Description and evaluation of the CASA dual-Doppler system

2011 Spring.Includes bibliographical references.Long range weather surveillance radars are designed for observing weather events for hundreds of kilometers from the radar and operate over a large coverage domain independently of weather conditions. As a result a loss in spatial resolution and limited temporal sampling of the weather phenomenon occurs. Due to the curvature of the Earth, long-range weather radars tend to make the majority of their precipitation and wind observations in the middle to upper troposphere, resulting in missed features associates with severe weather occurring in the lowest three kilometers of the troposphere. The spacing of long-range weather radars in the United States limits the feasibility of using dual-Doppler wind retrievals that would provide valuable information on the kinematics of weather events to end-users and researchers. The National Science Foundation Center for Collaborative Adapting Sensing of the Atmosphere (CASA) aims to change the current weather sensing model by increasing coverage of the lowest three kilometers of the troposphere by using densely spaced networked short-range weather radars. CASA has deployed a network of these radars in south-western Oklahoma, known as Integrated Project 1 (IP1). The individual radars are adaptively steered by an automated system known as the Meteorological Command and Control (MCC). The geometry of the IP1 network is such that the coverage domains of the individual radars are overlapping. A dual-Doppler system has been developed for the IP1 network which takes advantage of the overlapping coverage domains. The system is comprised of two subsystems, scan optimization and wind field retrieval. The scan strategy subsystem uses the DCAS model and the number of dual-Doppler pairs in the IP1 network to minimizes the normalized standard deviation in the wind field retrieval. The scan strategy subsystem also minimizes the synchronization error between two radars. The retrieval itself is comprised of two steps, data resampling and the retrieval process. The resampling step map data collected in radar coordinates to a common Cartesian grid. The retrieval process uses the radial velocity measurements to estimate the northward, eastward, and vertical component of the wind. The error in the retrieval is related to the beam crossing angle. The best retrievals occur at beam crossing angles greater than 30 degrees. During operations statistics on the scan strategy and wind field retrievals are collected in real-time. For the scan strategy subsystem statistics on the beam crossing angels, maximum elevation angle, number of elevation angles, maximum observable height, and synchronization time between radars in a pair are collected by the MCC. These statistics are used to evaluate the performance of the scan strategy subsystem. Observations of a strong wind event occurring on April 2, 2010 are used to evaluate the decision process associated with the scan strategy optimization. For the retrieval subsystem, the normalized standard deviation for the wind field retrieval is used to evaluate the quality of the retrieval. Wind fields from an EF2 tornado observed on May 14, 2009 are used to evaluate the quality of the wind field retrievals in hazardous wind events. Two techniques for visualizing vector fields are available, streamlines and arrows. Each visualization technique is evaluated based on the task of visualizing small and large scale phenomenon. Applications of the wind field retrievals include the computation of the vorticity and divergence fields. Vorticity and divergence for an EF2 tornado observed on May 14, 2009 are evaluated against vorticity and divergence for other observed tornadoes

Washed Away: The Study of Natural Disasters and Weather Stations in the Central Pacific Basin of Costa Rica

This report addresses the problems in Costa Rican communities during natural disasters and the selection of locations of new weather stations in the Central Pacific Basin. Currently, flash floods and landslides cause a devastating amount of damage, especially to communities that are not warned. Climate change is causing an increase in the number of flash floods and landslides in Costa Rica. There is a need for more weather stations in the Central Pacific Basin to help prevent damage or injury caused by these destructive events. Our goal was to investigate the problems communities face during natural disasters and to choose locations for eighteen new weather stations. This goal was accomplished through interviews and groundtruthing

Unveiling a Rich System of Faint Dwarf Galaxies in the Next Generation Fornax Survey

