Natural,modified DNA bases

The four canonical bases that make up genomic DNA are subject to a variety of chemical modifications in living systems. Recent years have witnessed the discovery of various new modified bases and of the enzymes responsible for their processing. Here, we review the range of DNA base modifications currently known and recent advances in chemical methodology that have driven progress in this field, in particular regarding their detection and sequencing. Elucidating the cellular functions of modifications remains an ongoing challenge; we discuss recent contributions to this area before exploring their relevance in medicine.     

Variation in the methods leads to variation in the interpretation of biodiversity–ecosystem multifunctionality relationships

生物多样性常常和生态系统多功能性(生态系统同时提供多个生态系统功能的能力)正相关。然而,生物多样性与生态系统多功能性的关系是否依赖于生态系统功能的数目有诸多争议。其中,生物多样性对生态系统多功能性的影响或许不随生态系统功能数目的变化而变化,或者随生态系统功能数目的增多而增强。我们期望通过研究不同生态系统多功能性指数的统计原理来解决这些争议。 我们使用了模型模拟和一系列来自不同空间尺度(从局域到全球)和不同生物群系(温带和高寒草地、森林和干旱地)的经验数据。我们回顾了量化生态系统多功能性的三种方法,包括平均值法、加和法和阈值法。我们发现随着生态系统功能数目的增加,生物多样性与生态系统多功能性的关系要么不变,要么增强。这些结果可由平均和加和的多功能性指数的统计原理来解释。具体来讲,当利用生态系统功能的平均值计算多功能性指数时,由于多样性对多功能性的效应等于多样性对单个生态系统功能效应的平均值,所以不会随生态系统功能数目的变化而变化。同样的道理,当利用单个生态系统的加和值计算多功能性指数时,多样性的效应会随着生态系统功能数目的增加而增强。我们提出了一个改进的多功能性指数,将平均或加和多功能性指数转化为标准化的多功能性指数, 以便于对不同研究的结果进行比较。此外,我们提出了基于变量数值范围的标准化方法来解决阈值法的数学假象问题(多样性效应随生态系统功能数目的增加而增强)。我们的研究结果表明,量化多功能性指数的方法不同,结果也不同。因此,有必要加深对不同方法数理基础的理解。而标准化的多功能性指数为比较不同研究中的生物多样性与生态系统多功能性的关系提供了有效的方法。     

污染场地土壤生态风险评估研究进展

随着我国快速城市化以及产业结构的调整,遗留下了大量的污染场地,发展和实施污染场地土壤生态风险评估是进行大规模污染场地修复行动的必要条件。本文围绕污染场地土壤生态风险评估的科学原理、框架构建及技术方法等方面的关键问题: 1)评估框架的场地实际针对性;2)概念模型的不确定性;3)土壤复合污染毒性机制;4)评估终点筛选;5)评估方法和框架构建等展开讨论,指出土壤复合污染的制毒机制,即污染物生物有效性和联合效应是污染场地土壤生态风险评估的关键科学问题。耦合美国环保局四步法和欧盟层级法的“证据-权重法”评估框架适用于野外复杂环境条件下的土壤污染生态风险评估。建议今后重点开展以下5个方面的工作: 1)污染场地土壤生态风险评估技术框架与风险管控技术框架之间的联合;2)概念模型研究;3)基于过程的场地土壤污染物反应运移模型研究;4)场地土壤复合污染生态毒理学机制研究;5)生态系统高水平生态风险评估终点研究。旨在为形成我国本土污染场地土壤生态风险评估技术指南提供理论基础和构架。     

三江源区生态系统和土壤保持服务对未来气候变化的响应特征

气候变化条件下的生态系统响应特征对生态系统服务的提升和生态环境保护具有重要意义。现有气候变化评估多以全球或区域大尺度研究为主,不适合局地小尺度。以2015年为基准,根据局地特征改进了综合顺序分类系统（CSCS）,模拟了未来不同温室气体排放模式下三江源地区自然植被分布,同时分析了植被覆盖度及土壤保持功能的时空变化。研究结果表明：①在2080年的不同排放情境下,三江源地区的降水和气温增长主要发生在生长季（5—9月）和半湿润地区,其中,高排放情境的增幅最大（42.21 mm和4.93℃）;②三江源地区潜在自然植被主要由草地转化为森林,植被覆盖度和土壤保持服务在不同排放情境下均呈现由西北向东南增加的趋势,与水热规律一致,其中高排放情境的增幅最大,低排放最小;③ 利用三江源地区原生裸地演替特点和多年NPP改进的CSCS模型,模拟精度提高了24%。研究成果为局地小尺度生态系统气候响应特征提供了必要的手段和规律认识。     

