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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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九种不同能量玉米副产物的膳食纤维组成与能量、粗纤维和猪氨基酸消化率的关系(待续)

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中国饲料 2016年第23期 40-43页

作者： n.A.Gutierrez n.v.l.serao B.J.Kerr R.T.Zijlstra J.F.Patience 爱荷华州立大学动物科技学院埃姆斯50011 美国农业部农业与环境国家实验室埃姆斯爱荷华州50011 阿尔伯塔大学农业食品与营养科学系

本试验旨在确定最佳拟合膳食纤维组成,以评估膳食纤维(DF)水平对能量、粗纤维和氨基酸消化率的影响。9种玉米副产物分别为:玉米皮(37.0%总非淀粉多糖[nSP]);玉米皮可溶物(17.1%nSP);玉米干酒糟及可溶物(DDGS;20.4%nSP);脱脂DDGS(25.0%nS... 详细信息

本试验旨在确定最佳拟合膳食纤维组成,以评估膳食纤维(DF)水平对能量、粗纤维和氨基酸消化率的影响。9种玉米副产物分别为:玉米皮(37.0%总非淀粉多糖[nSP]);玉米皮可溶物(17.1%nSP);玉米干酒糟及可溶物(DDGS;20.4%nSP);脱脂DDGS(25.0%nSP);未煮过的DDGS(22.0%nSP);高蛋白干酒糟(21.9%nSP);脱壳,脱胚玉米(1.1%nSP);玉米胚芽粕(44.4%nSP);和玉米蛋白粉(4.9%nSP)。试验选用初始体重为(25.9±2.5)kg、回肠末端装有T型瘘管生长猪20头,随机分配给10种日粮处理,每个处理8个重复。玉米-豆粕基础日粮为对照日粮,70%基础日粮+30%评估原料组成9种试验日粮。评估原料中11种膳食纤维成分是酸性洗涤纤维(ADF),中性洗涤纤维(nDF),总日粮纤维,半纤维素,总非淀粉多糖,nSP阿拉伯糖,nSP木糖,nSP甘露糖,nSP葡聚糖,nSP半乳糖,阿拉伯木聚糖。测定原料中总能(GE),干物质(DM),nDF的表观回肠消化率(AID)、表观全肠道消化率(ATTD),并测定氨基酸的AID。对每种原料种最佳纤维组分进行评估并排序,结果显示:阿拉伯木聚糖含量与GE(R^2=0.65;三次曲线,PnSP木糖残基与GE(R^2=0.80;三次曲线,PnDF(R^2=0.63;三次曲线,P0.05)。结论,阿拉伯木聚糖和nSP木糖残基可以解释由于日粮纤维水平改变引起的变化,可用于预测玉米副产物中除赖氨酸AID以外的纤维能量消化率,以及消化能和代谢能。

关键词：玉米副产物日粮纤维消化率能量猪

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九种不同能量玉米副产物的膳食纤维组成与能量、粗纤维和猪氨基酸消化率的关系(续)

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中国饲料 2016年第24期 35-39页

作者： n.A.Gutierrez n.v.l.serao B.J.Kerr R.T.Zijlstra J.F.Patience 爱荷华州立大学动物科技学院美国农业部农业与环境国家实验室阿尔伯塔大学农业食品与营养科学系

3.3指标的表观回肠消化率和能量含量不同原料之间GE和DM的AID和ATTD有差异(P0.05)。正如预期,DDC和CGn M中GE的ATTD最大(P<0.05),分别是99.6%和91.6%。相比之下,CB-S和CB中GE和DM的ATTD最低,但两个原料的AID值相似,说明两种原料均高度... 详细信息

3.3指标的表观回肠消化率和能量含量不同原料之间GE和DM的AID和ATTD有差异(Pn M中大部分干物质分别为淀粉和蛋白质,因此在所有原料中GE和DM的AID最大(P0.05)。正如预期,DDC和CGn M中GE的ATTD最大(P<0.05),分别是99.6%和91.6%。相比之下,CB-S和CB中GE和DM的ATTD最低,但两个原料的AID值相似,说明两种原料均高度耐后肠

关键词：氨基酸消化率 ME DE 粗纤维必需氨基酸 AID 阿拉伯木聚糖 DDGS 玉米副产物

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Silk-based nerve guidance conduits with macroscopic holes modulate the vascularization of regenerating rat sciatic nerve

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neural Regeneration Research 2025年第6期20卷 1789-1800页

