Stratification

分层
  • 文章类型: Journal Article
    背景:在持续性心房颤动(AF)患者中,用于衬底改性的广泛烧蚀,除了肺静脉隔离术(PVI)外,线性消融或复杂分割心房电描记图消融仍存在争议.先前研究广泛消融的研究已经证明了其不同的疗效,提示其功效可能存在异质性。衰老是房颤的主要危险因素,并与心房重构相关。我们旨在比较广泛消融策略与单纯PVI策略在年轻和老年患者中的疗效和安全性。
    方法:本研究是对多中心的事后分析,随机对照,非劣效性试验研究了单纯PVI(单独PVI组)与广泛消融(PVI+组)在持续性房颤患者中的疗效和安全性(EARNEST-PVI试验).我们根据年龄将总体人群分为两组,并评估治疗效果。
    结果:在年轻组(年龄<65岁,N=206),单独PVI组和PVI+组之间的复发率没有显着差异[风险比(HR):1.00,95CI:0.57-1.73,p=0.987],而老年组(年龄≥65岁,N=291)(HR:0.47,95CI:0.29-0.76,p=0.0021)(相互作用p=0.0446)。没有致命的手术并发症。
    结论:在持续性房颤患者中,在老年患者中,广泛消融策略比单纯PVI策略更有效,而两种方法在年轻患者中的有效性相当。
    背景:URL:https://clinicaltrials.gov;唯一标识符:NCT03514693。URL:https://center6。乌明。AC.jp/cgi-open-bin/ctr_e/ctr_view。cgi?recptno=R000022454唯一ID由UMIN:UMIN000019449发行。
    BACKGROUND: In patients with persistent atrial fibrillation (AF), extensive ablation for substrate modification, such as linear ablation or complex fractionated atrial electrogram ablation in addition to pulmonary vein isolation (PVI) remains controversial. Previous studies investigating extensive ablation have demonstrated its varying efficacy, suggesting the possible heterogeneity of its efficacy. Aging is a major risk factor for AF and is associated with atrial remodeling. We aimed to compare the efficacy and safety of the extensive ablation strategy compared with PVI alone strategy between young and elderly patients.
    METHODS: This study is a post-hoc analysis of the multicenter, randomized controlled, noninferiority trial investigating the efficacy and safety of PVI-only (PVI-alone arm) compared with extensive ablation (PVI-plus arm) in patients with persistent AF (EARNEST-PVI trial). We divided the overall population into 2 groups based on age and assessed treatment effects.
    RESULTS: In the young group (age < 65 years, N = 206), there was no significant difference in the recurrence rate between the PVI-alone group and PVI-plus group [hazard ratio (HR): 1.00, 95%CI: 0.57-1.73, p = 0.987], whereas the recurrence rate was significantly lower in the PVI-plus group compared to the PVI-alone group in the elderly group (age ≥ 65 years, N = 291) (HR: 0.47, 95%CI: 0.29-0.76, p = 0.0021) (p for interaction = 0.0446). There were no fatal procedural complications.
    CONCLUSIONS: In patients with persistent AF, the extensive ablation strategy was more effective than the PVI-alone strategy in elderly patients, while the effectiveness of both approaches was comparable in young patients.
    BACKGROUND: URL: https://clinicaltrials.gov; Unique identifier: NCT03514693. URL: https://center6.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000022454 Unique ID issued by UMIN: UMIN000019449.
