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Synthetic and Systems Biotechnology 2021年第4期6卷 402-413页

作者： Helena engel Felix Guischard Fabian Krause Janina Nandy Paulina Kaas Nico Hofflin Maja Kohn Normann Kilb Karsten Voigt Steffen Wolf Tahira Aslan Fabian Baezner Salom´e Hahne Carolin Ruckes Joshua Weygant Alisa Zinina emir Bora Akmeriç enoch B.Antwi Dennis Dombrovskij Philipp Franke Klara L.Lesch Niklas Vesper Daniel Weis Nicole Gensch Barbara Di Ventura Mehmet Ali Oztürk Signalling Research Centres BIOSS and CIBSS University of FreiburgSchanzlestr.1879104FreiburgGermany Institute of Biology III Faculty of BiologyUniversity of FreiburgSchanzlestr.179104FreiburgGermany Institute of Biology II Faculty of BiologyUniversity of FreiburgSchanzlestr.179104FreiburgGermany AG Roth-Lab for MicroarrayCopying ZBSA-Centre for Biological Systems AnalysisUniversity of FreiburgHabsburgerstrasse 4979104FreiburgGermany Biomolecular Dynamics Institute of PhysicsUniversity of FreiburgHermann-Herder-Strasse 3a79104FreiburgGermany Core Facility Signalling Factory Centre for Biological Signaling Studies(BIOSS)University of FreiburgSchanzlestr.1879104FreiburgGermany Spemann Graduate School of Biology and Medicine(SGBM) University of FreiburgAlbertstraße 19A79104FreiburgGermany Internal Medicine IV Department of MedicineMedical CenterUniversity of FreiburgHugstetter Straße 5579106FreiburgGermany Institute for Biochemistry University of FreiburgAlbertstr.2179104FreiburgGermany

In the rapidly expanding field of peptide therapeutics,the short in vivo half-life of peptides represents a considerable limitation for drug action.D-peptides,consisting entirely of the dextrorotatory enantiomers of naturally occurring levorotatory amino acids(AAs),do not suffer from these shortcomings as they are intrinsically resistant to proteolytic degradation,resulting in a favourable pharmacokinetic *** experimentally identify D-peptide binders to interesting therapeutic targets,so-called mirror-image phage display is typically performed,whereby the target is synthesized in D-form and L-peptide binders are screened as in conventional phage *** technique is extremely powerful,but it requires the synthesis of the target in D-form,which is challenging for large *** we present finDr,a novel web server for the computational identification and optimization of D-peptide ligands to any protein structure(https://***/).finDr performs molecular docking to virtually screen a library of helical 12-mer peptides extracted from the RCSB Protein Data Bank(PDB)for their ability to bind to the *** a separate,heuristic approach to search the chemical space of 12-mer peptides,finDr executes a customizable evolutionary algorithm(eA)for the de novo identification or optimization of D-peptide *** a proof of principle,we demonstrate the validity of our approach to predict optimal binders to the pharmacologically relevant target phenol soluble modulin alpha 3(PSMα3),a toxin of methicillin-resistant Staphylococcus aureus(MRSA).We validate the predictions using in vitro binding assays,supporting the success of this *** to conventional methods,finDr provides a low cost and easy-to-use alternative for the identification of D-peptide ligands against protein targets of choice without size *** believe finDr will facilitate D-peptide discovery with implications in biotechnology and biomedicine.

关键词： D-peptide Web server evolutionary algorithm Peptide design Molecular docking Mirror-image phage display

Observatory science with eXTP

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Science China(Physics,Mechanics & Astronomy) 2019年第2期62卷 97-138页