作者： Carina Hromada Patrick Heimel Markus Kerbl lászlóGál Sylvia nürnberger Barbara Schaedl James Ferguson nicole Swiadek Xavier Monforte Johannes C.Heinzel Antal nógrádi Andreas H.Teuschl-Woller David Hercher Department life Science Engineering University of Applied Sciences Technikum WienViennaAustria Austrian Cluster for Tissue Regeneration ViennaAustria ludwig Boltzmann Institute for Traumatology The Research Center in Cooperation with AUVAViennaAustria University Clinic of Dentistry Medical University of ViennaViennaAustria Department of Plastic Reconstructive and Aesthetic SurgeryLandesklinikum Wiener Neustadt2700 Wiener NeustadtAustria Department of Anatomy Histology and EmbryologyAlbert Szent-Györgyi Medical SchoolUniversity of SzegedSzegedHungary Medical University of vienna Department of Orthopedics and Trauma SurgeryDevision of Trauma SurgeryViennaAustria Department of Hand- PlasticReconstructive and Burn SurgeryBG Unfallklinik TuebingenUniversity of TuebingenTuebingenGermany

Peripheral nerve injuries induce a severe motor and sensory deficit. Since the availability of autologous nerve transplants for nerve repair is very limited, alternative treatment strategies are sought, including the use of tubular nerve guidance conduits(tnGCs). However, the use of tnGCs results in poor functional recovery and central necrosis of the regenerating tissue, which limits their application to short nerve lesion defects(typically shorter than 3 cm). Given the importance of vascularization in nerve regeneration, we hypothesized that enabling the growth of blood vessels from the surrounding tissue into the regenerating nerve within the tnGC would help eliminate necrotic processes and lead to improved regeneration. In this study, we reported the application of macroscopic holes into the tubular walls of silk-based tnGCs and compared the various features of these improved silk^(+) tnGCs with the tubes without holes(silk^(–) tnGCs) and autologous nerve transplants in an 8-mm sciatic nerve defect in rats. Using a combination of micro-computed tomography and histological analyses, we were able to prove that the use of silk^(+) tnGCs induced the growth of blood vessels from the adjacent tissue to the intraluminal neovascular formation. A significantly higher number of blood vessels in the silk^(+) group was found compared with autologous nerve transplants and silk^(–), accompanied by improved axon regeneration at the distal coaptation point compared with the silk^(–) tnGCs at 7 weeks postoperatively. In the 15-mm(critical size) sciatic nerve defect model, we again observed a distinct ingrowth of blood vessels through the tubular walls of silk^(+) tnGCs, but without improved functional recovery at 12 weeks postoperatively. Our data proves that macroporous tnGCs increase the vascular supply of regenerating nerves and facilitate improved axonal regeneration in a short-defect model but not in a critical-size defect model. This study suggests that further optimizatio

关键词： axon regeneration blood vessel functional recovery macroporous nerve lesion peripheral nerve repair sciatic nerve silk-based nerve guidance conduit vascularization

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Dendritic spine degeneration:a primary mechanism in the aging process

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neural Regeneration Research 2025年第6期20卷 1696-1698页

作者： Gonzalo Flores leonardo Aguilar-Hernández Fernado García-Dolores Humberto nicolini Andrea Judith vázquez-Hernández Hiram Tendilla-Beltrán Instituto de Fisiología Benemérita Universidad Autónoma de Puebla(BUAP)PueblaMexico Instituto de Ciencias Forenses(InCIFO) Tribunal Superior de Justicia de la Ciudad de México(TSJCDMX).Mexico CityMexico Instituto nacional de Medicina Genómica(InMEGEn) Mexico CityMexico

Recent reports suggest that aging is not solely a physiological process in living beings;instead, it should be considered a pathological process or disease(Amorim et al., 2022). Consequently, this process involves a wide range of factors, spanning from genetic to environmental factors, and even includes the gut microbiome(GM)(Mayer et al., 2022). All these processes coincide at some point in the inflammatory process, oxidative stress, and apoptosis, at different degrees in various organs and systems that constitute a living organism(Mayer et al., 2022;AguilarHernández et al., 2023).

