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The GATK joint genotyping workflow is appropriate for calling variants in RNA-seq experiments

Journal of Animal Science and Biotechnology 2019年第3期10卷 811-816页

作者： jean-simon brouard Flavio Schenkel Andrew Marete Nathalie Bissonnette Sherbrooke Research and Development Centre Agriculture and Agri-Food CanadaSherbrookeQC J1M 0C8Canada Center of Genetic Improvement of Livestock University of GuelphGuelphON N1G 2W1Canada

The Genome Analysis Toolkit(GATK) is a popular set of programs for discovering and genotyping variants from next-generation sequencing *** current GATK recommendation for RNA sequencing(RNA-seq) is to perform variant calling from individual samples,with the drawback that only variable positions are *** 3.0 and above of GATK offer the possibility of calling DNA variants on cohorts of samples using the HaplotypeCaller algorithm in Genomic Variant Call Format(GVCF) *** this approach,variants are called individually on each sample,generating one GVCF file per sample that lists genotype likelihoods and their genome *** a second step,variants are called from the GVCF files through a joint genotyping *** strategy is more flexible and reduces computational challenges in comparison to the traditional joint discovery *** a GVCF workflow for mining SNP in RNA-seq data provides substantial advantages,including reporting homozygous genotypes for the reference allele as well as missing *** advantage of RNA-seq data derived from primary macrophages isolated from 50 cows,the GATK joint genotyping method for calling variants on RNA-seq data was validated by comparing this approach to a so-called "per-sample" *** addition,pair-wise comparisons of the two methods were performed to evaluate their respective sensitivity,precision and accuracy using DNA genotypes from a companion study including the same 50 cows genotyped using either genotyping-by-sequencing or with the Bovine SNP50 Beadchip(imputed to the Bovine high density).Results indicate that both approaches are very close in their capacity of detecting reference variants and that the joint genotyping method is more sensitive than the per-sample *** that the joint genotyping method is more flexible and technically easier,we recommend this approach for variant calling in RNA-seq experiments.

关键词： GATK GVCF Joint genotyping RNA-seq SNP

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A reinforcement learning approach for thermostat setpoint preference learning

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Building Simulation 2024年第1期17卷 131-146页

作者： Hussein Elehwany Mohamed Ouf Burak Gunay Nunzio Cotrufo jean-simon Venne Department of Environmental Engineering Carleton UniversityOttawaCanada Departmentof Building Civiland Environmental EngineeringConcordia UniversityMontrealCanada BrainBox Al Inc. MontrealCanada

Occupant-centric controls(OcC)is an indoor climate control approach whereby occupant feedback is used in the sequence of operation of building energy *** OcC has been used in a wide range of building applications,an OcC category that has received considerable research interest is learning occupants'thermal preferences through their thermostat interactions and adapting temperature setpoints *** recent studies used reinforcement learning(RL)as an agent for OcC to optimize energy use and occupant *** studies depended on predicted mean vote(PMV)models or constant comfort ranges to represent comfort,while only few of them used thermostat *** paper addresses this gap by introducing a new off-policy reinforcement learning(RL)algorithm that imitates the occupant behaviour by utilizing unsolicited occupant thermostat *** algorithm is tested with a number of synthetically generated occupant behaviour models implemented via the Python APl of *** simulation results indicate that the RL algorithm could rapidly learn preferences for all tested occupant behaviour scenarios with minimal exploration *** substantial energy savings were observed with most occupant scenarios,the impact on the energy savings varied depending on occupants'preferences and thermostat use behaviour stochasticity.

关键词： reinforcement learning preference learning occupant-centric controls smart thermostats off-policy learning

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The GATK joint genotyping workflow is appropriate for calling variants in RNA-seq experiments.

