Using density surface models to estimate spatio-temporal changes in population densities and trend

Precise measures of population abundance and trend are needed for species conservation; these are most difficult to obtain for rare and rapidly changing populations. We compare uncertainty in densities estimated from spatio–temporal models with that from standard design-based methods. Spatio–temporal models allow us to target priority areas where, and at times when, a population may most benefit. Generalised additive models were fitted to a 31-year time series of point-transect surveys of an endangered Hawaiian forest bird, the Hawai‘i ‘ākepa Loxops coccineus. This allowed us to estimate bird densities over space and time. We used two methods to quantify uncertainty in density estimates from the spatio–temporal model: the delta method (which assumes independence between detection and distribution parameters) and a variance propagation method. With the delta method we observed a 52% decrease in the width of the design-based 95% confidence interval (CI), while we observed a 37% decrease in CI width when propagating the variance. We mapped bird densities as they changed across space and time, allowing managers to evaluate management actions. Integrating detection function modelling with spatio–temporal modelling exploits survey data more efficiently by producing finer-grained abundance estimates than are possible with design-based methods as well as producing more precise abundance estimates. Model-based approaches require switching from making assumptions about the survey design to assumptions about bird distribution. Such a switch warrants consideration. In this case the model-based approach benefits conservation planning through improved management efficiency and reduced costs by taking into account both spatial shifts and temporal changes in population abundance and distribution.     

Genetic variants and underlying mechanisms influencing variance heterogeneity in maize

Traditional genetic studies focus on identifying genetic variants associated with the mean difference in a quantitative trait. Because genetic variants also influence phenotypic variation via heterogeneity, we conducted a variance‐heterogeneity genome‐wide association study to examine the contribution of variance heterogeneity to oil‐related quantitative traits. We identified 79 unique variance‐controlling single nucleotide polymorphisms (vSNPs) from the sequences of 77 candidate variance‐heterogeneity genes for 21 oil‐related traits using the Levene test (P < 1.0 × 10^?5). About 30% of the candidate genes encode enzymes that work in lipid metabolic pathways, most of which define clear expression variance quantitative trait loci. Of the vSNPs specifically associated with the genetic variance heterogeneity of oil concentration, 89% can be explained by additional linked mean‐effects genetic variants. Furthermore, we demonstrated that gene × gene interactions play important roles in the formation of variance heterogeneity for fatty acid compositional traits. The interaction pattern was validated for one gene pair (GRMZM2G035341 and GRMZM2G152328) using yeast two‐hybrid and bimolecular fluorescent complementation analyses. Our findings have implications for uncovering the genetic basis of hidden additive genetic effects and epistatic interaction effects, and we indicate opportunities to stabilize efficient breeding and selection of high‐oil maize (Zea mays L.).     

The Bio3D packages for structural bioinformatics

Bio3D is a family of R packages for the analysis of biomolecular sequence, structure, and dynamics. Major functionality includes biomolecular database searching and retrieval, sequence and structure conservation analysis, ensemble normal mode analysis, protein structure and correlation network analysis, principal component, and related multivariate analysis methods. Here, we review recent package developments, including a new underlying segregation into separate packages for distinct analysis, and introduce a new method for structure analysis named ensemble difference distance matrix analysis (eDDM). The eDDM approach calculates and compares atomic distance matrices across large sets of homologous atomic structures to help identify the residue wise determinants underlying specific functional processes. An eDDM workflow is detailed along with an example application to a large protein family. As a new member of the Bio3D family, the Bio3D‐eddm package supports both experimental and theoretical simulation‐generated structures, is integrated with other methods for dissecting sequence‐structure–function relationships, and can be used in a highly automated and reproducible manner. Bio3D is distributed as an integrated set of platform independent open source R packages available from: http://thegrantlab.org/bio3d/ .     