作者： Jean J.M.in 't Zand enrico Bozzo JinLu Qu Xiang-Dong Li Lorenzo Amati Yang Chen Immacolata Donnarumma Victor Doroshenko Stephen A.Drake Margarita Hernanz Peter A.Jenke Thomas J.Maccarone Simin Mahmoodifar Domitilla de Martino Alessandra De Rosa elena M.Rossi Antonia Rowlinson Gloria Sala Giulia Stratta Thomas M.Tauris Joern Wilms XueFeng Wu Ping Zhou Iván Agudo Diego Altamirano Jean-Luc Atteia Nils A.andersson M.Cristina Baglio David R.Ballantyne Altan Baykal ehud Behar Tomaso Belloni Sudip Bhattacharyya Stefano Bianchi Anna Bilous Pere Blay Joao Braga Sφren Brandt edward F.Brown Niccolo Bucciantini Luciano Burderi edward M.Cackett Riccardo Campana Sergio Campana Piergiorgio Casella Yuri Cavecchi Frank Chambers Liang Chen Yu-Peng Chen Jér?me Chenevez maria Chernyakova ChiChuan Jin Riccardo Ciolfi elisa Costantini Andrew Cumming Antonino D'Aì Zi-Gao Dai Filippo D'Ammando Massimiliano De Pasquale Nathalie Degenaar Melania Del Santo Valerio D'elia Tiziana Di Salvo Gerry Doyle Maurizio Falanga XiLong Fan Robert D.Ferdman Marco Feroci Federico Fraschetti Duncan K.Galloway Angelo F.Gambino Poshak Gandhi MingYu Ge Bruce Gendre Ramandeep Gill Diego G?tz Christian Gouiffès Paola Grandi Jonathan Granot Manuel Güdel Alexander Heger Craig O.Heinke Jeroen Homan Rosario Iaria Kazushi Iwasawa Luca Izzo Long Ji Peter G.Jonker Jordi José Jelle S.Kaastra emrah Kalemci Oleg Kargaltsev Nobuyuki Kawai Laurens Keek Stefanie Komossa Ingo Kreykenbohm Lucien Kuiper Devaky Kunneriath Gang Li en-Wei Liang Manuel Linares Francesco Longo FangJun Lu Alexander A.Lutovinov Denys Malyshev Julien Malzac Antonios Manousakis Ian McHardy Missagh Mehdipour YunPeng Men mariano Méndez Roberto P.Mignani Romana Mikusincova M.Coleman Miller Giovanni Miniutti Christian Motch Joonas Nättilä emanuele Nardini Torsten Neubert Paul T.O'Brien Mauro Orlandini Julian P.Osborne Luigi Pacciani Stéphane Paltani Maurizio Paolillo Iossif e.Papadakis Biswajit Paul Alberto Pellizzoni Uria Peretz Miguel A.Pérez Torres emanuele Perinati Chanda Prescod-Weinstein Pablo Reig SRON Netherlands Institute for Space Research Department of Astronomy University of Geneva Key Laboratory for Particle Astrophysics Institute of High Energy PhysicsChinese Academy of Sciences School of Astronomy and Space Science Nanjing University INAF-IASF Bologna ASI Via del Politecnico snc INAF-Istituto di Astrofisica e Planetologie Spaziali Institut für Astronomie und Astrophysik Tübingen Universit?t Tübingen NASA Goddard Space Flight Center ICReA&Institute of Space Sciences(IeeC-CSIC) Campus UABCarrer de Can Magrans CSPAR SPA University of Alabama in Huntsville Department of Physics Texas Tech University INAF Osservatorio Astronomico di Capodimonte Leiden Observatory Leiden University Anton Pannekoek Institute University of Amsterdam ASTRON Netherlands Institute for Radio Astronomy Universitat Politecnica de Catalunya(UPC-IeeC) Universitádegli Studi di Urbino‘Carlo Bo’ Max-Planck-Institut für Radioastronomie Dr.Karl-Remeis-Sternwarte and erlangen Centre for Astroparticle Physics(eCAP) Friedrich Alexander Universit?t Erlangen-Nurnberg Purple Mountain Observatory Chinese Academy of Sciences Instituto de Astrofysíca de Andalucia-CSIC Department of Physics and Astronomy University of Southampton IRAP Universitéde ToulouseCNRSUPSCNES Mathematical Sciences and STAG Research Centre University of Southampton New York University Abu Dhabi Center for Relativistic Astrophysics School of PhysicsGeorgia Institute of Technology Physics Department Middle East Technical University Department of Physics Technion-Israel Institute of Technology INAF Osservatorio Astronomico di Brera Tata Institute of Fundamental Research Dipartimento di Matematica e Fisica Universitàdegli Studi Roma Tre Instituto de Astrofísica de Canarias Instituto Nacional de Pesquisas espaciais-INPe National Space Institute Technical University of Denmark(DTU Space) Department of Physics and Astronomy Michigan State University INAF Osservatorio Astrofisico di Arcetri Dipartimento di Fisica Universitádegli Studi di Cagliari Department of Physics and A

