Internal transport barriers in the National Spherical Torus Experiment

In the National Spherical Torus Experiment [M. Ono , Nucl. Fusion 41, 1435 (2001)], internal transport barriers (ITBs) are observed in reversed (negative) shear discharges where diffusivities for electron and ion thermal channels and momentum are reduced. While neutral beam heating can produce ITBs in both electron and ion channels, high harmonic fast wave heating can also produce electron ITBs (e-ITBs) under reversed magnetic shear conditions without momentum input. Interestingly, the location of the e-ITB does not necessarily match that of the ion ITB (i-ITB). The e-ITB location correlates best with the magnetic shear minima location determined by motional Stark effect constrained equilibria, whereas the i-ITB location better correlates with the location of maximum ExB shearing rate. Measured electron temperature gradients in the e-ITB can exceed critical gradients for the onset of electron thermal gradient microinstabilities calculated by linear gyrokinetic codes. A high-k microwave scattering diagnostic shows locally reduced density fluctuations at wave numbers characteristic of electron turbulence for discharges with strongly negative magnetic shear versus weakly negative or positive magnetic shear. Reductions in fluctuation amplitude are found to be correlated with the local value of magnetic shear. These results are consistent with nonlinear gyrokinetic simulations predicting a reduction in electron turbulence under negative magnetic shear conditions despite exceeding critical gradients.X1128sciescopu

Investigating Microtopographic and Soil Controls on a Mountainous Meadow Plant Community Using High-Resolution Remote Sensing and Surface Geophysical Data

This study aims to investigate the microtopographic controls that dictate the heterogeneity of plant communities in a mountainous floodplain-hillslope system, using remote sensing and surface geophysical techniques. Working within a lower montane floodplain-hillslope study site (750 m × 750 m) in the Upper Colorado River Basin, we developed a new data fusion framework, based on machine learning and feature engineering, that exploits remote sensing optical and light detection and ranging (LiDAR) data to estimate the distribution of key plant meadow communities at submeter resolution. We collected surface electrical resistivity tomography data to explore the variability in soil properties along a floodplain-hillslope transect at 0.50-m resolution and extracted LiDAR-derived metrics to model the rapid change in microtopography. We then investigated the covariability among the estimated plant community distributions, soil information, and topographic metrics. Results show that our framework estimated the distribution of nine plant communities with higher accuracy (87% versus 80% overall; 85% versus 60% for shrubs) compared to conventional classification approaches. Analysis of the covariabilities reveals a strong correlation between plant community distribution, soil electric conductivity, and slope, indicating that soil moisture is a primary control on heterogeneous spatial distribution. At the same time, microtopography plays an important role in creating particular ecosystem niches for some of the communities. Such relationships could be exploited to provide information about the spatial variability of soil properties. This highly transferable framework can be employed within long-term monitoring to capture community-specific physiological responses to perturbations, offering the possibility of bridging local plot-scale observations with large landscape monitoring

Genome re-annotation: a wiki solution?

The annotation of most genomes becomes outdated over time, owing in part to our ever-improving knowledge of genomes and in part to improvements in bioinformatics software. Unfortunately, annotation is rarely if ever updated and resources to support routine reannotation are scarce. Wiki software, which would allow many scientists to edit each genome's annotation, offers one possible solution

Prompt photon and associated heavy quark production at hadron colliders with kt-factorization

In the framework of the kt-factorization approach, the production of prompt photons in association with a heavy (charm or beauty) quarks at high energies is studied. The consideration is based on the O(\alpha \alpha_s^2) off-shell amplitudes of gluon-gluon fusion and quark-(anti)quark interaction subprocesses. The unintegrated parton densities in a proton are determined using the Kimber-Martin-Ryskin prescription. The analysis covers the total and differential cross sections and extends to specific angular correlations between the produced prompt photons and muons originating from the semileptonic decays of associated heavy quarks. Theoretical uncertainties of our evaluations are studied and comparison with the results of standard NLO pQCD calculations is performed. Our numerical predictions are compared with the recent experimental data taken by the D0 and CDF collaborations at the Tevatron. Finally, we extend our results to LHC energies.Comment: 14 pages, 10 figure

Mechanical slowing-down of cytoplasmic diffusion allows in vivo counting of proteins in individual cells.

