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Can we promote neural regeneration through microbiota-targeted strategies? Introducing the new concept of neurobiotics

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Neural Regeneration Research 2022年第9期17卷 1965-1966页

作者： Celia Herrera-Rincon Julia Murciano-Brea Stefano Geuna Department of Biodiversity Ecology&Evolutionand ModelingData Analysis&Computational Tools for Biology Research GroupBiomathematics UnitComplutense University of MadridMadridSpain Department of Clinical and Biological Sciences and Cavalieri Ottolenghi Neuroscience InstituteUniversity of TurinTurinItaly

The human body is populated by a large number of microbial colonies,with an estimated 10-100 trillion *** total genome size of human microbial colonies by far overwhelms the size of the host’s *** heterogenous group of microbial colonies(primarily bacteria,but also archaea,eukaryotes and viruses)is referred to with the term microbiota,and although most of them populate the gut,microbes are also detectable in many other organs of the body,especially in the distal tracts of the genitourinary system and the *** the last years,an increasing amount of evidence has been accumulated on how the microbiota exerts a significant influence on the development and physiology of the human body.

关键词： neural organs size

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Cross-Validation Approach to Evaluate Clustering Algorithms: An Experimental Study Using Multi-Label datasets

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SN Computer Science 2020年第5期1卷 1-9页

作者： Tarekegn, Adane Nega Michalak, Krzysztof Giacobini, Mario Modelling and Data Science Department of Mathematics University of Turin Turin Italy Department of Information Technologies Wroclaw University of Economics Wroclaw Poland Data Analysis and Modeling Unit Department of Veterinary Sciences University of Turin Turin Italy

Clustering validation is one of the most important and challenging parts of clustering analysis, as there is no ground truth knowledge to compare the results with. Up till now, the evaluation methods for clustering algorithms have been used for determining the optimal number of clusters in the data, assessing the quality of clustering results through various validity criteria, comparison of results with other clustering schemes, etc. It is also often practically important to build a model on a large amount of training data and then apply the model repeatedly to smaller amounts of new data. This is similar to assigning new data points to existing clusters which are constructed on the training set. However, very little practical guidance is available to measure the prediction strength of the constructed model to predict cluster labels for new samples. In this study, we proposed an extension of the cross-validation procedure to evaluate the quality of the clustering model in predicting cluster membership for new data points. The performance score was measured in terms of the root mean squared error based on the information from multiple labels of the training and testing samples. The principal component analysis (PCA) followed by k-means clustering algorithm was used to evaluate the proposed method. The clustering model was tested using three benchmark multi-label datasets and has shown promising results with overall RMSE of less than 0.075 and MAPE of less than 12.5% in three datasets. © 2020, Springer Nature Singapore Pte Ltd.

关键词： Clustering analysis Clustering validation Cross-validation Multi-label data

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An elementary approach based on variational inequalities for modelling a friction-based locomotion problem

arXiv

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arXiv 2024年

作者： Chen, Panyu González, Álvaro Mateos Mertz, Laurent Department of Computer Science Duke University United States University of Michigan-Shanghai Jiao Tong University Joint Institute Shanghai Jiao Tong University Shanghai200240 China Modeling Data Analysis & Computational Tools for Biology Research Group Biomathematics Unit Department of Biodiversity Ecology & Evolution Faculty of Biological Sciences Complutense University of Madrid Madrid28040 Spain Department of Mathematics City University of Hong Kong Kowloon Hong Kong

We propose an elementary proof based on a penalization technique to show the existence and uniqueness of the solution to a system of variational inequalities modelling the friction-based motion of a two-body crawling ... 详细信息

关键词： Friction

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BACTERIAL CONTACT INDUCES MORPHOLOGICAL AND FUNCTIONAL CHANGES IN PRIMARY NEURAL CORTICAL CELL CULTURES

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IBRO Neuroscience Reports 2023年 15卷 S227-S228页

