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Multivariate Developmental Pattern of Cortical Thickness, Brain Functional Connectivity and Behaviour: a Multi-Block Partial Least Square Discriminant Analysis

Multivariate Developmental Pattern of Cortical Thickness, Br...

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Metrology for Extended Reality, Artificial Intelligence and Neural Engineering (MetroXRAINE), IEEE International Conference on

作者： Emma Tassi Federica Goffi Carolina Bonivento Maddalena Mauri Nivedita Agarwal Rossano Girometti Yvan Torrente Anna Maria Bianchi Maria Nobile Eleonora Maggioni Paolo Brambilla Dept. of Neurosciences and Mental Health IRCCS Ca’ Granda Ospedale Maggiore Policlinico Milan Italy Department of Electronics Information and Bioengineering Politecnico di Milano Milan Italy Polo FVG Scientific Institute IRCCS ‘Eugenio Medea’ Pasian di Prato Udine Italy Child Psychopathology Unit Scientific Institute IRCCS Eugenio Medea Bosisio Parini Italy PhD program in Neuroscience School of Medicine and Surgery University of Milano-Bicocca Milan Italy Neuroimaging Lab Scientific Institute IRCCS E. Medea Bosisio Parini Italy Department of Medicine Institute of Radiology University of Udine Udine Italy Department of Pathophysiology and Transplantation Universita degli Studi di Milano Milan Italy

ISBN: (数字)9798350378009

ISBN: (纸本)9798350378016

The intricate relationship between emotional and behavioral traits and brain anatomy and function during childhood and adolescence is crucial for elucidating the neurobiological basis of diverse psychopathological disorders but it still largely unknown. In this study, we aimed to quantitatively evaluate the multivariate patterns of association between brain activity, cortical brain characteristics, and core clinical and behavioral features in a sample of forty subjects with age ranging between 11–21 years who were referred for emotional-behavioral problems. By exploiting a multi-block partial least square discriminant analysis (MBPLS-DA) framework, we attempt to explain the multivariate relations among the Child Behavior Checklist (CBCL) and brain structure and function assessed via magnetic resonance imaging (MRI). Based on individual importance of each block, our findings showed a prominent contribution of regional cortical thickness data in explaining the variance of CBCL scales. By analyzing each block's loadings individually, a prominent positive association was found among regional cortical thickness in paracentral, lateral occipital cortex, precuneus and CBCL composite scores of psychotic, autism spectrum disorder risk profiles and withdrawn scale. Furthermore, the same CBCL scores were also found positively associated with functional connections involving regions of anterior and median cingulate cortex, caudate nucleus, inferior parietal lobule and angular gyrus. Our investigation suggests a key role of brain structure and function in shaping behavioral traits that might be predispose to psychopathology during childhood and adolescence. The proposed MBPLS-DA application promotes broader adoption of this technique across diverse and multimodal MRI and clinical datasets.

关键词： Brain Magnetic resonance imaging Computed tomography Loading Neural engineering Focusing Metrology Resonance Thickness measurement Periodic structures

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Towards decoding the coupled decision-making of metabolism and epithelial-mesenchymal transition in cancer

arXiv

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arXiv 2020年

作者： Jia, Dongya Park, Jun Hyoung Kaur, Harsimran Jung, Kwang Hwa Yang, Sukjin Tripathi, Shubham Galbraith, Madeline Deng, Youyuan Jolly, Mohit Kumar Kaipparettu, Benny Abraham Onuchic, José N. Levine, Herbert Center for Theoretical Biological Physics Rice University HoustonTX77005 United States Department of Molecular and Human Genetics Baylor College of Medicine HoustonTX77030 United States Centre for BioSystems Science and Engineering Indian Institute of Science BangaloreKarnataka560012 India PhD Program in Systems Synthetic and Physical Biology Rice University HoustonTX77005 United States Department of Physics Northeastern University BostonMA02115 United States Department of Physics and Astronomy Rice University HoustonTX77005 United States Applied Physics Graduate Program Rice University HoustonTX77005 United States Dan L. Duncan Comprehensive Cancer Center Baylor College of Medicine HoustonTX77030 United States Department of Chemistry Rice University HoustonTX77005 United States Department of Biosciences Rice University HoustonTX77005 United States Department of Bioengineering Northeastern University BostonMA02115 United States

