Geiger-Mode Avalanche Photodiodes in Particle Detection

It is well known that avalanche photodiodes operated in the Geiger mode above the breakdown voltage offer a virtually infinite sensitivity and time accuracy in the picosecond range that can be used for single photon detection. However, their performance in particle detection remains still unexplored. In this contribution, we are going to expose the different steps that we have taken in order to prove the efficiency of Geiger mode avalanche photodiodes in the aforementioned field. In particular, we will present an array of pixels of 1mmx1mm fabricated with a standard CMOS technology for characterization in a test beam.Comment: 7 pages, 2 figures, Proceedings of LCWS1

Extracting Hα\alpha flux from photometric data in the J-PLUS survey

We present the main steps that will be taken to extract H$\alpha$ emission flux from Javalambre Photometric Local Universe Survey (J-PLUS) photometric data. For galaxies with $z\lesssim0.015$, the H$\alpha$+[NII] emission is covered by the J-PLUS narrow-band filter $F660$. We explore three different methods to extract the H$\alpha$ + [NII] flux from J-PLUS photometric data: a combination of a broad-band and a narrow-band filter ($r'$ and $F660$), two broad-band and a narrow-band one ($r'$, $i'$ and $F660$), and a SED-fitting based method using 8 photometric points. To test these methodologies, we simulated J-PLUS data from a sample of 7511 SDSS spectra with measured H$\alpha$ flux. Based on the same sample, we derive two empirical relations to correct the derived H$\alpha$+[NII] flux from dust extinction and [NII] contamination. We find that the only unbiased method is the SED fitting based one. The combination of two filters underestimates the measurements of the H$\alpha$ + [NII] flux by a 28%, while the three filters method by a 9%. We study the error budget of the SED-fitting based method and find that, in addition to the photometric error, our measurements have a systematic uncertainty of a 4.3%. Several sources contribute to this uncertainty: differences between our measurement procedure and the one used to derive the spectroscopic values, the use of simple stellar populations as templates, and the intrinsic errors of the spectra, which were not taken into account. Apart from that, the empirical corrections for dust extinction and [NII] contamination add an extra uncertainty of 14%. Given the J-PLUS photometric system, the best methodology to extract H$\alpha$ + [NII] flux is the SED-fitting based one. Using this method, we are able to recover reliable H$\alpha$ fluxes for thousands of nearby galaxies in a robust and homogeneous way.Comment: 11 pages, 14 figures. Minor changes to match the published versio

ncRNA orthologies in the vertebrate lineage.

Annotation of orthologous and paralogous genes is necessary for many aspects of evolutionary analysis. Methods to infer these homology relationships have traditionally focused on protein-coding genes and evolutionary models used by these methods normally assume the positions in the protein evolve independently. However, as our appreciation for the roles of non-coding RNA genes has increased, consistently annotated sets of orthologous and paralogous ncRNA genes are increasingly needed. At the same time, methods such as PHASE or RAxML have implemented substitution models that consider pairs of sites to enable proper modelling of the loops and other features of RNA secondary structure. Here, we present a comprehensive analysis pipeline for the automatic detection of orthologues and paralogues for ncRNA genes. We focus on gene families represented in Rfam and for which a specific covariance model is provided. For each family ncRNA genes found in all Ensembl species are aligned using Infernal, and several trees are built using different substitution models. In parallel, a genomic alignment that includes the ncRNA genes and their flanking sequence regions is built with PRANK. This alignment is used to create two additional phylogenetic trees using the neighbour-joining (NJ) and maximum-likelihood (ML) methods. The trees arising from both the ncRNA and genomic alignments are merged using TreeBeST, which reconciles them with the species tree in order to identify speciation and duplication events. The final tree is used to infer the orthologues and paralogues following Fitch's definition. We also determine gene gain and loss events for each family using CAFE. All data are accessible through the Ensembl Comparative Genomics ('Compara') API, on our FTP site and are fully integrated in the Ensembl genome browser, where they can be accessed in a user-friendly manner.Database URL: http://www.ensembl.org

Influence of continuous and intermittent water regimes on methane emissions from irrigated rice crops in southeast Brazil.

Irrigated rice crops in Brazil correspond to 35% of the total rice area and the preferred irrigation method is continuous flooding. In this study two water management systems ? continuous and intermittent flooding ? were monitored for the purpose of comparing their methane emission potential. Intermittent flooding was characterized by alternating flooding and draining periods during the rice cropping cycle. In both systems nitrogen fertilizers were applied twice (NPK and urea alone). Methane fluxes were determined using a closed chamber method (boxes 60x60 cm), and analyzed by GC-FID. Samples were collected from 4 boxes (2 boxes for each water management system) twice a week, for a weekly total of 46 samples. Measurements of air and soil temperature, soil and water pH, redox potential, plant biomass were done. After 104 days the accumulated fluxes resulted in a mean methane emission of 21.1 9 g CH4 m-2 d-1 under the continuous flooding regime and 23.9 g CH4 m-2 d-1 under the intermittent flooding regime. After the two N fertilizer application, methane fluxes decreased in all boxes, with a more marked reduction occurring in the intermittent regime stands. Total accumulated methane emissions, as well as grain yield, were evaluated for each water management system at the end of the cropping season, showing 13% higher productivity in the field under intermittent flooding system. The objectives of the present study were (i) to improve methane emission estimates and compare the emission potential of traditionally managed crop systems and (ii) to study the possibility of minimizing water consumption and the influence on the methane fluxes without deleterious effects to the crop

Emissão de N2O de um latossolo vermelho sob consórcio sorgo e braquiária no Cerrado.

