, and the temporal pattern of wheel-running behaviour to be derived from a single trace. We further tested this system with a running-wheel behavioural paradigm that can be used for investigating the neuronal mechanisms of procedural learning and postural stability, and discuss other potentially useful applications. This system and its ability to evaluate multiple wheel-running parameters may become a useful tool for screening new potentially important therapeutic compounds related to many neurological conditions.

Voluntary exercise at the expense of reproductive success in Djungarian hamsters ( Phodopus sungorus)

NASA Astrophysics Data System (ADS)

Petri, Ines; Scherbarth, Frank; Steinlechner, Stephan

2010-09-01

Energy demands of gestation and lactation represent a severe challenge for small mammals. Therefore, additional energetic burdens may compromise successful breeding. In small rodents, food restriction, cold exposure (also in combination) and wheel running to obtain food have been shown to diminish reproductive outcome. Although exhibited responses such as lower incidence of pregnancy, extended lactation periods and maternal infanticide were species dependent, their common function is to adjust energetic costs to the metabolic state reflecting the trade-off between maternal investment and self-maintenance. In the present study, we sought to examine whether voluntary exercise affects reproduction in Djungarian hamsters ( Phodopus sungorus), which are known for their high motivation to run in a wheel. Voluntary exercise resulted in two different effects on reproduction; in addition to increased infanticide and cannibalism, which was evident across all experiments, the results of one experiment provided evidence that free access to a running wheel may prevent successful pregnancy. It seems likely that the impact of voluntary wheel running on reproduction was associated with a reduction of internal energy resources evoked by extensive exercise. Since the hamsters were neither food-restricted nor forced to run in the present study, an energetic deficit as reason for infanticide in exercising dams would emphasise the particularly high motivation to run in a wheel.

WinHPC System | High-Performance Computing | NREL

Science.gov Websites

System WinHPC System NREL's WinHPC system is a computing cluster running the Microsoft Windows operating system. It allows users to run jobs requiring a Windows environment such as ANSYS and MATLAB

First Operational Experience With a High-Energy Physics Run Control System Based on Web Technologies

NASA Astrophysics Data System (ADS)

Bauer, Gerry; Beccati, Barbara; Behrens, Ulf; Biery, Kurt; Branson, James; Bukowiec, Sebastian; Cano, Eric; Cheung, Harry; Ciganek, Marek; Cittolin, Sergio; Coarasa Perez, Jose Antonio; Deldicque, Christian; Erhan, Samim; Gigi, Dominique; Glege, Frank; Gomez-Reino, Robert; Gulmini, Michele; Hatton, Derek; Hwong, Yi Ling; Loizides, Constantin; Ma, Frank; Masetti, Lorenzo; Meijers, Frans; Meschi, Emilio; Meyer, Andreas; Mommsen, Remigius K.; Moser, Roland; O'Dell, Vivian; Oh, Alexander; Orsini, Luciano; Paus, Christoph; Petrucci, Andrea; Pieri, Marco; Racz, Attila; Raginel, Olivier; Sakulin, Hannes; Sani, Matteo; Schieferdecker, Philipp; Schwick, Christoph; Shpakov, Dennis; Simon, Michal; Sumorok, Konstanty; Yoon, Andre Sungho

2012-08-01

Run control systems of modern high-energy particle physics experiments have requirements similar to those of today's Internet applications. The Compact Muon Solenoid (CMS) collaboration at CERN's Large Hadron Collider (LHC) therefore decided to build the run control system for its detector based on web technologies. The system is composed of Java Web Applications distributed over a set of Apache Tomcat servlet containers that connect to a database back-end. Users interact with the system through a web browser. The present paper reports on the successful scaling of the system from a small test setup to the production data acquisition system that comprises around 10.000 applications running on a cluster of about 1600 hosts. We report on operational aspects during the first phase of operation with colliding beams including performance, stability, integration with the CMS Detector Control System and tools to guide the operator.

