Event reconstruction for KM3NeT/ORCA using convolutional neural networks

The KM3NeT research infrastructure is currently under construction at two locations in the Mediterranean Sea. The KM3NeT/ORCA water-Cherenkov neutrino de tector off the French coast will instrument several megatons of seawater with photosensors. Its main objective is the determination of the neutrino mass ordering. This work aims at demonstrating the general applicability of deep convolutional neural networks to neutrino telescopes, using simulated datasets for the KM3NeT/ORCA detector as an example. To this end, the networks are employed to achieve reconstruction and classification tasks that constitute an alternative to the analysis pipeline presented for KM3NeT/ORCA in the KM3NeT Letter of Intent. They are used to infer event reconstruction estimates for the energy, the direction, and the interaction point of incident neutrinos. The spatial distribution of Cherenkov light generated by charged particles induced in neutrino interactions is classified as shower-or track-like, and the main background processes associated with the detection of atmospheric neutrinos are recognized. Performance comparisons to machine-learning classification and maximum-likelihood reconstruction algorithms previously developed for KM3NeT/ORCA are provided. It is shown that this application of deep convolutional neural networks to simulated datasets for a large-volume neutrino telescope yields competitive reconstruction results and performance improvements with respect to classical approaches

Event reconstruction for KM3NeT/ORCA using convolutional neural networks

The KM3NeT research infrastructure is currently under construction at two locations in the Mediterranean Sea. The KM3NeT/ORCA water-Cherenkov neutrino detector off the French coast will instrument several megatons of seawater with photosensors. Its main objective is the determination of the neutrino mass ordering. This work aims at demonstrating the general applicability of deep convolutional neural networks to neutrino telescopes, using simulated datasets for the KM3NeT/ORCA detector as an example. To this end, the networks are employed to achieve reconstruction and classification tasks that constitute an alternative to the analysis pipeline presented for KM3NeT/ORCA in the KM3NeT Letter of Intent. They are used to infer event reconstruction estimates for the energy, the direction, and the interaction point of incident neutrinos. The spatial distribution of Cherenkov light generated by charged particles induced in neutrino interactions is classified as shower- or track-like, and the main background processes associated with the detection of atmospheric neutrinos are recognized. Performance comparisons to machine-learning classification and maximum-likelihood reconstruction algorithms previously developed for KM3NeT/ORCA are provided. It is shown that this application of deep convolutional neural networks to simulated datasets for a large-volume neutrino telescope yields competitive reconstruction results and performance improvements with respect to classical approaches

Discutindo a educação ambiental no cotidiano escolar: desenvolvimento de projetos na escola formação inicial e continuada de professores

A presente pesquisa buscou discutir como a Educação Ambiental (EA) vem sendo trabalhada, no Ensino Fundamental e como os docentes desta escola compreendem e vem inserindo a EA no cotidiano escolar., em uma escola estadual do município de Tangará da Serra/MT, Brasil. Para tanto, realizou-se entrevistas com os professores que fazem parte de um projeto interdisciplinar de EA na escola pesquisada. Verificou-se que o projeto da escola não vem conseguindo alcançar os objetivos propostos por: desconhecimento do mesmo, pelos professores; formação deficiente dos professores, não entendimento da EA como processo de ensino-aprendizagem, falta de recursos didáticos, planejamento inadequado das atividades. A partir dessa constatação, procurou-se debater a impossibilidade de tratar do tema fora do trabalho interdisciplinar, bem como, e principalmente, a importância de um estudo mais aprofundado de EA, vinculando teoria e prática, tanto na formação docente, como em projetos escolares, a fim de fugir do tradicional vínculo “EA e ecologia, lixo e horta”.Facultad de Humanidades y Ciencias de la Educació

Il genoma delle Tuberaceae : analisi funzionale di sequenze espresse durante la morfogenesi di Tuber borchii Vittad.

