High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome

<p>Abstract</p> <p>Background</p> <p>Benefits from high-throughput sequencing using 454 pyrosequencing technology may be most apparent for species with high societal or economic value but few genomic resources. Rapid means of gene sequence and SNP discovery using this novel sequencing technology provide a set of baseline tools for genome-level research. However, it is questionable how effective the sequencing of large numbers of short reads for species with essentially no prior gene sequence information will support contig assemblies and sequence annotation.</p> <p>Results</p> <p>With the purpose of generating the first broad survey of gene sequences in <it>Eucalyptus grandis</it>, the most widely planted hardwood tree species, we used 454 technology to sequence and assemble 148 Mbp of expressed sequences (EST). EST sequences were generated from a normalized cDNA pool comprised of multiple tissues and genotypes, promoting discovery of homologues to almost half of <it>Arabidopsis</it> genes, and a comprehensive survey of allelic variation in the transcriptome. By aligning the sequencing reads from multiple genotypes we detected 23,742 SNPs, 83% of which were validated in a sample. Genome-wide nucleotide diversity was estimated for 2,392 contigs using a modified theta (θ) parameter, adapted for measuring genetic diversity from polymorphisms detected by randomly sequencing a multi-genotype cDNA pool. Diversity estimates in non-synonymous nucleotides were on average 4x smaller than in synonymous, suggesting purifying selection. Non-synonymous to synonymous substitutions (Ka/Ks) among 2,001 contigs averaged 0.30 and was skewed to the right, further supporting that most genes are under purifying selection. Comparison of these estimates among contigs identified major functional classes of genes under purifying and diversifying selection in agreement with previous researches.</p> <p>Conclusion</p> <p>In providing an abundance of foundational transcript sequences where limited prior genomic information existed, this work created part of the foundation for the annotation of the <it>E. grandis </it>genome that is being sequenced by the US Department of Energy. In addition we demonstrated that SNPs sampled in large-scale with 454 pyrosequencing can be used to detect evolutionary signatures among genes, providing one of the first genome-wide assessments of nucleotide diversity and Ka/Ks for a non-model plant species.</p

Avaliação de serviços em saúde mental no Brasil: revisão sistemática da literatura

ResumoA avaliação em saúde mental é um mecanismo capaz de produzir informações que contribuam positivamente para a tomada de decisão na área. Logo, é preciso apropriar-se das discussões existentes, refletindo sobre desafios e possibilidades na produção de conhecimento neste campo. Realizou-se uma revisão sistemática da produção científica brasileira sobre avaliação de serviços em saúde mental, identificando e discutindo métodos, perspectivas avaliativas e resultados. A busca de artigos ocorreu nas bases de dados IBECS, Lilacs e Scielo, com recorte temporal da publicação da lei 10.216. Foram encontrados 35 artigos por meio dos descritores e critérios de inclusão e exclusão utilizados. A produção da área concentrou-se nas regiões Sul e Sudeste, com diversos âmbitos e participantes, visando contribuir para o aprimoramento de serviços e decisões na área. Destacam-se os avanços no cuidado, com tratamento humanizado, participativo e comunitário, mas carecendo de maiores investimentos, qualificação profissional e melhorias organizacionais. Postula-se maior integração entre pesquisas, com as avaliações ultrapassando aspectos estruturais e a comparação com modelos hospitalocêntricos

The BINGO project: II. Instrument description

Context. The measurement of diffuse 21-cm radiation from the hyperfine transition of neutral hydrogen (Hi signal) in different redshifts is an important tool for modern cosmology. However, detecting this faint signal with non-cryogenic receivers in single-dish telescopes is a challenging task. The BINGO (Baryon Acoustic Oscillations from Integrated Neutral Gas Observations) radio telescope is an instrument designed to detect baryonic acoustic oscillations (BAOs) in the cosmological Hi signal, in the redshift interval 0:127 ≤ z ≤ 0:449. Aims. This paper describes the BINGO radio telescope, including the current status of the optics, receiver, observational strategy, calibration, and the site. Methods. BINGO has been carefully designed to minimize systematics, being a transit instrument with no moving dishes and 28 horns operating in the frequency range 980 ≤ v ≤ 1260 MHz. Comprehensive laboratory tests were conducted for many of the BINGO subsystems and the prototypes of the receiver chain, horn, polarizer, magic tees, and transitions have been successfully tested between 2018-2020. The survey was designed to cover ∼13% of the sky, with the primary mirror pointing at declination δ = -15°. The telescope will see an instantaneous declination strip of 14:75. Results. The results of the prototype tests closely meet those obtained during the modeling process, suggesting BINGO will perform according to our expectations. After one year of observations with a 60% duty cycle and 28 horns, BINGO should achieve an expected sensitivity of 102μK per 9.33MHz frequency channel, one polarization, and be able to measure the Hi power spectrum in a competitive time frame

Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV

The performance of muon reconstruction, identification, and triggering in CMS has been studied using 40 inverse picobarns of data collected in pp collisions at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection criteria covering a wide range of physics analysis needs have been examined. For all considered selections, the efficiency to reconstruct and identify a muon with a transverse momentum pT larger than a few GeV is above 95% over the whole region of pseudorapidity covered by the CMS muon system, abs(eta) < 2.4, while the probability to misidentify a hadron as a muon is well below 1%. The efficiency to trigger on single muons with pT above a few GeV is higher than 90% over the full eta range, and typically substantially better. The overall momentum scale is measured to a precision of 0.2% with muons from Z decays. The transverse momentum resolution varies from 1% to 6% depending on pseudorapidity for muons with pT below 100 GeV and, using cosmic rays, it is shown to be better than 10% in the central region up to pT = 1 TeV. Observed distributions of all quantities are well reproduced by the Monte Carlo simulation.Comment: Replaced with published version. Added journal reference and DO