Quantitative measurement of pass-by noise radiated by vehicles running at high speeds

NASA Astrophysics Data System (ADS)

Yang, Diange; Wang, Ziteng; Li, Bing; Luo, Yugong; Lian, Xiaomin

2011-03-01

It has been a challenge in the past to accurately locate and quantify the pass-by noise source radiated by the running vehicles. A system composed of a microphone array is developed in our current work to do this work. An acoustic-holography method for moving sound sources is designed to handle the Doppler effect effectively in the time domain. The effective sound pressure distribution is reconstructed on the surface of a running vehicle. The method has achieved a high calculation efficiency and is able to quantitatively measure the sound pressure at the sound source and identify the location of the main sound source. The method is also validated by the simulation experiments and the measurement tests with known moving speakers. Finally, the engine noise, tire noise, exhaust noise and wind noise of the vehicle running at different speeds are successfully identified by this method.

Data-driven modelling of vertical dynamic excitation of bridges induced by people running

NASA Astrophysics Data System (ADS)

Racic, Vitomir; Morin, Jean Benoit

2014-02-01

With increasingly popular marathon events in urban environments, structural designers face a great deal of uncertainty when assessing dynamic performance of bridges occupied and dynamically excited by people running. While the dynamic loads induced by pedestrians walking have been intensively studied since the infamous lateral sway of the London Millennium Bridge in 2000, reliable and practical descriptions of running excitation are still very rare and limited. This interdisciplinary study has addressed the issue by bringing together a database of individual running force signals recorded by two state-of-the-art instrumented treadmills and two attempts to mathematically describe the measurements. The first modelling strategy is adopted from the available design guidelines for human walking excitation of structures, featuring perfectly periodic and deterministic characterisation of pedestrian forces presentable via Fourier series. This modelling approach proved to be inadequate for running loads due to the inherent near-periodic nature of the measured signals, a great inter-personal randomness of the dominant Fourier amplitudes and the lack of strong correlation between the amplitudes and running footfall rate. Hence, utilising the database established and motivated by the existing models of wind and earthquake loading, speech recognition techniques and a method of replicating electrocardiogram signals, this paper finally presents a numerical generator of random near-periodic running force signals which can reliably simulate the measurements. Such a model is an essential prerequisite for future quality models of dynamic loading induced by individuals, groups and crowds running under a wide range of conditions, such as perceptibly vibrating bridges and different combinations of visual, auditory and tactile cues.

Run 263 with Black Thunder Mine subbituminous coal and dispersed molybdenum catalysts. Technical progress report

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

Not Available

This report presents the results of Run 263 performed at the Advanced Coal Liquefaction R&D Facility in Wilsonville, Alabama. The run started on October 31, 1991 and continued until February 23, 1992. Tests were conducted by operating the reactors in the Close-Coupled Integrated Two-Stage Liquefaction mode and by processing Black Thunder Mine subbituminous coal from Wyodak-Anderson seam in Wyoming Powder River Basin. Half volume reactors were used for the entire run. In the first part of Run 263, a dispersed molybdenum catalyst was evaluated for its performance without a supported catalyst in the second stage. Molyvan L and Molyvan 822more » (commercially available as friction reducing lubricants) were used as precursors for the dispersed molybdenum catalyst. The effect of the dispersed catalyst on eliminating the solids buildup was also evaluated. For the second part of the run, the hybrid catalyst system was tested with supported Criterion 324 1/1611 catalyst in the second stage at catalyst replacement rates of 2 and 3 lb/ton of MF coal. The molybdenum concentration was 100--200 ppm based on MF coal. Iron oxide was used as a slurry catalyst precursor at a rate of 1--2 wt % MF coal throughout the run with dimethyl disulfide (DMDS) as the sulfiding agent. The close-coupled reactor unit was on-stream for 2482 hours for an on-stream factor of 91.2% and the ROSE-SR{sup sm} unit was on-feed for 2126 hours for an on-stream factor of 96.4% for the entire run.« less

Run 263 with Black Thunder Mine subbituminous coal and dispersed molybdenum catalysts

