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Evaluating the potential of(epi)genotype‑by‑low pass nanopore sequencing in dairy cattle:a study on direct genomic value and methylation analysis

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Journal of Animal Science and Biotechnology 2023年第6期14卷 2276-2289页

作者： Oscar Gonzalez‑Recio Adrian Lopez‑Catalina Ramon Peiro‑Pastor alicia nieto‑valle Monica Castro Almudena Fernandez Dpt.Mejora Genetica Animal INIA-CSICCtra La Coruna Km 7.528040 MadridSpain. ETSIAAB Universidad Politecnica de Madrid.Ciudad Universitaria S/N28040 MadridSpain.

Background Genotype-by-sequencing has been proposed as an alternative to SNP genotyping arrays in genomic selection to obtain a high density of markers along the genome.It requires a low sequencing depth to be cost effective,which may increase the error at the genotype assigment.Third generation nanopore sequencing technology offers low cost sequencing and the possibility to detect genome methylation,which provides added value to genotype-by-sequencing.The aim of this study was to evaluate the performance of genotype-by-low pass nanopore sequencing for estimating the direct genomic value in dairy cattle,and the possibility to obtain methylation marks simultaneously.Results Latest nanopore chemistry(LSK14 and Q20)achieved a modal base calling accuracy of 99.55%,whereas previous kit(LSK109)achieved slightly lower accuracy(99.1%).The direct genomic value accuracy from genotype-by-low pass sequencing ranged between 0.79 and 0.99,depending on the trait(milk,fat or protein yield),with a sequencing depth as low as 2×and using the latest chemistry(LSK114).Lower sequencing depth led to biased estimates,yet with high rank correlations.The LSK109 and Q20 achieved lower accuracies(0.57-0.93).More than one million high reliable methylated sites were obtained,even at low sequencing depth,located mainly in distal intergenic(87%)and promoter(5%)regions.Conclusions This study showed that the latest nanopore technology in useful in a LowPass sequencing framework to estimate direct genomic values with high reliability.It may provide advantages in populations with no available SNP chip,or when a large density of markers with a wide range of allele frequencies is needed.In addition,low pass sequencing provided nucleotide methylation status of>1 million nucleotides at≥10×,which is an added value for epigenetic studies.

关键词： Genomic selection Genomic values Low pass sequencing Low sequencing imputation Polygenic risk score

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Estimation of Displacement and Extension due to Reverse Drag of Normal Faults: Forward Method

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International Journal of Geosciences 2024年第1期15卷 25-39页

作者： Shunshan Xu Angel Francisco nieto-Samaniego Huilong Xu Susana alicia Alaniz-Álvarez Universidad Nacional Autónoma de México Centro de Geociencias Apartado Postal 1-742 Querétaro Qro. México South China Sea Institute of Oceanology Chinese Academy of Sciences Guangzhou China

In the case of reverse drag of normal faulting, the displacement and horizontal extension are determined based on the established equations for the three mechanisms: rigid body, vertical shear and inclined shear. There are three sub-cases of basal detachment for the rigid body model: horizontal detachment, antithetic detachment and synthetic detachment. For the rigid body model, the established equations indicate that the total displacement on the synthetic base (Dt2) is the largest, that on the horizontal base (Dt1) is moderate, and that on the antithetic base (Dt3) is the smallest. On the other hand, the value of (Dt1) is larger than the displacement for the vertical shear (Dt4). The value of (Dt1) is larger than or less than the displacement for the inclined shear (Dt5) depending on the original fault dip δ0, bedding angle θ, and the angle of shear direction β. For all original parameters, the value of Dt5 is less than the value of Dt4. Also, by comparing three rotation mechanisms, we find that the inclined shear produces largest extension, the rigid body model with horizontal detachment produces the smallest extension, and the vertical shear model produces moderate extension.

关键词： Fault Rotation Fault Drag Fault Displacement Extension Forward Model

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Cosmological Model in Four Time and Four Space Dimensions

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Journal of Applied Mathematics and Physics 2024年第3期12卷 829-840页

作者： Juan Antonio nieto Facultad de Ciencias Físico-Matemáticas de la Universidad Autónoma de Sinaloa Culiacán Sinaloa México

We develop a cosmological model in a physical background scenario of four time and four space dimensions ((4+4)-dimensions or (4+4)-universe). We show that in this framework the (1+3)-universe is deeply connected with the (3+1)-universe. We argue that this means that in the (4+4)-universe there exists a duality relation between the (1+3)-universe and the (3+1)-universe.