O objetivo desse trabalho foi avaliar os fluxos de N2O em Latossolo Vermelho sob consórcio de sorgo (Sorghum bicolor) e braquiária piatã (Brachiaria brizantha cv. Piatã) em sucessão à soja em área de sequeiro, correlacionandoos com dados de precipitação, temperatura e umidade do solo. O experimento foi conduzido na Embrapa Cerrados em blocos ao acaso com duas repetições. Os tratamentos foram constituídos por: sistema de lavoura contínua sob plantio direto (1), lavoura contínua sob plantio convencional (2) e sistema de integração lavoura pecuária (3), tendo o Cerrado Nativo como referência. O plantio de sorgo foi realizado em consórcio com Piatã, após a colheita da soja. As amostras de N2O foram coletadas no período de 21/03/2014 a 04/07/2014 em câmaras do tipo estática fechada e analisadas em cromatógrafo gasoso. O fluxo de N2O foi maior logo após o plantio, a adubação de cobertura e precipitação para todos os sistemas de manejo avaliados. Os maiores fluxos foram verificados no sistema 2 com valores médios de 90,55 μg m-2 h-1, enquanto que nos sistemas 1 e 3 os fluxos médios foram 46,49 e 45,29 μg m-2 h-1, respectivamente

Postictal serotonin levels are associated with peri-ictal apnea.

ObjectiveTo determine the relationship between serum serotonin (5-HT) levels, ictal central apnea (ICA), and postconvulsive central apnea (PCCA) in epileptic seizures.MethodsWe prospectively evaluated video EEG, plethysmography, capillary oxygen saturation (SpO2), and ECG for 49 patients (49 seizures) enrolled in a multicenter study of sudden unexpected death in epilepsy (SUDEP). Postictal and interictal venous blood samples were collected after a clinical seizure for measurement of serum 5-HT levels. Seizures were classified according to the International League Against Epilepsy 2017 seizure classification. We analyzed seizures with and without ICA (n = 49) and generalized convulsive seizures (GCS) with and without PCCA (n = 27).ResultsPostictal serum 5-HT levels were increased over interictal levels for seizures without ICA (p = 0.01), compared to seizures with ICA (p = 0.21). In patients with GCS without PCCA, serum 5-HT levels were increased postictally compared to interictal levels (p < 0.001), but not in patients with seizures with PCCA (p = 0.22). Postictal minus interictal 5-HT levels also differed between the 2 groups with and without PCCA (p = 0.03). Increased heart rate was accompanied by increased serum 5-HT levels (postictal minus interictal) after seizures without PCCA (p = 0.03) compared to those with PCCA (p = 0.42).ConclusionsThe data suggest that significant seizure-related increases in serum 5-HT levels are associated with a lower incidence of seizure-related breathing dysfunction, and may reflect physiologic changes that confer a protective effect against deleterious phenomena leading to SUDEP. These results need to be confirmed with a larger sample size study

Obtenção de marcadores moleculares por meio de PCR-RFLP de genes relacionados com qualidade em café.

A qualidade de bebida do café é fator fundamental para sua comercialização, pois agrega valor ao produto, garantindo maior competitividade e melhores preços no mercado. A composição química do café é um dos fatores que determinam a qualidade da bebida. Seu sabor e seu aroma são resultantes da presença combinada de vários constituintes, dentre os quais os ácidos clorogênicos, os diterpenos e os açúcares. O objetivo deste trabalho foi buscar polimorfismos a partir de PCR-RFLP utilizando primers baseados em sequências ESTs de genes relacionados com a qualidade de bebida. Para isso foi utilizado o DNA de uma população F2 formada a partir da autofecundação de um híbrido interespecífico de Coffea arabica e C. canephora. Os resultados revelaram um total de doze marcas polimórficas na população. Dentre essas marcas, quatro foram obtidas através da presença e da ausência da amplificação dos genes. Oito combinações polimórficas foram obtidas através da clivagem do produto de PCR por quatro enzimas de restrição (TaqI, BsuRI, RsaI e HhaI). Com a validação dos polimorfismos encontrados nos amplicons, essas marcas estão sendo utilizadas para trabalhos de mapeamento na população de arabustas com objetivo de identificar QTLs relacionados à concentração de compostos como cafeína, ácidos clorogênicos, diterpenos, açúcares, bem como de proteases

Factors associated with risk behavior in travelers to tropical and subtropical regions

BACKGROUND: Recent decades have seen a rise in population movements and, therefore, the spread of tropical diseases and changes in the epidemiology of global disease patterns. Only 50% of travelers to tropical areas receive pre-travel advice and most of them present risk behaviors for acquiring infections. The aim of this study was to describe the clinical and epidemiological characteristics of travelers and identify factors associated with risk behaviors. METHODS: We made a retrospective, descriptive and analytical study of 772 travelers consulting a tropical medicine clinic in Barcelona in 2010. Data on demographic and clinical variables, travel characteristics and risk behaviors were collected. RESULTS: Among all travelers studied, 65.8% (466/708) received pre-travel advice and 30.7% (209/680) took malaria prophylaxis. At least one risk behavior was reported by 82.6% (587/711) of travelers. People travelling for 1-6 months had a 3-fold higher likelihood of experiencing risk behaviors than people travelling for <1 month (95% CI 1.54-5.81, p=0.001), and those travelling for >6 months had a 13-fold higher likelihood (95% CI 3.11-56.14, p<0.001) compared with the same group. Increasing age was associated with presenting less risk behaviors. CONCLUSIONS: Younger travelers and those making longer trips have a higher number of risk behaviors. Strategies emphasizing advice on risk behavior should focus on these groups

Caracterização morfológica e estimativa da distância genética de acessos de pimenta do banco ativo de germoplasma de Capsicum da Embrapa Clima Temperado.

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