Cancer cells have the plasticity to adjust their metabolic phenotypes for survival and metastasis. During metastasis, a developmental program known as the epithelial-mesenchymal transition (EMT) plays a critical role. There is extensive cross-talk between metabolism and EMT, but how this leads to coordinated physiological changes is still uncertain. The elusive connection between metabolism and EMT compromises the efficacy of metabolic therapies targeting metastasis. In this review, we aim for clarifying causation between metabolism and EMT based on recent experimental studies and propose integrated theoretical-experimental efforts to better understand the coupled decision-making of metabolism and EMT. © 2020, CC-BY-NC-ND.

关键词： Metabolism

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Epigenetic factor competition reshapes the EMT landscape

arXiv

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arXiv 2022年

作者： Ali Al-Radhawi, M. Tripathi, Shubham Zhang, Yun Sontag, Eduardo D. Levine, Herbert Department of Electrical and Computer Engineering Northeastern University BostonMA02115 United States Center for Theoretical Biological Physics Northeastern University BostonMA02115 United States PhD Program in Systems Synthetic and Physical Biology Rice University HoustonTX77005 United States Whitehead Institute for Biomedical Research CambridgeMA02142 United States Department of Bioengineering Northeastern University BostonMA02115 United States Department of Physics Northeastern University BostonMA02115 United States Laboratory of Systems Pharmacology Harvard Medical School BostonMA02115 United States State Key Laboratory of Molecular Oncology National Cancer Center National Clinical Research Center for Cancer Cancer Hospital Chinese Academy of Medical Sciences Peking Union Medical College Beijing100021 China

The emergence of and transitions between distinct phenotypes in isogenic cells can be attributed to the intricate interplay of epigenetic marks, external signals, and gene regulatory elements. These elements include chromatin remodelers, histone modifiers, transcription factors, and regulatory RNAs. Mathematical models known as Gene Regulatory Networks (GRNs) are an increasingly important tool to unravel the workings of such complex networks. In such models, epigenetic factors are usually proposed to act on the chromatin regions directly involved in the expression of relevant genes. However, it has been well-established that these factors operate globally and compete with each other for targets genome-wide. Therefore, a perturbation of the activity of a regulator can redistribute epigenetic marks across the genome and modulate the levels of competing regulators. In this paper, we propose a conceptual and mathematical modeling framework that incorporates both local and global competition effects between antagonistic epigenetic regulators in addition to local transcription factors, and show the counter-intuitive consequences of such interactions. We apply our approach to recent experimental findings on the Epithelial-Mesenchymal Transition (EMT). We show that it can explain the puzzling experimental data as well provide new verifiable predictions. © 2022, CC BY-NC-ND.

关键词： Transcription factors

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Erratum to “Detergent-Enzymatic Decellularization of Swine Blood Vessels: Insight on Mechanical Properties for Vascular Tissue Engineering”

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BioMed Research International 2014年第1期2014卷 412838-412838页

作者： Alessandro F. Pellegata M. Adelaide Asnaghi Ilaria Stefani Anna Maestroni Silvia Maestroni Tommaso Dominioni Sandro Zonta Gianpaolo Zerbini Sara Mantero Department of Chemistry Materials and Chemical Engineering “Giulio Natta” Politecnico di Milano Piazza Leonardo da Vinci 32 20133 Milano Italypolimi.it PhD Program in Bioengineering Politecnico di Milano Piazza Leonardo da Vinci 32 20133 Milano Italypolimi.it Complication of Diabetes Unit Division of Metabolic and Cardiovascular Sciences San Raffaele Scientific Institute Milan Italyunisr.it General Surgery I Fondazione IRCCS Pol. San Matteo Pavia ***

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Fixational eye movements enhance the precision of visual information transmitted by the primate retina

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Nature Communications 2024年第1期15卷 7964页

