Integrative sediment quality assessment using a biomarker approach: review of 3 years of field research

Recent research efforts in sediment and dredged material assessment research have focused on the inclusion of sublethal endpoints (biomarkers) in acute and long-term bioassays for dredged material characterisation and management. The incorporation of biomarkers as a new line of evidence in a weight of evidence approach allows the determination of more sensitive, longer-term biological information for use in laboratory and in situ sediment/tissue quality guidelines.     

基于微流控芯片的InDel快速族群推断体系研究

目的 QuickTargSeq全集成法医DNA现场快速检测系统是国内首台自主研制的现场快检仪,可应用于InDel族群推断检测,2 h左右完成“样本进-结果出”的快速自动化InDel分型。本文对InDel族群推断微流控芯片检测体系的性能进行评估,以期为实践应用提供参考。方法 使用InDel族群推断微流控芯片检测体系,对体系的灵敏度、干扰物耐受性、成功率、分型准确率、精确性、准确性、峰平衡性及检材适应性进行验证评估,同时对测试样本的族群来源进行推断。结果 138份样本的全集成检测成功率为95.65%,分型准确率为98.85%;DNA模板量≥5 ng时,可获得完整InDel分型,口腔拭子样本最佳采集次数为口腔内壁左右两侧各刮擦8次,血卡样本最佳检测方式为6片（Φ=2 mm）;所有基因座的平均杂合子峰高比值为0.86;10次运行的等位基因分型标准物（allelic ladder）片段大小标准差均在0.3 bp以内,测试样本等位基因和相应的等位基因分型标准物之间的片段准确性均在0.5 bp以内。结论 该体系可实现对口腔拭子、血卡、唾液卡及烟蒂样本的准确分型,能够准确推断样本的族群来源。     

A Decision-Making System with Reject Option for Atrial Fibrillation Prediction Without ECG Signals

ObjectivesThis paper presents a new method for Atrial Fibrillation detection based on the belief functions theory.Materials and methodsThe theoretical framework allows to handle missing and uncertain data, to aggregate evidence in an independent order of sources of information and to reject a decision in case of insufficient supporting evidence. The proposed method is evaluated on real signals acquired from Intensive Care Units available in the MIMIC-III database and compared to state-of-the-art technologies and methods.ResultsThe precision of the suggested method is 90.03%, which is 2% more than existing methods in the literature.ConclusionWhile almost all existing methods rely on high frequency sampled ECG signals, mainly at 125 Hz, to achieve a good accuracy, our proposed approach achieves a comparable performance using low frequency sampled physiological signals at 0.016 Hz without the need for an ECG which allows for a significant reduction in energy consumption, in data size and in processing complexity.     

On the need of legal frameworks for assessing restoration projects success: new perspectives from São Paulo state (Brazil)

Despite growing worldwide commitment to large‐scale ecosystem restoration, national public policies on restoration are few, and those that exist tend to be vague. Brazil and especially São Paulo state stand out. In a pioneering attempt to improve restoration projects and their outcomes, the Secretariat for the Environment of the State of São Paulo has enacted a legal instrument to drive planning and to assess whether the goals and targets of mandatory ecological restoration are being achieved. Regardless of the restoration techniques applied, the effectiveness of mandatory or public‐funded projects will henceforth be assessed by using three ecological indicators: (1) ground coverage with native vegetation; (2) density of native plants spontaneously regenerating; and (3) number of spontaneously regenerating native plant species. We analyze how this science‐based legal framework is expected to promote greater restoration success, improve cost‐effectiveness, and help bridge the all‐too‐familiar knowledge‐action gap in environmental policies. Notably, scientists, professionals, public agents, and stakeholders from different institutions have collaborated to advance the refinement and rolling out of this legal instrument. By 2037, it is expected that more than 300,000 restoration projects will be carried out in São Paulo state and monitored using this set of indicators. We also suggest that this approach could be usefully applied to the growing number of ecological restoration programs being carried out worldwide, especially in the context of offset policies intended to achieve serious compensation for environmental degradation or loss of biodiversity.     