作者： Juan Lombardo-Hernández David Muñoz-Rodríguez Marwane Bourqqia-Ramzi Pablo Garcia-Pérez Antonio Murciano Stefano Geuna Francisco Conejero Alvaro Mateos González M.T Garcia-Esteban Celia Herrera-Rincón Complutense University of Madrid Department Of Biodiversity Ecology & Evolution And Modeling Data Analysis & Computational Tools For Biology Research Group Biomathematics Unit Madrid Spain University of Turin Clinical And Biological Sciences Torino Italy NYU Shanghai Research Mathematics Shanghai China Complutense University of Madrid Microbiology Madrid Spain

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CSIG-11. TUMOR-CELL INTRINSIC CALCIUM OSCILLATIONS DRIVE BRAIN METASTASIS

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Neuro-Oncology 2024年第SUPPLEMENT_8期26卷 viii65–viii66页

作者： Hebach, Nils R Olshausen, Niels Schlag, Joana S Bang, Severin Kraft, Theresa Mayer, Chanté Linke, Zoe Westphal, Dana Seifert, Michael Timmer, Jens Wick, Wolfgang Winkler, Frank Karreman, Matthia A Clinical Cooperation Unit Neurooncology German Cancer Research Center Heidelberg Germany Neurology Clinic and National Center for Tumor Diseases Heidelberg Germany Institute of Physics University of Freiburg Freiburg Germany Freiburg Center for Data Analysis and Modeling (FDM) Freiburg Germany Institute for Medical Informatics and Biometry (IMB) Carl Gustav Carus Faculty of Medicine Dresden Germany National Center for Tumor Diseases (NCT) Dresden Germany Department of Dermatology Medical Faculty and University Hospital Carl Gustav Carus Dresden Germany

Calcium is a ubiquitous secondary messenger which regulates many cellular processes. Recently, we have shown that a subpopulation of glioblastoma cells can intrinsically generate calcium oscillations which drive proliferative signalling. Here, we set out to investigate whether such cancer cell autonomous oscillations are also present in secondary brain tumours. Employing longitudinal intravital two-photon microscopy in awake mice, we demonstrate that brain metastases of melanoma and lung cancer exhibit spontaneous calcium oscillationsin vivoalong the metastatic cascade. These oscillations are already observed during intravascular arrest and inin vitromonocultures, suggesting a tumour-cell intrinsic origin. We developed a fully automatic image analysis pipeline to accurately quantify calcium oscillations bothin vivoandin vitro. Mathematical modelling of cytosolic and ER calcium stores can predict stable calcium oscillations with similar frequency and peak characteristics as those experimentally observed. We discovered that these oscillations are tightly regulated by an interplay of calcium-induced calcium release and store-operated calcium entry (SOCE). Similarly, SOCE-related ion channels are enriched in tissue from human melanoma brain metastases compared to healthy brain controls and calcium activity can also be observedex vivoin patient-derived brain metastasis resections. Finally, by correlating calcium activity and EdU incorporation we discovered that the presence of calcium oscillations predicts their proliferative potentialin vitro. Importantly, by intravital two-photon microscopy we show that calcium activity correlates with metastasis size in preclinical models, suggesting a potential new therapeutic angle from which to target brain metastases.

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Corrigendum to "Risk factors of early spontaneous preterm birth despite carrying a cervical pessary in singleton pregnancies with a short cervix: Development of a risk prediction model" [Eur J Obstet Gynecol Reprod Biol X 22 (2024) 100305]

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European journal of obstetrics & gynecology and reproductive biology: X 2024年 23卷 100325页

作者： Carme Merced Laia Pratcorona Teresa Higueras Mireia Vargas Esther Del Barco Judit Solà Elena Carreras Maria Goya Department of Obstetrics Hospital Universitari de Vic Consorci Hospitalari de Vic Barcelona Spain. Department of Obstetrics Hospital Germans Trias I Pujol Universitat Autònoma de Barcelona Barcelona Spain. Maternal Fetal Medicine Unit Department of Obstetrics Hospital Universitari Vall d'Hebron Universitat Autònoma de Barcelona Barcelona Spain. Department of Obstetrics Althaia Xarxa Assistencial Universitària de Manresa Barcelona Spain. Data Analysis and Modeling Research Group Universitat de Vic-Universitat Central de Catalunya Vic Barcelona Spain.

[This corrects the article DOI: 10.1016/***.2024.100305.].