关键词： aging process stress

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MicroRnAs as potential diagnostic biomarkers for bipolar disorder

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neural Regeneration Research 2025年第6期20卷 1681-1695页

作者： Bridget Martinez Philip v.Peplow Department of Pharmacology University of Nevada-RenoRenoNVUSA Department of Medicine University of Nevada-RenoRenoNVUSA Department of Anatomy University of OtagoDunedinNew Zealand

Abnormal expression of microRnAs is connected to brain development and disease and could provide novel biomarkers for the diagnosis and prognosis of bipolar disorder. We performed a PubMed search for microRnA biomarkers in bipolar disorder and found 18 original research articles on studies performed with human patients and published from January 2011 to June 2023. These studies included microRnA profiling in bloodand brain-based materials. From the studies that had validated the preliminary findings,potential candidate biomarkers for bipolar disorder in adults could be miR-140-3p,-30d-5p,-330-5p,-378a-5p,-21-3p,-330-3p,-345-5p in whole blood, miR-19b-3p,-1180-3p,-125a-5p, let-7e-5p in blood plasma, and miR-7-5p,-23b-5p,-142-3p,-221-5p,-370-3p in the blood serum. Two of the studies had investigated the changes in microRnA expression of patients with bipolar disorder receiving treatment. One showed a significant increase in plasma miR-134 compared to baseline after 4 weeks of treatment which included typical antipsychotics, atypical antipsychotics, and benzodiazepines. The other study had assessed the effects of prescribed medications which included neurotransmitter receptorsite binders(drug class B) and sedatives, hypnotics, anticonvulsants, and analgesics(drug class C) on microRnA results. The combined effects of the two drug classes increased the significance of the results for miR-219 and-29c with miR-30e-3p and-526b* acquiring significance. MicroRnAs were tested to see if they could serve as biomarkers of bipolar disorder at different clinical states of mania, depression, and euthymia. One study showed that upregulation in whole blood of miR-9-5p,-29a-3p,-106a-5p,-106b-5p,-107,-125a-3p,-125b-5p and of miR-107,-125a-3p occurred in manic and euthymic patients compared to controls, respectively, and that upregulation of miR-106a-5p,-107 was found for manic compared to euthymic patients. In two other studies using blood plasma,downregulation of miR-134 was observed i

关键词： biomarker bipolar disorder blood leukocytes blood plasma blood plasma extracellular vesicles/exosomes blood serum brain tissue brain tissue extracellular vesicles/exosomes lymphoblastoid cell lines microRnA neural progenitor cells whole blood

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Autism spectrum disorder:difficulties in diagnosis and microRnA biomarkers

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neural Regeneration Research 2025年第10期20卷 2776-2786页

We performed a PubMed search for microRnAs in autism spectrum disorder that could serve as diagnostic biomarkers in patients and selected 17 articles published from January 2008 to December 2023,of which 4 studies were performed with whole blood,4 with blood plasma,5 with blood serum,1 with serum neural cell adhesion molecule l1-captured extracellular vesicles,1 with blood cells,and 2 with peripheral blood mononuclear *** of the studies involved children and the study cohorts were largely *** of the studies had performed microRnA sequencing or quantitative polymerase chain reaction assays to measure microRnA *** five studies had used real-time polymerase chain reaction assay to validate microRnA expression in autism spectrum disorder subjects compared to *** microRnAs that were validated in these studies may be considered as potential candidate biomarkers for autism spectrum disorder and include miR-500a-5p,-197-5p,-424-5p,-664a-3p,-365a-3p,-619-5p,-664a-3p,-3135a,-328-3p,and-500a-5p in blood plasma and miR-151a-3p,-181b-5p,-320a,-328,-433,-489,-572,-663a,-101-3p,-106b-5p,-19b-3p,-195-5p,and-130a-3p in blood serum of children,and miR-15b-5p and-6126 in whole blood of *** important limitations were identified in the studies reviewed,and need to be taken into account in future *** studies are warranted with children and adults having different levels of autism spectrum disorder severity and consideration should be given to using animal models of autism spectrum disorder to investigate the effects of suppressing or overexpressing specific microRnAs as a novel therapy.

