Monitoring a problem: evaluating the ecological status of the invasive Nile Monitor in Florida and forecasting population expansion using computational GIS

The state of Florida is an epicenter for the introduction of exotic terrestrial and marine species, often which are attributed to the pet industry. Identifying the threats posed by exotics that may become invasive is critical to manage and protect indigenous species and habitats. One such exotic that is now invasive in Florida is the Nile Monitor (Varanus niloticus). The Nile monitor is a large, predatory lizard native to central and southern Africa that is thought to have been introduced to Florida via both intentional and unintentional releases associated with the exotic pet trade. Since their introduction, Nile monitors have infiltrated much of central and southern Florida despite ongoing eradication efforts. The broad ecological plasticity and generalist diet of the Nile monitor affords them the potential to establish novel environments and to disrupt the trophic stability of a wide range of habitats. Unfortunately, there has been inadequate study of the metapopulation dynamics of the lizard in Florida as well as absent detailed analyses in the literature of their potential expansion and the ecological cost of their establishment. In this study, verified, georeferenced observations and specimen capture records of the monitor in Florida will be analyzed to quantify their present distribution and spatio-temporal dynamics of the invasive population. Through multivariate analysis of bioclimatic data for localities where the lizards have been recorded, information will be assembled conferring the physiological preferences and distribution correlations of the Nile monitor in their invasive range. Capture and observation records for the monitor will be linked to a habitat classification map, developed through GIS analysis of land cover, to identify ecotype preferences of the invasive population. Knowledge of habitats presently utilized by Nile monitors in Florida, in combination with bioclimatic factors and projections on future climatic conditions, can inform corridors of population spread and assess habitats at greater risk for invasion. Identifying areas at risk for Nile monitor incursion and corridors of spread will allow resource managers to act swiftly and precisely to prevent negative impacts to native fauna and also help prevent the establishment of additional breeding populations

Exploring the Complex Folding Free Energy Landscapes of a Series of β-rich Proteins

Protein aggregation is deleterious to human health and detrimental to therapeutic shelf-life. The physical processes that induce aggregation are the same processes that drive productive folding reactions. As such, protein aggregation is a non-productive form of protein folding. To gain insight into the steps that serve as a partition between the folding and aggregation reactions, the folding mechanisms of several β-rich proteins with links to human disease or medicine were examined. In the ALS-linked protein, SOD1, a subpopulation of the unfolded ensemble is found to be a common source of both nonnative structure and frustrated folding. These behaviors are only observed upon the reduction of the intrinsic disulfide bond, indicating that this covalent interaction wards against aggregation. The nonnative structure presents an attractive target for the development of new therapeutic agents. In VH domains from therapeutic mAbs, the intramolecular disulfide bond protects against aggregation. However, it can also introduce complexity to the folding mechanism. This complexity is linked to the formation of a strained orientation of the disulfide bond. This strained orientation of the disulfide in certain VH domains is energetically unfavorable enough to disrupt the formation of the disulfide in the full length mAbs. The novel relationship observed between disulfide orientation, folding complexity, and incomplete oxidation warrants further examination in other Ig domains. Overall, these results demonstrate that mapping the folding free energy landscape for proteins with roles in human disease or therapeutics can provide valuable insights for developing and improving treatment options

Evaluating the Ecological Status of the Introduced Nile Monitor (Varanus niloticus) in Florida: Forecasting Presence and Population Expansion Using Computational Geographic Information Systems

The Nile monitor (Varanus niloticus) is a large, carnivorous lizard that has become a notorious invasive species in Florida, USA. Initially released in the 1980s from the pet trade, the species has since established at least three breeding populations and spread throughout much of southern Florida. While current control efforts have failed to eradicate V. niloticus, it is important to attain a better understanding of its invasive dynamics to guide and inform better control strategies. In this study, available georeferenced records of V. niloticus in Florida were compiled and linked to a habitat classification map to evaluate ecotype preferences. Factored with bioclimatic data, the regional spread of V. niloticus was modelled for contemporary and projected (i.e., in the year 2050) presence using Maxent and Mahalanobis Distance models. Study results indicate that V. niloticus maintains a strong presence in eastern Lee County on the southwestern coast. Populations in Palm Beach and Miami-Dade counties on the southeastern coast may be interconnected, contrary to current descriptions that they are separated from each another. Model forecasts of conditions for the year 2050 identify widespread expansion of V. niloticus in Florida, particularly northward with the establishment of a new population center in Pasco County in the western central peninsula. This is the first known modelling study of V. niloticus in Florida and identifies regions at greater risk for future population expansion

Unsupervised Bilingual POS Tagging with Markov Random Fields

In this paper, we give a treatment to the problem of bilingual part-of-speech induction with parallel data. We demonstrate that naïve optimization of log-likelihood with joint MRFs suffers from a severe problem of local maxima, and suggest an alternative – using contrastive estimation for estimation of the parameters. Our experiments show that estimating the parameters this way, using overlapping features with joint MRFs performs better than previous work on the 1984 dataset.

