Showing papers by "Colorado State University published in 2011"

AIC model selection and multimodel inference in behavioral ecology: some background, observations, and comparisons

Abstract: We briefly outline the information-theoretic (I-T) approaches to valid inference including a review of some simple methods for making formal inference from all the hypotheses in the model set (multimodel inference). The I-T approaches can replace the usual t tests and ANOVA tables that are so inferentially limited, but still commonly used. The I-T methods are easy to compute and understand and provide formal measures of the strength of evidence for both the null and alternative hypotheses, given the data. We give an example to highlight the importance of deriving alternative hypotheses and representing these as probability models. Fifteen technical issues are addressed to clarify various points that have appeared incorrectly in the recent literature. We offer several remarks regarding the future of empirical science and data analysis under an I-T framework.

Benchmark map of forest carbon stocks in tropical regions across three continents.

Abstract: Developing countries are required to produce robust estimates of forest carbon stocks for successful implementation of climate change mitigation policies related to reducing emissions from deforestation and degradation (REDD). Here we present a “benchmark” map of biomass carbon stocks over 2.5 billion ha of forests on three continents, encompassing all tropical forests, for the early 2000s, which will be invaluable for REDD assessments at both project and national scales. We mapped the total carbon stock in live biomass (above- and belowground), using a combination of data from 4,079 in situ inventory plots and satellite light detection and ranging (Lidar) samples of forest structure to estimate carbon storage, plus optical and microwave imagery (1-km resolution) to extrapolate over the landscape. The total biomass carbon stock of forests in the study region is estimated to be 247 Gt C, with 193 Gt C stored aboveground and 54 Gt C stored belowground in roots. Forests in Latin America, sub-Saharan Africa, and Southeast Asia accounted for 49%, 25%, and 26% of the total stock, respectively. By analyzing the errors propagated through the estimation process, uncertainty at the pixel level (100 ha) ranged from ±6% to ±53%, but was constrained at the typical project (10,000 ha) and national (>1,000,000 ha) scales at ca. ±5% and ca. ±1%, respectively. The benchmark map illustrates regional patterns and provides methodologically comparable estimates of carbon stocks for 75 developing countries where previous assessments were either poor or incomplete.

Indication of Electron Neutrino Appearance from an Accelerator-produced Off-axis Muon Neutrino Beam

Abstract: The T2K experiment observes indications of nu(mu) -> nu(mu) e appearance in data accumulated with 1.43 x 10(20) protons on target. Six events pass all selection criteria at the far detector. In a three-flavor neutrino oscillation scenario with |Delta m(23)(2)| = 2.4 x 10(-3) eV(2), sin(2)2 theta(23) = 1 and sin(2)2 theta(13) = 0, the expected number of such events is 1.5 +/- 0.3(syst). Under this hypothesis, the probability to observe six or more candidate events is 7 x 10(-3), equivalent to 2.5 sigma significance. At 90% C.L., the data are consistent with 0.03(0.04) < sin(2)2 theta(13) < 0.28(0.34) for delta(CP) = 0 and a normal (inverted) hierarchy.

Temperature and soil organic matter decomposition rates – synthesis of current knowledge and a way forward

Abstract: The response of soil organic matter (OM) decomposition to increasing temperature is a critical aspect of ecosystem responses to global change The impacts of climate warming on decomposition dynamics have not been resolved due to apparently contradictory results from field and lab experiments, most of which has focused on labile carbon with short turnover times But the majority of total soil carbon stocks are comprised of organic carbon with turnover times of decades to centuries Understanding the response of these carbon pools to climate change is essential for forecasting longer-term changes in soil carbon storage Herein, we briefly synthesize information from recent studies that have been conducted using a wide variety of approaches In our effort to understand research to-date, we derive a new conceptual model that explicitly identifies the processes controlling soil OM availability for decomposition and allows a more explicit description of the factors regulating OM decomposition under different circumstances It explicitly defines resistance of soil OM to decomposition as being due either to its chemical conformation (quality )o r its physico-chemical protection from decomposition The former is embodied in the depolymerization process, the latter by adsorption/desorption and aggregate turnover We hypothesize a strong role for variation in temperature sensitivity as a function of reaction rates for both We conclude that important advances in understanding the temperature response of the processes that control substrate availability, depolymerization, microbial efficiency, and enzyme production will be needed to predict the fate of soil carbon stocks in a warmer world

