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Efficient scar-free knock-ins of several kilobases in plants by engineered CRISPR-Cas endonucleases

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Molecular Plant 2024年第5期17卷 824-837页

作者： Tom Schreiber Anja Prange petra Schafer Thomas Iwen Ramona Grutzner Sylvestre Marillonnet Aurelie Lepage Marie Javelle Wyatt Paul Alain Tissier Department of Cell and Metabolic Biology Leibniz Institute of Plant BiochemistryWeinberg 306120 Halle(Saale)Germany Limagrain Centre de RechercheRoute d’EnnezatCS 9012663720 ChappesFrance

In plants and mammals,non-homologous end-joining is the dominant pathway to repair DNA doublestrand breaks,making it challenging to generate knock-in events.In this study,we identified two groups of exonucleases from the herpes virus and the bacteriophage T7 families that conferred an up to 38-fold increase in homology-directed repair frequencies when fused to Cas9/Cas12a in a tobacco mosaic virus-based transient assay in Nicotiana benthamiana.We achieved precise and scar-free insertion of several kilobases of DNA both in transient and stable transformation systems.In Arabidopsis thaliana,fusion of Cas9 to a herpes virus family exonuclease led to 10-fold higher frequencies of knock-ins in the first generation of transformants.In addition,we demonstrated stable and heritable knock-ins in wheat in 1%of the primary transformants.Taken together,our results open perspectives for the routine production of heritable knock-in and gene replacement events in plants.

关键词： homology-directed repair knockin gene replacement CRISPR-Cas 50 exonuclease plants

Whole miRNome-wide Differential Co-expression of MicroRNAs

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Genomics, Proteomics & Bioinformatics 2012年第5期10卷 285-294页

作者： Cord F.Stehler Andreas Keller petra leidinger Christina Backes Anoop Chandran Jerg Wischhusen Benjamin Meder Eckart Meese Siemens Healthcare Strategy Department of Human Genetics Saarland University Interdisciplinary Center for Clinical Research University of Wuerzburg Department of Internal Medicine III Heidelberg University

Co-regulation of genes has been extensively analyzed, however, rather limited knowledge is available on co-regulations within the miRNome. We investigated differential co-expression of microRNAs （miRNAs） based on miRNome profiles of whole blood from 540 individuals. These include patients suffering from different cancer and non-cancer diseases, and unaffected controls. Using hierarchi- cal clustering, we found 9 significant clusters of co-expressed miRNAs containing 2-36 individual miRNAs. Through analyzing multiple sequencing alignments in the clusters, we found that co-expression of miRNAs is associated with both sequence similarity and genomic co-localization. We calculated correlations for all 371,953 pairs of miRNAs for all 540 individuals and identified 184 pairs of miRNAs with high correlation values. Out of these 184 pairs of miRNAs, 16 pairs （8.7%） were differentially co-expressed in unaffected controls, cancer patients and patients with non-cancer diseases. By computing correlated and anti-correlated miRNA pairs, we constructed a net- work with 184 putative co-regulations as edges and 100 miRNAs as nodes. Thereby, we detected specific clusters of miRNAs with high and low correlation values. Our approach represents the most comprehensive co-regulation analysis based on whole miRNome-wide expression profiling. Our findings further decrypt the interactions of miRNAs in normal and human pathological processes.

关键词： Co-expression Microarray MicroRNA Network analysis

Fetal lung growth predicts the risk for early-life respiratory infections and childhood asthma

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World Journal of Pediatrics 2024年第5期20卷 481-495页

作者： Dimitra E.Zazara Olympia Giannou Steven Schepanski Mirja Pagenkemper Anastasios D.Giannou Maike Pincus Ioannis Belios Stefan Bonn Ania C.Muntau Kurt Hecher Anke Diemert petra Clara Arck Division for Experimental Feto-Maternal Medicine Department of Obstetrics and Fetal MedicineUniversity Medical Center Hamburg-Eppendorf(UKE)Martinistraße 5220251HamburgGermany University Children’s Hospital UKEHamburgGermany Computer Engineering and Informatics Department Polytechnic SchoolUniversity of PatrasPatrasGreece Institute of Developmental Neurophysiology Center for Molecular Neurobiology Hamburg(ZMNH)UKEHamburgGermany Department of Obstetrics and Fetal Medicine UKEHamburgGermany Department of General Visceral and Thoracic SurgeryUKEHamburgGermany Section of Molecular Immunology and Gastroenterology I.Department of MedicineUKEHamburgGermany Pediatrics and Pediatric Pneumology Practice BerlinGermany Institute of Medical Systems Biology ZMNHUKEHamburgGermany Hamburg Center for Translational Immunology UKEHamburgGermany

