Coincidence between transcriptome analyses on different microarray platforms using a parametric framework

A parametric framework for the analysis of transcriptome data is demonstrated to yield coincident results when applied to data acquired using two different microarray platforms. Discrepancies among transcriptome studies are frequently reported, casting doubt on the reliability of collected data. The inconsistency among observations can be largely attributed to differences among the analytical frameworks employed for data analysis. The existing frameworks normalizes data against a standard determined from the data to be analyzed. In the present study, a parametric framework based on a strict model for normalization is applied to data acquired using an in-house printed chip and GeneChip. The framework is based on a common statistical characteristic of microarray data, and each data is normalized on the basis of a linear relationship with this model. In the proposed framework, the expressional changes observed and genes selected are coincident between platforms, achieving superior universality of data compared to other methods

Search for the decay KL0→3γK_L^0 \rightarrow 3\gamma

We performed a search for the decay $K_L^0 \rightarrow 3\gamma$ with the E391a detector at KEK. In the data accumulated in 2005, no event was observed in the signal region. Based on the assumption of $K_L^0 \rightarrow 3\gamma$ proceeding via parity-violation, we obtained the single event sensitivity to be $(3.23\pm0.14)\times10^{-8}$, and set an upper limit on the branching ratio to be $7.4\times10^{-8}$ at the 90% confidence level. This is a factor of 3.2 improvement compared to the previous results. The results of $K_L^0 \rightarrow 3\gamma$ proceeding via parity-conservation were also presented in this paper

Experimental study of the decay KL0→π0ννˉK_L^0\to\pi^0\nu\bar{\nu}

The first dedicated search for the rare neutral-kaon decay $K_L^0\to\pi^0\nu\bar{\nu}$ has been carried out in the E391a experiment at the KEK 12-GeV proton synchrotron. The final upper limit of 2.6 $\times 10^{-8}$ at the 90% confidence level was set on the branching ratio for the decay.Comment: 23 pages, 27 figures, accepted for publication as a regular article in Physical Review

Reef fish and benthic assemblages of the Trindade and Martin Vaz Island group, southwestern Atlantic

O conjunto insular de Trindade e Martin Vaz (CITMV) está localizado a aproximadamente 1.120 km da costa brasileira. Apesar de sua importância, salientada pela presença de diversas espécies endêmicas de peixes, não existem informações detalhadas sobre as assembléias de peixes e bentos do CITMV. É apresentada aqui a primeira caracterização quantitativa das assembléias de peixes e bentos do CITMV em um gradiente de profundidade entre 5 e 45 m. Informações qualitativas adicionais sobre assembléias recifais entre 45 e 100 m foram obtidas utilizando-se técnicas avançadas de mergulho (TRIMIX) e um veículo de operação remota (VOR). Assim como outras ilhas oceânicas brasileiras, a CITMV possui assembléias depauperadas de peixes e bentos, possivelmente devido ao seu isolamento e pequeno tamanho em comparação ao continente. A profundidade foi o fator que mais afetou a estrutura das assembléias de peixes, com a densidade da maioria das espécies declinando com o aumento da profundidade. Os recifes profundos (>; 45 m) foram caracterizados pela presença de bancos extensivos de rodolitos e recifes rochosos esparsamente cobertos por algas coralináceas incrustantes, corais negros (Cirripathes sp.) e alguns corais massivos e em de forma de placa. Peixes parcialmente ou obrigatoriamente planctívoros (e.g. Cephalopholis furcifer and Clepticus brasiliensis) também dominaram em recifes profundos. Características similares foram registradas para recifes mesofóticos ao longo do Atlântico Ocidental. Evidências de sobrepesca (obtidas aqui e em outros estudos recentes), a presença de quatro espécies de peixes endêmicas e com distribuição restrita, e o aumento no número de espécies novas ainda não descritas, indicam que a adoção de medidas de conservação baseadas no princípio da precaução é urgentemente necessária para garantir a manutenção dos ecossistemas frágeis e únicos do CITMV.The Trindade and Martin Vaz island group (TMVIG) is located at about 1,120 km off the Brazilian coast. Despite its importance, highlighted by the presence of several endemic fish species, the TMVIG lacks detailed information on the structure of fish and benthic assemblages. Presented here is the first quantitative assessment of reef fish and benthic assemblages of the TMVIG in a depth gradient ranging from 5 to 45 m. Additional qualitative information on reef assemblages between 45 and 100 m was obtained using advanced gas diving techniques (TRIMIX) and a remotely operated vehicle (ROV). Similarly to other Brazilian oceanic islands, the TMVIG possesses depauperated fish and benthic assemblages, possibly due to its isolation and small size in comparison to the mainland. Depth was the most important factor affecting the structure of fish assemblages, with the density of most fish species declining with depth. Deep reefs (>; 45 m) were characterized by the presence of extensive rhodolith beds and rocky reefs sparsely covered with crustose coralline algae, black coral (Cirripathes sp.) and a few massive or plate-like reef corals. Part-time or obligatory planktivorous fishes (e.g. Cephalopholis furcifer and Clepticus brasiliensis) also dominated deep reefs. Similar characteristics were recorded in mesophotic reef ecosystems across the Western Atlantic. Evidence of overfishing (obtained here and in other recent studies), the presence of four endemic and restricted range fish species, as well as the increase in number of new (and still undescribed) endemic taxa, indicates that the adoption of precautionary conservation measures are urgently needed in order to maintain the fragile and unique ecosystems of the TMVIG