关键词： Cosmological Model (4+4)-Dimensions Duality Symmetry

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Electrifying Ba_(0.5)Sr_(0.5)Co_(0.8)Fe_(0.2)O_(3-δ) for focalized heating in oxygen transport membranes

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Journal of Energy Chemistry 2024年第4期91卷 99-110页

作者： Marwan Laqdiem Julio García-Fayos Laura Almar Alfonso J.Carrillo Álvaro Represa JoséM.López nieto Sonia Escolástico David Catalán-Martinez Jose M.Serra Instituto de Tecnología Química(Universitat Politècnica de València–Consejo Superior de Investigaciones Científicas) Av.Los Naranjos s/nE-46022 ValenciaSpain

Industry decarbonization requires the development of highly efficient and flexible technologies relying on renewable energy resources,especially biomass and solar/wind electricity.In the case of pure oxygen production,oxygen transport membranes(OTMs)appear as an alternative technology for the cryogenic distillation of air,the industrially-established process of producing oxygen.Moreover,OTMs could provide oxygen from different sources(air,water,CO_(2),etc.),and they are more flexible in adapting to current processes,producing oxygen at 700^(-1)000℃.Furthermore,OTMs can be integrated into catalytic membrane reactors,providing new pathways for different processes.The first part of this study was focused on electrification on a traditional OTM material(Ba_(0.5)Sr_(0.5)Co_(0.8)Fe_(0.2)O_(3-δ)),imposing different electric currents/voltages along a capillary membrane.Thanks to the emerging Joule effect,the membrane-surface temperature and the associated O_(2) permeation flux could be adjusted.Here,the OTM is electrically and locally heated and reaches 900℃on the surface,whereas the surrounding of the membrane was maintained at 650℃.The O_(2)permeation flux reached for the electrified membranes was~3.7 NmL min^(-1)cm^(-2),corresponding to the flux obtained with an OTM non-electrified at 900℃.The influence of depositing a porous Ce_(0.8)Tb_(0.2)O_(2-δ) catalytic/protective layer on the outer membrane surface revealed that lower surface temperatures(830℃)were detected at the same imposed electric power.Finally,the electrification concept was demonstrated in a catalytic membrane reactor(CMR)where the oxidative dehydrogenation of ethane(ODHE)was carried out.ODHE reaction is very sensitive to temperature,and here,we demonstrate an improvement of the ethylene yield by reaching moderate temperatures in the reaction chamber while the O_(2) injection into the reaction can be easily fine-tuned.

关键词： Oxygen permeation Oxidative dehydrogenation of ethane Oxygen transport membranes Joule effect Mixed ionic-electronic conductors Catalytic membrane reactors

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The outcomes and safety of patients undergoing endoscopic retrograde cholangiopancreatography combining a single-use cholangioscope and a single-use duodenoscope:A multicenter retrospective international study

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Hepatobiliary & Pancreatic Diseases International 2024年第1期23卷 71-76页

作者： Alessandro Fugazza Matteo Colombo Michel Kahaleh V.Raman Muthusamy Bick Benjamin Wim Laleman Carmelo Barbera Carlo Fabbri Jose nieto Abed Al-Lehibi Mohan Ramchandani Amy Tyberg Haroon Shahid Avik Sarkar Dean Ehrlich Stuart Shermand Cecilia Binda Marco Spadaccini Andrea Iannone Kareem Khalaf Nageshwar Reddy Andrea Anderloni Alessandro Repici Division of Gastroenterology and Digestive Endoscopy Humanitas Research Hospital-IRCCSVia Manzoni 5620089RozzanoMilanoItaly Gastroenterology Rutgers Robert Wood JohnsonNew BrunswickNew JerseyUSA Vatche and Tamar Manoukian Division of Digestive Diseases University of CaliforniaLos Angeles School of Medicine at UCLALos AngelesCaliforniaUSA Division of Digestive and Liver Disorders Indiana University School of MedicineIndianapolisINUSA Department of Gastroenterology and Hepatology University Hospitals LeuvenKU Leuven3000 LeuvenBelgium U.O.C.di Gastroenterologia ed Endoscopia Digestiva Ospedale Giuseppe MazziniASL TeramoItaly Gastroenterology and Digestive Endoscopy Unit Forlì-Cesena HospitalsAUSL RomagnaForlì-CesenaItaly Borland Groover Clinic JacksonvilleFloridaUSA Department of Gastroenterology and Hepatology King Fahad Medical CityRiyadhSaudi Arabia Asian Institute of Gastroenterology HyderabadIndia Section of Gastroenterology Department of Emergency and Organ TransplantationUniversity of BariBari 70124Italy Department of Biomedical Sciences Humanitas UniversityVia Rita Levi Montalcini 420090Pieve EmanueleMilanItaly