Background Early-life respiratory infections and asthma are major health burdens during childhood.Markers predicting an increased risk for early-life respiratory diseases are sparse.Here,we identified the predictive value of ultrasound-monitored fetal lung growth for the risk of early-life respiratory infections and asthma.Methods Fetal lung size was serially assessed at standardized time points by transabdominal ultrasound in pregnant women participating in a pregnancy cohort.Correlations between fetal lung growth and respiratory infections in infancy or early-onset asthma at five years were examined.Machine-learning models relying on extreme gradient boosting regressor or classifier algorithms were developed to predict respiratory infection or asthma risk based on fetal lung growth.For model development and validation,study participants were randomly divided into a training and a testing group,respectively,by the employed algorithm.Results Enhanced fetal lung growth throughout pregnancy predicted a lower early-life respiratory infection risk.Male sex was associated with a higher risk for respiratory infections in infancy.Fetal lung growth could also predict the risk of asthma at five years of age.We designed three machine-learning models to predict the risk and number of infections in infancy as well as the risk of early-onset asthma.The models’R2 values were 0.92,0.90 and 0.93,respectively,underscoring a high accuracy and agreement between the actual and predicted values.Influential variables included known risk factors and novel predictors,such as ultrasound-monitored fetal lung growth.Conclusion Sonographic monitoring of fetal lung growth allows to predict the risk for early-life respiratory infections and asthma.

关键词： Asthma Child risk Early-life respiratory infections Prenatal lung development Sexual dimorphism

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高效节能的污泥干化处理方案

流程工业 2024年第1期 28-29页

作者： petra Schlachter Harter干燥技术公司

欧洲一些法律规定从2029年起,在污泥中提取磷的过程中,需要保持污泥的干燥状态。然而,传统的污泥干化方法耗费大量能源,成本过高。利用冷凝干化技术可以帮助污水处理厂降低能耗和成本,奥地利某污水处理协会的试点项目展示了该技术的应... 详细信息

欧洲一些法律规定从2029年起,在污泥中提取磷的过程中,需要保持污泥的干燥状态。然而,传统的污泥干化方法耗费大量能源,成本过高。利用冷凝干化技术可以帮助污水处理厂降低能耗和成本,奥地利某污水处理协会的试点项目展示了该技术的应用方式。

关键词：污水处理厂污泥干化干燥状态干化技术高效节能技术的应用试点项目奥地利

Predicting Amazon customer reviews with deep confidence using deep learning and conformal prediction

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Journal of Management Analytics 2022年第1期9卷 1-16页

作者： Ulf Norinder petra Norinder Department of Computer and Systems Sciences Stockholm UniversityKistaSweden Stockholm Business School Stockholm UniversityStockholmSweden

In this investigation,we have shown that the combination of deep learning,including natural language processing,and conformal prediction results in highly predictive and efficient temporal test set sentiment estimates for 12 categories of Amazon product reviews using either in-category predictions,i.***.the model and the test set are from the same review category or cross-category predictions,i.***.using a model of another review category for predicting the test set.The similar results from in-and cross-category predictions indicate high degree of generalizability across product review categories.The investigation also shows that the combination of deep learning and conformal prediction gracefully handles class imbalances without explicit class balancing measures.

关键词： Amazon customer reviews machine learning conformal prediction deep learning natural language processing temporal test sets

Sharing the post-earthquake situation for emergency response management in transborder areas: The e-Atlas tool

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Journal of Safety Science and Resilience 2022年第1期3卷 72-86页

作者： Stefano Grimaz petra Malisan Andrea Pividori SPRINT-Lab Polytechnic Department of Engineering and ArchitectureUniversity of Udine33100UdineItaly

