Critical note on the application of the “two-third” spline

The “two-third spline” (2/3S) is a frequently applied method to detrend tree-ring series. It fits a spline with a 50% frequency cutoff at a frequency equal to two-thirds of each sample length in a dataset. It was introduced to ensure a minimum loss of low-frequency variance, which is resolvable during the detrending of ring-width series.In this paper I show potential problems that arise when rusing this method. The 2/3S runs counter the strengths of using a digital filter to detrend – i.e. one is giving up full control over the frequency-removing characteristics of the growth curve and each individual time series retains a different amount of low frequency. Thus, the 2/3S is less suitable for reconstructing climate or to compare environmental impacts on tree growth between groups – both of which comprise the majority of dendrochronological analyses – as it will likely introduce a temporal frequency bias. Within a long chronology it will result in decreasing power to resolve low frequencies towards present in a living-only trees setting, especially when the youngest segment lengths are 100 years and shorter, and more generally during the period where the chronology is constructed from samples with shorter segment lengths compared to the period with longer segment lengths. The frequency bias will also significantly impact regression slopes and correlation coefficients, possibly distorting analyses investigating multiple groups with different mean segment lengths. Highlighting these potential biases, I recommend the community to not use this method on an individual basis but rather to use a fixed spline stiffness for all samples based on the n% criterion (n = 67) of e.g. the mean segment length of the entire dataset.     

Zinc tolerance in populations ofDeschampsia cespitosa (Gramineae) beneath electricity pylons

Patterns of zinc tolerance were examined in eightDeschampsia cespitosa (L.)Beauv. populations from normal and zinc-contaminated soils, using solution culture methods. Zinc-tolerant populations have evolved beneath pylons, and their tolerance patterns (degree, variance, heritability) vary. Tolerance is genetically based in all of them. In contrast to the cases of other species previously reported, some within-population differences are considerable, and may be due to both heterogeneity of the soils zinc contents, various gene combinations and gene recombinations between genotypes. One control population contains many tolerant plants, an original result which is discussed.     

A chromosome‐level genome assembly reveals the genetic basis of cold tolerance in a notorious rice insect pest,Chilo suppressalis

The rice stem borer, Chilo suppressalis, is one of the most damaging insect pests to rice production worldwide. Although C. suppressalis has been the focus of numerous studies examining cold tolerance and diapause, plant–insect interactions, pesticide targets and resistance, and the development of RNAi‐mediated pest management, the absence of a high‐quality genome has limited deeper insights. To address this limitation, we generated a draft C. suppressalis genome constructed from both Illumina and PacBio sequences. The assembled genome size was 824.35 Mb with a contig N₅₀ of 307 kb and a scaffold N₅₀ of 1.75 Mb. Hi‐C scaffolding assigned 99.2% of the bases to one of 29 chromosomes. Based on universal single‐copy orthologues (BUSCO), the draft genome assembly was estimated to be 97% complete and is predicted to encompass 15,653 protein‐coding genes. Cold tolerance is an extreme survival strategy found in animals. However, little is known regarding the genetic basis of the winter ecology of C. suppressalis. Here, we focused our orthologous analysis on those gene families associated with animal cold tolerance. Our finding provided the first genomic evidence revealing specific cold‐tolerant strategies in C. suppressalis, including those involved in glucose‐originated glycerol biosynthesis, triacylglycerol‐originated glycerol biosynthesis, fatty acid synthesis and trehalose transport‐intermediate cold tolerance. The high‐quality C. suppressalis genome provides a valuable resource for research into a broad range of areas in molecular ecology, and subsequently benefits developing modern pest control strategies.     