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

Not Available

This report presents the results of Run 263 performed at the Advanced Coal Liquefaction R D Facility in Wilsonville, Alabama. The run started on October 31, 1991 and continued until February 23, 1992. Tests were conducted by operating the reactors in the Close-Coupled Integrated Two-Stage Liquefaction mode and by processing Black Thunder Mine subbituminous coal from Wyodak-Anderson seam in Wyoming Powder River Basin. Half volume reactors were used for the entire run. In the first part of Run 263, a dispersed molybdenum catalyst was evaluated for its performance without a supported catalyst in the second stage. Molyvan L and Molyvanmore » 822 (commercially available as friction reducing lubricants) were used as precursors for the dispersed molybdenum catalyst. The effect of the dispersed catalyst on eliminating the solids buildup was also evaluated. For the second part of the run, the hybrid catalyst system was tested with supported Criterion 324 1/1611 catalyst in the second stage at catalyst replacement rates of 2 and 3 lb/ton of MF coal. The molybdenum concentration was 100--200 ppm based on MF coal. Iron oxide was used as a slurry catalyst precursor at a rate of 1--2 wt % MF coal throughout the run with dimethyl disulfide (DMDS) as the sulfiding agent. The close-coupled reactor unit was on-stream for 2482 hours for an on-stream factor of 91.2% and the ROSE-SR[sup sm] unit was on-feed for 2126 hours for an on-stream factor of 96.4% for the entire run.« less

Rapid and accurate pyrosequencing of angiosperm plastid genomes

PubMed Central

Moore, Michael J; Dhingra, Amit; Soltis, Pamela S; Shaw, Regina; Farmerie, William G; Folta, Kevin M; Soltis, Douglas E

2006-01-01

Background Plastid genome sequence information is vital to several disciplines in plant biology, including phylogenetics and molecular biology. The past five years have witnessed a dramatic increase in the number of completely sequenced plastid genomes, fuelled largely by advances in conventional Sanger sequencing technology. Here we report a further significant reduction in time and cost for plastid genome sequencing through the successful use of a newly available pyrosequencing platform, the Genome Sequencer 20 (GS 20) System (454 Life Sciences Corporation), to rapidly and accurately sequence the whole plastid genomes of the basal eudicot angiosperms Nandina domestica (Berberidaceae) and Platanus occidentalis (Platanaceae). Results More than 99.75% of each plastid genome was simultaneously obtained during two GS 20 sequence runs, to an average depth of coverage of 24.6× in Nandina and 17.3× in Platanus. The Nandina and Platanus plastid genomes shared essentially identical gene complements and possessed the typical angiosperm plastid structure and gene arrangement. To assess the accuracy of the GS 20 sequence, over 45 kilobases of sequence were generated for each genome using conventional sequencing. Overall error rates of 0.043% and 0.031% were observed in GS 20 sequence for Nandina and Platanus, respectively. More than 97% of all observed errors were associated with homopolymer runs, with ~60% of all errors associated with homopolymer runs of 5 or more nucleotides and ~50% of all errors associated with regions of extensive homopolymer runs. No substitution errors were present in either genome. Error rates were generally higher in the single-copy and noncoding regions of both plastid genomes relative to the inverted repeat and coding regions. Conclusion Highly accurate and essentially complete sequence information was obtained for the Nandina and Platanus plastid genomes using the GS 20 System. More importantly, the high accuracy observed in the GS 20 plastid genome sequence was generated for a significant reduction in time and cost over traditional shotgun-based genome sequencing techniques, although with approximately half the coverage of previously reported GS 20 de novo genome sequence. The GS 20 should be broadly applicable to angiosperm plastid genome sequencing, and therefore promises to expand the scale of plant genetic and phylogenetic research dramatically. PMID:16934154

GEM-AC, a stratospheric-tropospheric global and regional model for air quality and climate change: evaluation of gas phase properties

NASA Astrophysics Data System (ADS)

Kaminski, J. W.; Semeniuk, K.; McConnell, J. C.; Lupu, A.; Mamun, A.

