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TICA: Transcriptional Interaction and Coregulation Analyzer

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Genomics, Proteomics & Bioinformatics 2018年第5期16卷 342-353页

作者： stefano perna Pietro Pinoli stefano Ceri Limsoon Wong Dipartimento di Elettronica Informazione e Bioingegneria Politecnico di Milano School of Computing National University of Singapore

Transcriptional regulation is critical to cellular processes of all organisms. Regulatory mechanisms often involve more than one transcription factor(TF) from different families, binding together and attaching to the DNA as a single complex. However, only a fraction of the regulatory partners of each TF is currently known. In this paper, we present the Transcriptional Interaction and Coregulation Analyzer(TICA), a novel methodology for predicting heterotypic physical interaction of TFs. TICA employs a data-driven approach to infer interaction phenomena from chromatin immunoprecipitation and sequencing(ChIP-seq) data. Its prediction rules are based on the distribution of minimal distance couples of paired binding sites belonging to different TFs which are located closest to each other in promoter regions. Notably, TICA uses only binding site information from input ChIP-seq experiments, bypassing the need to do motif calling on sequencing data. We present our method and test it on ENCODE ChIP-seq datasets, using three cell lines as reference including HepG2, GM12878, and K562. TICA positive predictions on ENCODE ChIP-seq data are strongly enriched when compared to protein complex(CORUM) and functional interaction(BioGRID) databases. We also compare TICA against both motif/ChIP-seq based methods for physical TF–TF interaction prediction and published literature. Based on our results, TICA offers significant specificity(average 0.902) while maintaining a good recall(average 0.284) with respect to CORUM, providing a novel technique for fast analysis of regulatory effect in cell lines. Furthermore, predictions by TICA are complementary to other methods for TF–TF interaction prediction(in particular, TACO and CENTDIST). Thus, combined application of these prediction tools results in much improved sensitivity in detecting TF–TF interactions compared to TICA alone(sensitivity of 0.526 when combining TICA with TACO and 0.585 when combining with CENTDIST)with little compromise in specificity(specificity 0.760 when combining

关键词： Transcription factors Coregulation Protein–protein interactions Machine learning Data-driven analysis

Physical exercise and traumatic brain injury: is it question of time?

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Neural Regeneration Research 2024年第3期19卷 475-476页

作者： Valentina Mastrorilli stefano Farioli Vecchioli Institute of Biochemistry and Cell Biology Institute of Biochemistry and Cell BiologyNational Research Council(IBBC/CNR)MonterotondoRomeItaly Plaisant S.R.L. RomeItaly

Is it better to be safe than sorry?This Hamletic dilemma has always stimulated medical-scientific debates in numerous fields of biomedicine.And among these,the preventive-therapeutic approach to the treatment of brain trauma is one of the most striking examples.Traumatic brain injury(TBI)is a leading cause of brain damage among young and elderly populations with a very high hospitalization and death rate.TBI is characterized by two pathologically distinct but strictly consequential phases:a first characterized by an immediate and highly variable mechanical dysfunction of the brain tissue,which involves widespread cell death and tissue degeneration,followed by a second phase which can last from days to even years depending on the severity of the TBI and the patient’s pre-existing health status.Secondary processes,including inflammatory phenomena,oxidative stress associated with metabolic,vascular,and neuro-modulatory deficits,are very often responsible for neuro-motor and psychological deficits leading to long-term disabilities(Kaur and Sharma,2018).

