Application of the β-expectation tolerance interval to method validation of the M30 and M65 ELISA cell death biomarker assays

Method validation should focus on demonstrating that an assay is fit for its intended purpose. We have applied the β-expectation tolerance interval - a statistical approach that predicts the accuracy of assay measurements in the future - to the validation of two different cell death biomarker assays, the M30 and M65 ELISAs. A meta-analysis was conducted on a total of 57 different M30 and M65 assays run over a 2 year period. All code utilised in calculations was developed using MATLAB. The optimal fit to the calibration curve for the M30 assay was shown to be a quartic curve which yielded a β-expectation tolerance interval of +20.5% and -23.6% at β=95% over a wide range of QC standards (88-810 U/L). However, such a fit required at least 7 points to avoid problems with over fitting. A linear fit to the M65 calibration curve normally produced a tolerance interval of less than ±20%, however, marked inter-batch variations were evident. Amelioration of batch to batch variations was accomplished by fitting M65 calibration data preferably to a 4-parameter logistic function or a cubic spline. The minimum number of QC replicates and different assays required to produce reliable accuracy profiles was determined. The β-expectation tolerance interval approach has resulted in further optimisation of the M30 and M65 ELISAs as biomarker assays that should translate into greater accuracy in results generated from clinical trials samples.     

Thermal tolerance and geographical range size in the Agabus brunneus group of European diving beetles (Coleoptera: Dytiscidae)

Aim Within clades, most taxa are rare, whilst few are common, a general pattern for which the causes remain poorly understood. Here we investigate the relationship between thermal performance (tolerance and acclimation ability) and the size of a species’ geographical range for an assemblage of four ecologically similar European diving beetles (the Agabus brunneus group) to examine whether thermal physiology relates to latitudinal range extent, and whether Brown’s hypothesis and the environmental variability hypothesis apply to these taxa. Location Europe. Methods In order to determine the species tolerances to either low or high temperatures we measured the lethal thermal limits of adults, previously acclimated at one of two temperatures, by means of thermal ramping experiments (± 1°C min^?1). These measures of upper and lower thermal tolerances (UTT and LTT respectively) were then used to estimate each species’ thermal tolerance range, as total thermal tolerance polygons and marginal UTT and LTT thermal polygons. Results Overall, widespread species have higher UTTs and lower LTTs than restricted ones. Mean upper lethal limits of the Agabus brunneus group (43 to 46°C), are similar to those of insects living at similar latitudes, whilst mean lower lethal limits (?6 to ?9°C) are relatively high, suggesting that this group is not particularly cold‐hardy compared with other mid‐temperate‐latitude insects. Widespread species possess the largest thermal tolerance ranges and have a relatively symmetrical tolerance to both high and low temperatures, when compared with range‐restricted relatives. Over the temperature range employed, adults did not acclimate to either high or low temperatures, contrasting with many insect groups, and suggesting that physiological plasticity has a limited role in shaping distribution. Main conclusions Absolute thermal niche appears to be a good predictor of latitudinal range, supporting both Brown’s hypothesis and the environmental variability hypothesis. Restricted‐range species may be more susceptible to the direct effect of climate change than widespread species, notwithstanding the possibility that even ‘thermally‐hardy’, widespread species may be influenced by the indirect effects of climate change such as reduction in habitat availability in Mediterranean areas.     

不同光敏色素分子的特异感光性

简要综述两种光敏色素（ＰｈｙＡ、ＰｈｙＢ） 的分子特性、感光性及作用模式等方面的研究进展。光敏色素是一种调节植物中许多光反应的色素蛋白复合体。不同光敏色素分子具有特异的感光性。ＰｈｙＡ负责‘甚低辐照反应’和远红光‘高辐照反应’; 而ＰｈｙＢ则调节‘低辐照反应’及红光‘高辐照反应’。另外, 讨论了ＰｈｙＡ和ＰｈｙＢ在光周期感受中的作用。     

Minimum required number of specimen records to develop accurate species distribution models