2012-12-01

The Global Environmental Multiscale model for Air Quality and climate change (GEM-AC) is a global general circulation model based on the GEM model developed by the Meteorological Service of Canada for operational weather forecasting. It can be run with a global uniform (GU) grid or a global variable (GV) grid where the core has uniform grid spacing and the exterior grid expands. With a GV grid high resolution regional runs can be accomplished without a concern for boundary conditions. The work described here uses GEM version 3.3.2. The gas-phase chemistry consists in detailed reactions of Ox, NOx, HOx, CO, CH4, NMVOCs, halocarbons, ClOx and BrO. We have recently added elements of the Global Modal-aerosol eXtension (GMXe) scheme to address aerosol microphysics and gas-aerosol partitioning. The evaluation of the MESSY GMXe aerosol scheme is addressed in another poster. The Canadian aerosol module (CAM) is also available. Tracers are advected using the semi-Lagrangian scheme native to GEM. The vertical transport includes parameterized subgrid scale turbulence and large scale convection. Dry deposition is implemented as a flux boundary condition in the vertical diffusion equation. For climate runs the GHGs CO2, CH4, N2O, CFCs in the radiation scheme are adjusted to the scenario considered. In GV regional mode at high resolutions a lake model, FLAKE is also included. Wet removal comprises both in-cloud and below-cloud scavenging. With the gas phase chemistry the model has been run for a series of ten year time slices on a 3°×3° global grid with 77 hybrid levels from the surface to 0.15 hPa. The tropospheric and stratospheric gas phase results are compared with satellite measurements including, ACE, MIPAS, MOPITT, and OSIRIS. Current evaluations of the ozone field and other stratospheric fields are encouraging and tropospheric lifetimes for CH4 and CH3CCl3 are in reasonable accord with tropospheric models. We will present results for current and future climate conditions forced by SST for 2050.

CMSA: a heterogeneous CPU/GPU computing system for multiple similar RNA/DNA sequence alignment.

PubMed

Chen, Xi; Wang, Chen; Tang, Shanjiang; Yu, Ce; Zou, Quan

2017-06-24

The multiple sequence alignment (MSA) is a classic and powerful technique for sequence analysis in bioinformatics. With the rapid growth of biological datasets, MSA parallelization becomes necessary to keep its running time in an acceptable level. Although there are a lot of work on MSA problems, their approaches are either insufficient or contain some implicit assumptions that limit the generality of usage. First, the information of users' sequences, including the sizes of datasets and the lengths of sequences, can be of arbitrary values and are generally unknown before submitted, which are unfortunately ignored by previous work. Second, the center star strategy is suited for aligning similar sequences. But its first stage, center sequence selection, is highly time-consuming and requires further optimization. Moreover, given the heterogeneous CPU/GPU platform, prior studies consider the MSA parallelization on GPU devices only, making the CPUs idle during the computation. Co-run computation, however, can maximize the utilization of the computing resources by enabling the workload computation on both CPU and GPU simultaneously. This paper presents CMSA, a robust and efficient MSA system for large-scale datasets on the heterogeneous CPU/GPU platform. It performs and optimizes multiple sequence alignment automatically for users' submitted sequences without any assumptions. CMSA adopts the co-run computation model so that both CPU and GPU devices are fully utilized. Moreover, CMSA proposes an improved center star strategy that reduces the time complexity of its center sequence selection process from O(mn 2 ) to O(mn). The experimental results show that CMSA achieves an up to 11× speedup and outperforms the state-of-the-art software. CMSA focuses on the multiple similar RNA/DNA sequence alignment and proposes a novel bitmap based algorithm to improve the center star strategy. We can conclude that harvesting the high performance of modern GPU is a promising approach to accelerate multiple sequence alignment. Besides, adopting the co-run computation model can maximize the entire system utilization significantly. The source code is available at https://github.com/wangvsa/CMSA .

The influence of successive matches on match-running performance during an under-23 international soccer tournament: The necessity of individual analysis.

