Interpretability of bi-level variable selection methods

Variable selection is usually performed to increase interpretability, as sparser models are easier to understand than full models. However, a focus on sparsity is not always suitable, for example, when features are related due to contextual similarities or high correlations. Here, it may be more appropriate to identify groups and their predictive members, a task that can be accomplished with bi-level selection procedures. To investigate whether such techniques lead to increased interpretability, group exponential LASSO (GEL), sparse group LASSO (SGL), composite minimax concave penalty (cMCP), and least absolute shrinkage, and selection operator (LASSO) as reference methods were used to select predictors in time-to-event, regression, and classification tasks in bootstrap samples from a cohort of 1001 patients. Different groupings based on prior knowledge, correlation structure, and random assignment were compared in terms of selection relevance, group consistency, and collinearity tolerance. The results show that bi-level selection methods are superior to LASSO in all criteria. The cMCP demonstrated superiority in selection relevance, while SGL was convincing in group consistency. An all-round capacity was achieved by GEL: the approach jointly selected correlated and content-related predictors while maintaining high selection relevance. This method seems recommendable when variables are grouped, and interpretation is of primary interest.     

Mosquito control actions affect chironomid diversity in temporary wetlands of the Upper Rhine Valley

The Upper Rhine Valley, a “hotspot of biodiversity” in Germany, has been treated with the biocide Bacillus thuringiensis var. israelensis (Bti) for mosquito control for decades. Previous studies discovered Bti nontarget effects in terms of severe chironomid abundance reductions. In this study, we investigated the impact of Bti on species level and addressed the community composition of the nontarget family Chironomidae by use of community metabarcoding. Chironomid emergence data were collected in three mosquito‐control relevant wetland types in the Upper Rhine Valley. For all three sites the chironomid species composition, based on operational taxonomic units (OTUs), was different to varying degrees in the Bti‐treated samples versus control samples, ranging from a significant 63% OTU reduction to an OTU replacement. We assumed that predatory chironomids are less prone to Bti than filter feeders, as the latter feed on floating particles leading to direct ingestion of Bti. However, a comparable percentage of predators and filter feeders (63% and 65%, respectively) was reduced in the Bti samples, suggesting that the feeding strategy is not the main driver for Bti sensitivity in chironomids. Finally, our data was compared to a three‐year‐old data set, indicating possible chironomid community recovery due to species recolonization a few years after the last Bti application. Considering the currently discussed worldwide insect decline we recommend a rethinking of the usage of the biocide Bti, and to prevent its ongoing application especially in nature protection reserves to enhance ecological resilience and to prevent boosting the current biodiversity loss.     

高压力制备柯萨奇病毒疫苗

以HeLa细胞和BALB／c小鼠为模型,研究了高压力对柯萨B组病毒（CVB）感染活性和免疫原性的影响,发现在230MPa压力下,结合其他相应的物理条件,CVB的感染活性可完全消失。该CVB仍具有抗原性,可诱导小鼠产生CVB特异性抗性,效价可达1：1500。用高压力处理的CVB免疫小鼠,再用正常CVB攻击,其生存率为67％,具有疫苗的特性。这些结果表明,高压力处理的CVB具有免疫保护作用,可作为一种具有潜在应用前景的病毒疫苗。     

Molecular modeling of glycosyltransferases involved in the biosynthesis of blood group A,blood group B,Forssman, and iGb3 antigens and their interaction with substrates

A terminal alpha1-3 linked Gal or GalNAc sugar residue is the common structure found in several oligosaccharide antigens, such as blood groups A and B, the xeno-antigen, the Forssman antigen, and the isogloboside 3 (iGb3) glycolipid. The enzymes involved in the addition of this residue display strong amino acid sequence similarities, suggesting a common fold. From a recently solved crystal structure of the bovine alpha3-galactosyltransferase complexed with UDP, homology modeling methods were used to build the four other enzymes of this family in their locked conformation. Nucleotide-sugars, the Mn2+ ion, and oligosaccharide acceptors were docked in the models. Nine different amino acid regions are involved in the substrate binding sites. After geometry optimization of the complexes and analysis of the predicted structures, the basis of the specificities can be rationalized. In the nucleotide-sugar binding site, the specificity between Gal or GalNAc transferase activity is due to the relative size of two clue amino acids. In the acceptor site, the presence of up to three tryptophan residues define the complexity of the oligosaccharide that can be specifically recognized. The modeling study helps in rationalizing the crystallographic data obtained in this family and provides insights on the basis of substrate and donor recognition.     

