Comparison of complex modeling strategies for prediction of a binary outcome based on a few,highly correlated predictors

Motivated by a clinical prediction problem, a simulation study was performed to compare different approaches for building risk prediction models. Robust prediction models for hospital survival in patients with acute heart failure were to be derived from three highly correlated blood parameters measured up to four times, with predictive ability having explicit priority over interpretability. Methods that relied only on the original predictors were compared with methods using an expanded predictor space including transformations and interactions. Predictors were simulated as transformations and combinations of multivariate normal variables which were fitted to the partly skewed and bimodally distributed original data in such a way that the simulated data mimicked the original covariate structure. Different penalized versions of logistic regression as well as random forests and generalized additive models were investigated using classical logistic regression as a benchmark. Their performance was assessed based on measures of predictive accuracy, model discrimination, and model calibration. Three different scenarios using different subsets of the original data with different numbers of observations and events per variable were investigated. In the investigated setting, where a risk prediction model should be based on a small set of highly correlated and interconnected predictors, Elastic Net and also Ridge logistic regression showed good performance compared to their competitors, while other methods did not lead to substantial improvements or even performed worse than standard logistic regression. Our work demonstrates how simulation studies that mimic relevant features of a specific data set can support the choice of a good modeling strategy.     

Alternative pathways of liana communities in the forests of northwestern Argentina

Liana dynamics in secondary and mature forests are well known in tropical areas dominated by native tree species. Outside the tropics and in secondary forests invaded by exotic species, knowledge is scarce. In this study, we compare liana communities between secondary and mature forests dominated by native species in a subtropical montane area of Sierra de San Javier, Tucuman, Argentina. Additionally, we evaluate changes of liana communities in secondary forests with increasing densities of Ligustrum lucidum and Morus alba, two of the most invasive exotic trees of the area. We surveyed liana species richness and density in three 30-year secondary patches, four 60-year secondary patches, and four mature patches dominated by native tree species, to analyze changes in liana communities with forest age. Within each patch, we sampled 10–25 20 × 20 m quadrats. Additionally, we surveyed liana density and species richness in secondary forest patches with different densities of L. lucidum and M. alba. In native-dominated forests, liana species richness increased and showed a tendency of increasing basal area from 30-year secondary forests to mature forests. Liana density was highly variable, and most of the species were shared between native-dominated secondary and mature forests. Liana density and species richness decreased with L. lucidum density, whereas in secondary forests highly dominated by M. alba, lianas increased in density. Overall, lianas followed different pathways influenced by native forest succession and exotic tree invasions.     

Continental estimates of forest cover and forest cover changes in the dry ecosystems of Africa between 1990 and 2000

Aim

This study provides regional estimates of forest cover in dry African ecoregions and the changes in forest cover that occurred there between 1990 and 2000, using a systematic sample of medium‐resolution satellite imagery which was processed consistently across the continent.

Location

The study area corresponds to the dry forests and woodlands of Africa between the humid forests and the semi‐arid regions. This area covers the Sudanian and Zambezian ecoregions.

Methods

A systematic sample of 1600 Landsat satellite imagery subsets, each 20 km × 20 km in size, were analysed for two reference years: 1990 and 2000. At each sample site and for both years, dense tree cover, open tree cover, other wooded land and other vegetation cover were identified from the analysis of satellite imagery, which comprised multidate segmentation and automatic classification steps followed by visual control by national forestry experts.

Results

Land cover and land‐cover changes were estimated at continental and ecoregion scales and compared with existing pan‐continental, regional and local studies. The overall accuracy of our land‐cover maps was estimated at 87%. Between 1990 and 2000, 3.3 million hectares (Mha) of dense tree cover, 5.8 Mha of open tree cover and 8.9 Mha of other wooded land were lost, with a further 3.9 Mha degraded from dense to open tree cover. These results are substantially lower than the 34 Mha of forest loss reported in the FAO's 2010 Global Forest Resources Assessment for the same period and area.

Main conclusions

Our method generates the first consistent and robust estimates of forest cover and change in dry Africa with known statistical precision at continental and ecoregion scales. These results reduce the uncertainty regarding vegetation cover and its dynamics in these previously poorly studied ecosystems and provide crucial information for both science and environmental policies.     

