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MINI-EX:Integrative inference of single-cell gene regulatory networks in plants

Molecular Plant 2022年第11期15卷 1807-1824页

作者： Camilla Ferrari nicol.s Manosalva Pérez Klaas Vandepoele Department of Plant Biotechnology and Bioinformatics Ghent University9052 GhentBelgium Center for Plant Systems Biology VIB9052 GhentBelgium Bioinformatics Institute Ghent Ghent University9052 GhentBelgium

Multicellular organisms,such as plants,are characterized by highly specialized and tightly regulated cell populations,establishing specific morphological structures and executing distinct *** regulatory networks(GRNs)describe condition-specific interactions of transcription factors(TFs)regulating the expression of target genes,underpinning these specific *** efficient and validated methods to identify cell-type-specific GRNs from single-cell data in plants are lacking,limiting our understanding of the organization of specific cell types in both model species and crops,we developed MINI-EX(Motif-Informed Network Inference based on single-cell EXpression data),an integrative approach to infer cell-type-specific networks in ***-EX uses single-cell transcriptomic data to define expression-based networks and integrates TF motif information to filter the inferred regulons,resulting in networks with increased ***,regulons are assigned to different cell types,leveraging cell-specific expression,and candidate regulators are prioritized using network centrality measures,functional annotations,and expression *** embedded prioritization strategy offers a unique and efficient means to unravel signaling cascades in specific cell types controlling a biological process of *** demonstrate the stability of MINI-EX toward input data sets with low number of cells and its robustness toward missing data,and show that it infers state-of-the-art networks with a better performance compared with other related single-cell network ***-EX successfully identifies key regulators controlling root development in Arabidopsis and rice,leaf development in Arabidopsis,and ear development in maize,enhancing our understanding of cell-type-specific regulation and unraveling the roles of different regulators controlling the development of specific cell types in plants.

关键词： single-cell RNA-seq gene regulatory network transcription factors systems biology

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Isoxazolone Reactivity Explained by Computed Electronic Structure Analysis

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Chinese Journal of Chemistry 2020年第2期38卷 163-168页

作者： Giovanni Bella Antonio Santoro Massimiliano Cordaro Francesco nicol. Giuseppe Bruno Department of Chemical BiologicalPharmaceutical and Environmental SciencesUniversity of MessinaViale F.Stagno d'Alcontres 3198166 MessinaItaly

Summary of main observation and conclusion lsoxazol(2H)-5-one was chosen as a model molecule to study the structural features(a,p angles and carbonyl bond length)regarding lactone moiety in the isoxazolone species by computational *** method with B3LYP 6-311++G(2df,2p)basis set was used to carry out the optimization on a series(A and B families)of isoxazolones suitably substituted on double bond.

关键词： calculation. moiety substituted

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Empirical mode decomposition of multiphase flows in porous media:characteristic scales and speed of convergence

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Petroleum Science 2020年第1期17卷 153-167页

作者： nicol.s Echebarrena Pablo D.Mininni Gustavo A.Moreno YPF-Technology EnsenadaBuenos AiresArgentina CONICET Buenos AiresArgentina Physics Department IFIBASchool of Exact and Natural SciencesUniversity of Buenos AiresCONICETUniversity Campus1428 Buenos AiresArgentina

We apply a proper orthogonal decomposition(POD)to data stemming from numerical simulations of a fingering instability in a multiphase flow passing through obstacles in a porous medium,to study water injection processes in the production of hydrocarbon *** show that the time evolution of a properly defined flow correlation length can be used to identify the onset of the fingering *** of characteristic lengths for each of the modes resulting from the POD provides further information on the dynamics of the ***,using numerical simulations with different viscosity ratios,we show that the convergence of the POD depends non-trivially on whether the fingering instability develops or *** result has implications on proposed methods to decrease the dimensionality of the problem by deriving reduced dynamical systems after truncating the system’s governing equations to a few POD modes.

关键词： Two-phase flow Empirical mode decomposition Viscous fingering Porous media

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Application of PROTAC strategy to TTR-Aβ protein-protein interaction for the development of Alzheimer's disease drugs

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Neural Regeneration Research 2021年第8期16卷 1554-1555页

作者： nicol.Tonali Susanna Nencetti Elisabetta Orlandini Lidia Ciccone Université Paris-Saclay CNRSBioCISChâtenay-MalabryFrance Department of Pharmacy University of PisaPisaItaly Department of Earth Sciences Research Center“E.Piaggio”University of PisaPisaItaly

Alzheimer's disease(AD) is a complex and multifaced neurodegenerative disorder for which the precise pathological molecular mechanisms are still not completely known. In last years, rational multi-target drug design methods, which combine multiple molecules having complementary modes of action, have been increasingly used in the development of anti-AD drugs.