We report the discovery of 158 previously undetected dwarf galaxies in the Fornax cluster central regions using a deep coadded $u, g$ and $i$-band image obtained with the DECam wide-field camera mounted on the 4-meter Blanco telescope at the Cerro Tololo Interamerican Observatory as part of the {\it Next Generation Fornax Survey} (NGFS). The new dwarf galaxies have quasi-exponential light profiles, effective radii $0.1\!<\!r_e\!<\!2.8$ kpc and average effective surface brightness values $22.0\!<\!\mu_i\!<\!28.0$ mag arcsec$^{-2}$. We confirm the existence of ultra-diffuse galaxies (UDGs) in the Fornax core regions that resemble counterparts recently discovered in the Virgo and Coma galaxy clusters.~We also find extremely low surface brightness NGFS dwarfs, which are several magnitudes fainter than the classical UDGs. The faintest dwarf candidate in our NGFS sample has an absolute magnitude of $M_i\!=\!-8.0$\,mag. The nucleation fraction of the NGFS dwarf galaxy sample appears to decrease as a function of their total luminosity, reaching from a nucleation fraction of $>\!75\%$ at luminosities brighter than $M_i\!\simeq\!-15.0$ mag to $0\%$ at luminosities fainter than $M_i\!\simeq\!-10.0$ mag. The two-point correlation function analysis of the NGFS dwarf sample shows an excess on length scales below $\sim\!100$ kpc, pointing to the clustering of dwarf galaxies in the Fornax cluster core.Comment: 6 pages, 3 figures. Accepted for publication in The Astrophysical Journal Letters. Download the high-resolution version of the paper from the following link: https://www.dropbox.com/s/xb9vz8s29wlzjgf/ms.pdf?dl=

Comparative analysis of mycobacterium and related actinomycetes yields insight into the evolution of mycobacterium tuberculosis pathogenesis

<p>Abstract</p> <p>Background</p> <p>The sequence of the pathogen <it>Mycobacterium tuberculosis </it>(<it>Mtb</it>) strain <it>H37Rv </it>has been available for over a decade, but the biology of the pathogen remains poorly understood. Genome sequences from other <it>Mtb </it>strains and closely related bacteria present an opportunity to apply the power of comparative genomics to understand the evolution of <it>Mtb </it>pathogenesis. We conducted a comparative analysis using 31 genomes from the Tuberculosis Database (TBDB.org), including 8 strains of <it>Mtb </it>and <it>M. bovis</it>, 11 additional Mycobacteria, 4 Corynebacteria, 2 Streptomyces, <it>Rhodococcus jostii RHA1, Nocardia farcinia, Acidothermus cellulolyticus, Rhodobacter sphaeroides, Propionibacterium acnes</it>, and <it>Bifidobacterium longum</it>.</p> <p>Results</p> <p>Our results highlight the functional importance of lipid metabolism and its regulation, and reveal variation between the evolutionary profiles of genes implicated in saturated and unsaturated fatty acid metabolism. It also suggests that DNA repair and molybdopterin cofactors are important in pathogenic Mycobacteria. By analyzing sequence conservation and gene expression data, we identify nearly 400 conserved noncoding regions. These include 37 predicted promoter regulatory motifs, of which 14 correspond to previously validated motifs, as well as 50 potential noncoding RNAs, of which we experimentally confirm the expression of four.</p> <p>Conclusions</p> <p>Our analysis of protein evolution highlights gene families that are associated with the adaptation of environmental Mycobacteria to obligate pathogenesis. These families include fatty acid metabolism, DNA repair, and molybdopterin biosynthesis. Our analysis reinforces recent findings suggesting that small noncoding RNAs are more common in Mycobacteria than previously expected. Our data provide a foundation for understanding the genome and biology of <it>Mtb </it>in a comparative context, and are available online and through TBDB.org.</p

Psychosocial Predictors of Non-Adherence and Treatment Failure in a Large Scale Multi-National Trial of Antiretroviral Therapy for HIV: Data from the ACTG A5175/PEARLS Trial