Exploring the relationship between dental wear and status in late medieval subadults from England

Dental wear patterns were recorded on 458 deciduous molar teeth, of 142 subadults from late medieval (AD 1086–1539) England, to explore the relationship between dental wear and burial status of children. A new ordinal method for scoring dental wear stages on the deciduous molar teeth was devised. It was postulated that if a discernible relationship between dental wear stage and burial location could be seen then this could reflect a difference in diet between those receiving higher or lower status burial. The dental wear stages recorded were statistically similar for the dentitions of subadults from different cemeteries, as well as from different burial locations, indicating a comparable diet for the children studied. Am J Phys Anthropol, 2013. © 2013 Wiley Periodicals, Inc.     

铬对中国林蛙蝌蚪生长发育的毒性效应

为评价水域环境中铬元素对两栖动物幼体的急性毒性,将中国林蛙(Rana chensinensis)28～29期蝌蚪分别暴露于30～35 mg·L-1Cr(Ⅲ)6个不同浓度和10 ～ 45mg·L-1Cr(Ⅵ)6个不同浓度的水体中,分别在24、48、72和96 h统计蝌蚪的死亡率及半致死浓度(LC50).结果表明:暴露24、48、72和96 h,Cr(Ⅲ)对蝌蚪的LC50分别为34.09±1.06、33.47±0.65、32.58±0.11和(32.05±0.20) mg·L-1,安全浓度(SC)为(3.21±0.02)mg·L-1;Cr(Ⅵ)对蝌蚪的LC50分别为91.97±5.32、51.19±4.62、35.79±1.40和(28.81±1.87) mg·L-1,安全浓度(SC)为(2.88±0.19) rng·L-1.观察表明:Cr(Ⅲ)的急性毒性是通过与蝌蚪皮肤表面的分泌物结合后粘附在鳃部,导致呼吸障碍致死;而Cr(Ⅵ)的强氧化性可导致蝌蚪的表皮溃变,鳃部萎缩致死;另外,将28～29期蝌蚪暴露于安全浓度(SC)以下的含铬水体进行慢性实验,通过检测蝌蚪的体长、体重和完全变态时间显示,低浓度的Cr(Ⅲ)和Cr(Ⅵ)对蝌蚪的生长发育仍具有一定的抑制作用,并可导致畸型发生,其作用强度呈现剂量效应,但时间累积效应不规律.     

川西亚高山不同海拔森林土壤活性氮库及净氮矿化的季节动态

研究了川西理县毕棚沟不同海拔梯度(3600 m、3300 m和3000 m)森林群落土壤活性氮库及土壤净氮矿化速率的季节动态.结果表明: 研究区森林土壤活性氮库(铵态氮、硝态氮、微生物生物量氮和可溶性有机氮)及净氮矿化速率存在明显的季节变化,但不同形态土壤活性氮库的季节动态有一定差异.4个采样时期(非生长季与生长季初期、中期及末期)各海拔土壤硝态氮浓度(8.38～89.60 mg·kg^-1)均显著高于铵态氮浓度(0.44～8.43 mg·kg^-1).生长季初期各海拔梯度的土壤净氮矿化速率均表现为负值(-0.77～-0.56 mg·kg^-1·d^-1),而非生长季、生长季中期和末期均为正值.除硝态氮外,不同海拔的土壤铵态氮、微生物生物量氮和可溶性有机氮浓度的差异极显著,海拔对它们的影响与季节变化有关.该区土壤净氮矿化以硝化为主,且氮矿化过程不受海拔梯度的影响.冬季土壤净氮矿化明显(0.42～099 mg·kg^-1·d^-1),早春高的土壤无机氮可能为植物生长提供基础养分,也可能通过淋溶方式从系统中丢失.     

Neogene origins and implied warmth tolerance of Amazon tree species

Tropical rain forest has been a persistent feature in South America for at least 55 million years. The future of the contemporary Amazon forest is uncertain, however, as the region is entering conditions with no past analogue, combining rapidly increasing air temperatures, high atmospheric carbon dioxide concentrations, possible extreme droughts, and extensive removal and modification by humans. Given the long‐term Cenozoic cooling trend, it is unknown whether Amazon forests can tolerate air temperature increases, with suggestions that lowland forests lack warm‐adapted taxa, leading to inevitable species losses. In response to this uncertainty, we posit a simple hypothesis: the older the age of a species prior to the Pleistocene, the warmer the climate it has previously survived, with Pliocene (2.6–5 Ma) and late‐Miocene (8–10 Ma) air temperature across Amazonia being similar to 2100 temperature projections under low and high carbon emission scenarios, respectively. Using comparative phylogeographic analyses, we show that 9 of 12 widespread Amazon tree species have Pliocene or earlier lineages (>2.6 Ma), with seven dating from the Miocene (>5.6 Ma) and three >8 Ma. The remarkably old age of these species suggest that Amazon forests passed through warmth similar to 2100 levels and that, in the absence of other major environmental changes, near‐term high temperature‐induced mass species extinction is unlikely.     