Many key regulatory proteins in bacteria are present in too low numbers to be detected with conventional methods, which poses a particular challenge for single-cell analyses because such proteins can contribute greatly to phenotypic heterogeneity. Here we develop a microfluidics-based platform that enables single-molecule counting of low-abundance proteins by mechanically slowing-down their diffusion within the cytoplasm of live Escherichia coli (E. coli) cells. Our technique also allows for automated microscopy at high throughput with minimal perturbation to native physiology, as well as viable enrichment/retrieval. We illustrate the method by analysing the control of the master regulator of the E. coli stress response, RpoS, by its adapter protein, SprE (RssB). Quantification of SprE numbers shows that though SprE is necessary for RpoS degradation, it is expressed at levels as low as 3-4 molecules per average cell cycle, and fluctuations in SprE are approximately Poisson distributed during exponential phase with no sign of bursting

Theoretical Aspects of Particle Production

These lectures describe some of the latest data on particle production in high-energy collisions and compare them with theoretical calculations and models based on QCD. The main topics covered are: fragmentation functions and factorization, small-x fragmentation, hadronization models, differences between quark and gluon fragmentation, current and target fragmentation in deep inelastic scattering, and heavy quark fragmentation.Comment: 26 pages, 27 figures. Lectures at International Summer School on Particle Production Spanning MeV and TeV Energies, Nijmegen, The Netherlands, August 199

Simulating the Mammalian Blastocyst - Molecular and Mechanical Interactions Pattern the Embryo

Mammalian embryogenesis is a dynamic process involving gene expression and mechanical forces between proliferating cells. The exact nature of these interactions, which determine the lineage patterning of the trophectoderm and endoderm tissues occurring in a highly regulated manner at precise periods during the embryonic development, is an area of debate. We have developed a computational modeling framework for studying this process, by which the combined effects of mechanical and genetic interactions are analyzed within the context of proliferating cells. At a purely mechanical level, we demonstrate that the perpendicular alignment of the animal-vegetal (a-v) and embryonic-abembryonic (eb-ab) axes is a result of minimizing the total elastic conformational energy of the entire collection of cells, which are constrained by the zona pellucida. The coupling of gene expression with the mechanics of cell movement is important for formation of both the trophectoderm and the endoderm. In studying the formation of the trophectoderm, we contrast and compare quantitatively two hypotheses: (1) The position determines gene expression, and (2) the gene expression determines the position. Our model, which couples gene expression with mechanics, suggests that differential adhesion between different cell types is a critical determinant in the robust endoderm formation. In addition to differential adhesion, two different testable hypotheses emerge when considering endoderm formation: (1) A directional force acts on certain cells and moves them into forming the endoderm layer, which separates the blastocoel and the cells of the inner cell mass (ICM). In this case the blastocoel simply acts as a static boundary. (2) The blastocoel dynamically applies pressure upon the cells in contact with it, such that cell segregation in the presence of differential adhesion leads to the endoderm formation. To our knowledge, this is the first attempt to combine cell-based spatial mechanical simulations with genetic networks to explain mammalian embryogenesis. Such a framework provides the means to test hypotheses in a controlled in silico environment

Effectiveness of moving on: an Australian designed generic self-management program for people with a chronic illness

