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LIBRA:an adaptative integrative tool for paired single-cell multi-omics data

Quantitative Biology 2023年第3期11卷 246-259页

作者： Xabier Martinez-de-Morentin Sumeer AKhan Robert Lehmann Sisi Qu Alberto Maillo Narsis AKiani Felipe Prosper Jesper Tegner david gomez-Cabrero Navarrabiomed Complejo Hospitalario de Navarra(CHN)Universidad Pública de Navarra(UPNA)IdiSNAPamplona 31001Spain Biological and Environmental Sciences and Engineering Division King Abdullah University of Science and TechnologyThuwal 23955Saudi Arabia Algorithmic Dynamic Lab Department of Oncology and PathologyCenter for Molecular MedicineKarolinska InstituteStockholm 17177Sweden Division of Hemato-Oncology Center for Applied Medical Research CIMACancer Center University of Navarra(CCUN)Navarra Institute for Health Research(IDISNA)CIBERONCPamplona 31008Spain Department of Hematology Clinica Universidad de NavarraCIBERONC Pamplona 31008Spain Computer Electrical and Mathematical Sciences and Engineering DivisionKing Abdullah University of Science and TechnologyThuwal 23955Saudi Arabia

Background:Single-cell multi-omics technologies allow a profound system-level biology understanding of cells and ***,an integrative and possibly systems-based analysis capturing the different modalities is *** response,bioinformatics and machine learning methodologies are being developed for multi-omics single-cell *** is unclear whether current tools can address the dual aspect of modality integration and prediction across modalities without requiring extensive parameter ***:We designed LIBRA,a neural network based framework,to learn translation between paired multi-omics profiles so that a shared latent space is ***,we implemented a variation,aLIBRA,that allows automatic fine-tuning by identifying parameter combinations that optimize both the integrative and predictive *** model parameters and evaluation metrics are made available to users with minimal user ***,aLIBRA allows experienced users to implement custom *** LIBRA toolbox is freely available as R and Python libraries at GitHub(TranslationalBioinformaticsUnit/LIBRA).Results:LIBRA was evaluated in eight multi-omic single-cell data-sets,including three combinations of *** observed that LIBRA is a state-of-the-art tool when evaluating the ability to increase cell-type(clustering)resolution in the integrated latent ***,when assessing the predictive power across data modalities,such as predictive chromatin accessibility from gene expression,LIBRA outperforms existing *** expected,adaptive parameter optimization(aLIBRA)significantly boosted the performance of learning predictive models from paired ***:LIBRA is a versatile tool that performs competitively in both“integration”and“prediction”tasks based on single-cell multi-omics *** is a data-driven robust platform that includes an adaptive learning scheme.

关键词： single-cell multi-omic Autoencoder auto-finetuning

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Cardiovascular risk burden and disability:findings from the International Mobility in Aging Study(IMIAS)

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Journal of Geriatric Cardiology 2024年第3期21卷 331-339页

作者： Juan-david Martinez-Aristizábal Carmen-Lucia Curcio Juliana Fernandes Afshin Vafael Cristiano dos Santos Gomes Fernando gomez Internal Medicine Critical Care DepartmentPablo Tobón Uribe HospitalMedellínColombia Research Group in Geriatrics and Gerontology Faculty of Health SciencesUniversidad de CaldasManizalesColombia Laboratory of Physical Therapy and Collective Health Physical Therapy DepartmentFederal University of PernambucoJornalista Aníbal Fernandes Avenue RecifeBrazil Department of Public Health Sciences Queen’s UniversityKingstonONCanada Department of Physiotherapy University of PernambucoBR 203KmBrazil