A trait-based approach predicting community assembly and dominance of microbial invasive species

Understanding the mechanisms underlying community assembly helps to define success and susceptibility to biological invasions. Here, we explored phytoplankton community assembly following niche and neutral paradigms and using a trait-based approach. Under the hypothesis that the morphology-based functional groups (MBFG) clusters species with similar niche, we analysed how trait-related differences in fitness influence dominance of an invasive species. This was based on literature review, field data and model simulations. We predict that invading species can be dominant if: 1) do not belong to the local MBFG but use unexploited areas of the niche, or 2) belong to the resident MBFG but exhibit a higher fitness due to a particular combination of traits. The invasive dinoflagellate Ceratium furcoides was used as the model species to evaluate these hypotheses, its morphological (e.g. volume) and physiological (e.g. growth rates) traits were compared with species from the same (V: photosynthetic flagellates) and different (VII: colonial cyanobacteria) MBFG. Fitness was estimated using models parametrized with MBFG rates (R*, ability to draw down phosphate) under different environmental conditions (i.e. flushing). Results contributed to support both hypotheses. First, the alternation of C. furcoides and cyanobacteria dominance was explained by the use of different niches. Secondly, species from MBFG V were dominant under similar environments. Within this group V C. furcoides showed higher fitness under low flushing and high predation, advantage provided by a distinctive combination of traits. The application of trait-based approaches to represent the niche and estimate fitness along environmental gradients was useful to evaluate community assembly and can be used to predict the dominance of microbial species invasions.     

改良乳腺癌根治术后切口感染的病原学特征、影响因素及其凝血纤溶功能研究

摘要 目的：探讨改良乳腺癌根治术后切口感染的病原学特征、影响因素及其对凝血纤溶功能的影响。方法：选取我院于2016年6月~2020年9月期间收治的390例行改良乳腺癌根治术的乳腺癌患者,分析改良乳腺癌根治术后切口感染的病原学特征、影响因素及术后切口感染对凝血纤溶功能的影响。结果：390例行改良乳腺癌根治术的乳腺癌患者,术后发生切口感染28例,术后切口感染率为7.18%（28/390）,将未发生术后切口感染的患者纳为未感染组（n=362）,发生的纳为感染组（n=28）。28例发生感染的患者共分离培养病原菌36株,其中革兰阳性菌14株,占比38.89%（14/36）,以金黄色葡萄球菌、粪肠球菌为主。革兰阴性菌21株,占比58.33%（21/36）,以大肠埃希菌、铜绿假单胞菌为主。改良根治术后乳腺癌患者切口感染的影响因素包括手术时间、术后住院时间、合并基础疾病、引流时间、年龄、白蛋白（P<0.05）。多因素Logistic回归分析发现：合并基础疾病、年龄≥60岁、白蛋白＜35 g/L、手术时间≥120 min均是改良乳腺癌根治术后切口感染的影响因素（P＜0.05）。两组术后30 d凝血酶原时间（PT）、活化部分凝血活酶时间（APTT）、凝血酶时间（TT）升高,且未感染组高于感染组（P<0.05）,纤维蛋白原（FIB）降低,且未感染组低于感染组（P<0.05）。结论：改良乳腺癌根治术后切口感染较为常见,致病菌以革兰阴性菌为主,年龄、合并基础疾病、白蛋白、手术时间均是其影响因素,同时术后切口感染的发生可影响凝血纤溶功能的恢复,临床医生应积极采取措施预防术后切口感染的发生,从而保证手术治疗效果。     

Revisiting of Carex sect. Confertiflorae s.l. (Cyperaceae): New data from molecular and morphological evidence and first insights on Carex biogeography in East Asia

