Maximum Likelihood Estimates for Binary Data with Random Effects

The purpose of this paper is to present a procedure for obtaining approximate maximum likelihood estimates for compound binary response models. The extra binomial variation is incorporated into the model by adding random effects to the fixed effects on the probit (or logit) scale. Numerical integration techniques are used to arrive at a solution of the likelihood equations. The paper also presents an illustrating numerical example based on a large toxicological data set. The computations are carried out within the GLIM statistical package.     

Estimation of Sample Size for Reference Interval Studies

The currently used criterion for sample size calculation in a reference interval study is not well stated and leads to imprecise control of the ratio in question. We propose a generalization of the criterion used to determine sufficient sample size in reference interval studies. The generalization allows better estimation of the required sample size when the reference interval estimation will be using a power transformation or is nonparametric. Bootstrap methods are presented to estimate sample sizes required by the generalized criterion. Simulation of several distributions both symmetric and positively skewed is presented to compare the sample size estimators. The new method is illustrated on a data set of plasma glucose values from a 50‐g oral glucose tolerance test. It is seen that the sample sizes calculated from the generalized criterion leads to more reliable control of the desired ratio.     

Population Indices Versus Correlated Density Estimates of Black-Footed Ferret Abundance

ABSTRACT Estimating abundance of carnivore populations is problematic because individuals typically are elusive, nocturnal, and dispersed across the landscape. Rare or endangered carnivore populations are even more difficult to estimate because of small sample sizes. Considering behavioral ecology of the target species can drastically improve survey efficiency and effectiveness. Previously, abundance of the black-footed ferret (Mustela nigripes) was monitored by spotlighting and generating indices of relative abundance because reintroduced populations were slow to establish. Indices, however, lack variance estimates and are costly to generate for the black-footed ferret. We therefore used spotlight surveys and live-trapping in conjunction with a robust mark-recapture estimator to improve abundance monitoring for the black-footed ferret, one of North America's most endangered carnivores. We estimated abundance of the black-footed ferret at Shirley Basin, Wyoming, USA, using correlated density estimates and Program MARK. We compared our results to 2 indices of relative abundance, minimum number alive and predicted number of ferrets from litter counts. The correlated density estimate for the black-footed ferret (N̂_R = 229; 95% CI = 161–298) was similar to minimum number alive (N̂_R = 192) and predicted number of ferrets from litter counts (N̂_R= 235). The efficiency and effectiveness of survey methods we used for the black-footed ferret were high by carnivoran standards. Our results suggest that the sampling approach we utilized can be implemented for a fraction of the cost and effort required to generate 2 indices of relative abundance for the black-footed ferret. Although we recommend managers implement a similar survey approach to monitor abundance of reintroduced populations of the black-footed ferret, analysis with sparse data sets will be problematic. Until the black-footed ferret becomes widespread and abundant at a reintroduction site, spotlighting will remain preferable as a means to generate indices of distribution and relative abundance for the black-footed ferret.     

Generalized Walker-Duncan Procedure for Obtaining Maximum Likelihood Estimates of Parameters of Logistic Discriminant Function

A recursive method of obtaining the maximum likelihood estimates of the parameters of the quadratic logistic discriminant function is presented. This method is an extension of the Walker and Duncan procedure (1967) proposed for the linear logistic discriminant function in a dichotomous case. A generalization of the method to the problem of discrimination between several populations is also given in the paper. It works for both linear and quadratic logistic discriminant function. After an estimation of the parameters of the logistic function a classification can be performed. An example of application of the method to automatic diagnosis of some respiratory diseases is presented. Comparison with the standard procedures used for the estimation is done by a short simulation study.     

