Eliciting and encoding expert knowledge on variable selection into classical or Bayesian species distribution models

The quality of species distribution models (SDMs) relies to a large degree on the quality of the input data, from bioclimatic indices to environmental and habitat descriptors (Austin, 2002). Recent reviews of SDM techniques, have sought to optimize predictive performance e.g. Elith et al., 2006. In general SDMs employ one of three approaches to variable selection. The simplest approach relies on the expert to select the variables, as in environmental niche models Nix, 1986 or a generalized linear model without variable selection (Miller and Franklin, 2002). A second approach explicitly incorporates variable selection into model fitting, which allows examination of particular combinations of variables. Examples include generalized linear or additive models with variable selection (Hastie et al. 2002); or classification trees with complexity or model based pruning (Breiman et al., 1984, Zeileis, 2008). A third approach uses model averaging, to summarize the overall contribution of a variable, without considering particular combinations. Examples include neural networks, boosted or bagged regression trees and Maximum Entropy as compared in Elith et al. 2006. Typically, users of SDMs will either consider a small number of variable sets, via the first approach, or else supply all of the candidate variables (often numbering more than a hundred) to the second or third approaches. Bayesian SDMs exist, with several methods for eliciting and encoding priors on model parameters (see review in Low Choy et al. 2010). However few methods have been published for informative variable selection; one example is Bayesian trees (O’Leary 2008). Here we report an elicitation protocol that helps makes explicit a priori expert judgements on the quality of candidate variables. This protocol can be flexibly applied to any of the three approaches to variable selection, described above, Bayesian or otherwise. We demonstrate how this information can be obtained then used to guide variable selection in classical or machine learning SDMs, or to define priors within Bayesian SDMs.

New genetic loci link adipose and insulin biology to body fat distribution

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10−8). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms.

The cause, distribution and economic importance of fruit speckle of banana in north Queensland

Banana Fruit Speckle.

Factors affecting the synthesis and distribution of beta-lactamase in Mycobacterium smegmatis SN2 cultures

A high level of extracellular beta-lactamase activity was detected in cultures ofMycobacterium smegmatis SN2. The extracellular distribution of the enzyme varied with growth conditions such as additional carbon source and pH of the medium. Addition of chloramphenicol tothe culture inhibited the increase in the extracellular beta-lactamase activity. Cell wall damage or autolysis may be responsible for the extracellular beta-lactamase activity.

Distribution of the angle of rotation plane random walks

We study the probability distribution of the angle by which the tangent to the trajectory rotates in the course of a plane random walk. It is shown that the determination of this distribution function can be reduced to an integral equation, which can be rigorously transformed into a differential equation of Hill's type. We derive the asymptotic distribution for very long walks.

Investigation of the distribution and incidence of Avocado sunblotch

Investigation of the distribution and incidence of Avocado sunblotch.

Continuum percolation with discs having a distribution of radii

It is shown that for continuum percolation with overlapping discs having a distribution of radii, the net areal density of discs at percolation threshold depends non-trivially on the distribution, and is not bounded by any finite constant. Results of a Monte Carlo simulation supporting the argument are presented.

Analysis of the distribution of the number of bidders in construction contract auctions

The number of bidders, N, involved in a construction procurement auction is known to have an important effect on the value of the lowest bid and the mark up applied by bidders. In practice, for example, it is important for a bidder to have a good estimate of N when bidding for a current contract. One approach, instigated by Friedman in 1956, is to make such an estimate by statistical analysis and modelling. Since then, however, finding a suitable model for N has been an enduring problem for researchers and, despite intensive research activity in the subsequent thirty years little progress has been made - due principally to the absence of new ideas and perspectives. This paper resumes the debate by checking old assumptions, providing new evidence relating to concomitant variables and proposing a new model. In doing this and in order to assure universality, a novel approach is developed and tested by using a unique set of twelve construction tender databases from four continents. This shows the new model provides a significant advancement on previous versions. Several new research questions are also posed and other approaches identified for future study.

Brownian particles in stationary and moving traps: The mean and variance of the heat distribution function

A recent theoretical model developed by Imparato et al. Phys of the experimentally measured heat and work effects produced by the thermal fluctuations of single micron-sized polystyrene beads in stationary and moving optical traps has proved to be quite successful in rationalizing the observed experimental data. The model, based on the overdamped Brownian dynamics of a particle in a harmonic potential that moves at a constant speed under a time-dependent force, is used to obtain an approximate expression for the distribution of the heat dissipated by the particle at long times. In this paper, we generalize the above model to consider particle dynamics in the presence of colored noise, without passing to the overdamped limit, as a way of modeling experimental situations in which the fluctuations of the medium exhibit long-lived temporal correlations, of the kind characteristic of polymeric solutions, for instance, or of similar viscoelastic fluids. Although we have not been able to find an expression for the heat distribution itself, we do obtain exact expressions for its mean and variance, both for the static and for the moving trap cases. These moments are valid for arbitrary times and they also hold in the inertial regime, but they reduce exactly to the results of Imparato et al. in appropriate limits. DOI: 10.1103/PhysRevE.80.011118 PACS.