Species distribution models (SDMs) are widely used to predict the occurrence of species. Because SDMs generally use presence‐only data, validation of the predicted distribution and assessing model accuracy is challenging. Model performance depends on both sample size and species’ prevalence, being the fraction of the study area occupied by the species. Here, we present a novel method using simulated species to identify the minimum number of records required to generate accurate SDMs for taxa of different pre‐defined prevalence classes. We quantified model performance as a function of sample size and prevalence and found model performance to increase with increasing sample size under constant prevalence, and to decrease with increasing prevalence under constant sample size. The area under the curve (AUC) is commonly used as a measure of model performance. However, when applied to presence‐only data it is prevalence‐dependent and hence not an accurate performance index. Testing the AUC of an SDM for significant deviation from random performance provides a good alternative. We assessed the minimum number of records required to obtain good model performance for species of different prevalence classes in a virtual study area and in a real African study area. The lower limit depends on the species’ prevalence with absolute minimum sample sizes as low as 3 for narrow‐ranged and 13 for widespread species for our virtual study area which represents an ideal, balanced, orthogonal world. The lower limit of 3, however, is flawed by statistical artefacts related to modelling species with a prevalence below 0.1. In our African study area lower limits are higher, ranging from 14 for narrow‐ranged to 25 for widespread species. We advocate identifying the minimum sample size for any species distribution modelling by applying the novel method presented here, which is applicable to any taxonomic clade or group, study area or climate scenario.     

Ecological and physiological thermal niches to understand distribution of Chagas disease vectors in Latin America

In order to assess how triatomines (Hemiptera, Reduviidae), Chagas disease vectors, are distributed through Latin America, we analysed the relationship between the ecological niche and the limits of the physiological thermal niche in seven species of triatomines. We combined two methodological approaches: species distribution models, and physiological tolerances. First, we modelled the ecological niche and identified the most important abiotic factor for their distribution. Then, thermal tolerance limits were analysed by measuring maximum and minimum critical temperatures, upper lethal temperature, and ‘chill‐coma recovery time’. Finally, we used phylogenetic independent contrasts to analyse the link between limiting factors and the thermal tolerance range for the assessment of ecological hypotheses that provide a different outlook for the geo‐epidemiology of Chagas disease. In triatomines, thermo‐tolerance range increases with increasing latitude mainly due to better cold tolerances, suggesting an effect of thermal selection. In turn, physiological analyses show that species reaching southernmost areas have a higher thermo‐tolerance than those with tropical distributions, denoting that thermo‐tolerance is limiting the southern distribution. Understanding the latitudinal range along its physiological limits of disease vectors may prove useful to test ecological hypotheses and improve strategies and efficiency of vector control at the local and regional levels.     

Effects of population density on alienicolae of Aphis fabae Scop.

A technique for rearing aphids in dense populations is described. Apterae were reared in high (‘C’) and low (‘U’) population densities and the proportions of alatae among their progenies were compared. Proportions of alatae were larger among progenies of ‘C’ apterae, and the proportions also increased as the density of the population in which the progenies were reared increased. Progenies of alatae never became alatae.     

Carbohydrates of the antarctic brown seaweed Ascoseira mirabilis

Mannitol, sucrose and four monosaccharides were obtained from an ethanolic extract of Ascoseira mirabilis. Sequential extraction with aqueous calcium chloride, dilute acid and dilute alkali gave mixtures of laminaran, ‘fucan’ and alginic acid. Laminarans fractionated from the extracts contained different proportions of uniformly (1 → 3) and (1 → 6) linked chains of β-D-glucose residues. The ‘fucan’ contained varying proportions of fucose, galactose and glucuronic acid, small amounts of xylose, mannose, glucose, half ester sulphate and protein. Extraction of the weed under mild alkaline conditions gave a yield of 13.4% of low molecular weight calcium alginate with a mannuronate to guluronate ratio of 30:70 and only a small proportion of sequences of alternating residues. Selective extraction and fractionation gave alginate fractions rich (> 80%) in mannuronate or guluronate.     