Numerical Continuation Methods: An Introduction

Abstract: 1 Introduction.- 2 The Basic Principles of Continuation Methods.- 2.1 Implicitly Defined Curves.- 2.2 The Basic Concepts of PC Methods.- 2.3 The Basic Concepts of PL Methods.- 3 Newton's Method as Corrector.- 3.1 Motivation.- 3.2 The Moore-Penrose Inverse in a Special Case.- 3.3 A Newton's Step for Underdetermined Nonlinear Systems.- 3.4 Convergence Properties of Newton's Method.- 4 Solving the Linear Systems.- 4.1 Using a QR Decomposition.- 4.2 Givens Rotations for Obtaining a QR Decomposition.- 4.3 Error Analysis.- 4.4 Scaling of the Dependent Variables.- 4.5 Using LU Decompositions.- 5 Convergence of Euler-Newton-Like Methods.- 5.1 An Approximate Euler-Newton Method.- 5.2 A Convergence Theorem for PC Methods.- 6 Steplength Adaptations for the Predictor.- 6.1 Steplength Adaptation by Asymptotic Expansion.- 6.2 The Steplength Adaptation of Den Heijer & Rheinboldt.- 6.3 Steplength Strategies Involving Variable Order Predictors.- 7 Predictor-Corrector Methods Using Updating.- 7.1 Broyden's "Good" Update Formula.- 7.2 Broyden Updates Along a Curve.- 8 Detection of Bifurcation Points Along a Curve.- 8.1 Simple Bifurcation Points.- 8.2 Switching Branches Via Perturbation.- 8.3 Branching Off Via the Bifurcation Equation.- 9 Calculating Special Points of the Solution Curve.- 9.1 Introduction.- 9.2 Calculating Zero Points f(c(s)) = 0.- 9.3 Calculating Extremal Points minsf((c(s)).- 10 Large Scale Problems.- 10.1 Introduction.- 10.2 General Large Scale Solvers.- 10.3 Nonlinear Conjugate Gradient Methods as Correctors.- 11 Numerically Implementable Existence Proofs.- 11.1 Preliminary Remarks.- 11.2 An Example of an Implementable Existence Theorem.- 11.3 Several Implementations for Obtaining Brouwer Fixed Points.- 11.4 Global Newton and Global Homotopy Methods.- 11.5 Multiple Solutions.- 11.6 Polynomial Systems.- 11.7 Nonlinear Complementarity.- 11.8 Critical Points and Continuation Methods.- 12 PL Continuation Methods.- 12.1 Introduction.- 12.2 PL Approximations.- 12.3 A PL Algorithm for Tracing H(u) = 0.- 12.4 Numerical Implementation of a PL Continuation Algorithm.- 12.5 Integer Labeling.- 12.6 Truncation Errors.- 13 PL Homotopy Algorithms.- 13.1 Set-Valued Maps.- 13.2 Merrill's Restart Algorithm.- 13.3 Some Triangulations and their Implementations.- 13.4 The Homotopy Algorithm of Eaves & Saigal.- 13.5 Mixing PL and Newton Steps.- 13.6 Automatic Pivots for the Eaves-Saigal Algorithm.- 14 General PL Algorithms on PL Manifolds.- 14.1 PL Manifolds.- 14.2 Orientation and Index.- 14.3 Lemke's Algorithm for the Linear Complementarity Problem.- 14.4 Variable Dimension Algorithms.- 14.5 Exploiting Special Structure.- 15 Approximating Implicitly Defined Manifolds.- 15.1 Introduction.- 15.2 Newton's Method and Orthogonal Decompositions Revisited.- 15.3 The Moving Frame Algorithm.- 15.4 Approximating Manifolds by PL Methods.- 15.5 Approximation Estimates.- 16 Update Methods and their Numerical Stability.- 16.1 Introduction.- 16.2 Updates Using the Sherman-Morrison Formula.- 16.3 QR Factorization.- 16.4 LU Factorization.- P1 A Simple PC Continuation Method.- P2 A PL Homotopy Method.- P3 A Simple Euler-Newton Update Method.- P4 A Continuation Algorithm for Handling Bifurcation.- P5 A PL Surface Generator.- P6 SCOUT - Simplicial Continuation Utilities.- P6.1 Introduction.- P6.2 Computational Algorithms.- P6.3 Interactive Techniques.- P6.4 Commands.- P6.5 Example: Periodic Solutions to a Differential Delay Equation.- Index and Notation.