关键词： autism spectrum disorder biomarker blood cells blood plasma blood serum diagnosis microRnA peripheral blood mononuclear cells serum neural cell adhesion molecule l1-captured extracellular vesicles whole blood

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MicroRnAs as potential biomarkers for diagnosis of post-traumatic stress disorder

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neural Regeneration Research 2025年第7期20卷 1957-1970页

Post-traumatic stress disorder is a mental disorder caused by exposure to severe traumatic life ***,there are no validated biomarkers or laboratory tests that can distinguish between trauma survivors with and without post-traumatic stress *** addition,the heterogeneity of clinical presentations of post-traumatic stress disorder and the overlap of symptoms with other conditions can lead to misdiagnosis and inappropriate *** suggests that this condition is a multisystem disorder that affects many biological systems,raising the possibility that peripheral markers of disease may be used to diagnose post-traumatic stress *** performed a PubMed search for microRnAs(miRnAs)in post-traumatic stress disorder(PTSD)that could serve as diagnostic biomarkers and found 18 original research articles on studies performed with human patients and published January 2012 to December *** included four studies with whole blood,seven with peripheral blood mononuclear cells,four with plasma extracellular vesicles/exosomes,and one with serum *** of these studies had also used whole *** studies were excluded as they did not involve microRnA *** of the studies had collected samples from adult male veterans who had returned from deployment and been exposed to combat,and only two were from recently traumatized adult *** measuring miRnA expression levels,many of the studies had used microarray miRnA analysis,miRnA Seq analysis,or nanoString *** six studies had used real time polymerase chain reaction assay to determine/validate miRnA expression in PTSD subjects compared to *** miRnAs that were found/validated in these studies may be considered as potential candidate biomarkers for PTSD and include miR-3130-5p in whole blood;miR-193a-5p,-7113-5p,-125a,-181c,and-671-5p in peripheral blood mononuclear cells;miR-10b-5p,-203a-3p,-4488,-502-3p,-874-3p,-5100,and-7641 in plasma extracellular vesicles/

关键词： biomarker diagnosis microRnA peripheral blood mononuclear cells plasma extracellular vesicles/exosomes post-traumatic stress disorder serum exosomes whole blood whole plasma

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Genetic analysis of reproductive performance in sows during porcine reproductive and respiratory syndrome(PRRS)and porcine epidemic diarrhea(PED)outbreaks

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Journal of Animal Science and Biotechnology 2019年第2期10卷 327-338页

作者： Cassandra l.Scanlan Austin M.Putz Kent A.Gray nick v.l.serao Department of Animal Science Iowa State UniversityAmesIA 50011USA Department of Animal Science North Carolina State UniversityRaleighNC 27607USA Genetic Research and Development Smithfield Premium GeneticsRose HillNC 28458USA.

Background: Porcine reproductive and respiratory syndrome(PRRS) is one of the most infectious swine diseases in the world, resulting in over 600 million dollars of economic loss in the USA alone. More recently, the USA swine industry has been having additional major economic losses due to the spread of porcine epidemic diarrhea(PED).However, information regarding the amount of genetic variation for response to diseases in reproductive sows is still very limited. The objectives of this study were to identify periods of infection with of PRRS virus(PRRSv) and/or PED virus(PEDv), and to estimate the impact their impact on the phenotypic and genetic reproductive performance of commercial ***: Disease(PRRS or PED) was significant(P ll traits analyzed except for total piglets *** estimates for traits during Clean(without any disease), PRRS, and PED ranged from 0.01(number of mummies;Clean and PED) to 0.41(abortion;PED). Genetic correlations between traits within disease statuses ranged from-0.99(proportion born dead with number weaned;PRRS) to 0.99(number born dead with born alive;Clean). Within trait, between disease statuses, estimates ranged from-0.17(number weaned between PRRS and PED) to 0.99(abortion between Clean and PRRS).Conclusion: Results indicate that selection for improved performance during PRRS and PED in commercial sows is possible and would not negatively impact performance in Clean environments.

关键词： Genetic evaluation Porcine epidemic diarrhea Porcine reproductive and respiratory syndrome Reproductive performance Swine

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nucleoside modified mRnA-lipid nanoparticles as a new delivery platform for the repair of the injured spinal cord

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neural Regeneration Research 2025年第8期20卷 2311-2312页

作者： Krisztián Pajer Tamás Bellák Antal nógrádi Department of Anatomy Histology and EmbryologyAlbert Szent-Györgyi Medical SchoolUniversity of SzegedSzegedHungary

Spinal cord injury and treatment opportunities:The adult mammalian spinal cord has a very limited capacity for spontaneous regeneration due to various intrinsic molecular and cellular *** the spinal cord neurons have the capacity to regenerate their axons,the expression of growth inhibitory factors,lack or suppression of proper guidance cues,and profound inflammatory responses do not permit successful regeneration(Khyeam et al.,2021).

关键词： injured capacity modified

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