A method for adjusting allele frequencies in the case of microsatellite allele drop‐out

A new method is proposed to adjust allele frequencies when allelic drop‐out is common. This method assumes Hardy–Weinberg equilibrium (HWE), and treats the problematic alleles as a one‐locus two‐allele system with dominance. By assuming that the homozygote frequency of the ‘recessive’ allele is measured correctly, we can back calculate the allele frequency of the ‘dominant’ allele, and adjust the heterozygote frequency accordingly. The drawback is that multilocus genotypes cannot be constructed and tests that use deviations from Hardy–Weinberg such as tests for bottlenecks become impossible. An example is given where a large homozygote excess (F_IS = 0.44) is adjusted to a reasonable level (F_IS = 0.046). The effect of scoring error was set in relation to sampling error and while F_IS values can be seriously biased, F_ST values are not necessarily so, if scoring error and sample size are both low. As sample size increases, the effect of scoring error increases.     

Effects of iodine deficiency on mental and psychomotor abilities

The allometric relationships between canine base area, first molar and summed molar crown area, and the glabella–opisthocranion distance, and the direct allometric relationships between canine and molar size have been established in five primate taxa. Separate sex and combined sex ‘intraspecific’, and ‘interspecific’ regression and ‘best fit’ allometry coefficients were computed. This analysis showed that for any increase in glabella–opisthocranion length, the rate of increase in canine size exceeds the rate of increase in molar area, and ‘best fit’ solutions indicate that canine base area is positively allometric when related directly to molar crown area. These results were compared with data available for the ‘gracile’ australopithecine, A. africanus, and two ‘robust’ australopithecine taxa, A. boisei and A. robustus. The differences in canine and molar size which occur between the ‘gracile’ taxon and the two ‘robust’ taxa do not correspond to any of the trends in the comparative allometric models. Data on glabella–opisthocranion length for the fossils, meagre though they are, show that while the proportional increase in molar crown area between the taxa corresponds to comparative allometry models, the reduced canine size in the ‘robust’ taxa is against comparative allometric trends. These results indicate that, at least in terms of canine/molar proportions, the differences between the ‘gracile’ and ‘robust’ australopithecines are not merely allometric and may indicate significant dietary or behavioural differences.     

Low levels of extraneous agents in vaccine starting materials

There are different ways to define the concept of ‘low levels’ of extraneous agents in vaccines and vaccine starting materials, based on the amount of extraneous agents as such, the sensitivity of the detection method and the probability approach linked to the sampling method. None of these approaches, however, is entirely satisfactory – a general definition of a ‘low level’ cannot be provided. Since the main point is the safety of medicinal products, the risk analysis approach to ‘low level’ contaminations can be considered as a way to overcome the abovementioned deadlock. But as too many variables impact the risk analysis, it cannot be properly performed either. In practice, seeds are tested to show freedom from extraneous agents, the other raw materials are inactivated through a validated method. However, there are technical and regulatory limits in both cases, and neither testing nor inactivation entirely guarantees freedom from extraneous agents. Despite this unsatisfactory situation, it should be acknowledged that no truly significant disease outbreak linked to an extraneous agent has been identified until today. Regulatory actions are mainly undertaken when a sanitary problem occurs. In the end, companies remain responsible for their products.     

山西不同生态型大豆品种苗期耐低温性综合评价

为探明山西不同生态型大豆(Glycine max)品种对苗期低温胁迫的应答表现, 寻求大豆苗期耐低温性综合评价指标和评价方法, 选取了山西普遍种植的‘晋大53’、‘晋大70’和‘晋豆24’ 3个不同生态型大豆品种, 在苗期将材料分别置于14、17和20 ℃人工气候箱中, 保持昼夜恒温, 进行低温胁迫处理。分别测定了各品种光合与产量性状值, 用基因型主效应及其与环境互作(GGE)双标图分析各性状对品种的效应及性状间的相关性, 应用隶属函数法综合评价各品种的苗期耐低温性。结果显示: 低温胁迫下不同生态型大豆品种苗期延长1-12天; 苗期光合性状值均下降, 其中, 叶片气孔导度(G_s)和蒸腾速率(T_r)下降最明显; 产量性状值均呈下降趋势, 单株生物量和单株荚数下降最明显; 各项性状在不同品种中对低温的应答效应不同, 且性状间存在明显的相关性, 可作为耐低温性的评价指标。品种‘晋大70’的耐低温性最佳。     