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Recent advances in T-cell receptor repertoire analysis: Bridging the gap with multimodal single-cell RNA sequencing

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ImmunoInformatics 2022年 5卷

作者： Sebastiaan Valkiers Nicky de Vrij Sofie Gielis Sara Verbandt Benson Ogunjimi Kris Laukens Pieter Meysman Adrem Data Lab Department of Computer Science University of Antwerp Antwerp Belgium Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS) University of Antwerp Antwerp Belgium Clinical Immunology Unit Department of Clinical Sciences Institute of Tropical Medicine Antwerp Belgium Molecular Digestive Oncology Department of Oncology Katholieke Universiteit Leuven Leuven Belgium Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID) Vaccine & Infectious Disease Institute (VAXINFECTIO) University of Antwerp Antwerp Belgium Antwerp Center for Translational Immunology and Virology (ACTIV) Vaccine and Infectious Disease Institute (VAXINFECTIO) University of Antwerp Antwerp Belgium Department of Paediatrics Antwerp University Hospital Antwerp Belgium

T cells exercise a multitude of functions such as cytotoxicity, secretion of immunomodulating cytokines or regulation of tolerance, collectively resulting in an effective control of immune-related disease. Through the unique mechanism of V(D)J recombination, T cells express a highly specific receptor complex known as the T-cell receptor (TCR). Single-cell sequencing technologies have paved the road for interrogating the transcriptome and the paired αβ TCR repertoire of a single T cell in tandem. In contrast, conventional bulk methods are restricted to only one layer of information. This combination of transcriptomic- and repertoire information can provide novel insight into the functional character of T cell immunity. Recently, single-cell technologies have gained in popularity due to improvements in throughput, decrease in cost and the ability for multimodal experiments that integrate different information layers. Consequently, this prompts the need for the development of novel computational tools that integrate transcriptomic profiles and corresponding features of the TCR repertoire. Here we discuss the current progress in the field of single-cell T cell sequencing, with a focus on the multimodality of new approaches that allow the paired profiling of cellular phenotype and clonotype information. In addition, this review provides detailed descriptions of recent computational developments for analyzing single-cell TCR sequencing data in an integrative manner using novel computational approaches. Finally, we present an overview of the available software tools that can be used to perform integrative analysis of gene expression and TCR profiles.

关键词： Single-cell sequencing Single-cell immune profiling Single-cell gene expression T-cell receptor repertoire Multi-omics

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Plotting time: On the usage of CNNs for time series classification

arXiv

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arXiv 2021年

作者： Rodrigues, Nuno M. Batista, João E. Trujillo, Leonardo Duarte, Bernardo Giacobini, Mario Vanneschi, Leonardo Silva, Sara LASIGE Faculdade de Ciências da Universidade de Lisboa Campo Grande Lisboa1749-016 Portugal Departamento de Ingeniería Eléctrica y Electrónica Tecnológico Nacional Mexico IT de Tijuana Mexico MARE Marine and Environmental Sciences Centre Faculdade de Ciências da Universidade de Lisboa Campo Grande Lisboa1749-016 Portugal Departamento de Biologia Vegetal Faculdade de Ciências da Universidade de Lisboa Campo Grande Lisboa1749-016 Portugal Data Analysis and Modeling Unit Department of Veterinary Sciences University of Torino Italy Universidade Nova de Lisboa Campus de Campolide Lisboa1070-312 Portugal

We present a novel approach for time series classification where we represent time series data as plot images and feed them to a simple CNN, outperforming several state-of-the-art methods. We propose a simple and highly replicable way of plotting the time series, and feed these images as input to a non-optimized shallow CNN, without any normalization or residual connections. These representations are no more than default line plots using the time series data, where the only pre-processing applied is to reduce the number of white pixels in the image. We compare our method with different state-of-the-art methods specialized in time series classification on two real-world non public datasets, as well as 98 datasets of the UCR dataset collection. The results show that our approach is very promising, achieving the best results on both real-world datasets and matching / beating the best state-of-the-art methods in six UCR datasets. We argue that, if a simple naive design like ours can obtain such good results, it is worth further exploring the capabilities of using image representation of time series data, along with more powerful CNNs, for classification and other related tasks. © 2021, CC BY.