Texte intégral accessible uniquement aux membres de l'Université de LorraineThe ripening of a truffle fruitbody leads to drastic changes in its size, morphology, cellular organization and aroma production. To explore the gene expression in Tuber borchii during fruitbody development, cDNA libraries from fruitbodies at two stages of maturation were constructed, 3000 cDNA clones were isolated, 2043 were used for constructing cDNA arrays and 641 ESTs of high quality were produced. The results demonstrate that 1) the molecular machinery which allows the truffle ripening mostly consists of orphan genes; 2) truffles have an intense metabolism where pathways belonging to the primary and secondary metabolism are active; 3) some stress-related genes can be identified as markers for fruitbody formation. Furthermore the expression pattern of a cDNA sequence, isolated from ripe fruitbody, showing a good similarity to a Neurospora crassa blue-light inducible gene, was studied using Real-Time RT-PCR assay. The data obtained suggest a light-dependent response in T. borchii.La formation de l'ascocarpe des truffes conduit à des modifications de leur taille, de l'organisation cellulaire et de la production des arômes. La réalisation de deux banques d'ADNc à partir de fructifications à deux stades de maturation différent a permis la production de 2043 clones d'ADNc et de 641 ESTs. La comparaison de l'expression génique sur filtre d'ADNc dans le mycélium et dans différents stades de maturation de l'ascocarpe montre que : 1) la majorité des gènes régulés lors de la formation de l'ascocarpe ont une fonction inconnue ; 2) un certain nombre de transcrits codent pour des enzymes impliquées dans les voies du métabolisme primaire et secondaire ; 3) des gènes impliqués dans la résistance aux stress sont les plus stimulés. Enfin, la caractérisation d'un EST de T. borchii présentant une similarité avec le gène bli-3 de Neurospora crassa suggère que la truffe perçoit la lumière

Le génome des Tuberaceae (analyse fonctionnelle des séquences exprimées durant la morphogénèse de Tuber borchii Vittad.)

La formation de l'ascocarpe des truffes conduit à des modifications de leur taille, de l'organisation cellulaire et de la production des arômes. La réalisation de deux banques d'ADNc à partir de fructifications à deux stades de maturation différent a permis la production de 2043 clones d'ADNc et de 641 ESTs. La comparaison de l'expression génique sur filtre d'ADNc dans le mycélium et dans différents stades de maturation de l'ascocarpe montre que : 1) la majorité des gènes régulés lors de la formation de l'ascocarpe ont une fonction inconnue ; 2) un certain nombre de transcrits codent pour des enzymes impliquées dans les voies du métabolisme primaire et secondaire ; 3) des gènes impliqués dans la résistance aux stress sont les plus stimulés. Enfin, la caractérisation d'un EST de T. borchii présentant une similarité avec le gène bli-3 de Neurospora crassa suggère que la truffe perçoit la lumière.The ripening of a truffle fruitbody leads to drastic changes in its size, morphology, cellular organization and aroma production. To explore the gene expression in Tuber borchii during fruitbody development, cDNA libraries from fruitbodies at two stages of maturation were constructed, 3000 cDNA clones were isolated, 2043 were used for constructing cDNA arrays and 641 ESTs of high quality were produced. The results demonstrate that 1) the molecular machinery which allows the truffle ripening mostly consists of orphan genes; 2) truffles have an intense metabolism where pathways belonging to the primary and secondary metabolism are active; 3) some stress-related genes can be identified as markers for fruitbody formation. Furthermore the expression pattern of a cDNA sequence, isolated from ripe fruitbody, showing a good similarity to a Neurospora crassa blue-light inducible gene, was studied using Real-Time RT-PCR assay. The data obtained suggest a light-dependent response in T. borchii.NANCY1-SCD Sciences & Techniques (545782101) / SudocSudocFranceF

Ruolo del sequenziamento diretto nella tipizzazione di HCV-RNA a fini clinico-epidemiologici

