The ecodist Package for Dissimilarity-based Analysis of Ecological Data

Ecologists are concerned with the relationships between species composition and environmental framework incorporating space explicitly is an extremely flexible tool for answering these questions. The R package ecodist brings together methods for working with dissimilarities, including some not available in other R packages. We present some of the features of ecodist, particularly simple and partial Mantel tests, and make recommendations for their effective use. Although the partial Mantel test is often used to account for the effects of space, the assumption of linearity greatly reduces its effectiveness for complex spatial patterns. We introduce a modification of the Mantel correlogram designed to overcome this restriction and allow consideration of complex nonlinear structures. This extension of the method allows the use of partial multivariate correlograms and tests of relationship between variables at different spatial scales. Some of the possibilities are demonstrated using both artificial data and data from an ongoing study of plant community composition in grazinglands of the northeastern United States.

The ecodist Package for Dissimilarity-based Analysis of Ecological Data

Ecologists are concerned with the relationships between species composition and environmental framework incorporating space explicitly is an extremely flexible tool for answering these questions. The R package ecodist brings together methods for working with dissimilarities, including some not available in other R packages. We present some of the features of ecodist, particularly simple and partial Mantel tests, and make recommendations for their effective use. Although the partial Mantel test is often used to account for the effects of space, the assumption of linearity greatly reduces its effectiveness for complex spatial patterns. We introduce a modification of the Mantel correlogram designed to overcome this restriction and allow consideration of complex nonlinear structures. This extension of the method allows the use of partial multivariate correlograms and tests of relationship between variables at different spatial scales. Some of the possibilities are demonstrated using both artificial data and data from an ongoing study of plant community composition in grazinglands of the northeastern United States

Forest pattern, fire, and climatic change in the Sierra Nevada

In the Sierra Nevada, distributions of forest tree species are largely controlled by the soil-moisture balance. Changes in temperature or precipitation as a result of increased greenhouse gas concentrations could lead to changes in species distributions. In addition, climatic change could increase the frequency and severity of wildfires. We used a forest gap model developed for Sierra Nevada forests to investigate the potential sensitivity of these forests to climatic change, including a changing fire regime. Fuel moisture influences the fire regime and couples fire to climate. Fires are also affected by fuel loads, which accumulate according to forest structure and composition. These model features were used to investigate the complex interactions between climate, fire, and forest dynamics. Eight hypothetical climate-change scenarios were simulated, including two general circulation model (GCM) predictions of a 2 3 CO2 world. The response of forest structure, species composition, and the fire regime to these changes in the climate were examined at four sites across an elevation gradient. Impacts on woody biomass and species composition as a result of climatic change were site specific and depended on the environmental constraints of a site and the environmental tolerances of the tree species simulated. Climatic change altered the fire regime both directly and indirectly. Fire frequency responded directly to climate’s influence on fuel moisture, whereas fire extent was affected by changes that occurred in either woody biomass or species composition. The influence of species composition on fuel-bed bulk density was particularly important. Future fires in the Sierra Nevada could be both more frequent and of greater spatial extent if GCM predictions prove true.Keywords: Spatial pattern, Fire regime, Connectivity, Forest gap model, Climatic chang

Forest pattern, fire, and climatic change in the Sierra Nevada

In the Sierra Nevada, distributions of forest tree species are largely controlled by the soil-moisture balance. Changes in temperature or precipitation as a result of increased greenhouse gas concentrations could lead to changes in species distributions. In addition, climatic change could increase the frequency and severity of wildfires. We used a forest gap model developed for Sierra Nevada forests to investigate the potential sensitivity of these forests to climatic change, including a changing fire regime. Fuel moisture influences the fire regime and couples fire to climate. Fires are also affected by fuel loads, which accumulate according to forest structure and composition. These model features were used to investigate the complex interactions between climate, fire, and forest dynamics. Eight hypothetical climate-change scenarios were simulated, including two general circulation model (GCM) predictions of a 2 × CO₂ world. The response of forest structure, species composition, and the fire regime to these changes in the climate were examined at four sites across an elevation gradient. Impacts on woody biomass and species composition as a result of climatic change were site specific and depended on the environmental constraints of a site and the environmental tolerances of the tree species simulated. Climatic change altered the fire regime both directly and indirectly. Fire frequency responded directly to climate's influence on fuel moisture, whereas fire extent was affected by changes that occurred in either woody biomass or species composition. The influence of species composition on fuel-bed bulk density was particularly important. Future fires in the Sierra Nevada could be both more frequent and of greater spatial extent if GCM predictions prove true.Keywords: forest gap model, fire regime, spatial pattern, climatic change, connectivit

An assessment of high carbon stock and high conservation value approaches to sustainable oil palm cultivation in Gabon