Flow-cytometric Studies of the Phagocytic Capacities of Equine Neutrophils

Methodological aspects of flow-cytometric evaluation of the phagocytic properties of equine neutrophils were elucidated. The kinetics of attachment and ingestion were studied, and the phagocytic process was more rapidly completed when serum-opsonized yeast cells were used than with use of IgG-opsonized yeast cells. Trypan blue was successfully used to quench fluorescence of non-ingested yeast cells. There were only minor differences in the kinetics of phagocytosis between quenched and un-quenched samples, indicating that attachment is rapidly followed by ingestion. Trypan blue quenching caused loss of cells with light scattering properties of granulocytes, although this did not affect the determined frequencies of truly phagocytic neutrophils. Aggregation of yeast cells proved to be a disturbance but not an obstacle to the determination of frequencies of actively phagocytic cells. Flow cytometry is well suited for studies of phagocytosis of yeast cells by equine neutrophils, and the trypan blue quenching provides a means of eliminating false-positive events due to aggregation of yeast cells. The main advantage of the flow-cytometric method is the possibility of rapid processing of a large number of samples, making the method useful for studies of herds.     

Effects of Temperature and Water Loss on Terrestrial Locomotor Performance in Land Crabs: Integrating Laboratory and Field Studies

SYNOPSIS. Terrestrial and semi-terrestrial crustaceans are exposedto fluctuations in ambient temperature and conditions that favorevaporative water loss. These environmental stresses alter performancelimits in the laboratory and behavior in the field. The maximalrate of oxygen consumption, maximum aerobic speed, and endurancecapacity are greater at a body temperature (T_b) of 24°Cthan at 15°C or 30°C in the ghost crab, Ocypode quadrata.The total metabolic cost to move at the same relative speedis greater at a T_b of 24°C than at 15°C. Slower aerobickinetics at 15°C result in a smaller relative contributionof oxidative metabolism to total metabolic cost. However, therelative contributions from accelerated glycolysis are similarat both temperatures. When locomotion is intermittent, the totaldistance traveled before fatigue can be similar at Tbs of 15and 24°C but result from different movement and pause durationsat these temperatures. Performance limits of the ghost crabare negatively affected by dehydration and are sensitive torates of water loss. In the laboratory, endurance capacity ofthe fiddler crab, Uca pugilator, is greater at a T_b of 30°Cthan at 25°C. In the field, freely moving fiddler crabswith a T_b of 30°C travel at faster mean preferred speeds,as determined by motion analysis, than crabs at 25°C. Datafor land crabs support and advance general ectothermic modelsfor the effects of temperature and dehydration on locomotorperformance.     

Physiological Costs of Repetitive Courtship Displays in Cockroaches Handicap Locomotor Performance

Courtship displays are typically thought to have evolved via female choice, whereby females select mates based on the characteristics of a display that is expected to honestly reflect some aspect of the male’s quality. Honesty is typically enforced by mechanistic costs and constraints that limit the level at which a display can be performed. It is becoming increasingly apparent that these costs may be energetic costs involved in the production of dynamic, often repetitive displays. A female attending to such a display may thus be assessing the physical fitness of a male as an index of his quality. Such assessment would provide information on his current physical quality as well as his ability to carry out other demanding activities, qualities with which a choosy female should want to provision her offspring. In the current study we use courtship interactions in the Cuban burrowing cockroach, Byrsotria fumigata to directly test whether courtship is associated with a signaler’s performance capacity. Males that had produced courtship displays achieved significantly lower speeds and distances in locomotor trials than non-courting control males. We also found that females mated more readily with males that produced a more vigorous display. Thus, males of this species have developed a strategy where they produce a demanding courtship display, while females choose males based on their ability to produce this display. Courtship displays in many taxa often involve dynamic repetitive actions and as such, signals of stamina in courtship may be more widespread than previously thought.     

Planning and Assessment of Activity Budget Studies Employing Instantaneous Sampling

To obtain accurate estimates of activity budget parameters, samples must be unbiased and precise. Many researchers have considered how biased data may affect their ability to draw conclusions and examined ways to decrease bias in sampling efforts, but few have addressed the implications of not considering estimate precision. We propose a method to assess whether the number of instantaneous samples collected is sufficient to obtain precise activity budget parameter estimates. We draw on sampling theory to determine the number of observations per animal required to reach a desired bound on the error of estimation based on a stratified random sample, with individual animals acting as strata. We also discuss the optimal balance between the number of individuals sampled and the number of observations sampled per individual for a variety of sampling conditions. We present an empirical dataset on pronghorn (Antilocapra americana) as an example of the utility of the method. The required numbers of observation to reach precise estimates for pronghorn varied between common and rare behaviors, but precise estimates were achieved with <255 observations per individual for common behaviors. The two most apparent factors affecting the required number of observations for precise estimates were the number of individuals sampled and the complexity of the activity budget. This technique takes into account variation associated with individual activity budgets and population variation in activity budget parameter estimates, and helps to ensure that estimates are precise. The method can also be used for planning future sampling efforts.     