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  • 文章类型: Journal Article
    背景:运动困难在许多地方都很常见,但不是全部,自闭症患者。这些困难可能与其他问题同时发生,比如语言的延迟,知识分子,和适应性功能。支撑这种困难的生物机制不太清楚。在携带高度渗透的罕见基因突变的个体中,运动技能差往往更常见。这种机制可能具有改变神经生理兴奋-抑制平衡的下游后果,并导致行为运动噪声增强。
    方法:这项研究结合了自闭症患者的公开数据集和内部数据集(n=156),典型的发展(TD,n=149),和发育协调障碍(DCD,n=23)儿童(3-16岁)。根据《儿童运动评估电池》第2版测量的运动能力模式,确定了自闭症运动亚型。基于稳定性的相对聚类验证用于识别自闭症运动亚型并评估保留数据中的泛化准确性。自闭症电机亚型进行了电机噪声的差异测试,操作为在简单的触地任务中记录的重复运动运动轨迹之间的不相似程度。
    结果:可以检测到相对的“高”(n=87)与“低”(n=69)自闭症运动亚型,并且在保留数据中以89%的准确率进行推广。相对“低”亚型的一般智力较低,在独立行走年龄较大,但在第一个单词的年龄或自闭症特征或症状学上没有差异。与“高”(科恩的d=0.77)或TD儿童(科恩的d=0.85)相比,“低”亚型的电机噪声要高得多,但自闭症儿童和TD儿童之间相似(科恩的d=0.08)。在到达动作的前馈阶段,\'低\'亚型中增强的电动机噪声也最为明显。
    结论:这项工作的样本量有限。未来在较大样本中的工作以及独立复制非常重要。仅在一个特定的电机任务上测量电机噪声。因此,需要对许多其他电机任务中的电机噪声进行更全面的评估。
    结论:自闭症可以分为至少两种离散的运动亚型,其特征是运动噪声水平不同。这表明自闭症运动亚型可能受到不同生物学机制的支持。
    BACKGROUND: Motor difficulties are common in many, but not all, autistic individuals. These difficulties can co-occur with other problems, such as delays in language, intellectual, and adaptive functioning. Biological mechanisms underpinning such difficulties are less well understood. Poor motor skills tend to be more common in individuals carrying highly penetrant rare genetic mutations. Such mechanisms may have downstream consequences of altering neurophysiological excitation-inhibition balance and lead to enhanced behavioral motor noise.
    METHODS: This study combined publicly available and in-house datasets of autistic (n = 156), typically-developing (TD, n = 149), and developmental coordination disorder (DCD, n = 23) children (age 3-16 years). Autism motor subtypes were identified based on patterns of motor abilities measured from the Movement Assessment Battery for Children 2nd edition. Stability-based relative clustering validation was used to identify autism motor subtypes and evaluate generalization accuracy in held-out data. Autism motor subtypes were tested for differences in motor noise, operationalized as the degree of dissimilarity between repeated motor kinematic trajectories recorded during a simple reach-to-drop task.
    RESULTS: Relatively \'high\' (n = 87) versus \'low\' (n = 69) autism motor subtypes could be detected and which generalize with 89% accuracy in held-out data. The relatively \'low\' subtype was lower in general intellectual ability and older at age of independent walking, but did not differ in age at first words or autistic traits or symptomatology. Motor noise was considerably higher in the \'low\' subtype compared to \'high\' (Cohen\'s d = 0.77) or TD children (Cohen\'s d = 0.85), but similar between autism \'high\' and TD children (Cohen\'s d = 0.08). Enhanced motor noise in the \'low\' subtype was also most pronounced during the feedforward phase of reaching actions.
    CONCLUSIONS: The sample size of this work is limited. Future work in larger samples along with independent replication is important. Motor noise was measured only on one specific motor task. Thus, a more comprehensive assessment of motor noise on many other motor tasks is needed.
    CONCLUSIONS: Autism can be split into at least two discrete motor subtypes that are characterized by differing levels of motor noise. This suggests that autism motor subtypes may be underpinned by different biological mechanisms.
