Group structure

组结构
  • 文章类型: Journal Article
    许多合作育种物种生活在具有复杂结构的群体中-大群体规模,低且可变的亲属结构,和多个繁殖对。由于这些混合亲属群体通常是由于男女无关个体的移民以及有限的后代散布而形成的,分散模式的差异会导致群体结构的变化,甚至在同一物种或种群内。这里,我们研究了环境介导的扩散模式如何影响多元育种高超八哥(Lamprotornissuperbus)中群体结构的变化,一种鸟类合作育种者,该育种者生活在时空变化的稀树草原环境中,并形成具有可变群体大小的混合亲属群体,每组多于一个繁殖对。使用4068个全基因组多态性位点和精细尺度,来自肯尼亚中部近200平方公里环境梯度的22个群体的遥感生态数据,我们发现不仅在两性中频繁和长距离传播(低隔离距离和弱遗传结构)的证据,而且还可以从低质量生境中具有低归一化植被指数(NDVI)的小群体定向扩散到具有高NDVI的高质量生境中的大群体。此外,我们在低质量的栖息地中发现了更强的遗传结构,在较高质量的栖息地中,遗传多样性较高,群体相关性较低。先前使用来自同一群体中的群体的长期数据的工作表明,具有较低亲缘关系的群体更大,并且具有更多的繁殖对。长途,因此,定向分散以最大程度地提高个人适应性,可以在质量较低的栖息地中导致更小,更简单的基于亲属的社会群体,但是在更高质量的栖息地中,更大,更复杂的混合亲属群体。这样的特异性,群体结构的种群内部变化,包括社会群体亲属结构的变化,可能对进化机制的相对重要性(即直接与间接健身效益)是合作社会形成的基础。
    Many cooperatively breeding species live in groups with complex structure-large group sizes, low and variable kin structure, and multiple breeding pairs. Since these mixed-kin groups typically form because of immigration of unrelated individuals of both sexes in addition to limited offspring dispersal, differences in patterns of dispersal can generate variation in group structure, even within the same species or population. Here, we examine how environmentally mediated dispersal patterns influence variation in group structure in the plural breeding superb starling (Lamprotornis superbus), an avian cooperative breeder that inhabits a spatiotemporally variable savanna environment and forms mixed-kin groups with variable group sizes and more than one breeding pair per group. Using 4068 genome-wide polymorphic loci and fine-scale, remotely sensed ecological data from 22 groups sampled across a nearly 200 km2 environmental gradient in central Kenya, we find evidence of not only frequent and long-distance dispersal in both sexes (low isolation-by-distance and weak genetic structure), but also directional dispersal from small groups in lower quality habitat with low normalised difference vegetation index (NDVI) to large groups in higher quality habitat with high NDVI. Additionally, we find stronger genetic structure among groups in lower quality habitat, and higher genetic diversity and lower relatedness of groups in higher quality habitat. Previous work using long-term data from groups in the same population has shown that groups with lower relatedness are larger and have more breeding pairs. Long-distance, directional dispersal to maximise individual fitness can thus lead to smaller and simpler kin-based social groups in lower quality habitat, but larger and more complex mixed-kin groups in higher quality habitat. Such intraspecific, within-population variation in group structure, including variation in kin structure of social groups, could have profound implications for the relative importance of the evolutionary mechanisms (i.e. direct vs. indirect fitness benefits) underlying the formation of cooperative societies.
