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MARS and RNAcmap3:The Master Database of All Possible RNA Sequences Integrated with RNAcmap for RNA Homology Search

Genomics, Proteomics & Bioinformatics 2024年第1期22卷 143-150页

作者： Ke Chen thomas Litfin Jaswinder Singh Jian Zhan Yaoqi Zhou Institute of Systems and Physical Biology Shenzhen Bay LaboratoryShenzhen 518055China Peking University Shenzhen Graduate School Shenzhen 518055China University of Science and Technology of China Hefei 230026China Suzhou Institute for Advanced Research University of Science and Technology of ChinaSuzhou 215123China Institute for Glycomics Griffith UniversitySouthportQLD 4222Australia

sequences found in the huge,integrated database of protein sequences(Big Fantastic Database).In contrast,the existing nucleotide databases were not consolidated to facilitate wider and deeper homology ***,we built a comprehensive database by incorporating the non-coding RNA(ncRNA)sequences from RNAcentral,the transcriptome assembly and metagenome assembly from metagenomics RAST(MG-RAST),the genomic sequences from Genome Warehouse(GWH),and the genomic sequences from MGnify,in addition to the nucleotide(nt)database and its subsets in National Center of Biotechnology Information(NCBI).The resulting Master database of All possible RNA sequences(MARS)is 20-fold larger than NCBI’s nt database or 60-fold larger than *** new dataset along with a new split-search strategy allows a substantial improvement in homology search over existing state-of-the-art *** also yields more accurate and more sensitive multiple sequence alignments(MSAs)than manually curated MSAs from Rfam for the majority of structured RNAs mapped to *** results indicate that MARS coupled with the fully automatic homology search tool RNAcmap will be useful for improved structural and functional inference of ncRNAs and RNA language models based on *** is accessible at https://***/omix/release/OMIX003037,and RNAcmap3 is accessible at http://***/download/.

关键词： RNA sequence database Homology search Secondary structure MARS RNAcmap3

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Impact of increasing one-carbon metabolites on traumatic brain injury outcome using pre-clinical models

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Neural Regeneration Research 2024年第8期19卷 1728-1733页

作者： Sanika M.Joshi Theresa Currier thomas Nafisa M.Jadavji College of Osteopathic Medicine Midwestern UniversityGlendaleCAUSA Department of Biomedical Sciences Midwestern UniversityGlendaleCAUSA Department of Child Health College of Medicine–PhoenixUniversity of ArizonaPhoenixAZUSA College of Veterinary Medicine Midwestern UniversityGlendaleCAUSA Department of Neuroscience Carleton UniversityOttawaCanada

Traumatic brain injury is a major cause of death and disability worldwide,affecting over 69 million individuals ***-carbon metabolism has been shown to have beneficial effects after brain damage,such as ischemic ***,whether increasing one-carbon metabolite vitamins impacts traumatic brain injury outcomes in patients requires more *** aim of this review is to evaluate how one-carbon metabolites impact outcomes after the onset of traumatic brain ***,Web of Science,and Google Scholar databases were searched for studies that examined the impact of B-vitamin supplementation on traumatic brain injury *** search terms included combinations of the following words:traumatic brain injury,dietary supplementation,one-carbon metabolism,and *** focus of each literature search was basic science *** year of publication in the literature searches was not *** analysis of the literature has shown that dietary supplementation of B-vitamins has significantly improved the functional and behavioral recove ry of animals with traumatic brain injury compared to *** r,this improvement is dosage-dependent and is contingent upon the onset of supplementation and whether there is a sustained or continuous delive ry of vitamin supplementation post-traumatic brain *** details of supplementation post-traumatic brain injury need to be further ***,we conclude that B-vitamin supplementation improves behavioral outcomes and reduces cognitive impairment post-traumatic brain injury in animal model *** investigation in a clinical setting should be stro ngly considered in co njunction with current medical treatments for traumatic brain injury-affected individuals.

