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In silico analysis of lncRNA-miRNA-mRNA signatures related to Sorafenib effectiveness in liver cancer cells

World Journal of Gastroenterology 2025年第3期31卷 84-102页

作者： Patricia de la Cruz-Ojeda Ester Parras-Martínez Raquel Rey-Pérez jordi Muntané Functional Genomics of Solid Tumors Laboratory Centre de Recherche des CordeliersParis 75006France Department of Oncology Surgery Cell Therapy and Organ TransplantationInstitute of Biomedicine of SevilleVirgen del Rocio University HospitalSeville 41013Spain Biomedical Research Center for Hepatic and Digestive Diseases CIBERehdMadrid 28029Spain Department of Medical Physiology and Biophysics University of SevilleSeville 41009Spain

BACKGROUND Hepatocellular carcinoma(HCC)is the most common subtype of primary liver cancer with varied incidence and epidemiology *** is still a recommended treatment for a large proportion of patients with advanced *** patterns of treatment responsiveness have been identified in differentiated hepatoblastoma HepG2 cells and metastatic HCC SNU449 *** To define the long non-codingRNA-microRNA-mRNA(lncRNA-miRNA-mRNA)predicted signatures related to selected hallmarks of cancer(apoptosis,autophagy,cell stress,cell dedifferentiation and invasiveness)in RNAseq studies using Sorafenib-treated HepG2 and SNU449 *** available software analyses allowed us to establish the lncRNA-miRNA-mRNA regulatory axes following treatment in HepG2 and SNU449 *** HepG2 and SNU449 cells were treated with Sorafenib(10μmol/L)for 24 *** RNA,including small and long RNA,was extracted with a commercial miRNeasy *** was carried out for the identification of changes in lncRNA-miRNA-mRNA regulatory *** MALAT,THAP9-AS1 and SNGH17 appeared to coordinately regulate miR-374b-3p and miR-769-5p that led to upregulation of SMAD7,TIRARP,TFAP4 and FAXDC2 in HepG2 ***12,EPB41 L4A-AS1,LINC01578,SNHG12 and GAS5 interacted with let-7b-3p,miR-195-5p and VEGFA in SNU449 *** axes MALAT1/hsamir-374b-3p/SMAD7 and MALAT1/hsa-mir-769-5p/TFAP4 were of high relevance for Sorafenib response in HepG2 cells,whereas PVT1/hsa-miR-195-5p/VEGFA was responsible for the differential response of SNU449 cells to Sorafenib *** Critical lncRNAs acting as sponges of miRNA were identified that regulated mRNA expression,whose proteins mainly increased the antitumor effectiveness of the treatment(SMAD7,TIRARP,TFAP4,FAXDC2 and ADRB2).However,the broad regulatory axis leading to increased VEGFA expression may be related to the side effect of Sorafenib in SNU449 cells.

关键词： Cell culture Hepatocellular carcinoma Non-coding RNA RNAseq Sorafenib

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国际卒中遗传学联盟的推荐意见（第1部分）：标准化表型数据收集

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国际脑血管病杂志 2015年第9期23卷 645-650页

作者： Jennifer J. Majersik John W.Cole Jonathan Golledge Natalia S. Rost Yu-Feng Yvonne Chan M. Edip Gurol Ame G. Lindgren Daniel Woo Israel Fernandez-Cadenas Donna T. Chen Vincent Thijs Bradford B. Worrall Ayeesha Kamal Paul Bentley Joanna M. Wardlaw Ynte M. Ruigrok Thomas W.K Battey Reinhold Schmidt Joan Montaner Anne-Katrin Giese Jaume Roquer jordi jimenez-conde Chaeyoung Lee Hakan Ay Juan Jose Martin 李海峰岳耀先徐军不详山东大学齐鲁医院神经内科济南250012

与几乎所有复杂疾病一样,卒中的患病风险和临床转归也是多基因作用的[1]。探索相关基因突变有望为新型个体化治疗方法奠定基础,从而显著减少卒中对全球健康造成的毁灭性影响。为了达到足够的统计学效能以确认多个风险性等位基因,需要很... 详细信息