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  • 文章类型: News
    小猿,长臂猿和siamangs,是一夫一妻制的物种,其社会群体由父母和后代组成。因此,失去一个成员可能会引起的压力反应,其余的成员,由于他们的强债券。糖皮质激素(GC)一直是压力的有用指标,但是当单独测量这些激素时,区分急性和慢性应激可能是有限的。肾上腺激素硫酸脱氢表雄酮(DHEAS),GC拮抗剂,与应激反应的调节有关。因此,这些激素的伴随测量可以帮助检查事件,例如失去一个小组成员,引起了应激反应。在这份简短的报告中,我们讨论了该组成年男性死亡后,两个动物园饲养的北部白颊长臂猿(Nomascusleuogenys)(1名青春期男性和他的母亲)的荷尔蒙反应。基线粪便样本是在5个月前从这两个人那里机会主义地收集的,以及小组成员死亡后3个月。通过酶免疫测定(EIA)对总共25个样品的粪便GC代谢物(FGCM)和DHEAS进行定量,以计算FGCM:DHEAS比率。我们的结果表明FGCM和FGCM的增加:青少年男性的DHEAS,但不是成年女性,在死亡之后。我们的发现表明,FGCM和DHEAS测量的整合可以提供有价值的信息来解释个体压力水平对群体社会结构突然变化的影响。
    The small apes, gibbons and siamangs, are monogamous species with their social groups comprising of both parents and their offspring. Therefore, the loss of a member may elicit a stress response in the remaining members due to their strong bonds. Glucocorticoids (GCs) have been useful indicators of stress, but distinguishing between acute versus chronic stress may be limited when measuring these hormones alone. The adrenal hormone dehydroepiandrosterone-sulfate (DHEAS), a GC antagonist, has been implicated in the regulation of the stress response. Thus, the concomitant measurement of these hormones can help examine whether an event, such as the loss of a group member, elicited a stress response. In this brief report, we discuss the hormonal response of two zoo-housed northern white-cheeked gibbons (Nomascus leucogenys) (1 adolescent male and his mother) after the death of the adult male of the group. Baseline fecal samples were collected opportunistically from these two individuals 5 months prior, and 3 months following the death of their group member. A total of 25 samples were quantified for fecal GC metabolites (FGCMs) and DHEAS by enzyme immunoassay (EIA) to calculate the FGCMs:DHEAS ratio. Our results indicate an increase in FGCMs and FGCMs:DHEAS for the adolescent male, but not the adult female, following the death. Our findings suggest that the integration of FGCMs and DHEAS measurements can provide valuable information to interpret individual stress levels to the sudden change in the group\'s social structure.
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  • 文章类型: Journal Article
    橡胶树,巴西橡胶树(威尔德。前Adr.deJuss.)穆勒。Arg.,是世界上唯一用于商业生产天然橡胶的工厂。经过多年的繁殖,橡胶树存在广泛的种质分化。橡胶树种质资源多样性和种群结构的探索,在建立核心种质资源的同时,有助于阐明遗传背景并促进这些资源的有效利用和管理。通过使用SNP分子标记技术,扩增了195棵橡胶树资源,他们的遗传多样性分析,随后构建了指纹图谱。通过这个过程,鉴定了橡胶树的耐寒核心种质。结果显示,PIC,他,和pi值分别为0.0905至0.3750、0.095至0.5000和0.0953至0.5013。群体结构分析和聚类分析都将种质划分为两组,表示一个简单的组结构。建立核心种质资源库,抽样比例为10%,由21个种质组成,分为两个种群。G1人口由20个国家组成,而人口G2包括1个登录名。研究结果导致了分子数据库的创建,该数据库有望为橡胶树种质的管理和后续育种应用做出贡献。
    The rubber tree, Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell. Arg., is the sole plant worldwide utilized for the commercial production of natural rubber. Following years of breeding, there exists a wide array of germplasm differentiation in rubber trees. The exploration of diversity and population structure within rubber tree germplasm resources, alongside the establishment of core germplasm resources, is instrumental in elucidating the genetic background and facilitating the effective utilization and management of these resources. By employing SNP molecular marker technology, 195 rubber tree resources were amplified, their genetic diversity analyzed, and a fingerprint map was subsequently constructed. Through this process, the cold-resistant core germplasm of rubber trees was identified. The results revealed that the PIC, He, and pi values ranged from 0.0905 to 0.3750, 0.095 to 0.5000, and 0.0953 to 0.5013, respectively. Both group structure analysis and cluster analysis delineated the accessions into two groups, signifying a simple group structure. A core germplasm bank was established with a sampling ratio of 10%, comprising 21 accessions divided into two populations. Population G1 consists of 20 accessions, while population G2 comprises 1 accession. The research findings have led to the creation of a molecular database that is anticipated to contribute to the management and subsequent breeding applications of rubber tree accessions.
