Weighted averaging partial least squares regression (WA-PLS): an improved method for reconstructing environmental variables from species assemblages

Weighted averaging regression and calibration form a simple, yet powerful method for reconstructing environmental variables from species assemblages. Based on the concepts of niche-space partitioning and ecological optima of species (indicator values), it performs well with noisy, species-rich data that cover a long ecological gradient (>3 SD units). Partial least squares regression is a linear method for multivariate calibration that is popular in chemometrics as a robust alternative to principal component regression. It successively selects linear components so as to maximize predictive power. In this paper the ideas of the two methods are combined. It is shown that the weighted averaging method is a form of partial least squares regression applied to transformed data that uses the first PLS-component only. The new combined method, ast squares, consists of using further components, namely as many as are useful in terms of predictive power. The further components utilize the residual structure in the species data to improve the species parameters (optima) in the final weighted averaging predictor. Simulations show that the new method can give 70% reduction in prediction error in data sets with low noise, but only a small reduction in noisy data sets. In three real data sets of diatom assemblages collected for the reconstruction of acidity and salinity, the reduction in prediction error was zero, 19% and 32%.     

BME-1生物医用电子微分器

本文介绍了一个用国产高输入阻抗运算放大器制成的生物医用电子微分器。电路由同步输入、延时、三角波发生器、微分单元和滤波单元组成。微分时间常数20μs—50ms;校正电压变化率±0.1v/s—±200v/s;延时20μs—10s。微分器可为外来正脉冲触发,也可手动触发,它已用于微分心肌细胞动作电位、心腔压力等多种生物讯号。     

Older than New Caledonia emergence? A molecular phylogenetic study of the eneopterine crickets (Orthoptera: Grylloidea)

Aim A New Caledonian insect group was studied in a world‐wide phylogenetic context to test: (1) whether local or regional island clades are older than 37 Ma, the postulated re‐emergence time of New Caledonia; (2) whether these clades show evidence for local radiations or multiple colonizations; and (3) whether there is evidence for relict taxa with long branches in phylogenetic trees that relate New Caledonian species to geographically distant taxa. Location New Caledonia, south‐west Pacific. Methods We sampled 43 cricket species representing all tribes of the subfamily Eneopterinae and 15 of the 17 described genera, focusing on taxa distributed in the South Pacific and around New Caledonia. One nuclear and three mitochondrial genes were analysed using Bayesian and parsimony methods. Phylogenetic divergence times were estimated using a relaxed clock method and several calibration criteria. Results The analyses indicate that, under the most conservative dating scenario, New Caledonian eneopterines are 5–16 million years old. The largest group in the Pacific region dates to 18–29 Ma. New Caledonia has been colonized in two phases: the first around 10.6 Ma, with the subsequent diversification of the endemic genus Agnotecous, and the second with more recent events around 1–4 Ma. The distribution of the sister group of Agnotecous and the lack of phylogenetic long branches in the genus refute an assumption of major extinction events in this clade and the hypothesis of local relicts. Main conclusions Our phylogenetic studies invalidate a simple scenario of local persistence of this group in New Caledonia since 80 Ma, either by survival on the New Caledonian island since its rift from Australia, or, if one accepts the submergence of New Caledonia, by local island‐hopping among other subaerial islands, now drowned, in the region during periods of New Caledonian submergence.     

Assessing the response of forest productivity to climate extremes in Switzerland using model–data fusion

The response of forest productivity to climate extremes strongly depends on ambient environmental and site conditions. To better understand these relationships at a regional scale, we used nearly 800 observation years from 271 permanent long‐term forest monitoring plots across Switzerland, obtained between 1980 and 2017. We assimilated these data into the 3‐PG forest ecosystem model using Bayesian inference, reducing the bias of model predictions from 14% to 5% for forest stem carbon stocks and from 45% to 9% for stem carbon stock changes. We then estimated the productivity of forests dominated by Picea abies and Fagus sylvatica for the period of 1960–2018, and tested for productivity shifts in response to climate along elevational gradient and in extreme years. Simulated net primary productivity (NPP) decreased with elevation (2.86 ± 0.006 Mg C ha^?1 year^?1 km^?1 for P. abies and 0.93 ± 0.010 Mg C ha^?1 year^?1 km^?1 for F. sylvatica). During warm–dry extremes, simulated NPP for both species increased at higher and decreased at lower elevations, with reductions in NPP of more than 25% for up to 21% of the potential species distribution range in Switzerland. Reduced plant water availability had a stronger effect on NPP than temperature during warm‐dry extremes. Importantly, cold–dry extremes had negative impacts on regional forest NPP comparable to warm–dry extremes. Overall, our calibrated model suggests that the response of forest productivity to climate extremes is more complex than simple shift toward higher elevation. Such robust estimates of NPP are key for increasing our understanding of forests ecosystems carbon dynamics under climate extremes.     

Straightforward method for calibration of mechanistic cation exchange chromatography models for industrial applications

Mechanistic modeling of chromatography processes is one of the most promising techniques for the digitalization of biopharmaceutical process development. Possible applications of chromatography models range from in silico process optimization in early phase development to in silico root cause investigation during manufacturing. Nonetheless, the cumbersome and complex model calibration still decelerates the implementation of mechanistic modeling in industry. Therefore, the industry demands model calibration strategies that ensure adequate model certainty in a limited amount of time. This study introduces a directed and straightforward approach for the calibration of pH-dependent, multicomponent steric mass action (SMA) isotherm models for industrial applications. In the case investigated, the method was applied to a monoclonal antibody (mAb) polishing step including four protein species. The developed strategy combined well-established theories of preparative chromatography (e.g. Yamamoto method) and allowed a systematic reduction of unknown model parameters to 7 from initially 32. Model uncertainty was reduced by designing two representative calibration experiments for the inverse estimation of remaining model parameters. Dedicated experiments with aggregate-enriched load material led to a significant reduction of model uncertainty for the estimates of this low-concentrated product-related impurity. The model was validated beyond the operating ranges of the final unit operation, enabling its application to late-stage downstream process development. With the proposed model calibration strategy, a systematic experimental design is provided, calibration effort is strongly reduced, and local minima are avoided.     

