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Whyand how tousethe SeqCode

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mLife 2024年第1期3卷 1-13页

作者： Wiliam B.Whitman maria Chuvochina Brian P.Hedlund Konstantinos T.Konstantinidis marike Palmer Luis m.rodriguez-R lain Sutcliffe Fengping Wang Deparment of microbioogy University of GeorgiaAthensGeorgiaUAA Schoolof Chemistry and molecular Biosciences Australian CentreforEogenomicsThe Universty of QueenslandSt LuciaAustralia University of Nevada Las Vegas Las VegasNevadaUSA Schol of Civil and Environmental Engineering and School of Biological SciencesGeorgia Institute of TechnologyAtlantaGeorgiaUSA Department of microbiology University of ManitobaWinnipegManitobaCanada School of Life Sciences University of Nevada Las VegasLas VegasNevadaUSA Department of microbiology and Digital Science Center(DiSC) University of InnsbruckInnsbruckAustria Faculty of Health&Life Sciences Northumbria UniversityNewcastle upon TyneUK School of Oceanography International Center for Deep Life InvestigationShanghai Jiao Tong UniversityShanghaiChina

The SeqCode,formally called the Code of Nomenclature of Prokaryotes Described from Sequence Data,is a new code of nomenclature in which genome sequences are the nomenclatural types for the names of prokaryotic species.While similar to the International Code of Nomenclature of Prokaryotes(ICNP)in structure and rules of priority,it does not require the deposition of type strains in international culture collections.Thus,it allows for the formation of permanent names for uncultured prokaryotes whose nearly complete genome sequences have been obtained directly from environmental DNA as well as other prokaryotes that cannot be deposited in culture collections.Because the diversity of uncultured prokaryotes greatly exceeds that of readily culturable prokaryotes,the SeqCode is the only code suitable for naming the majority of prokaryotic species.The start date of the SeqCode was January 1,2022,and the online Registry(https://seqco.del)was created to ensure valid publication of names.The SeqCode recognizes all names validly published under the ICNP before 2022.After that date,names validly published under the SeqCode compete with ICNP names for priority.As a result,species can have only one name,either from the SeqCode or ICNP,enabling effective communication and the creation of unified taxonomies of uncultured and cultured prokaryotes.The SeqCode is administered by the SeqCode Committee,which is comprised of the SeqCode Community and elected administrative components.Anyone with an interest in the systematics of prokaryotes is encouraged to join the SeqCode Community and participate in the development of this resource.

关键词： genome sequences metagenome-assembled genomes nomenclature SeqCode

Estimates of voluntary activation in individuals with anterior cruciate ligament reconstruction:Effects of type of stimulator,number of stimuli,and quantification technique

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Journal of Sport and Health Science 2022年第1期11卷 85-93页

作者： Steven A.Garcia Kazandra m.rodriguez Scott R.Brown Riann m.Palmieri-Smith Chandramouli Krishnan School of Kinesiology University of MichiganAnn ArborMI 48109USA Neuromuscular and Rehabilitation Robotics Laboratory(NeuRRo Lab) Department of Physical Medicine and RehabilitationUniversity of MichiganAnn ArborMI 48108USA Department of Orthopaedic Surgery Michigan MedicineUniversity of MichiganAnn ArborMI 48109USA Robotics Institute University of MichiganAnn ArborMI 48109USA

Background:Accurate quantification of voluntary activation is important for understanding the extent of quadriceps dysfunction in individuals with anterior cruciate ligament reconstruction(ACLR).Voluntary activation has been quantified using both percent activation derived from the interpolated twitch technique and central activation ratio(CAR)derived from the burst superimposition technique,as well as by using different types of electrical stimulators and pulse train conditions.However,it is unclear how these parameters affect voluntary activation estimates in individuals with ACLR.This study was performed to fill this important knowledge gap in the anterior cruciate ligament literature.methods:Quadriceps strength and voluntary activation were examined in 18 ACLR participants(12 quadriceps/patellartendon graft,6 hamstring tendon graft;time since ACLR:1.06±0.82 years,mean±SD)at 90°of knee flexion using 2 stimulators(Digitimer and Grass)and pulse train conditions(3-pulse and 10-pulse).Voluntary activation was quantified by calculating both CAR and percent activation.Results:Results indicated that voluntary activation was significantly overestimated by CAR when compared with percent activation(pmates were not affected by pulse train conditions when using percent activation;however,3-pulse stimuli resulted in greater overestimation than 10-pulse stimuli when using CAR(p=0.003).Voluntary activation did not differ between stimulators(p>0.05);however,the Digitimer evoked greater torque at rest than the Grass(pm the interpolated twitch technique provides superior estimates of voluntary activation than CAR derived from burst superimposition and is less affected by pulse train conditions or stimulators in individuals with ACLR.