Global species–energy relationship in forest plots: role of abundance,temperature and species climatic tolerances

Aim To evaluate the strength of evidence for hypotheses explaining the relationship between climate and species richness in forest plots. We focused on the effect of energy availability which has been hypothesized to influence species richness: (1) via the effect of productivity on the total number of individuals (the more individuals hypothesis, MIH); (2) through the effect of temperature on metabolic rate (metabolic theory of biodiversity, MTB); or (3) by imposing climatic limits on species distributions. Location Global. Methods We utilized a unique ‘Gentry‐style’ 370 forest plots data set comprising tree counts and individual stem measurements, covering tropical and temperate forests across all six forested continents. We analysed variation in plot species richness and species richness controlled for the number of individuals by using rarefaction. Ordinary least squares (OLS) regression and spatial regressions were used to explore the relative performance of different sets of environmental variables. Results Species richness patterns do not differ whether we use raw number of species or number of species controlled for number of individuals, indicating that number of individuals is not the proximate driver of species richness. Productivity‐related variables (actual evapotranspiration, net primary productivity, normalized difference vegetation index) perform relatively poorly as correlates of tree species richness. The best predictors of species richness consistently include the minimum temperature and precipitation values together with the annual means of these variables. Main conclusion Across the world's forests there is no evidence to support the MIH, and a very limited evidence for a prominent role of productivity as a driver of species richness patterns. The role of temperature is much more important, although this effect is more complex than originally assumed by the MTB. Variation in forest plot diversity appears to be mostly affected by variation in the minimum climatic values. This is consistent with the ‘climatic tolerance hypothesis’ that climatic extremes have acted as a strong constraint on species distribution and diversity.     

Genetic analyses using GGE model and a mixed linear model approach,and stability analyses using AMMI bi-plot for late-maturity alpha-amylase activity in bread wheat genotypes

Low falling number and discounting grain when it is downgraded in class are the consequences of excessive late-maturity α-amylase activity (LMAA) in bread wheat (Triticum aestivum L.). Grain expressing high LMAA produces poorer quality bread products. To effectively breed for low LMAA, it is necessary to understand what genes control it and how they are expressed, particularly when genotypes are grown in different environments. In this study, an International Collection (IC) of 18 spring wheat genotypes and another set of 15 spring wheat cultivars adapted to South Dakota (SD), USA were assessed to characterize the genetic component of LMAA over 5 and 13 environments, respectively. The data were analysed using a GGE model with a mixed linear model approach and stability analysis was presented using an AMMI bi-plot on R software. All estimated variance components and their proportions to the total phenotypic variance were highly significant for both sets of genotypes, which were validated by the AMMI model analysis. Broad-sense heritability for LMAA was higher in SD adapted cultivars (53%) compared to that in IC (49%). Significant genetic effects and stability analyses showed some genotypes, e.g. ‘Lancer’, ‘Chester’ and ‘LoSprout’ from IC, and ‘Alsen’, ‘Traverse’ and ‘Forefront’ from SD cultivars could be used as parents to develop new cultivars expressing low levels of LMAA. Stability analysis using an AMMI bi-plot revealed that ‘Chester’, ‘Lancer’ and ‘Advance’ were the most stable across environments, while in contrast, ‘Kinsman’, ‘Lerma52’ and ‘Traverse’ exhibited the lowest stability for LMAA across environments.     