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  • 文章类型: Journal Article
    背景:心房颤动(AF)是全球最常见的心律失常,与较高的死亡率和发病率风险有关。预测房颤和房颤相关并发症,临床风险评分通常采用,但是它们的预测准确性通常是有限的,考虑到房颤患者固有的复杂性和异质性。通过将房颤的不同表现分类为连贯且可管理的临床表型,可以促进制定量身定制的预防和治疗策略。在这项研究中,我们提出了一种基于人工智能(AI)的方法,以在普通和重症监护人群中得出有意义的房颤临床表型。
    方法:我们的方法采用了生成地形图,概率机器学习方法,识别具有相似特征的患者的微集群。然后使用Ward的最小方差方法识别潜在空间中的宏簇区域(临床表型)。我们将其应用于代表普通和重症监护人群的两个大型队列数据库(UK-Biobank和MIMIC-IV)。
    结果:所提出的方法学表明其能够获得有意义的房颤临床表型。因为它的概率基础,它可以增强患者分层的鲁棒性。它还产生了复杂的高维数据的可解释可视化,加强对衍生表型及其关键特征的理解。使用我们的方法,我们在不同患者人群中鉴定并表征了房颤的临床表型.
    结论:我们的方法对噪声是稳健的,可以发现隐藏的模式和子组,并且可以阐明更具体的患者概况,有助于更可靠的患者分层,这可以促进针对每种表型的预防和治疗方案的定制。它还可以应用于其他数据集以得出其他病症的临床上有意义的表型。
    背景:本研究由DECIPHER项目(LJMUQR-PSF)和欧盟项目TARGET(10113624)资助。
    BACKGROUND: Atrial fibrillation (AF) is the most common heart arrhythmia worldwide and is linked to a higher risk of mortality and morbidity. To predict AF and AF-related complications, clinical risk scores are commonly employed, but their predictive accuracy is generally limited, given the inherent complexity and heterogeneity of patients with AF. By classifying different presentations of AF into coherent and manageable clinical phenotypes, the development of tailored prevention and treatment strategies can be facilitated. In this study, we propose an artificial intelligence (AI)-based methodology to derive meaningful clinical phenotypes of AF in the general and critical care populations.
    METHODS: Our approach employs generative topographic mapping, a probabilistic machine learning method, to identify micro-clusters of patients with similar characteristics. It then identifies macro-cluster regions (clinical phenotypes) in the latent space using Ward\'s minimum variance method. We applied it to two large cohort databases (UK-Biobank and MIMIC-IV) representing general and critical care populations.
    RESULTS: The proposed methodology showed its ability to derive meaningful clinical phenotypes of AF. Because of its probabilistic foundations, it can enhance the robustness of patient stratification. It also produced interpretable visualisation of complex high-dimensional data, enhancing understanding of the derived phenotypes and their key characteristics. Using our methodology, we identified and characterised clinical phenotypes of AF across diverse patient populations.
    CONCLUSIONS: Our methodology is robust to noise, can uncover hidden patterns and subgroups, and can elucidate more specific patient profiles, contributing to more robust patient stratification, which could facilitate the tailoring of prevention and treatment programs specific to each phenotype. It can also be applied to other datasets to derive clinically meaningful phenotypes of other conditions.
    BACKGROUND: This study was funded by the DECIPHER project (LJMU QR-PSF) and the EU project TARGET (10113624).