Probable non-vector-borne transmission of Zika virus, Colorado, USA.

Abstract: Clinical and serologic evidence indicate that 2 American scientists contracted Zika virus infections while working in Senegal in 2008. One of the scientists transmitted this arbovirus to his wife after his return home. Direct contact is implicated as the transmission route, most likely as a sexually transmitted infection.

Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1 , an unannotated lincRNA implicated in disease progression

Abstract: Noncoding RNAs (ncRNAs) are emerging as key molecules in human cancer, with the potential to serve as novel markers of disease and to reveal uncharacterized aspects of tumor biology. Here we discover 121 unannotated prostate cancer-associated ncRNA transcripts (PCATs) by ab initio assembly of high-throughput sequencing of polyA(+) RNA (RNA-Seq) from a cohort of 102 prostate tissues and cells lines. We characterized one ncRNA, PCAT-1, as a prostate-specific regulator of cell proliferation and show that it is a target of the Polycomb Repressive Complex 2 (PRC2). We further found that patterns of PCAT-1 and PRC2 expression stratified patient tissues into molecular subtypes distinguished by expression signatures of PCAT-1-repressed target genes. Taken together, our findings suggest that PCAT-1 is a transcriptional repressor implicated in a subset of prostate cancer patients. These findings establish the utility of RNA-Seq to identify disease-associated ncRNAs that may improve the stratification of cancer subtypes.

The dynamical core, physical parameterizations, and basic simulation characteristics of the atmospheric component AM3 of the GFDL global coupled model CM3

Abstract: The Geophysical Fluid Dynamics Laboratory (GFDL) has developed a coupled general circulation model (CM3) for the atmosphere, oceans, land, and sea ice. The goal of CM3 is to address emerging issues in climate change, including aerosol–cloud interactions, chemistry–climate interactions, and coupling between the troposphere and stratosphere. The model is also designed to serve as the physical system component of earth system models and models for decadal prediction in the near-term future—for example, through improved simulations in tropical land precipitation relative to earlier-generation GFDL models. This paper describes the dynamical core, physical parameterizations, and basic simulation characteristics of the atmospheric component (AM3) of this model. Relative to GFDL AM2, AM3 includes new treatments of deep and shallow cumulus convection, cloud droplet activation by aerosols, subgrid variability of stratiform vertical velocities for droplet activation, and atmospheric chemistry driven by emiss...

The HadGEM2-ES implementation of CMIP5 centennial simulations

Abstract: . The scientific understanding of the Earth's climate system, including the central question of how the climate system is likely to respond to human-induced perturbations, is comprehensively captured in GCMs and Earth System Models (ESM). Diagnosing the simulated climate response, and comparing responses across different models, is crucially dependent on transparent assumptions of how the GCM/ESM has been driven – especially because the implementation can involve subjective decisions and may differ between modelling groups performing the same experiment. This paper outlines the climate forcings and setup of the Met Office Hadley Centre ESM, HadGEM2-ES for the CMIP5 set of centennial experiments. We document the prescribed greenhouse gas concentrations, aerosol precursors, stratospheric and tropospheric ozone assumptions, as well as implementation of land-use change and natural forcings for the HadGEM2-ES historical and future experiments following the Representative Concentration Pathways. In addition, we provide details of how HadGEM2-ES ensemble members were initialised from the control run and how the palaeoclimate and AMIP experiments, as well as the "emission-driven" RCP experiments were performed.