Trubs,but no trianas: filled and empty regions of angiosperm stem length‐diameter‐mechanics space

Discrete plant habit categories such as ‘tree’, ‘shrub’, and ‘liana’ belie continuous variation in nature. To study the evolution of this continuous variation, we gathered data on stem length, diameter and tissue mechanical stiffness across a highly morphologically diverse highland xerophytic scrub on a lava flow in central Mexico. With stem allometric and mechanical data from 1216 segments from 50 species, we examined relationships between stem length–diameter proportions and tissue mechanical stiffness using linear mixed‐effects models. Rather than a series of discrete clouds in stem length–diameter–tissue stiffness space, corresponding to traditional habit categories, the plants of this xerophytic scrub formed a single continuous one. Within this cloud, self‐supporting plants had stems that became predictably longer and tissues that became stiffer for a given diameter increase, and there was no paucity of intermediates between trees and shrubs (‘trubs’). Non self‐supporting plants had a steeper stem length–diameter slope and their tissues did not increase in stiffness with stem size. The area between self‐ and non self‐supporting plants was sparsely occupied as stem size increased. We predict that this ‘empty’ space between lianas and trees is developmentally accessible but of low fitness, meaning that there should be few ‘trianas’ in nature. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 361–373.     

Determination of the precision of spike timing in the visual cortex of anaesthetised cats

Neuronal cortical spike trains contain precisely replicating patterns whose presence cannot be accounted for by chance production. A comparison of the number of triplets of spikes present two times with the number of doublets replicated three times in the same window duration gives a frequency-insensitive measure of this type of fine temporal organisation. By varying the tolerance with which such precisely replicating patterns are detected, one can evaluate the accuracy of spike timing in spike trains. In the sample of data here analysed, it was found that replicating patterns were best seen in the precision range 0.4–1.4 ms (a result evidently at variance with a simple ‘integrate and fire’ model of neurons). Surprisingly, the fine temporal structure of spike trains thus evidenced was stronger at relatively low firing rate discharges and was present in both the ‘spontaneous’ and ‘evoked’ responses.     

Scaling of long bones in ruminants with respect to the scapula

The significance of the scapula for locomotion is becoming more and more established. Studies of locomotion in small and medium‐sized mammals show a considerable amplitude of the scapula and a large contribution to step length. Taking this into account, long bone studies of forelimb movement restricted to the ‘arm’ miss one important segment. A regression model (reduced major axis) was used for analysis of a sample of 77 species of ruminants. This sample was divided according to (1) phylogenetic relationships and (2) habitat. The proximal elements of the limbs, scapula and humerus in the anterior extremity, femur in the hindlimb, show a similar scaling in the different analyses. The changes to limb proportions in the different subsamples are caused by the variability of the distal segments. The anterior extremity scales with a higher coefficient than the hindlimb in all analyses. Concepts like elastic or geometric similarity are inadequate for long bone scaling when the full range of body size in the sample is used. Taking all analyses into account, the differences in limb proportions are due more to phylogenetic relationships than to habitat.     

A framework for controlling false discovery rates and minimizing the amount of genotyping in the search for disease mutations

OBJECTIVES: To develop a method for designing studies to find disease mutations that can achieve a set of goals with respect to proportions of false and true discoveries with the minimum amount of genotyping. METHODS: Derivation of an analytical framework supplemented with simulation techniques. The approach is illustrated for a fine mapping study and a whole-genome linkage disequilibrium scan. RESULTS: The use of multiple stages where earlier stages are characterized by very high false discovery rates (FDR) followed by an abrupt change to the required FDR in the final stage results in a 50-75% reduction in genotyping. The proportion of true discoveries is a much more important determinant of the genotyping burden than the FDR. Neither sample size nor controlling the false discoveries will present major problems in whole-genome LD scans but the amount of genotyping will be extremely large even if the study is completely designed to minimize genotyping. CONCLUSIONS: The proposed statistical framework presents a simple and flexible approach to determine the design parameters (e.g. sample size, p values at which tests need to be performed at each stage) that minimize the genotyping burden given a set of goals for the percentage of true and false discoveries.     