关键词： Anterior cruciate ligament Central activation Inhibition Knee strength Triplet Twitch interpolation

Liver expression of steroid hormones and Apolipoprotein D receptors in hepatocellular carcinoma

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World Journal of Gastroenterology 2007年第23期13卷 3221-3227页

作者： FJ Vizoso m rodriguez A Altadill mL González-Diéguez A Linares LO González S Junquera F Fresno-Forcelledo mD Corte L Rodrigo Unidad de Investigación. Fundación Hospital de Jove. Gijón Spain Gastroenterology Service. Hospital Universitario Central de Asturias. Oviedo Spain Instituto Universitario de Oncología del Principado de Asturias. Oviedo Spain Pathology Service. Hospital Universitario Central de Asturias. Oviedo Spain

AIm: To evaluate the tissular expression of Androgen (A), Estrogen (E) and Progesterone (Pg) receptors, and Apolipoprotein D (ApoD), in liver tumors from resected hepatocellular carcinoma (HCC) cases in order to assess their possible relationship to prognosis. mETHODS: We performed an immunohistochemical study using tissue microarrays (containing more than 260 cancer specimens, from 31 HCC patients and controls) to determine the presence of specif ic antibodies against AR, ER, PgR and ApoD, correlating their findings with several clinico-pathological and biological variables. The staining results were categorized using a semi-quantitive score based on their intensity, and the percentage of immunostained cells was measured. RESULTS: A total of 21 liver tumors (67.7%) were positive for AR; 16 (51.6%) for ER; 26 (83.9%) for PgR and 12 (38.7%) stained for ApoD. We have found a wide variability in the immunostaining score values for each protein, with a median (range) of 11.5 (11.5-229.5) for AR; 11.1 (8.5-65) for ER; 14.2 (4-61) for PgR; and 37.7 (13.8-81.1) for ApoD. A history of heavy ethanol consumption, correlated positively with AR and PgR and negatively with ER status. HCV chronic infection also correlated positively with AR and PgR status. However, the presence of ApoD immunostaining did not correlate with any of these variables. Tumors with a positive immuno-staining for PgR showed a better prognosis. CONCLUSION: Our results indicate a moderate clinical value of the steroid receptor status in HCC, emphasizing the need to perform further studies in order to evaluate the possible role of new hormonal-based therapies.

关键词：雄激素雌激素孕酮载脂蛋白肝细胞癌

microRNA-502-3p regulates GABAergic synapse function in hippocampal neurons

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Neural Regeneration Research 2024年第12期19卷 2698-2707页

作者： Bhupender Sharma melissa mTorres Sheryl rodriguez Laxman Gangwani Subodh Kumar Center of Emphasis in Neuroscience Department of Molecular and Translational MedicinePaul L.Foster School of MedicineTexas Tech University Health Sciences CenterEl PasoTXUSA Bond Life Sciences Center and Department of Veterinary Pathobiology University of MissouriColumbiaMOUSA L.Frederick Francis Graduate School of Biomedical Sciences Texas Tech University Health Sciences CenterEl PasoTXUSA

Gamma-aminobutyric acid(GABA)ergic neurons,the most abundant inhibitory neurons in the human brain,have been found to be reduced in many neurological disorders,including Alzheimer's disease and Alzheimer's disease-related dementia.Our previous study identified the upregulation of microRNA-502-3p(miR-502-3p)and downregulation of GABA type A receptor subunitα-1 in Alzheimer's disease synapses.This study investigated a new molecular relationship between miR-502-3p and GABAergic synapse function.In vitro studies were perfo rmed using the mouse hippocampal neuronal cell line HT22 and miR-502-3p agomiRs and antagomiRs.In silico analysis identified multiple binding sites of miR-502-3p at GABA type A receptor subunitα-1 mRNA.Luciferase assay confirmed that miR-502-3p targets the GABA type A receptor subunitα-1 gene and suppresses the luciferase activity.Furthermore,quantitative reve rse transcription-polymerase chain reaction,miRNA in situ hybridization,immunoblotting,and immunostaining analysis confirmed that overexpression of miR-502-3p reduced the GABA type A receptor subunitα-1 level,while suppression of miR-502-3p increased the level of GABA type A receptor subunitα-1 protein.Notably,as a result of the overexpression of miR-502-3p,cell viability was found to be reduced,and the population of necrotic cells was found to be increased.The whole cell patch-clamp analysis of human-GABA receptor A-α1/β3/γ2L human embryonic kidney(HEK)recombinant cell line also showed that overexpression of miR-502-3p reduced the GABA current and overall GABA function,suggesting a negative correlation between miR-502-3p levels and GABAergic synapse function.Additionally,the levels of proteins associated with Alzheimer s disease were high with miR-502-3p overexpression and reduced with miR-502-3p suppression.The present study provides insight into the molecular mechanism of regulation of GABAergic synapses by miR-502-3p.We propose that micro-RNA,in particular miR-502-3p,could be a potential therapeutic to rget to modulate GABAergic synapse f