关键词： injury striking modulator

CBE Clima Tool:A free and open-source web application for climate analysis tailored to sustainable building design

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Building Simulation 2024年第3期17卷 493-508页

作者： Giovanni Betti Federico Tartarini Christine Nguyen stefano Schiavon Center for the Built Environment University of California BerkeleyBerkeleyUSA Berkeley Education Alliance for Research in Singapore SingaporeSingapore Heat and Health Research Incubator Faculty of Medicine and HealthThe University of SydneyCamperdownAustralia College of Letters and Sciences University of California BerkeleyBerkeleyUSA

Climate-responsive building design holds immense potential for enhancing comfort,energy efficiency,and environmental sustainability.However,many social,cultural,and economic obstacles might prevent the wide adoption of designing climate-adapted buildings.One of these obstacles can be removed by enabling practitioners to easily access,visualize and analyze local climate data.The CBE Clima Tool(Clima)is a free and open-source web application that offers easy access to publicly available weather files and has been created for building energy simulation and design.It provides a series of interactive visualizations of the variables contained in the EnergyPlus Weather Files and several derived ones like the UTCI or the adaptive comfort indices.It is aimed at students,educators,and practitioners in the architecture and engineering fields.Since its inception,Clima’s user base has exhibited robust growth,attracting over 25,000 unique users annually from across 70 countries.Our tool is poised to revolutionize climate-adaptive building design,transcending geographical boundaries and fostering innovation in the architecture and engineering fields.

关键词： architectural design climate analysis sustainable building design web application building energy simulation open-source software

Integrated CO_(2)capture and reduction catalysis:Role ofγ-Al_(2)O_(3)support,unique state of potassium and synergy with copper

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Journal of Environmental Sciences 2024年第6期140卷 113-122页

作者： Donato Pinto stefano Minorello Zhouping Zhou Atsushi Urakawa Catalysis Engineering Department of Chemical EngineeringDelft University of TechnologyDelft2629HZNetherlands

Carbon dioxide capture and reduction(CCR)process emerges as an efficient catalytic strategy for CO_(2)capture and conversion to valuable chemicals.K-promoted Cu/Al_(2)O_(3)catalysts exhibited promising CO_(2)capture efficiency and highly selective conversion to syngas(CO+H_(2)).The dynamic nature of the Cu-K system at reaction conditions complicates the identification of the catalytically active phase and surface sites.The present work aims at more precise understanding of the roles of the potassium and copper and the contribution of the metal oxide support.Whileγ-Al_(2)O_(3)guarantees high dispersion and destabilisation of the potassium phase,potassium and copper act synergistically to remove CO_(2)from diluted streams and promote fast regeneration of the active phase for CO_(2)capture releasing CO while passing H_(2).A temperature of 350℃is found necessary to activate H_(2)dissociation and generate the active sites for CO_(2)capture.The effects of synthesis parameters on the CCR activity are also described by combination of ex-situ characterisation of the materials and catalytic testing.

关键词： Carbon dioxide Carbon capture and utilisation CO_(2)capture and reduction Solid CO_(2)sorbents Heterogeneous catalysis Potassium Copper catalysts Aluminium oxide

Estimating wood quality attributes from dense airborne LiDAR point clouds

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Forest Ecosystems 2024年第2期11卷 226-235页

作者： Nicolas Cattaneo stefano Puliti Carolin Fischer Rasmus Astrup Norwegian Institute of Bioeconomy Research(NIBIO) Division of Forest and Forest ResourcesHøgskoleveien 81433ÅsNorway

Mapping individual tree quality parameters from high-density LiDAR point clouds is an important step towards improved forest inventories.We present a novel machine learning-based workflow that uses individual tree point clouds from drone laser scanning to predict wood quality indicators in standing trees.Unlike object reconstruction methods,our approach is based on simple metrics computed on vertical slices that summarize information on point distances,angles,and geometric attributes of the space between and around the points.Our models use these slice metrics as predictors and achieve high accuracy for predicting the diameter of the largest branch per log (DLBs) and stem diameter at different heights (DS) from survey-grade drone laser scans.We show that our models are also robust and accurate when tested on suboptimal versions of the data generated by reductions in the number of points or emulations of suboptimal single-tree segmentation scenarios.Our approach provides a simple,clear,and scalable solution that can be adapted to different situations both for research and more operational mapping.