黄瓜苗期耐低温性及相关生理指标遗传分析

选取耐低温弱光性不同的6份黄瓜材料9504、9507、9506、9517、9511、9514按Griffing方法Ⅱ配制完全双列杂交组合,对亲本及F1进行低温弱光处理(昼/夜温度12℃/8℃,每天光照7.5 h,光照强度30μmol·m-2·s-1)14 d后调查幼苗耐低温性、保护酶(POD和SOD)活性、渗透调节物质(可溶性蛋白质和脯氨酸)含量等生理指标,分析其遗传规律.结果显示,黄瓜亲本9504、9507及其组合F1幼苗的耐寒性较强,保护酶活性和脯氨酸含量较高,黄瓜幼苗耐寒性与其保护酶活性和渗透调节物质含量关系密切;黄瓜幼苗耐低温性、POD和SOD活性、可溶性蛋白质和脯氨酸含量所有性状的遗传符合加性-显性模型,它们的广义遗传力分别达82.133%、93.351%、97.368%、59.230%、93.460%,狭义遗传力达73.170%、53.191%、26.316%、58.587%、45.963%.研究表明,黄瓜耐低温性、POD和SOD活性、脯氨酸含量适于早代选择;幼苗可溶性蛋白质含量受生长环境的影响较大,可晚代选择.     

THE POWER OF THE " A" -" NOT A" METHOD

The " A" - " Not A" method is a rating method with two categories. It is often treated as a discrimination method. Unlike forced choice procedures, the Thurstonian model for this method involves a choice criterion. In statistical tests, it is treated as a comparison of two proportions. In this paper, the power for hypothesis tests involving the monadic and replicated monadic " A" - " Not A" method is discussed. The power functions and the sample sizes needed for 80% power are given based on Thurstone's δ. Designs with equal and unequal allocations for A and A (Not A) samples are considered. The power of the method is also compared with that of four forced choice methods under the assumption that the perceptual variance is identical among methods. The comparison shows that, in general, the power for the five methods ranks from high to low: the 3-AFC, 2-AFC, " A" - " Not A", triangular and duo-trio. The comparison also shows that, based on the same number of panelists and/or the same sample size for the A and A⁻ samples for the methods, if the panelists are not too discrepant and the choice criterion in the " A" - " Not A" method is not too strict or too lax, the power of the " A" - " Not A" method is very close to that of the 2-AFC method.     

Rethinking patch size and isolation effects: the habitat amount hypothesis

I challenge (1) the assumption that habitat patches are natural units of measurement for species richness, and (2) the assumption of distinct effects of habitat patch size and isolation on species richness. I propose a simpler view of the relationship between habitat distribution and species richness, the ‘habitat amount hypothesis’, and I suggest ways of testing it. The habitat amount hypothesis posits that, for habitat patches in a matrix of non‐habitat, the patch size effect and the patch isolation effect are driven mainly by a single underlying process, the sample area effect. The hypothesis predicts that species richness in equal‐sized sample sites should increase with the total amount of habitat in the ‘local landscape’ of the sample site, where the local landscape is the area within an appropriate distance of the sample site. It also predicts that species richness in a sample site is independent of the area of the particular patch in which the sample site is located (its ‘local patch’), except insofar as the area of that patch contributes to the amount of habitat in the local landscape of the sample site. The habitat amount hypothesis replaces two predictor variables, patch size and isolation, with a single predictor variable, habitat amount, when species richness is analysed for equal‐sized sample sites rather than for unequal‐sized habitat patches. Studies to test the hypothesis should ensure that ‘habitat’ is correctly defined, and the spatial extent of the local landscape is appropriate, for the species group under consideration. If supported, the habitat amount hypothesis would mean that to predict the relationship between habitat distribution and species richness: (1) distinguishing between patch‐scale and landscape‐scale habitat effects is unnecessary; (2) distinguishing between patch size effects and patch isolation effects is unnecessary; (3) considering habitat configuration independent of habitat amount is unnecessary; and (4) delineating discrete habitat patches is unnecessary.