Sensitivity to Basis Mismatch in Compressed Sensing

Abstract: The theory of compressed sensing suggests that successful inversion of an image of the physical world (broadly defined to include speech signals, radar/sonar returns, vibration records, sensor array snapshot vectors, 2-D images, and so on) for its source modes and amplitudes can be achieved at measurement dimensions far lower than what might be expected from the classical theories of spectrum or modal analysis, provided that the image is sparse in an apriori known basis. For imaging problems in spectrum analysis, and passive and active radar/sonar, this basis is usually taken to be a DFT basis. However, in reality no physical field is sparse in the DFT basis or in any apriori known basis. No matter how finely we grid the parameter space the sources may not lie in the center of the grid cells and consequently there is mismatch between the assumed and the actual bases for sparsity. In this paper, we study the sensitivity of compressed sensing to mismatch between the assumed and the actual sparsity bases. We start by analyzing the effect of basis mismatch on the best k-term approximation error, which is central to providing exact sparse recovery guarantees. We establish achievable bounds for the l1 error of the best k -term approximation and show that these bounds grow linearly with the image (or grid) dimension and the mismatch level between the assumed and actual bases for sparsity. We then derive bounds, with similar growth behavior, for the basis pursuit l1 recovery error, indicating that the sparse recovery may suffer large errors in the presence of basis mismatch. Although, we present our results in the context of basis pursuit, our analysis applies to any sparse recovery principle that relies on the accuracy of best k-term approximations for its performance guarantees. We particularly highlight the problematic nature of basis mismatch in Fourier imaging, where spillage from off-grid DFT components turns a sparse representation into an incompressible one. We substantiate our mathematical analysis by numerical examples that demonstrate a considerable performance degradation for image inversion from compressed sensing measurements in the presence of basis mismatch, for problem sizes common to radar and sonar.

Signatures of the Antarctic ozone hole in Southern Hemisphere surface climate change

Abstract: Roughly 90% of atmospheric ozone is found in the lower stratosphere in the ozone layer Since about the 1970s, anthropogenic emissions of ozone-depleting gases have led to depletion of ~3–4% of the total overhead ozone averaged over the globe 1 The strongest depletion is found over Antarctica during spring, when photochemical processes combine with a unique set of meteorological conditions to greatly increase the effectiveness of ozone-depleting gases, and more than half of the total overhead ozone is destroyed Characteristics of the resulting Antarctic ozone hole are reviewed in refs 1 and 2, and the identification and attribution of the phenomenon was recently celebrated in a special edition of Nature (http://wwwnaturecom/nature/focus/ ozonehole/) The Antarctic ozone hole is evident in ozone observations taken every spring since about the early 1980s 1 Its annual onset coincides with the return of sunlight to the cold polar stratosphere during September/October, and its decay with the collapse of the stratospheric vortex during November/December 1,2 The most obvious surface impact is an increase in ultraviolet radiation reaching the surface 1 Over the past decade, however, it has become clear that the ozone hole is also associated with widespread changes in the Southern Hemisphere tropospheric circulation and surface climate Our purpose here is to review the evidence that suggests that the Antarctic ozone hole has had a demonstrable effect on the surface climate of the Southern Hemisphere The ozone hole and Southern Hemisphere circulation Ozone absorbs incoming solar radiation Hence the depletion of ozone over Antarctica leads to cooling of the polar stratosphere 2,3

Receptor-mediated activation of ceramidase activity initiates the pleiotropic actions of adiponectin

Abstract: The adipocyte-derived secretory factor adiponectin promotes insulin sensitivity, decreases inflammation and promotes cell survival. No unifying mechanism has yet explained how adiponectin can exert such a variety of beneficial systemic effects. Here, we show that adiponectin potently stimulates a ceramidase activity associated with its two receptors, AdipoR1 and AdipoR2, and enhances ceramide catabolism and formation of its antiapoptotic metabolite--sphingosine-1-phosphate (S1P)--independently of AMP-dependent kinase (AMPK). Using models of inducible apoptosis in pancreatic beta cells and cardiomyocytes, we show that transgenic overproduction of adiponectin decreases caspase-8-mediated death, whereas genetic ablation of adiponectin enhances apoptosis in vivo through a sphingolipid-mediated pathway. Ceramidase activity is impaired in cells lacking both adiponectin receptor isoforms, leading to elevated ceramide levels and enhanced susceptibility to palmitate-induced cell death. Combined, our observations suggest a unifying mechanism of action for the beneficial systemic effects exerted by adiponectin, with sphingolipid metabolism as its core upstream signaling component.

