On the use of partial area under the ROC curve for comparison of two diagnostic tests

Evaluation of diagnostic performance is typically based on the receiver operating characteristic (ROC) curve and the area under the curve (AUC) as its summary index. The partial area under the curve (pAUC) is an alternative index focusing on the range of practical/clinical relevance. One of the problems preventing more frequent use of the pAUC is the perceived loss of efficiency in cases of noncrossing ROC curves. In this paper, we investigated statistical properties of comparisons of two correlated pAUCs. We demonstrated that outside of the classic model there are practically reasonable ROC types for which comparisons of noncrossing concave curves would be more powerful when based on a part of the curve rather than the entire curve. We argue that this phenomenon stems in part from the exclusion of noninformative parts of the ROC curves that resemble straight‐lines. We conducted extensive simulation studies in families of binormal, straight‐line, and bigamma ROC curves. We demonstrated that comparison of pAUCs is statistically more powerful than comparison of full AUCs when ROC curves are close to a “straight line”. For less flat binormal ROC curves an increase in the integration range often leads to a disproportional increase in pAUCs’ difference, thereby contributing to an increase in statistical power. Thus, efficiency of differences in pAUCs of noncrossing ROC curves depends on the shape of the curves, and for families of ROC curves that are nearly straight‐line shaped, such as bigamma ROC curves, there are multiple practical scenarios in which comparisons of pAUCs are preferable.     

Introducing the vectorial Kappa: An index to quantify congruence between vectorial mosaics

This paper introduces the vectorial Kappa (κ_v) that one can utilize to assess congruence between two vectorial mosaics. The vectorial Kappa extends for vectorial mosaics the approach of the so-called Cohen's Kappa index, commonly used to compare raster mosaics. By comparing both approaches, we aim to demonstrate how efficient and convenient a vector-based congruence may be when working on vectorial mosaics.     

Characterization of eukaryotic-like kinase activity in Escherichia coli using the gene-protein database

Abstract The gene-protein database was used to obtain the two-dimensional polyacrylamide gel coordinates of proteins phosphorylated in extracts of Escherichia coli including those phosphorylated by eukaryotic-like kinase activities. These suggest that the phosphoproteins correspond to, or co-migrate with, the product of an open reading frame at 1.3 min (Orf80), Enzyme 1 of the phosphoenolpyruvate-dependent phosphotransferase system (Ptsl), the tRNA synthetase for histidine (HisS), and proteins involved in the response to carbon starvation and quinone treatment.     

Increased abundance of native and non-native spiders with habitat fragmentation

Habitat fragmentation and invasive species often contribute to the decline of native taxa. Since the penetration of non‐native species into natural habitat may be facilitated by habitat fragmentation, it is important to examine how these two factors interact. Previous research documented that, in contrast to most other arthropod taxa, spiders increased in density and morphospecies richness with decreasing fragment area and increasing fragment age (time since insularization) in urban habitat fragments in San Diego County, California, USA. We tested whether a specific mechanism, an increase in non‐native species with fragmentation, is responsible for this pattern. We found that both native and non‐native taxa contributed to the pattern. Abundance of native spiders per pitfall trap sample increased significantly with decreasing fragment size (i.e. a negative density–area relationship) and abundance of non‐natives increased significantly with increasing fragment age. The proportion of non‐native individuals also increased significantly with age. One non‐native species, Oecobius navus, comprised the majority of non‐native individuals (82.2%) and a significant proportion of total individuals (25.1%). Richness of spider families per sample (family density) increased with fragment age due to an increase in the occurrence of non‐natives in older fragments, however, native family richness did not vary with age or area. Due to increasing dominance by non‐native and some native families, family evenness declined with decreasing fragment size and increasing fragment age. Native and non‐native abundance covaried positively arguing against strong negative interactions between the two groups. O. navus had a strong positive association with another common non‐native arthropod, the Argentine ant (Linepitheme humile), suggesting a possible direct interaction. In contrast, abundance of native spiders was negatively correlated with Argentine ant abundance. We hypothesize that fragmentation in this semiarid habitat increases productivity in smaller and older fragments enhancing the density of both native and non‐native taxa.     

