Measures and models for angular correlation and angular-linear correlation

Population models for dependence between two angular measurements and for dependence between an angular and a linear observation are proposed. The method of canonical correlations first leads to new population and sample measures of dependence in this latter situation. An example relating wind direction to the level of a pollutant is given. Next, applied to pairs of angular measurements, the method yields previously proposed sample measures in some special cases and a new sample measure in general

A Multimetric Assessment of Stream Condition in the Northern Lakes and Forests Ecoregion Using Spatially Explicit Statistical Modeling and Regional Normalization

We sampled fish communities, water temperature, water chemistry, physical habitat, and catchment characteristics for 94 stream sites selected randomly throughout the Northern Lakes and Forests ecoregion and used those data to explicitly model reference conditions and assess ecological stream condition at each site via a regional normalization framework. The streams we sampled were first order through fourth order, and the catchments ranged from 0.9 to 458 km2. We developed multiple linear regression (MLR) models that predicted fish community metrics, water chemistry characteristics, and local physical habitat from catchment characteristics; we used these models to compare existing conditions with the conditions that would be expected based on the regression models. Our results indicated that the fish communities were relatively unimpaired because the catchment variables associated with human‐induced land use change were important in only 1 of the 10 fish metric models. Agricultural land use was a significant variable in the MLR equation for species of Lepomis (sunfish). Agricultural land use and urban land use were both significant variables in all of the MLR models predicting water chemistry variables; urban land use was a significant variable in the MLR model predicting the percent coverage of all instream cover types. Regional normalization indicated that none of the sites were impaired based on fish community attributes. However, our analysis based on water chemistry metrics indicated that 22– 35% of the sites were impaired and that, based on physical habitat, 6–14% of the sites were impaired. A comparison with other published studies of the ecoregion suggested that the regional normalization process correctly characterized stream condition.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141590/1/tafs0697.pd

Exploring wind direction and SO2 concentration by circular-linear density estimation

The study of environmental problems usually requires the description of variables with different nature and the assessment of relations between them. In this work, an algorithm for flexible estimation of the joint density for a circular-linear variable is proposed. The method is applied for exploring the relation between wind direction and SO2 concentration in a monitoring station close to a power plant located in Galicia (NW-Spain), in order to compare the effectiveness of precautionary measures for pollutants reduction in two different years.Comment: 17 pages, 7 figures, 2 table

A Landscapeâ Based Classification of Fish Assemblages in Sampled and Unsampled Lakes

We related fish species patterns and landscapeâ scale environmental data from 216 Michigan lakes to identify repeatable types of fish assemblages, identify environmental factors related to assemblage types, and classify fish assemblages in unsampled lakes. Multivariate regression tree modeling of fish species abundances identified six assemblage types that were explained by degreeâ days during the iceâ free period, lake surface area, and mean lake surface temperature. Warmwater species dominated southern lakes, while coolwater and coldwater species had higher abundances in northern lakes. Coolwater species were present in large southern lakes, whereas warmwater species were excluded from northern lakes that had low mean surface temperatures or low degreeâ days. These results suggest that patterns of lake fish assemblages are shaped by differences in climate as well as lakeâ specific differences in surface temperature regimes and in vertical availability of coldwater and coolwater habitats. Because we related fish patterns to readily available landscapeâ level data, our approach can be used to characterize fish assemblages in all lakes across broad geographic extents.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/142256/1/tafs0414.pd

Developing User‐Friendly Habitat Suitability Tools from Regional Stream Fish Survey Data

We developed user‐friendly fish habitat suitability tools (plots) for fishery managers in Michigan; these tools are based on driving habitat variables and fish population estimates for several hundred stream sites throughout the state. We generated contour plots to show patterns in fish biomass for over 60 common species (and for 120 species grouped at the family level) in relation to axes of catchment area and low‐flow yield (90% exceedance flow divided by catchment area) and also in relation to axes of mean and weekly range of July temperatures. The plots showed distinct patterns in fish habitat suitability at each level of biological organization studied and were useful for quantitatively comparing river sites. We demonstrate how these plots can be used to support stream management, and we provide examples pertaining to resource assessment, trout stocking, angling regulations, chemical reclamation of marginal trout streams, indicator species, instream flow protection, and habitat restoration. These straightforward and effective tools are electronically available so that managers can easily access and incorporate them into decision protocols and presentations.Received April 9, 2010; accepted November 8, 2010Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141005/1/nafm0041.pd

