Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species

We developed a fast, integrative pipeline to identify cis natural antisense transcripts (cis-NATs) at genome scale. The pipeline mapped mRNAs and ESTs in UniGene to genome sequences in GoldenPath to find overlapping transcripts and combining information from coding sequence, poly(A) signal, poly(A) tail and splicing sites to deduce transcription orientation. We identified cis-NATs in 10 eukaryotic species, including 7830 candidate sense–antisense (SA) genes in 3915 SA pairs in human. The abundance of SA genes is remarkably low in worm and does not seem to be caused by the prevalence of operons. Hundreds of SA pairs are conserved across different species, even maintaining the same overlapping patterns. The convergent SA class is prevalent in fly, worm and sea squirt, but not in human or mouse as reported previously. The percentage of SA genes among imprinted genes in human and mouse is 24–47%, a range between the two previous reports. There is significant shortage of SA genes on Chromosome X in human and mouse but not in fly or worm, supporting X-inactivation in mammals as a possible cause. SA genes are over-represented in the catalytic activities and basic metabolism functions. All candidate cis-NATs can be downloaded from

CEAS: cis-regulatory element annotation system

The recent availability of high-density human genome tiling arrays enables biologists to conduct ChIP–chip experiments to locate the in vivo-binding sites of transcription factors in the human genome and explore the regulatory mechanisms. Once genomic regions enriched by transcription factor ChIP–chip are located, genome-scale downstream analyses are crucial but difficult for biologists without strong bioinformatics support. We designed and implemented the first web server to streamline the ChIP–chip downstream analyses. Given genome-scale ChIP regions, the cis-regulatory element annotation system (CEAS) retrieves repeat-masked genomic sequences, calculates GC content, plots evolutionary conservation, maps nearby genes and identifies enriched transcription factor-binding motifs. Biologists can utilize CEAS to retrieve useful information for ChIP–chip validation, assemble important knowledge to include in their publication and generate novel hypotheses (e.g. transcription factor cooperative partner) for further study. CEAS helps the adoption of ChIP–chip in mammalian systems and provides insights towards a more comprehensive understanding of transcriptional regulatory mechanisms. The URL of the server is

Miniature high speed compressor having embedded permanent magnet motor

A high speed centrifugal compressor for compressing fluids includes a permanent magnet synchronous motor (PMSM) having a hollow shaft, the being supported on its ends by ball bearing supports. A permanent magnet core is embedded inside the shaft. A stator with a winding is located radially outward of the shaft. The PMSM includes a rotor including at least one impeller secured to the shaft or integrated with the shaft as a single piece. The rotor is a high rigidity rotor providing a bending mode speed of at least 100,000 RPM which advantageously permits implementation of relatively low-cost ball bearing supports

Systems Design, Fabrication, and Testing of a High-Speed Miniature Motor for Cryogenic Cooler

The long-term storage of liquid hydrogen for space missions is of considerable interest to NASA. To this end, the Reverse Turbo-Brayton Cryocooler (RTBC) is considerably lighter than conventional designs and a potentially viable and attractive solution for NASA's long-term Zero-Boil-off (ZBO) hydrogen storage system for future space missions. We present the systems design, fabrication, and performance evaluation of the Permanent Magnet Synchronous Motor (PMSM) powering a cryocooler capable of removing 20 W of heat at 18 K with a COP of 0.005 and driven by two 2-kW permanent magnet synchronous motors operating at 200 000 rpm and at room temperature and 77 K. Structural, thermal, and rotordynamic aspects of system design are considered

The Rapidly Flaring Afterglow of the Very Bright and Energetic GRB 070125

We report on multi-wavelength observations, ranging from the X-ray to radio wave bands, of the IPN-localized gamma-ray burst GRB 070125. Spectroscopic observations reveal the presence of absorption lines due to O I, Si II, and C IV, implying a likely redshift of z = 1.547. The well-sampled light curves, in particular from 0.5 to 4 days after the burst, suggest a jet break at 3.7 days, corresponding to a jet opening angle of ~7.0 degrees, and implying an intrinsic GRB energy in the 1 - 10,000 keV band of around E = (6.3 - 6.9)x 10^(51) erg (based on the fluences measured by the gamma-ray detectors of the IPN network). GRB 070125 is among the brightest afterglows observed to date. The spectral energy distribution implies a host extinction of Av < 0.9 mag. Two rebrightening episodes are observed, one with excellent time coverage, showing an increase in flux of 56% in ~8000 seconds. The evolution of the afterglow light curve is achromatic at all times. Late-time observations of the afterglow do not show evidence for emission from an underlying host galaxy or supernova. Any host galaxy would be subluminous, consistent with current GRB host-galaxy samples. Evidence for strong Mg II absorption features is not found, which is perhaps surprising in view of the relatively high redshift of this burst and the high likelihood for such features along GRB-selected lines of sight.Comment: 50 pages, 9 figures, 5 tables Accepted to the Astrophysical Journa

Infection status and risk factors of HIV, HBV, HCV, and syphilis among drug users in Guangdong, China - a cross-sectional study

<p>Abstract</p> <p>Background</p> <p>China has witnessed a remarkable increase in sexually transmitted infections (STIs) and HIV. The study is to assess the prevalence of HIV, HBV, HCV and syphilis and related risk factors among drug users in mandatory detoxification center Qingyuan, Guangdong, China.</p> <p>Method</p> <p>A cross-sectional study on drug use behaviors, sex behaviors, and presence of antibodies to HIV, HCV, Treponema pallidum, and surface antigen of HBV (HBsAg) was conducted among drug users recruited from 3 detoxification centers in Qingyuan, Guangdong, China. Risk factors for each of four infections were analyzed with logistic regression model.</p> <p>Results</p> <p>A total of 740 subjects were recruited, the median age was 31 years old (range 24-38). The seroprevalence rates of HIV, HBsAg, HCV and syphilis were 4.6%, 19.3%, 71.6% and 12.6%, respectively. Risk factors for HIV were intravenous drug use and co-infection with syphilis. Having a regular sexual partner who was a drug user was considered to be a risk factor for HBV. Intravenous drug use was a risk factor for HCV. However, the consistent use of condoms with commercial sex partners was protective for HCV infection. Compared to drug users living in urban area, those living in rural areas were more likely to be infected with syphilis, and there was an association between commercial sex and syphilis.</p> <p>Conclusion</p> <p>The prevalence of HIV, HBV, HCV and syphilis were high among drug users in detoxification centers in Qingyuan, thus, risk reduction programs for the drug user population is urgently required.</p