BACKGROUND The association of cardiovascular risk burden with disability is *** examined the association between trajectories of the Framingham general cardiovascular disease risk score(FGCRS)with the trajectories of limitations of physical function in older *** A total of 1219 participants with no disabilities from the International Mobility in Aging Study(IMIAS)study who had up to three repeated measures of FGCRS between 2012–2016 and without a history of stroke or coronary heart disease at baseline and follow-up were *** at baseline was assessed and categorized into *** function was evaluated with the Short Physical Performance Battery(SPPB).The data were analyzed using linear mixed-effects *** At baseline,FGCRS ranged between 3–94(mean score:24±15.8),participants were 32(2.6%),502(41.2%)and 685(56.2%)in lowest,middle,and highest tertiles,*** the trajectories of limitations of physical function,the lowest FGCRS had no differences,while the middle and highest had a decrease in physical performance between 2012–2014(P=0.0001).Age,being female,living in Andes Mountains,having middle and highest FGCRS,higher alcohol consumption,being obese,lack of exercise and cognitive impairment increase the probability of disability(P<0.05).Alternatively,living in more developed regions and having a higher educational level reduced the probability of disability during the follow-up time(P<0.05).CONCLUSIONS Higher cardiovascular risk burden is associated with decreased physical performance,especially in *** suggest SPPB may provide a measure of cardiovascular health in older adults.

关键词： finding Battery burden

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Role of sex on psychological distress,quality of life,and coping of patients with advanced colorectal and non-colorectal cancer

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World Journal of Gastrointestinal Oncology 2022年第10期14卷 2025-2037页

作者： Vilma Pacheco-Barcia david gomez Berta Obispo Luka Mihic Gongora Raquel Hernandez San Gil Patricia Cruz-Castellanos Mireia Gil-Raga Vicente Villalba Ismael Ghanem Paula Jimenez-Fonseca Caterina Calderon Department of Medical Oncology School of MedicineAlcala University(UAH)Hospital Central de la Defensa Gómez UllaMadrid 28047Spain Department of Medical Oncology Hospital Universitario de NavarraPamplona 31008Spain Department of Medical Oncology Hospital Universitario Infanta LeonorMadrid 28031Spain Department of Medical Oncology Hospital Universitario Central de AsturiasOviedo 33011Spain Department of Medical Oncology Hospital Universitario de CanariasTenerife 38320Spain Department of Medical Oncology Hospital Universitario La PazMadrid 28046Spain Department of Medical Oncology Hospital General Universitario de ValenciaCIBERONCValencia 46014Spain Department of Clinical Psychology and Psychobiology Faculty of PsychologyUniversity of BarcelonaBarcelona 08007Spain Department of Medical Oncology Hospital Universitario Central de AsturiasISPAOviedo 33007Spain Department of Clinical Psychology and Psychobiology University of BarcelonaBarcelona 08007Spain

BACKGROUNDPatients with advanced gastrointestinal cancer must cope with the negative effects of cancer and *** To evaluate psychological distress,quality of life,and coping strategies in patients with advanced colorectal cancer compared to non-colorectal cancer based on *** A prospective,transversal,multicenter study was conducted in 203 patients;101(50%)had a colorectal and 102(50%)had digestive,non-colorectal advanced *** completed questionnaires evaluating psychological distress(Brief Symptom Inventory-18),quality of life(EORTC QLQ-C30),and coping strategies(Mini-Mental Adjustment to Cancer)before starting systemic cancer *** The study included 42.4%*** exhibited more depressive symptoms,anxiety,functional limitations,and anxious preoccupation than *** with non-colorectal digestive cancer and women showed more somatization and physical symptoms than subjects with colorectal cancer and *** with colorectal cancer reported the best health *** The degree of disease acceptance in gastrointestinal malignancies may depend on sex and location of the primary digestive *** interventions should specifically address sex and tumor site differences in individuals with advanced digestive cancer.