The T2K Experiment

Abstract: The T2K experiment is a long-baseline neutrino oscillation experiment Its main goal is to measure the last unknown lepton sector mixing angle {\theta}_{13} by observing { u}_e appearance in a { u}_{\mu} beam It also aims to make a precision measurement of the known oscillation parameters, {\Delta}m^{2}_{23} and sin^{2} 2{\theta}_{23}, via { u}_{\mu} disappearance studies Other goals of the experiment include various neutrino cross section measurements and sterile neutrino searches The experiment uses an intense proton beam generated by the J-PARC accelerator in Tokai, Japan, and is composed of a neutrino beamline, a near detector complex (ND280), and a far detector (Super-Kamiokande) located 295 km away from J-PARC This paper provides a comprehensive review of the instrumentation aspect of the T2K experiment and a summary of the vital information for each subsystem

Caspase 3-mediated stimulation of tumor cell repopulation during cancer radiotherapy

Abstract: In cancer treatment, apoptosis is a well-recognized cell death mechanism through which cytotoxic agents kill tumor cells. Here we report that dying tumor cells use the apoptotic process to generate potent growth-stimulating signals to stimulate the repopulation of tumors undergoing radiotherapy. Furthermore, activated caspase 3, a key executioner in apoptosis, is involved in the growth stimulation. One downstream effector that caspase 3 regulates is prostaglandin E(2) (PGE(2)), which can potently stimulate growth of surviving tumor cells. Deficiency of caspase 3 either in tumor cells or in tumor stroma caused substantial tumor sensitivity to radiotherapy in xenograft or mouse tumors. In human subjects with cancer, higher amounts of activated caspase 3 in tumor tissues are correlated with markedly increased rate of recurrence and death. We propose the existence of a cell death-induced tumor repopulation pathway in which caspase 3 has a major role.

Coping with Stresses: Roles of Calcium- and Calcium/Calmodulin-Regulated Gene Expression

Abstract: Abiotic and biotic stresses are major limiting factors of crop yields and cause billions of dollars of losses annually around the world. It is hoped that understanding at the molecular level how plants respond to adverse conditions and adapt to a changing environment will help in developing plants that can better cope with stresses. Acquisition of stress tolerance requires orchestration of a multitude of biochemical and physiological changes, and most of these depend on changes in gene expression. Research during the last two decades has established that different stresses cause signal-specific changes in cellular Ca2+ level, which functions as a messenger in modulating diverse physiological processes that are important for stress adaptation. In recent years, many Ca2+ and Ca2+/calmodulin (CaM) binding transcription factors (TFs) have been identified in plants. Functional analyses of some of these TFs indicate that they play key roles in stress signaling pathways. Here, we review recent progress in this area with emphasis on the roles of Ca2+- and Ca2+/CaM-regulated transcription in stress responses. We will discuss emerging paradigms in the field, highlight the areas that need further investigation, and present some promising novel high-throughput tools to address Ca2+-regulated transcriptional networks.

Lipid-induced insulin resistance mediated by the proinflammatory receptor TLR4 requires saturated fatty acid-induced ceramide biosynthesis in mice.

Abstract: Obesity is associated with an enhanced inflammatory response that exacerbates insulin resistance and contributes to diabetes, atherosclerosis, and cardiovascular disease. One mechanism accounting for the increased inflammation associated with obesity is activation of the innate immune signaling pathway triggered by TLR4 recognition of saturated fatty acids, an event that is essential for lipid-induced insulin resistance. Using in vitro and in vivo systems to model lipid induction of TLR4-dependent inflammatory events in rodents, we show here that TLR4 is an upstream signaling component required for saturated fatty acid–induced ceramide biosynthesis. This increase in ceramide production was associated with the upregulation of genes driving ceramide biosynthesis, an event dependent of the activity of the proinflammatory kinase IKKβ. Importantly, increased ceramide production was not required for TLR4-dependent induction of inflammatory cytokines, but it was essential for TLR4-dependent insulin resistance. These findings suggest that sphingolipids such as ceramide might be key components of the signaling networks that link lipid-induced inflammatory pathways to the antagonism of insulin action that contributes to diabetes.

