Fire,landscape change and models of small mammal habitat suitability at multiple spatial scales

Fire is an important process in many ecosystems, but inappropriate fire regimes can adversely affect biodiversity. We identified a naturally flammable heathy woodland ecosystem where the use of planned fire had increased the extent of older vegetation, and quantified the abundance of two small native mammals in this landscape (silky mouse Pseudomys apodemoides and heath rat P. shortridgei). We defined four time‐since‐fire (TSF) categories representing a 2‐ to 55‐year post‐fire sequence and, on the basis of a habitat accommodation model, predicted that both species would select younger age‐classes over older ones. We also predicted that (i) much of the variance in vegetation structure would remain unexplained by TSF and (ii) statistical models of mammal abundance and occupancy including structural variables as predictors would be better than models including TSF. Pseudomys apodemoides selected 17‐ to 23‐year‐old sites, while there was no evidence that P. shortridgei selected a particular TSF category, findings that were inconsistent with our predictions. In line with our predictions, relatively large portions of the variance in vegetation structure remained unexplained by TSF (adjustedr² for four structural variables: 0.24, 0.29, 0.35 and 0.57), and in three of four cases there was strong evidence that statistical models of mammal abundance and occupancy including structural variables were better than those including TSF. At the site scale (hectares), P. shortridgei abundance was positively related to the cover of dead material at the base of Xanthorrhoea plants and at the trap scale (metres), the trapability of both species was significantly related to vegetation volume at 0–20 cm. Our findings suggest that TSF may not be a good proxy for either vegetation structure or species abundance/occupancy.     

Homology and ontogeny: pattern and process in comparative developmental biology

In this article the interface between development and homology is discussed. Development is here interpreted as a sequence of evolutionarily independent stages. Any approach stressing the importance of specific developmental stages is rejected. A homology definition is favoured which includes similarity, and complexity serves as a test for homology. Complexity is seen as the possibility of subdividing a character into evolutionarily independent corresponding substructures. Topology as a test for homology is critically discussed because corresponding positions are not necessarily indicative of homology. Complexity can be used twofold for homology assessments of development: either stages or processes of development are homologised. These two approaches must not be conflated. This distinction leads to the conclusion that there is no ontogenetic homology “criterion”.     

Parametric spatial cure rate models for interval-censored time-to-relapse data

Several recent papers (e.g., Chen, Ibrahim, and Sinha, 1999, Journal of the American Statistical Association 94, 909-919; Ibrahim, Chen, and Sinha, 2001a, Biometrics 57, 383-388) have described statistical methods for use with time-to-event data featuring a surviving fraction (i.e., a proportion of the population that never experiences the event). Such cure rate models and their multivariate generalizations are quite useful in studies of multiple diseases to which an individual may never succumb, or from which an individual may reasonably be expected to recover following treatment (e.g., various types of cancer). In this article we extend these models to allow for spatial correlation (estimable via zip code identifiers for the subjects) as well as interval censoring. Our approach is Bayesian, where posterior summaries are obtained via a hybrid Markov chain Monte Carlo algorithm. We compare across a broad collection of rather high-dimensional hierarchical models using the deviance information criterion, a tool recently developed for just this purpose. We apply our approach to the analysis of a smoking cessation study where the subjects reside in 53 southeastern Minnesota zip codes. In addition to the usual posterior estimates, our approach yields smoothed zip code level maps of model parameters related to the relapse rates over time and the ultimate proportion of quitters (the cure rates).     

Value of heartburn for diagnosing gastroesophageal reflux disease in severely obese patients

Objective : To evaluate the prevalence of gastroesophageal reflux disease (GERD) in severely obese patients and the association between symptoms and objective data of GERD in this population. Research Methods and Procedures : A total of 158 consecutive severely obese patients (BMI ≥ 40 kg/m²) were prospectively evaluated. Symptoms were evaluated by a structured clinical questionnaire. Objective assessment was made by ambulatory 24‐hour esophageal pH monitoring and endoscopy. GERD was defined by the presence of symptoms or complications (esophagitis). The clinical criterion defining GERD was the presence of at least two episodes of heartburn per week. Results : The mean age of the 138 patients subjected to complete study was 42.6 ± 10.2 years, with a BMI of 50.1 ± 6.9 kg/m² (range, 40.6 to 69.4 kg/m²); 78% were women. The prevalence of GERD evaluated by symptoms and/or esophagitis was 33.3% (46/138). Clinical criteria of GERD were present in 31/138 cases (22.5%), and 26 (18.8%) had esophagitis. In 69/138 patients (50%), pHmetry was abnormal. Fifty‐three patients with esophagitis and/or abnormal pHmetry were asymptomatic. The sensitivity of heartburn as a diagnostic criterion of GERD in patients with severe obesity was 29.3%, with a specificity of 85.7%. No significant association was observed between severe obesity grade and the prevalence of symptoms and/or objective data. Discussion : Asymptomatic gastroesophageal reflux (abnormal esophageal acid exposure and/or reflux esophagitis) is more common than symptomatic gastroesophageal reflux in severely obese patients. Increased BMI is not associated with a greater prevalence of GERD in these patients.     

Variable selection for logistic regression using a prediction-focused information criterion

In biostatistical practice, it is common to use information criteria as a guide for model selection. We propose new versions of the focused information criterion (FIC) for variable selection in logistic regression. The FIC gives, depending on the quantity to be estimated, possibly different sets of selected variables. The standard version of the FIC measures the mean squared error of the estimator of the quantity of interest in the selected model. In this article, we propose more general versions of the FIC, allowing other risk measures such as the one based on L(p) error. When prediction of an event is important, as is often the case in medical applications, we construct an FIC using the error rate as a natural risk measure. The advantages of using an information criterion which depends on both the quantity of interest and the selected risk measure are illustrated by means of a simulation study and application to a study on diabetic retinopathy.     