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  • 文章类型: Journal Article
    分层薄膜提供高性能和多功能,然而,实现完全分层的电影仍然是一个挑战。逐层方法,涉及每一层的顺序沉积,已普遍用于分层薄膜制造。然而,这种方法很耗时,劳动密集型,并且容易在薄膜内留下缺陷。或者,利用干燥二元胶体混合物的自分层过程最近得到了广泛的发展,但是它依赖于严格的操作条件,通常产生异质夹层。在这项研究中,介绍了一种用于创建完全分层的纳米颗粒(NP)膜的主动界面分层过程。该技术利用在空气-水界面处具有变化的界面活性的NP。在消耗压力的帮助下,NP混合物在界面处的横向压缩会导致界面活性较低的NP单独解吸到子相中,而更多的界面活性NP保留在界面处。这种简单的压缩导致具有可控性的近乎完美的分层NP膜,普遍性,和可扩展性。结合溶剂退火工艺,主动分层方法使得能够制造在NP层顶上包含聚合物层的分层膜。这项工作为设计药物封装和控释提供了深刻的启示,以及制造透明和柔性电极。
    Stratified films offer high performance and multifunctionality, yet achieving fully stratified films remains a challenge. The layer-by-layer method, involving the sequential deposition of each layer, has been commonly utilized for stratified film fabrication. However, this approach is time-consuming, labor-intensive, and prone to leaving defects within the film. Alternatively, the self-stratification process exploiting a drying binary colloidal mixture is intensively developed recently, but it relies on strict operating conditions, typically yielding a heterogeneous interlayer. In this study, an active interfacial stratification process for creating completely stratified nanoparticle (NP) films is introduced. The technique leverages NPs with varying interfacial activity at the air-water interface. With the help of depletion pressure, the lateral compression of NP mixtures at the interface induces individual desorption of less interfacial active NPs into the subphase, while more interfacial active NPs remain at the interface. This simple compression leads to nearly perfect stratified NP films with controllability, universality, and scalability. Combined with a solvent annealing process, the active stratification process enables the fabrication of stratified films comprising a polymeric layer atop a NP layer. This work provides insightful implications for designing drug encapsulation and controlled release, as well as manufacturing transparent and flexible electrodes.
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  • 文章类型: Journal Article
    在过去的十年中,限制平均生存时间(RMST)的分析在生物医学研究中变得越来越普遍,作为评估治疗或对生存的协变量影响的手段。RMST相对于危险比(HR)的优势包括增加的可解释性和对通常脆弱的比例危险假设的依赖。一些作者认为RMST回归通常应该是前线分析,而不是基于计数过程增量的方法。然而,为了使RMST的使用更加主流,有必要扩大可以应用相关方法的数据结构的范围。在这份报告中,我们从两个角度来解决这个问题。首先,直接建模RMST的大多数现有方法发展都集中在乘法模型上。由于拟合和/或参数解释的良好性,加法模型可能是优选的。第二,现在遇到的许多设置都具有高维分类(令人讨厌)协变量,最好避免参数估计。出于这些考虑,我们提出了用于直接RMST分析的分层加性模型。所提出的方法具有加性协变量效应。此外,干扰因素可以从估计中考虑,类似于Cox回归中的分层,这样可以将重点适当地授予主要兴趣的参数。推导了所提出的估计量的大样本性质,并进行了仿真研究以评估有限样本的性能。此外,我们提供了在风险区分度和预测准确性方面评估拟合模型的技术。然后将提出的方法应用于肝移植数据,以估计供体特征对移植后存活时间的影响。
    Analysis of the restricted mean survival time (RMST) has become increasingly common in biomedical studies during the last decade as a means of estimating treatment or covariate effects on survival. Advantages of RMST over the hazard ratio (HR) include increased interpretability and lack of reliance on the often tenuous proportional hazards assumption. Some authors have argued that RMST regression should generally be the frontline analysis as opposed to methods based on counting process increments. However, in order for the use of the RMST to be more mainstream, it is necessary to broaden the range of data structures to which pertinent methods can be applied. In this report, we address this issue from two angles. First, most of existing methodological development for directly modeling RMST has focused on multiplicative models. An additive model may be preferred due to goodness of fit and/or parameter interpretation. Second, many settings encountered nowadays feature high-dimensional categorical (nuisance) covariates, for which parameter estimation is best avoided. Motivated by these considerations, we propose stratified additive models for direct RMST analysis. The proposed methods feature additive covariate effects. Moreover, nuisance factors can be factored out of the estimation, akin to stratification in Cox regression, such that focus can be appropriately awarded to the parameters of chief interest. Large-sample properties of the proposed estimators are derived, and a simulation study is performed to assess finite-sample performance. In addition, we provide techniques for evaluating a fitted model with respect to risk discrimination and predictive accuracy. The proposed methods are then applied to liver transplant data to estimate the effects of donor characteristics on posttransplant survival time.