Background: This paper presents the evaluation of “Moving On”, a generic self-management program for people with a chronic illness developed by Arthritis NSW. The program aims to help participants identify their need for behavior change and acquire the knowledge and skills to implement changes that promote their health and quality of life. Method: A prospective pragmatic randomised controlled trial involving two group programs in community settings: the intervention program (Moving On) and a control program (light physical activity). Participants were recruited by primary health care providers across the north-west region of metropolitan Sydney, Australia between June 2009 and October 2010. Patient outcomes were self-reported via pre- and post-program surveys completed at the time of enrolment and sixteen weeks after program commencement. Primary outcomes were change in self-efficacy (Self-efficacy for Managing Chronic Disease 6-Item Scale), self-management knowledge and behaviour and perceived health status (Self-Rated Health Scale and the Health Distress Scale). Results: A total of 388 patient referrals were received, of whom 250 (64.4%) enrolled in the study. Three patients withdrew prior to allocation. 25 block randomisations were performed by a statistician external to the research team: 123 patients were allocated to the intervention program and 124 were allocated to the control program. 97 (78.9%) of the intervention participants commenced their program. The overall attrition rate of 40.5% included withdrawals from the study and both programs. 24.4% of participants withdrew from the intervention program but not the study and 22.6% withdrew from the control program but not the study. A total of 62 patients completed the intervention program and follow-up evaluation survey and 77 patients completed the control program and follow- up evaluation survey. At 16 weeks follow-up there was no significant difference between intervention and control groups in self-efficacy; however, there was an increase in self-efficacy from baseline to follow-up for the intervention participants (t=−1.948, p=0.028). There were no significant differences in self-rated health or health distress scores between groups at follow-up, with both groups reporting a significant decrease in health distress scores. There was no significant difference between or within groups in self-management knowledge and stage of change of behaviours at follow-up. Intervention group attenders had significantly higher physical activity (t=−4.053, p=0.000) and nutrition scores (t=2.315, p= 0.01) at follow-up; however, these did not remain significant after adjustment for covariates. At follow-up, significantly more participants in the control group (20.8%) indicated that they did not have a self-management plan compared to those in the intervention group (8.8%) (X2=4.671, p=0.031). There were no significant changes in other self-management knowledge areas and behaviours after adjusting for covariates at follow-up. Conclusions: The study produced mixed findings. Differences between groups as allocated were diluted by the high proportion of patients not completing the program. Further monitoring and evaluation are needed of the impact and cost effectiveness of the program. Trial registration: Australian New Zealand Clinical Trials Registry: ACTRN1260900029821

The usefulness of a free self-test for screening albuminuria in the general population: a cross-sectional survey

<p>Abstract</p> <p>Background</p> <p>In this study we evaluated the usefulness of a free self-test for screening albuminuria in the general population.</p> <p>Methods</p> <p>Dutch adults were invited by the Dutch Kidney Foundation to order a free albuminuria self-test, consisting of three semi quantitative dipstick tests, via the Internet. Results were classified in negative, low-positive and high-positive. In case of a positive test result, the tester was recommended to visit a GP for supplementary examination and/or treatment. Participants of the programme were sent a questionnaire for evaluation by e-mail eight weeks after receiving the self-test.</p> <p>Results</p> <p>During the first 30 days of the self-test programme, 996,927 self-tests were ordered. In total, 71,714 participants completed the questionnaire: 79% had a negative test result and 21% had a positive test result (20% low-positive and 1% high-positive). Of the positive testers, 25% visited a GP after testing for albuminuria. Among the 3,983 participants who visited a GP, 193 new diseases were detected: 25 chronic renal failure, 152 hypertension and 31 diabetes mellitus.</p> <p>Conclusion</p> <p>Using a free self-test for screening albuminuria in the general population resulted in a large response and a number of newly detected diseases. However, we found a very high percentage of positive testers of which probably a large part is false positive. Furthermore, only a small part of the positive testers visited a GP for additional examination and/or treatment. The efficiency of such a campaign could be increased by embedding the testing in health care to reduce the number of false-positive results and to ensure follow-up and treatment in case of a positive test result.</p

Consistent phenological shifts in the making of a biodiversity hotspot: the Cape flora

Background The best documented survival responses of organisms to past climate change on short (glacial-interglacial) timescales are distributional shifts. Despite ample evidence on such timescales for local adaptations of populations at specific sites, the long-term impacts of such changes on evolutionary significant units in response to past climatic change have been little documented. Here we use phylogenies to reconstruct changes in distribution and flowering ecology of the Cape flora - South Africa's biodiversity hotspot - through a period of past (Neogene and Quaternary) changes in the seasonality of rainfall over a timescale of several million years. Results Forty-three distributional and phenological shifts consistent with past climatic change occur across the flora, and a comparable number of clades underwent adaptive changes in their flowering phenology (9 clades; half of the clades investigated) as underwent distributional shifts (12 clades; two thirds of the clades investigated). Of extant Cape angiosperm species, 14-41% have been contributed by lineages that show distributional shifts consistent with past climate change, yet a similar proportion (14-55%) arose from lineages that shifted flowering phenology. Conclusions Adaptive changes in ecology at the scale we uncover in the Cape and consistent with past climatic change have not been documented for other floras. Shifts in climate tolerance appear to have been more important in this flora than is currently appreciated, and lineages that underwent such shifts went on to contribute a high proportion of the flora's extant species diversity. That shifts in phenology, on an evolutionary timescale and on such a scale, have not yet been detected for other floras is likely a result of the method used; shifts in flowering phenology cannot be detected in the fossil record