Assimilation of Wind Profiles from Multiple Doppler Radar Wind Profilers for Space Launch Vehicle Applications

Space launch vehicles utilize atmospheric winds in design of the vehicle and during day-of-launch (DOL) operations to assess affects of wind loading on the vehicle and to optimize vehicle performance during ascent. The launch ranges at NASA's Kennedy Space Center co-located with the United States Air Force's (USAF) Eastern Range (ER) at Cape Canaveral Air Force Station and USAF's Western Range (WR) at Vandenberg Air Force Base have extensive networks of in-situ and remote sensing instrumentation to measure atmospheric winds. Each instrument's technique to measure winds has advantages and disadvantages in regards to use for vehicle engineering assessments. Balloons measure wind at all altitudes necessary for vehicle assessments, but two primary disadvantages exist when applying balloon output on DOL. First, balloons need approximately one hour to reach required altitude. For vehicle assessments this occurs at 60 kft (18.3 km). Second, balloons are steered by atmospheric winds down range of the launch site that could significantly differ from those winds along the vehicle ascent trajectory. Figure 1 illustrates the spatial separation of balloon measurements from the surface up to approximately 55 kft (16.8 km) during the Space Shuttle launch on 10 December 2006. The balloon issues are mitigated by use of vertically pointing Doppler Radar Wind Profilers (DRWPs). However, multiple DRWP instruments are required to provide wind data up to 60 kft (18.3 km) for vehicle trajectory assessments. The various DRWP systems have different operating configurations resulting in different temporal and spatial sampling intervals. Therefore, software was developed to combine data from both DRWP-generated profiles into a single profile for use in vehicle trajectory analyses. Details on how data from various wind measurement systems are combined and sample output will be presented in the following sections

Eliminating Fatigue in Surface-Bound Spiropyrans

This paper describes an experimental approach to eliminating the loss of reversibility that surface-bound spiropyrans exhibit when switched with light. Although such fatigue can be controlled in other contexts, on surfaces, the photochromic compounds are held in close proximity to each other and relatively few molecules modulate the properties of a device, leading to a loss of functionality after only a few switching cycles. The switching process was characterized by photoelectron spectroscopy and differences in tunneling currents in the spiropyran and merocyanine forms using eutectic Ga-In. Self-assembled monolayers comprising only the photochromic compounds degraded rapidly, while mixed monolayers with hexanethiol showed different behaviors depending on the relative humidity. Under dry conditions, no chemical degradation was observed and the switching process was reversible over at least 100 cycles. Under humid conditions, no degradation occurred, but the switching process became irreversible. The absence of degradation observed in mixed monolayers is ascribed to the lack of solvation, which increases the barrier to a key bond rotation past the available thermal energy. These results highlight important differences in the contexts in which photochromic compounds are utilized and demonstrate that they can be leveraged to extract device-relevant functionality from surface-bound switches by suppressing fatigue and irreversibility

An operon for production of bioactive gibberellin A4 phytohormone with wide distribution in the bacterial rice leaf streak pathogen Xanthomonas oryzae pv. oryzicola

• Phytopathogens have developed elaborate mechanisms to attenuate the defense response of their host plants, including convergent evolution of complex pathways for production of the gibberellin (GA) phytohormones, which were actually first isolated from the rice fungal pathogen Gibberella fujikuroi. The rice bacterial pathogen Xanthomonas oryzae pv. oryzicola (Xoc) has been demonstrated to contain a biosynthetic operon with cyclases capable of producing the universal GA precursor ent-kaurene. Genetic (knock-out) studies indicate that the derived diterpenoid serves as a virulence factor for this rice leaf streak pathogen, serving to reduce the jasmonic acid (JA) mediated defense response. • Here the function of the remaining genes in the Xoc operon are elucidated and the distribution of the operon in X. oryzae investigated in over 100 isolates. • The Xoc operon leads to production of the bioactive GA4, an additional step beyond production of the penultimate precursor GA9 mediated by the homologous operons recently characterized from rhizobia. Moreover, this GA biosynthetic operon was found to be widespread in Xoc (\u3e90%), but absent in the other major oryzae pathovar. • These results indicate selective pressure for production of GA4 in the distinct lifestyle of Xoc, and the importance of GA to both fungal and bacterial pathogens of rice

Macromolecular crowding and decellularization method increase the growth factor binding potential of cell-secreted extracellular matrices

