A generalized discriminant rule when training population and test population differ on their descriptive parameters

Standard discriminant analysis methods make the assumption that both the labeled sample used to estimate the discriminant rule and the nonlabeled sample on which this rule is applied arise from the same population. In this work, we consider the case where the two populations are slightly different. In the multinormal context, we establish that both populations are linked through linear mapping. Estimation of the nonlabeled sample discriminant rule is then obtained by estimating parameters of this linear relationship. Several models describing this relationship are proposed and associated estimated parameters are given. An experimental illustration is also provided in which sex of birds that differ morphometrically over their geographical range is to be deterrmined and a comparison with the standard allocation rule is performed. Extension to a partially labeled sample is also discussed.     

Highly efficient labeling of DNA polymerases by a binary system of photoaffinity reagents

A binary system of photoaffinity reagents was proposed earlier for highly efficient labeling of DNA polymerases by 5"-[³²P]DNA primers. In the present study we demonstrate the feasibility of this approach to increase the efficiency of DNA polymerase labeling. A photoactive 2,3,5,6-tetrafluoro-4-azidobenzoyl (FAB) group was incorporated at the 3"-end of 5"-[³²P]DNA primers synthesized by DNA polymerase or Tte in the presence of one of the dTTP analogs—FAB-4-dUTP, FAB-9-dUTP, or FAB-4-ddUTP. The reaction mixture was irradiated by light with wavelength of 334-365 nm (direct labeling) or 365-450 nm in the presence of photosensitizer, one of dTTP analogs containing a pyrene moiety, Pyr-6-dUTP or Pyr-8-dUTP. In the case of the binary system of photoaffinity reagents, a FAB group is activated by energy transfer from sensitizer localized in the dNTP-binding site of DNA polymerase in the triple complex, comprised by reagent, DNA polymerase, and Pyr-6(8)-dUTP. Direct activation of the FAB group under these conditions is negligible. The most efficient photolabeling of DNA polymerases was observed with a primer containing a FAB-4-dUMP group at the 3"-end, and Pyr-6-dUTP as a photosensitizer. Using 10-fold molar excess of photoreagent to DNA polymerase , the labeling efficiency was shown to achieve 60%, which is 2-fold higher than the efficiency of the direct DNA polymerase labeling under harsher conditions (334-365 nm).     

The compliance score as a regressor in randomized trials

The compliance score in randomized trials is a measure of the effect of randomization on treatment received. It is in principle a group-level pretreatment variable and so can be used where individual-level measures of treatment received can produce misleading inferences. The interpretation of models with the compliance score as a regressor of interest depends on the link function. Using the identity link can lead to valid inference about the effects of treatment received even in the presence of nonrandom noncompliance; such inference is more problematic for nonlinear links. We illustrate these points with data from two randomized trials.     

Estimation and testing with overdispersed proportions using the beta-logistic regression model of Heckman and Willis

Methods are presented for modeling dose-related effects in proportion data when extra-binomial variability is a concern. Motivation is taken from experiments in developmental toxicology, where similarity among conceptuses within a litter leads to intralitter correlations and to overdispersion in the observed proportions. Appeal is made to the well-known beta-binomial distribution to represent the overdispersion. From this, an exponential function of the linear predictor is used to model the dose-response relationship. The specification was introduced previously for econometric applications by Heckman and Willis; it induces a form of logistic regression for the mean response, together with a reciprocal biexponential model for the intralitter correlation. Large-sample, likelihood-based methods for estimating and testing the joint proportion-correlation response are studied. A developmental toxicity data set illustrates the methods.     

Species richness and assemblage structure of Trichoptera in Danish streams

• 1 Species richness and assemblages of Trichoptera from 157 ‘pristine’ Danish lowland stream sites were analyzed, for dependence on geographical position of the sites and simple physical variables, using two way indicator species analysis and detrended correspondence analysis.
• 2 A total of 106 species were recorded, representing ≈ 90% of the species pool known from Danish streams. Only seven species occurred at more than half the sites, whereas an additional 11 species were found at more than a quarter of the sites.
• 3 Although sites showed significant regional differences in environmental variables (stream order, width, slope and presence/absence of riparian forest), species richness and assemblages were primarily correlated with stream order, width and slope. Maximum richness was found at the largest (5th order) stream sites.
• 4 Regional differences in species assemblages were found, with several species being absent from the islands Funen and Bornholm. Species assemblages also differed between forested and non‐forested stream sites.
• 5 We found evidence that stream temperature may be of only minor importance in determining Trichoptera species richness and assemblage composition in Danish streams compared to other size‐related physical factors.