关键词： folic acid nicotinamide one-carbon metabolism riboflavin traumatic brain injury vitamin B12 vitamin B2 vitamin B3

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Characterization of the infectivity of an Indonesian Zika virus strain in mammalian cell lines

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Asian Pacific Journal of Tropical Biomedicine 2024年第5期14卷 215-224页

作者： Justus thomas Obiajulu Sievers Anom Bowolaksono R.Tedjo Sasmono Graduate School of Biology Department of BiologyFaculty of Mathematics and Natural SciencesUniversitas IndonesiaDepok 16424Indonesia Eijkman Research Center for Molecular Biology National Research and Innovation AgencyCibinong 16911Indonesia Cellular and Molecular Mechanisms in Biological System Research Group Department of BiologyFaculty of Mathematics and Natural SciencesUniversitas IndonesiaDepok 16424Indonesia

Objective:To characterize the infection patterns and growth characteristics of the Zika virus(ZIKV)strain JMB-185 from Indonesia in various mammalian cell ***:ZIKV was grown in human(A549,HEK293,HepG2,Huh7,Jurkat,and THP-1)and non-human mammalian(RAW264.7,Vero,and Vero76)cell *** replication kinetics were measured using plaque assay,while intra-and extracellular viral RNA concentrations were assessed using *** cytometry was used to quantify the infected cells and cell viability was measured using an MTT *** ability of ZIKV to infect cell lines was visualized using a fluorescence immunostaining ***:This ZIKV strain preferentially infected the lung,kidney,and liver cell lines A549,HEK293,Huh7,Vero,and Vero76,but not the immune cells Jurkat,RAW264.7,and *** contrast,the ZIKV showed no sign of infection in HepG2 cells,while maintaining viral titer over 3 days post-infection,with no infection recorded in immunostaining,no increase in viral RNA,and no indication of cell ***:The Indonesian ZIKV strain has a similar infection profile as other strains,except for its poor infectivity on HepG2 *** on the growth characteristics of Indonesia ZIKV will help expand our understanding of the biology of ZIKV which will be useful for various applications including antiviral discovery.

关键词： Zika virus Infectivity Replication Cell lines In vitro

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Reversed charge transfer induced by nickel in Fe-Ni/Mo_(2)C@nitrogen-doped carbon nanobox for promoted reversible oxygen electrocatalysis

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Journal of Energy Chemistry 2024年第1期88卷 202-212,I0005页

作者： Zhicheng Nie Lei Zhang Qiliang Zhu Zhifan Ke Yingtang Zhou thomas Wågberg Guangzhi Hu School of Materials Science and Engineering Anhui University of Science and TechnologyHuainan 232001AnhuiChina Institute for Ecological Research and Pollution Control of Plateau Lakes School of Ecology and Environmental ScienceYunnan UniversityKunming 650504YunnanChina National Engineering Research Center for Marine Aquaculture Marine Science and Technology CollegeZhejiang Ocean UniversityZhoushan 316004ZhejiangChina Department of Physics UmeåUniversityUmeåS-90187Sweden

The interaction between metal and support is critical in oxygen catalysis as it governs the charge transfer between these two entities,influences the electronic structures of the supported metal,affects the adsorption energies of reaction intermediates,and ultimately impacts the catalytic *** this study,we discovered a unique charge transfer reversal phenomenon in a metal/carbon nanohybrid ***,electrons were transferred from the metal-based species to N-doped carbon,while the carbon support reciprocally donated electrons to the metal domain upon the introduction of *** led to the exceptional electrocatalytic performances of the resulting Ni-Fe/Mo_(2)C@nitrogen-doped carbon catalyst,with a half-wave potential of 0.91 V towards oxygen reduction reaction(ORR)and a low overpotential of 290 m V at 10 mA cm^(-2)towards oxygen evolution reaction(OER)under alkaline ***,the Fe-Ni/Mo_(2)C@carbon heterojunction catalyst demonstrated high specific capacity(794 mA h g_(Zn)~(-1))and excellent cycling stability(200 h)in a Zn-air *** calculations revealed that Mo_(2)C effectively inhibited charge transfer from Fe to the support,while secondary doping of Ni induced a charge transfer reversal,resulting in electron accumulation in the Fe-Ni alloy *** local electronic structure modulation significantly reduced energy barriers in the oxygen catalysis process,enhancing the catalytic efficiency of both ORR and ***,our findings underscore the potential of manipulating charge transfer reversal between the metal and support as a promising strategy for developing highly-active and durable bi-functional oxygen electrodes.