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  • 文章类型: Journal Article
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  • 文章类型: Journal Article
    英国生物银行是一项大型队列研究,在2006-2010年在英国22个评估中心招募了超过500,000名年龄在40-69岁之间的英国参与者。自我报告的健康结果和入院数据是两种类型的记录,包括参与者的疾病状态。冠状动脉疾病(CAD)是英国生物银行队列中最常见的死亡原因。在区分所有英国生物银行参与者的患病率和发病率CAD事件后,我们确定了各评估中心之间CAD年龄标准化率的地域差异.使用Mann-Whitney检验,来自英格兰和苏格兰的UKBiobank参与者的汇总队列方程得分之间发现了显着的分布差异。使用置换测试,来自英格兰和苏格兰以及来自不同评估中心的英国生物银行参与者的多基因风险评分存在显着差异。我们的目的是通过收集疾病相关危险因素的数据来区分不同疾病发生率的评估中心。然而,仅依靠个体水平的预测并平均它们来获得群体水平的预测被证明是无效的,特别是由于参与偏差导致的相关协变量的存在。通过使用Mundlak模型,通过在模型中包含自变量的组均值来估计随机效应回归,我们有效地解决了这些问题。此外,我们设计了一个仿真实验来演示Mundlak模型的功能。我们的发现应用于公共卫生资金和战略,因为我们的方法可以用来预测未来的病例率,因为人口结构和生活方式的变化都不确定。
    The UK Biobank (UKB) is a large cohort study that recruited over 500,000 British participants aged 40-69 in 2006-2010 at 22 assessment centers from across the United Kingdom. Self-reported health outcomes and hospital admission data are 2 types of records that include participants\' disease status. Coronary artery disease (CAD) is the most common cause of death in the UKB cohort. After distinguishing between prevalence and incidence CAD events for all UKB participants, we identified geographical variations in age-standardized rates of CAD between assessment centers. Significant distributional differences were found between the pooled cohort equation scores of UKB participants from England and Scotland using the Mann-Whitney test. Polygenic risk scores of UKB participants from England and Scotland and from different assessment centers differed significantly using permutation tests. Our aim was to discriminate between assessment centers with different disease rates by collecting data on disease-related risk factors. However, relying solely on individual-level predictions and averaging them to obtain group-level predictions proved ineffective, particularly due to the presence of correlated covariates resulting from participation bias. By using the Mundlak model, which estimates a random effects regression by including the group means of the independent variables in the model, we effectively addressed these issues. In addition, we designed a simulation experiment to demonstrate the functionality of the Mundlak model. Our findings have applications in public health funding and strategy, as our approach can be used to predict case rates in the future, as both population structure and lifestyle changes are uncertain.