关键词： Alzheimer's disease GABAergic synapse gamma-aminobutyric acid type A receptor subunitα-1(GABRα1) microRNA-502-3p(miR-502-3p) miRNA in situ hybridization Patch-clamp

In‑depth proteome characterization of endometrium and extraembryonic membranes during implantation in pig

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Journal of Animal Science and Biotechnology 2024年第3期15卷 1027-1055页

作者： maria A.Gil Josep m.Cambra Heriberto rodriguez‑martinez Cristina Cuello Inmaculada Parrilla Emilio A.martinez Department of medicine and Animal Surgery International Excellence Campus for Higher Education and Research“Campus Mare Nostrum”University of MurciaMurciaSpain Institute for Biomedical Research of murcia(ImIB-Pascual Parrilla) MurciaSpain Technical University of munich MunichGermany Department of Biomedical&Clinical Sciences(BKV) BKH/Obstetrics&GynaecologyLinkoping UniversityLinkopingSweden

Background Proteome characterization of the porcine endometrium and extraembryonic membranes is important to understand mother-embryo cross-communication.In this study,the proteome of the endometrium and cho-rioallantoic membrane was characterized in pregnant sows(PS)during early gestation(d 18 and 24 of gestation)and in the endometrium of non-pregnant sows(NPS)during the same days using LC-mS/mS analysis.The UniProtKB database and ClueGO were used to obtain functional Gene Ontology annotations and biological and functional networks,respectively.Results Our analysis yielded 3,254 and 3,457 proteins identified in the endometrium of PS and NPS,respectively;of these,1,753 being common while 1,501 and 1,704 were exclusive to PS and NPS,respectively.In addition,we iden-tified 3,968 proteins in the extraembryonic membranes of PS.Further analyses of function revealed some proteins had relevance for the immune system process and biological adhesion in endometrium while the embryonic chorion displayed abundance of proteins related to cell adhesion and cytoskeletal organization,suggesting they dominated the moment of endometrial remodeling,implantation and adhesion of the lining epithelia.Data are available via Pro-teomeXchange with identifier PXD042565.Conclusion This is the first in-depth proteomic characterization of the endometrium and extraembryonic mem-branes during weeks 3 to 4 of gestation;data that contribute to the molecular understanding of the dynamic environ-ment during this critical period,associated with the majority of pregnancy losses.

关键词： Endometrium Extraembryonic membranes Implantation Pig Proteome

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How does anterior cruciate ligament reconstruction affect the functioning of the brain and spinal cord?A systematic review with meta-analysis

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Journal of Sport and Health Science 2021年第2期10卷 172-181页

作者： Kazandra m.rodriguez Riann m.Palmieri-Smith Chandramouli Krishnan School of Kinesiology University of MichiganAnn ArborMI 48109USA Department of Orthopaedic Surgery Michigan MedicineAnn ArborMI 48109USA Department of Physical medicine and Rehabilitation Michigan MedicineAnn ArborMI 48108USA Biomedical Engineering University of MichiganAnn ArborMI 48109USA michigan Robotics Institute University of MichiganAnn ArborMI 48109USA

Objective:To examine the effect of anterior cruciate ligament(ACL)reconstruction on spinal-reflex and corticospinal excitability of the quadriceps muscle.methods:A comprehensive electronic database search was performed to identify studies that objectively measured Hoffmann reflex to muscle response ratio,motor threshold,and motor evoked potentials after ACL reconstruction.Pooled standardized mean differences(SmDs)were computed using a random effects meta-analysis model.Results:A total of 13 studies were eligible for analysis.The Hoffmann reflex to muscle response ratio was significantly higher on both the reconstructed and non-reconstructed legs when compared with the healthy control leg(SmD=0.28,95%confidence interval(95%CI):0.08-0.49,p=0.006 and SmD=0.22,95%CI:0.04-0.40,p=0.016,respectively)but did not differ between legs(SmD=0.10,95%CI:-0.01 to 0.21,p=0.078).The motor threshold was significantly higher on both the reconstructed(SmD=0.76,95%CI:0.40-1.12,pmD=0.47,95%CI:0.00-0.95,p=0.049)when compared with the legs of healthy controls.The reconstructed leg also had a higher motor threshold when compared with the non-reconstructed leg(SmD=0.20,95%CI:0.06-0.34,p=0.005).These changes were paralleled by bilateral reductions in quadriceps strength(ACL reconstructed:SmD=-0.78,95%CI:-1.07 to-0.49,pmD=-0.32,95%CI:-0.63 to-0.01,p=0.042)and quadriceps voluntary activation(ACL reconstructed:SmD=-0.73,95%CI:-0.97 to-0.50,pmD=-0.55,95%CI:-0.82 to-0.27,pmpared with healthy controls.Conclusion:There is increased excitability of the spinal-reflex pathways and reduced excitability of the corticospinal pathways following ACL reconstruction.These changes are paralleled by reductions in quadriceps strength and voluntary activation,suggesting that rehabilitation interventions should focus on normalizing the excitability of neural pathways to effectively address quadriceps dysfunction after ACL reconstruction.