关键词： Metal-support interaction Charge transfer reversal Oxygen reduction reaction Oxygen evolution reaction Zinc-air battery

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Energy and blast performance of beryllium in a model thermobaric composition in comparison with aluminum and magnesium

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Defence Technology（防务技术） 2024年第6期36卷 13-19页

作者： thomas M.Klapotke Stanisław Cudziło Waldemar A.Trzcinski Jozef Paszula Energetic Materials Research Department of ChemistryUniversity of Munich(LMU)Butenandtstrasse 5-13(D)81377MunichGermany Military University of Technology Faculty of Advanced Technologies and ChemistrySylwester Kaliski Str.200-908WarsawPoland

A direct comparison is made between the effectiveness of Al,Mg,and Be powders as additional fuels in model thermobaric compositions containing 20%fuel,20%ammonium perchlorate,and 60%RDX(1,3,5-Trinitro-1,3,5-triazacyclohexane)passivated with *** determined calorimetric measurements of the heat of detonation,along with the overpressure histories in an explosion chamber filled with nitrogen,were used to determine the quasi-static pressure(QSP)under anaerobic *** measurements were also performed in a semi-closed bunker,and all blast wave parameters generated after the detonation of 500 g charges of the tested explosives were *** calorimetry results,QSP values,and blast wave parameters(pressure amplitude,specific and total impulses)clearly indicate that Be is much more effective as an additional fuel than either Al or Mg in both anaerobic post-detonation reactions as well as the subsequent aerobic *** heat of detonation of the RDXwax/AP/Be explosive mixture is over 40%and 50%higher than that of the mixture containing aluminum and magnesium instead of beryllium,***,the TNT equivalent of the Be-containing composition due to the overpressure in the nitrogen-filled explosion chamber is 1.66,while the equivalent calculated using an air shock wave-specific impulse at a distance of 2.5 m is equal to *** high values of these parameters confirm the high reactivity of beryllium in both the anaerobic and aerobic stages of the thermobaric explosion.

关键词： Thermobaric explosives Beryllium Heat of detonation Quasi-static overpressure Blast wave parameters

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Numerical study of novel OME_(1-6) combustion mechanism and spray combustion at changed ambient environments

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Frontiers in Energy 2024年第4期18卷 483-505页

作者： Frederik WIESMANN Zeyan QIU Dong HAN Lukas STRAUβ Sebastian RIEβ Michael WENSING thomas LAUER Institute of Powertrains and Automotive Technology TU Wien1060 ViennaAustria Key Laboratory for Power Machinery and Engineering of Ministry of Education Shanghai Jiao Tong UniversityShanghai 200240China Professorship for Fluid Systems Technology Friedrich-AlexanderUniversität Erlangen-Nürnberg91058 ErlangenGermany

For a climate-neutral future mobility,the socalled e-fuels can play an essential ***,oxygenated e-fuels containing oxygen in their chemical formula have the additional potential to burn with significantly lower soot *** particular,polyoxymethylene dimethyl ethers or oxymethylene ethers(PODEs or OMEs)do not contain carbon-carbon bonds,prohibiting the production of soot precursors like acetylene(C_(2)H_(2)).These properties make OMEs a highly interesting candidate for future climate-neutral compression-ignition ***,to fully leverage their potential,the auto-ignition process,flame propagation,and mixing regimes of the combustion need to be *** achieve this,efficient oxidation mechanisms suitable for computational fluid dynamics(CFD)calculations must be developed and *** present work aims to highlight the improvements made by developing an adapted oxidation mechanism for OME1-6 and introducing it into a validated spray combustion CFD model for *** simulations were conducted for single-and multi-injection patterns,changing ambient temperatures,and oxygen *** results were validated against high-pressure and high-temperature constantpressure chamber ****-chemiluminescence measurements accomplished the characterization of the auto-ignition *** experiments and simulations were conducted for two different *** improvements concerning the prediction of the ignition delay time were accomplished while also retaining an excellent agreement for the flame lift-off *** spatial zones of high-temperature reaction activity were also affected by the adaption of the reaction *** showed a greater tendency to form OH^(*) radicals within the center of the spray in accordance with the experiments.