单核细胞趋化蛋白-1、高迁移率族蛋白B1与溃疡性结肠炎患者肠道菌群变化的相关性

目的 探讨单核细胞趋化蛋白-1（MCP-1）、高迁移率族蛋白B1（HMGB1）与溃疡性结肠炎（UC）患者肠道菌群变化的相关性。方法 选取2016年9月‒2018年1月遂宁市中心医院收治的98例UC患者资料,根据Mayo评分系统将UC患者分为活动期组（n=50）和缓解期组（n=48）。选取同期进行体检的健康人50例作为对照组。比较各组间肠道菌群,血清MCP-1、HMGB1水平,并进行Pearson相关分析。结果 活动期组患者肠道乳杆菌、双歧杆菌含量[（5.34±0.87）、（5.81±0.83）CFU/g]显著低于缓解期组和对照组[（8.07±0.86）、（8.35±0.88）CFU/g;（8.13±0.91）、（8.46±0.95）CFU/g]（F=12.035,P0.05）。活动期组和缓解期组患者血清MCP-1、HMGB1水平[（267.42±23.51）、（21.35±2.26）ng/mL;（188.15±20.73）、（6.28±1.38）ng/mL]显著高于对照组[（106.38±15.92）、（2.13±0.41）ng/mL]（F=84.163,P<0.001;F=25.386,P<0.001）;活动期组患者血清MCP-1、HMGB1水平[（267.42±23.51）、（21.35±2.26）ng/mL]显著高于缓解期组[（188.15±20.73）、（6.28±1.38）ng/mL]（t=17.676、39.641,均P<0.05）。经过Pearson相关性分析,MCP-1、HMGB1与UC患者乳杆菌、双歧杆菌含量呈负相关（r=‒0.715、‒0.659,r=‒0.703、‒0.614,均P<0.001）,与大肠埃希菌、肠球菌、拟杆菌含量呈正相关（r=0.783、0.702,r=0.762、0.735,r=0.653、0.612,均P<0.001）。结论 MCP-1、HMGB1作为促炎因子可介导肠黏膜炎性反应,引起UC患者肠道菌群的紊乱。     

新疆艾比湖湿地自然保护区植物的生态分组

应用列联表的χ~2检验和Spearman相关系数研究了艾比湖湿地自然保护区植物的种间联结性和相关性.依据测定结果,将艾比湖湿地自然保护区的植物划分为4个生态种组:梭梭+盐节木+白麻+盐爪爪+琵琶柴+碱蓬+花花柴+骆驼刺+绢蒿+白刺+芦苇、小獐茅+多枝柽柳+滨藜+小叶碱蓬+盐豆木+鹅绒藤+盐穗木、胡杨+白梭梭、奶浆草+甘草+西北天门冬+赖草+罗布麻.各生态种组内,物种间具备最大的种问联结性和相关性.长期的演替过程使各生态种组对生境有最大的适应能力,各自分别生活于过渡带的盐化平原低地、湖滨盐沼地、荒漠和荒漠优势种间的阳斑.今后在艾比湖湿地自然保护区植物的保护和恢复中,以整个生态种组的角度出发较单个植物的保护和恢复更为有效.     

兽疫链球菌透明质酸合成相关基因hasB的克隆以及性质研究

透明质酸是链球菌荚膜的主要组成部分,有着重要的生理功能。UDP-葡萄糖脱氢酶(HasB)是透明质酸合成中的一个关键酶,而C类链球菌的UDP-葡萄糖脱氢酶编码基因(hasB)尚未被克隆。通过hasB基因的上下游序列设计引物从兽疫链球茵的基因组中克隆出一段序列,测序结果显示其包含一个由1206个碱基组成的开放阅读框,所编码的蛋白序列同化脓链球菌和乳链球菌的UDP-葡萄糖脱氢酶蛋白序列分别有63．1％和70．6％的相似性。将这段基因置于T7启动子下,并在大肠杆菌中进行表达,能够得到一个约47kDa的蛋白,酶活测定显示其具有UDP-葡萄糖脱氢酶活性。这些结果表明所克隆的基因是兽疫链球菌的UDP-葡萄糖脱氢酶编码基因。