Modeling large scale species abundance with latent spatial processes

Modeling species abundance patterns using local environmental features is an important, current problem in ecology. The Cape Floristic Region (CFR) in South Africa is a global hot spot of diversity and endemism, and provides a rich class of species abundance data for such modeling. Here, we propose a multi-stage Bayesian hierarchical model for explaining species abundance over this region. Our model is specified at areal level, where the CFR is divided into roughly $37{,}000$ one minute grid cells; species abundance is observed at some locations within some cells. The abundance values are ordinally categorized. Environmental and soil-type factors, likely to influence the abundance pattern, are included in the model. We formulate the empirical abundance pattern as a degraded version of the potential pattern, with the degradation effect accomplished in two stages. First, we adjust for land use transformation and then we adjust for measurement error, hence misclassification error, to yield the observed abundance classifications. An important point in this analysis is that only $28$ of the grid cells have been sampled and that, for sampled grid cells, the number of sampled locations ranges from one to more than one hundred. Still, we are able to develop potential and transformed abundance surfaces over the entire region. In the hierarchical framework, categorical abundance classifications are induced by continuous latent surfaces. The degradation model above is built on the latent scale. On this scale, an areal level spatial regression model was used for modeling the dependence of species abundance on the environmental factors.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS335 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Identifying hotspots for plant invasions and forecasting focal points of further spread

1. To ensure the successful detection, control and eradication of invasive plant species, we need information that can identify areas prone to invasions and criteria that can point out which particular populations may become foci of further spread. Specifically, our work aimed to develop statistical models that identify hotspots of invasive plant species and evaluate the conditions that give rise to successful populations of invasive species. 2. We combined extensive data sets on invasive species richness and on species per cent ground cover, together with climate, local habitat and land cover data. We then estimated invasive species richness as a function of those environmental variables by developing a spatially explicit generalized linear model within a hierarchical Bayesian framework. In a second analysis, we used an ordinal logistic regression model to quantify invasive species abundance as a function of the same set of predictor variables. 3. Our results show which locations in the studied region, north-eastern USA, are prone to plant species invasions given the combination of climatic and land cover conditions particular to the sites. Predictions were also generated under a range of climate scenarios forecasted for the region, which pointed out at an increase in invasive species incidence under the most moderate forecast. Predicted abundance for some of the most common invasive plant species, Berberis thumbergii , Celastrus orbiculatus , Euonymus alata , Elaeagnus umbellata and Rosa multiflora , allowed us to identify the specific conditions that promote successful population growth of these species, populations that could become foci of further spread. 4. Synthesis and applications. Reliable predictions of plants’ invasive potential are crucial for the successful implementation of control and eradication management plans. By following a multivariate approach the parameters estimated in this study can now be used on targeted locations to evaluate the risk of invasions given the local climate and landscape structure; they can also be applied under different climate scenarios and changing landscapes providing an array of possible outcomes. In addition, this modelling approach can be easily used in other regions and for other species.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/78698/1/j.1365-2664.2009.01736.x.pd

Statistical Downscaling and Bias Correction of Climate Model Outputs for Climate Change Impact Assessment in the U.S. Northeast

Statistical downscaling can be used to efficiently downscale a large number of General Circulation Model (GCM) outputs to a fine temporal and spatial scale. To facilitate regional impact assessments, this study statistically downscales (to 18deg spatial resolution) and corrects the bias of daily maximum and minimum temperature and daily precipitation data from six GCMs and four Regional Climate Models (RCMs) for the northeast United States (US) using the Statistical Downscaling and Bias Correction (SDBC) approach. Based on these downscaled data from multiple models, five extreme indices were analyzed for the future climate to quantify future changes of climate extremes. For a subset of models and indices, results based on raw and bias corrected model outputs for the present-day climate were compared with observations, which demonstrated that bias correction is important not only for GCM outputs, but also for RCM outputs. For future climate, bias correction led to a higher level of agreements among the models in predicting the magnitude and capturing the spatial pattern of the extreme climate indices. We found that the incorporation of dynamical downscaling as an intermediate step does not lead to considerable differences in the results of statistical downscaling for the study domain