In this White Paper we present the potential of the enhanced X-ray Timing and Polarimetry(eXTP) mission for studies related to Observatory Science targets. These include flaring stars, supernova remnants, accreting white dwarfs, low and high mass X-ray binaries, radio quiet and radio loud active galactic nuclei, tidal disruption events, and gamma-ray bursts. eXTP will be excellently suited to study one common aspect of these objects: their often transient nature. Developed by an international Consortium led by the Institute of High energy Physics of the Chinese Academy of Science, the eXTP mission is expected to be launched in the mid 2020s.

关键词： space research in struments nuclear astrophysics flare stars accretion and accretion disks mass loss and stellar winds cataclysmic binaries X-ray binaries supernova remnants active galactic nuclei X-ray bursts gamma-ray bursts gravitational waves

Notes for genera:Ascomycota

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Fungal Diversity 2017年第5期86卷 1-594页

作者： Nalin N.Wijayawardene Kevin D.Hyde Kunhiraman C.Rajeshkumar David L.Hawksworth Hugo Madrid Paul M.Kirk Uwe Braun Rajshree V.Singh Pedro W.Crous Martin Kukwa Robert Lücking Cletus P.Kurtzman Andrey Yurkov Danny Haelewaters Andre´Aptroot H.Thorsten Lumbsch einar Timdal Damien ertz Javier etayo Alan J.L.Phillips Johannes Z.Groenewald Moslem Papizadeh Laura Selbmann Monika C.Dayarathne Gothamie Weerakoon e.B.Gareth Jones Satinee Suetrong Qing Tian Rafael F.Castanda-Ruiz Ali H.Bahkali Ka-Lai Pang Kazuaki Tanaka Dong Qin Dai Jariya Sakayaroj Martina Hujslová Lorenzo Lombard Belle D.Shenoy Ave Suija Sajeewa S.N.Maharachchikumbura Kasun M.Thambugala Dhanushka N.Wanasinghe Bharati O.Sharma Subhash Gaikwad Gargee Pandit Laura Zucconi Silvano Onofri eleonora egidi Huzefa A.Raja Rampai Kodsueb Marcela e.S.Caceres Sergio Perez-Ortega Patrícia O.Fiuza Josiane Santana Monteiro Larissa N.Vasilyeva Roger G.Shivas maria Prieto Mats Wedin Ibai Olariaga Adebola Azeez Lateef Yamini Agrawal Seyed Abolhassan Shahzadeh Fazeli Mohammad Ali Amoozegar Guo Zhu Zhao Walter P.Pfliegler Gunjan Sharma Magdalena Oset Mohamed A.Abdel-Wahab Susumu Takamatsu Konstanze Bensch Nimali Indeewari de Silva AndréDe Kesel Anuruddha Karunarathna Saranyaphat Boonmee Donald H.Pfister Yong-Zhong Lu Zong-Long Luo Nattawut Boonyuen Dinushani A.Daranagama Indunil C.Senanayake Subashini C.Jayasiri Milan C.Samarakoon Xiang-Yu Zeng Mingkwan Doilom Luis Quijada Sillma Rampadarath Gabriela Heredia Asha J.Dissanayake Ruvishika S.Jayawardana Rekhani H.Perera Li Zhou Tang Chayanard Phukhamsakda Margarita Hernańdez-Restrepo Xiaoya Ma Saowaluck Tibpromma Luis F.P.Gusmao Darshani Weerahewa Samantha C.Karunarathna Key Laboratory for Plant Diversity and Biogeography of east Asia Kunming Institute of BotanyChinese Academy of ScienceKunming 650201YunnanPeople’s Republic of China Center of excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand World Agroforestry Centre East and Central AsiaKunming 650201YunnanPeople’s Republic of China Mushroom Research Foundation 128 M.3 Ban Pa Deng T.Pa PaeA.Mae TaengChiang Mai 50150Thailand National Fungal Culture Collection of India(NFCCI) Biodiversity and Palaeobiology(Fungi)GroupAgharkar Research InstitutePuneMaharashtra 411004India Royal Botanic Gardens KewRichmondSurrey TW93DSUK Department of Life Sciences The Natural History MuseumCromwell RoadLondon SW75BDUK Jilin Agricultural University Changchun 130118JilinPeople’s Republic of China Centro de Geno´mica y Bioinforma´tica Facultad de CienciasUniversidad Mayor de ChileCamino La Pira´mide 5750HuechurabaSantiagoChile Martin-Luther-Universita¨t Institut fu¨r BiologieBereich Geobotanik und Botanischer GartenHerbariumNeuwerk 2106099 Halle(Saale)Germany Westerdijk Fungal Biodiversity Institute Uppsalalaan 83584 CT UtrechtThe Netherlands Department of Plant Taxonomy and Nature Conservation Faculty of BiologyUniversity of Gdan´skWita Stwosza 5980-308 Gdan´skPoland Botanic Garden and Botanical Museum Königin-Luise-Str.6-814195 BerlinGermany Mycotoxin Prevention and Applied Microbiology Research Unit National Center for Agricultural Utilization ResearchAgricultural Research ServiceU.S.Department of AgriculturePeoriaIL 61604USA Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures Inhoffenstraße 7B38124 BrunswickGermany Farlow Reference Library and Herbarium of Cryptogamic Botany Harvard University22 Divinity AvenueCambridgeMA 02138USA Department of Organismic and evolutionary Biology Harvard University22 Divinity AvenueCambridgeMA 02138USA ABL Herbarium G.v.d.Veenstraat 1073762 XK SoestThe Netherlands Science&education The Field Museum1400