关键词： Classification (of information)

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Correction: Clinical and laboratory features associated with macrophage activation syndrome in Still's disease: data from the international AIDA Network Still's Disease Registry

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Internal and emergency medicine 2024年第1期19卷 255-257页

作者： Paola Triggianese Antonio Vitale Giuseppe Lopalco Henrique Ayres Mayrink Giardini Francesco Ciccia Ibrahim Al-Maghlouth Piero Ruscitti Petros Paul Sfikakis Florenzo Iannone Isabele Parente de Brito Antonelli Martina Patrone Kazi Nur Asfina Ilenia Di Cola Katerina Laskari Carla Gaggiano Abdurrahman Tufan Paolo Sfriso Lorenzo Dagna Roberto Giacomelli Andrea Hinojosa-Azaola Gaafar Ragab Lampros Fotis Haner Direskeneli Veronica Spedicato Marilia Ambiel Dagostin Daniela Iacono Hebatallah Hamed Ali Paola Cipriani Jurgen Sota Riza Can Kardas Sara Bindoli Corrado Campochiaro Luca Navarini Stefano Gentileschi Eduardo Martín-Nares Jiram Torres-Ruiz Moustafa Ali Saad Katerina Kourtesi Fatma Alibaz-Oner Gizem Sevik Annamaria Iagnocco Joanna Makowska Marcello Govoni Sara Monti Maria Cristina Maggio Francesco La Torre Emanuela Del Giudice José Hernández-Rodríguez Elena Bartoloni Giacomo Emmi Maria Sole Chimenti Armin Maier Gabriele Simonini Giovanni Conti Alma Nunzia Olivieri Maria Tarsia Amato De Paulis Alberto Lo Gullo Ewa Więsik-Szewczyk Ombretta Viapiana Benson Ogunjimi Samar Tharwat Sukran Erten Rossana Nuzzolese Anastasios Karamanakos Micol Frassi Alessandro Conforti Valeria Caggiano Achille Marino Gian Domenico Sebastiani Antonio Gidaro Enrico Tombetti Francesco Carubbi Giovanni Rubegni Alessandra Cartocci Alberto Balistreri Claudia Fabiani Bruno Frediani Luca Cantarini Rheumatology Allergology and Clinical Immunology Department of Systems Medicine University of Rome Tor Vergata Rome Italy. University of Rome Tor Vergata Rome Italy. Department of Medical Sciences Surgery and Neurosciences Research Center of Systemic Autoinflammatory Diseases Behçet's Disease Clinic and Rheumatology-Ophthalmology Collaborative Uveitis Center University of Siena Siena Italy. vitale.reumatologia@***. UOC Reumatologia Azienda Ospedaliero-Universitaria Senese ERN-RITA Center Siena Italy. vitale.reumatologia@***. Policlinico "Le Scotte" Viale Bracci 1 53100 Siena Italy. vitale.reumatologia@***. Rheumatology Unit Department of Emergency and Organ Transplantation University of Bari Bari Italy. Rheumatology Division Faculdade de Medicina Hospital das Clínicas Universidade de São Paulo São Paulo Brazil. Department of Precision Medicine Università Degli Studi Della Campania Luigi Vanvitelli Naples Italy. Rheumatology Unit Department of Medicine College of Medicine King Saud University Riyadh Saudi Arabia. College of Medicine Research Center College of Medicine King Saud University Riyadh Saudi Arabia. Rheumatology Unit Department of Biotechnological and Applied Clinical Sciences University of L'Aquila L'Aquila Italy. Joint Academic Rheumatology Program National and Kapodistrian University of Athens Medical School Athens Greece. Department of Medical Sciences Surgery and Neurosciences Research Center of Systemic Autoinflammatory Diseases Behçet's Disease Clinic and Rheumatology-Ophthalmology Collaborative Uveitis Center University of Siena Siena Italy. UOC Reumatologia Azienda Ospedaliero-Universitaria Senese ERN-RITA Center Siena Italy. Division of Rheumatology Department of Internal Medicine Gazi University Faculty of Medicine Ankara Turkey. Rheumatology Unit Department of Medicine (DIMED) University of Padova Padua Italy. Unit of Immunology Rheumatology Allergy and Rare Diseases IRCCS San Raffaele Hospital Milan Italy. Vita-Salute Sa