链球菌病类活疫苗活菌计数参考品的研制

研制链球菌病类活疫苗活菌计数参考品,可以更加科学地评价活菌计数结果的准确性和有效性。首先,制备了一批链球菌病类活疫苗活菌计数参考品,对其物理性状、纯粹性、真空度、剩余水分进行检验,并对其均一性、运输稳定性、热稳定性进行测定,另组织3家单位通过协作标定的方式对参考品活菌数进行赋值,用协作标定法统计参考品在12个月内的保存期。参考品的性状检查、纯粹检验、真空度测定和剩余水分测定结果均符合《中国兽药典》的规定;均一性试验结果显示,参考品计数结果的变异系数小于10%,均一性良好;运输稳定性试验证明,参考品在夏季和冬季用泡沫盒加冰袋的方式运输3日内数值仍能保持稳定;加速热稳定性试验验证,参考品在–20 ℃条件下保存3个月、4 ℃条件下保存21 d内均可活菌数稳定;通过协作标定,统计出参考品活菌数的赋值范围为 (8.5–12.1)×107 CFU/支;保存期试验结果证实,参考品在–70 ℃以下保存一年内活菌数可维持稳定状态。链球菌病类活疫苗活菌计数参考品,不仅可以为链球菌病类活疫苗的活菌计数实验提供参照物,而且可以用于评价马丁琼脂培养基的质量,为兽用生物制品质量控制提供保障。     

基于实测高光谱与Sentinel-2B数据的银北土壤Na+含量估测

为了探讨不同传感器对土壤Na⁺含量的估测能力,本研究以宁夏银北地区典型样点土壤实测光谱和Sentinel-2B影像光谱为对象,运用逐步回归(SR)和主成分回归分析(PCA)方法对光谱数据进行敏感参量筛选,然后采用偏最小二乘回归(PLSR)、支持向量机(SVM)和反向传播神经网络模型(BPNN)分别建立实测光谱和影像数据的土壤Na⁺含量估算模型。结果表明: 除Band9外,实测重采样数据与影像数据呈极显著相关。基于SR筛选方式建立的模型估算精度普遍高于PCA(SVM模型除外),PCA-SVM模型为影像最佳Na⁺含量估算模型,预测精度为0.792;SR-BPNN模型为实测最佳Na⁺含量估算模型,预测精度达到0.908。经重采样实测光谱模型校正后的SR-PLSR影像光谱土壤Na⁺含量估算模型精度从0.481提高到0.798,有效提高了较大尺度下的土壤Na⁺含量估算精度。本研究实现了遥感监测土壤Na⁺含量由点向面的空间转换,为Sentinel-2B影像监测盐渍化土壤Na⁺含量提供了科学参考。     

Validation of discrete time-to-event prediction models in the presence of competing risks

Clinical prediction models play a key role in risk stratification, therapy assignment and many other fields of medical decision making. Before they can enter clinical practice, their usefulness has to be demonstrated using systematic validation. Methods to assess their predictive performance have been proposed for continuous, binary, and time-to-event outcomes, but the literature on validation methods for discrete time-to-event models with competing risks is sparse. The present paper tries to fill this gap and proposes new methodology to quantify discrimination, calibration, and prediction error (PE) for discrete time-to-event outcomes in the presence of competing risks. In our case study, the goal was to predict the risk of ventilator-associated pneumonia (VAP) attributed to Pseudomonas aeruginosa in intensive care units (ICUs). Competing events are extubation, death, and VAP due to other bacteria. The aim of this application is to validate complex prediction models developed in previous work on more recently available validation data.     

Fossil grebes from the Truckee Formation (Miocene) of Nevada and a new phylogenetic analysis of Podicipediformes (Aves)

Podicipediformes is a cosmopolitan clade of foot‐propelled diving birds that, despite inhabiting marine and lacustrine environments, have a poor fossil record. In this contribution, we describe three new grebe fossils from the diatomite beds of the Late Miocene Truckee Formation (10.2 ± 0.2 Ma) of Nevada (USA). Two postcranial skeletons and an associated set of wing elements indicate that at least two distinct grebe species occupied the large, shallow Lake Truckee during the Miocene. Phylogenetic analysis of morphological data supports a basal divergence between a clade uniting the dabchicks (Tachybaptus, Limnodytes, Poliocephalus) and a clade uniting Podilymbus, Rollandia, Podiceps and Aechmophorus. Missing data, combined with a paucity of informative skeletal characters, make it difficult to place the Truckee grebes within either of these major clades. Given the weak projection of the cnemial crests compared with extant grebes, it also remains plausible that these specimens represent stem lineage grebes. Although more material is needed to resolve the phylogenetic position of the Truckee grebes, our analysis offers insight into the tempo of grebe evolution by placing the Miocene taxon Thiornis sociata within the dabchick clade. Thiornis sociata provides a minimum age calibration of 8.7 Ma for the basal divergence among dabchicks. Based on the recovery of a nonmonophyletic Tachybaptus and placement of the Western Hemisphere ‘Tachybaptus’ dominicus as the basal member of the otherwise exclusively Eastern Hemisphere dabchick clade, we resurrect the genus Limnodytes for this extant species (Limnodytes dominicus). Our results also nest the large, long‐necked Aechmophorus grebes within the genus Podiceps, as the sister taxon to Podiceps major.