Knowledge of the relationships and thus the classification of fungi,has developed rapidly with increasingly widespread use of molecular techniques,over the past 10–15 years,and continues to *** genera have been found to be polyphyletic,and their generic concepts have subsequently been *** names have thus been introduced for species which are phylogenetically distinct from the type species of particular *** ending of the separate naming of morphs of the same species in 2011,has also caused changes in fungal generic *** order to facilitate access to all important changes,it was desirable to compile these in a single *** present article provides a list of generic names of Ascomycota(approximately 6500 accepted names published to the end of 2016),including those which are *** and summaries of the changes since the last edition of‘Ainsworth&Bisby’s Dictionary of the Fungi’in 2008 are *** notes include the number of accepted species,classification,type species(with location of the type material),culture availability,life-styles,distribution,and selected publications that have appeared since *** work is intended to provide the foundation for updating the ascomycete component of the"Without prejudice list of generic names of Fungi"published in 2013,which will be developed into a list of protected generic *** will be subjected to the XIXth International Botanical Congress in Shenzhen in July 2017 agreeing to a modification in the rules relating to protected lists,and scrutiny by procedures determined by the Nomenclature Committee for Fungi(NCF).The previously invalidly published generic names Barriopsis,Collophora(as Collophorina),Cryomyces,Dematiopleospora,Heterospora(as Heterosporicola),Lithophila,Palmomyces(as Palmaria)and Saxomyces are validated,as are two previously invalid family names,Bartaliniaceae and *** species of Lalaria,which were invalidly published are trans

关键词： Article 59 Classification One name Pleomorphic fungi Taxonomy

Challenges for the Characterization of Genetically Modified Animals by the qPCR Technique in the era of Genomic editing

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Veterinary Science Research 2021年第1期3卷 1-11页

作者： Ribrio Ivan Tavares Pereira Batista Darcio Italo Alves Teixeira Vicente Jose de Figueiredo Freitas Luciana Magalhaes Melo Joanna maria Goncalves Souza-Fabjan Laboratorio de Fisiologia e Controle da Reproducao Faculdade de VeterinariaUniversidade Estadual do Ceara(UECE)Av.Dr.Silas Munguba 1700FortalezaCE60740-903Brazil Faculdade de Veterinaria Universidade Federal Fluminense(UFF)Rua Vital Brazil Filho64NiteroiRJ24230-340Brazil Molecular Genetics Research Unit University Center Fametro(Unifametro)Rua Conselheiro Estelita500FortalezaCE60010-260Brazil

Characterization of genetically modified organisms through determination of zygosity and transgene integration concerning both copy number and genome site is important for breeding a transgenic line and the use of these organisms in the purpose for which it was *** blot,fluorescence in situ hybridization or mating are demanding and time-consuming techniques traditionally used in the characterization of transgenic organisms and,with the exception of mating,give ambiguous *** the emergence of the real-time quantitative PCR technology,different applications have been described for the analysis of transgenic organisms by determination of several parameters to transgenic ***,the accuracy in quantitation by this method can be influenced in all steps of *** review focuses on the aspects that influence pre-analytical steps(DNA extraction and DNA quantification methods),quantification strategies and data analysis in quantification of copy number and zygosity in transgenic animals.