黄山松土壤可溶性有机质对氮添加的响应及其与细菌群落的关联

为探究黄山松土壤可溶性有机质(DOM)数量和质量对短期氮(N)添加的响应及其与细菌群落的关联,在福建戴云山自然保护区设置不同N添加水平(0、40和80 kg N·hm^-2·a^-1)试验,采用三维荧光与平行因子联用法,并结合高通量测序手段分别对土壤DOM和细菌群落进行分析。结果表明: 与对照相比,N添加整体降低了0～10和10～20 cm土层可溶性有机碳(DOC)含量和DOM腐殖化指数(HIX),其中,高氮(80 kg N·hm^-2·a^-1)添加下均显著降低。平行因子分析法进一步表明N添加下DOM中类腐殖质组分(C1、C2)的相对含量降低。此外,N添加减少了富营养细菌(变形菌门、酸微菌纲)的相对丰度,而增加了贫营养细菌(斯巴达杆菌纲)的相对丰度。富营养细菌的相对丰度与HIX、C1、C2呈显著正相关,与相对易分解的类富里酸组分(C3)呈显著负相关;而贫营养细菌的情况则相反。说明N添加下不同生活策略的细菌类群对DOM中难分解和易分解组分存在明显的偏好性。我们推测N沉降加剧背景下土壤微生物生活策略的转变可能有助于DOM组分的塑造。     

Redundancy or heterogeneity in the electric activity of the biceps brachii muscle? Added value of PCA-processed multi-channel EMG muscle activation estimates in a parallel-fibered muscle

Conventional bipolar EMG provides imprecise muscle activation estimates due to possibly heterogeneous activity within muscles and due to improper alignment of the electrodes with the muscle fibers. Principal component analysis (PCA), applied on multi-channel monopolar EMG yielded substantial improvements in muscle activation estimates in pennate muscles. We investigated the degree of heterogeneity in muscle activity and the contribution of PCA to muscle activation estimates in biceps brachii (BB), which has a relatively simply parallel-fibered architecture. EMG-based muscle activation estimates were assessed by comparison to elbow flexion forces in isometric, two-state isotonic contractions in eleven healthy male subjects. Monopolar EMG was collected over the entire surface of the BB with about 63 electrodes. Estimation quality of different combinations of EMG channels showed that heterogeneous activation was found mainly in medio-lateral direction, whereas adding channels in the longitudinal direction added largely redundant information. Multi-channel bipolar EMG amplitude improved muscle activation estimates by 5–14% as compared to a single bipolar. PCA-processed monopolar EMG amplitude yielded a further improvement of (12–22%). Thus multi-channel EMG, processed with PCA, substantially improves the quality of muscle activation estimates compared conventional bipolar EMG in BB.     

基于主成分分析法探讨人体测量学参数与青少年血糖关系的研究

目的:调查分析人体测量学参数包括体重指数(BMI)、腰围(WC)、臀围(HC)、腰围/臀围比(WHR)及腰围/身高比(WHtR)对南昌地区青少年空腹血糖的影响。方法:在南昌地区进行随机抽样检查731例12-18岁之间的青少年,测量身高、体重、BMI、WC、HC、WHR、WHtR和空腹血糖,用SAS软件进行统计分析。结果:男女性的五项人体测量学指标和空腹血糖间均呈显著正相关,相关系数为0.14-0.38;通过主成分分析得到四个主成分,多重回归分析结果表明联合四个主成分比单独使用其中任何一个更能解释空腹血糖的变异。结论:BMI、WC、HC、WHR、WHtR与男性和女性空腹血糖都有一定相关性,并且联合这五项测量学指标比单独使用其中任何一个能更精确预测空腹血糖。     

Objective classification of scapular kinematics in participants with movement faults of the scapula on clinical assessment

The aim of this study was to assess the potential of employing a classification tool to objectively classify participants with clinically assessed movement faults (MFs) of the scapula. Six participants with a history of shoulder pain with MFs of the scapula and 12 healthy participants with no movement faults (NMFs) performed a flexion movement control test of the scapula, while scapular kinematic data were collected. Principal component scores and discrete kinematic variables were used as input into a classifier. Five out of the six participants with a history of pain were successfully classified as having scapular MFs with an accuracy of 72%. Variables related to the upward rotation of the scapula had the most influence on the classification. The results of the study demonstrate the potential of adopting a multivariate approach in objective classification of participants with altered scapular kinematics in pathological groups.     

