Uncovering the expression patterns of chimeric transcripts using surveys of affymetrix GeneChips.

BACKGROUND: A chimeric transcript is a single RNA sequence which results from the transcription of two adjacent genes. Recent studies estimate that at least 4% of tandem human gene pairs may form chimeric transcripts. Affymetrix GeneChip data are used to study the expression patterns of tens of thousands of genes and the probe sequences used in these microarrays can potentially map to exotic RNA sequences such as chimeras. RESULTS: We have studied human chimeras and investigated their expression patterns using large surveys of Affymetrix microarray data obtained from the Gene Expression Omnibus. We show that for six probe sets, a unique probe mapping to a transcript produced by one of the adjacent genes can be used to identify the expression patterns of readthrough transcripts. Furthermore, unique probes mapping to an intergenic exon present only in the MASK-BP3 chimera can be used directly to study the expression levels of this transcript. CONCLUSIONS: We have attempted to implement a new method for identifying tandem chimerism. In this analysis unambiguous probes are needed to measure run-off transcription and probes that map to intergenic exons are particularly valuable for identifying the expression of chimeras

Preliminary Limits on the WIMP-Nucleon Cross Section from the Cryogenic Dark Matter Search (CDMS)

We are conducting an experiment to search for WIMPs, or weakly-interacting massive particles, in the galactic halo using terrestrial detectors. This generic class of hypothetical particles, whose properties are similar to those predicted by extensions of the standard model of particle physics, could comprise the cold component of non-baryonic dark matter. We describe our experiment, which is based on cooled germanium and silicon detectors in a shielded low-background cryostat. The detectors achieve a high degree of background rejection through the simultaneous measurement of the energy in phonons and ionization. Using exposures on the order of one kilogram-day from initial runs of our experiment, we have achieved (preliminary) upper limits on the WIMP-nucleon cross section that are comparable to much longer runs of other experiments.Comment: 5 LaTex pages, 5 eps figs, epsf.sty, espcrc2dsa2.sty. Proceedings of TAUP97, Gran Sasso, Italy, 7-11 Sep 1997, Nucl. Phys. Suppl., A. Bottino, A. di Credico and P. Monacelli (eds.). See also http://cfpa.berkeley.ed

Spectroscopic analysis of finite size effects around a Kondo quantum dot

We consider a simple setup in which a small quantum dot is strongly connected to a finite size box. This box can be either a metallic box or a finite size quantum wire.The formation of the Kondo screening cloud in the box strongly depends on the ratio between the Kondo temperature and the box level spacing. By weakly connecting two metallic reservoirs to the quantum dot, a detailed spectroscopic analysis can be performed. Since the transport channels and the screening channels are almost decoupled, such a setup allows an easier access to the measure of finite-size effects associated with the finite extension of the Kondo cloud.Comment: contribution to Les Houches proceeding, ``Quantum magnetism'' 200

Photosynthesis by six portuguese maize cultivars during drought stress and recovery

Photosynthesis, chlorophyll fluorescence and leaf water parameters were measured in six Portuguese maize (Zea mays L.) cultivars during and following a period of drought stress. The leaf relative water content (RWC) responded differently among cultivars but, except for cultivar PB369, recovered close to initial values after watering was restored. Photosynthetic rate and stomatal conductance decreased with drought but more slowly in cultivars PB269 and PB260 than in cultivars AD3R, PB64, PB304 and PB369. Water use efficiency (WUE) decreased during the water stress treatment although with cultivar PB260 the decrease was marked only when the RWC fell below 40%. Recovery of WUE was seen with all cultivars except PB369. The maximum quantum efficiency of photosystem II, the photochemical quenching coefficient, the electron transport rate in PSII and the estimated functional plastoquinone pool tended to decrease with drought, while the non -photochemical quenching coefficient increased. The parameters estimated from chlorophyll fluorescence did not recover in PB369, during re - watering. The results show that PB260 and PB269 were the most tolerant and PB369 was the least tolerant cultivars to water stress. The variation found amongst the cultivars tested suggests the existence of valuable genetic resources for crop improvement in relation to drought tolerance

Knowledge and practices regarding child development among primary healthcare professionals