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  • 文章类型: Journal Article
    背景:在亨廷顿病临床试验中,招募和分层方法主要依赖于遗传负荷,认知和运动评估得分。他们不太关注体内脑成像标记,在临床诊断之前很好地反映了神经病理学。机器学习方法提供了一定程度的复杂性,可以通过利用来自大型数据集的多模态生物标志物来显着改善预后和分层。这种专门针对HD基因扩增载体定制的模型可以进一步增强分层过程的功效。
    目的:改善亨廷顿病患者的临床试验分层。
    方法:我们使用了先前发表的队列中451名患有亨廷顿病的基因阳性个体(包括预见性和诊断性)的数据(PREDICT,TRACK,TrackON,和图像)。我们将全脑分割应用于纵向脑部扫描,并测量侧脑室扩大的速度,超过3年,它被用作我们的预后随机森林回归模型的目标变量。模型在基线时对特征的各种组合进行了训练,包括遗传负荷,认知和运动评估评分生物标志物,以及脑成像衍生的特征。此外,我们建立了一个简化的分层模型,根据预期的心室扩大率将个体分为两个同质组(低危和高危).
    结果:通过整合脑成像特征和遗传负荷,预后模型的预测准确性大大提高,认知和运动生物标志物:交叉验证的平均绝对误差减少24%,产生530mm3/年的误差。分层模型在区分中等和快速进展者方面的交叉验证准确性为81%(精度=83%,召回=80%)。
    结论:这项研究验证了机器学习在根据心室扩大率区分低危和高危个体方面的有效性。这些模型是使用HD个体的特征进行专门训练的,这提供了更多的疾病特异性,简化,与依赖从健康对照组中提取的特征相比,预后富集的准确方法,正如以前的研究所做的那样。所提出的方法有可能通过以下方式提高临床效用:i)使更有针对性地招募个人进行临床试验,ii)改善对个人的事后评估,和iii)最终通过个性化治疗选择为个人带来更好的结果。
    BACKGROUND: In Huntington\'s disease clinical trials, recruitment and stratification approaches primarily rely on genetic load, cognitive and motor assessment scores. They focus less on in vivo brain imaging markers, which reflect neuropathology well before clinical diagnosis. Machine learning methods offer a degree of sophistication which could significantly improve prognosis and stratification by leveraging multimodal biomarkers from large datasets. Such models specifically tailored to HD gene expansion carriers could further enhance the efficacy of the stratification process.
    OBJECTIVE: To improve stratification of Huntington\'s disease individuals for clinical trials.
    METHODS: We used data from 451 gene positive individuals with Huntington\'s disease (both premanifest and diagnosed) from previously published cohorts (PREDICT, TRACK, TrackON, and IMAGE). We applied whole-brain parcellation to longitudinal brain scans and measured the rate of lateral ventricular enlargement, over 3 years, which was used as the target variable for our prognostic random forest regression models. The models were trained on various combinations of features at baseline, including genetic load, cognitive and motor assessment score biomarkers, as well as brain imaging-derived features. Furthermore, a simplified stratification model was developed to classify individuals into two homogenous groups (low risk and high risk) based on their anticipated rate of ventricular enlargement.
    RESULTS: The predictive accuracy of the prognostic models substantially improved by integrating brain imaging features alongside genetic load, cognitive and motor biomarkers: a 24 % reduction in the cross-validated mean absolute error, yielding an error of 530 mm3/year. The stratification model had a cross-validated accuracy of 81 % in differentiating between moderate and fast progressors (precision = 83 %, recall = 80 %).