Usually,the response after a disastrous event requires decision-makers in emergency operative rooms to quickly outline and understand the current post-event situation,for planning and defining strategies for a contextualized response.Moreover,in many cases,disastrous events affect cross-border territories and/or involve multiple orga-nizations in responding to the demand generated by the event.These cases require a harmonized and coordinated response by all the institutions/subjects involved in emergency management.To address this challenge,this pa-per proposes the e-Atlas(emergency atlas)tool for showing and sharing information that embraces a response management perspective to explicitly support decision-makers in managing the criticalities of a post-earthquake situation.The e-Atlas has been designed and tested to:i)acquire sensible information for allowing decision-makers to understand in almost real-time the post-earthquake situational picture,and ii)share the representation of the situational picture among different users,allowing each of them to use it according to its specific require-ments.Applications of the tool are illustrated,to show how it is used in a transborder context in the North-East area of Italy.

关键词： Emergency response management GIS Seismic emergency Decision-making support e-Atlas

Performance and potential of porous carbons derived of electrospun metal-organic frameworks for supercapacitor applications

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Journal of Energy Chemistry 2022年第10期31卷 348-353,I0008页

作者： petra Agota Szilagyi Ana Jorge Sobrido School of Engineering and Materials Science Queen Mary University of LondonLondon E14NSUK

Supercapacitors(SCs) are energy storage devices with the ability to charge and discharge at very high rates. The fast accumulation and release of charges occurs either electrostatically or electrochemically. There are two types of capacitors: electric double layer capacitors(EDLCs) and pseudocapacitors. EDLCs are the most commercially available.

关键词： Electrospinning MOFs Porous carbons Supercapacitors Electrodes Energy storage

Inland-coastal demographic transformations in a karst area:a case study of the surroundings of Krka National Park(Croatia)

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Journal of Mountain Science 2022年第2期19卷 305-321页

作者： TELBISZ Tamas RADELJAK KAUFMANN petra BOCIC Neve Department of Physical Geography Eotvos Lorand UniversityPazmany Peter setany 1/CBudapest 1117Hungary Department of Geography Faculty of ScienceUniversity of ZagrebMarulicev trg 19/IIZagreb 10000Croatia

According to geographic possibilism,environment does not determine socio-economic development.However,the environment sets certain constraints and limitations for development.How do natural settings influence population dynamics?In this study,we examine this question using the example of?ibenik-Knin County,which includes Krka National Park(NP)with a GIS-based statistical approach.The following parameters represent natural factors:elevation,slope,distance from water,and proportion of karst areas.In addition,distance from Krka NP was also added as an independent seminatural factor(despite the fact that it is a social construction).The dependent social parameters are population density for selected historical dates,population change,year of maximum population,natural increase,migration,and age index.The analysis units are the 199 settlements found in the county,and the 20 local administrative units(LAU2).The study period can be divided into five phases:from the first census in 1857 to 1921,there was a slow increase in most settlements;then a relatively constant phase up to 1961(some settlements began shrinking in this period);a slow decrease until 1991;arapid decrease during the next decade;and relative stabilisation to present day.These processes were also accompanied by significant inner and outer migrations.As for the relationships between natural and demographic factors,we found that although the coastal-inland area dichotomy is dominant in the study area,elevation has the highest correlation with most population parameters.However,distance from water is also significantly correlated with population change and migration in certain periods.In the inland areas,there are statistically significant differences between the demographic processes of fully-karstic and partially-karstic areas,while in the coastal zone,the karst effect is overshadowed by other social processes.The impact of Krka NP on the demographic characteristics of the surrounding settlements was statistically not detectable.Our final conclusion is tha

关键词： Geographic possibilism Karst National park Population density Migration

Plant growth and soil microbial community structure of legumes and grasses grown in monoculture or mixture

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Journal of Environmental Sciences 2008年第10期20卷 1231-1237页

作者： MARSCHNER petra Soil and Land System School of Earth and Environmental Sciences The University of AdelaideAdelaide 5005 Australia

A greenhouse pot experiment was conducted to investigate the in?uence of soil moisture content on plant growth and the rhizosphere microbial community structure of four plant species (white clover, alfalfa, sudan grass, tall fescue), grown individually or in a mixture. The soil moisture content was adjusted to 55% or 80% water holding capacity (WHC). The results indicated that the total plant biomass of one pot was lower at 55% WHC. At a given soil moisture, the total plant biomass of white clover and tall ...

关键词： legumes grasses the Chinese Loess Plateau microbial communities phospholipid fatty acid （PLFA）