Background: Duodenoscope-related multidrug-resistant organism(MDRO) infections raise concerns. Disposable duodenoscopes have been recently introduced in the market and approved by regulatory agencies with the aim to reduce the risk of endoscopic retrograde cholangiopancreatography(ERCP) associated infections. The aim of this study was to evaluate the outcome of procedures performed with single-use duodenoscopes in patients with clinical indications to single-operator cholangiopancreatoscopy. Methods: This is a multicenter international, retrospective study combining all patients who underwent complex biliopancreatic interventions using the combination of a single-use duodenoscope and a single-use cholangioscope. The primary outcome was technical success defined as ERCP completion for the intended clinical indication. Secondary outcomes were procedural duration, rate of cross-over to reusable duodenoscope, operator-reported satisfaction score(1 to 10) on performance rating of the single-use duodenoscope, and adverse event(AE) rate. Results: A total of 66 patients(26, 39.4% female) were included in the study. ERCP was categorized according to ASGE ERCP grading system as 47(71.2%) grade 3 and 19(28.8%) grade 4. The technical success rate was 98.5%(65/66). Procedural duration was 64(interquartile range 15-189) min, cross-over rate to reusable duodenoscope was 1/66(1.5%). The satisfaction score of the single-use duodenoscope classified by the operators was 8.6 ± 1.3 points. Four patients(6.1%) experienced AEs not directly related to the single-use duodenoscope, namely 2 post-ERCP pancreatitis(PEP), 1 cholangitis and 1 bleeding.Conclusions: Single-use duodenoscope is effective, reliable and safe even in technically challenging procedures with a non-inferiority to reusable duodenoscope, making these devices a viable alternative to standard reusable equipment.

关键词： Single-operator cholangioscopy Single-use duodenoscope Endoscopic retrograde cholangiopancreatography Indeterminate biliary stricture Difficult biliary stones

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Landscape of global urban environmental resistome and its association with local socioeconomic and medical status

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Science China(Life Sciences) 2024年第6期67卷 1292-1301页

作者： Jun Wu Yige Hu Michael H Perlin David Danko Jun Lu Manuela Oliveira Johannes Werner Maria M Zambrano Maria A Sierra Olayinka O Osuolale PawełŁabaj Nicolás Rascovan Nur Hazlin Hazrin-Chong Soojin Jang Haruo Suzuki Marina nieto-Caballero Bharath Prithiviraj Patrick K H Lee Agnieszka Chmielarczyk Anna Różańska Yongxiang Zhao Lan Wang Christopher E Mason Tieliu Shi Center for Bioinformatics and Computational Biology and the Institute of Biomedical SciencesSchool of Life SciencesEast China Normal UniversityShanghai 200241China Department of Biology Program on Disease EvolutionUniversity of LouisvilleLouisville 40292USA Weill Cornell Medicine New York 10065USA The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine New York 10065USA Department of Pulmonary Medicine Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghai 200025China i3S-Instituto de Investiga玢o e Inova玢o em Saúde Universidade do PortoPorto 4050-290Portugal Ipatimup-Instituto de Patologia e Imunologia Molecular da Universidade do Porto Porto 4200-465Portugal Departamento de Biologia Faculdade de CiênciasUniversidade do PortoPorto 4050-290Portugal High Performance and Cloud Computing Group Zentrum für Datenverarbeitung(ZDV)Eberhard Karls University of TübingenW鋍hterstra遝7672074TübingenGermany Corporación Corpogen Research Center Bogotá110311Colombia Applied Environmental Metagenomics and Infectious Diseases Research(AEMIDR) Department of Biological SciencesElizade UniversityIlara-Mokin 340271Nigeria Maopolska Centre of Biotechnology Jagiellonian UniversityKraków 30-005Poland Aix-Marseille Université Mediterranean Institute of OceanologyUniversitéde ToulonCNRSIRDUM 110Marseille 83041France Department of Biological Sciences and Biotechnology Faculty of Science and TechnologyUniversiti Kebangsaan Malaysia43600 UKM BangiSelangor Institut Pasteur Korea Seoul 13488Republic of Korea Faculty of Environment and Information Studies Keio UniversityFujisawaKanagawa 252-0882Japan University of Colorado at Boulder CivilEnvironmental and Architectural DepartmentBoulder 80303USA Brooklyn College of the City University of New York Brooklyn 11210USA School of Energy and Environment City University of Hong KongHong Kong 999077China Department of Microbiology Faculty of MedicineJagiellonian UniversityKraków 30-005Poland Biological Targeting Diagnosis and The