OBJECTIVE: To evaluate the knowledge and practices regarding child development among physicians working in primary healthcare units. METHOD: Cross-sectional descriptive study carried out at primary healthcare units in Embu, São Paulo, Brazil. Study procedures: 1) Evaluation of knowledge: test consisting of 20 multiple-choice questions on child development applied to all 31 physicians who were providing pediatric care at the primary healthcare units; 2) Evaluation of practices: semi-structured interview applied to a sample of 154 mothers/caregivers of children aged up to 36 months during follow-up visits at primary healthcare units in the municipality. For the comparisons of categorical variables (evaluation/advices about development in visits of children at different ages), the chi-square test was employed. RESULTS: The mean number of correct responses among physicians was 14.8. The error rate for seven questions was greater than 30% (sensory development, language acquisition, physiology of the nervous system, clinical and laboratory diagnosis of congenital infections and innate errors of metabolism) and the rate of correct responses was greater than 85% for four questions (motor and personal-social development markers, risk factors and genetic syndromes). Regarding practices, in 69 (45%) visits, the doctor asked the mother/caregiver's opinion about the child's development; in 80 (52%), the mother/caregiver said that the doctor assessed the development; and in 64 (42%), the mother/caregiver said that the doctor advised them on practices for child's stimulation. CONCLUSIONS: Faulty knowledge and practices regarding child development were identified among primary care professionals, indicating the need for continued education.OBJETIVO: Avaliar o conhecimento e as práticas sobre desenvolvimento infantil de médicos que atuam em Unidades Básicas de Saúde (UBS). MÉTODO: Estudo transversal, descritivo, realizado nas UBS de Embu (SP). Procedimentos do estudo: 1) avaliação do conhecimento por teste contendo 20 questões de múltipla escolha sobre desenvolvimento da criança aplicado a 31 médicos (universo) que prestam assistência pediátrica em UBS; 2) avaliação das práticas - entrevista semiestruturada aplicada para uma amostra de 154 mães/cuidadores que acompanhavam crianças com idade menor ou igual a 36 meses em consulta médica agendada em UBS do município. Para comparação de variáveis categóricas (avaliação/orientações sobre desenvolvimento em consultas de crianças de diferentes faixas etárias), utizou-se o qui-quadrado. RESULTADOS: A média de acertos dos médicos foi de 14,8 questões; sete questões apresentaram índices de erros superiores a 30% (desenvolvimento sensorial, aquisição de linguagem, fisiologia do sistema nervoso, diagnóstico clínico e laboratorial de infecções congênitas, erros inatos do metabolismo) e quatro questões apresentaram acertos acima de 85% (marcos do desenvolvimento motor, pessoal-social, fatores de risco e síndrome genética). Quanto às práticas, em 69 (45%) consultas o médico perguntou a opinião da mãe/cuidador sobre o desenvolvimento da criança, em 80 (52%) a mãe/cuidador referiu que o médico fez alguma pergunta e/ou avaliou o desenvolvimento e em 64 (42%) orientou sobre como estimular a criança. CONCLUSÕES: Identificaram-se falhas de conhecimento e nas práticas dos profissionais referentes ao desenvolvimento da criança, o que indica a necessidade de implementar educação permanente.UNIFESP Curso de MedicinaUNIFESP Projeto DesenvolverSecretaria Municipal de Saúde do EmbuUNIFESP Departamento de Pediatria Disciplina de Pediatria Geral e ComunitáriaUNIFESP, Curso de MedicinaUNIFESP, Projeto DesenvolverUNIFESP, Depto. de Pediatria Disciplina de Pediatria Geral e ComunitáriaSciEL

Detection of Gamma-Ray Emission from the Starburst Galaxies M82 and NGC 253 with the Large Area Telescope on Fermi

We report the detection of high-energy gamma-ray emission from two starburst galaxies using data obtained with the Large Area Telescope on board the Fermi Gamma-ray Space Telescope. Steady point-like emission above 200 MeV has been detected at significance levels of 6.8 sigma and 4.8 sigma respectively, from sources positionally coincident with locations of the starburst galaxies M82 and NGC 253. The total fluxes of the sources are consistent with gamma-ray emission originating from the interaction of cosmic rays with local interstellar gas and radiation fields and constitute evidence for a link between massive star formation and gamma-ray emission in star-forming galaxies.Comment: Submitted to ApJ Letter

Fermi Gamma-ray Imaging of a Radio Galaxy

The Fermi Gamma-ray Space Telescope has detected the gamma-ray glow emanating from the giant radio lobes of the radio galaxy Centaurus A. The resolved gamma-ray image shows the lobes clearly separated from the central active source. In contrast to all other active galaxies detected so far in high-energy gamma-rays, the lobe flux constitutes a considerable portion (>1/2) of the total source emission. The gamma-ray emission from the lobes is interpreted as inverse Compton scattered relic radiation from the cosmic microwave background (CMB), with additional contribution at higher energies from the infrared-to-optical extragalactic background light (EBL). These measurements provide gamma-ray constraints on the magnetic field and particle energy content in radio galaxy lobes, and a promising method to probe the cosmic relic photon fields.Comment: 27 pages, includes Supplementary Online Material; corresponding authors: C.C. Cheung, Y. Fukazawa, J. Knodlseder, L. Stawar

Fermi Large Area Telescope observations of PSR J1836+5925

The discovery of the gamma-ray pulsar PSR J1836+5925, powering the formerly unidentified EGRET source 3EG J1835+5918, was one of the early accomplishments of the Fermi Large Area Telescope (LAT). Sitting 25 degrees off the Galactic plane, PSR J1836+5925 is a 173 ms pulsar with a characteristic age of 1.8 million years, a spindown luminosity of 1.1$\times10^{34}$ erg s$^{-1}$, and a large off-peak emission component, making it quite unusual among the known gamma-ray pulsar population. We present an analysis of one year of LAT data, including an updated timing solution, detailed spectral results and a long-term light curve showing no indication of variability. No evidence for a surrounding pulsar wind nebula is seen and the spectral characteristics of the off-peak emission indicate it is likely magnetospheric. Analysis of recent XMM observations of the X-ray counterpart yields a detailed characterization of its spectrum, which, like Geminga, is consistent with that of a neutron star showing evidence for both magnetospheric and thermal emission.Comment: Accepted to Astrophysical Journa