Defending Activists at Risk: Protecting Human Rights Defenders from Threats and Violence

This paper seeks to identify protection and security strategies that can be utilized to support human rights defenders. With the intention of making this paper useful to both human rights practitioners and grantmakers, we discuss important legislation, highlight case studies and conclude with a series of best practices drawn from our experience and the recommendations of experts in the field. We hope this work stimulates needed dialogue, enhancing the safety of human rights defenders and making them more effective in their tireless efforts on behalf of others

Cartan subalgebras of root-reductive Lie algebras

Root-reductive Lie algebras are direct limits of finite-dimensional reductive Lie algebras under injections which preserve the root spaces. It is known that a root-reductive Lie algebra is a split extension of an abelian Lie algebra by a direct sum of copies of finite-dimensional simple Lie algebras as well as copies of the three simple infinite-dimensional root-reductive Lie algebras sl_infty, so_infty, and sp_infty. As part of a structure theory program for root-reductive Lie algebras, Cartan subalgebras of the Lie algebra gl_infty were introduced and studied in a paper of Neeb and Penkov. In the present paper we refine and extend the results of [N-P] to the case of a general root-reductive Lie algebra g. We prove that the Cartan subalgebras of g are the centralizers of maximal toral subalgebras and that they are nilpotent and self-normalizing. We also give an explicit description of all Cartan subalgebras of the simple Lie algebras sl_infty, so_infty, and sp_infty. We conclude the paper with a characterization of the set of conjugacy classes of Cartan subalgebras of the Lie algebras gl_infty, sl_infty, so_infty, and sp_infty with respect to the group of automorphisms of the natural representation which preserve the Lie algebra.Comment: 28 pages, 1 figur

Capacity Management in Rental Businesses With Two Customer Bases

We consider the allocation of capacity in a system in which rental equipment is accessed by two classes of customers. We formulate the problem as a continuous-time analogue of the one-shot allocation problems found in the more traditional literature on revenue management, and we analyze a queueing control model that approximates its dynamics. Our investigation yields three sets of results. First, we use dynamic programming to characterize properties of optimal capacity allocation policies. We identify conditions under which “complete sharing”—in which both classes of customers have unlimited access to the rental fleet—is optimal. Next, we develop a computationally efficient “aggregate threshold” heuristic that is based on a fluid approximation of the original stochastic model. We obtain closed-form expressions for the heuristic’s control parameters and show that the heuristic performs well in numerical experiments. The closed-form expressions also show that, in the context of the fluid approximation, revenues are concave and increasing in the fleet size. Finally, we consider the effect of the ability to allocate capacity on optimal fleet size. We show that the optimal fleet size under allocation policies may be lower, the same as, or higher than that under complete sharing. As capacity costs increase, allocation policies allow for larger relative fleet sizes. Numerical results show that, even in cases in which dollar profits under complete sharing may be close to those under allocation policies, the capacity reductions enabled by allocation schemes can help to lift profit margins significantly

Nonnative structure in a peptide model of the unfolded state of SOD1: Implications for ALS-linked aggregation

Dozens of mutations throughout the sequence of the gene encoding superoxide dismutase 1 (SOD1) have been linked to toxic protein aggregation in the neurodegenerative disease amyotrophic lateral sclerosis (ALS). A parsimonious explanation for numerous genotypes resulting in a common phenotype would be mutation-induced perturbation of the folding free-energy surface that increases the populations of high-energy states prone to aggregation. The absence of intermediates in the folding of monomeric SOD1 suggests that the unfolded ensemble is a potential source of aggregation. To test this hypothesis, here we dissected SOD1 into a set of peptides end-labeled with FRET probes to model the local behavior of the corresponding sequences in the unfolded ensemble. Using time-resolved FRET, we observed that the peptide corresponding to the loop VII-beta8 sequence at the SOD1 C-terminus was uniquely sensitive to denaturant. Utilizing a two-dimensional form of maximum entropy modeling, we demonstrate that the sensitivity to denaturant is the surprising result of a two-state-like transition from a compact to an expanded state. Variations of the peptide sequence revealed that the compact state involves a nonnative interaction between the disordered N-terminus and the hydrophobic C-terminus of the peptide. This nonnative intramolecular structure could serve as a precursor for intermolecular association and result in aggregation associated with ALS. We propose that this precursor would provide a common molecular target for therapeutic intervention in the dozens of ALS-linked SOD1 mutations