作者： Wu, Eric G. Brackbill, Nora Rhoades, Colleen Kling, Alexandra Gogliettino, Alex R. Shah, Nishal P. Sher, Alexander Litke, Alan M. Simoncelli, Eero P. Chichilnisky, E.J. Department of Electrical Engineering Stanford University Stanford CA United States Department of Physics Stanford University Stanford CA United States Department of Bioengineering Stanford University Stanford CA United States Department of Neurosurgery Stanford University Stanford CA United States Department of Ophthalmology Stanford University Stanford CA United States Hansen Experimental Physics Laboratory Stanford University 452 Lomita Mall Stanford 94305 CA United States Neurosciences PhD Program Stanford University Stanford CA United States Santa Cruz Institute for Particle Physics University of California Santa Cruz Santa Cruz CA United States Flatiron Institute Simons Foundation New York NY United States Center for Neural Science New York University New York NY United States Courant Institute of Mathematical Sciences New York University New York NY United States

Fixational eye movements alter the number and timing of spikes transmitted from the retina to the brain, but whether these changes enhance or degrade the retinal signal is unclear. To quantify this, we developed a Bayesian method for reconstructing natural images from the recorded spikes of hundreds of retinal ganglion cells (RGCs) in the macaque retina (male), combining a likelihood model for RGC light responses with the natural image prior implicitly embedded in an artificial neural network optimized for denoising. The method matched or surpassed the performance of previous reconstruction algorithms, and provides an interpretable framework for characterizing the retinal signal. Reconstructions were improved with artificial stimulus jitter that emulated fixational eye movements, even when the eye movement trajectory was assumed to be unknown and had to be inferred from retinal spikes. Reconstructions were degraded by small artificial perturbations of spike times, revealing more precise temporal encoding than suggested by previous studies. Finally, reconstructions were substantially degraded when derived from a model that ignored cell-to-cell interactions, indicating the importance of stimulus-evoked correlations. Thus, fixational eye movements enhance the precision of the retinal representation. © The Author(s) 2024.

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Assessment of circulating extracellular vesicles from calorie-restricted mice and humans in ischaemic injury models

Journal of Extracellular Biology

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Journal of Extracellular Biology 2023年第5期2卷 e86页

作者： Jaimes, Manuel S. V. Liao, Chia-Te Chen, Max M. Czosseck, Andreas Lee, Tsung-Lin Chou, Yu-Hsiang Chen, Yung-Ming Lin, Shuei-Liong Lai, James J. Lundy, David J. Graduate Institute of Biomedical Materials & Tissue Engineering Taipei Medical University Taipei Taiwan Division of Nephrology Department of Internal Medicine Shuang Ho Hospital Taipei Medical University New Taipei Taiwan Division of Nephrology Department of Internal Medicine School of Medicine College of Medicine Taipei Medical University Taipei Taiwan TMU Research Center of Urology and Kidney (TMU-RCUK) Taipei Medical University Taipei Taiwan Division of Nephrology Department of Internal Medicine National Taiwan University Hospital College of Medicine National Taiwan University Taipei Taiwan Graduate Institute of Physiology College of Medicine National Taiwan University Taipei Taiwan Department of Bioengineering University of Washington Seattle WA United States Department of Materials Science and Engineering National Taiwan University of Science and Technology Taipei Taiwan International PhD Program in Biomedical Engineering Taipei Medical University Taipei Taiwan Center for Cell Therapy Taipei Medical University Hospital Taipei Taiwan

Calorie restriction (CR) and fasting affect lifespan, disease susceptibility and response to acute injury across multiple animal models, including ischaemic injuries such as myocardial infarction or kidney hypoxia. The cargo and function of circulating extracellular vesicles (EV) respond to changes in host physiology, including exercise, injury, and other interventions. Thus, we hypothesised that EVs induced following CR may reflect some of the beneficial properties of CR itself. In a pilot study, EVs were isolated from mice following 21 days of 30 % CR, and from eight human donors after 72 h water-only fasting. EV size, concentration and morphology were profiled by NTA, western blot and cryoEM, and their function was assessed using multiple assays related to ischaemic diseases. We found that EVs from post-fasting samples better protected cardiac cells from hypoxia/reperfusion (H/R) injury compared to pre-fasting EVs. However, there was no difference when used to treat H/R-injured kidney epithelial cells. Post-fasting derived EVs slowed the rate of fibroblast migration and slightly reduced macrophage inflammatory gene expression compared to pre-fasting derived EVs. Lastly, we compared miRNA cargos of pre- and post-fasting human serum EVs and found significant changes in a small number of miRNAs. We conclude that fasting appears to influence EV cargo and function, with varied effects worthy of further exploration. © 2023 The Authors. Journal of Extracellular Biology published by Wiley Periodicals, LLC on behalf of the International Society for Extracellular Vesicles.