关键词： ACLR Cortical excitability H-reflex Transcranial magnetic stimulation TmS

Symmetry in optics and photonics:a group theory approach

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Science Bulletin 2018年第4期63卷 244-251页

作者： B.m.rodriguez-Lara Ramy EI-Ganainy Julio Guerrero Tecnologico de monterrey.Escuela de Ingenieria y Ciencias Monterrey 64849Mexico Instituto Nacional de Astrofisica Optica y Electr6nicaPueblaCP 72840Mexico Department of Physics and Hexes Center for Quantum Phenomena Michigan Technological UniversityHoughton.MI 49931USA Departamento de matematicas Facultad de Ciendas Experimentales y de la SaludCampus Las LagunillasUniversidad de Jaen23071JaenSpain Departamento de Ingenierfa y Tecnologia de Computadores Facultad de lnformdticaCampus EspinardoUnivesidad de Murcia30100 MurciaSpain

Group theory(GT) provides a rigorous framework for studying symmetries in various disciplines in physics ranging from quantum field theories and the standard model to fluid mechanics and chaos theory. To date, the application of such a powerful tool in optical physics remains limited. Over the past few years however, several quantum-inspired symmetry principles(such as parity-time invariance and supersymmetry) have been introduced in optics and photonics for the first time. Despite the intense activities in these new research directions, only few works utilized the power of group theory. motivated by this status quo, here we present a brief overview of the application of GT in optics, deliberately choosing examples that illustrate the power of this tool in both continuous and discrete setups. We hope that this review will stimulate further research that exploits the full potential of GT for investigating various symmetry paradigms in optics, eventually leading to new photonic devices.

关键词：对称原则光学调查混乱理论液体力学标准模型光物理工具时间

Thermodynamic Study for Arsenic Removal from Freshwater by Using Electrocoagulation Process

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Advances in Chemical Engineering and Science 2014年第4期4卷 548-556页

作者： J. R. Parga J. L. Valenzuela G. T. munive V. m. Vazquez m. rodriguez Department of materials Science Technological Institute of Saltillo Saltillo Coahuila Mexico Department of Chemical Engineering and metallurgy University of Sonora Hermosillo Mexico

Insert Industrial treatment of mineral-processing and non-ferrous metal-smelting acid wastewater effluents is becoming an enormous worldwide problem. In mexico, heavy metalscontaminated natural waters, including freshwater, surface water and ground water, are a significant problem as some of these compounds are known as toxic, mutagenic, and carcinogenic. A very promising electrochemical treatment technique that does not require chemical additions to remove arsenic is electrocoagulation (EC) with air injection. The proposed electrochemical process is efficient because used low cost iron electrodes and promising in industrial application. Theoretical the purpose of this research was to investigate the thermodynamic of arsenic adsorption on iron species using the Langmuir’s Isotherm. Also, thermodynamic parameters such as , and were calculated and the adsorption process was found to be exothermic and spontaneous. X-ray Diffraction and Scanning Electron microscopy, were used to characterize the solid products formed during EC. The results of this study suggest that magnetite particles and amorphous iron oxyhydroxides are present in the examined EC products and this study indicate that arsenic can be successfully adsorbed on iron species by electrocoagulation process. Field pilot-scale study demonstrated the removal of As(III)/As(V) with an efficiency of more than 99% from both wastewater and wells.

关键词： Coprecipitation Electrocoagulation magnetite Particles

Twists and Gromov Hyperbolicity of Riemann Surfaces

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Acta mathematica Sinica,English Series 2011年第1期27卷 29-44页

作者： Katsuhiko mATSUZAKI Jose m. rodriguez Department of mathematics School of Education Waseda University Shinjuku Tokyo 169-8050 Japan Departamento de matemdticas Universidad Carlos IH de Madrid Avenida de la Universidad 30 28911 Legangs Madrid Spain

The main aim of this paper is to study whether the Gromov hyperbolicity is preserved under some transformations on Riemann surfaces （with their Poincare metrics）. We prove that quasiconformal maps between Riemann surfaces preserve hyperbolicity; however, we also show that arbitrary twists along simple closed geodesics do not preserve it, in general.

关键词： Quasiconformal maps Riemann surfaces Gromov hyperbolicity