DISCUSSION OF THE EFFECTS OF RECESSION ON THE RURAL-FARM ECONOMY

Community/Rural/Urban Development,

FUEL-INSULATION TRADEOFFS FOR ARKANSAS BROILER HOUSES

Livestock Production/Industries,

Using Administrative Data to Count Local Populations

There is growing evidence that official population statistics based on the decennial census are inaccurate at the local authority level—the fundamental administrative unit of the UK. This paper investigates the use of locally available administrative data sets for counting populations. The method uses truth tables for combining different data sources with different population coverage according to a defined and therefore replicable set of rules. The result is timelier and geographically more flexible data which is more cost-effective to produce than a survey-based census. Associated techniques for linking diverse data sources at individual and household level are briefly discussed. The methodology is then applied to administrative data from a London borough with about 170,000 people. The results are evaluated and compared with other population sources. The paper concludes by discussing potential improvements including scaling up the work to cover multiple local authorities. The practicalities of using alternative central government data sets are briefly considered. A sequel paper in this journal provides examples of key applications of this approach at local level

Projections of Agricultural and Fish and Wildlife Water Demand in the Ouachita River Basin: A Linear Programming Approach

The availability of an abundant water supply has been a major resource of the Ouachita River Basin. In recent years, water requirements for a number of uses have increased, raising the concern that future water shortages could occur in the basin. The purpose of the study reported here was to estimate future water demand for irrigation, commercial fisheries, and fish and wildlife uses

First-principles study of orthorhombic CdTiO3 perovskite

In this work we perform an ab-initio study of CdTiO3 perovskite in its orthorhombic phase using FLAPW method. Our calculations help to decide between the different cristallographic structures proposed for this perovskite from X-Ray measurements. We compute the electric field gradient tensor (EFG) at Cd site and obtain excellent agreement with available experimental information from a perturbed angular correlation (PAC) experiment. We study EFG under an isotropic change of volume and show that in this case the widely used "point charge model approximation" to determine EFG works quite well.Comment: 4 pages, 1 figure. Accepted in Physical Review

FLORA: a novel method to predict protein function from structure in diverse superfamilies

Predicting protein function from structure remains an active area of interest, particularly for the structural genomics initiatives where a substantial number of structures are initially solved with little or no functional characterisation. Although global structure comparison methods can be used to transfer functional annotations, the relationship between fold and function is complex, particularly in functionally diverse superfamilies that have evolved through different secondary structure embellishments to a common structural core. The majority of prediction algorithms employ local templates built on known or predicted functional residues. Here, we present a novel method (FLORA) that automatically generates structural motifs associated with different functional sub-families (FSGs) within functionally diverse domain superfamilies. Templates are created purely on the basis of their specificity for a given FSG, and the method makes no prior prediction of functional sites, nor assumes specific physico-chemical properties of residues. FLORA is able to accurately discriminate between homologous domains with different functions and substantially outperforms (a 2–3 fold increase in coverage at low error rates) popular structure comparison methods and a leading function prediction method. We benchmark FLORA on a large data set of enzyme superfamilies from all three major protein classes (α, β, αβ) and demonstrate the functional relevance of the motifs it identifies. We also provide novel predictions of enzymatic activity for a large number of structures solved by the Protein Structure Initiative. Overall, we show that FLORA is able to effectively detect functionally similar protein domain structures by purely using patterns of structural conservation of all residues

Detrital zircon age and provenance constraints on late Paleozoic ice-sheet growth and dynamics in Western and Central Australia

U–Pb dating and Hf-isotope provenance analysis of detrital zircons from the glaciogenic lower Permian Grant Group of the Canning Basin indicate sources principally from basement terranes in central Australia, with subordinate components from terranes to the south and north. Integrating these data with field outcrop and subsurface evidence for ice sheets, including glacial valleys and striated pavements along the southern and northern margins of the basin, suggests that continental ice sheets extended over several Precambrian upland areas of western and central Australia during the late Paleozoic ice age (LPIA). The youngest zircons constrain the maximum age for contemporaneous ice sheet development to the late Carboniferous (Kasimovian), whereas palynology provides a minimum age of early Permian (Asselian–Sakmarian). Considering the palynological age of the Grant Group within the context of regional and global climate proxies, the main phase of continental ice sheet growth was possibly in the Ghzelian–Asselian. The presence of ice sheets older than Kasimovian in western and central Australia remains difficult to prove given a regional gap in deposition possibly covering the mid-Bashkirian to early Ghzelian within the main depocentres and even larger along basin margins, and the poor evidence for older Carboniferous glacial facies. There is also no evidence for extensive glacial facies younger than mid-Sakmarian in this region as opposed to eastern Australia where the youngest regional glacial phase was Guadalupian