与几乎所有复杂疾病一样,卒中的患病风险和临床转归也是多基因作用的[1]。探索相关基因突变有望为新型个体化治疗方法奠定基础,从而显著减少卒中对全球健康造成的毁灭性影响。为了达到足够的统计学效能以确认多个风险性等位基因,需要很大的样本量。尽管卒中是全世界范围内第二大致死病因和成年人致残的主要原因[2],但没有任何一家研究机构能独立收集到足够的样本。在认识到这一挑战之后,来自世界各地的卒中研究者们于2007年成立了国际卒中遗传学联盟（ International Stroke Genetics Consortium, ISGC； http：//www. ***）,其使命是通过研究在全球多个研究机构入组的患者来识别影响卒中患病风险、临床预后和治疗效果的遗传学因素。尽管先前已取得了一些成功[3-5],仍有大量工作有待进行,这不仅是为了发现风险性等位基因从而达到卒中个体化医疗的最终目标,更是为了开发综合性卒中风险评估手段以及得到足以改变临床实践的结果[6]。根据糖尿病和冠状动脉疾病等其他复杂疾病的研究进展,为了识别与卒中相关的所有基因突变,需要100000～200000个样本。为了达到这个样本量,需要进行更为广泛的协作。

关键词：遗传学因素数据收集卒中国际标准化个体化医疗表型冠状动脉疾病

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Hankel operators on exponential Bergman spaces

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Science China Mathematics 2022年第2期65卷 421-442页

作者： Zhangjian Hu jordi Pau Department of Mathematics Huzhou UniversityHuzhou 313000China Departament de Matematiques i Informatica Universitat de BarcelonaBarcelona 08007Spain

We completely describe the boundedness and compactness of Hankel operators with general symbols acting on Bergman spaces with exponential type weights.

关键词： weighted Bergman space Hankel operator ?-equation

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Sigma-1 receptor: a new player in neuroprotection against chemotherapy-induced peripheral neuropathy

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Neural Regeneration Research 2018年第5期13卷 775-778页

作者： jordi Bruna Roser Velasco Neuro-Oncology Unit Hospital Universitari de Bellvitge-ICO L'Hospitalet IDIBELL (Institut d'Investigació Biomèdica de Bellvitge) Institute of Neurosciences Department of Cell Biology Physiology and Immunology Universitat Autonoma de Barcelona and Centro de Investigación Biomedica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)

Chemotherapy-induced peripheral neuropathy is a very frequent neurological complication in cancer. Oxaliplatin（OXA） is a platinum analogue used as a first-line agent in the treatment of colorectal cancer. OXA induced peripheral neuropathy（OIN） is the main toxicity both during and after the completion of chemotherapy that presents as two distinct syndromes： acute and chronic neuropathy. None of the neuroprotective agents previously tested had prevented or limited the acute and/or chronic OIN. MR309（previously developed as E-52862） is a novel selective sigma-1 receptor（S1R） antagonist with preclinical analgesic activity in OXA-induced neuropathic pain in animal models. This review analyzes the results of the recently published phase Ⅱ, randomized, double-blind, placebo-controlled clinical trial including 124 patients with colorectal cancer（CRC） treated with MR309. This study shows encouraging findings in the setting of neuroprotection against OIN with an acceptable safety profile. The study demonstrated MR309 usefulness in decreasing acute OIN, by reducing cold hypersensitivity experienced by patients, and pointed to the amelioration of chronic OIN by lowering the proportion of patients who developed severe chronic OIN. In addition, we provide a summary and discussion on the pathways that can be modulated by the S1R to explain the observed clinical benefits in the OIN.

关键词： oxaliplatin chemotherapy-induced peripheral neuropathy sigma-1 receptor neurotoxicity MR309 E-52862

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Chemokine ligand 2 and paraoxonase-1 in non-alcoholic fatty liver disease:The search for alternative causative factors

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World Journal of Gastroenterology 2015年第10期21卷 2875-2882页

作者： jordi Camps Jorge Joven Unitat de Recerca Biomèdica Hospital Universitari de Sant Joan Institut d’Investigació Sanitària Pere Virgili Universitat Rovira i Virgili

The incidence and prevalence of non-alcoholic fatty liver disease(NAFLD)is constantly *** this is apparently associated with the growing increase in obesity,insulin resistance and obesity-related metabolic disturbances their presence is not a necessary or sufficient condition to explain the accumulation of fatin the ***,NAFLD is a predictor of other metabolic *** is currently the most frequent chronic liver disease but should not be considered benign or anecdotic because a considerable proportion of patients with NAFLD progress to cirrhosis and endstage liver ***,the search for alternative molecular mechanisms with therapeutic implications in NAFLD and associated disorders deserves a careful *** are possible targets as these organelles generate energy from nutrient *** findings,generated in patients with extreme obesity and in murine models,support the notion that NAFLD could be a mitochondrial *** is plausible because mitochondrial dysfunction affects the accumulation of lipids in hepatocytes and promotes lipid peroxidation,the production of reactive oxygen species,the release of cytokines causing inflammation and cell *** we discuss basic research and mechanistic studies targeting the role of chemokine ligand 2 in liver inflammation and that of the paraoxonases in the oxidative *** combination and association with mitochondrial dysfunction may uncover mechanisms underlying the progression of NAFLD and may help to identify novel therapeutic targets.