关键词： oxygenated fuels reaction kinetics oxidation mechanisms computational fluid dynamics(CFD) oxymethylene ethers(OME) e-fuels multiinjection spray-combustion

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Health economics for intra-capsular hip fractures undertaking fixation

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World Journal of Orthopedics 2024年第1期15卷 30-38页

作者： Anatole Wiik thomas Ashdown Ian Holloway Department of Surgery Trauma and OrthopaedicsLondon North West University HealthcareLondon HA13UJUnited Kingdom Department of Surgery Trauma and OrthopaedicsLondon North West University HospitalLondon HA13UJUnited Kingdom

BACKGROUND Hip fracture is a common musculoskeletal injury in the elderly requiring surgery *** operative mainstay of intra-capsular hip fractures is arthroplasty with a smaller proportion for *** To determine the most beneficial method of fixation for patients with intracapsular hip *** A registered audit from 2012-2018 was conducted on all intra-capsular hip fractures treated with 2 commonly used fixation *** notes,electronic records and clinical codes for cost benefit were evaluated.A validated quality of life measure was collected at least 1 year after *** A total of 83 patients were identified with intra-capsular fractures undergoing fixation during the retrospective *** were 47 cannulated cancellous screw and 36 sliding hip screw fixations with the case mix comparable for age,gender,co-morbidities and fracture *** was no significant difference in blood loss,tip apex distance,radiation exposure,length of stay,radiological union time,collapse,avascular necrosis or re-operation between fixation *** regression analysis demonstrated displaced intracapsular hip fractures correlated significantly with an undesirable outcome conferring a relative odds ratio of *** were 9(19%)and 4(11%)patients respectively,who required *** was no significant difference in health resource group tariff and implant cost with comparable EQ-5D and visual CONCLUSION No significant advantage was identified with differing fixation type,but irrespective there were a high number of patients requiring *** was predicted by initial fracture displacement and patient *** may need to be carefully considered for health economics and patient benefit.

关键词： Hip fracture Fixation Patient reported outcome measure Cost

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BLE beacons for sample position estimation in a life science automation laboratory

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Transportation Safety and Environment 2024年第3期6卷 111-123页

作者： Haiping Wu Steffen Junginger thomas Roddelkopf Hui Liu Kerstin Thurow Institute of Artificial Intelligence&Robotics(IAIR) Key Laboratory of Traffic Safety on Track of Ministry of EducationSchool of Traffic and Transportation EngineeringCentral South UniversityChangsha 410075HunanChina Institute of Automation(IAT) University of Rostock18119 RostockGermany Center of Life Science Automation(celisca) University of Rostock18119 RostockGermany

Estimation of the sample position is essential for working process monitoring and management in the life science automation lab*** low-energy(BLE)beacons have the advantages of low price,small size and low energy consumption,which make them a promising solution for sample position estimation in the automated *** fingerprinting models have been proposed to achieve indoor localization with the received signal strength(RSS)***,most of the research depends on intensive beacon *** estimation,which depends entirely on one beacon,is more suitable for sample position estimation in large automated *** complexity of the life science automation laboratory environment brings challenges to the traditional path loss model(PLM),which is a widely used radio wave propagation model-based proximity estimation *** this paper,BLE sensing devices for sample position estimation are *** BLE beacon-based proximity estimation is discussed in the framework of machine learning,in which the support vector regression(SVR)is utilized to model the nonlinear relationship between the RSS data and distance,and the Kalman filter is utilized to decrease the RSS data *** experimental results over different environments indicate that the SVR outperforms the PLM significantly,and provides 1 m absolute errors for more than 95%of the testing *** Kalman filter brings benefits to stable distance *** from proximity-based sample position estimation,the proposed framework turned out to be effective in position estimation between parallel workbenches and position estimation on an automated workstation.