PubMed

Varley, Matthew C; Di Salvo, Valter; Modonutti, Mattia; Gregson, Warren; Mendez-Villanueva, Alberto

2018-03-01

This study investigated the effects of successive matches on match-running in elite under-23 soccer players during an international tournament. Match-running data was collected using a semi-automated multi-camera tracking system during an international under-23 tournament from all participating outfield players. Players who played 100% of all group stage matches were included (3 matches separated by 72 h, n = 44). Differences in match-running performance between matches were identified using a generalised linear mixed model. There were no clear effects for total, walking, jogging, running, high-speed running and sprinting distance between matches 1 and 3 (effect size (ES); -0.32 to 0.05). Positional analysis found that sprint distance was largely maintained from matches 1 to 3 across all positions. Attackers had a moderate decrease in total, jogging and running distance between matches 1 and 3 (ES; -0.72 to -0.66). Classifying players as increasers or decreasers in match-running revealed that match-running changes are susceptible to individual differences. Sprint performance appears to be maintained over successive matches regardless of playing position. However, reductions in other match-running categories vary between positions. Changes in match-running over successive matches affect individuals differently; thus, players should be monitored on an individual basis.

Magnetic plucking of piezoelectric bimorphs for a wearable energy harvester

NASA Astrophysics Data System (ADS)

Pozzi, Michele

2016-04-01

A compact and low-profile energy harvester designed to be worn on the outside of the knee-joint is presented. Frequency up-conversion has been widely adopted in recent times to exploit the high frequency response of piezoelectric transducers within environments where only low frequencies are present. Contactless magnetic plucking is here introduced, in a variable reluctance framework, with the aim of improving the mechanical energy transfer into the transducers, which is sub-optimal with contact plucking. FEA and experiments were used to design an optimal arrangement of ferromagnetic teeth to interact with the magnets fixed to the piezoelectric beams. A prototype was made and extensively tested in a knee-joint simulator controlled with gait data available in the literature. Energy and power produced were measured for walking and running steps. A power management unit was developed using off-the-shelf components, permitting the generation of a stable and regulated supply of 26 mW at 3.3 V during walking. Record levels of rectified (unregulated) electrical power of over 50 and 70 mW per walking and running steps, respectively, were measured.

A distributed control system for the lower-hybrid current drive system on the Tokamak de Varennes

NASA Astrophysics Data System (ADS)

Bagdoo, J.; Guay, J. M.; Chaudron, G.-A.; Decoste, R.; Demers, Y.; Hubbard, A.

1990-08-01

An rf current drive system with an output power of 1 MW at 3.7 GHz is under development for the Tokamak de Varennes. The control system is based on an Ethernet local-area network of programmable logic controllers as front end, personal computers as consoles, and CAMAC-based DSP processors. The DSP processors ensure the PID control of the phase and rf power of each klystron, and the fast protection of high-power rf hardware, all within a 40 μs loop. Slower control and protection, event sequencing and the run-time database are provided by the programmable logic controllers, which communicate, via the LAN, with the consoles. The latter run a commercial process-control console software. The LAN protocol respects the first four layers of the ISO/OSI 802.3 standard. Synchronization with the tokamak control system is provided by commercially available CAMAC timing modules which trigger shot-related events and reference waveform generators. A detailed description of each subsystem and a performance evaluation of the system will be presented.

Approaches in highly parameterized inversion - GENIE, a general model-independent TCP/IP run manager

USGS Publications Warehouse

Muffels, Christopher T.; Schreuder, Willem A.; Doherty, John E.; Karanovic, Marinko; Tonkin, Matthew J.; Hunt, Randall J.; Welter, David E.