    CONCLUSIONS: This study validated the effectiveness of machine learning in differentiating between low- and high-risk individuals based on the rate of ventricular enlargement. The models were exclusively trained using features from HD individuals, which offers a more disease-specific, simplified, and accurate approach for prognostic enrichment compared to relying on features extracted from healthy control groups, as done in previous studies. The proposed method has the potential to enhance clinical utility by: i) enabling more targeted recruitment of individuals for clinical trials, ii) improving post-hoc evaluation of individuals, and iii) ultimately leading to better outcomes for individuals through personalized treatment selection.
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  • 文章类型: Journal Article
    与失业相关的不良生活过程事件会对个人未来的劳动力市场前景产生负面影响。未授权状态,以及随后未经授权的就业,可以类似地操作,即使移民改变了法律地位,也会损害他们的劳动力市场前景。然而,目前尚不清楚与先前未经授权的身份相关的任何持久劣势如何以及为什么会因性别而异。鉴于法律地位和性别重叠影响移徙和分层,这是一个重要的缺点。使用来自全国代表性合法永久居民样本的纵向数据,我们发现与先前暴露于未经授权的状态相关的持久缺点,尤其是女性。相对于从未未经授权的男性,先前接触过未经授权的男性会经历持续的职业劣势。然而,与从未获得过未经授权的女性相比,暴露于未经授权身份的女性随着时间的推移会经历越来越大的职业劣势。人力资本和法律程序有助于解释这种模式。
    Adverse life course events associated with unemployment can negatively affect individuals\' future labor market prospects. Unauthorized status, and subsequent unauthorized employment, may operate similarly, marring immigrants\' labor market prospects even after they change legal status. However, it is unclear how and why any durable disadvantage associated with prior unauthorized status operates differently by gender. This is an important shortcoming given that legal status and gender overlap to influence both migration and stratification. Using longitudinal data from a nationally-representative sample of lawful permanent residents, we find durable disadvantage associated with prior exposure to unauthorized status, especially among women. Men with prior exposure to unauthorized status experience persistent occupational disadvantage over time relative to men who were never unauthorized. However, women with exposure to unauthorized status experience widening occupational disadvantage over time relative to women who were never unauthorized. Human capital and legal processes help to explain this pattern.
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  • 文章类型: Journal Article
    地球上最敌对的海洋栖息地之一是南太平洋环流(SPG)的表面,具有高太阳辐射的特点,营养极度枯竭和生产力低下。在SO-245“UltraPac”巡航通过超贫营养SPG中心期间,通过荧光原位杂交检测到海洋α-蛋白质细菌组AEGEAN169,其相对丰度高达最上层水层总微生物群落的6%,具有两个不同的种群(念珠菌Nemonibacter和Ca。Indimonas).分裂细胞的高频率与高转录水平相结合,这表明这两种进化枝可能具有高度代谢活性。AEGEAN169的比较宏基因组和代谢组学分析显示,与竞争对手SAR11,SAR86,SAR116和Prochloroccocus相比,它们对这种极端环境编码了微妙但独特的代谢适应。两种AEGEAN169进化枝每个预测蛋白的转运蛋白百分比最高(9.5%和10.6%,分别)。特别是,ABC转运蛋白与蛋白视紫红质的高表达和分解代谢途径的检测,建议两种AEGEAN169进化枝的潜在清除生活方式。尽管两个AEGEAN169进化枝可能共享利用膦酸盐作为磷源的基因组潜力,它们的碳和氮代谢途径不同。Ca.Nemonibacter可能使用甘氨酸甜菜碱,而Ca。氨单胞菌可能会分解尿素,肌酸,和狗娘养的。总之,两种进化枝的不同潜在代谢策略表明,两者都很好地适应了资源有限的条件,并与SPG地表水最上层的其他优势微生物进化枝竞争良好。