关键词： calorie restriction cardiomyocyte diet extracellular vesicle fasting hypoxia ketone macrophage microRNA serum

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Author Correction: Low-intensity pulsed ultrasound stimulation (LIPUS) modulates microglial activation following intracortical microelectrode implantation

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Nature communications 2024年第1期15卷 7618页

作者： Fan Li Jazlyn Gallego Natasha N Tirko Jenna Greaser Derek Bashe Rudra Patel Eric Shaker Grace E Van Valkenburg Alanoud S Alsubhi Steven Wellman Vanshika Singh Camila Garcia Padilla Kyle W Gheres John I Broussard Roger Bagwell Maureen Mulvihill Takashi D Y Kozai Department of Bioengineering University of Pittsburgh Pittsburgh PA USA. Center for Neural Basis of Cognition Pittsburgh PA USA. Computational Modeling and Simulation PhD Program University of Pittsburgh Pittsburgh PA USA. Department of Biochemistry and Molecular Biology Pennsylvania State University University Park PA USA. Actuated Medical Bellefonte PA USA. Washington University in St. Louis St. Louis MO USA. Department of Neuroscience University of Pittsburgh Pittsburgh PA USA. Columbia University New York NY USA. Department of Bioengineering University of Pittsburgh Pittsburgh PA USA. TK.Kozai@pitt.edu. Center for Neural Basis of Cognition Pittsburgh PA USA. TK.Kozai@pitt.edu. Center for Neuroscience University of Pittsburgh Pittsburgh PA USA. TK.Kozai@pitt.edu. McGowan Institute of Regenerative Medicine University of Pittsburgh Pittsburgh PA USA. TK.Kozai@pitt.edu. NeuroTech Center University of Pittsburgh Brain Institute Pittsburgh PA USA. TK.Kozai@pitt.edu.

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Publisher Correction: Immune landscape in invasive ductal and lobular breast cancer reveals a divergent macrophage-driven microenvironment

Nature cancer

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Nature cancer 2023年第4期4卷 582页

作者： Sayali Onkar Jian Cui Jian Zou Carly Cardello Anthony R Cillo Mostofa Rafid Uddin April Sagan Marion Joy Hatice U Osmanbeyoglu Katherine L Pogue-Geile Priscilla F McAuliffe Peter C Lucas George C Tseng Adrian V Lee Tullia C Bruno Steffi Oesterreich Dario A A Vignali Department of Immunology University of Pittsburgh School of Medicine Pittsburgh PA USA. Tumor Microenvironment Center UPMC Hillman Cancer Center Pittsburgh PA USA. Graduate Program in Microbiology and Immunology University of Pittsburgh School of Medicine Pittsburgh PA USA. Department of Biostatistics University of Pittsburgh Pittsburgh PA USA. Computational Biology Department Carnegie Mellon University Pittsburgh PA USA. Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational Biology Pittsburgh PA USA. Department of Biomedical Informatics University of Pittsburgh Pittsburgh PA USA. UPMC Hillman Cancer Center Pittsburgh PA USA. NSABP Foundation Pittsburgh PA USA. Department of Bioengineering University of Pittsburgh Pittsburgh PA USA. Section of Breast Surgery Division of Surgical Oncology Department of Surgery University of Pittsburgh College of Medicine Magee Women's Hospital of UPMC Pittsburgh PA USA. Women's Cancer Research Center UPMC Hillman Cancer Center Magee-Womens Research Institute University of Pittsburgh Pittsburgh PA USA. Department of Pathology University of Pittsburgh Pittsburgh PA USA. Cancer Biology Program UPMC Hillman Cancer Center Pittsburgh PA USA. Department of Pharmacology and Chemical Biology University of Pittsburgh Pittsburgh PA USA. Cancer Immunology and Immunotherapy Program UPMC Hillman Cancer Center Pittsburgh PA USA. Women's Cancer Research Center UPMC Hillman Cancer Center Magee-Womens Research Institute University of Pittsburgh Pittsburgh PA USA. oesterreichs@upmc.edu. Cancer Biology Program UPMC Hillman Cancer Center Pittsburgh PA USA. oesterreichs@upmc.edu. Department of Pharmacology and Chemical Biology University of Pittsburgh Pittsburgh PA USA. oesterreichs@upmc.edu. Department of Immunology University of Pittsburgh School of Medicine Pittsburgh PA USA. dvignali@pitt.edu. Tumor Microenvironment Center UPMC Hillman Cancer Center Pittsburgh PA USA. dvignali@pi

