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| 1 | Discriminating mild from critical COVID-19 by innate and adaptive immune single-cell profiling of bronchoalveolar lavages显示文摘How the innate and adaptive host immune system miscommunicate to worsen COVID-19 immunopathology has not been fully elucidated.Here,we perform single-cell deep-immune profiling of bronchoalveolar lavage(BAL)samples from 5 patients with mild and 26 with critical COVID-19 in comparison to BALs from non-COVID-19 pneumonia and normal lung.We use pseudotime inference to build T-cell and monocyte-to-macrophage trajectories and model gene expression changes along them.In mild COVID-19,CD8^(+)resident-memory(TRM)and CD4^(+)T-helper-17(T_(H17))cells undergo active(presumably antigen-driven)expansion towards the end of the trajectory,and are characterized by good effector functions,while in critical COVID-19 they remain more naïve.Vice versa,CD4^(+)T-cells with T-helper-1 characteristics(TH1-like)and CD8^(+)T-cells expressing exhaustion markers(T_(EX)-like)are enriched halfway their trajectories in mild COVID-19,where they also exhibit good effector functions,while in critical COVID-19 they show evidence of inflammation-associated stress at the end of their trajectories.Monocyte-to-macrophage trajectories show that chronic hyperinflammatory monocytes are enriched in critical COVID-19,while alveolar macrophages,otherwise characterized by anti-inflammatory and antigen-presenting characteristics,are depleted.In critical COVID-19,monocytes contribute to an ATP-purinergic signaling-inflammasome footprint that could enable COVID-19 associated fibrosis and worsen disease-severity.Finally,viral RNA-tracking reveals infected lung epithelial cells,and a significant proportion of neutrophils and macrophages that are involved in viral clearance. | Els Wauters Pierre Van Mol Abhishek Dinkarnath Garg Sander Jansen Yannick Van Herck Lore Vanderbeke Ayse Bassez Bram Boeckx Bert Malengier-Devlies Anna Timmerman Thomas Van Brussel Tina Van Buyten Rogier Schepers Elisabeth Heylen Dieter Dauwe Christophe Dooms Jan Gunst Greet Hermans Philippe Meersseman Dries Testelmans Jonas Yserbyt Sabine Tejpar Walter De Wever Patrick Matthys CONTAGIOUS collaborators Johan Neyts Joost Wauters Junbin Qian Diether Lambrechts | 2021 | Cell Research2021，31，3： | 11 |
| 2 | A pan-cancer blueprint of the heterogeneous tumor microenvironment revealed by single-cell profiling显示文摘The stromal compartment of the tumor microenvironment consists of a heterogeneous set of tissue-resident and tumor-infiltrating cells,which are profoundly moulded by cancer cells.An outstanding question is to what extent this heterogeneity is similar between cancers affecting different organs.Here,we profile 233,591 single cells from patients with lung,colorectal,ovary and breast cancer(n=36)and construct a pan-cancer blueprint of stromal cell heterogeneity using different single-cell RNA and protein-based technologies.We identify 68 stromal cell populations,of which 46 are shared between cancer types and 22 are unique.We also characterise each population phenotypically by highlighting its marker genes,transcription factors,metabolic activities and tissue-specific expression differences.Resident cell types are characterised by substantial tissue specificity,while tumor-infiltrating cell types are largely shared across cancer types.Finally,by applying the blueprint to melanoma tumors treated with checkpoint immunotherapy and identifying a naive CD4+T-cell phenotype predictive of response to checkpoint immunotherapy,we illustrate how it can serve as a guide to interpret scRNA-seq data.In conclusion,by providing a comprehensive blueprint through an interactive web server,we generate the first panoramic view on the shared complexity of stromal cells in different cancers. | Junbin Qian Siel Olbrecht Bram Boeckx Hanne Vos Damya Laoui Emre Etlioglu Els Wauters Valentina Pomella Sara Verbandt Pieter Busschaert Ayse Bassez Amelie Franken Marlies Vanden Bempt Jieyi Xiong Birgit Weynand Yannick van Herck Asier Antoranz Francesca Maria Bosisio Bernard Thienpont Giuseppe Floris Ignace Vergote Ann Smeets Sabine Tejpar Diether Lambrechts | 2020 | Cell Research2020，30，9： | 11 |