关键词： Absolute quantification Copy number DNA extraction Relative quantification Zygosity

Altered molecular pattern of mucosal healing in Crohn's disease fibrotic stenosis

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World Journal of Gastrointestinal Pathophysiology 2013年第3期4卷 53-58页

作者： enzo Ierardi Floriana Giorgio Domenico Piscitelli mariabeatrice Principi Santina Cantatore maria Grazia Fiore Roberta Rossi Michele Barone Alfredo Di Leo Carmine Panella Gastroenterology Department of Medical and Surgical Sciences University of Foggia 71100 Foggia Italy Gastroenterology Department of Emergency and Organ Transplantation University of Bari 70124 Bari Italy

AIM: To investigate tumor necrosis factor-α (TNF-α), syndecan 1 and basic fibroblast growth factor (bFGF) balance in Crohn's disease (CD) strictures. MeTHODS: Our study was performed on 24 surgical specimens of CD fibrotic stenosis. Ten histological normal surgical samples were retrieved for both the large and small bowel from patients with benign conditions and healthy tissue represented control collection. Sex and age in controls did not differ from CD group. Three endoscopic biopsy specimens taken after informed consent in subjects with normal colon were also used as negative controls. TNF-α, syndecan 1 and bFGF were detected by both reverse transcriptase reverse transcriptase polymerase chain reaction after mRNA extraction (results expressed as fold-change) and ***: TNF-α did not show any significant difference between CD and control specimens (1.54 ± 1.19; P > 0.05). Very high levels of bFGF were observed in CD (11.76 ± 4.65; P e syndecan 1 which showed a moderate increase (5.53 ± 2.18; P e (ANOVA) plus Student-NeumannKeuls showed: bFGF > syndecan 1 > TNF-α = control. Immunoreactivity for bFGF was observed in epithelial, stromal, endothelial cells and even in the muscular layer, whilst in normal tissue it was almost unexpressed. Syndecan 1 and TNF-α staining was confined to mucosal epithelial and stromal cells, while in controls syndecan 1 was found in its normal site, i.e. , basolateral area of the crypts and TNF-α very poorly expressed. CONCLUSION: Fibrotic stenosis of CD may be the final result of an irreversible transformation of different cells into fibrogenic phenotype no longer inhibited by posttranscriptional regulation.

关键词： Crohn’s disease Fibrotic stenosis Tumor necrosis factor-α Syndecan 1 Basic fibroblast growth factor

历史性视角下后工业区景观认知及实践变革研究

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风景园林 2020年第7期27卷 8-17页

作者： [德]卢卡·玛丽亚·弗朗西斯科·法布里斯李梦一欣米兰理工大学北京建筑大学北京建筑大学建筑与城市规划学院

随着社会变迁、文化更迭、环境伦理观演变,后工业区经历了50年的更新与发展。在这一背景下,探究全球后工业区更新的4个嬗变历程:初现变革、剧烈变革、结构变革、整合性变革,以揭示后工业景观变革在风景园林设计实践、社会与法规、生态... 详细信息

随着社会变迁、文化更迭、环境伦理观演变,后工业区经历了50年的更新与发展。在这一背景下,探究全球后工业区更新的4个嬗变历程:初现变革、剧烈变革、结构变革、整合性变革,以揭示后工业景观变革在风景园林设计实践、社会与法规、生态主义思想、创新理念方面的不断发展和完善。通过历时性分析,重新解读50年变革历程中的代表性案例,揭示风景园林实践进程中后工业区更新的多元化探索。从历史研究的角度出发,构建基于历史分期—变革内涵—里程碑案例的后工业景观研究脉络,以期为当下中国后工业景观理论及实践的发展提供指导与借鉴。