关键词： Anxiety Colorectal cancer Depression Gastrointestinal cancer Sex

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Protective effects of cyclosporine and its analog NIM-811 in a murine model of hepatic ischemia-reperfusion injury

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Liver Research 2024年第1期8卷 46-53页

作者： Joshua Hefler Rena Pawlick Braulio A.Marfil-Garza Aducio Thiesen Nerea Cuesta-gomez Sanaz Hatami Darren H.Freed Constantine Karvellas david L.Bigam A.M.James Shapiro Department of Surgery Faculty of Medicine&DentistryUniversity of AlbertaEdmontonABCanada Department of Medicine Faculty of Medicine&DentistryUniversity of AlbertaEdmontonABCanada CHRISTUS-LatAm Hub Excellence&Innovation Center MonterreyMexico Alberta Diabetes Institute University of AlbertaEdmontonABCanada Clinical Islet Transplant Program University of AlbertaEdmontonABCanada Department of Laboratory Medicine&Pathology Faculty of Medicine&DentistryUniversity of AlbertaEdmontonABCanada

Background and aim:The liver is susceptible to ischemia-reperfusion injury(IRI)during hepatic surgery,when the vessels are compressed to control bleeding,or liver transplantation,when there is an obligate period of *** hallmark of IRI comprises mitochondrial dysfunction,which generates reactive oxygen species,and cell death through necrosis or ***(CsA),which is a well-known immunosuppressive agent that inhibits calcineurin,has the additional effect of inhibiting the mito-chondrial permeability transition pore(mPTP),thereby,preventing mitochondrial swelling and ***-811,which is the nonimmunosuppressive analog of CsA,has a similar effect on the *** this study,we tested the effect of both agents on mitigating warm hepatic IRI in a murine *** and methods:Before ischemic insult,the mice were administered with intraperitoneal normal saline(control);CsA at 2.5,10,or 25 mg/kg;or NIM-811 at 10 mg/***,the mice were subjected to partial warm hepatic ischemia by selective pedicle clamping for 60 min,followed by 6 h of recovery after *** alanine transaminase(ALT)was measured,and the liver tissue was examined histologically for the presence of apoptosis and the levels of inflammatory ***:Compared with the control mice,the mice treated with 10 and 25 mg/kg of CsA and NIM-811 had significantly lower ALT levels(P<0.001,0.007,and 0.031,respectively).Moreover,the liver tissue showed reduced histological injury scores after treatment with CsA at 2.5,10,and 25 mg/kg and NIM-811(P=0.041,<0.001,0.003,and 0.043,respectively)and significant decrease in apoptosis after treatment with CsA at all doses(P=0.012,0.007,and<0.001,respectively).Levels of the pro-inflammatory cyto-kines,particularly interleukin(IL)-1β,IL-2,IL-4,IL-10,and keratinocyte chemoattractant/human growth-regulated oncogene significantly decreased in the mice treated with the highest dose of CsA(25 mg/kg)than those in the control ***

关键词： Cyclosporine(CsA) Cyclosporine analogue Liver surgery Ischemia-reperfusion injury(IRI) Animal model NIM-811

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Changes in physical activity and cardiovascular mortality in older adults

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Journal of Geriatric Cardiology 2017年第4期14卷 287-288页

作者： Sara Higueras-Fresnillo Pilar Guallar-Castillon Veronica Cabanas-Sanchez Jose R. Banegas Femando Rodriguez-Artalejo david Martinez-gomez Department of Physical Education Sport and Human Movement Faculty of Teacher Training and Education Universidad Aut6noma de Madrid Madrid Spain Department of Preventive Medicine and Public Health School of Medicine Universidad Autonoma de Madrid/IdiPAZ CIBER of Epidemiology and Public Health (CIBERESP) Spain IMDEA-Food Institute. CEI UAM+CSIC Madrid Spain

Cardiovascular disease (CVD) is the main cause of death in older adults. There is strong evidence that regular physical activity (PA) reduces the risk of CVD mortality in this population group. However, these studies used baseline data and do not account for potential changes in PA. Previous research on the mortality effect of changes in PA focused on all-cause deaths; hence, this is the first study aimed to examine the association of changes in PA with subsequent CVD mortality in older adults.