Phylogenetic relationships among loliginid squids (Cephalopoda: Myopsida) based on analyses of multiple data sets

The phylogenetic relationships among the loliginid squids, a species-rich group of shallowwater muscular squids, have been investigated recently using several approaches, including allozyme electrophoresis and analyses of morphological and DNA sequence data, yet no consensus has been reached. This study examines the effects of combining multiple data sets (morphology, allozymes and DNA sequence data from two mitochondrial genes) on estimates of loliginid phylogeny. Various data combinations were analysed under three maximum parsimony weighting schemes: equal weights for all characters, successive approximations and implicit weights parsimony. When feasible, support for branches within trees was assessed with nonparametric bootstrapping and decay analysis. Some ingroup relationships were consistent across all analyses, but relationships among outgroup taxa and basal ingroup taxa varied. Combining data increased bootstrap support for several nodes. Methods that downweight highly variable characters (i.e. successive approximations and implicit weights parsimony) produced very similar trees which included two major clades: a clade consisting of all species sampled from American waters (except Sepioteuthis ), and a clade of several east Atlantic species ( Loligo forbesi Steenstrup, Loligo vulgaris Lamarck and Loligo reynaudi d'Orbigny) plus several Indo-West Pacific species in the genera Uroteuthis and Loliolus. The Sepioteuthis species occupied a basal position within Loliginidae, but Sepioteuthis itself was not always monophyletic. The position of a clade of a few Lolliguncula species and Loligo (Alloteuthis) also varied across analyses. A new loliginid classification is proposed based on these findings.     

Evolutionary Sparse Learning for Phylogenomics

We introduce a supervised machine learning approach with sparsity constraints for phylogenomics, referred to as evolutionary sparse learning (ESL). ESL builds models with genomic loci—such as genes, proteins, genomic segments, and positions—as parameters. Using the Least Absolute Shrinkage and Selection Operator, ESL selects only the most important genomic loci to explain a given phylogenetic hypothesis or presence/absence of a trait. ESL models do not directly involve conventional parameters such as rates of substitutions between nucleotides, rate variation among positions, and phylogeny branch lengths. Instead, ESL directly employs the concordance of variation across sequences in an alignment with the evolutionary hypothesis of interest. ESL provides a natural way to combine different molecular and nonmolecular data types and incorporate biological and functional annotations of genomic loci in model building. We propose positional, gene, function, and hypothesis sparsity scores, illustrate their use through an example, and suggest several applications of ESL. The ESL framework has the potential to drive the development of a new class of computational methods that will complement traditional approaches in evolutionary genomics, particularly for identifying influential loci and sequences given a phylogeny and building models to test hypotheses. ESL’s fast computational times and small memory footprint will also help democratize big data analytics and improve scientific rigor in phylogenomics.     

新种祁门过路黄的核型证据

对新种祁门过路黄及其近缘种巴东过路黄和光叶巴东过路黄的核型在居群水平上进行了比较研究。结果表明这两种植物的核型特征在种内是稳定的,同一物种的不同居群间核型无明显差异。祁门过路黄的核型为2n=2x=24=6m+6sm+6st+6t;巴东过路黄和光叶巴东过路黄的核型均为2n=2x=24=6m+4sm+6st+8t;两物种间核型差异显著,核型特征支持将祁门过路黄作为新种处理。     

Y染色体短串联重复序列微流控芯片复合扩增检测体系研究

目的 构建Y染色体短串联重复序列（Y-STR）微流控芯片扩增检测试剂,并进行性能验证,实现Y-STR基因座的快速全集成检测。方法 使用Y-STR微流控芯片检测体系,对其灵敏度、成功率和分型准确率、峰平衡性、精准性和准确性、检材适应性、混合物检测能力和抗抑制性进行验证评估。结果 DNA标准品9948的模板量≥8 ng,血卡片数≥3片以及口腔拭子刮擦次数≥7次时可获得Y-STR完整分型;165份样本的全集成检测成功率为91.52%,分型准确率为99.74%;不同荧光通道之间的峰高比值为89.81%;10次运行的等位基因分型标准品的片段大小标准差均在0.5 bp以内,20份样本全集成检测的等位基因片段和相应的等位基因标准品之间的片段准确性均在0.5 bp以内;能够对口腔拭子、血卡、唾液卡、烟蒂、血棉签、布片精斑等检材进行准确分型;混合样本中较小贡献者与较大贡献者在1∶3的比例时可获得完整基因分型;在不同浓度的腐殖酸（50～400 mg/L）、靛蓝（20～100 nmol/L）、血红蛋白（100～500μmol/L）等抑制物的干扰下,该体系可获得完整基因分型。结论 该体系可应用于国产Quick...     

Using DNA from non-invasive samples to identify individuals and census populations: an evidential approach tolerant of genotyping errors

DNA extracted from hair or faeces shows increasing promise for censusing populations whose individuals are difficult to locate. To date, the main problem with this approach has been that genotyping errors are common. If these errors are not identified, counting genotypes is likely to overestimate the number of individuals in a population. Here, we describe an algorithm that uses maximum likelihood estimates of genotyping error rates to calculate the evidence that samples came from the same individual. We test this algorithm with a hypothetical model of genotyping error and show that this algorithm works well with substantial rates of genotyping error and reasonable amounts of data. Additional work is necessary to develop statistical models of error in empirical data.