Deletion of parasite immune modulatory sequences combined with immune activating signals enhances vaccine mediated protection against filarial nematodes

<p>Background: Filarial nematodes are tissue-dwelling parasites that can be killed by Th2-driven immune effectors, but that have evolved to withstand immune attack and establish chronic infections by suppressing host immunity. As a consequence, the efficacy of a vaccine against filariasis may depend on its capacity to counter parasite-driven immunomodulation.</p> <p>Methodology and Principal Findings: We immunised mice with DNA plasmids expressing functionally-inactivated forms of two immunomodulatory molecules expressed by the filarial parasite Litomosoides sigmodontis: the abundant larval transcript-1 (LsALT) and cysteine protease inhibitor-2 (LsCPI). The mutant proteins enhanced antibody and cytokine responses to live parasite challenge, and led to more leukocyte recruitment to the site of infection than their native forms. The immune response was further enhanced when the antigens were targeted to dendritic cells using a single chain Fv-αDEC205 antibody and co-administered with plasmids that enhance T helper 2 immunity (IL-4) and antigen-presenting cell recruitment (Flt3L, MIP-1α). Mice immunised simultaneously against the mutated forms of LsALT and LsCPI eliminated adult parasites faster and consistently reduced peripheral microfilaraemia. A multifactorial analysis of the immune response revealed that protection was strongly correlated with the production of parasite-specific IgG1 and with the numbers of leukocytes present at the site of infection.</p> <p>Conclusions: We have developed a successful strategy for DNA vaccination against a nematode infection that specifically targets parasite-driven immunosuppression while simultaneously enhancing Th2 immune responses and parasite antigen presentation by dendritic cells.</p&gt

Shower development of particles with momenta from 15 GeV to 150 GeV in the CALICE scintillator-tungsten hadronic calorimeter

We present a study of showers initiated by electrons, pions, kaons, and protons with momenta from 15 GeV to 150 GeV in the highly granular CALICE scintillator-tungsten analogue hadronic calorimeter. The data were recorded at the CERN Super Proton Synchrotron in 2011. The analysis includes measurements of the calorimeter response to each particle type as well as measurements of the energy resolution and studies of the longitudinal and radial shower development for selected particles. The results are compared to Geant4 simulations (version 9.6.p02). In the study of the energy resolution we include previously published data with beam momenta from 1 GeV to 10 GeV recorded at the CERN Proton Synchrotron in 2010.Comment: 35 pages, 21 figures, 8 table

Hadron shower decomposition in the highly granular CALICE analogue hadron calorimeter

The spatial development of hadronic showers in the CALICE scintillator-steel analogue hadron calorimeter is studied using test beam data collected at CERN and FNAL for single positive pions and protons with initial momenta in the range from 10 to 80 GeV/c. Both longitudinal and radial development of hadron showers are parametrised with two-component functions. The parametrisation is fit to test beam data and simulations using the QGSP_BERT and FTFP_BERT physics lists from Geant4 version 9.6. The parameters extracted from data and simulated samples are compared for the two types of hadrons. The response to pions and the ratio of the non-electromagnetic to the electromagnetic calorimeter response, h/e, are estimated using the extrapolation and decomposition of the longitudinal profiles.Comment: 38 pages, 19 figures, 5 tables; author list changed; submitted to JINS

Measurement and comparison of individual external doses of high-school students living in Japan, France, Poland and Belarus -- the "D-shuttle" project --

Twelve high schools in Japan (of which six are in Fukushima Prefecture), four in France, eight in Poland and two in Belarus cooperated in the measurement and comparison of individual external doses in 2014. In total 216 high-school students and teachers participated in the study. Each participant wore an electronic personal dosimeter "D-shuttle" for two weeks, and kept a journal of his/her whereabouts and activities. The distributions of annual external doses estimated for each region overlap with each other, demonstrating that the personal external individual doses in locations where residence is currently allowed in Fukushima Prefecture and in Belarus are well within the range of estimated annual doses due to the background radiation level of other regions/countries