    One of the most hostile marine habitats on Earth is the surface of the South Pacific Gyre (SPG), characterized by high solar radiation, extreme nutrient depletion, and low productivity. During the SO-245 \"UltraPac\" cruise through the center of the ultra-oligotrophic SPG, the marine alphaproteobacterial group AEGEAN169 was detected by fluorescence in situ hybridization at relative abundances up to 6% of the total microbial community in the uppermost water layer, with two distinct populations (Candidatus Nemonibacter and Ca. Indicimonas). The high frequency of dividing cells combined with high transcript levels suggests that both clades may be highly metabolically active. Comparative metagenomic and metatranscriptomic analyses of AEGEAN169 revealed that they encoded subtle but distinct metabolic adaptions to this extreme environment in comparison to their competitors SAR11, SAR86, SAR116, and Prochlorococcus. Both AEGEAN169 clades had the highest percentage of transporters per predicted proteins (9.5% and 10.6%, respectively). In particular, the high expression of ABC transporters in combination with proteorhodopsins and the catabolic pathways detected suggest a potential scavenging lifestyle for both AEGEAN169 clades. Although both AEGEAN169 clades may share the genomic potential to utilize phosphonates as a phosphorus source, they differ in their metabolic pathways for carbon and nitrogen. Ca. Nemonibacter potentially use glycine-betaine, whereas Ca. Indicimonas may catabolize urea, creatine, and fucose. In conclusion, the different potential metabolic strategies of both clades suggest that both are well adapted to thrive resource-limited conditions and compete well with other dominant microbial clades in the uppermost layers of SPG surface waters.
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  • 文章类型: Journal Article
    微生物群落,其中包括原核生物和原生生物,在水生生态系统中发挥重要作用,影响生态过程。为了了解这些社区,元编码提供了一个强大的工具来评估它们的分类组成和跟踪海洋和淡水环境中的时空动态。虽然海洋生态系统已经被广泛研究,在了解温带湖泊中的真核微生物群落方面存在显著的研究空白。我们的研究通过调查罗希湖(波兰)的自由生活细菌和小型原生群落来解决这一差距,一个不协调的温带湖泊。代谢编码分析显示,细菌和原生群落都表现出不同的季节性模式,不一定由优势类群塑造。此外,机器学习和统计方法确定了每个季节特有的关键扩增子序列变体(ASV)。此外,我们在缺氧性低血中发现了一个独特的群落。我们还表明,塑造所分析群落组成的关键因素是温度,氧和硅的浓度。在气候变化可能影响混合模式并导致长期分层的背景下,了解这些社区结构和潜在因素非常重要。
    Microbial communities, which include prokaryotes and protists, play an important role in aquatic ecosystems and influence ecological processes. To understand these communities, metabarcoding provides a powerful tool to assess their taxonomic composition and track spatio-temporal dynamics in both marine and freshwater environments. While marine ecosystems have been extensively studied, there is a notable research gap in understanding eukaryotic microbial communities in temperate lakes. Our study addresses this gap by investigating the free-living bacteria and small protist communities in Lake Roś (Poland), a dimictic temperate lake. Metabarcoding analysis revealed that both the bacterial and protist communities exhibit distinct seasonal patterns that are not necessarily shaped by dominant taxa. Furthermore, machine learning and statistical methods identified crucial amplicon sequence variants (ASVs) specific to each season. In addition, we identified a distinct community in the anoxic hypolimnion. We have also shown that the key factors shaping the composition of analysed community are temperature, oxygen, and silicon concentration. Understanding these community structures and the underlying factors is important in the context of climate change potentially impacting mixing patterns and leading to prolonged stratification.