Seemingly unrelated measurement error models, with application to nutritional epidemiology

Motivated by an important biomarker study in nutritional epidemiology, we consider the combination of the linear mixed measurement error model and the linear seemingly unrelated regression model, hence Seemingly Unrelated Measurement Error Models. In our context, we have data on protein intake and energy (caloric) intake from both a food frequency questionnaire (FFQ) and a biomarker, and wish to understand the measurement error properties of the FFQ for each nutrient. Our idea is to develop separate marginal mixed measurement error models for each nutrient, and then combine them into a larger multivariate measurement error model: the two measurement error models are seemingly unrelated because they concern different nutrients, but aspects of each model are highly correlated. As in any seemingly unrelated regression context, the hope is to achieve gains in statistical efficiency compared to fitting each model separately. We show that if we employ a "full" model (fully parameterized), the combination of the two measurement error models leads to no gain over considering each model separately. However, there is also a scientifically motivated "reduced" model that sets certain parameters in the "full" model equal to zero, and for which the combination of the two measurement error models leads to considerable gain over considering each model separately, e.g., 40% decrease in standard errors. We use the Akaike information criterion to distinguish between the two possibilities, and show that the resulting estimates achieve major gains in efficiency. We also describe theoretical and serious practical problems with the Bayes information criterion in this context.     

The effect of thermopreference on circadian thermoregulation in sprague-dawley and fisher 344 rats

Interstrain differences in thermoregulation of rats are important in biomedical research because subtleties in thermoregulatory sensitivities may greatly affect data collected. Little is known regarding how individual rodent strains differentially utilize behavioral thermal preference to regulate core temperature (Tc). Sprague-Dawley (SD) and Fischer 344 (F344) rats are known to have differences in thermoregulation including heat tolerance and are useful models to study interstrain differences in thermoregulation. Adult male SD and F344 rats of similar body size were implanted with radiotelemetry thermoprobes (DSI) to measure Tc and MA and housed in either a longitudinal temperature gradient with an ambient temperature (Ta) range of ∼15–40 °C to measure selected Ta (STa) or control environment maintained at a Ta of 23 °C. When continuously monitored for 48 h, Tc and MA increased at night, while STa decreased, according to their normal circadian cycle in both strains. SD rats were more active than F344 rats throughout the circadian cycle (SD gradient: day=12.9±1.2 m/h, night=32.1±2.4 m/h; F344 gradient: day=4.1±0.6 m/h, night=16.8±1.8 m/h; p<0.05 interstrain and circadian effects). The STa of each strain was greater during the daytime (SD: 26.4±0.2 °C; F344: 27.8±0.3 °C) than at night (SD: 24.7±0.3 °C; F344: 25.7±0.3 °C) confirming past studies that thermopreference during the day and night is greater than standard room temperature (∼23 °C). Correlations between MA and Tc suggest that MA has a greater effect on Tc in the F344 but not the SD strain when housed in a temperature gradient. There were significant strain differences in Tc depending on whether rats were housed in a temperature gradient. That is, the control F344 rats had a lower Tc during the transition from dark to light compared to rats housed in a gradient. Tc of the SD strain was unaffected by housing in the gradient. Rats are typically housed at a standard room temperature of 23 °C. However, the results demonstrate that when given the opportunity to behaviorally thermoregulate in a temperature gradient, the F344 strain selects a warmer environment that affects the regulation of Tc. This may be important in the experimenters' choice of ambient temperatures to house and study rats and other rodents.     

Disruptive effects of prefeeding and haloperidol administration on multiple measures of food-maintained behavior in rats

Four rats responded under a choice reaction-time procedure. At the beginning of each trial, the rats were required to hold down a center lever for a variable duration, release it following a high- or low-pitched tone, and press either a left or right lever, conditionally on the tone. Correct choices were reinforced with a probability of .95 or .05 under blinking or static houselights, respectively. After performance stabilized, disruptive effects of free access to food pellets prior to sessions (prefeeding) and intraperitoneal injection of haloperidol were examined on multiple behavioral measures (i.e., the number of trials completed, percent of correct responses, and reaction time). Resistance to prefeeding depended on the probability of food delivery for the number of trials completed and reaction time. Resistance to haloperidol, on the other hand, was not systematically affected by the probability of food delivery for all dependent measures.     

Quantifying personality in the terrestrial hermit crab: Different measures, different inferences

There is much interest in studying animal personalities but considerable debate as to how to define and evaluate them. We assessed the utility of one proposed framework while studying personality in terrestrial hermit crabs (Coenobita clypeatus). We recorded the latency of individuals to emerge from their shells over multiple trials in four unique manipulations. We used the specific testing situations within these manipulations to define two temperament categories (shyness-boldness and exploration-avoidance). Our results identified individual behavioral consistency (i.e., personality) across repeated trials of the same situations, within both categories. Additionally, we found correlations between behaviors across contexts (traits) that suggested that the crabs had behavioral syndromes. While we found some correlations between behaviors that are supposed to measure the same temperament trait, these correlations were not inevitable. Furthermore, a principal component analysis (PCA) of our data revealed new relationships between behaviors and provided the foundation for an alternate interpretation: measured behaviors may be situation-specific, and may not reflect general personality traits at all. These results suggest that more attention must be placed on how we infer personalities from standardized methods, and that we must be careful to not force our data to fit our frameworks.