关键词：死亡率心血管老年人体力

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A comprehensive look at the psychoneuroimmunoendocrinology of spinal cord injury and its progression: mechanisms and clinical opportunities

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Military Medical Research 2024年第2期11卷 228-267页

作者： Miguel A.Ortega Oscar Fraile-Martinez Cielo García-Montero Sergio Haro Miguel Ángel Álvarez-Mon Diego De Leon-Oliva Ana M.gomez-Lahoz Jorge Monserrat Mar Atienza-Pérez david Díaz Elisa Lopez-Dolado Melchor Álvarez-Mon Department of Medicine and Medical Specialities University of Alcala28801 Alcala de HenaresSpain Ramón y Cajal Institute of Sanitary Research(IRYCIS) 28034 MadridSpain Department of Psychiatry and Mental Health Hospital Universitario Infanta Leonor28031 MadridSpain Service of Rehabilitation National Hospital for Paraplegic PatientsCarr.de la PeraledaS/N45004 ToledoSpain Immune System Diseases‑Rheumatology Service and Internal Medicine University Hospital Príncipe de Asturias(CIBEREHD)28806 Alcala de HenaresSpain

Spinal cord injury(SCI)is a devastating and disabling medical condition generally caused by a traumatic event(primary injury).This initial trauma is accompanied by a set of biological mechanisms directed to ameliorate neural damage but also exacerbate initial damage(secondary injury).The alterations that occur in the spinal cord have not only local but also systemic consequences and virtually all organs and tissues of the body incur important changes after SCI,explaining the progression and detrimental consequences related to this ***(PNIE)is a growing area of research aiming to integrate and explore the interactions among the different systems that compose the human organism,considering the mind and the body as a *** initial traumatic event and the consequent neurological disruption trigger immune,endocrine,and multisystem dysfunction,which in turn affect the patient's psyche and *** the present review,we will explore the most important local and systemic consequences of SCI from a PNIE perspective,defining the changes occurring in each system and how all these mechanisms are ***,potential clinical approaches derived from this knowledge will also be collectively presented with the aim to develop integrative therapies to maximize the clinical management of these patients.

关键词： Spinal cord injury(SCI) Psychoneuroimmunoendocrinology(PNIE) Secondary injury Immunoinflammatory dysfunction Gut microbiota Translational opportunities

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Changes in Human Hair Induced by UV- and Gamma Irradiation

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Advances in Bioscience and Biotechnology 2016年第1期7卷 19-27页

作者： Ervin Palma david gomez Eugene Galicia Viktor Stolc Yuri Griko Evergreen Valley College San Jose CA USA Carnegie Melon University Moffett Field CA USA Division of Space Biosciences NASA Ames Research Center Moffett Field CA USA

The effect of UV- and 137Cs gamma radiation on the structural and chemical integrity of human hair was studied to determine the feasibility of using human hair as a non-invasive biomarker of radiation exposure to ionized gamma- and non-ionized UV-radiation. Steady state tryptophan (Trp) fluorescence and chemical analytical methods were used to evaluate the molecular integrity of Trp fluorophores and SH-groups in hair proteins and to assess the radiation induced damage quantitatively. It was found that human hair fibers were progressively damaged by exposure to both UV- and ionized gamma radiation. Damage to the hair was evidenced by a decrease in the fluorescence intensity as a result of observed depletion of the amino acid tryptophan as well as significant reduction in a number of free SH-groups in hair proteins. Hair damage was dose-dependent for exposures between 0 and 10.0 Gy and 0 - 20 J/cm2 of UV-radiation. Additional results demonstrate that hair-fibers exposed to gamma rays, with much higher quantum energy than UV, undergo a smaller extent of changes in Trp fluorescence than when exposed to lower or equal energy of UV-irradiation. The stable Trp fluorophore appears to be extremely sensitive to UV-radiation in contrast to the ionized gamma radiation whose damage is originated from the reaction of free radicals and direct deposition of energy. We conclude that fluorescence spectroscopy represents a useful tool in the quantitative evaluation of the radiation exposure and could also be used for the rapid and non-invasive assessment of radiation dose i.e. biodosimeter. The approach is simple, non-invasive and appears to have considerable potential that enables quantitative evaluation of radiation dose exposure in a single hair fiber.