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  • 文章类型: Journal Article
    丹江口水库是南水北调工程的重要水源,拥有不同深度的浮游细菌群落,对其氮磷循环和相关驱动因素的理解仍然有限。在这项研究中,我们选取丹江口水库内的5个生态点进行宏基因组学分析,研究浮游细菌群落在地表的垂直分布,中间,和底层。此外,我们分析和预测了氮和磷循环的功能,以及他们的驱动因素。我们的发现揭示了变形杆菌的优势,放线菌,和丹江口水库的植物。在不同深度的浮游细菌群落结构中观察到显著差异,随着温度(T),氧化还原电位(ORP),溶解氧(DO),Chla被确定为影响浮游细菌组成的主要因素。氮循环功能基因的分析鉴定出39个基因,包括gltB,glnA,gltd,gdha,NRT,等。,涉及七个主要途径,包括固氮,硝化,反硝化,和异化硝酸盐还原。磷循环功能基因分析确定了54个基因,包括pstS,ppx-gppA,glpQ,ppk1等。,主要参与六个主要途径,包括有机磷矿化,无机P增溶,和监管。聚类分析表明,不同深度是影响氮磷循环功能基因组成和丰度的显著因素。表层和底层氮磷循环功能基因的组成和丰度不同,并且普遍高于中间层。异常球菌,Hydrogenophaga,Limnohabitans,Clavibacter,其他物种被确定为参与氮磷循环的关键物种。此外,我们发现氮磷循环功能基因与环境因子如DO,pH值,T,总溶解固体(TDS),电导率(EC),还有Chla.此外,这些环境因素的含量在丹江口水库中表现出与深度相关的变化,导致浮游细菌氮和磷循环功能基因的垂直分布模式。总的来说,这项研究揭示了成分,函数,丹江口水库不同层浮游细菌群落及其影响因素,为这个重要的水库生态系统中浮游细菌的生态功能和多样性保护提供了有价值的见解。
    Danjiangkou Reservoir is a critical water source for the South-to-North Water Diversion Project, which harbors a diverse bacterioplankton community with varying depths, and the understanding of its nitrogen and phosphorus cycle and associated driving factors remains limited. In this study, we selected five ecological sites within Danjiangkou Reservoir and conducted metagenomics analysis to investigate the vertical distribution of bacterioplankton communities in the surface, middle, and bottom layers. Furthermore, we analyzed and predicted the function of nitrogen and phosphorus cycles, along with their driving factors. Our findings revealed the dominance of Proteobacteria, Actinobacteria, and Planctomycetes in the Danjiangkou Reservoir. Significant differences were observed in the structure of bacterioplankton communities across different depths, with temperature (T), oxidation-reduction potential (ORP), dissolved oxygen (DO), and Chla identified as primary factors influencing the bacterioplankton composition. Analysis of nitrogen cycle functional genes identified 39 genes, including gltB, glnA, gltD, gdhA, NRT, etc., which were involved in seven main pathways, encompassing nitrogen fixation, nitrification, denitrification, and dissimilatory nitrate reduction. Phosphorus cycle function gene analysis identified 54 genes, including pstS, ppx-gppA, glpQ, ppk1, etc., primarily participating in six main pathways, including organic P mineralization, inorganic P solubilization, and regulatory. Cluster analysis indicated that different depths were significant factors influencing the composition and abundance of nitrogen and phosphorus cycle functional genes. The composition and abundance of nitrogen and phosphorus cycle functional genes in the surface and bottom layers differed and were generally higher than those in the middle layer. Deinococcus, Hydrogenophaga, Limnohabitans, Clavibacter, and others were identified as key species involved in the nitrogen and phosphorus cycle. Additionally, we found significant correlations between nitrogen and phosphorus cycle functional genes and environmental factors such as DO, pH, T, total dissolved solids (TDS), electrical conductivity (EC), and Chla. Furthermore, the content of these environmental factors exhibited depth-related changes in the Danjiangkou Reservoir, resulting in a distinct vertical distribution pattern of bacterioplankton nitrogen and phosphorus cycle functional genes. Overall, this study sheds light on the composition, function, and influencing factors of bacterioplankton communities across different layers of Danjiangkou Reservoir, offering valuable insights for the ecological function and diversity protection of bacterioplankton in this crucial reservoir ecosystem.
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