| 3 | Maize biochars accelerate short-term soil nitrogen dynamics in a loamy sand soil显示文摘 | Victoria Nelissen Tobias Rütting Dries Huygens Jeroen Staelens Greet Ruysschaert Pascal Boeckx | 2012 | Soil Biology and Biochemistry2012，，： | 4 |
| 4 | Methane emission from a landfill and the methane oxidising capacity of its covering soil显示文摘 | Pascal Boeckx Oswald van Cleemput Ida Villaralvo | 1996 | Soil Biology and Biochemistry1996，，10： | 2 |
| 5 | 高浓度CO_2处理后土壤N_2O排放特征显示文摘土壤被认为是大气氧化亚氮(N_2O)的重要生物排放源。随着大气CO_2浓度升高,土壤N_2O排放规律可能发生改变。无锡FACE(Free-air CO_2 Enrichment)基地至2003年已运行2年,分别采集Ambien(t背景大气CO_2浓度处理)和FACE(背景大气CO_2浓度+200mmol·mol-1处理)农田土壤,调节含水量至40%WFPS,在25℃室内有氧预培养7d后,按250μgN·g-1添加NH4NO3,将含水量调节至80%WFPS,在25℃进行有氧培养7d。在此培养期间,定期测定施肥后土壤N_2O和CO_2排放速率,探讨来自田间Ambient和FACE土壤N_2O排放差异及其可能的影响因素。结果表明,所有土壤N_2O和CO_2排放速率均随培养时间延长而迅速递减,来自Ambient处理的土壤N_2O和CO_2排放速率均高于来自FACE处理的土壤相应排放量,且土壤N_2O与CO_2排放速率存在显著正相关。通过比较培养前后土壤交换态NH_(4+)和NO_(3-)含量的变化,显示培养过程中可能存在相当量的微生物氮固持,有必要加强相关研究。 | 徐仲均 王迎红 徐星凯 Pascal Boeckx Oswald Van Cleemput 朱建国 王跃思 | 2008 | 农业环境科学学报2008，27，5： | 2 |
| 6 | Sustained nitrite accumulation in a membraneassisted bioreactor(MBR) for the treatment of ammonium rich wastewater显示文摘 | Wyffels S Boeckx P | 2003 | ChemTechnol Biotechnol2003，78，4： | 1 |
| 7 | Identification and quantification of nitrogen removal in a rotating biological contactor by 15N tracer techniques显示文摘 | Wyffels S Pynaert K Boeckx P | 2003 | Water Research2003，37，6： | 1 |
| 8 | Intranasal sutentanil for pre - operative sedation显示文摘 | Vereauteren M Boeckx E Hanegreeis G | 1988 | Anaesthesia1988，43，4： | 1 |
| 9 | Soil nitrogen conserva- tion mechanisms in a pristine south Chilean Nothofagus forest eco- system 显示文摘 | Huygens D RUtting T Boeckx P | 2007 | Soil Biology Biochemistry2007，39，： | 1 |
| 10 | High Prognostic Impact of Flow Cytometric Minimal Residual Disease Detection in Acute Myeloid Leukemia: Data From the HOVON/SAKK AML 42A Study显示文摘 | Monique Terwijn Wim L.J. van Putten Angèle Kelder Vincent H.J. van der Velden Rik A. Brooimans Thomas Pabst Johan Maertens Nancy Boeckx Georgine E. de Greef Peter J.M. Valk Frank W.M.B. Preijers Peter C. Huijgens Angelika M. Dr?ger Urs Schanz Mojca Jongen | 2013 | Journal of Clinical Oncology2013，，31： | 1 |
| 11 | The epithelium of human hydrosalpinges: a light optical and scanning electron microscopic study 显示文摘 | Vasquez G Winston RM Boeckx W | 1983 | Br J Obstet Gynaeeol1983，90，8： | 1 |
| 12 | Floc-based sequential partial nitritation and anammox at full scale with contrasting N 2 O emissions显示文摘 | Joachim Desloover Haydée De Clippeleir Pascal Boeckx Gijs Du Laing Joop Colsen Willy Verstraete Siegfried E. Vlaeminck | 2011 | Water Research2011，，9： | 1 |
| 13 | Changes in donor site selection in lower limb free flap reconstru-ctions显示文摘 | Boeckx W van den Hof B van Holder C | 1996 | Microsurgery1996，17，7： | 1 |
| 14 | Soil nitrogen conservation mechanisms in a pristine south Chilean Nothofagus forest ecosystem 显示文摘 | HUYGENS D RUTTING T BOECKX P | 2007 | Soil Biology and Biochemistry2007，39，： | 1 |
| 15 | Late results of burn wound scar after cerium nitrate-silver sulfadiazine and compressive therapu: scanning eletronmicroscopy evaluation of keloid scar显示文摘 | Selvaggi G Boeckx W De WulfM | 2007 | Plast Reconstr Surg2007，119，6： | 1 |
| 16 | Biological denitrification in microbial fuel cells 显示文摘 | Clauwaert P Rabaey K Aelterman P Schamphelaire LD Pham TH Boeckx P Boon N Verstraete W | 2007 | Environ Sci Teehnol2007，41，9： | 1 |
| 17 | Mechanisms for re- tention of bioavailable nitrogen in volcanic rainforest soils显示文摘 | Huygens D Boeckx P Templer P | 2008 | Nature Geoscience2008，1，8： | 1 |
| 18 | Manipulating the N release from 15N labelled celery residues by using straw and vinasses 显示文摘 | CHAVES B DE NEVE S BOECKX P | 2006 | Soil Biology and Biochemistry2006，38，： | 1 |
| 19 | Refinements in free flap breast reconstrnc- tion:The free bilateral deep inferior epigastric perforator flap anasto- mosed to the internal mammary artery显示文摘 | Blondeel PN Boeckx WD | 1994 | Br J Plast Surg1994，47，49： | 1 |
| 20 | Neoangiogenesis in adhesion formation and peritoneal healing显示文摘 | Bigatti G Boeckx W Gruft L | 1995 | Human Reproduction1995，10，9： | 1 |
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