Antimicrobial resistance(AMR)poses a critical threat to global health and development,with environmental factors—particularly in urban areas—contributing significantly to the spread of antibiotic resistance genes(ARGs).However,most research to date has been conducted at a local level,leaving significant gaps in our understanding of the global status of antibiotic resistance in urban environments.To address this issue,we thoroughly analyzed a total of 86,213 ARGs detected within 4,728 metagenome samples,which were collected by the Meta SUB International Consortium involving diverse urban environments in 60 cities of 27 countries,utilizing a deep-learning based methodology.Our findings demonstrated the strong geographical specificity of urban environmental resistome,and their correlation with various local socioeconomic and medical conditions.We also identified distinctive evolutionary patterns of ARG-related biosynthetic gene clusters(BGCs)across different countries,and discovered that the urban environment represents a rich source of novel antibiotics.Our study provides a comprehensive overview of the global urban environmental resistome,and fills a significant gap in our knowledge of large-scale urban antibiotic resistome analysis.

关键词： urban environment metagenome antibiotic resistance resistance diversity biosynthetic gene clusters

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The complex Maxwell stress tensor theorem:The imaginary stress tensor and the reactive strength of orbital momentum.A novel scenery underlying electromagnetic optical forces

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Light(Science & Applications) 2022年第11期11卷 2655-2675页

作者： Manuel nieto-Vesperinas Xiaohao Xu Instituto de Ciencia de Materiales de Madrid Consejo Superior de Investigaciones Cintificas.Campus de CantoblancoMadrid 28049Spain State Key Laboratory of Transient Optics and Photonics Xi'an Institute of Optics and Precision MechanicsChinese Academy of SciencesXi'an 710119China Institute of Nanophotonics Jinan UniversityGuangzhou 511443China

We uncover the existence of a universal phenomenon concerning the electromagnetic optical force exerted by light or other electromagnetic waves on a distribution of charges and currents in general,and of particles in particular.This conveys the appearence of underlying reactive quantities that hinder radiation pressure and currently observed timeaveraged forces.This constitutes a novel paradigm of the mechanical effciency of light on matter,and completes the landscape of the optical,and generally electromagnetic,force in photonics and classical electrodynamics;widening our understanding in the design of both llumination and particles in optical manipulation without the need of increasing the illuminating power,and thus lowering dissipation and heating.We show that this may be accomplished through the minimization of what we establish as the reactive strength of orbital(or canonical)momentum,which plays against the optical force a role analogous to that of the reactive power versus the radiation effciency of an antenna.This long time overlooked quantity,important for current progress of optical manipulation,and that stems from the complex Maxwell theorem of conservation of complex momentum that we put forward,as well as its alternating flow associated to the imaginary part of the complex Maxwell stress tensor,conform the imaginary Lorentz force that we introduce in this work,and that like the reactive strength of orbital momentum,is antagonistic to the well-known time-averaged force;thus making this reactive Lorentz force indirectly observable near wavelengths at which the time-averaged force is lowered.The Minkowski and Abraham momenta are also addressed.

关键词： imaginary tensor orbital

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Oleanolic acid:a promising neuroprotective agent for cerebral ischemia

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Neural Regeneration Research 2015年第4期10卷 540-541页

作者： Caltana Laura nieto María Luisa Brusco alicia Instituto de Biología Celulary Neurociencia IBCN(UBA-CONICET)Buenos AiresArgentina Instituto Biologíay Genética Molecular CSIC-UVAValladolidSpain

Stroke is considered the most common and severely disabling neurological disease. It is one of the leading causes of death after heart disease and cancer, causing 10% deaths worldwide and involving risk factors such as smoking, obesity and nutritional disbalance. Disability affects 75% of stroke survivors through severe mental and/or physical impairment depending on the affected brain area （Go et al., 2014）.