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畜牧与生物技术杂志(英文版) 2019年第3期

作者： jean-simon brouard Flavio Schenkel Andrew Marete Nathalie Bissonnette Sherbrooke Research and Development Centre，Agriculture and Agri-Food Canada Center of Genetic Improvement of Livestock，University of Guelph

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Birds’Diversity in Kalfou Forest Reserve and Its Peripheral Zone, Far North, Cameroon

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Open Journal of Animal Sciences 2024年第2期14卷 137-155页

作者： Ghislain Noé Kougoum Piebeng simon A. Tamungang Daksala Wansang jean Tonleu Laurentine Soufo Muhammad Bilal Awa II Taku Alexis Teguia Department of Biological Sciences Faculty of Science University of Maroua Maroua Cameroon Department of Animal Biology Faculty of Science University of Dschang Dschang Cameroon Department of Forestry and Wildlife Technology College of Technology University of Bamenda Bamenda Cameroon Department of Environmental Sciences Higher Polytechnical Training School University of Maroua Maroua Cameroon Department of Biology Virtual University of Pakistan Rawalpindi Campus Punjab Pakistan Department of Animal Production Faculty of Agronomy and Agricultural Science University of Dschang Dschang Cameroon

The Far North Region of Cameroon is home to a great diversity of bird species, which unfortunately remains very little explored. This work was initiated to establish an inventory of birds and the factors affecting their diversity and distribution for sustainable management in the Kalfou Forest Reserve (KFR) and its periphery. Two methods were used for sampling, linear strip transects from which direct counts and indirect observations were made and the mist netting to complement the first. In total, 2525 birds were observed, including 149 species, belonging to 20 orders and 55 families. Accipitridae had the greatest number of species (11). The species richness was greater in the KFR (117 species) compared to the periphery (95 species). The specific richness was higher in wooded savannah compared to other habitats. Shannon index was significantly higher in the KFR (3.99) compared to that obtained in the periphery (3.80). The value of the Simpson index was higher on the outskirts of the KFR than on the periphery. The indices of species diversity were greater in the wooded savannah compared to other vegetation types. The seasons had no influence on bird diversity. Among the human activities encountered, the pressure indices were more important for grazing (7.3 contacts/km). Human activities have resulted in a significant decrease in specific richness. Six endangered species were encountered, four belonging to the Accipitridae family. The greater bird diversity in the reserve compared to the periphery shows that protected areas are a long-term solution for biodiversity conservation.

关键词： Bird Diversity Habitats Bird Species Human Activities Conservation Kalfou

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Mobility of Major and Trace Elements during the Bauxitization Processes in Ngaoundal Area (Adamawa Cameroon): Implication on Mining Perspectives

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Open Journal of Geology 2024年第1期14卷 81-100页

作者： André Sini Harouna Boukari Ondoa Augustin Désiré Balla Djetenbe Beral Salomon Wangmené Awé simon Djakba Basga jean Pierre Nguetnkam Department of Mining Engineering School of Geology and Mining Engineering University of Ngaoundere Ngaoundere Cameroon Department of Mining Engineering and Environment School of Mining Industry and Geology University of Abdou-Moumouni Niamey Niger Department of Earth Sciences Faculty of Science University of Ngaoundere Ngaoundere Cameroon Department of Mining Engineering Saint Jerome Polytechnic Saint Jerome Catholic University Institute of Douala Douala Cameroon Institute of Agricultural Research for Development (IRAD) Garoua Cameroon

This study was focused to assess major and trace elements in bauxitic duricrusts from Ngaoundal and its surroundings in order to establish their mining interest. To this end, fieldworks, mineralogical and geochemical analyses were carried out. Four facies of duricrust were identified and characterized from the summit to the top of the slope of the Ngaoundal mountain: scoriaceous, pisolitic, nodular and massive. Mineralogical and geochemical analyses performed on 16 samples, revealed a significant concentration of Al2O3 mainly in the scoriaceous facies (over 45% in grade), moderate in Fe2O3 (averaging 23.69%) and SiO2 (averaging 21.7%). Trace elements were generally low, excluding Cr (421 ppm on average), Zr (327 ppm on average and V (213 ppm on average). In addition, the limited quantities of alkalis (Na2O, K2O) and alkaline earths metals (MgO, CaO) coupled with the very high values of Chemical Index of Alteration (CIA) and Mineralogical Index of Alteration (MIA), (more than 99%) attest to the intense weathering of the studied materials. Allitization and monosiallitization constituted the crystallochemical phenomena that have led to the development of bauxitic minerals. More than 90% of gibbsite in scoriaceous facies, 52.21% - 76.01% of kaolinite in pisolitic facies and more than 40% of hematite in nodular facies were quantified. The relationships between the constitutive components indicated their interdependency during the bauxitization phenomenon. The mineralogical and geochemical properties highlighted the mining interest of the studied duricrusts to be valorized.