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Patterns of somatic structural variation in human cancer genomes (vol 578, pg 112, 2020)

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NATURE 2023年第7948期614卷 E38-E38页

作者： Li, Yilong Roberts, Nicola D. Wala, Jeremiah A. Shapira, Ofer Schumacher, Steven E. Kumar, Kiran Khurana, Ekta Waszak, Sebastian Korbel, Jan O. Haber, James E. Imielinski, Marcin Weischenfeldt, Joachim Beroukhim, Rameen Campbell, Peter J. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK Totient Inc Cambridge MA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Haematology University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Korea Advanced Institute of Science and Technology Daejeon South Korea Department of Zoology Genetics and Physical Anthropology University of Santiago de Compostela Santiago de Compostela Spain Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) University of Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) University of Vigo Vigo Spain Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain Department of Zoology Genetics and Physical Anthropology (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) Universidade de Vigo Vigo Spain The Broad Institute of Harvard and MIT Cambridge MA USA Bioinformatics and Integrative Genomics Harvard University Cambridge MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Broad Institute of MIT and Harvard Cambridge MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Harvard Medical School Boston MA USA Massachusetts General Hospital Center for Cancer Research Charlestown MA USA Dana-Farber Cancer Institute Boston MA USA Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute and Harvard Medical School Boston MA USA Weill Cornell Medical College New York NY USA Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Controlled Department and Institution New York NY USA Englander Institute for Precision Medicine Weill Cornell Medicine Ne

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Author Correction: Genomic footprints of activated telomere maintenance mechanisms in cancer (Dec, 10.1038/s41467-019-13824-9, 2022)

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NATURE COMMUNICATIONS 2022年第1期13卷 1-1页

作者： Sieverling, Lina Hong, Chen Koser, Sandra D. Ginsbach, Philip Kleinheinz, Kortine Hutter, Barbara Braun, Delia M. Cortes-Ciriano, Isidro Xi, Ruibin Kabbe, Rolf Park, Peter J. Eils, Roland Schlesner, Matthias Brors, Benedikt Rippe, Karsten Jones, David T. W. Feuerbach, Lars Division of Applied Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Faculty of Biosciences Heidelberg University 69120 Heidelberg Germany Division of Applied Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Biosciences Heidelberg University Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Department for Bioinformatics and Functional Genomics Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant 69120 Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Institute of Pharmacy and Molecular Biotechnology and BioQuant Heidelberg University Heidelberg Germany German Cancer Consortium (DKTK) Heidelberg Germany National Center for Tumor Diseases (NCT) Heidelberg Heidelberg Germany Heidelberg Center for Personalized Oncology (DKFZ-HIPO) German Cancer Research Center (DKFZ) Heidelberg Germany German Cancer Consortium (DKTK) German Cancer Research Center (DKFZ) Heidelberg Germany Division of Chromatin Networks German Cancer Research Center (DKFZ) and BioQuant 69120 Heidelberg Germany Department of Biomedical Informatics Harvard Medical School Boston Massachusetts 02115 USA Department of Chemistry Centre for Molecular Science Informatics University of Cambridge Cambridge CB2 1EW UK Ludwig Center at Harvard Medical School Boston Massachusetts 02115 USA Department of Biomedical Informatics Harvard Medical School Boston MA USA Department of Chemistry Centre for Molecular Science Informatics University of Cambridge Cambridge UK Ludwig Center at Harvard Medical School Boston MA USA School of Mathematical Sciences and Center for Statistical Science Peking University Beijing 100871 China Heidelberg University Heidelberg Germany New BIH Digital Health Center Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin Berlin Germany Bioi

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