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Regularized quantile regression for SNP marker estimation of pig growth curves

Journal of Animal Science and Biotechnology 2017年第4期8卷 824-832页

作者： L.M.A.Barroso M.Nascimento A.C.C.Nascimento1 f.f.silva N.V.L.Serao C.D.Cruz M.D.V.Resende f.L.silva C.f.Azevedo P.S.Lopes S.E.f.Guimaraes Department of Statistics Federal University of Vicosa Av. P H Rolfs s/nUniversity Campus Vicosa MG 36570-000 Brazil Department of Animal Science Federal University of Vicosa Av. P H Rolfs s/n University CampusVicosa MG 36570-000 Brazil Department of Animal Science Iowa State University Kildee Hall 50011 Ames Iowa USA Department of General Biology Federal University of Vicosa Av. P H Rolfs s/n University CampusVicosa MG 36570-000 Brazil Embrapa forestry Estrada da Ribeira km 111Colombo PR Brazil. Department of Plant Science Federal University of Vicosa Av. P H Rolfs s/n University Campus Vicosa MG 36570-000 Brazil

Background: Genomic growth curves are general y defined only in terms of population mean; an alternative approach that has not yet been exploited in genomic analyses of growth curves is the Quantile Regression(QR). This methodology allows for the estimation of marker effects at different levels of the variable of interest. We aimed to propose and evaluate a regularized quantile regression for SNP marker effect estimation of pig growth curves, as well as to identify the chromosome regions of the most relevant markers and to estimate the genetic individual weight trajectory over time(genomic growth curve) under different quantiles(levels).Results: The regularized quantile regression(RQR) enabled the discovery, at different levels of interest(quantiles), of the most relevant markers al owing for the identification of QTL regions. We found the same relevant markers simultaneously affecting different growth curve parameters(mature weight and maturity rate): two(ALGA0096701 and ALGA0029483)for RQR(0.2), one(ALGA0096701) for RQR(0.5), and one(ALGA0003761) for RQR(0.8). Three average genomic growth curves were obtained and the behavior was explained by the curve in quantile 0.2, which differed from the ***: RQR allowed for the construction of genomic growth curves, which is the key to identifying and selecting the most desirable animals for breeding purposes. furthermore, the proposed model enabled us to find, at different levels of interest(quantiles), the most relevant markers for each trait(growth curve parameter estimates) and their respective chromosomal positions(identification of new QTL regions for growth curves in pigs). These markers can be exploited under the context of marker assisted selection while aiming to change the shape of pig growth curves.

关键词： Genome association Growth curve Pig QTL Regularized quantile regression

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Adsorption of yttrium(Y^(3+)) and concentration of rare earth elements from phosphogypsum using chitin and chitin aerogel

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Journal of Rare Earths 2024年第4期42卷 775-782页

作者： Glaydson S.dos Reis Diana Pinto Sabrina f.Lütke Eder C.Lima Luis f.O.silva Irineu A.S.De Brum Guilherme L.Dotto Department of forest Biomaterials and Technology Biomass Technology Centre Swedish University of Agricultural SciencesUmeaE13Swedn Universidad De La Costa Calle 58#55-66080002BarranquillaAtlanticoColombia Research Group on Adsorptive and Catalytic Process Engineering(ENGEPAC) Federal University of Santa MariaAv.Roraima100079705900Santa MariaRSBrazil Institute of Chemistry Federal University of Rio Grande do Sul90040060Porto AlegreBrazil

Chitin powder and chitin-aerogel were prepared from shrimp wastes and used to uptake Y^(3+)from aqueous solutions and concentrate this rare earth element from phosphogypsum(PG).Chitin aerogel displays a specific surface area of 945 m^(2)/g,while chitin powder is 3.6 m^(2)/g,which largely influences its adsorption *** the adsorption in synthetic solutions,the effect of pH on Y^(3+)removal is strong for chitin powder *** contrast,no big pH influence was detected for chitin *** interactions and chelation can highlight the proposed mechanism of Y^(3+)on chitin adsorbents for the powder and ***,in addition to these interactions,pore filling/pore diffusion is the main mechanism of Y^(3+)removal in the chitin *** aerogel is efficient in concentrating 8 times the Y^(3+)from PG,a very complex *** complex chitin aerogel-Y^(3+)can be a secondary source of rare earth elements for other applications.