Background/Aims: Genotyping and subtyping of hepatitis C virus (HCV) is epidemiologically and clinically relevant to prognosis and therapeutical management of HCV infection.Aim was to study the feasibility of an “in house” direct sequencing method for the genotyping and subtyping of HCV strains compared with a commercially available genotyping assay (Inno-LiPA,VERSANT® HCV Genotype 2.0 Assay, Bayer). Methods: 74 clinical plasma samples cross-representing HCV genotypes 1 to 5 typed with the line probe assay Inno-LiPA (LiPA) were subjected to a laboratory-developed 5’UTR direct sequencing protocol (5’UTR Seq).A NS5B direct sequencing protocol (NS5B Seq) was apply to 23/74 samples (17 negative by the 5’UTR).Two libraries of 5’UTR and NS5B HCV prototypes were constructed; BioEdit 7.0.0 and ClustalW were used for alignments and phylogenetic analysis. Results: 5’UTR Seq typed 47/74 LiPA positive samples (64%). Concordance between the two assays was 91% (43/47) and 72% (31/43) for HCV genotyping and subtyping, respectively. LiPA and 5’UTR Seq discordant samples were typed by NS5B Seq. NS5B Seq typed 13/17 samples negative with 5’UTR Seq.All genotypes and subtypes detected with NS5B Seq were concordant with LiPA. 5’UTR and NS5B direct sequencing pointed out a wider HCV subtype distribution than LiPA for genotype 1, 2 and 4. By the combination of 5’UTR and NS5B direct sequencing, 81% (60/74) of LiPA positive samples were typed. Conclusion: HCV typing and subtyping with the line probe assay Inno-LiPA is highly recommended for clinical purposes.A more detailed HCV typing for epidemiologic purposes can by achieved by the direct sequencing of a region with a moderate degree of genetic variability such as NS5B. HCV NS5B analysis is more efficient in resolving viral strain genetic variability than direct sequencing of a highly conserved region such as 5’UTR

Real-time PCR per HBV DNA: valutazione del nuovo sistema automatizzato COBAS AMPLIPREP™/COBAS TAQMAN™ HBV

Success of antiviral therapy for chronic hepatitis B is supported by highly sensitive PCR-based assays for Hepatitis B virus (HBV) DNA. Nucleic acid extraction from biologic specimens is technically demanding and reliable PCR results depend it. Performances of the fully automatic system COBAS AmpliPrep™/COBAS TaqMan™ 48 (CAP/CTM) (Roche, Branchburg, NJ) for HBV DNA extraction and real -time PCR quantification were assessed and compared with the end-point PCR COBAS AMPLICOR HBV Monitor (CAHBM, Roche). Analytical evaluation with a proficiency panel showed that CAP/CTM quantitated HBV DNA levels in one single run over a wide dynamic range (7 logs) with a close correlation between expected and observed values (r=0.976, interassay variability below 5%). Clinical evaluation as tested with samples from 92 HBsAg-positive patients, demonstrated excellent correlation with CAHBM (r=0.966, mean difference in quantitation: 0.36 log10 IU/ml). CAP/CTM detected 10% more viremic patients and longer period of residual viremia in those on therapy. In lamivudine (LAM)-resistant patients, reduction of HBV DNA after 12 months of Adefovir (ADF) was higher in the combination (LAM+ADF) schedule than in ADF monotherapy (5.1 vs. 3.5 logs) suggesting a benefit in continuing LAM. In conclusion,CAP/CTM can improve the management of HBV infection, the assessment of antiviral therapy and drug resistance, supporting further insights in the emerging area of drug resistance

Transcript Profiling Reveals Novel Marker Genes Involved in Fruiting Body Formation in Tuber borchii

cDNA arrays were used to explore mechanisms controlling fruiting body development in the truffle Tuber borchii. Differences in gene expression were higher between reproductive and vegetative stage than between two stages of fruiting body maturation. We suggest hypotheses about the importance of various physiological processes during the development of fruiting bodies