关键词： Biomarkers Cytokines Inflammation Metabolism Mitoc

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Machine learning applications on lunar meteorite minerals:From classification to mechanical properties prediction

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International Journal of Mining Science and Technology 2024年第9期34卷 1283-1292页

作者： Eloy Peña-Asensio Josep M.Trigo-Rodríguez jordi Sort jordi Ibáñez-Insa Albert Rimola Department of Aerospace Science and Technology Politecnico di MilanoMilano 20156Italy Institut de Ciències de l’Espai(ICE-CSIC) Campus UAB08193 Cerdanyola del VallèsSpain Institut d’Estudis Espacials de Catalunya(IEEC) Barcelona 08034Spain Departament de Física Universitat Autònoma de BarcelonaCerdanyola del Vallès E-08193Spain InstitucióCatalana de Recerca i Estudis Avançats(ICREA) Barcelona E-08010Spain Geosciences Barcelona(GEO3BCN-CSIC) E-08028 BarcelonaSpain Departament de Química Universitat Autònoma de BarcelonaBellaterra 08193Spain

Amid the scarcity of lunar meteorites and the imperative to preserve their scientific value,nondestructive testing methods are *** translates into the application of microscale rock mechanics experiments and scanning electron microscopy for surface composition *** study explores the application of Machine Learning algorithms in predicting the mineralogical and mechanical properties of DHOFAR 1084,JAH 838,and NWA 11444 lunar meteorites based solely on their atomic percentage *** a prior-data fitted network model,we achieved near-perfect classification scores for meteorites,mineral groups,and individual *** regressor models,notably the KNeighbor model,provided an outstanding estimate of the mechanical properties—previously measured by nanoindentation tests—such as hardness,reduced Young’s modulus,and elastic *** considerations on the nature and physical properties of the minerals forming these meteorites,including porosity,crystal orientation,or shock degree,are essential for refining *** findings underscore the potential of Machine Learning in enhancing mineral identification and mechanical property estimation in lunar exploration,which pave the way for new advancements and quick assessments in extraterrestrial mineral mining,processing,and research.

关键词： Meteorites Moon Mineralogy Machine learning Mechanical properties

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A model for the control of DNA integrity by the sperm nuclear matrix

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Asian Journal of Andrology 2015年第4期17卷 610-615页

作者： Joanna E Gawecka jordi Ribas-Maynou jordi Benet W Steven Ward Clinical and Translational Research Program Universityof Hawaii Cancer Center Honolulu HI USA Cell BiologyUnit Cell Biology Phisiology and Immunology DepartmentMedicine Faculty Universitat Autonoma de Barcelona08193 Bellaterra Spain Center of Male Infertility andAnalysis de Barcelona Edifici Eureka PBM5 Parc deRecerca de la UAB Campus de la UAB 08193 BellaterraSpain Institute for Biogenesis Research Departmentof Anatomy Biochemistry and Physiology Honolulu HIUSA Department of Obstetrics Gynecology and Women'sHealth John A. Burns School of Medicine University ofHawaii at Manoa. Honolulu. HI 96822. USA.

The highly condensed chromatin of mammalian spermatozoa is usually considered to be biologically inert before fertilization. However, we have demonstrated that even in this compacted state, sperm chromatin is subject to degradation at open configurations associated with the nuclear matrix through a process we have termed sperm chromatin fragmentation （SCF）. ＂[his suggests that a mechanism exists to monitor the health of spermatozoa during transit through the male reproductive tract and to destroy the genome of defective sperm cells. The site of DNA damage in SCF, the matrix attachment sites, are the same that we hypothesize initiate DNA synthesis in the zygote. When sperm that have damaged DNA are injected into the oocyte, the newly created zygote responds by delaying DNA synthesis in the male pronudeus and, if the damage is severe enough, arresting the embryo＇s development. Here we present a model for paternal DNA regulation by the nuclear matrix that begins during sperm maturation and continues through early embryonic development.