2012-01-01

GENIE is a model-independent suite of programs that can be used to generally distribute, manage, and execute multiple model runs via the TCP/IP infrastructure. The suite consists of a file distribution interface, a run manage, a run executer, and a routine that can be compiled as part of a program and used to exchange model runs with the run manager. Because communication is via a standard protocol (TCP/IP), any computer connected to the Internet can serve in any of the capacities offered by this suite. Model independence is consistent with the existing template and instruction file protocols of the widely used PEST parameter estimation program. This report describes (1) the problem addressed; (2) the approach used by GENIE to queue, distribute, and retrieve model runs; and (3) user instructions, classes, and functions developed. It also includes (4) an example to illustrate the linking of GENIE with Parallel PEST using the interface routine.

Running Improves Pattern Separation during Novel Object Recognition.

PubMed

Bolz, Leoni; Heigele, Stefanie; Bischofberger, Josef

2015-10-09

Running increases adult neurogenesis and improves pattern separation in various memory tasks including context fear conditioning or touch-screen based spatial learning. However, it is unknown whether pattern separation is improved in spontaneous behavior, not emotionally biased by positive or negative reinforcement. Here we investigated the effect of voluntary running on pattern separation during novel object recognition in mice using relatively similar or substantially different objects.We show that running increases hippocampal neurogenesis but does not affect object recognition memory with 1.5 h delay after sample phase. By contrast, at 24 h delay, running significantly improves recognition memory for similar objects, whereas highly different objects can be distinguished by both, running and sedentary mice. These data show that physical exercise improves pattern separation, independent of negative or positive reinforcement. In sedentary mice there is a pronounced temporal gradient for remembering object details. In running mice, however, increased neurogenesis improves hippocampal coding and temporally preserves distinction of novel objects from familiar ones.

The LHCb Run Control

NASA Astrophysics Data System (ADS)

Alessio, F.; Barandela, M. C.; Callot, O.; Duval, P.-Y.; Franek, B.; Frank, M.; Galli, D.; Gaspar, C.; Herwijnen, E. v.; Jacobsson, R.; Jost, B.; Neufeld, N.; Sambade, A.; Schwemmer, R.; Somogyi, P.

2010-04-01

LHCb has designed and implemented an integrated Experiment Control System. The Control System uses the same concepts and the same tools to control and monitor all parts of the experiment: the Data Acquisition System, the Timing and the Trigger Systems, the High Level Trigger Farm, the Detector Control System, the Experiment's Infrastructure and the interaction with the CERN Technical Services and the Accelerator. LHCb's Run Control, the main interface used by the experiment's operator, provides access in a hierarchical, coherent and homogeneous manner to all areas of the experiment and to all its sub-detectors. It allows for automated (or manual) configuration and control, including error recovery, of the full experiment in its different running modes. Different instances of the same Run Control interface are used by the various sub-detectors for their stand-alone activities: test runs, calibration runs, etc. The architecture and the tools used to build the control system, the guidelines and components provided to the developers, as well as the first experience with the usage of the Run Control will be presented

Analysis Of Rearfoot Motion In Running Shoes

NASA Astrophysics Data System (ADS)

Cooper, Les

1986-12-01

In order to produce better shoes that cushion athletes from the high impact forces of running and still provide stability to the foot it is essential to have a method of quickly and reliably evaluating the performance of prototype shoes. The analysis of rear-foot motion requires the use of film or video recordings of test subjects running on a treadmill. Specific points on the subject are tracked to give a measure of inversion or eversion of the heel. This paper describes the testing procedure and its application to running shoe design. A comparison of film and video systems is also discussed.

Minimal algorithm for running an internal combustion engine

NASA Astrophysics Data System (ADS)

Stoica, V.; Borborean, A.; Ciocan, A.; Manciu, C.

2018-01-01

The internal combustion engine control is a well-known topic within automotive industry and is widely used. However, in research laboratories and universities the use of a control system trading is not the best solution because of predetermined operating algorithms, and calibrations (accessible only by the manufacturer) without allowing massive intervention from outside. Laboratory solutions on the market are very expensive. Consequently, in the paper we present a minimal algorithm required to start-up and run an internal combustion engine. The presented solution can be adapted to function on performance microcontrollers available on the market at the present time and at an affordable price. The presented algorithm was implemented in LabView and runs on a CompactRIO hardware platform.