关键词：风景园林后工业化环境设计后工业公园废弃地更新

Boron nitride nanoresonators for phonon-enhanced molecular vibrational spectroscopy at the strong coupling limit

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Light(Science & Applications) 2017年第1期6卷 55-62页

作者： Marta Autore Peining Li Irene Dolado Francisco J Alfaro-Mozaz Ruben esteban Ainhoa Atxabal Fèlix Casanova Luis e Hueso Pablo Alonso-González Javier Aizpurua Alexey Y Nikitin Saül Vélez Rainer Hillenbrand CIC nanoGUNe Donostia-San Sebastián 20018Spain Donostia International Physics Center(DIPC) Donostia-San Sebastián 20018Spain IKeRBASQUe Basque Foundation for ScienceBilbao 48013Spain Departamento de Física Universidad de OviedoOviedo 33007Spain Centro de Física de Materiales(MPC CSIC-UPV/EHU)Donostia-San Sebastián 20018Spain Current address:Department of Materials ETH ZürichZürich 8093Switzerland CIC nanoGUNe and UPV/eHU Donostia-San Sebastián 20018Spain

enhanced light-matter interactions are the basis of surface-enhanced infrared absorption(SeIRA)spectroscopy,and conventionally rely on plasmonic materials and their capability to focus light to nanoscale spot *** polariton nanoresonators made of polar crystals could represent an interesting alternative,since they exhibit large quality factors,which go far beyond those of their plasmonic *** recent emergence of van der Waals crystals enables the fabrication of highquality nanophotonic resonators based on phonon polaritons,as reported for the prototypical infrared-phononic material hexagonal boron nitride(h-BN).In this work we use,for the first time,phonon-polariton-resonant h-BN ribbons for SeIRA spectroscopy of small amounts of organic molecules in Fourier transform infrared ***,the interaction between phonon polaritons and molecular vibrations reaches experimentally the onset of the strong coupling regime,while numerical simulations predict that vibrational strong coupling can be fully *** polariton nanoresonators thus could become a viable platform for sensing,local control of chemical reactivity and infrared quantum cavity optics experiments.

关键词： boron nitride phonon polaritons strong coupling surface-enhanced infrared absorption spectroscopy SeIRA

A combined computational pipeline to detect circular RNAs in human cancer cells under hypoxic stress

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Journal of Molecular Cell Biology 2019年第10期11卷 829-844页

作者： Antonella Di Liddo Camila de Oliveira Freitas Machado Sandra Fischer Stefanie ebersberger Andreas WHeumliller Julia eWeigand Michaela Muller-McNicoll Kathi Zarnack Buchmann Institute for Molecular Life Sciences Goethe University FrankfurtFrankfurt am MainGermany Institute of Cell Biology and Neuroscience Goethe University FrankfurtFrankfurt am MainGermany Institute for Cardiovascular Regeneration Goethe University FrankfurtFrankfurt am MainGermany Department of Biology Technical University DarmstadtGermany Institute of Molecular Biology(IMB) MainzGermany

Hypoxia is associated with several diseases,including *** that are deprived of adequate oxygen supply trigger tran-scriptional and post-transcriptional responses,which control cellular pathways such as angiogenesis,proliferation,and metabolic *** RNAs(circRNAs)are a novel class of mainly non-coding RNAs,which have been implicated in multiple cancers and attract increasing attention as potential ***,we characterize the circRNA signatures of three different cancer cell lines from cervical(HeLa),breast(MCF-7),and lung(A549)cancer under *** order to reliably detect circRNAs,we integrate available tools with custom approaches for quantification and statistical analysis?Using this consolidated computational pipeline,we identify?12000 circRNAs in the three cancer *** molecular characteristics point to an involvement of complementary RNA sequences as well as trans-acting factors in circRNA biogenesis,such as the RNA-binding protein HNRNPC-Notably,we detect a number of circRNAs that are more abundant than their linear *** addition,64 circRNAs significantly change in abundance upon hypoxia,in most cases in a cell type-specific *** summary,we present a comparative circRNA profiling in human cancer cell lines,which promises novel insights into the biogenesis and function of circRNAs under hypoxic stress.

关键词： circular RNA computational pipeline differential expression cancer cells hypoxia RNA-Seq

Diffusion models for the description of seedless grape drying using analytical andnumerical solutions

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