Recombinant growth factors are used in tissue engineering to stimulate cell proliferation, migration, and differentiation. Conventional methods of growth factor delivery for therapeutic applications employ large amounts of these bioactive cues. Effective, localized growth factor release is essential to reduce the required dose and potential deleterious effects. The endogenous extracellular matrix (ECM) sequesters native growth factors through its negatively charged sulfated glycosaminoglycans. Mesenchymal stromal cells secrete an instructive extracellular matrix that can be tuned by varying culture and decellularization methods. In this study, mesenchymal stromal cell-secreted extracellular matrix was modified using λ-carrageenan as a macromolecular crowding (MMC) agent and decellularized with DNase as an alternative to previous decellularized extracellular matrices (dECM) to improve growth factor retention. Macromolecular crowding decellularized extracellular matrix contained 7.7-fold more sulfated glycosaminoglycans and 11.7-fold more total protein than decellularized extracellular matrix, with no significant difference in residual DNA. Endogenous BMP-2 was retained in macromolecular crowding decellularized extracellular matrix, whereas BMP-2 was not detected in other extracellular matrices. When implanted in a murine muscle pouch, we observed increased mineralized tissue formation with BMP-2-adsorbed macromolecular crowding decellularized extracellular matrix in vivo compared to conventional decellularized extracellular matrix. This study demonstrates the importance of decellularization method to retain endogenous sulfated glycosaminoglycans in decellularized extracellular matrix and highlights the utility of macromolecular crowding to upregulate sulfated glycosaminoglycan content. This platform has the potential to aid in the delivery of lower doses of BMP-2 or other heparin-binding growth factors in a tunable manner

Professional Development and the Informal Curriculum in End-of-Life Care

Although professionalism has emerged as a key competency for today’s physicians, there exists little insight into how best to teach medical students the relevant skills or instill in them the commitment required to practice according to the highest professional standards. Ten UCSF medical students were interviewed at three time points (second, third, and fourth years of school). Interviews focused on students’ learning and development regarding end-of-life care (EOLC). Students described varying steps in their professional development from their second to fourth years of school, including feeling confused about the definition of professionalism and integrating their personal and professional identities. In addition to professional development, four other themes contributed to the development of medical student understanding of how to provide EOLC as a professional: (1) curricular discordance, (2) role models, (3) the tightrope between trained versus human reactions, and (4) ethical dilemmas. These five themes represent dilemmas that students often learned how to respond to over the course of school. Professional development in EOLC required the acquisition of skills necessary to balance the tension between and navigate conflicting messages present in medical student training

Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A

Background: Xanthomonas oryzae pv. oryzae causes bacterial blight of rice (Oryza sativa L.), a major disease that constrains production of this staple crop in many parts of the world. We report here on the complete genome sequence of strain PXO99A and its comparison to two previously sequenced strains, KACC10331 and MAFF311018, which are highly similar to one another. Results: The PXO99 A genome is a single circular chromosome of 5,240,075 bp, considerably longer than the genomes of the other strains (4,941,439 bp and 4,940,217 bp, respectively), and it contains 5083 protein-coding genes, including 87 not found in KACC10331 or MAFF311018. PXO99A contains a greater number of virulence-associated transcription activator-like effector genes and has at least ten major chromosomal rearrangements relative to KACC10331 and MAFF311018. PXO99 A contains numerous copies of diverse insertion sequence elements, members of which are associated with 7 out of 10 of the major rearrangements. A rapidly-evolving CRISPR (clustered regularly interspersed short palindromic repeats) region contains evidence of dozens of phage infections unique to the PXO99A lineage. PXO99A also contains a unique, near-perfect tandem repeat of 212 kilobases close to the replication terminus. Conclusion: Our results provide striking evidence of genome plasticity and rapid evolution within Xanthomonas oryzae pv. oryzae. The comparisons point to sources of genomic variation and candidates for strain-specific adaptations of this pathogen that help to explain the extraordinary diversity of Xanthomonas oryzae pv. oryzae genotypes and races that have been isolated from around the world. © 2008 Salzberg et al; licensee BioMed Central Ltd