关键词： acid Oleanolic acid

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Carbamazepine degradation by visible-light-driven photocatalyst Ag_(3)PO_(4)/GO:Mechanism and pathway

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Environmental Science and Ecotechnology 2022年第1期9卷 17-26页

作者： Guanhan Chen Wenyi Dong Hongjie Wang Zilong Zhao Feng Wang Feifei Wang Cesar nieto-Delgado School of Civil and Environmental Engineering Harbin Institute of Technology ShenzhenShenzhen518055PR China Shenzhen Key Laboratory of Water Resource Utilization and Environmental Pollution Control Shenzhen518055PR China State Key Laboratory of Urban Water Resource and Environment School of EnvironmentHarbin Institute of TechnologyHarbin150090PR China Division de Ciencias Ambientales Instituto Potosino de Investigacion Científica y TecnologicaIPICyT.Camino a la Presa San Jose 2055.San Luis PotosíSLP 78216Mexico

Carbamazepine(CBZ),as one of the most frequently detected pharmaceuticals,is of great concern due to its potential impact on the ecosystem and human health.This study provides an effective approach to remove CBZ by using photocatalyst silver phosphate combined with graphene oxide(Ag_(3)PO_(4)/GO)under visible irradiation.The morphology,composition,and optical properties of Ag_(3)PO_(4)/GO were characterized employing SEM,XRD,and DRS.Graphene oxide could improve the visible-light utilization and promote electron's charge to enhance the photocatalytic performance of Ag_(3)PO_(4)/GO.With the optimal reaction condition of 5.86 mW/cm_(2)light intensity,15-25℃ temperature,5-7 pH,and 0.5 mg/L catalytic dosages,5 mg/L CBZ could be completely degraded in 30 min,and the apparent rate constant could reach 0.12 min^(-1).Additionally,the radical trapping experiments indicated·OH and O_(2)^(-)· were the main reactive oxygen species employed to eliminate CBZ.The decay pathways of CBZ had been proposed accordingly,and the main product was the low-molecular products.

关键词： Carbamazepine Ag_(3)PO_(4)/GO Visible light Photocatalysis

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Advances in spray products for skin regeneration

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Bioactive Materials 2022年第10期7卷 187-203页

作者： Paula Pleguezuelos-Beltran Patricia Galvez-Martín Daniel nieto-Garcí Juan Antonio Marchal Elena Lopez-Ruiz Biopathology and Regenerative Medicine Institute(IBIMER) Centre for Biomedical Research(CIBM)University of GranadaGranadaSpain Department of Human Anatomy and Embryology Faculty of MedicineUniversity of GranadaGranadaSpain BioFab i3D Lab-Biofabrication and 3D(bio)printing Laboratory GranadaSpain Excellence Research Unit“Modeling Nature”(MNat) University of GranadaGranadaSpain Biosanitary Research Institute of Granada(ibs.GRANADA) University Hospitals of Granada-University of GranadaGranadaSpain R&D Human Health Bioib´erica S.A.UBarcelonaSpain Department of Pharmacy and Pharmaceutical Technology Faculty of PharmacyUniversity of GranadaGranadaSpain Complex Tissue Regeneration Department MERLN Institute for Technology Inspired Regenerative MedicineUniversiteitssingel 406229ER Maastrichtthe Netherlands Department of Health Sciences University of Ja´enJa´enSpain

To date,skin wounds are still an issue for healthcare professionals.Although numerous approaches have been developed over the years for skin regeneration,recent advances in regenerative medicine offer very promising strategies for the fabrication of artificial skin substitutes,including 3D bioprinting,electrospinning or spraying,among others.In particular,skin sprays are an innovative technique still under clinical evaluation that show great potential for the delivery of cells and hydrogels to treat acute and chronic wounds.Skin sprays present significant advantages compared to conventional treatments for wound healing,such as the facility of application,the possibility to treat large wound areas,or the homogeneous distribution of the sprayed material.In this article,we review the latest advances in this technology,giving a detailed description of investigational and currently commercially available acellular and cellular skin spray products,used for a variety of diseases and applying different experimental materials.Moreover,as skin sprays products are subjected to different classifications,we also explain the regulatory pathways for their commercialization and include the main clinical trials for different skin diseases and their treatment conditions.Finally,we argue and suggest possible future trends for the biotechnology of skin sprays for a better use in clinical dermatology.

关键词： Skin Spray Tissue engineering Fibrin Hydrogel

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