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INTRODUCTION

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Bulletin of the American Meteorological Society 2024年第8期105卷 S1-S11页

作者： Boyer, T. Blunden, J. Dunn, R.J.H. NOAA/NESDIS National Centers for Environmental Information Silver Spring Maryland NOAA/NESDIS National Centers for Environmental Information Asheville North Carolina Met Office Hadley Centre Exeter United Kingdom European Centre for Medium-Range Weather Forecasts Reading United Kingdom University of Maryland College Park Maryland Scripps Institution of Oceanography University of California San Diego La Jolla California NOAA/NWS National Centers for Environmental Prediction Climate Prediction Center College Park Maryland Brandenburg University of Technology (BTU) Cottbus-Senftenberg Germany Servicio Meteorológico Nacional Buenos Aires Argentina NOAA/OAR Physical Sciences Laboratory Boulder Colorado European Centre for Medium-Range Weather Forecasts Bonn Germany Center for Geophysical Research and School of Physics University of Costa Rica San José Costa Rica Department of Meteorology and National Centre for Earth Observation University of Reading Reading United Kingdom Centro Nacional de Monitoramento e Alertas de Desastres Naturais CEMADEN São Paulo Brazil Université Grenoble Alpes Institut des Géosciences de l’Environnement IRD CNRS Grenoble INP Grenoble France Hampton University Hampton Virginia Seychelles Meteorological Authority Mahe Seychelles Section for Glaciers Ice and Snow Norwegian Water Resources and Energy Directorate Oslo Norway National Research Institute for Agriculture Food and Environment (INRAE) CARRTEL Université Savoie Mont Blanc Thonon les Bains France Graduate School of Agriculture Osaka Metropolitan University Sakai Japan Science Faculty Universidad Nacional de Colombia Bogotá Colombia University of Bremen Bremen Germany NOAA Global Monitoring Laboratory Boulder Colorado Servicio Nacional de Meteorología e Hidrología del Perú Lima Perú Centro de Investigaciones sobre Desertificación – Spanish National Research Council (CSIC-UV-GVA) Valencia Spain Hydro-Climate Extremes Lab (H-CEL) Ghent University Ghent Belgium Department o

In 2023, La Niña conditions that generally prevailed in the eastern Pacific Ocean from mid-2020 into early 2023 gave way to a strong El Niño by October. Atmospheric concentrations of Earth’s major greenhouse gases—carbon dioxide, methane, and nitrous oxide—all increased to record-high levels. The annual global average carbon dioxide concentration in the atmosphere rose to 419.3±0.1 ppm, which is 50% greater than the pre-industrial level. The growth from 2022 to 2023 was 2.8 ppm, the fourth highest in the record since the 1960s. The combined short-term effects of El Niño and the long-term effects of increasing levels of heat-trapping gases in the atmosphere contributed to new records for many essential climate variables reported here. The annual global temperature across land and oceans was the highest in records dating as far back as 1850, with the last seven months (June–December) having each been record warm. Over land, the globally averaged temperature was also record high. Dozens of countries reported record or near-record warmth for the year, including China and continental Europe as a whole (warmest on record), India and Russia (second warmest), and Canada (third warmest). Intense and widespread heatwaves were reported around the world. In Vietnam, an all-time national maximum temperature record of 44.2°C was observed at Tuong Duong on 7 May, surpassing the previous record of 43.4°C at Huong Khe on 20 April 2019. In Brazil, the air temperature reached 44.8°C in Araçuaí in Minas Gerais on 20 November, potentially a new national record and 12.8°C above normal. The effect of rising temperatures was apparent in the cryosphere, where snow cover extent by June 2023 was the smallest in the 56-year record for North America and seventh smallest for the Northern Hemisphere overall. Heatwaves contributed to the greatest average mass balance loss for Alpine glaciers around the world since the start of the record in 1970. Due to rapid volume loss beginning in 2021, St. A

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