Industrial-scale oil palm cultivation is rapidly expanding in Gabon, where it has the potential to drive economic growth, but also threatens forest, biodiversity and carbon resources. The Gabonese government is promoting an ambitious agricultural expansion strategy, while simultaneously committing to minimize negative environmental impacts of oil palm agriculture. This study estimates the extent and location of suitable land for oil palm cultivation in Gabon, based on an analysis of recent trends in plantation permitting. We use the resulting suitability map to evaluate two proposed approaches to minimizing negative environmental impacts: a High Carbon Stock (HCS) approach, which emphasizes forest protection and climate change mitigation, and a High Conservation Value (HCV) approach, which focuses on safeguarding biodiversity and ecosystems. We quantify the forest area, carbon stock, and biodiversity resources protected under each approach, using newly developed maps of priority species distributions and forest biomass for Gabon. We find 2.7–3.9 Mha of suitable or moderately suitable land that avoid HCS areas, 4.4 million hectares (Mha) that avoid HCV areas, and 1.2–1.7 Mha that avoid both. This suggests that Gabon's oil palm production target could likely be met without compromising important ecosystem services, if appropriate safeguards are put in place. Our analysis improves understanding of suitability for oil palm in Gabon, determines how conservation strategies align with national targets for oil palm production, and informs national land use planning

Signaling via interleukin-4, receptor alpha chain is required for successful vaccination against schistosomiasis in BALB/c mice

Radiation-attenuated (RA) schistosome larvae are potent stimulators of innate immune responses at the skin site of exposure (pinna) that are likely to be important factors in the development of Th1-mediated protective immunity. In addition to causing an influx of neutrophils, macrophages, and dendritic cells (DCs) into the dermis, RA larvae induced a cascade of chemokine and cytokine secretion following in vitro culture of pinna biopsy samples. While macrophage inflammatory protein 1 and interleukin-1 (IL-1) were produced transiently within the first few days, the Th1-promoting cytokines IL-12 and IL-18 were secreted at high levels until at least day 14. Assay of C3H/HeJ mice confirmed that IL-12 secretion was not due to lipopolysaccharide contaminants binding Toll-like receptor 4. Significantly, IL-12 p40 secretion was sustained in pinnae from vaccinated mice but not in those from nonprotected infected mice. In contrast, IL-10 was produced from both vaccinated and infected mice. This cytokine regulates IL-12-associated dermal inflammation, since in vaccinated IL-10/ mice, pinna thickness was greatly increased concurrent with elevated levels of IL-12 p40. A significant number of IL-12 p40 cells were detected as emigrants from in vitro-cultured pinnae, and most were within a population of rare large granular cells that were Ia, consistent with their being antigen-presenting cells. Labeling of IL-12 cells for CD11c, CD205, CD8, CD11b, and F4/80 indicated that the majority were myeloid DCs, although a proportion were CD11c F4/80, suggesting that macrophages were an additional source of IL-12 in the skin

Causes and Implications of the Correlation between Forest productivity and Tree Mortality Rates

At global and regional scales, tree mortality rates are positively correlated with forest net primary productivity (NPP). Yet causes of the correlation are unknown, in spite of potentially profound implications for our understanding of environmental controls of forest structure and dynamics and, more generally, our understanding of broad-scale environmental controls of population dynamics and ecosystem processes. Here we seek to shed light on the causes of geographic patterns in tree mortality rates, and we consider some implications of the positive correlation between mortality rates and NPP. To reach these ends, we present seven hypotheses potentially explaining the correlation, develop an approach to help distinguish among the hypotheses, and apply the approach in a case study comparing a tropical and temperate forest. Based on our case study and literature synthesis, we conclude that no single mechanism controls geographic patterns of tree mortality rates. At least four different mechanisms may be at play, with the dominant mechanisms depending on whether the underlying productivity gradients are caused by climate or soil fertility. Two of the mechanisms are consequences of environmental selection for certain combinations of life-history traits, reflecting trade-offs between growth and defense (along edaphic productivity gradients) and between reproduction and persistence (as manifested in the adult tree stature continuum along climatic and edaphic gradients). The remaining two mechanisms are consequences of environmental influences on the nature and strength of ecological interactions: competition (along edaphic gradients) and pressure from plant enemies (along climatic gradients). For only one of these four mechanisms, competition, can high mortality rates be considered to be a relatively direct consequence of high NPP. The remaining mechanisms force us to adopt a different view of causality, in which tree growth rates and probability of mortality can vary with at least a degree of independence along productivity gradients. In many cases, rather than being a direct cause of high mortality rates, NPP may remain high in spite of high mortality rates. The independent influence of plant enemies and other factors helps explain why forest biomass can show little correlation, or even negative correlation, with forest NPP