     

Subterranean rodents of the genus Ctenomys (Caviomorpha, Ctenomyidae) follow the converse to Bergmann's rule

Aim We analysed body‐size variation in relation to latitude, longitude, elevation and environmental variables in Ctenomys (tuco‐tucos), subterranean rodents in the Ctenomyidae (Caviomorpha). We tested the existence of inter‐ and intraspecific size clines to determine if these rodents follow Bergmann's rule, to compare intra‐ and interspecific size trends and to assess the relevance of the subterranean lifestyle on these trends. Location South America, south of 15° latitude. Methods This paper is based on 719 specimens of tuco‐tucos from 133 localities of Argentina, Bolivia, Chile, Paraguay, Peru and Uruguay, representing 47 named species and 32 undescribed forms. Intraspecific analyses were performed for Ctenomys talarum Thomas, 1898 and the Ctenomys perrensi Thomas, 1896 species complex. Head and body length and weight were used for estimating body size. Geographical independent variables included latitude, longitude and altitude. Environmental independent variables were mean minimal and maximal monthly temperature, mean annual temperature, mean minimal and maximal precipitation, and total annual precipitation. To estimate seasonality, the annual variability of the climatic factors was calculated as their coefficients of variation and the difference between maximum and minimum values. Mean annual actual evapotranspiration (AET), and mean annual, January (summer) and July (winter) potential evapotranspiration (PET) values were also calculated for each locality, as well as annual, summer and winter water balance (WB). Statistical analyses consisted of simple and multiple regression and nonparametric correlation. Results Body size of Ctenomys decreases interspecifically from 15°00′ S to 48°15′ S and from 56°33′ W to 71°46′ W, and is positively correlated with ambient temperature and precipitation. The best predictors of body size according to multiple regression analyses were mean annual temperature, the difference between mean maximum and minimum annual temperatures, annual PET, the difference between summer and winter PET, and annual and winter water balance. These patterns are repeated, but not identically, at a smaller geographical scale within the species C. talarum and the superspecies C. perrensi. Main conclusions Tuco‐tucos follow the converse to Bergmann's rule at the interspecific level. At the intraspecific level some parallel trends were observed, but the smaller scale of these analyses, involving a very reduced variation of environmental factors, necessitates caution in interpreting results. The subterranean lifestyle probably insulates these rodents from the external temperature. The observed latitudinal body‐size gradients are more probably related to seasonality, ambient energy, primary productivity and/or intensity of predation.     

Predicting fine‐scale distributions of peripheral aquatic species in headwater streams

Headwater species and peripheral populations that occupy habitat at the edge of a species range may hold an increased conservation value to managers due to their potential to maximize intraspecies diversity and species' adaptive capabilities in the context of rapid environmental change. The southern Appalachian Mountains are the southern extent of the geographic range of native Salvelinus fontinalis and naturalized Oncorhynchus mykiss and Salmo trutta in eastern North America. We predicted distributions of these peripheral, headwater wild trout populations at a fine scale to serve as a planning and management tool for resource managers to maximize resistance and resilience of these populations in the face of anthropogenic stressors. We developed correlative logistic regression models to predict occurrence of brook trout, rainbow trout, and brown trout for every interconfluence stream reach in the study area. A stream network was generated to capture a more consistent representation of headwater streams. Each of the final models had four significant metrics in common: stream order, fragmentation, precipitation, and land cover. Strahler stream order was found to be the most influential variable in two of the three final models and the second most influential variable in the other model. Greater than 70% presence accuracy was achieved for all three models. The underrepresentation of headwater streams in commonly used hydrography datasets is an important consideration that warrants close examination when forecasting headwater species distributions and range estimates. Additionally, it appears that a relative watershed position metric (e.g., stream order) is an important surrogate variable (even when elevation is included) for biotic interactions across the landscape in areas where headwater species distributions are influenced by topographical gradients.     

Association Models for Clustered Data with Binary and Continuous Responses

Summary .  We consider analysis of clustered data with mixed bivariate responses, i.e., where each member of the cluster has a binary and a continuous outcome. We propose a new bivariate random effects model that induces associations among the binary outcomes within a cluster, among the continuous outcomes within a cluster, between a binary outcome and a continuous outcome from different subjects within a cluster, as well as the direct association between the binary and continuous outcomes within the same subject. For the ease of interpretations of the regression effects, the marginal model of the binary response probability integrated over the random effects preserves the logistic form and the marginal expectation of the continuous response preserves the linear form. We implement maximum likelihood estimation of our model parameters using standard software such as PROC NLMIXED of SAS . Our simulation study demonstrates the robustness of our method with respect to the misspecification of the regression model as well as the random effects model. We illustrate our methodology by analyzing a developmental toxicity study of ethylene glycol in mice.