Fungal disease incidence along tree diversity gradients depends on latitude in European forests

European forests host a diversity of tree species that are increasingly threatened by fungal pathogens, which may have cascading consequences for forest ecosystems and their functioning. Previous experimental studies suggest that foliar and root pathogen abundance and disease severity decrease with increasing tree species diversity, but evidences from natural forests are rare. Here, we tested whether foliar fungal disease incidence was negatively affected by tree species diversity in different forest types across Europe. We measured the foliar fungal disease incidence on 16 different tree species in 209 plots in six European countries, representing a forest‐type gradient from the Mediterranean to boreal forests. Forest plots of single species (monoculture plots) and those with different combinations of two to five tree species (mixed species plots) were compared. Specifically, we analyzed the influence of tree species richness, functional type (conifer vs. broadleaved) and phylogenetic diversity on overall fungal disease incidence. The effect of tree species richness on disease incidence varied with latitude and functional type. Disease incidence tended to increase with tree diversity, in particular in northern latitudes. Disease incidence decreased with tree species richness in conifers, but not in broadleaved trees. However, for specific damage symptoms, no tree species richness effects were observed. Although the patterns were weak, susceptibility of forests to disease appears to depend on the forest site and tree type.     

Does stream flow structure woody riparian vegetation in subtropical catchments?

The primary objective of this study was to test the relevance of hydrological classification and class differences to the characteristics of woody riparian vegetation in a subtropical landscape in Queensland, Australia. We followed classification procedures of the environmental flow framework ELOHA – Ecological Limits of Hydrologic Alteration. Riparian surveys at 44 sites distributed across five flow classes recorded 191 woody riparian species and 15, 500 individuals. There were differences among flow classes for riparian species richness, total abundance, and abundance of regenerating native trees and shrubs. There were also significant class differences in the occurrence of three common tree species, and 21 indicator species (mostly native taxa) further distinguished the vegetation characteristics of each flow class. We investigated the influence of key drivers of riparian vegetation structure (climate, depth to water table, stream‐specific power, substrate type, degree of hydrologic alteration, and land use) on riparian vegetation. Patterns were explained largely by climate, particularly annual rainfall and temperature. Strong covarying drivers (hydrology and climate) prevented us from isolating the independent influences of these drivers on riparian assemblage structure. The prevalence of species considered typically rheophytic in some flow classes implies a more substantial role for flow in these classes but needs further testing. No relationships were found between land use and riparian vegetation composition and structure. This study demonstrates the relevance of flow classification to the structure of riparian vegetation in a subtropical landscape, and the influence of covarying drivers on riparian patterns. Management of environmental flows to influence riparian vegetation assemblages would likely have most potential in sites dominated by rheophytic species where hydrological influences override other controls. In contrast, where vegetation assemblages are dominated by a diverse array of typical rainforest species, and other factors including broad‐scale climatic gradients and topographic variables have greater influence than hydrology, riparian vegetation is likely to be less responsive to environmental flow management.     

Tree Height Reduction After Selective Logging in a Tropical Forest

By harvesting scattered large trees, selective logging increases light availability and thereby stimulates growth and crown expansion at early‐life stage among remnant trees. We assessed the effects of logging on total and merchantable bole (i.e., lowest branch at crown base) heights on 952 tropical canopy trees in French Guiana. We observed reductions in both total (mean, ?2.3 m) and bole (mean, ?2.0 m) heights more than a decade after selective logging. Depending on local logging intensity, height reductions resulted in 2–13 percent decreases in aboveground tree biomass and 3–17 percent decreases in bole volume. These results highlight the adverse effects of logging at both tree and stand levels. This decrease in height is a further threat to future provision of key environmental services, such as timber production and carbon sequestration.