The Biological Response to Nanometre-sized Polymer Particles

Recently, nanometre-sized UHMWPE particles generated from hip and knee replacements have been identified in vitro and in vivo. UHMWPE particles in the 0.1-1.0 µm size range have been shown to be more biologically active than larger particles, provoking an inflammatory response implicated in late aseptic loosening of total joint replacements. The biological activity of nanometre-sized particles has not previously been studied. The biological response to clinically-relevant UHMWPE wear particles including nanometre-sized and micrometre-sized, along with polystyrene particles (FluoSpheres 20 nm, 60 nm, 200 nm and 1.0 µm), and nanometre-sized model polyethylene particles (Ceridust 3615®), was determined in terms of osteolytic cytokine release from primary human peripheral blood mononuclear cells (PBMNC’s). Nanometre-sized UHMWPE wear particles, nanometre-sized Ceridust 3615® and 20 nm FluoSpheres had no significant effect on TNF-α, IL-1β, IL-6 and IL-8 release from PBMNC’s at a concentration of 100 μm3 particles per cell after 12 and 24 hours. The micrometre-size UHMWPE wear particles (0.1-1.0 μm) and 60 nm, 200 nm and 1.0 µm FluoSpheres caused significantly elevated osteolytic cytokine release from PBMNC’s. These results indicated that particles below circa 50 nm fail to activate PBMNC’s and that particle size, composition and morphology played a crucial role in cytokine release by particle stimulated macrophages

Causes and implications of the correlation between forest productivity and tree mortality rates

At global and regional scales, tree mortality rates are positively correlated with forest net primary productivity (NPP). Yet causes of the correlation are unknown, in spite of potentially profound implications for our understanding of environmental controls of forest structure and dynamics and, more generally, our understanding of broad-scale environmental controls of population dynamics and ecosystem processes. Here we seek to shed light on the causes of geographic patterns in tree mortality rates, and we consider some implications of the positive correlation between mortality rates and NPP. To reach these ends, we present seven hypotheses potentially explaining the correlation, develop an approach to help distinguish among the hypotheses, and apply the approach in a case study comparing a tropical and temperate forest. Based on our case study and literature synthesis, we conclude that no single mechanism controls geographic patterns of tree mortality rates. At least four different mechanisms may be at play, with the dominant mechanisms depending on whether the underlying productivity gradients are caused by climate or soil fertility. Two of the mechanisms are consequences of environmental selection for certain combinations of life-history traits, reflecting trade-offs between growth and defense (along edaphic productivity gradients) and between reproduction and persistence (as manifested in the adult tree stature continuum along climatic and edaphic gradients). The remaining two mechanisms are consequences of environmental influences on the nature and strength of ecological interactions: competition (along edaphic gradients) and pressure from plant enemies (along climatic gradients). For only one of these four mechanisms, competition, can high mortality rates be considered to be a relatively direct consequence of high NPP. The remaining mechanisms force us to adopt a different view of causality, in which tree growth rates and probability of mortality can vary with at least a degree of independence along productivity gradients. In many cases, rather than being a direct cause of high mortality rates, NPP may remain high in spite of high mortality rates. The independent influence of plant enemies and other factors helps explain why forest biomass can show little correlation, or even negative correlation, with forest NPP.Keywords: Functional traits, Plant enemies, Forest dynamics, Temperate forest, Net primary productivity, Tropical forest, Competition, Consumer controls, Tree growth, Life-history trade-offs, Tree mortality, Permanent sample plotsThis is the publisher’s final pdf. The published article is copyrighted by Ecological Society of America and can be found at: www.esa.org

Generation of a large volume of clinically relevant nanometre-sized ultra-high-molecular-weight polyethylene wear particles for cell culture studies.

It has recently been shown that the wear of ultra-high-molecular-weight polyethylene in hip and knee prostheses leads to the generation of nanometre-sized particles, in addition to micron-sized particles. The biological activity of nanometre-sized ultra-high-molecular-weight polyethylene wear particles has not, however, previously been studied due to difficulties in generating sufficient volumes of nanometre-sized ultra-high-molecular-weight polyethylene wear particles suitable for cell culture studies. In this study, wear simulation methods were investigated to generate a large volume of endotoxin-free clinically relevant nanometre-sized ultra-high-molecular-weight polyethylene wear particles. Both single-station and six-station multidirectional pin-on-plate wear simulators were used to generate ultra-high-molecular-weight polyethylene wear particles under sterile and non-sterile conditions. Microbial contamination and endotoxin levels in the lubricants were determined. The results indicated that microbial contamination was absent and endotoxin levels were low and within acceptable limits for the pharmaceutical industry, when a six-station pin-on-plate wear simulator was used to generate ultra-high-molecular-weight polyethylene wear particles in a non-sterile environment. Different pore-sized polycarbonate filters were investigated to isolate nanometre-sized ultra-high-molecular-weight polyethylene wear particles from the wear test lubricants. The use of the filter sequence of 10, 1, 0.1, 0.1 and 0.015 µm pore sizes allowed successful isolation of ultra-high-molecular-weight polyethylene wear particles with a size range of < 100 nm, which was suitable for cell culture studies