Particle kinetic simulation of high altitude hypervelocity flight

In this grant period, the focus has been on the effects of thermo-chemical nonequilibrium in low-density gases, and on interactions between such gases and solid surfaces. Such conditions apply to hypersonic flows of re-entry vehicles, and to the expansion plumes of small rockets. Due to the nonequilibrium nature of these flows, a particle approach has been adopted. The method continues to undergo refinement and application to typical flows of interest. A number of studies have been performed for flows in thermo-chemical nonequilibrium. The effects of vibrational nonequilibrium on the rate of dissociation were studied for diatomic nitrogen. It was found that a new model reproduced the nonequilibrium behavior observed experimentally

Increasing Transit Ridership: Lessons from the Most Successful Transit Systems in the 1990s, MTI Report-01-22

This study systematically examines recent trends in public transit ridership in the U.S. during the 1990s. Specifically, this analysis focuses on agencies that increased ridership during the latter half of the decade. While transit ridership increased steadily by 13 percent nationwide between 1995 and 1999, not all systems experienced ridership growth equally. While some agencies increased ridership dramatically, some did so only minimally, and still others lost riders. What sets these agencies apart from each other? What explains the uneven growth in ridership

miBLAST: scalable evaluation of a batch of nucleotide sequence queries with BLAST

A common task in many modern bioinformatics applications is to match a set of nucleotide query sequences against a large sequence dataset. Exis-ting tools, such as BLAST, are designed to evaluate a single query at a time and can be unacceptably slow when the number of sequences in the query set is large. In this paper, we present a new algorithm, called miBLAST, that evaluates such batch workloads efficiently. At the core, miBLAST employs a q-gram filtering and an index join for efficiently detecting similarity between the query sequences and database sequences. This set-oriented technique, which indexes both the query and the database sets, results in substantial performance improvements over existing methods. Our results show that miBLAST is significantly faster than BLAST in many cases. For example, miBLAST aligned 247 965 oligonucleotide sequences in the Affymetrix probe set against the Human UniGene in 1.26 days, compared with 27.27 days with BLAST (an improvement by a factor of 22). The relative performance of miBLAST increases for larger word sizes; however, it decreases for longer queries. miBLAST employs the familiar BLAST statistical model and output format, guaranteeing the same accuracy as BLAST and facilitating a seamless transition for existing BLAST users

Quantitative Analysis of Dynamic Protein Interactions during Transcription Reveals a Role for Casein Kinase II in Polymerase-associated Factor (PAF) Complex Phosphorylation and Regulation of Histone H2B Monoubiquitylation

Using affinity purification MS approaches, we have identified a novel role for casein kinase II (CKII) in the modification of the polymerase associated factor complex (PAF-C). Our data indicate that the facilitates chromatin transcription complex (FACT) interacts with CKII and may facilitate PAF complex phosphorylation. Posttranslational modification analysis of affinity-isolated PAF-C shows extensive CKII phosphorylation of all five subunits of PAF-C, although CKII subunits were not detected as interacting partners. Consistent with this, recombinant CKII or FACT-associated CKII isolated from cells can phosphorylate PAF-C in vitro, whereas no intrinsic kinase activity was detected in PAF-C samples. Significantly, PAF-C purifications combined with stable isotope labeling in cells (SILAC) quantitation for PAF-C phosphorylation from wild-type and CKII temperature-sensitive strains (cka1Δ cka2–8) showed that PAF-C phosphorylation at consensus CKII sites is significantly reduced in cka1Δ cka2–8 strains. Consistent with a role of CKII in FACT and PAF-C function, we show that decreased CKII function in vivo results in decreased levels of histone H2B lysine 123 monoubiquitylation, a modification dependent on FACT and PAF-C. Taken together, our results define a coordinated role of CKII and FACT in the regulation of RNA polymerase II transcription through chromatin via phosphorylation of PAF-C

Trainee teachers' use of blogs as private reflections for professional development

A collaborative research project between Sheffield Hallam University and Nottingham Trent University in the UK investigated the use of blogs with trainee teachers as an alternative to reflective paper-based diaries. An action research case study, involving focus groups of post-graduate (secondary) trainee teachers (one group from each University) was undertaken to determine attitudes and perceptions of blogging as an appropriate tool to support reflective professional development. The findings indicate that the use of blogs by the trainee teachers had a positive impact overall, and provide concrete evidence of their development as emerging professional teachers. Unlike traditional paper-based systems, blogs provided ongoing opportunities for the tutor to assist the trainees in their development as reflective practitioners. This paper seeks to share the findings of this research which the authors believe could be applicable to other areas of Higher Education.</p

Second-harmonic generation induced by electric currents in GaAs

We demonstrate a new, nonlinear optical effect of electric currents. First, a steady current is generated by applying a voltage on a doped GaAs crystal. We demonstrate that this current induces second-harmonic generation of a probe laser pulse. Second, we optically inject a transient current in an undoped GaAs crystal by using a pair of ultrafast laser pulses, and demonstrate that it induces the same second-harmonic generation. In both cases, the induced second-order nonlinear susceptibility is proportional to the current density. This effect can be used for nondestructive, noninvasive, and ultrafast imaging of currents. These advantages are illustrated by the real-time observations of a coherent plasma oscillation and spatial resolution of current distribution in a device. This new effect also provides a mechanism for electrical control of the optical response of materials.Comment: 5 pages, 3 figure