关键词： UAV laser scanning Wood quality Machine learning Point cloud metrics

A quantitative analysis of the US materials flow methodology and comparison to the EU methodology for MSW statistics

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Waste Disposal and Sustainable Energy 2024年第1期6卷 85-94页

作者： Demetra Tsiamis Fabio Poretti stefano Consonni Marco J.Castaldi Earth Engineering Center Department of Chemical EngineeringThe City College of New YorkNew YorkNYUSA Dipartimento Di Energetica Politecnico Di MilanoPiazza Leonardo da Vinci 3220133MilanItaly

The European Union(EU)and the United States(US)determine municipal solid waste(MSW)statistics differently.The EU applies a site-specific methodology that directly measures waste whereas the US employs a materials flow methodology that estimates MSW statistics indirectly based on production and recovery data from industries.This study dissects the materials flow methodology and presents quantitative materials flow Sankey diagrams for the primary MSW materials to highlight data gaps that can be addressed to improve the methodology’s accuracy.Private industry plastics data were applied to the materials flow methodology,and the results were within 10%of the plastics statistics reported by the US Environmental Protection Agency(US EPA).Drawbacks to the methodologies include EU measurement inaccuracies due to double-counting and not accounting for residual waste in the US.The latter may partially explain why landfilling tonnages reported by the US EPA were approximately 60%less than the tonnages reported by the Waste to Energy Research and Technology Council(WTERT)in its national MSW survey that applied the EU methodology in the US.Unlike the EU,there is no US national policy that requires states to measure and report state-level waste data to the US EPA.Future improvements in US MSW statistics rely heavily on the implementation of national policies to homogenize the measurement and collection of waste data from states.

关键词： Materials flow methodology Site-specific methodology United States European Union Municipal solid waste Discrepancy

Endoscopic treatment of scarred polyps with a non-thermal device(Endorotor):A review of the literature

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World Journal of Gastroenterology 2024年第12期30卷 1706-1713页

作者： Mariam Zaghloul Hameed Rehman stefano Sansone Konstantinos Argyriou Adolfo Parra-Blanco Department of Hepatology Gastroenterology and Infectious DiseasesKafrelsheikh UniversitKafr-Elshikh 33516Egypt Department of Gastroenterology Service Nottingham City Hospital CampusNottingham University Hospitals NHS TrustNottingham NG51PBUnited Kingdom Department of Gastroenterology University Hospital of LarissaLarissa 41334Greece NIHR Nottingham Biomedical Research Centre Nottingham University Hospitals NHS Trust and University of NottinghamNottingham NG72UHUnited Kingdom

Endoscopic resection(ER)of colorectal polyps has become a daily practice in most endoscopic units providing a colorectal cancer screening program and requires the availability of local experts and high-end endoscopic devices.ER procedures have evolved over the past few years from endoscopic mucosal resection(EMR)to more advanced techniques,such as endoscopic submucosal dissection and endo-scopic full-thickness resection.Complete resection and disease eradication are the ultimate goals of ER-based techniques,and novel devices have been developed to achieve these goals.The EndoRotor®Endoscopic Powered Resection System(Interscope Medical,Inc.,Northbridge,Massachusetts,United States)is one such device.The EndoRotor is a powered resection tool for the removal of alimentary tract mucosa,including post-EMR persistent lesions with scarring,and has both CE Mark and FDA clearance.This review covers available published evidence documenting the usefulness of EndoRotor for the management of recurrent colorectal polyps.