Predicting protein linkages in bacteria: Which method is best depends on task

<p>Abstract</p> <p>Background</p> <p>Applications of computational methods for predicting protein functional linkages are increasing. In recent years, several bacteria-specific methods for predicting linkages have been developed. The four major genomic context methods are: Gene cluster, Gene neighbor, Rosetta Stone, and Phylogenetic profiles. These methods have been shown to be powerful tools and this paper provides guidelines for when each method is appropriate by exploring different features of each method and potential improvements offered by their combination. We also review many previous treatments of these prediction methods, use the latest available annotations, and offer a number of new observations.</p> <p>Results</p> <p>Using <it>Escherichia coli </it>K12 and <it>Bacillus subtilis</it>, linkage predictions made by each of these methods were evaluated against three benchmarks: functional categories defined by COG and KEGG, known pathways listed in EcoCyc, and known operons listed in RegulonDB. Each evaluated method had strengths and weaknesses, with no one method dominating all aspects of predictive ability studied. For functional categories, as previous studies have shown, the Rosetta Stone method was individually best at detecting linkages and predicting functions among proteins with shared KEGG categories while the Phylogenetic profile method was best for linkage detection and function prediction among proteins with common COG functions. Differences in performance under COG versus KEGG may be attributable to the presence of paralogs. Better function prediction was observed when using a weighted combination of linkages based on reliability versus using a simple unweighted union of the linkage sets. For pathway reconstruction, 99 complete metabolic pathways in <it>E. coli </it>K12 (out of the 209 known, non-trivial pathways) and 193 pathways with 50% of their proteins were covered by linkages from at least one method. Gene neighbor was most effective individually on pathway reconstruction, with 48 complete pathways reconstructed. For operon prediction, Gene cluster predicted completely 59% of the known operons in <it>E. coli </it>K12 and 88% (333/418)in <it>B. subtilis</it>. Comparing two versions of the <it>E. coli </it>K12 operon database, many of the unannotated predictions in the earlier version were updated to true predictions in the later version. Using only linkages found by both Gene Cluster and Gene Neighbor improved the precision of operon predictions. Additionally, as previous studies have shown, combining features based on intergenic region and protein function improved the specificity of operon prediction.</p> <p>Conclusion</p> <p>A common problem for computational methods is the generation of a large number of false positives that might be caused by an incomplete source of validation. By comparing two versions of a database, we demonstrated the dramatic differences on reported results. We used several benchmarks on which we have shown the comparative effectiveness of each prediction method, as well as provided guidelines as to which method is most appropriate for a given prediction task.</p

Genetic Diversity and Protective Efficacy of the RTS,S/AS01 Malaria Vaccine.

BACKGROUND: The RTS,S/AS01 vaccine targets the circumsporozoite protein of Plasmodium falciparum and has partial protective efficacy against clinical and severe malaria disease in infants and children. We investigated whether the vaccine efficacy was specific to certain parasite genotypes at the circumsporozoite protein locus. METHODS: We used polymerase chain reaction-based next-generation sequencing of DNA extracted from samples from 4985 participants to survey circumsporozoite protein polymorphisms. We evaluated the effect that polymorphic positions and haplotypic regions within the circumsporozoite protein had on vaccine efficacy against first episodes of clinical malaria within 1 year after vaccination. RESULTS: In the per-protocol group of 4577 RTS,S/AS01-vaccinated participants and 2335 control-vaccinated participants who were 5 to 17 months of age, the 1-year cumulative vaccine efficacy was 50.3% (95% confidence interval [CI], 34.6 to 62.3) against clinical malaria in which parasites matched the vaccine in the entire circumsporozoite protein C-terminal (139 infections), as compared with 33.4% (95% CI, 29.3 to 37.2) against mismatched malaria (1951 infections) (P=0.04 for differential vaccine efficacy). The vaccine efficacy based on the hazard ratio was 62.7% (95% CI, 51.6 to 71.3) against matched infections versus 54.2% (95% CI, 49.9 to 58.1) against mismatched infections (P=0.06). In the group of infants 6 to 12 weeks of age, there was no evidence of differential allele-specific vaccine efficacy. CONCLUSIONS: These results suggest that among children 5 to 17 months of age, the RTS,S vaccine has greater activity against malaria parasites with the matched circumsporozoite protein allele than against mismatched malaria. The overall vaccine efficacy in this age category will depend on the proportion of matched alleles in the local parasite population; in this trial, less than 10% of parasites had matched alleles. (Funded by the National Institutes of Health and others.)

So Small, So Loud: Extremely High Sound Pressure Level from a Pygmy Aquatic Insect (Corixidae, Micronectinae)

To communicate at long range, animals have to produce intense but intelligible signals. This task might be difficult to achieve due to mechanical constraints, in particular relating to body size. Whilst the acoustic behaviour of large marine and terrestrial animals has been thoroughly studied, very little is known about the sound produced by small arthropods living in freshwater habitats. Here we analyse for the first time the calling song produced by the male of a small insect, the water boatman Micronecta scholtzi. The song is made of three distinct parts differing in their temporal and amplitude parameters, but not in their frequency content. Sound is produced at 78.9 (63.6–82.2) SPL rms re 2.10−5 Pa with a peak at 99.2 (85.7–104.6) SPL re 2.10−5 Pa estimated at a distance of one metre. This energy output is significant considering the small size of the insect. When scaled to body length and compared to 227 other acoustic species, the acoustic energy produced by M. scholtzi appears as an extreme value, outperforming marine and terrestrial mammal vocalisations. Such an extreme display may be interpreted as an exaggerated secondary sexual trait resulting from a runaway sexual selection without predation pressure