Managing Dynamic User Communities in a Grid of Autonomous Resources

One of the fundamental concepts in Grid computing is the creation of Virtual Organizations (VO's): a set of resource consumers and providers that join forces to solve a common problem. Typical examples of Virtual Organizations include collaborations formed around the Large Hadron Collider (LHC) experiments. To date, Grid computing has been applied on a relatively small scale, linking dozens of users to a dozen resources, and management of these VO's was a largely manual operation. With the advance of large collaboration, linking more than 10000 users with a 1000 sites in 150 counties, a comprehensive, automated management system is required. It should be simple enough not to deter users, while at the same time ensuring local site autonomy. The VO Management Service (VOMS), developed by the EU DataGrid and DataTAG projects[1, 2], is a secured system for managing authorization for users and resources in virtual organizations. It extends the existing Grid Security Infrastructure[3] architecture with embedded VO affiliation assertions that can be independently verified by all VO members and resource providers. Within the EU DataGrid project, Grid services for job submission, file- and database access are being equipped with fine- grained authorization systems that take VO membership into account. These also give resource owners the ability to ensure site security and enforce local access policies. This paper will describe the EU DataGrid security architecture, the VO membership service and the local site enforcement mechanisms Local Centre Authorization Service (LCAS), Local Credential Mapping Service(LCMAPS) and the Java Trust and Authorization Manager.Comment: Talk from the 2003 Computing in High Energy and Nuclear Physics (CHEP03), La Jolla, Ca, USA, March 2003, 7 pages, LaTeX, 5 eps figures. PSN TUBT00

Beyond seasonal climate: statistical estimation of phenological responses to weather

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/117250/1/eap20142471793.pd

Optical frequency comb Fourier transform spectroscopy of formaldehyde in the 1250 to 1390 cm−1 range: Experimental line list and improved MARVEL analysis

We use optical frequency comb Fourier transform spectroscopy to record high-resolution, low-pressure, room-temperature spectra of formaldehyde (H212C16O) in the range of 1250 to 1390 cm−1. Through line-by-line fitting, we retrieve line positions and intensities of 747 rovibrational transitions: 558 from the ν6 band, 129 from the ν4 band, and 14 from the ν3 band, as well as 46 from four different hot bands. We incorporate the accurate and precise line positions (0.4 MHz median uncertainty) into the MARVEL (measured active vibration-rotation energy levels) analysis of the H2CO spectrum. This increases the number of MARVEL-predicted energy levels by 82 and of rovibrational transitions by 5382, and substantially reduces uncertainties of MARVEL-derived H2CO energy levels over a large range: from pure rotational levels below 200 cm−1 up to multiply excited vibrational levels at 6000 cm−1. This work is an important step toward filling the gaps in formaldehyde data in the HITRAN database

Scaling up: linking field data and remote sensing with a hierarchical model

Ecologists often seek to understand patterns and processes across multiple spatial and temporal scales ranging from centimeters to hundreds of meters and from seconds to years. Hierarchical statistical models offer a framework for sampling design and analysis that can be used to incorporate the information collected at finer scales while allowing comparison at coarser scales. In this study we use a Hierarchical Bayesian model to assess the relationship between measurements collected on the ground at centimeter scales nested within 2 × 3 m quadrats, which are in turn nested within much larger (0.1-12 ha) plots. We compare these measurements with the Normalized Difference Vegetation Index (NDVI) derived from radiometrically and geometrically corrected 30-m resolution LANDSAT ETM+ data to assess the NDVI-Biomass relationship in the Cape Floristic Region of South Africa. Our novel modeling approach allows the data observed at submeter scales to be incorporated directly into the model and thus all the data (and variability) collected at finer scales are represented in the estimates of biomass at the LANDSAT scale. The model reveals that there is a strong correlation between NDVI and biomass, which supports the use of NDVI in spatiotemporal analysis of vegetation dynamics in Mediterranean shrubland ecosystems. The methods developed here can be easily generalized to other ecosystems and ecophysiological parameters

A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia coli

Gene expression is subject to random perturbations that lead to fluctuations in the rate of protein production. As a consequence, for any given protein, genetically identical organisms living in a constant environment will contain different amounts of that particular protein, resulting in different phenotypes. This phenomenon is known as “phenotypic noise.” In bacterial systems, previous studies have shown that, for specific genes, both transcriptional and translational processes affect phenotypic noise. Here, we focus on how the promoter regions of genes affect noise and ask whether levels of promoter-mediated noise are correlated with genes' functional attributes, using data for over 60% of all promoters in Escherichia coli. We find that essential genes and genes with a high degree of evolutionary conservation have promoters that confer low levels of noise. We also find that the level of noise cannot be attributed to the evolutionary time that different genes have spent in the genome of E. coli. In contrast to previous results in eukaryotes, we find no association between promoter-mediated noise and gene expression plasticity. These results are consistent with the hypothesis that, in bacteria, natural selection can act to reduce gene expression noise and that some of this noise is controlled through the sequence of the promoter region alon

CIRCULAR COMPARISON OF CONVENTIONAL PRESSURE STANDARDS USING A TRANSPORTABLE OPTICAL REFRACTOMETER: PREPARATION AND TRANSPORTATION

Using a transportable Fabry-Pérot cavity refractometer, a circular comparison of existing primary standards at several national metrology institutes is currently underway. This paper provides information about the refractometer, the preparation for the comparison, and the transportation procedur