Genetic basis of kernel nutritional traits during maize domestication and improvement

The nutritional traits of maize kernels are important for human and animal nutrition, and these traits have undergone selection to meet the diverse nutritional needs of humans. However, our knowledge of the genetic basis of selecting for kernel nutritional traits is limited. Here, we identified both single and epistatic quantitative trait loci (QTLs) that contributed to the differences of oil and carotenoid traits between maize and teosinte. Over half of teosinte alleles of single QTLs increased the values of the detected oil and carotenoid traits. Based on the pleiotropism or linkage information of the identified single QTLs, we constructed a trait–locus network to help clarify the genetic basis of correlations among oil and carotenoid traits. Furthermore, the selection features and evolutionary trajectories of the genes or loci underlying variations in oil and carotenoid traits revealed that these nutritional traits produced diverse selection events during maize domestication and improvement. To illustrate more, a mutator distance–relative transposable element (TE) in intron 1 of DXS2, which encoded a rate‐limiting enzyme in the methylerythritol phosphate pathway, was identified to increase carotenoid biosynthesis by enhancing DXS2 expression. This TE occurs in the grass teosinte, and has been found to have undergone selection during maize domestication and improvement, and is almost fixed in yellow maize. Our findings not only provide important insights into evolutionary changes in nutritional traits, but also highlight the feasibility of reintroducing back into commercial agricultural germplasm those nutritionally important genes hidden in wild relatives.     

Quantitative assessment of the accuracy for three interpolation techniques in kinematic analysis of human movement

Marker obstruction during human movement analyses requires interpolation to reconstruct missing kinematic data. This investigation quantifies errors associated with three interpolation techniques and varying interpolated durations. Right ulnar styloid kinematics from 13 participants performing manual wheelchair ramp ascent were reconstructed using linear, cubic spline and local coordinate system (LCS) interpolation from 11–90% of one propulsive cycle. Elbow angles (flexion/extension and pronation/supination) were calculated using real and reconstructed kinematics. Reconstructed kinematics produced maximum elbow flexion/extension errors of 37.1 (linear), 23.4 (spline) and 9.3 (LCS) degrees. Reconstruction errors are unavoidable [minimum errors of 6.7 mm (LCS); 0.29 mm (spline); 0.42 mm (linear)], emphasising careful motion capture system setup must be performed to minimise data interpolation. For the observed movement, LCS-based interpolation (average error of 14.3 mm; correlation of 0.976 for elbow flexion/extension) was most suitable for reconstructing durations longer than 200 ms. Spline interpolation was superior for shorter durations.     

Optimization of the hydrolysis of lignocellulosic residues by using radial basis functions modeling and particle swarm optimization

The concentrations of glucose and total reducing sugars obtained by chemical hydrolysis of three different lignocellulosic feedstocks were maximized. Two response surface methodologies were applied to model the amount of sugars produced: (1) classical quadratic least-squares fit (QLS), and (2) artificial neural networks based on radial basis functions (RBF). The results obtained by applying RBF were more reliable and better statistical parameters were obtained. Depending on the type of biomass, different results were obtained. Improvements in fit between 35% and 55% were obtained when comparing the coefficients of determination (R²) computed for both QLS and RBF methods. Coupling the obtained RBF models with particle swarm optimization to calculate the global desirability function, allowed to perform multiple response optimization. The predicted optimal conditions were confirmed by carrying out independent experiments.     

Core concepts of spatial prioritisation in systematic conservation planning

Systematic conservation planning (SCP) is a field of conservation biology concerned with delivering on‐the‐ground actions that achieve conservation goals. It describes a set of operational models that cover both design and implementation of conservation, with a strong focus on mobilising the collective action typically required to implement conservation. SCP, as it was originally described, was composed of six different stages: collection of data, identification of conservation goals, evaluation of the existing protected area network, design of expansions, implementation of conservation action, and long‐term maintenance of biodiversity in the network. Since then, the operational model has been expanded into several different variants. Conservation actions applied inside SCP include establishment and expansion of reserve networks and allocation of habitat restoration and management. Within the broader context of SCP, there is a fundamental biogeographic‐economic analysis frequently called spatial conservation prioritisation or conservation assessment, which is used for identifying where important areas for biodiversity are and how conservation goals might be achieved efficiently. Here, we review the usage and meaning of the 12 biogeographic‐economic core concepts of SCP: adequacy, complementarity, comprehensiveness, effectiveness, efficiency, flexibility, irreplaceability, replacement cost, representation, representativeness, threat, and vulnerability. Some of the concepts have clear definitions whereas others may have alternative and possibly conflicting definitions. With a comprehensive literature review literature, we elucidate the historical backgrounds of these concepts, the first definitions and usages, alternative later definitions, key applications, and prior reviews. This review reduces linguistic uncertainty in the application of SCP. Since SCP is a global activity with a multitude of different stakeholders involved, it is vital that those involved can speak the same language. Through these concepts, this review serves as a source of information about the historical development of SCP. It provides a comprehensive review for anyone wishing to understand the key concepts of spatial prioritisation within SCP.     