Exact Maximum Likelihood Estimates of Cox's Regression Parameters Based on Categorized Factorial Data

This paper describes how Cox's Proportional Hazards model may be used to analyze dichotomized factorial data obtained from a right-censored epidemiological study where time to response is of interest. Exact maximum likelihood estimates of the relative mortality rates are obtained for any number of prognostic factors, as well as their joint asymptotic sampling distribution. These rates represent excess mortality due to the various levels of the prognostic factors. The results are used to discuss the effect of the factors on the survival probability distribution of a cohort of industrial workers who have been exposed to a carcinogen. Kaplan-Meier estimates of the survival function of the internal control population are used to determine the expected number of deaths in the study population. This method differs from the usual lite-table procedure. Asymptotic tests are proposed for some simultaneous and conditional statistical hypotheses.     

Studies of the Enzymic Capacities and Transport Properties of Pea Root Plastids

Plastids have been isolated from pea (Pisum sativum L.) roots with a high degree of purity and intactness. In these plastids, the activity of enzymes involved in carbohydrate metabolism have been analyzed and corrected for cytosolic contamination. The results show that fructose-1,6-bisphosphatase, NAD-glyceraldehyde phosphate dehydrogenase, and phosphoglyceromutase are not present in pea root plastids. Transport measurements revealed that inorganic phosphate, dihydroxyacetone phosphate (DHAP), 3-phosphoglycerate, 2-phosphoglycerate, phosphoenolpyruvate, and glucose-6-phosphate (Glc6p) are transported across the envelope in a counterexchange mode. Transport of glucose-1-phosphate was definitely excluded. The oxidation of Glc6P by intact plastids resulted almost exclusively in the formation of DHAP. The parallel measurement of DHAP formation and NO2- consumption during Glc6P-supported nitrite reduction yielded a ratio of NO2-reduced/DHAP formed of 1.6, which is relatively close to the theoretical value of 2.0. These results show that the oxidation of Glc6P, involving the uptake of Glc6P and the release of DHAP, and the reduction of NO2- are very tightly coupled to each other.     

四种利用不同生境蜥蜴运动能力的形态特征相关性

动物体态特征、功能表现和生境利用之间是否存在相关性是当前生态形态学领域的一个研究焦点。在实验室条件下测定分别利用开阔地面、草丛、岩石、树丛生境的 4种蜥蜴 (中国石龙子、北草蜥、山地麻蜥和变色树蜥 )的形态特征和运动能力 ,着重探讨蜥蜴运动能力与形态特征之间的相关性。 4种蜥蜴的头体长大小依次为 :中国石龙子 >变色树蜥 >北草蜥 >山地麻蜥。就相对体长而言 ,中国石龙子 >山地麻蜥和北草蜥 >变色树蜥 ,而头大小、附肢长度和尾长的种间差异趋势则相反 ;体高的种间差异为北草蜥 >中国石龙子和变色树蜥 >山地麻蜥。在平面上 ,山地麻蜥和北草蜥的速度显著大于中国石龙子和变色树蜥 ;在斜面上 ,变色树蜥和山地麻蜥的速度显著高于中国石龙子。变色树蜥斜面附着能力最强 ,中国石龙子最弱。生境利用不同的蜥蜴形态迥异 ,运动能力亦因此有显著的差异。本研究结果支持动物形态特征与其功能表现相关的观点。     