关键词： drugs Alzheimer Aβ

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From unstructured texts to semantic story maps

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International Journal of Digital Earth 2023年第1期16卷 234-250页

作者： Valentina Bartalesi Gianpaolo Coro Emanuele Lenzi Pasquale Pagano nicol.Pratelli Istituto di Scienza e Tecnologie dell’Informazione‘A.Faedo’del Consiglio Nazionale delle Ricerche PisaItaly

Digital maps greatly support storytelling about territories,especially when enriched with data describing cultural,societal,and ecological aspects,conveying emotional messages that describe the territory as a *** maps are interactive online digital narratives that can describe a territory beyond its map by enriching the map with text,pictures,videos,and other multimedia *** paper presents a semi-automatic workflow to produce story maps from textual documents containing territory *** expertfirst assembles one territory-contextual document containing text and ***,automatic processes use natural language processing and Wikidata services to(i)extract key concepts(entities)and geospatial coordinates associated with the territory,(ii)assemble a logically-ordered sequence of enriched story-map events,and(iii)openly publish online story maps and an interoperable Linked Open Data semantic knowledge base for event exploration and inter-story correlation *** workflow uses an Open Science-oriented methodology to publish all processes and *** our workflow,we produced story maps for the value chains and territories of 23 rural European areas of 16 *** numerical evaluation,we demonstrated that territory experts considered the story maps effective in describing their territories,and appropriate for communicating with citizens and stakeholders.

关键词： Story maps semantic web ontology natural language processing narratives e-infrastructures virtual research environments

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Vascular injury during laparoscopic cholecystectomy:An oftenoverlooked complication

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World Journal of Gastrointestinal Surgery 2023年第3期15卷 338-345页

作者： Antonio Pesce nicol. Fabbri Carlo Vittorio Feo Department of Surgery University of FerraraAzienda USL of FerraraAzienda USL of FerraraLagosanto 44023FerraraItaly

Laparoscopic cholecystectomy is one of the most frequently performed procedures in gastrointestinal surgery *** complications due to vascular injuries represent an important cause of morbidity and mortality,especially when facing major bleeding during laparoscopy,where bleeding control can be technically challenging in inexperienced ***,the reported incidence rate of conversion to open surgery due to vascular lesions is approximately 0%-1.9%,with a mortality rate of approximately 0.02%.The primary aim of this article was to perform an up-to-date overview regarding the incidence and surgical management of vascular injuries during laparoscopic cholecystectomy according to the available scientific evidence.

关键词： Laparoscopic cholecystectomy Vascular injury Vascular anomalies Surgical management Specialized hepatobiliary centers

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Parallel pathways:A chronicle of evolution in rectal and breast cancer surgery

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World Journal of Gastrointestinal Oncology 2024年第4期16卷 1091-1096页

作者： Antonio Pesce nicol.Fabbri Diletta Iovino Carlo Vittorio Feo Unit of General Surgery University of FerraraAzienda USL of FerraraFerrara 44023LagosantoItaly

In this editorial,we have analyzed the historical evolution of rectal and breast cancer surgery,focusing on the progressive reduction of demolitive approaches and the increasing use of more conservative strategies,accompanied by a growing emphasis on perioperative treatments aimed at enhancing surgical *** of these changes have been made possible due to an increased awareness and understanding of oncological diseases and improved perioperative treatments.

关键词： Rectal cancer History Breast surgery Demolitive treatment Conservative surgery

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Diagnostic detection with cardiac tomography and resonance of extremely rare coronary anomaly:A case report and review of literature

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World Journal of Clinical Cases 2019年第5期7卷 628-635页

作者： nicol. Schicchi Marco Fogante Gian Marco Giuseppetti Andrea Giovagnoni Department of Radiology Azienda Ospedaliero-Universitaria Ospedali Riuniti Department of Radiology Università Politecnica delle Marche