Integrating sorghum whole genome sequence information with a compendium of sorghum QTL studies reveals uneven distribution of QTL and of gene-rich regions with significant implications for crop improvement.

A comprehensive analysis was conducted using 48 sorghum QTL studies published from 1995 to 2010 to make information from historical sorghum QTL experiments available in a form that could be more readily used by sorghum researchers and plant breeders. In total, 771 QTL relating to 161 unique traits from 44 studies were projected onto a sorghum consensus map. Confidence intervals (CI) of QTL were estimated so that valid comparisons could be made between studies. The method accounted for the number of lines used and the phenotypic variation explained by individual QTL from each study. In addition, estimated centimorgan (cM) locations were calculated for the predicted sorghum gene models identified in Phytozome (JGI GeneModels SBI v1.4) and compared with QTL distribution genome-wide, both on genetic linkage (cM) and physical (base-pair/bp) map scales. QTL and genes were distributed unevenly across the genome. Heterochromatic enrichment for QTL was observed, with approximately 22% of QTL either entirely or partially located in the heterochromatic regions. Heterochromatic gene enrichment was also observed based on their predicted cM locations on the sorghum consensus map, due to suppressed recombination in heterochromatic regions, in contrast to the euchromatic gene enrichment observed on the physical, sequence-based map. The finding of high gene density in recombination-poor regions, coupled with the association with increased QTL density, has implications for the development of more efficient breeding systems in sorghum to better exploit heterosis. The projected QTL information described, combined with the physical locations of sorghum sequence-based markers and predicted gene models, provides sorghum researchers with a useful resource for more detailed analysis of traits and development of efficient marker-assisted breeding strategies.

Mile-a-minute (Mikania micrantha): its distribution, growth and physical and socio-economic impacts in Papua New Guinea

Mikania micrantha, Kunth. H.B.K (Asteraceae) or mile-a-minute is a weed of Neotropical origin in 17 Pacific Island countries. It is becoming increasingly regarded as an invasive weed in Papua New Guinea and is now the focus of an Australian Government-funded biological control program. As part of the program, growth rates, distribution and physical and socia-economic impacts were studied to obtain baseline data and to assist with the field release of biological control agents. Through public awareness campaigns and dedicated surveys, mikania has been reported in most lowland provinces. It is particularly widespread in East New Britain and West New Britain Province. In field trials, mikania grew more than 1 metre per month in open sunny areas but slightly slower when growing under cocoa. The weed invades a wide range of land types, impacting on plantations and food gardens, smothering pawpaw, young cocoa, banana, taro, young oil palms and ornamental plants. In socia-economic surveys, mikania was found to have severe impacts on crop production and income generated through reduced yields and high weeding costs. These studies suggest that there would be substantial benefits to the community if biological control of mikania is successful.

Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution

Waist-hip ratio (WHR) is a measure of body fat distribution and a predictor of metabolic consequences independent of overall adiposity. WHR is heritable, but few genetic variants influencing this trait have been identified. We conducted a meta-analysis of 32 genome-wide association studies for WHR adjusted for body mass index (comprising up to 77,167 participants), following up 16 loci in an additional 29 studies (comprising up to 113,636 subjects). We identified 13 new loci in or near RSPO3, VEGFA, TBX15-WARS2, NFE2L3, GRB14, DNM3-PIGC, ITPR2-SSPN, LY86, HOXC13, ADAMTS9, ZNRF3-KREMEN1, NISCH-STAB1 and CPEB4 (P = 1.9 × 10−9 to P = 1.8 × 10−40) and the known signal at LYPLAL1. Seven of these loci exhibited marked sexual dimorphism, all with a stronger effect on WHR in women than men (P for sex difference = 1.9 × 10−3 to P = 1.2 × 10−13). These findings provide evidence for multiple loci that modulate body fat distribution independent of overall adiposity and reveal strong gene-by-sex interactions.

Mikania micrantha Kunth (Asteraceae) (Mile-a-Minute): Its Distribution and Physical and Socioeconomic Impacts in Papua New Guinea

Mikania micrantha or mile-a-minute is regarded as a major invasive weed in Papua New Guinea (PNG) and is now the target of a biological control program. As part of the program, distribution and physical and socioeconomic impacts of M. micrantha were studied to obtain baseline data and to assist with field release of biological control agents. Through public awareness campaigns and dedicated surveys, M. micrantha has been reported in all 15 lowland provinces. It is particularly widespread in East New Britain, as well as in West New Britain and New Ireland. A CLIMEX model suggests that M. micrantha has the potential to continue to spread throughout all lowland areas in PNG. The weed was found in a wide range of land uses, impacting on plantations and food gardens and smothering papaya, young cocoa, banana, taro, young oil palms, and ornamental plants. In socioeconomic surveys, M. micrantha was found to have severe impacts on crop production and income generated through reduced yields and high weeding costs, particularly in subsistence mixed cropping systems. About 89% of all respondents had M. micrantha on their land, and 71% of respondents had to weed monthly. Approximately 96% of respondents in subsistence mixed cropping systems used only physical means of control compared with 68% of respondents in other farming systems. About 45% of all respondents estimated that M. micrantha causes yield losses in excess of 30%. These studies suggest that there would be substantial benefits to landholders if biological control of M. micrantha were to be successful.