Ways of Learning: Observational Studies Versus Experiments

Abstract Manipulative experimentation that features random assignment of treatments, replication, and controls is an effective way to determine causal relationships. Wildlife ecologists, however, often must take a more passive approach to investigating causality. Their observational studies lack one or more of the 3 cornerstones of experimentation: controls, randomization, and replication. Although an observational study can be analyzed similarly to an experiment, one is less certain that the presumed treatment actually caused the observed response. Because the investigator does not actively manipulate the system, the chance that something other than the treatment caused the observed results is increased. We reviewed observational studies and contrasted them with experiments and, to a lesser extent, sample surveys. We identified features that distinguish each method of learning and illustrate or discuss some complications that may arise when analyzing results of observational studies. Findings from observational studies are prone to bias. Investigators can reduce the chance of reaching erroneous conclusions by formulating a priori hypotheses that can be pursued multiple ways and by evaluating the sensitivity of study conclusions to biases of various magnitudes. In the end, however, professional judgment that considers all available evidence is necessary to render a decision regarding causality based on observational studies. (JOURNAL OF WILDLIFE MANAGEMENT 72(1):4–13; 2008)     

Adjusting for Heritable Covariates Can Bias Effect Estimates in Genome-Wide Association Studies

In recent years, a number of large-scale genome-wide association studies have been published for human traits adjusted for other correlated traits with a genetic basis. In most studies, the motivation for such an adjustment is to discover genetic variants associated with the primary outcome independently of the correlated trait. In this report, we contend that this objective is fulfilled when the tested variants have no effect on the covariate or when the correlation between the covariate and the outcome is fully explained by a direct effect of the covariate on the outcome. For all other scenarios, an unintended bias is introduced with respect to the primary outcome as a result of the adjustment, and this bias might lead to false positives. Here, we illustrate this point by providing examples from published genome-wide association studies, including large meta-analysis of waist-to-hip ratio and waist circumference adjusted for body mass index (BMI), where genetic effects might be biased as a result of adjustment for body mass index. Using both theory and simulations, we explore this phenomenon in detail and discuss the ramifications for future genome-wide association studies of correlated traits and diseases.     

Maximum Running Speed of Captive Bar-Headed Geese Is Unaffected by Severe Hypoxia

While bar-headed geese are renowned for migration at high altitude over the Himalayas, previous work on captive birds suggested that these geese are unable to maintain rates of oxygen consumption while running in severely hypoxic conditions. To investigate this paradox, we re-examined the running performance and heart rates of bar-headed geese and barnacle geese (a low altitude species) during exercise in hypoxia. Bar-headed geese (n = 7) were able to run at maximum speeds (determined in normoxia) for 15 minutes in severe hypoxia (7% O₂; simulating the hypoxia at 8500 m) with mean heart rates of 466±8 beats min⁻¹. Barnacle geese (n = 10), on the other hand, were unable to complete similar trials in severe hypoxia and their mean heart rate (316 beats.min⁻¹) was significantly lower than bar-headed geese. In bar-headed geese, partial pressures of oxygen and carbon dioxide in both arterial and mixed venous blood were significantly lower during hypoxia than normoxia, both at rest and while running. However, measurements of blood lactate in bar-headed geese suggested that anaerobic metabolism was not a major energy source during running in hypoxia. We combined these data with values taken from the literature to estimate (i) oxygen supply, using the Fick equation and (ii) oxygen demand using aerodynamic theory for bar-headed geese flying aerobically, and under their own power, at altitude. This analysis predicts that the maximum altitude at which geese can transport enough oxygen to fly without environmental assistance ranges from 6,800 m to 8,900 m altitude, depending on the parameters used in the model but that such flights should be rare.     

Biasing Factors for Simple Soil Ingestion Estimates in Mass Balance Studies of Soil Ingestion

Soil ingestion estimates from mass balance soil ingestion studies can be used in Monte Carlo Risk assessment. We develop and describe a simulation model based on four mass balance soil ingestion studies that enables food ingestion, soil ingestion, and transit time to be mimicked. We use the simulation to evaluate potential biases that exist in current estimates of the distribution of daily soil ingestion in children (constructed from subject specific average daily estimates). The simulation identifies the importance of the study duration on the bias in the upper percentile soil ingestion estimates, indicating that the 95% soil ingestion estimate may be positively biased by over 100%. Misspecification of play areas for soil sampling is shown to have no biasing effect, and absorption of trace elements in food of up to 30% is shown to bias the soil ingestion distribution by less than 20 mg/d. The results, based on Al and Si trace element estimates, define the limits of previously published soil ingestion estimates, and provide insight for future study design and estimation methods.     