关键词： BLE beacon position estimation proximity estimation received signal strength(RSS) support vector regression(SVR) life science automation laboratory

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Clean,but not green:Emission assessment,forecast modelling and policy solutions for plastic microbeads from personal care products in India

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Emerging Contaminants 2024年第3期10卷 124-133页

作者： Riya Kumbukattu Alex thomas Maes Suja Purushothaman Devipriya School of Environmental Studies Cochin University of Science and Technology682022India GRID-Arendal Teaterplassen 34836ArendalNorway

Intentionally added plastic microbeads in personal care products(PCP)are an underestimated source of *** microbeads are added as fillers,to increase product volume or aesthetics and allegedly have the purpose of cleansing and *** assess and forecast microbead emissions in India,this study analysed 45 items from four different categories of personal care products:face wash,face scrub,shower gel and body scrub available in the Indian market and determined microbead abundance,size,colour,shape and polymer ***,an emission estimation and time-seriesbased forecast for 2030 was done using ARIMA(0,2,0)for individual categories and *** results indicate that 45.00%of the products contained irregular or smooth microplastics,with Polyethylene being the dominant polymer,followed by Polypropylene,Polystyrene,Polyurethane and Polycaprolactone.A significant number of products(23.33%)contained cellulose microbeads,with ambiguity regarding their *** identified microbeads were mainly irregular in shape and granular in texture,especially ***/transparent colour dominated the identified microbeads,followed by blue,pink,yellow,red and *** 1.34%of the total product contained plastic microbeads,with 5.04%and 0.04%being the highest and lowest percentages *** average size of microbeads was found to be 640.74 mm,452.45 mm,556.66 mm and 606.30 mm in different *** overall annual emission estimation was 3.51×10^(19)(highest),2.14×10^(18)(lowest)and 1.37×10^(19)(average)in 2021 and forecasted to be 4.12×10^(19)(highest),2.52×10^(18)(lowest)and 1.611019(average)in *** exorbitantly high value is due to India's significant population,globalisation,inefficient wastewater efficiency,growing economy and disposable income.A lack of policies and adequate regulations further add to *** study emphasises and recommends the development of stringent policies and other well-tailored mitig

关键词： Microplastic beads Time-series forecast Policy solutions Emission estimation Personal care products

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Key features of numerical models for the FE-simulation of deep tunnel advance by the NATM

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Underground Space 2024年第1期14卷 357-376页

作者： Peter Gamnitzer Matthias Neuner Magdalena Schreter-Fleischhacker Alexander Dummer thomas Mader Stefan Smaniotto Gunter Hofstetter Unit of Strength of Materials and Structural Analysis Institute of Basic Sciences in Engineering SciencesUniversitat InnsbruckTechnikerstraβe 13Innsbruck A-6020Austria

In the present work,important aspects of time-dependent nonlinear 3D finite element(FE)models for deep tunnel advance by the New Austrian Tunneling Method(NATM),characterized by repeated sequences of excavation,securing,and idle periods,are discussed on the example of a 3D finite element model of a stretch of the Brenner Base Tunnel,which is currently constructed between Austria and *** material models are utilized for representing the surrounding rock mass and the shotcrete *** on the finite element model,strategies for the efficient implementation into a parallel distributed memory numerical code are *** are essential to achieve reasonable computation times for numerical simulations of tunneling based on large 3D FE *** particular,the implementation of the construction procedure,parallel computing and communication specific details,and efficient linear solvers for the global equation system within the incremental-iterative Newton–Raphson scheme are ***,possible extensions of the material models for rock mass and shotcrete,used in the 3D FE model,are *** concern(i)a gradient-enhanced model for transversely isotropic rock and rock mass,taking into account hardening and softening behavior and(ii)the extension of the shotcrete model to nonlinear creep and damage due to *** possible benefits of the model extensions in numerical simulations of tunneling by the NATM are discussed.

关键词： NATM Finite element model Rock Shotcrete Damage-plasticity model

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