Three Dimensional Structure and Energy Balance of a Coronal Mass Ejection

The Ultraviolet Coronagraph Spectrometer (UVCS) observed Doppler shifted material of a partial Halo Coronal Mass Ejection (CME) on December 13 2001. The observed ratio of [O V]/O V] is a reliable density diagnostic important for assessing the state of the plasma. Earlier UVCS observations of CMEs found evidence that the ejected plasma is heated long after the eruption. We have investigated the heating rates, which represent a significant fraction of the CME energy budget. The parameterized heating and radiative and adiabatic cooling have been used to evaluate the temperature evolution of the CME material with a time dependent ionization state model. The functional form of a flux rope model for interplanetary magnetic clouds was also used to parameterize the heating. We find that continuous heating is required to match the UVCS observations. To match the O VI-bright knots, a higher heating rate is required such that the heating energy is greater than the kinetic energy. The temperatures for the knots bright in Ly$\alpha$ and C III emission indicate that smaller heating rates are required for those regions. In the context of the flux rope model, about 75% of the magnetic energy must go into heat in order to match the O VI observations. We derive tighter constraints on the heating than earlier analyses, and we show that thermal conduction with the Spitzer conductivity is not sufficient to account for the heating at large heights.Comment: 40 pages, 16 figures, accepted for publication in ApJ For associated mpeg file, please see https://www.cora.nwra.com/~jylee/mpg/f5.mp

Metabolite essentiality elucidates robustness of Escherichia coli metabolism

Complex biological systems are very robust to genetic and environmental changes at all levels of organization. Many biological functions of Escherichia coli metabolism can be sustained against single-gene or even multiple-gene mutations by using redundant or alternative pathways. Thus, only a limited number of genes have been identified to be lethal to the cell. In this regard, the reaction-centric gene deletion study has a limitation in understanding the metabolic robustness. Here, we report the use of flux-sum, which is the summation of all incoming or outgoing fluxes around a particular metabolite under pseudo-steady state conditions, as a good conserved property for elucidating such robustness of E. coli from the metabolite point of view. The functional behavior, as well as the structural and evolutionary properties of metabolites essential to the cell survival, was investigated by means of a constraints-based flux analysis under perturbed conditions. The essential metabolites are capable of maintaining a steady flux-sum even against severe perturbation by actively redistributing the relevant fluxes. Disrupting the flux-sum maintenance was found to suppress cell growth. This approach of analyzing metabolite essentiality provides insight into cellular robustness and concomitant fragility, which can be used for several applications, including the development of new drugs for treating pathogens.Comment: Supplements available at http://stat.kaist.ac.kr/publication/2007/PJKim_pnas_supplement.pd

THE USE OF INERTIAL MEASUREMENT UNITS TO IDENTIFY BIOMECHANICAL FACTORS OF PERFORMANCE IN CRICKET FAST BOWLERS

The role of a cricket bowler is to deliver the ball in such a way as to minimise batsmen scoring runs or get them out. Fast bowlers utilise the pace of delivery as a key tool to achieve this. The purpose of this study was to use inertial measurement units (IMUs) to investigate the relationship between IMU derived spinal kinematics, lower limb accelerations and ball release speed in cricket fast bowlers. Sacral vertical loading rate at back-foot impact and thoracic lateral flexion at front-foot impact displayed significant positive relationships with ball release speed (r=.521 and .629 respectively). Consequently, this study highlights IMUs are able to effectively identify trends in fast bowling performance and hence, larger accelerations at back-foot impact with increased lateral flexion at front-foot impact were effective strategies to increase ball release speed for the bowlers measured in this study

Preventing and Treating Type 2 Diabetes Through a Physically Active Lifestyle

By the late 1960s, the increasing number of type 2 diabetic cases in children and adolescents rapidly presented a signifi cant public health issue recognized by the American Diabetes Association (2000). Since then, the prevalence of pediatric type 2 diabetes appears to be on the rise not only in the United States but all around the world (Gungor et al., 2005). In the United States, an increase from fewer than four percent to more than 50 percent of new cases of type 2 diabetes in the pediatric population was reported between the years of 1982 and 1998 (American Diabetes Association, 2000). An increasing percentage of pediatric cases of newly diagnosed type 2 diabetes were also reported in population-based data (Gungor et al., 2005). Therefore, the purpose of this article is to discuss how regular physical activity can help to prevent and treat type 2 diabetes