关键词： Duricrust Bauxitization Phenomenon Mineralogical and Geochemical Characterization Major and Trace Elements Mining Potential

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Modeling of 3-D Losses and Deviations in a Throughflow Analysis Tool

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Journal of Thermal Science 2007年第3期16卷 208-214页

作者： jean-Fran■ois simon OlivierLéonard Techspace Aero-Aerodynamic Group University

This contribution is dedicated to the modeling of the end-wall flows in a throughflow model for turbomachinery applications. The throughflow model is based on the Euler or Navier-Stokes equations solved by a Finite-Volume technique. Two approaches are presented for the end-wall modeling. The first one is based on an inviscid formulation with dedicated 3-D distributions of loss coefficient and deviation in the end-wall regions. The second approach is directly based on a viscous formulation with no-slip boundary condition along the annular end-walls and blade force modification in the region close to the end-walls. The throughflow results are compared to a series of 3-D Navier-Stokes calculations averaged in the circumferential direction. These 3-D calculations were performed on the three rotors of a low pressure axial compressor, for a series of tip clearance values.

关键词： throughflow losses deviations axial compressors

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Psychological distress during the COVID-19 pandemic in France:a national assessment of at-risk populations

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General Psychiatry 2020年第6期33卷 400-405页

作者： Benjamin Chaix Guillaume Delamon Arthur Guillemasse Benoit brouard jean-Emmanuel Bibault ENT Department Hopital Gui de ChauliacMontpellierFrance University Montpellier 1 MontpellierFrance Hopital Pite-Salpetriere WefightBrain&Spine InstituteParisFrance Department of Radiation Oncology Hopital Europeen Georges Pompidou CancerologieParisFrance

Background Lockdowns were implemented to limit the spread of *** distress(PD)and post-traumatic stress disorder have been reported after traumatic events,but the specific effect of the pandemic is not well *** The aim of this study was to assess PD in France,a country where C0VID-19 had such a dramatic impact that it required a country-wide *** We recruited patients in four groups of chatbot users followed for breast cancer,asthma,depression and *** used the Psychological Distress Inventory(PDI),a validated scale to measure PD during traumatic events,and correlated PD risk with patients*characteristics in order to better identify the ones who were the most at *** The study included 1771 participants.91.25%(n=1616)were female with a mean age of 32.8(13.71)years and 7.96%(n=141)were male with a mean age of 28.0(8.14)*** total,38.06%(n=674)of the respondents had psychological distress(PDI>14).An analysis of variance showed that unemployment and depression were significantly associated with a higher PDI *** using their smartphones or computers for more than 1 hour a day also had a higher PDI score(p=0.026).Conclusion Prevalence of PD in at-risk patients is *** patients are also at an increased risk of developing post-traumatic stress *** steps should be implemented to monitor and prevent PD through dedicated mental health policies if we want to limit the public health impact of COVID-19 in time.

关键词： distress steps limit

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A Comparison of Hydrothermal Aging, SO₂ and Propene Poisoning Effects on NH₃-SCR over Cu-ZSM-5 and Cu-SAPO-34 Catalysts

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Journal of Materials Science and Chemical Engineering 2024年第5期12卷 10-28页

作者： Kouadio Brou Albert Koffi Konan Martin Zran Van Eric-simon Horo Kone Unité de Formation et de Recherche des Sciences et de Technologies (UFR ST) Universit&#233 Alassane Ouattara Bouak&#233 C&#244te d&#8217Ivoire Unité de Formation et de Recherche Environnement (UFR E) Universit&#233 Jean Lorougnon Gu&#233d&#233 Daloa C&#244te d&#8217Ivoire Unité de Formation et de Recherche des Sciences des Structures de la Mati&#232re et de Technologie (UFR SSMT) Abidjan C&#244te d&#8217Ivoire