Maturation-Induced Cloaking of Neutralization Epitopes on HIV-1 Particles

To become infectious, HIV-1 particles undergo a maturation process involving proteolytic cleavage of the Gag and Gag-Pol polyproteins. Immature particles contain a highly stable spherical Gag lattice and are impaired for fusion with target cells. The fusion impairment is relieved by truncation of the gp41 cytoplasmic tail (CT), indicating that an interaction between the immature viral core and gp41 within the particle represses HIV-1 fusion by an unknown mechanism. We hypothesized that the conformation of Env on the viral surface is regulated allosterically by interactions with the HIV-1 core during particle maturation. To test this, we quantified the binding of a panel of monoclonal antibodies to mature and immature HIV-1 particles by immunofluorescence imaging. Surprisingly, immature particles exhibited markedly enhanced binding of several gp41-specific antibodies, including two that recognize the membrane proximal external region (MPER) and neutralize diverse HIV-1 strains. Several of the differences in epitope exposure on mature and immature particles were abolished by truncation of the gp41 CT, thus linking the immature HIV-1 fusion defect with altered Env conformation. Our results suggest that perturbation of fusion-dependent Env conformational changes contributes to the impaired fusion of immature particles. Masking of neutralization-sensitive epitopes during particle maturation may contribute to HIV-1 immune evasion and has practical implications for vaccine strategies targeting the gp41 MPER

The Interferon Response Inhibits HIV Particle Production by Induction of TRIM22

Treatment of human cells with Type 1 interferons restricts HIV replication. Here we report that the tripartite motif protein TRIM22 is a key mediator. We used transcriptional profiling to identify cellular genes that were induced by interferon treatment and identified TRIM22 as one of the most strongly up-regulated genes. We confirmed, as in previous studies, that TRIM22 over-expression inhibited HIV replication. To assess the role of TRIM22 expressed under natural inducing conditions, we compared the effects of interferon in cells depleted for TRIM22 using RNAi and found that HIV particle release was significantly increased in the knockdown, implying that TRIM22 acts as a natural antiviral effector. Further studies showed that TRIM22 inhibited budding of virus-like particles containing Gag only, indicating that Gag was the target of TRIM22. TRIM22 did not block the release of MLV or EIAV Gag particles. Inhibition was associated with diffuse cytoplasmic staining of HIV Gag rather than accumulation at the plasma membrane, suggesting TRIM22 disrupts proper trafficking. Mutational analyses of TRIM22 showed that the catalytic amino acids Cys15 and Cys18 of the RING domain are required for TRIM22 antiviral activity. These data disclose a pathway by which Type 1 interferons obstruct HIV replication

Macrophage Replication Screen Identifies a Novel Francisella Hydroperoxide Resistance Protein Involved in Virulence

Francisella tularensis is a Gram-negative facultative intracellular pathogen and the causative agent of tularemia. Recently, genome-wide screens have identified Francisella genes required for virulence in mice. However, the mechanisms by which most of the corresponding proteins contribute to pathogenesis are still largely unknown. To further elucidate the roles of these virulence determinants in Francisella pathogenesis, we tested whether each gene was required for replication of the model pathogen F. novicida within macrophages, an important virulence trait. Fifty-three of the 224 genes tested were involved in intracellular replication, including many of those within the Francisella pathogenicity island (FPI), validating our results. Interestingly, over one third of the genes identified are annotated as hypothetical, indicating that F. novicida likely utilizes novel virulence factors for intracellular replication. To further characterize these virulence determinants, we selected two hypothetical genes to study in more detail. As predicted by our screen, deletion mutants of FTN_0096 and FTN_1133 were attenuated for replication in macrophages. The mutants displayed differing levels of attenuation in vivo, with the FTN_1133 mutant being the most attenuated. FTN_1133 has sequence similarity to the organic hydroperoxide resistance protein Ohr, an enzyme involved in the bacterial response to oxidative stress. We show that FTN_1133 is required for F. novicida resistance to, and degradation of, organic hydroperoxides as well as resistance to the action of the NADPH oxidase both in macrophages and mice. Furthermore, we demonstrate that F. holarctica LVS, a strain derived from a highly virulent human pathogenic species of Francisella, also requires this protein for organic hydroperoxide resistance as well as replication in macrophages and mice. This study expands our knowledge of Francisella's largely uncharacterized intracellular lifecycle and demonstrates that FTN_1133 is an important novel mediator of oxidative stress resistance

Langevin diffusions on the torus: estimation and applications

We introduce stochastic models for continuous-time evolution of angles and develop their estimation. We focus on studying Langevin diffusions with stationary distributions equal to well-known distributions from directional statistics, since such diffusions can be regarded as toroidal analogues of the Ornstein–Uhlenbeck process. Their likelihood function is a product of transition densities with no analytical expression, but that can be calculated by solving the Fokker–Planck equation numerically through adequate schemes. We propose three approximate likelihoods that are computationally tractable: (i) a likelihood based on the stationary distribution; (ii) toroidal adaptations of the Euler and Shoji–Ozaki pseudo-likelihoods; (iii) a likelihood based on a specific approximation to the transition density of the wrapped normal process. A simulation study compares, in dimensions one and two, the approximate transition densities to the exact ones, and investigates the empirical performance of the approximate likelihoods. Finally, two diffusions are used to model the evolution of the backbone angles of the protein G (PDB identifier 1GB1) during a molecular dynamics simulation. The software package sdetorus implements the estimation methods and applications presented in the paper