关键词： Rare earths Sustainable material Chitin powder Chitin porous aerogel Yttrium adsorption and recovery

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Assembly structures of coastal woody species of eastern South America:Patterns and drivers

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Plant Diversity 2024年第5期46卷 611-620页

作者： Eduardo Vinícius da silva Oliveira Myrna friederichs Landim Sidney f.Gouveia Graduate Program in Ecology and Conservation Federal University of SergipeSão CristovãoSergipeBrazil National Institute of Science and Technology Ecology Evolution and Conservation of Biodiversity(INCT-EECBio)GoiâniaGoiasBrazil Department of Biology Federal University of SergipeSão CristóvãoSergipeBrazil Department of Ecology Federal University of SergipeSão CristóvãoSergipeBrazil

Tropical regions have provided new insights into how ecological communities are *** dry coastal communities,water stress has been hypothesized to determine plant assembly structure by favoring preadapted lineages from neighboring ecosystems,consistent with functional ***,it is unclear whether this hypothesis is sufficient to explain how coastal communities in tropical ecosystems are ***,we test whether water stress or other factors drive community assembly in woody plant communities across the coastal zone of Brazil,a tropical *** characterized functional and phylogenetic structures of these communities and determined the underlying environmental factors(e.g.,water stress,historical climate stability,edaphic constraints,and habitat heterogeneity)that drive their community *** of coastal woody species show geographically varied patterns,including stochastic arrangements,clustering,and overdispersion of species relative to their traits and phylogenetic *** complexity,water vapor pressure,and soil nutrient availability best explained the gradient in the functional *** deficit,water vapor pressure,and soil organic carbon were the best predictors of variation in phylogenetic *** results support the water-stress conservatism hypothesis on functional and phylogenetic structure,as well as the effect of habitat heterogeneity on functional structure and edaphic constraints on functional and phylogenetic *** effects are associated with increased phenotypic and phylogenetic divergence of woody plant assemblages,which is likely mediated by abiotic filtering and niche opportunities,suggesting a complex pattern of ecological assembly.

关键词： Brazil Completeness Clustering Restinga vegetation Water constraints

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Bolstering integrity in environmental data science and machine learning requires understanding socioecological inequity

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frontiers of Environmental Science & Engineering 2024年第5期18卷 171-179页

作者： Joe f.Bozeman III School of Civil and Environmental Engineering Georgia Institute of TechnologyAtlantaGA30332USA School of Public Policy Georgia Institute of TechnologyAtlantaGA30332USA

Socioecological inequity in environmental data science—such as inequities deriving from data-driven approaches and machine learning(ML)—are current issues subject to debate and *** is growing consensus around embedding equity throughout all research and design domains—from inception to administration,while also addressing procedural,distributive,and recognitional ***,practically doing so may seem onerous or daunting to *** current perspective helps to alleviate these types of concerns by providing substantiation for the connection between environmental data science and socioecological inequity,using the Systemic Equity framework,and provides the foundation for a paradigmatic shift toward normalizing the use of equity-centered approaches in environmental data science and ML *** the integrity of environmental data science and ML is just beginning from an equity-centered tool development and rigorous application *** this end,this perspective also provides relevant future directions and challenges by overviewing some meaningful tools and strategies—such as applying the Wells-Du Bois Protocol,employing fairness metrics,and systematically addressing irreproducibility;emerging needs and proposals—such as addressing data-proxy bias and supporting convergence research;and establishes a ten-step path ***,the work that environmental scientists and engineers do ultimately affect the well-being of us all.

关键词： Equity Bias Machine Learning Data Science Justice Systemic Equity

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Premature axon-oligodendrocyte interaction contributes to stalling of experimental axon regeneration after injury to the white matter

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Neural Regeneration Research 2024年第3期19卷 469-470页

作者： Ephraim f.Trakhtenberg Department of Neuroscience University of Connecticut School of MedicineFarmingtonCTUSA

Studies from nearly 3 decades ago suggested that,in the central nervous system(CNS),myelination of axons by oligodendrocytes not only helps improve axonal conductivity but also stabilizes circuitry(Colello and Schwab,1994).Over the years,myelin sheaths produced by oligodendrocytes have been found to contain multiple molecules that are inhibitory to axonal growth(e.g.,MAG,NogoA,OMgp,Semaphorins)(Yiu and He,2006;Silver et al.,2014).After white matter injury in the adult CNS,myelin debris from damaged axons and dead oligodendrocytes accumulates in the forming glial scar and exposes these myelin-associated axon growth-inhibitory molecules to the injured axonal stumps,thereby contributing to the inhibition of axonal *** development,CNS axons reach their postsynaptic targets and stop growing before oligodendrocytes appear and myelinate them(foran and Peterson,1992;Dangata et al.,1996).Therefore,myelin-associated axon growth-inhibitory molecules interacting with already grown axons during myelination were thought to block axons from promiscuous sprouting and miswiring,thereby stabilizing neural circuitry in the CNS(Colello and Schwab,1994).

关键词： thereby white injury

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An unexpected cellular fountain of youth:platelets provide factors rejuvenating brain functions

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Signal Transduction and Targeted Therapy 2024年第1期9卷 16-18页

作者： Harald f.Langer Department of Cardiology AngiologyHaemostaseology and Medical Intensive CareUniversity Medical Centre MannheimMedical Faculty MannheimHeidelberg UniversityMannheimGermany German Centre for Cardiovascular Research(DZHK) Partner Site Heidelberg/MannheimMannheimGermany European Center for Angioscience Medical Faculty MannheimHeidelberg UniversityMannheimGermany Cardiovascular systems biology Medical Clinic IUniversity Heart Center LübeckLübeckGermany

In a recent manuscript published in Nature,Schroer et *** that platelets and in particular platelet derived Pf-4(CXCL4)are a novel factor,which can rejuvenate the mammalian neuronal system.1 These findings have the potential to trigger an entire new field of research opening new platelet-derived candidate effector molecules for supporting regeneration.