This study was aimed to investigate the effects of hydrothermal aging, propene and SO2 poisoning on the ammonia-selective catalytic reduction (NH3-SCR) performance of both Cu-SAPO-34 and Cu-ZSM-5. The catalytic activities of fresh, aged and poisoned samples were tested in ammonia-selective catalytic reduction (NH3-SCR) of NOx conditions. The XRD, TG and N2-desorption results showed that the structures of the Cu-SAPO-34 and Cu-ZSM-5 remained intact after 750˚C hydrothermally aged, SO2 and propene poisoned. After hydrothermal aging at 750˚C for 12 h, the NO reduction performance of Cu-ZSM-5 was significantly reduced at lower temperatures, while that of Cu-SAPO-34 was less affected. Moreover, Cu-SAPO-34 catalyst showed high NO conversion with SO2 or propene compared to Cu-ZSM-5. However, Cu-ZSM-5 showed a larger drop in catalytic activity with SO2 or propene compared to Cu-SAPO-34 catalyst. The H2-TPR results showed that Cu2 ions could be reduced to Cu and Cu0 for Cu-ZSM-5, while no significant transformation of copper species was observed for Cu-SAPO-34. Meanwhile, the UV-vis DRS results showed that CuO species were formed in Cu-ZSM-5, while little changes were observed for the Cu-SAPO-34. Cu-SAPO-34 showed high sulfur and hydrocarbon poison resistance compared to Cu-ZSM-5. In summary, Cu-SAPO-34 with small-pore zeolite showed higher hydrothermal stability and better hydrocarbon and sulfur poison resistant than Cu-ZSM-5 with medium-pore.

关键词： Hydrothermal Aging Propene and SO2Poisoning Ammonia-Selective Catalytic Reduction(NH3-SCR) Cu-SAPO-34 Cu-ZSM-5

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Differences in egg hatching time between cyclical and obligate parthenogenetic lineages of aphids

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Insect Science 2019年第1期26卷 135-141页

作者： Charles-Antoine Dedryver Joel Bonhomme jean-Francois Le Gallic jean-Christophe simon Unite Mixte de Recherche IGEPP 1349 INRAIAgrocampus OuestlUniversite Rennes 1Le Rheu cedexFrance

Many aphid species exhibit a variation in reproductive mode which is influenced by winter climate regimes,with cyclical parthenogenetic (CP)lines dominating in cold winter areas (because they produce cold-resistant eggs)and obligate parthenogenetic (OP) ones in mild winter regions (because of their parthenogenetic overwintering).Genetic studies on several aphid species have shown that the OP trait can be transmitted during sexual events involving the 2 types of *** genetic system could be considered as a local safeguarding mechanism for OP alleles in case severe frost would have killed all parthenogenetically overwintering ***,this strategy would only be efficient in restoring local polymorphism in breeding systems if the newly hatched OP recombinants remain competitive over their CP *** this study we compared egg hatching sequences of CP and OP F1 clones from several crosses obtained for 2 cereal aphid species,Sitobion avenae (constant 5℃,8 h of light)and Rhopalosiphum padi (winter outdoor conditions).For ***,we obtained F1 offspring from 6 crosses, involving 4 clones while in *** F1 were obtained from 11 crosses involving 14 clones. We showed that in both species proportions of OP clones were higher in the first half of the progeny relative to the second *** addition,F1 OP clones hatched in the mean about a week earlier than their CP sibs,which gives them a demographic advantage at the start of the growth *** then discussed the consequences of this fitness advantage for the maintenance and spread of the OP trait in aphid populations.

关键词： asexuality diapauses genetic variation insects overwintering strategies reproductive mode

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The promises and challenges of research on plant-insect-microbe interactions

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Insect Science 2017年第6期24卷 904-909页

作者： jean-Christophe simon Arjen Biere Akiko Sugio UMR 1349 Institut de Genetique Environnement et Protection des Plantes INRA Agrocampus Ouest Universite Rennes 1 Domaine de la Motte Le Rheu Cedex France Department of Terrestrial Ecology Netherlands Institute of Ecology NIOO-KNA W Wageningen the Netherlands

Ecological interactions are of paramount importance for the functioning and health of ecosystems. Phytophagous insects are part of complex ecological networks involving abiotic factors, host plants, natural enemies, and benefi- cial organisms （McLean et al., 2016）. Insects and plants are also associated durably or transitorily with a wealth of microbes including pathogens, commensals and beneficial partners from a vast array of microbial taxa （Sugio et al., 2015）. In recent years, evidence has accumulated that microbes directly or indirectly influence plant-insect interactions at individual, population and community levels.

关键词： SYMBIONTS FUNGI

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