Developmental stability and morphological differences in Plantago major L. leaves under contrasting environmental conditions

Abstract

In the present study, an additional combination of end‐points was applied on the natural populations of the common plantain, previously estimated using morphometric assays. Here, besides measuring developmental instability (DI), by determining the level of fluctuating asymmetry (FA) and the total amount of phenotypic variability (PV), we tried to distinguish the three natural populations under contrasting environmental conditions using the morphological data. Results obtained using both FA indices were the same; higher asymmetry levels in the reference than in the polluted environments were detected for leaf width, vein distances within a leaf and lobe length. The one‐way analysis of variance results revealed that there were significant differences in PV values among populations analysed for each character. When all leaf traits were considered together, the PV median value was significantly higher in Crni Lug leaves compared with leaves from other sites. The multivariate analysis of variance results revealed the significant effect of environment on both FA₄ and PV values. The component scores of first factor (PC1) were significantly different between the Karaburma and Crni Lug populations. Besides, component scores of both PC1 and PC2 were significantly different between the Zemun and Crni Lug samples. The stepwise discriminant functional analysis results allowed us to identify a set of four variables, with a sufficient discriminating ability (75%).     

Comparison of allometric relationships and morphological differences in Tilia cordata Mill. outer leaves exposed to different environmental conditions

The study is based on four leaf parameters: leaf width (LW), lobe length (LL), leaf size (LS) and leaf shape which is calculated as LW to leaf length (LW/LL) ratio. Under different environmental conditions, LL is an isometric character, LW shows positive allometry, whereas LW/LL shows negative allometry. Regression analysis results indicated that there is no significant difference either in slopes or in regression coefficients between investigated sites. Thus, in this study, we found that allometric relationships between leaf parameters and LS are character specific and that they tended not to differ significantly between Tilia cordata Mill. outer leaves exposed to different environmental conditions. Also, there are no significant interpopulation differences for both principal component PC1 and PC2 scores. The stepwise discriminant functional analysis results allowed us to identify a set of two leaf parameters (LS and LL) with a moderate discriminating ability (59.8%). T. cordata outer leaves are significantly larger and broader in the reference area (R-leaves) than leaves from polluted (P-leaves) site. The data also indicated that there is a relatively larger petiole size in R-leaves than in P-leaves. We found that in P-leaves, LW increased faster with increasing LS than in R-leaves.     

Variability of albumin adducts of 1,4-benzoquinone,a toxic metabolite of benzene,in human volunteers

Abstract

A putative haematotoxic and leukaemogenic metabolite of benzene, 1,4-benzoquinone (1,4-BQ), reacts rapidly with macromolecules. The authors previously characterized levels of the albumin (Alb) adduct (1,4-BQ-Alb) of this reactive species in populations of workers exposed to benzene. Since high levels of 1,4-BQ-Alb were also measured in unexposed workers from those investigations, the current study was initiated to determine potential sources of 1,4-BQ in the general population. A single blood sample was collected from 191 healthy subjects from the Research Triangle area, NC, USA, to determine the baseline 1,4-BQ-Alb levels and contributing sources. The median 1,4-BQ-Alb at baseline was 550?pmol?g^?1 Alb (interquartile range 435–814?pmol?g^?1). A second blood sample was collected approximately 3 months later from a subgroup of 33 subjects to estimate the within- and between-person variation in 1,4-BQ-Alb. Standardized questionnaires were administered to collect information about demographic, dietary and lifestyle factors. Multiple linear regression models identified several significant contributors to 1,4-BQ-Alb levels, including gender, body mass index (BMI), the gender–BMI interaction, automobile refuelling, smoking status, and consumption of fruit and the artificial sweetener, aspartame. The authors predicted that these background levels of 1,4-BQ-Alb were equivalent to occupational exposures between 1 and 3 parts per million of benzene. Mixed effects linear models indicated that the random variation in adduct levels was about equally divided between and within subjects. The observations indicate that levels of 1,4-BQ-Alb cover a wide range in the general population, and they support the hypotheses that demographic, diet and lifestyle factors are contributing sources.