BACKGROUND The association of two congenital coronary artery anomalies(CAAs) is extremely rare but represents one of the main cause of sudden cardiac death in young athletes. Although coronary angiography(CX-A) is still widely used in childhood, cardiac magnetic resonance(C-MRI) and cardiac computed tomography(C-CT) have recently taken on an increasing diagnostic role in early detection of CAAs and concomitant congenital cardiac *** SUMMARY A healthy 10-year-old male patient was referred to the Radiological Department of our Institution due to no evidence of left coronary artery in echocardiographic examination. With C-MRI was detected marked myocardial trabeculation and was suspected anomalous origin and course of left circumflex(LCx) artery and of left anterior descending(LAD) artery. With third generation Dual Source C-CT192x2-sections(SOMATOM Force, Siemens, Germany) was confirmed anomalous origin of LCx artery from right pulmonary artery associated with anomalous origin of LAD artery from right coronary artery with course in front of right ventricular outflow tract. The patient underwent surgical treatment with reimplantation of the anomalous LCX and LAD arteries into the wall of ascending aorta, with no postoperative complications. The patient remained asymptomatic and follow-up C-MRI scan four months after operation showed complete success of surgery *** This case highlights the diagnostic potential of C-CT and C-MRI in evaluation of CAAs and of cardiac morphology and functionality, with very low radiation dose and without the risks related to invasive procedure.

关键词： Coronary anomalies Cardiac computed tomography Cardiac magnetic resonance Case report Coronary artery anomalies

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The relationship between morphology and flight in Drosophila:a study of two pairs of sibling species from a natural population

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Insect Science 2024年第3期31卷 885-900页

作者： nicol.s Flaibani Victoría Estefania Ortiz Juan JoséFanara Valeria Paula Carreira Laboratorio de Evolucion Departamento de EcologiaGenética y Evolucion(DEGE)Facultad de Ciencias Exactas y Naturales(FCEN)Universidad de Buenos Aires(UBA)Instituto de GenéticaEcologia y Evolucion de Buenos Aires(IEGEBA)Consejo Nacional de Investigaciones Cientificasy Tecnicas(CONICET)-UBABuenos AiresArgentina

Insect flight is a complex trait involved in different behaviors,from the search for sexual partners,food,or breeding *** studies have postulated the adaptive advantages of certain morphological traits in relation to increased flight capacity,such as low values of wing loading or high values of wing:thorax ratio and wing-aspect ***,few studies have evaluated the relationship between variables related to flight and morphological traits in *** work aimed to study morphological traits in males and females of two pairs of sibling species:Drosophila buzzati Patterson and Wheeler-Drosophila koeferae Fontdevila and Wasserman,and Drosophila melanogaster Meigen-Drosophila simulans Sturtevant,and to analyze its relationship with *** detected the highest proportion of flight time in *** and *** compared to *** and ***,*** results also revealed sexual dimorphism,with males exhibiting a higher proportion of flight time than ***,we did not find a general pattern to explain the relationship between morphology and the proportion of flight time because associations varied depending upon the analyses(considering all groups together or each sex-species combination separately).Moreover,these associations explained a low percentage of variation,suggesting that other nonmorphological components related to flight,such as physiological variables,should be taken into *** work allowed us to show the variability and complexity of an aspect of flight,suggesting that the adaptive role of the morphological traits studied might have been overestimated.

关键词： morphological traits time in flight wing loading wing:thorax ratio wingaspect ratio wing second moment of area

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Macrophage phagocytosis of SARS-CoV-2-infected cells mediates potent plasmacytoid dendritic cell activation

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Cellular & Molecular Immunology 2023年第7期20卷 835-849页

作者： O.García-nicol.s A.Godel G.Zimmer A.Summerfield Institute of Virology and Immunology(IVI) Sensemattstrasse 2933147 MittelhäusernSwitzerland Department of Infectious Diseases and Pathobiology Vetsuisse FacultyUniversity of BernBernSwitzerland Multidisciplinary Center for Infectious Diseases University of BernBernSwitzerland.

Early and strong interferon type I (IFN-I) responses are usually associated with mild COVID-19 disease, whereas persistent orunregulated proinflammatory cytokine responses are associated with severe disease outcomes. Previous work suggested thatmonocyte-derived macrophages (MDMs) are resistant and unresponsive to SARS-CoV-2 infection. Here, we demonstrate that uponphagocytosis of SARS-CoV-2-infected cells, MDMs are activated and secrete IL-6 and TNF. Importantly, activated MDMs in turnmediate strong activation of plasmacytoid dendritic cells (pDCs), leading to the secretion of high levels of IFN-α and ***, pDC activation promoted IL-6 production by MDMs. This kind of pDC activation was dependent on direct integrinmediated cell‒cell contacts and involved stimulation of the TLR7 and STING signaling pathways. Overall, the present studydescribes a novel and potent pathway of pDC activation that is linked to the macrophage-mediated clearance of infected *** findings suggest that a high infection rate by SARS-CoV-2 may lead to exaggerated cytokine responses, which maycontribute to tissue damage and severe disease.

关键词： SARS-CoV-2 COVID-19 Monocyte-derived macrophages Plasmacytoid dendritic cell Interferon-α Inflammatory cytokines

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