Continued warming could transform Greater Yellowstone fire regimes by mid-21st century

Abstract: Climate change is likely to alter wildfire regimes, but the magnitude and timing of potential climate-driven changes in regional fire regimes are not well understood. We considered how the occurrence, size, and spatial location of large fires might respond to climate projections in the Greater Yellowstone ecosystem (GYE) (Wyoming), a large wildland ecosystem dominated by conifer forests and characterized by infrequent, high-severity fire. We developed a suite of statistical models that related monthly climate data (1972-1999) to the occurrence and size of fires >200 ha in the northern Rocky Mountains; these models were cross-validated and then used with downscaled (~12 km × 12 km) climate projections from three global climate models to predict fire occurrence and area burned in the GYE through 2099. All models predicted substantial increases in fire by midcentury, with fire rotation (the time to burn an area equal to the landscape area) reduced to <30 y from the historical 100-300 y for most of the GYE. Years without large fires were common historically but are expected to become rare as annual area burned and the frequency of regionally synchronous fires increase. Our findings suggest a shift to novel fire-climate-vegetation relationships in Greater Yellowstone by midcentury because fire frequency and extent would be inconsistent with persistence of the current suite of conifer species. The predicted new fire regime would transform the flora, fauna, and ecosystem processes in this landscape and may indicate similar changes for other subalpine forests.

Ergodic and nonergodic processes coexist in the plasma membrane as observed by single-molecule tracking

Abstract: Diffusion in the plasma membrane of living cells is often found to display anomalous dynamics. However, the mechanism underlying this diffusion pattern remains highly controversial. Here, we study the physical mechanism underlying Kv2.1 potassium channel anomalous dynamics using single-molecule tracking. Our analysis includes both time series of individual trajectories and ensemble averages. We show that an ergodic and a nonergodic process coexist in the plasma membrane. The ergodic process resembles a fractal structure with its origin in macromolecular crowding in the cell membrane. The nonergodic process is found to be regulated by transient binding to the actin cytoskeleton and can be accurately modeled by a continuous-time random walk. When the cell is treated with drugs that inhibit actin polymerization, the diffusion pattern of Kv2.1 channels recovers ergodicity. However, the fractal structure that induces anomalous diffusion remains unaltered. These results have direct implications on the regulation of membrane receptor trafficking and signaling.

Nonparametric Independence Screening in Sparse Ultra-High Dimensional Additive Models

Abstract: A variable screening procedure via correlation learning was proposed by Fan and Lv (2008) to reduce dimensionality in sparse ultra-high-dimensional models. Even when the true model is linear, the marginal regression can be highly nonlinear. To address this issue, we further extend the correlation learning to marginal nonparametric learning. Our nonparametric independence screening (NIS) is a specific type of sure independence screening. We propose several closely related variable screening procedures. We show that with general nonparametric models, under some mild technical conditions, the proposed independence screening methods have a sure screening property. The extent to which the dimensionality can be reduced by independence screening is also explicitly quantified. As a methodological extension, we also propose a data-driven thresholding and an iterative nonparametric independence screening (INIS) method to enhance the finite- sample performance for fitting sparse additive models. The simulation resul...

A low-cost, simple, and rapid fabrication method for paper-based microfluidics using wax screen-printing

Abstract: Wax screen-printing as a low-cost, simple, and rapid method for fabricating paper-based microfluidic devices (µPADs) is reported here. Solid wax was rubbed through a screen onto paper filters. The printed wax was then melted into the paper to form hydrophobic barriers using only a hot plate. We first studied the relationship between the width of a hydrophobic barrier and the width of the original design line. We also optimized the heating temperature and time and determined the resolution of structures fabricated using this technique. The minimum width of hydrophilic channel and hydrophobic barrier is 650 and 1300 µm, respectively. Next, our fabrication method was compared to a photolithographic method using the reaction between bicinchoninic acid (BCA) and Cu1+ to demonstrate differences in background reactivity. Photolithographically defined channels exhibited a high background while wax printed channels showed a very low background. Finally, the utility of wax screen-printing was demonstrated for the simultaneous determination of glucose and total iron in control human serum samples using an electrochemical method with glucose oxidase and a colorimetric method with 1,10-phenanthroline. This study demonstrates that wax screen-printing is an easy-to-use and inexpensive alternative fabrication method for µPAD, which will be especially useful in developing countries.