Integrating Water Flow,Locomotor Performance and Respiration of Chinese Sturgeon during Multiple Fatigue-Recovery Cycles

The objective of this study is to provide information on metabolic changes occurring in Chinese sturgeon (an ecologically important endangered fish) subjected to repeated cycles of fatigue and recovery and the effect on swimming capability. Fatigue-recovery cycles likely occur when fish are moving through the fishways of large dams and the results of this investigation are important for fishway design and conservation of wild Chinese sturgeon populations. A series of four stepped velocity tests were carried out successively in a Steffensen-type swimming respirometer and the effects of repeated fatigue-recovery on swimming capability and metabolism were measured. Significant results include: (1) critical swimming speed decreased from 4.34 bl/s to 2.98 bl/s; (2) active oxygen consumption (i.e. the difference between total oxygen consumption and routine oxygen consumption) decreased from 1175 mgO₂/kg to 341 mgO₂/kg and was the primary reason for the decrease in U _crit; (3) excess post-exercise oxygen consumption decreased from 36 mgO₂/kg to 22 mgO₂/kg; (4) with repeated step tests, white muscle (anaerobic metabolism) began contributing to propulsion at lower swimming speeds. Therefore, Chinese sturgeon conserve energy by swimming efficiently and have high fatigue recovery capability. These results contribute to our understanding of the physiology of the Chinese sturgeon and support the conservation efforts of wild populations of this important species.     

Fixed Versus Removable Microdialysis Probes for In Vivo Neurochemical Analysis: Implications for Behavioral Studies

Abstract: The levels of several neurochemicals, i.e., uric acid (UA), dopamine (DA), dihydroxyphenylacetic acid, and 5-hydroxyindoleacetic acid, collected daily from the rat striatum with either fixed or removable microdialysis probes for 7 days after surgery were compared. The implantation of the fixed cannula was followed by a 10-fold increase in the UA content in the dialysates collected from the first day after surgery onward and by a steady decrease in dihydroxyphenylacetic acid levels, whereas those of DA remained fairly stable. With the removable cannula system, only a smaller, transient increase in UA during the first 3 days after surgery was observed, with no change in DA or monoamine metabolites. The glial reaction around the cannula tracks was assessed by both quantitative histological techniques and measuring the glutamine levels in the dialysates collected at the time of surgery and 7 days later. Both the glial cell number and nuclear size, as well as the glutamine outflow, were considerably larger in the animals implanted with the fixed probes. It is, therefore, likely that the UA levels in the dialysate reflect the glial reaction to the probe. The suitability of the removable probe system for behavioral experiments involving repeated microdialysis sampling was illustrated in an experiment showing that the DA release in the nucleus accumbens of male rats assessed daily at postsurgery days 5–10 was virtually identical in three alternating sessions of sexual behavior as was the smaller release of this neurotransmitter detected during intervening nonsexual social interactions.     

The Role of Relative Spinal Motion during Feline Galloping for Speed Performance

Felines use their spinal column to increase their running speed at rapid locomotion performance. However, its motion profile behavior during fast gait locomotion has little attention. The goal of this study is to examine the relative spinal motion profile during two different galloping gait speeds. To understand this dynamic behavior trend, a dynamic motion of the feline animal （Felis catus domestica） was measured and analyzed by motion capture devices. Based on the experiments at two different galloping gaits, we observed a significant increase in speed （from 3.2 m.s-1 to 4.33 m.s-1） during the relative motion profile synchronization between the spinal （range： 118.86~ to 168.00~） and pelvic segments （range： 46.35~ to 91.13~） during the hindlimb stance phase （time interval： 0.495 s to 0.600 s）. Based on this discovery, the relative angular speed profile was applied to understand the possibility that the role of the relative motion match during high speed locomotion generates bigger ground reaction force.