Home on the Range: Factors Explaining Partial Migration of African Buffalo in a Tropical Environment

Partial migration (when only some individuals in a population undertake seasonal migrations) is common in many species and geographical contexts. Despite the development of modern statistical methods for analyzing partial migration, there have been no studies on what influences partial migration in tropical environments. We present research on factors affecting partial migration in African buffalo (Syncerus caffer) in northeastern Namibia. Our dataset is derived from 32 satellite tracking collars, spans 4 years and contains over 35,000 locations. We used remotely sensed data to quantify various factors that buffalo experience in the dry season when making decisions on whether and how far to migrate, including potential man-made and natural barriers, as well as spatial and temporal heterogeneity in environmental conditions. Using an information-theoretic, non-linear regression approach, our analyses showed that buffalo in this area can be divided into 4 migratory classes: migrants, non-migrants, dispersers, and a new class that we call “expanders”. Multimodel inference from least-squares regressions of wet season movements showed that environmental conditions (rainfall, fires, woodland cover, vegetation biomass), distance to the nearest barrier (river, fence, cultivated area) and social factors (age, size of herd at capture) were all important in explaining variation in migratory behaviour. The relative contributions of these variables to partial migration have not previously been assessed for ungulates in the tropics. Understanding the factors driving migratory decisions of wildlife will lead to better-informed conservation and land-use decisions in this area

Accurate Protein Structure Annotation through Competitive Diffusion of Enzymatic Functions over a Network of Local Evolutionary Similarities

High-throughput Structural Genomics yields many new protein structures without known molecular function. This study aims to uncover these missing annotations by globally comparing select functional residues across the structural proteome. First, Evolutionary Trace Annotation, or ETA, identifies which proteins have local evolutionary and structural features in common; next, these proteins are linked together into a proteomic network of ETA similarities; then, starting from proteins with known functions, competing functional labels diffuse link-by-link over the entire network. Every node is thus assigned a likelihood z-score for every function, and the most significant one at each node wins and defines its annotation. In high-throughput controls, this competitive diffusion process recovered enzyme activity annotations with 99% and 97% accuracy at half-coverage for the third and fourth Enzyme Commission (EC) levels, respectively. This corresponds to false positive rates 4-fold lower than nearest-neighbor and 5-fold lower than sequence-based annotations. In practice, experimental validation of the predicted carboxylesterase activity in a protein from Staphylococcus aureus illustrated the effectiveness of this approach in the context of an increasingly drug-resistant microbe. This study further links molecular function to a small number of evolutionarily important residues recognizable by Evolutionary Tracing and it points to the specificity and sensitivity of functional annotation by competitive global network diffusion. A web server is at http://mammoth.bcm.tmc.edu/networks

A Measure of the Promiscuity of Proteins and Characteristics of Residues in the Vicinity of the Catalytic Site That Regulate Promiscuity

Promiscuity, the basis for the evolution of new functions through ‘tinkering’ of residues in the vicinity of the catalytic site, is yet to be quantitatively defined. We present a computational method Promiscuity Indices Estimator (PROMISE) - based on signatures derived from the spatial and electrostatic properties of the catalytic residues, to estimate the promiscuity (PromIndex) of proteins with known active site residues and 3D structure. PromIndex reflects the number of different active site signatures that have congruent matches in close proximity of its native catalytic site, the quality of the matches and difference in the enzymatic activity. Promiscuity in proteins is observed to follow a lognormal distribution (μ = 0.28, σ = 1.1 reduced chi-square = 3.0E-5). The PROMISE predicted promiscuous functions in any protein can serve as the starting point for directed evolution experiments. PROMISE ranks carboxypeptidase A and ribonuclease A amongst the more promiscuous proteins. We have also investigated the properties of the residues in the vicinity of the catalytic site that regulates its promiscuity. Linear regression establishes a weak correlation (R2∼0.1) between certain properties of the residues (charge, polar, etc) in the neighborhood of the catalytic residues and PromIndex. A stronger relationship states that most proteins with high promiscuity have high percentages of charged and polar residues within a radius of 3 Å of the catalytic site, which is validated using one-tailed hypothesis tests (P-values∼0.05). Since it is known that these characteristics are key factors in catalysis, their relationship with the promiscuity index cross validates the methodology of PROMISE