Two new functions in the WormBase Enrichment Suite

Genome-wide experiments routinely generate large amounts of data that can be hard to interpret biologically. A common approach to interpreting these results is to employ enrichment analyses of controlled languages, known as ontologies, that describe various biological parameters such as gene molecular or biological function. In C. elegans, three distinct ontologies, the Gene Ontology (GO), Anatomy Ontology (AO), and the Worm Phenotype Ontology (WPO) are used to annotate gene function, expression and phenotype, respectively (Ashburner et al. 2000; Lee and Sternberg, 2003; Schindelman et al. 2011). Previously, we developed software to test datasets for enrichment of anatomical terms, called the Tissue Enrichment Analysis (TEA) tool (Angeles-Albores and Sternberg, 2016). Using the same hypergeometric statistical method, we extend enrichment testing to include WPO and GO, offering a unified approach to enrichment testing in C. elegans. The WormBase Enrichment Suite can be accessed via a user-friendly interface at http://www.wormbase.org/tools/enrichment/tea/tea.cgi. To validate the tools, we analyzed a previously published extracellular vesicle (EV)-releasing neuron (EVN) signature gene set derived from dissociated ciliated EV neurons (Wang et al. 2015) using WormBase Enrichment Suite based on the WS262 WormBase release. TEA correctly identified the CEM, hook sensillum and IL2 neuron as enriched tissues. The top phenotype associated with the EVN signature was chemosensory behavior. Gene Ontology enrichment analysis showed that cell projection and cell body were the most enriched cellular components in this gene set, followed by the biological processes neuropeptide signaling pathway and vesicle localization further down. The tutorial script used to generate the figure above can be viewed at: https://github.com/dangeles/TissueEnrichmentAnalysis/blob/master/tutorial/Tutorial.ipynb The addition of Gene Enrichment Analysis (GEA) and Phenotype Enrichment Analysis (PEA) to WormBase marks an important step towards a unified set of analyses that can help researchers to understand genomic datasets. These enrichment analyses will allow the community to fully benefit from the data curation ongoing at WormBase

Tissue enrichment analysis for C. elegans genomics

Background: Over the last ten years, there has been explosive development in methods for measuring gene expression. These methods can identify thousands of genes altered between conditions, but understanding these datasets and forming hypotheses based on them remains challenging. One way to analyze these datasets is to associate ontologies (hierarchical, descriptive vocabularies with controlled relations between terms) with genes and to look for enrichment of specific terms. Although Gene Ontology (GO) is available for Caenorhabditis elegans, it does not include anatomical information. Results: We have developed a tool for identifying enrichment of C. elegans tissues among gene sets and generated a website GUI where users can access this tool. Since a common drawback to ontology enrichment analyses is its verbosity, we developed a very simple filtering algorithm to reduce the ontology size by an order of magnitude. We adjusted these filters and validated our tool using a set of 30 gold standards from Expression Cluster data in WormBase. We show our tool can even discriminate between embryonic and larval tissues and can even identify tissues down to the single-cell level. We used our tool to identify multiple neuronal tissues that are down-regulated due to pathogen infection in C. elegans. Conclusions: Our Tissue Enrichment Analysis (TEA) can be found within WormBase, and can be downloaded using Python’s standard pip installer. It tests a slimmed-down C. elegans tissue ontology for enrichment of specific terms and provides users with a text and graphic representation of the results

Transcription Factor Nrf1 Mediates the Proteasome Recovery Pathway after Proteasome Inhibition in Mammalian Cells

In Saccharomyces cerevisiae, chemical or genetic inhibition of proteasome activity induces new proteasome synthesis promoted by the transcription factor RPN4. This ensures that proteasome activity is matched to demand. This transcriptional feedback loop is conserved in mammals, but its molecular basis is not understood. Here, we report that nuclear factor erythroid-derived 2-related factor 1 (Nrf1), a transcription factor of the cap “n” collar basic leucine zipper family, but not the related Nrf2, is necessary for induced proteasome gene transcription in mouse embryonic fibroblasts (MEFs). Promoter-reporter assays revealed the importance of antioxidant response elements in Nrf1-mediated upregulation of proteasome subunit genes. Nrf1^(−/−) MEFs were impaired in the recovery of proteasome activity after transient treatment with the covalent proteasome inhibitor YU101, and knockdown of Nrf1 in human cancer cells enhanced cell killing by YU101. Taken together, our results suggest that Nrf1-mediated proteasome homeostasis could be an attractive target for therapeutic intervention in cancer

Further studies on relic neutrino asymmetry generation II: a rigorous treatment of repopulation in the adiabatic limit

We derive an approximate relic neutrino asymmetry evolution equation that systematically incorporates repopulation processes from the full quantum kinetic equations (QKEs). It is shown that in the collision dominant epoch, the said equation reduces precisely to the expression obtained previously from the static/adiabatic approximation. The present treatment thus provides a rigorous justification for the seemingly incongruous assumptions of a negligible repopulation function and instantaneous repopulation sometimes employed in earlier works.Comment: RevTeX, 11 pages, no figure