Productivity Is a Poor Predictor of Plant Species Richness

Abstract: For more than 30 years, the relationship between net primary productivity and species richness has generated intense debate in ecology about the processes regulating local diversity. The original view, which is still widely accepted, holds that the relationship is hump-shaped, with richness first rising and then declining with increasing productivity. Although recent meta-analyses questioned the generality of hump-shaped patterns, these syntheses have been criticized for failing to account for methodological differences among studies. We addressed such concerns by conducting standardized sampling in 48 herbaceous-dominated plant communities on five continents. We found no clear relationship between productivity and fine-scale (meters−2) richness within sites, within regions, or across the globe. Ecologists should focus on fresh, mechanistic approaches to understanding the multivariate links between productivity and richness.

Do species’ traits predict recent shifts at expanding range edges?

Abstract: Although some organisms have moved to higher elevations and latitudes in response to recent climate change, there is little consensus regarding the capacity of different species to track rapid climate change via range shifts Understanding species' abilities to shift ranges has important implications for assessing extinction risk and predicting future community structure At an expanding front, colonization rates are determined jointly by rates of reproduction and dispersal In addition, establishment of viable populations requires that individuals find suitable resources in novel habitats Thus, species with greater dispersal ability, reproductive rate and ecological generalization should be more likely to expand into new regions under climate change Here, we assess current evidence for the relationship between leading-edge range shifts and species' traits We found expected relationships for several datasets, including diet breadth in North American Passeriformes and egg-laying habitat in British Odonata However, models generally had low explanatory power Thus, even statistically and biologically meaningful relationships are unlikely to be of predictive utility for conservation and management Trait-based range shift forecasts face several challenges, including quantifying relevant natural history variation across large numbers of species and coupling these data with extrinsic factors such as habitat fragmentation and availability

Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance

Abstract: Soils are immensely diverse microbial habitats with thousands of co-existing bacterial, archaeal, and fungal species. Across broad spatial scales, factors such as pH and soil moisture appear to determine the diversity and structure of soil bacterial communities. Within any one site however, bacterial taxon diversity is high and factors maintaining this diversity are poorly resolved. Candidate factors include organic substrate availability and chemical recalcitrance, and given that they appear to structure bacterial communities at the phylum level, we examine whether these factors might structure bacterial communities at finer levels of taxonomic resolution. Analyzing 16S rRNA gene composition of nucleotide analog-labeled DNA by PhyloChip microarrays, we compare relative growth rates on organic substrates of increasing chemical recalcitrance of >2,200 bacterial taxa across 43 divisions/phyla. Taxa that increase in relative abundance with labile organic substrates (i.e., glycine, sucrose) are numerous (>500), phylogenetically clustered, and occur predominantly in two phyla (Proteobacteria and Actinobacteria) including orders Actinomycetales, Enterobacteriales, Burkholderiales, Rhodocyclales, Alteromonadales, and Pseudomonadales. Taxa increasing in relative abundance with more chemically recalcitrant substrates (i.e., cellulose, lignin, or tannin-protein) are fewer (168) but more phylogenetically dispersed, occurring across eight phyla and including Clostridiales, Sphingomonadalaes, Desulfovibrionales. Just over 6% of detected taxa, including many Burkholderiales increase in relative abundance with both labile and chemically recalcitrant substrates. Estimates of median rRNA copy number per genome of responding taxa demonstrate that these patterns are broadly consistent with bacterial growth strategies. Taken together, these data suggest that changes in availability of intrinsically labile substrates may result in predictable shifts in soil bacterial composition.