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  • 文章类型: Journal Article
    对个体社会关系和群体结构的研究提供了对物种自然史的见解,并可以为人类护理中的动物提供管理决策。大猩猩康复和保护教育(GRACE)中心为14名格劳尔大猩猩(Gorillaberingeigraueri)提供永久庇护所,大猩猩属的极度濒危且研究不足的亚种,在刚果民主共和国。我们在八个月的时间里监测了GRACE大猩猩的关联模式,并在这里通过多个社交网络统计数据描述了它们的个体关系和群体结构。该群体高度联系,但个体之间的关联平均较弱。社交网络指标描述了成年女性是群体中最合群和社会中心的个体。事实上,平均而言,成年女性是最合群和社会中心的。群体水平的关联模式在研究期间和观察类型之间显著相关,表明该小组在八个月的研究期间社会稳定。本研究中收集的数据是由GRACE护理人员作为其日常饲养常规的一部分进行的,并提供了对该群体行为的重要见解,最终告知他们的护理,福利和未来发布的考虑。此处实施的方法方法很容易扩展到任何寻求使用数据来告知饲养和管理程序的灵长类动物保护区或护理设施。最后,我们的研究是第一个对Grauer大猩猩进行的社会网络分析,并提供了对这个研究不足的亚种的行为的初步见解。尽管需要更多的研究来评估这里的发现是否反映了这个亚种的自然史或群体的特质。
    The study of individual social relationships and group structure provides insights into a species\' natural history and can inform management decisions for animals living in human care. The Gorilla Rehabilitation and Conservation Education (GRACE) center provides permanent sanctuary for a group of 14 Grauer\'s gorillas (Gorilla beringei graueri), a critically endangered and poorly studied subspecies of the genus gorilla, in the Democratic Republic of the Congo. We monitored the association patterns of the gorillas at GRACE over eight months and here describe their individual relationships and group structure via multiple social network statistics. The group was highly connected but associations between individuals were weak on average. Social network metrics describe that an adult female was the most gregarious and socially central individual within the group. In fact, adult females were the most gregarious and socially central on average. Group level association patterns were significantly correlated over the study period and across observation types, suggesting the group was socially stable during the eight month study period. The data collected in this study were done so by GRACE caregivers as part of their daily husbandry routine and provided important insights into this group\'s behavior, ultimately informing on their care, welfare and future release considerations. The methodological approaches implemented here are easily scalable to any primate sanctuary or care facility seeking to use data to inform husbandry and management procedures. Lastly, our study is the first social network analysis to be conducted on Grauer\'s gorillas and provides tentative insights into the behavior of this poorly studied subspecies. Though more research is needed to evaluate if the findings here are reflective of this subspecies\' natural history or the idiosyncrasies of the group.
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  • 文章类型: Journal Article
    离子液体(IL)是一类具有物理化学性质的低熔点盐,使其适合于一系列工业应用。越来越多的证据表明,某些IL是细胞毒性和潜在的环境污染物,因此了解促进IL细胞毒性的结构特征很重要。两亲性离子液体(AmIL),一类具有亲脂性N-烷基链的IL,含有芳族头基的细胞毒性通常比它们的脂肪族头基更大,然而,其他头组属性的影响不太清楚。因此,这项研究旨在提供有关阳离子头部基团对AmIL细胞毒性作用的新的结构活性关系(SAR)见解。一系列AmIL,带有一系列结构上不同的芳族阳离子,charge,合成和亲脂性并针对人MDA-MB-231乳腺癌细胞进行筛选。发现更大和更亲脂性的头部基团增加细胞毒性,尽管变化的幅度不大。评估代表性IL的线粒体效应。AmIL在细胞毒性浓度下诱导MDA-MB-231细胞线粒体功能障碍,这表明它们的目标是线粒体.来自这项研究的新SAR信息可能有助于设计具有受控细胞毒性的AmIL。
    Ionic liquids (ILs) are a class of low melting point salts with physicochemical properties that make them suitable for a range of industrial applications. Accumulating evidence suggests that certain ILs are cytotoxic and potential environmental pollutants, thus understanding the structural features that promote IL cytotoxicity is important. Amphiphilic ionic liquids (AmILs), a class of ILs with lipophilic N-alkyl chains, containing aromatic head groups are generally more cytotoxic than their aliphatic counterparts, however the impact of other head group properties are less clear. This study therefore sought to provide new structure activity relationship (SAR) insights regarding the role of the cationic head group on AmIL cytotoxicity. A series of AmILs bearing a range of structurally diverse aromatic cations varying in size, charge, and lipophilicity was synthesised and screened against human MDA-MB-231 breast cancer cells. It was found that larger and more lipophilic head groups increased cytotoxicity, although the magnitude of the changes were modest. The mitochondrial effects of representative ILs were assessed. The AmILs induced mitochondrial dysfunction in MDA-MB-231 cells at cytotoxic concentrations, suggesting that they target mitochondria. The new SAR information from this study may assist in the design of AmILs with controlled cytotoxicity.