无融合生殖悬铃叶苎麻（Boehmeria tricuspis）多倍性发生的染色体行为研究

摘要：对无融合生殖悬铃叶苎麻（2n=42）和有性生殖悬铃叶苎麻(2n=28)花粉母细胞（PMC）减数分裂行为进行比较研究,从而推断两者之间的进化关系;探索无融合生殖悬铃叶苎麻（B.tricuspis）发生的细胞遗传学基础,为无融合生殖发生的遗传学研究提供理论依据。在无融合生殖类型经诱导所产生的PMC的减数分裂过程中,发现有丰富的三价体形成,属典型的同源三倍体减数分裂行为特征;而有性生殖类型 PMC的减数分裂行为绝大多数正常,但也存在少量异常现象。其中有些异常行为,可能与未减数配子（2n）的形成紧密相关。因而推断,在有性生殖类型的生殖过程中,可能发生了未减数配子（2n）与减数配子（n）的融合,产生了同源三倍体合子。这应该是无融合生殖悬铃叶苎麻发生的重要的细胞遗传学基础。     

Geometric morphometrics as a tool for interpreting evolutionary transitions in the black fly wing (Diptera: Simuliidae)

A geometric morphometric analysis was conducted on wing‐vein landmarks on exemplar species of the family Simuliidae of the following genera: Parasimulium, Gymnopais, Twinnia, Helodon, Prosimulium, Greniera, Stegopterna, Tlalocomyia, Cnephia, Ectemnia, Metacnephia, Austrosimulium, and Simulium. Generalized least squares superimposition was performed on landmarks, followed by a principal component analysis on resulting Procrustes distances. Patterns of shape change along the principal component axes were visualized using the thin‐plate spline. The analysis revealed wing shape diversity through (1) the insertion points of the subcosta and R₁, resulting in the terminus of the costa exhibiting a trend towards a more apical position on the wing, and (2) the insertion point of the humeral cross vein, resulting in the anterior branch of the media exhibiting a trend toward a more basal position on the wing. Canonical variates analysis of Procrustes distances successfully assigned all exemplar species into their a priori taxonomic groupings. The diversity in wing shape reveals a trend towards decreased length of basal radial cell and increased costalization of anterior wing veins in the evolutionary transition from plesiomorphic prosimuliines to more derived simuliines. The functional significance of these evolutionary transitions is discussed. © 2013 The Linnean Society of London     

Physiological model using diffuse reflectance spectroscopy for nonmelanoma skin cancer diagnosis

Diffuse reflectance spectroscopy (DRS) is a noninvasive, fast, and low‐cost technology with potential to assist cancer diagnosis. The goal of this study was to test the capability of our physiological model, a computational Monte Carlo lookup table inverse model, for nonmelanoma skin cancer diagnosis. We applied this model on a clinical DRS dataset to extract scattering parameters, blood volume fraction, oxygen saturation and vessel radius. We found that the model was able to capture physiological information relevant to skin cancer. We used the extracted parameters to classify (basal cell carcinoma [BCC], squamous cell carcinoma [SCC]) vs actinic keratosis (AK) and (BCC, SCC, AK) vs normal. The area under the receiver operating characteristic curve achieved by the classifiers trained on the parameters extracted using the physiological model is comparable to that of classifiers trained on features extracted via Principal Component Analysis. Our findings suggest that DRS can reveal physiologic characteristics of skin and this physiologic model offers greater flexibility for diagnosing skin cancer than a pure statistical analysis. Physiological parameters extracted from diffuse reflectance spectra data for nonmelanoma skin cancer diagnosis.