关键词： DNA mammalian spermatozoa

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AJAC: Atomic data calculation tool in Python

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Chinese Physics B 2013年第4期22卷 545-557页

作者： Amani Tahat jordi Marti Kaher Tahat Ali Khwaldeh Department of Physics and Nuclear Engineering Technical University of Catalonia Barcelona Spain Saudi Grown Investment Company Quai du Seujet 30 Geneva 1201 Switzerland Department of Computer Engineering Faculty of Engineering Philadelphia University Amman Jordan

In this work, new features and extensions of a currently used online atomic database management system are reported. A multiplatform flexible computation package is added to the present system, to allow the calculation of various atomic radiative and collisional processes, based on simplifying the use of some existing atomic codes adopted from the literature. The interaction between users and data is facilitated by a rather extensive Python graphical user interface working online and could be installed in personal computers of different classes. In particular, this study gives an overview of the use of one model of the package models （i.e., electron impact collisional excitation model）. The accuracy of computing capability of the electron impact collisional excitation in the adopted model, which follows the distorted wave approximation approach, is enhanced by implementing the Dirac R-matrix approximation approach. The validity and utility of this approach are presented through a comparison of the current computed results with earlier available theoretical and experimental results. Finally, the source code is made available under the general public license and being distributed freely in the hope that it will be useful to a wide community of laboratory and astrophysical plasma diagnostics.

关键词： software engineering atomic data atomic databases

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Pattern recognition and data mining software based on artificial neural networks applied to proton transfer in aqueous environments

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Chinese Physics B 2014年第4期23卷 410-421页

作者： Amani Tahat jordi Marti Ali Khwaldeh Kaher Tahat Department of Physics and Nuclear Engineering Technical University of Catalonia-Barcelona Tech B4-B5North Campus UPC08034 Barcelona Catalonia Spain Department of Computer Engineering Faculty of Engineering Philadelphia University Department of Graduate Business Studies Waterford Institute of TechnologyMain Campus Cork RoadWaterford Ireland

In computational physics proton transfer phenomena could be viewed as pattern classification problems based on a set of input features allowing classification of the proton motion into two categories： transfer ＇occurred＇ and transfer ＇not occurred＇. The goal of this paper is to evaluate the use of artificial neural networks in the classification of proton transfer events, based on the feed-forward back propagation neural network, used as a classifier to distinguish between the two transfer cases. In this paper, we use a new developed data mining and pattern recognition tool for automating, controlling, and drawing charts of the output data of an Empirical Valence Bond existing code. The study analyzes the need for pattern recognition in aqueous proton transfer processes and how the learning approach in error back propagation （multilayer perceptron algorithms） could be satisfactorily employed in the present case. We present a tool for pattern recognition and validate the code including a real physical case study. The results of applying the artificial neural networks methodology to crowd patterns based upon selected physical properties （e.g., temperature, density） show the abilities of the network to learn proton transfer patterns corresponding to properties of the aqueous environments, which is in turn proved to be fully compatible with previous proton transfer studies.

关键词： pattern recognition proton transfer chart pattern data mining artificial neural network empiricalvalence bond

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Sessile oak forest plant community changes on the NE Iberian Peninsula over recent decades

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Journal of Plant Ecology 2019年第5期12卷 894-906页

作者： jordi Bou Lluís Vilar LAGP-Flora and Vegetation Institute of the EnvironmentUniversity of GironaGironaCataloniaSpain

Aims Our aims were 3-fold:(i)to determine whether global change has altered the composition and structure of the plant community found in the sessile oak forests on the NE Iberian Peninsula over the last decades,(ii)to establish whether the decline in forest exploitation activities that has taken place since the mid-20th century has had any effect on the forests and(iii)to ascertain whether there is any evidence of impact from climate *** We assess changes in the plant community by comparing a cur-rent survey of sessile oak forest with a historical data set obtained from previous regional studies dating from 1962 to *** ana-lyse the regional changes in the community in terms of biodiversity variables,species composition and plant ***,plants traits such as plant life forms and chorological groups are used to discern any effects from land-use changes and climate warming on the plant *** Findingsthere has been a loss of diversity in the community and,in the hottest region,there is also a loss of species *** composition of the community suggests that,although significant changes have taken place over recent decades,these changes differ between regions as a result of the low impact global change has had in the western *** instance,while the tree canopy cover in the western sessile oak forests remains stable,the eastern sessile oak forests are still recovering from the former exploitation that led to a loss of their rich and abundant herbaceous *** fact,the recovery process in the catalan Pre-coastal Range has constituted an increase in the Euro-Siberian plants typical to this ***,in the eastern forests,there is evidence that climate warming has impacted the thermophilization of the sessile oak forests found on the coastal Range.

关键词： global change community ecology Quercus petraea forest ecology

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