关键词： supporting platelets finding

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The viscous strip approach to simplify the calculation of the surface acoustic wave generated streaming

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Applied Mathematics and Mechanics(English Edition) 2024年第4期45卷 711-724页

作者： f.JAZINI DORCHEH M.GHASSEMI fuel Cells and Nano Systems(fCNS)Laboratory Department of Mechanical EngineeringK.N.Toosi University of TechnologyTehran 19697Iran

In recent decades,the importance of surface acoustic waves,as a biocompatible tool to integrate with microfluidics,has been proven in various medical and biological *** numerical modeling of acoustic streaming caused by surface acoustic waves in microchannels requires the effect of viscosity to be considered in the equations which complicates the *** this paper,it is shown that the major contribution of viscosity and the horizontal component of actuation is concentrated in a narrow region alongside the actuation *** the inviscid equations are considerably easier to solve,a division into the viscous and inviscid domains would alleviate the computational load *** particles'traces calculated by this approximation are excellently alongside their counterparts from the completely viscous *** is also shown that the optimum thickness for the viscous strip is about 9-fold the acoustic boundary layer thickness for various flow patterns and amplitudes of actuation.

关键词： surface acoustic wave microfluidics numerical simulation particle tracing acoustic streaming

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Antimicrobial,antibiofilm,angiogenesis,anti-inflammatory,and wound healing activities of zinc nanoparticles green synthesized using ferula macrecolea extract

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Asian Pacific Journal of Tropical Biomedicine 2024年第6期14卷 259-268页

作者： Sultan f.Alnomasy Department of Medical Laboratories Sciences College of Applied Medical SciencesShaqra UniversityAl-Quwayiyah 19257Saudi Arabia

Objective:To assess the antimicrobial,antibiofilm,anti-inflammatory,angiogenic,and wound healing activities of zinc nanoparticles(ZNPs)green synthesized using ferula macrecolea ***:The green synthesis was conducted using the precipitation ***,the minimum inhibitory concentration(MIC),minimum bactericidal concentration(MBC),and minimum biofilm inhibition concentration 50%(MBIC50)of ZNPs against Staphylococcus aureus(***)and Pseudomonas aeruginosa(***)were *** effects of ZNPs on the gene expressions of Staphylococcus spp.[intracellular adhesion A(icaA)and D(icaD)]and ***(rhlI and rhlR)were investigated using quantitative real-time *** addition,the effects of ZNPs on wound healing,angiogenesis,and anti-inflammatory markers were ***:The green-synthesized ZNPs demonstrated significant antimicrobial efficacy against *** and *** biofilm formation in *** and *** was also inhibited by ZNPs with MBIC50 values of 3.30μg/mL and 2.08μg/mL,***,ZNPs downregulated the expression of biofilm-related genes icaA,icaD,rhlI,and rhlR in the tested *** also demonstrated promising in vitro wound healing effects by promoting fibroblast cell proliferation and wound closure in a dose-dependent manner.A significant increase in the expression of HLA-G5 and VEGf-A genes as well as a marked decrease in the expression of Nf-κB,IL-1β,and TNf-αgenes were observed in cells treated with ZNPs compared to the control group(Pffects against *** and *** and wound-healing effects by inhibiting biofilm formation,inducing angiogenesis,and reducing ***,further studies must be conducted to specify the accurate mechanisms of action and toxicity of ZNPs.

关键词： Wound healing Antibacterial Angiogenesis Nanomedicine ferula macrecolea Inflammation

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Cognition and movement in neurodegenerative disorders:a dynamic duo

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Neural Regeneration Research 2024年第10期19卷 2101-2102页

作者： Marit f.L.Ruitenberg Department of Health Medical and NeuropsychologyLeiden UniversityLeidenthe Netherlands Leiden Institute for Brain and Cognition Leidenthe Netherlands

People with neurodegenerative disorders often experience problems across a variety of functional domains,including cognition,movement,and psychosocial *** classification of these disorders is based on the phenotypical manifestations that represent the most prominent clinical *** example,Parkinson's disease and Huntington's disease are typically regarded as movement disorders,whereas Alzheimer's disease(AD) and other dementias are regarded as cognitive disorders.

关键词： disorders Huntington degenerative

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Attempts to restore loss of function in damaged ACD cells open the way to non-mutational oncogenesis

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Genes & Diseases 2024年第3期11卷 5-6页

作者： Vladimir f.Niculescu 86420 Diedorf Germany Kirschenweg

This correspondence to Gene&Diseases calls attention to the controversy between proponents of genetic modification in carcinogenesis and supporters of non-mutational *** from molecular cancer research and findings from evolutionary cancer cell biology support the latter claim and provide no rationale for the mutational origin of sporadic *** is more conceivable that the general susceptibility of asymmetric cell division(ACD)phenotypes to oxygen leads to irreparable DNA defects and dysregulated defective symmetric cell division(DscD)phenotypes.

关键词： rational latter finding

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