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  • 文章类型: Journal Article
    轻度认知障碍(MCI)是一种以认知障碍的发作和演变为特征的临床综合征,通常被认为是阿尔茨海默病(AD)的过渡阶段。经历快速进展为AD的MCI患者的遗传特征可以增强早期诊断能力并促进AD的药物发现。虽然全基因组关联研究(GWAS)是鉴定与疾病相关的单核苷酸多态性(SNP)的标准工具,由于对多重测试的严格控制,它未能检测到具有小效应大小的SNP。此外,该方法不考虑SNP的组结构,如基因或连锁不平衡区,这可以为遗传结构提供有价值的见解。为了解决这些限制,我们提出了一种贝叶斯双水平变量选择方法,该方法检测与从MCI到AD的转化时间相关的SNP。我们的方法将组包含指标集成到加速故障时间模型中,以识别重要的SNP组。此外,我们采用数据增强技术,利用预测后验估计删失时间值.我们调整Dirichlet-Laplace收缩先验,以纳入SNP水平变量选择的组结构。在模拟研究中,我们的方法在变量选择方面优于其他竞争方法。对阿尔茨海默病神经影像学计划(ADNI)数据的分析揭示了与AD直接或间接相关的几个基因,而经典GWAS没有鉴定出任何显著的SNP。
    Mild cognitive impairment (MCI) is a clinical syndrome characterized by the onset and evolution of cognitive impairments, often considered a transitional stage to Alzheimer\'s disease (AD). The genetic traits of MCI patients who experience a rapid progression to AD can enhance early diagnosis capabilities and facilitate drug discovery for AD. While a genome-wide association study (GWAS) is a standard tool for identifying single nucleotide polymorphisms (SNPs) related to a disease, it fails to detect SNPs with small effect sizes due to stringent control for multiple testing. Additionally, the method does not consider the group structures of SNPs, such as genes or linkage disequilibrium blocks, which can provide valuable insights into the genetic architecture. To address the limitations, we propose a Bayesian bi-level variable selection method that detects SNPs associated with time of conversion from MCI to AD. Our approach integrates group inclusion indicators into an accelerated failure time model to identify important SNP groups. Additionally, we employ data augmentation techniques to impute censored time values using a predictive posterior. We adapt Dirichlet-Laplace shrinkage priors to incorporate the group structure for SNP-level variable selection. In the simulation study, our method outperformed other competing methods regarding variable selection. The analysis of Alzheimer\'s Disease Neuroimaging Initiative (ADNI) data revealed several genes directly or indirectly related to AD, whereas a classical GWAS did not identify any significant SNPs.
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  • 文章类型: Journal Article
    目的:目前还没有发表的关于男科全球在线研究合作的例子。我们描述了发展,这种类型的第一个财团的概况和成员特征,全球男科论坛(GAF)。
    方法:发送给所有GAF成员的在线调查收集了人口统计信息(性别,年龄,经验,学术称号,度,国家,专业,专业)。它还利用了成员特征的数据,例如,研究技能,软件和统计;首选活动;时间承诺;预期角色;以及参与研究的兴趣,在GAF的科学活动和在线合作研究中。对调查结果进行了分析和列表。我们概述了成员的人口统计学和专业特征以及迄今为止的科学成就。叙述方法概述了GAF的结构和功能。
    结果:540名成员中共有418人完成了调查,并被纳入分析(77.4%的响应率)。样本主要包括泌尿科医师(34.2%),三分之一的受访者执业时间超过15年(33.3%)。高达86.1%的成员表示有兴趣积极参与撰写科学文章。样本的三分之一(37.1%)可以每周花费4至6小时。很少有受访者报告统计和艺术品技能(分别为2.6%和1.9%)。成员根据他们的专长和经验被分配到特定的角色。协同工作确保项目及时完成,同时保持质量。对于结果,GAF在创建后的一年内发表了29篇原创文章,作者来自48个国家,涉及的主题包括精索静脉曲张,精子DNA损伤,氧化应激,精液分析和男性不育,卵母细胞/胚胎,辅助生殖技术(ART)和男性不育评估的实验室问题。
    结论:GAF是一个成功的全球在线男科研究模型。已经发表了大量科学文章。鉴于如此有效,采用GAF模型对于希望创建和协调成功的国际在线研究小组的其他学科可能很有用。
    OBJECTIVE: There are no published examples of a global online research collaborative in andrology. We describe the development, profile and member characteristics of the first consortium of this type, the Global Andrology Forum (GAF).