A Mouse-Adapted SARS-Coronavirus Causes Disease and Mortality in BALB/c Mice

No single animal model for severe acute respiratory syndrome (SARS) reproduces all aspects of the human disease. Young inbred mice support SARS-coronavirus (SARS-CoV) replication in the respiratory tract and are available in sufficient numbers for statistical evaluation. They are relatively inexpensive and easily accessible, but their use in SARS research is limited because they do not develop illness following infection. Older (12- to 14-mo-old) BALB/c mice develop clinical illness and pneumonitis, but they can be hard to procure, and immune senescence complicates pathogenesis studies. We adapted the SARS-CoV (Urbani strain) by serial passage in the respiratory tract of young BALB/c mice. Fifteen passages resulted in a virus (MA15) that is lethal for mice following intranasal inoculation. Lethality is preceded by rapid and high titer viral replication in lungs, viremia, and dissemination of virus to extrapulmonary sites accompanied by lymphopenia, neutrophilia, and pathological changes in the lungs. Abundant viral antigen is extensively distributed in bronchial epithelial cells and alveolar pneumocytes, and necrotic cellular debris is present in airways and alveoli, with only mild and focal pneumonitis. These observations suggest that mice infected with MA15 die from an overwhelming viral infection with extensive, virally mediated destruction of pneumocytes and ciliated epithelial cells. The MA15 virus has six coding mutations associated with adaptation and increased virulence; when introduced into a recombinant SARS-CoV, these mutations result in a highly virulent and lethal virus (rMA15), duplicating the phenotype of the biologically derived MA15 virus. Intranasal inoculation with MA15 reproduces many aspects of disease seen in severe human cases of SARS. The availability of the MA15 virus will enhance the use of the mouse model for SARS because infection with MA15 causes morbidity, mortality, and pulmonary pathology. This virus will be of value as a stringent challenge in evaluation of the efficacy of vaccines and antivirals

Metering Best Practices, A Guide to Achieving Utility Resource Efficiency, Release 2.0

This release is an update and expansion of the information provided in Release 1.0 of the Metering Best Practice Guide that was issued in October 2007. This release, as was the previous release, was developed under the direction of the U.S. Department of Energy's Federal Energy Management Program (FEMP). The mission of FEMP is to facilitate the Federal Government's implementation of sound cost-effective energy management and investment practices to enhance the nation's energy security and environmental stewardship. Each of these activities is directly related to achieving requirements set forth in the Energy Policy Acts of 1992 and 2005, the Energy Independence and Security Act (EISA) of 2007, and the goals that have been established in Executive Orders 13423 and 13514 - and also those practices that are inherent in sound management of Federal financial and personnel resources

Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data

Genome-wide expression profiling is a powerful tool for implicating novel gene ensembles in cellular mechanisms of health and disease. The most popular platform for genome-wide expression profiling is the Affymetrix GeneChip. However, its selection of probes relied on earlier genome and transcriptome annotation which is significantly different from current knowledge. The resultant informatics problems have a profound impact on analysis and interpretation the data. Here, we address these critical issues and offer a solution. We identified several classes of problems at the individual probe level in the existing annotation, under the assumption that current genome and transcriptome databases are more accurate than those used for GeneChip design. We then reorganized probes on more than a dozen popular GeneChips into gene-, transcript- and exon-specific probe sets in light of up-to-date genome, cDNA/EST clustering and single nucleotide polymorphism information. Comparing analysis results between the original and the redefined probe sets reveals ∼30–50% discrepancy in the genes previously identified as differentially expressed, regardless of analysis method. Our results demonstrate that the original Affymetrix probe set definitions are inaccurate, and many conclusions derived from past GeneChip analyses may be significantly flawed. It will be beneficial to re-analyze existing GeneChip data with updated probe set definitions

Hyporesponsiveness to social and nonsocial sensory stimuli in children with autism, children with developmental delays, and typically developing children

This cross-sectional study seeks to (a) describe developmental correlates of sensory hyporesponsiveness to social and nonsocial stimuli, (b) determine whether hyporesponsiveness is generalized across contexts in children with autism relative to controls, and (c) test the associations between hyporesponsiveness and social communication outcomes. Three groups of children ages 11-105 months (N = 178; autism = 63, developmental delay = 47, typical development = 68) are given developmental and sensory measures including a behavioral orienting task (the Sensory Processing Assessment). Lab measures are significantly correlated with parental reports of sensory hyporesponsiveness. Censored regression models show that hyporesponsiveness decreased across groups with increasing mental age (MA). Group differences are significant but depend upon two-way interactions with MA and context (social and nonsocial). At a very young MA (e.g., 6 months), the autism group demonstrates more hyporesponsiveness to social and nonsocial stimuli (with larger effects for social) than developmental delay and typically developing groups, but at an older MA (e.g., 60 months) there are no significant differences. Hyporesponsiveness to social and nonsocial stimuli predicts lower levels of joint attention and language in children with autism. Generalized processes in attention disengagement and behavioral orienting may have relevance for identifying early risk factors of autism and for facilitating learning across contexts to support the development of joint attention and language