关键词： Hair Fluorescence Radiation Chemical Integrity

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Predicting a Failure of Public Speaking Performance Using Multidimensional Assessment

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Journal of Sports Science 2016年第4期4卷 197-209页

作者： Jiewen Hua Edith Filaire Tom Giraud david Antonio gomez Jauregui Mariette Soury Jean-Claude Martin Laurence Devillers Christine Le Scanff Department of CLAMS University of Paris-Sud Orsay 91405 France Department of CIAMS University of Orleans Orleans 45067 France Department of LIMSI-CNRS University of Paris-Sud Orsay 91405 France Department of LIMSI-CNRS University of Paris-Sorbonne Paris 75000 France

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Emissive displays with transfer-printed assemblies of 8 μm × 15 μm inorganic light-emitting diodes

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Photonics Research 2017年第2期5卷 23-29页

作者： CHRISTOPHER A.BOWER MATTHEW A.MEITL BROOK RAYMOND ERICH RADAUSCHER RONALD COK SALVATORE BONAFEDE david gomez TANYA MOORE CARL PREVATTE BRENT FISHER ROBERT ROTZOLL GEORGE A.MELNIK ALIN FECIORU ANTóNIO JOSé TRINDADE X-Celeprint Inc. Research Triangle Park X-Celeprint Ltd.

Displays using direct light emission from microscale inorganic light-emitting diodes(μILEDs)have the potential to be very bright and also very power ***-throughput technologies that accurately and cost-effectively assemble microscale devices on display substrates with high yield are key enablers forμILED *** stamp transfer printing is such a candidate assembly technology.A variety ofμILED displays have been designed and fabricated by transfer printing,including passive-matrix and active-matrix displays on glass and plastic substrates.

关键词： Emissive displays with transfer-printed assemblies of 8 m inorganic light-emitting diodes

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cysA,cysP,and rpoS mutations increase the power density in *** microbial fuel cells:Performing enhancement based on metabolic flux analysis

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Advances in Bioscience and Biotechnology 2013年第1期4卷 103-111页

作者： Juan Diego Mejia Cindy Stephany Rojas Laura Avellaneda Franco david Alejandro Urbina gomez Beatriz Helena Correa Arias Nubia Milena Velasco Rodriguez Maria Teresa Cortes Montanez Martha Josefina Vives-Florez Andres Fernando Gonzalez Barrios Grupo de Diseno de Productos y Procesos(GDPP) Departamento de Ingenieria QuimicaUniversidad de los AndesBogotaColombia Grupo de Investigacion en Produccion y Logistica(PYLO) Departamento de Ingenieria IndustrialUniversidad de los AndesBogotaColombia Laboratorio de Electroquimica y Materiales Polimericos Departamento de QuimicaUniversidad de los AndesBogotaColombia Centro de Investigaciones Microbiologicas(CIMIC) Departamento de Ciencias BiologicasUniversidad de los AndesBogotaColombia

This study presents the simulation of a MFC with Pseudomonas aeruginosa based on a metabolic flux analysis (MFA) which arises as a linear programming model that served as input for the fuel cell model. The linear model was implemented in Xpress MP? and the coupling model in Comsol Multiphysics?. The in silico model predicted maximum potentials of 0.135 V which were consistent with those obtained in the experimental cell. Afterwards, an optimization platform based on multiobjective optimization approach was implemented aimed to determine genes that increase the average cell power. cysA, cysP and rpoS mutants which were predicted to increase the power of the cell, were experimentally tested with an air cathode fuel cell finding an augment up to 35-fold in the average power density for the rpoS mutant. Power densities were obtained through experimentation in the range of [0.13 - 5] mW/m2. Electron shuttle rise was qualitative corroborated trough cyclic voltammetry tests, which allowed to visualize the augment of the peaks for rpoS mutation.

关键词： Component Formatting Style Styling Insert

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