    METHODS: An online survey sent to all GAF members collected demographic information (sex, age, experience, academic title, degrees, country, specialty, profession). It also tapped data on members\' characteristics e.g., skills in research, software and statistics; preferred activities; time commitments; expected roles; and interest in participating in research, in GAF\'s scientific activities and collaborative online research. The findings were analyzed and tabulated. We outline members\' demographic and professional characteristics and scientific achievements to date. A narrative approach outlined GAF\'s structure and functioning.
    RESULTS: A total of 418 out of 540 members completed the survey and were included in the analysis (77.4% response rate). The sample comprised mainly urologists (34.2%) and a third of the respondents had practiced for >15 years (33.3%). Up to 86.1% of the members expressed interest in being actively engaged in writing scientific articles. A third of the sample (37.1%) could dedicate 4 to 6 hours/week. Few respondents reported skills in statistics and artwork (2.6% and 1.9% respectively). Members were assigned to specific roles based on their expertise and experiences. Collaborative working ensured the timely completion of projects while maintaining quality. For outcomes, GAF published 29 original articles within one year of its creation, with authors from 48 countries spanning topics that included varicocele, sperm DNA damage, oxidative stress, semen analysis and male infertility, oocyte/embryo, and laboratory issues of assisted reproductive technique (ART) and male infertility evaluation.
    CONCLUSIONS: GAF is a successful global online andrology research model. A healthy number of scientific articles have been published. Given such effectiveness, adopting the GAF model could be useful for other disciplines that wish to create and coordinate successful international online research groups.
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    文章类型: Journal Article
    近年来,数据驱动的个性化决策问题受到了广泛的关注。特别是,决策者的目标是确定最佳的个性化治疗规则(ITR),以便最大化异质患者特定特征的平均预期指定结果。许多现有方法处理二元或中等数量的治疗臂,并且可能不考虑潜在的治疗效果结构。然而,当治疗臂的数量变大时,这些方法的有效性可能会恶化。在这篇文章中,我们提出了GRoup结果加权学习(GROWL),以通过单个优化来估计治疗空间中的潜在结构和最佳组结构ITR。特别是,为了估计群体结构的ITR,在基于加权角度的多类别分类框架下,我们利用基于强化角度的多类别支持向量机(RAMSVM)来学习基于组的决策规则。Fisher一致性,超额风险约束,并建立了值函数的收敛速度,为GROWL提供了理论保证。仿真研究和实际数据分析中的大量经验结果表明,GROWL比其他几种现有方法具有更好的性能。
    Data driven individualized decision making problems have received a lot of attentions in recent years. In particular, decision makers aim to determine the optimal Individualized Treatment Rule (ITR) so that the expected specified outcome averaging over heterogeneous patient-specific characteristics is maximized. Many existing methods deal with binary or a moderate number of treatment arms and may not take potential treatment effect structure into account. However, the effectiveness of these methods may deteriorate when the number of treatment arms becomes large. In this article, we propose GRoup Outcome Weighted Learning (GROWL) to estimate the latent structure in the treatment space and the optimal group-structured ITRs through a single optimization. In particular, for estimating group-structured ITRs, we utilize the Reinforced Angle based Multicategory Support Vector Machines (RAMSVM) to learn group-based decision rules under the weighted angle based multi-class classification framework. Fisher consistency, the excess risk bound, and the convergence rate of the value function are established to provide a theoretical guarantee for GROWL. Extensive empirical results in simulation studies and real data analysis demonstrate that GROWL enjoys better performance than several other existing methods.
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