Spectral composition of shade light in coastal-zone oak forests in SE Bulgaria,and relationships with leaf area index: a first overview

Major knowledge gaps exist with respect to light-quality regimes in the coastal-zone Strandzha Quercus frainetto (Q.f.) forest region adjoining the southern Bulgarian Black Sea. This paper presents preliminary results that help narrow these gaps. In conjunction with leaf area index (LAI) field campaigns we undertook measurements with an array of 7 broad-band (ca 40 nm) sensors covering the range 0.40–0.94 μm, plus 1 sensor for UVB (0.297 μm peak) and 1 for photosynthetically active radiation (PAR). Measurements focused on inside-forest shade conditions at sites 0 to ca 15 km from the Black Sea and at altitudes up to ca 120 m above sea level. Some of the sites were also studied using a high-resolution spectroradiometer. A sequential measuring strategy was necessary. This involves potentially large uncertainties, here addressed through estimations of the variability around the sinusoidal course of daylight. Light-quality regimes were found to be in general support of earlier studies of deciduous forests. Our data from the broad-band sensors and from the spectroradiometer are mutually supportive. They indicate a stronger red-shift below Q.f. canopies than below canopies in enclaves dominated by Fagus orientalis and Pinus sylvestris. Transmission in the range 0.50–0.55 μm increases beneath the three types of canopies, most pronounced in the Q.f. case. Analysis of relationships between the inside-forest to open-field irradiance ratio and LAI supports the use of Beer’s Law. We found a fairly strong relationship between the red (0.66 μm) to far-red (0.73 μm) irradiance ratios (R/FR) and LAI for the Q.f. forest. In quantitative terms, the result is new for this Q.f. region, and suggests further research to explore whether a two-sensor approach (0.66 and 0.73 μm) might offer possibilities for further low-cost mapping of the spatio-temporal patterns of R/FR and LAI in Strandzha. Such mapping would assist in further studies of the region’s forest biogeochemistry and vitality.     

Improving efficiency of breeding for higher crop yield

Summary Exclusive selection for yield raises, the harvest index of self-pollinated crops with little or no gain in total bipmass. In addition to selection for yield, it is suggested that efficient breeding for higher yield requires simultaneous selection for yield's three major, genetically controlled physiological components. The following are needed: (1) a superior rate of biomass accumulation. (2) a superior rate of actual yield accumulation in order to acquire a high harvest index, and (3) a time to harvest maturity that is neither shorter nor longer than the duration of the growing season. That duration is provided by the environment, which is the fourth major determinant of yield. Simultaneous selection is required because genetically established interconnections among the three major physiological components cause: (a) a correlation between the harvest index and days to maturity that is usually negative; (b) a correlation between the harvest index and total biomass that is often negative, and (c) a correlation between biomass and days to maturity that is usually positive. All three physiological components and the correlations among them can be quantified by yield system analysis (YSA) of yield trials. An additive main effects and multiplicative interaction (AMMI) statistical analysis can separate and quantify the genotype × environment interaction (G × E) effect on yield and on each physiological component that is caused by each genotype and by the different environment of each yield trial. The use of yield trials to select parents which have the highest rates of accumulation of both biomass and yield, in addition to selecting for the G × E that is specifically adapted to the site can accelerate advance toward the highest potential yield at each geographical site. Higher yield for many sites will raise average regional yield. Higher yield for multiple regions and continents will raise average yield on a world-wide basis. Genetic and physiological bases for lack of indirect selection for biomass from exclusive selection for yield are explained.     

唐古拉山以北地区生态资产核算

生态系统核算可以为生态文明建设提供定量性的决策依据,包括生态资产核算和生态系统服务核算两个方面,生态资产指生产和提供生态系统产品和服务的生态系统。以唐古拉山以北地区(简称唐北地区)为研究对象对其生态资产进行了核算,建立生态资产实物量及变化核算表、损益表,提出了生态资产综合指数。2015年唐北地区草地生态资产面积为21800.01 km~2,其中良级比重最高达68.46%,湿地生态资产面积为4763.01 km~2,其中优级比例最高为59.72%,野生动植物共有138种,其中重点保护动物10种。2015年唐北地区生态资产综合指数为79.77,比2000年降低了3.60%。2000—2015年,湿地、草地生态资产分别增加了164.23、2.82 km~2。2000—2015年湿地生态资产存量增加202.90 km~2,其中由湿地恢复导致面积增加最大为200.50 km~2,存量减少38.63 km~2,其中湿地退化是导致存量减少的主要原因,面积为36.23 km~2,草地存量增加了39.18 km~2,主要是由于湿地退化导致的草地扩张,存量减少36.26 km~2,主要由湿地恢复和荒漠化引起。研究中不同生态资产质量等级的核算以及生态资产综合指数的提出利于生态资产的全面核算和比较,对于建立离任责任制、生态文明建设意义重大。