关键词： EndoRotor Scarred polyps Recurrent polyps Colorectal cancer Colorectal polyps

A CFD Model to Evaluate Near-Surface Oil Spill from a Broken Loading Pipe in Shallow Coastal Waters

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Fluid Dynamics & Materials Processing 2024年第1期20卷 59-77页

作者： Portia Felix Lee Leon Derek Gay stefano Salon Hazi Azamathulla Department of Civil and Environmental Engineering The University of the West IndiesSt.AugustineTrinidad and Tobago National Institute of Oceanography and Experimental Geophysics-OGS TriesteItaly

Oil spills continue to generate various issues and concerns regarding their effect and behavior in the marine environment,owing to the related potential for detrimental environmental,economic and social implications.It is essential to have a solid understanding of the ways in which oil interacts with the water and the coastal ecosystems that are located nearby.This study proposes a simplified model for predicting the plume-like transport behavior of heavy Bunker C fuel oil discharging downward from an acutely-angled broken pipeline located on the water surface.The results show that the spill overall profile is articulated in three major flow areas.The first,is the source field,i.e.,a region near the origin of the initial jet,followed by the intermediate or transport field,namely,the region where the jet oil flow transitions into an underwater oil plume flow and starts to move horizontally,and finally,the far-field,where the oil re-surface and spreads onto the shore at a significant distance from the spill site.The behavior of the oil in the intermediate field is investigated using a simplified injection-type oil spill model capable of mimicking the undersea trapping and lateral migration of an oil plume originating from a negatively buoyant jet spill.A rectangular domain with proper boundary conditions is used to implement the model.The Projection approach is used to discretize a modified version of the Navier-Stokes equations in two dimensions.A benchmark fluid flow issue is used to verify the model and the results indicate a reasonable relationship between specific gravity and depth as well as agreement with the aerial data and a vertical temperature profile plot.

关键词： CFD model Navier-Stokes equations projection method water surface oil spill shallow coastal waters

Solid pseudopapillary tumor of the pancreas:A systematic review of clinical,surgical and oncological characteristics of 1384 patients underwent pancreatic surgery

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Hepatobiliary & Pancreatic Diseases International 2024年第4期23卷 331-338页

作者： Gennaro Mazzarella Edoardo Maria Muttillo Diego Coletta Biagio Picardi stefano Rossi Simone Rossi Del Monte Vito Gomes Irnerio Angelo Muttillo Division of General and Emergency Surgery San Filippo Neri Hospital00136 RomeItaly Department of Surgery“Pietro Valdoni” Sapienza University of RomeViale del Policlinico 15500161 RomeItaly Surgical and Medical Department of Translational Medicine Sant’Andrea HospitalSapienza University of Rome00185 RomeItaly Department of Surgical Sciences Umberto I University HospitalSapienza University of Rome00136 RomeItaly Department of General Surgery Ospedali Riuniti Marche Nord61121 PesaroItaly Department of Pathology San Filippo Neri Hospital00136 RomeItaly

Background:Pancreatic solid pseudopapillary tumors(SPTs)are rare clinical entity,with low malignancy and still unclear pathogenesis.They account for less than 2%of exocrine pancreatic neoplasms.This study aimed to perform a systematic review of the main clinical,surgical and oncological characteristics of pancreatic SPTs.Data sources:MEDLINE/PubMed,Web of Science and Scopus databases were systematically searched for the main clinical,surgical and oncological characteristics of pancreatic SPTs up to April 2021,in accordance with the preferred reporting items for systematic reviews and meta-analyses(PRISMA)standards.Primary endpoints were to analyze treatments and oncological outcomes.Results:A total of 823 studies were recorded,86 studies underwent full-text reviews and 28 met inclusion criteria.Overall,1384 patients underwent pancreatic surgery.Mean age was 30 years and 1181 patients(85.3%)were female.The most common clinical presentation was non-specific abdominal pain(52.6%of cases).Mean overall survival was 98.1%.Mean recurrence rate was 2.8%.Mean follow-up was 4.2 years.Conclusions:Pancreatic SPTs are rare,and predominantly affect young women with unclear pathogenesis.Radical resection is the gold standard of treatment achieving good oncological impact and a favorable prognosis in a yearly life-long follow-up.

关键词： Frantz’s tumor Pancreas Pancreatic neoplasms Pancreatic surgery Solid pseudopapillary tumor