Carex sect. Confertiflorae s.l. is a medium-sized species group (ca. 40 species) with its center of diversity in E Asia (China and Japan). According to morphological traits, the section has been proposed to split into two sections (sects. Confertiflorae sensu Ohwi and Molliculae Ohwi) up to five different ones (sects. Confertiflorae s.s., Molliculae, Dispalatae Ohwi, Ischnostachyae Ohwi, and Alliiformes Akiyama). Recent phylogenetic reconstructions showed Confertiflorae s.l. not to be monophyletic, as species traditionally considered part of it were found to belong to other clades, whereas species traditionally ascribed to other sections were nested within it. In this study, we investigated the phylogenetic structure, morphological affinities, and biogeographic history of sect. Confertiflorae s.l. We employed a taxon-based approach to explore the morphological affinities of the species considered in sect. Confertiflorae and compared the micromorphology of the nutlets of almost all the taxa using SEM. We included 40 samples representing 31 species/subspecies of sect. Confertiflorae s.l. and used two nuclear (ETS and ITS) and three plastid (trnL-F, matK, and rpl32-trnL ^UAG) molecular markers to reconstruct the phylogeny of the group. The phylogenetic analyses confirmed the polyphyly of sect. Confertiflorae s.l., whose representatives were found within five distinct clades. From these, two clades, sect. Confertiflorae and sect. Molliculae, were found to be closely related and contained the majority of the species. The composition of the two clades agreed with the morphological structure of the group, and we confirmed an exclusive combination of features (namely color of basal sheaths, presence of bract sheath, peduncle of lowest spike, inflorescence sex distribution, shape of pistillate glume apex, and color and veins of utricle, among others) characterizing each of the two clades. The origin of the two clades was found to be in the early Pliocene; however, the majority of the diversification events within each clade took place during the Pleistocene. This illustrates that although Asia has been regarded as having little potential ecological space for Carex to diversify due to its climate stability, groups of sedges sub-endemic from that area may have a fairly recent origin related to glaciations. We proposed the rearrangement of sect. Confertiflorae as previously conceived as three independent sections: the monotypic Alliiformes, sect. Molliculae, and sect. Paludosae.     

Clinical determinants of early spontaneous conversion to sinus rhythm in patients with atrial fibrillation

Netherlands Heart Journal - The current standard of care for acute atrial fibrillation (AF) focuses primarily on immediate restoration of sinus rhythm by cardioversion, although AF often terminates...     

Reunderstanding Cairo through urban metabolism: Formal versus informal districts resource flow performance in fast urbanizing cities

Urban expansion can be seen as the most pervasive human impact on the environment where its high resource use contributes negatively to climate change and resource scarcity crises. Many experts call for decoupling resource use, economic development, and related urban development especially within cities of the Global South. This paper focuses on investigating resource efficiency through the lens of urban metabolism. It investigates current resource flows, through material flow analysis, from source to sink, in two diverse districts in Cairo: a formal district and an informal one, regarding materials (waste) and mobility. Consequently, the paper discusses locally responsive interventions that address local priorities as opposing to citywide one‐size fits all solution. The paper relies on parcel audits, which are embedded in an Urban Metabolism Information System developed by the Ecocity Builders and their partners, through a joint project with Cairo University. The methodology couples crowd‐sourced data, parcel audits, and experts’ knowledge to better understand resource flows based on a bottom‐up approach, given the unavailability of governmental data on the local level. The paper further correlates the perceived quality of life with the actual resource flows. It utilizes fieldwork investigations to argue against the local misconceptions regarding the inefficiency of informal areas/systems versus the higher efficiency of planned areas/systems. The paper concludes by proposing integrated solutions that respond to local needs and resources. It highlights the challenges and lessons of this tailored bottom‐up approach and its applicability in other cities worldwide.     

Modified Fuzzy Q Learning Based Classifier for Pneumonia and Tuberculosis

This work proposes reinforcement learning for correctly identifying pneumonia and tuberculosis (TB) using a repository of X ray images. To our knowledge, this is a first attempt at employing reinforcement learning for pneumonia and TB classification. In particular, modified fuzzy Q learning (MFQL) algorithm in conjunction with wavelet based pre-processing has been used to build a classifier for identifying pneumonia and tuberculosis's severity. Proposed classifier is a self-learning one and uses pneumonia dataset (no pneumonia, mild pneumonia and severe pneumonia) and tuberculosis dataset (TB present, TB absent) samples to classify X ray images of subjects. Results indicate that MFQL based approach achieves high accuracy and fares much better over contemporary Support Vector Machine (SVM) and k-Nearest Neighbor (KNN) classifiers. Proposed classifier can be a useful tool for pneumonia and tuberculosis diagnosis in a practical setting.