A multistage tuberculosis vaccine that confers efficient protection before and after exposure

Abstract: All tuberculosis vaccines currently in clinical trials are designed as prophylactic vaccines based on early expressed antigens. We have developed a multistage vaccination strategy in which the early antigens Ag85B and 6-kDa early secretory antigenic target (ESAT-6) are combined with the latency-associated protein Rv2660c (H56 vaccine). In CB6F1 mice we show that Rv2660c is stably expressed in late stages of infection despite an overall reduced transcription. The H56 vaccine promotes a T cell response against all protein components that is characterized by a high proportion of polyfunctional CD4(+) T cells. In three different pre-exposure mouse models, H56 confers protective immunity characterized by a more efficient containment of late-stage infection than the Ag85B-ESAT6 vaccine (H1) and BCG. In two mouse models of latent tuberculosis, we show that H56 vaccination after exposure is able to control reactivation and significantly lower the bacterial load compared to adjuvant control mice.

Soil biodiversity and carbon cycling: A review and synthesis of studies examining diversity-function relationships

Abstract: Biodiversity and carbon (C) cycling have been the focus of much research in recent decades, partly because both change as a result of anthropogenic activities that are likely to continue. Soils are extremely species-rich and store approximately 80% of global terrestrial C. Soil organisms play a key role in C dynamics and a loss of species through global changes could influence global C dynamics. Here, we synthesize findings from published studies that have manipulated soil species richness and measured the response in terms of ecosystem functions related to C cycling (such as decomposition, respiration and the abundance or biomass of decomposer biota) to evaluate the impact of biodiversity loss on C dynamics. We grouped studies where one or more biotic groups had been manipulated to include a richness of 10 species in order to reflect 'low' and 'high' extents of diversity manipulations. There was a positive relationship between species richness and C cycling in 77-100% of low-diversity experiments, even when the richness of just one biotic group was manipulated, whereas positive relationships occurred less frequently in studies with greater richness (35-64%). Moreover, when positive relationships were observed, these often indicated functional redundancy at low extents of diversity or that community composition had a stronger influence on C cycling than did species richness. Initial reductions in soil species richness resulting from global changes are unlikely to alter C dynamics significantly unless particularly influential species are lost. However, changes in community composition, and the loss of species with an ability to facilitate specialized soil processes related to C cycling, as a result of global changes, may have larger impacts on C dynamics.

MAPPING JOURNALISM CULTURES ACROSS NATIONS: A comparative study of 18 countries

Abstract: This article reports key findings from a comparative survey of the role perceptions, epistemological orientations and ethical views of 1800 journalists from 18 countries. The results show that detachment, non-involvement, providing political information and monitoring the government are considered essential journalistic functions around the globe. Impartiality, the reliability and factualness of information, as well as adherence to universal ethical principles are also valued worldwide, though their perceived importance varies across countries. Various aspects of interventionism, objectivism and the importance of separating facts from opinion, on the other hand, seem to play out differently around the globe. Western journalists are generally less supportive of any active promotion of particular values, ideas and social change, and they adhere more to universal principles in their ethical decisions. Journalists from non-western contexts, on the other hand, tend to be more interventionist in their role perceptions and more flexible in their ethical views.

Relationships among net primary productivity, nutrients and climate in tropical rain forest: a pan‐tropical analysis

Abstract: Tropical rain forests play a dominant role in global biosphere-atmosphere CO2 exchange. Although climate and nutrient availability regulate net primary production (NPP) and decomposition in all terrestrial ecosystems, the nature and extent of such controls in tropical forests remain poorly resolved. We conducted a meta-analysis of carbon-nutrient-climate relationships in 113 sites across the tropical forest biome. Our analyses showed that mean annual temperature was the strongest predictor of aboveground NPP (ANPP) across all tropical forests, but this relationship was driven by distinct temperature differences between upland and lowland forests. Within lowland forests (< 1000 m), a regression tree analysis revealed that foliar and soil-based measurements of phosphorus (P) were the only variables that explained a significant proportion of the variation in ANPP, although the relationships were weak. However, foliar P, foliar nitrogen (N), litter decomposition rate (k), soil N and soil respiration were all directly related with total surface (0‐10 cm) soil P concentrations. Our analysis provides some evidence that P availability regulates NPP and other ecosystem processes in lowland tropical forests, but more importantly, underscores the need for a series of large-scale nutrient manipulations ‐ especially in lowland forests ‐ to elucidate the most important nutrient interactions and controls.