Background: PEARLS, a large scale trial of antiretroviral therapy (ART) for HIV (n = 1,571, 9 countries, 4 continents), found that a once-daily protease inhibitor (PI) based regimen (ATV+DDI+FTC), but not a once-daily non-nucleoside reverse transcriptase inhibitor/nucleoside reverse transcriptase inhibitor (NNRTI/NRTI) regimen (EFV+FTC/TDF), had inferior efficacy compared to a standard of care twice-daily NNRTI/NRTI regimen (EFV+3TC/ZDV). The present study examined non-adherence in PEARLS. Methods: Outcomes: non-adherence assessed by pill count and by self-report, and time to treatment failure. Longitudinal predictors: regimen, quality of life (general health perceptions = QOL-health, mental health = QOL-mental health), social support, substance use, binge drinking, and sexual behaviors. “Life-Steps” adherence counseling was provided. Results: In both pill-count and self-report multivariable models, both once-a-day regimens had lower levels of non-adherence than the twice-a-day standard of care regimen; although these associations attenuated with time in the self-report model. In both multivariable models, hard-drug use was associated with non-adherence, living in Africa and better QOL-health were associated with less non-adherence. According to pill-count, unprotected sex was associated with non-adherence. According to self-report, soft-drug use was associated with non-adherence and living in Asia was associated with less non-adherence. Both pill-count (HR = 1.55, 95% CI: 1.15, 2.09, p<.01) and self-report (HR = 1.13, 95% CI: 1.08, 1.13, p<.01) non-adherence were significant predictors of treatment failure over 72 weeks. In multivariable models (including pill-count or self-report nonadherence), worse QOL-health, age group (younger), and region were also significant predictors of treatment failure. Conclusion: In the context of a large, multi-national, multi-continent, clinical trial there were variations in adherence over time, with more simplified regimens generally being associated with better adherence. Additionally, variables such as QOL-health, regimen, drug-use, and region play a role. Self-report and pill-count adherence, as well as additional psychosocial variables, such QOL-health, age, and region, were, in turn, associated with treatment failure

Kepler eclipsing binary stars. VII. the catalogue of eclipsing binaries found in the entire Kepler data set

The primary Kepler Mission provided nearly continuous monitoring of ~200,000 objects with unprecedented photometric precision. We present the final catalog of eclipsing binary systems within the 105 deg2 Kepler field of view. This release incorporates the full extent of the data from the primary mission (Q0-Q17 Data Release). As a result, new systems have been added, additional false positives have been removed, ephemerides and principal parameters have been recomputed, classifications have been revised to rely on analytical models, and eclipse timing variations have been computed for each system. We identify several classes of systems including those that exhibit tertiary eclipse events, systems that show clear evidence of additional bodies, heartbeat systems, systems with changing eclipse depths, and systems exhibiting only one eclipse event over the duration of the mission. We have updated the period and galactic latitude distribution diagrams and included a catalog completeness evaluation. The total number of identified eclipsing and ellipsoidal binary systems in the Kepler field of view has increased to 2878, 1.3% of all observed Kepler targets

A Phase I Trial of Sirolimus with 7&3 Induction Chemotherapy in Patients with Newly Diagnosed Acute Myeloid Leukemia

Chemotherapy remains a primary treatment for younger AML patients, though many relapse. Data from our group have shown that highly phosphorylated S6 in blasts may predict response to sirolimus given with chemotherapy. We report the results of a phase I study of this combination in newly diagnosed AML and the pharmacodynamic analysis of pS6 before and after treatment. Subjects received sirolimus (12 mg on day 1, 4 mg daily, days 2-10), then idarubicin and cytarabine (days 4-10). Response was assessed at hematologic recovery or by day 42 using a modified IWG criteria. Fifty-five patients received sirolimus. Toxicity was similar to published 7 + 3 data, and 53% had high-, 27% intermediate-, and 20% favorable-risk disease. Forty-four percent of the high-risk patients entered into CR/CRp. Seventy-nine percent of the intermediate-risk subjects had a CR/CRp. All favorable-risk patients had a CR by day 42; 9/11 remained alive and in remission with a median follow-up of 660 days. Additionally, 41/55 patients had adequate samples for pharmacodynamic analysis. All patients demonstrated activation of S6 prior to therapy, in contrast to 67% seen in previous studies of relapsed AML. mTORC1 inhibition was observed in 66% of patients without enrichment among patients who achieved remission. We conclude that sirolimus and 7 + 3 is a well-tolerated and safe regimen. mTORC1 appears to be activated in almost all patients at diagnosis of AML. Inhibition of mTORC1 did not differ based on response, suggesting that AML cells may have redundant signaling pathways that regulate chemosensitivity in the presence of mTORC1 inhibition