A latent contingency table approach to dose finding for combinations of two agents

Summary .  Two-agent combination trials have recently attracted enormous attention in oncology research. There are several strong motivations for combining different agents in a treatment: to induce the synergistic treatment effect, to increase the dose intensity with nonoverlapping toxicities, and to target different tumor cell susceptibilities. To accommodate this growing trend in clinical trials, we propose a Bayesian adaptive design for dose finding based on latent 2 × 2 tables. In the search for the maximum tolerated dose combination, we continuously update the posterior estimates for the unknown parameters associated with marginal probabilities and the correlation parameter based on the data from successive patients. By reordering the dose toxicity probabilities in the two-dimensional space, we assign each coming cohort of patients to the most appropriate dose combination. We conduct extensive simulation studies to examine the operating characteristics of the proposed method under various practical scenarios. Finally, we illustrate our dose-finding procedure with a clinical trial of agent combinations at M. D. Anderson Cancer Center.     

Substrate Availability May Be More Important than Aquatic Insect Abundance in the Distribution of Riparian Orb-web Spiders in the Tropics

Spiders that are abundant along streams may depend on energy subsidies across land–water ecotones, but the effects of season and habitat structure on this trophic linkage remain poorly understood in the tropics. We carried out surveys and a manipulative experiment to investigate the effects of season and substrate availability on the distribution of riparian orb-web spiders in Hong Kong, southern China. In the surveys, spider abundance, prey, substrate use, and web orientation were recorded. The experiment involved installation of in-stream artificial substrates (ropes and bamboo poles) to increase substrate availability for web attachment. We found no seasonal difference in web abundance, but seasonal differences were observed for the prey on webs: aquatic insects (mostly Ephemeroptera and chironomid midges) contributed 69 percent of total prey collected during the wet season, but only 38 percent during the dry season. Most webs (50–80%) were < 0.5 m above the water and 45–51 percent of them tended to be orientated horizontally to the water surface and supported by overhanging vegetation and boulders. The addition of artificial substrates resulted in a 23–34 percent increase in the number of webs at the four treatment sites compared to controls, indicating that availability of web-building substrates is a critical determinant of the spider distribution. Our results suggest that riparian zones are potential 'hotspots' of food availability for spiders, and that the aquatic insect subsidy allows this habitat to support increased densities of spiders when the constraint of substrate availability is relaxed.     

LIKELIHOOD-BASED INFERENCE IN ISOLATION-BY-DISTANCE MODELS USING THE SPATIAL DISTRIBUTION OF LOW-FREQUENCY ALLELES

Estimating dispersal distances from population genetic data provides an important alternative to logistically taxing methods for directly observing dispersal. Although methods for estimating dispersal rates between a modest number of discrete demes are well developed, methods of inference applicable to "isolation-by-distance" models are much less established. Here, we present a method for estimating ρσ², the product of population density (ρ) and the variance of the dispersal displacement distribution (σ²). The method is based on the assumption that low-frequency alleles are identical by descent. Hence, the extent of geographic clustering of such alleles, relative to their frequency in the population, provides information about ρσ². We show that a novel likelihood-based method can infer this composite parameter with a modest bias in a lattice model of isolation-by-distance. For calculating the likelihood, we use an importance sampling approach to average over the unobserved intraallelic genealogies, where the intraallelic genealogies are modeled as a pure birth process. The approach also leads to a likelihood-ratio test of isotropy of dispersal, that is, whether dispersal distances on two axes are different. We test the performance of our methods using simulations of new mutations in a lattice model and illustrate its use with a dataset from Arabidopsis thaliana .     

Modifying living space: an experimental study of the influences of vegetation on aquatic invertebrate community structure

In temporary freshwater systems, the type of vegetation within a system can influence community structure. Vegetation not only provides physical structure, but can also contribute to changes in abundance and quality of food and in water quality through decomposition. An experiment was undertaken using natural and artificial vegetation in small mesocosms to examine the influence of the physical structure of vegetation on invertebrate community structure in terms of water quality, food abundance, and physical structure. It was predicted that invertebrate community structure would be identical in natural and artificial treatments if the effect of vegetative decomposition was negligible. Furthermore, invertebrate community structure in bare ground treatments would be identical to those with vegetation if the physical structure of vegetation has no significant effect. Five treatments were used: a bare ground control, artificial vegetation (×2), and natural vegetation treatments (grass, eucalypt leaf litter). Water quality, food abundance, and invertebrate abundance were examined after six weeks of inundation. All treatments had high water temperatures (34–40°C), and natural vegetation treatments had slightly higher conductivity (208–316 mS cm⁻¹) and lower turbidity (40–231 NTU) than other treatments (47–156 mS cm⁻¹ and 55–400 NTU, respectively). The physical structure of artificial vegetation did not significantly influence invertebrate community structure compared to the bare ground treatment, whereas treatments with decomposing natural vegetation had relatively low abundances of microcrustaceans (0–96 individuals/mesocosm) and relatively high abundances of chironomids (192–1576 individuals/mesocosm) compared to other treatments (>100 microcrustaceans/mesocosm if present, and <370 chironomids/mesocosm, respectively). This suggests that food availability had greater importance than physical structure in determining community structure in these small aquatic ecosystems. Handling editor: S. M. Thomaz     

Specific gravity as an alternative to creatinine for estimating urine concentration in captive and wild chimpanzee (Pan troglodytes) Samples

The measurement of hormones in urine has become a widely used technique in primatology. Because urine concentration varies according to fluid intake, concentration must be measured in each sample collected, and hormone values are always expressed per unit of concentration. Traditionally, creatinine has been used as a concentration index, but some studies in humans have shown that creatinine varies among populations and even within and between individuals within a population, and that it begins to degrade after just one freeze-thaw cycle. In addition, creatinine measurement is relatively time-consuming and expensive and creates hazardous waste. In this study, we tested the hypothesis that specific gravity, or the ratio of the density of a sample to that of water, is highly correlated with creatinine measurement in urine samples collected from captive chimpanzees at the New Iberia Research Center in Louisiana and wild chimpanzees at the Ngogo study site in the Kibale National Park, Uganda. We found that specific gravity and creatinine were highly correlated in both captive (N=124) and wild (N=13) chimpanzee samples, and that specific gravity measurement was robust to actual and simulated transport conditions and repeated freeze-thaw cycles. We recommend that researchers consider specific gravity measurement as a preferable alternative to creatinine measurement in their studies of primate endocrinology.     

Habitat level determinants of emergent macrophyte occurrence,extension and change in two large boreal lakes in Finland

Historical (1947–1950) and present day (1998–2000) aerial photograph data of aquatic vegetation were combined with soil, land use and habitat morphology variables in two lakes, oligotrophic L. Näsijärvi (256 km²) and eutrophic L. Pyhäjärvi (122 km²), with regulated water levels in southern Finland. Multivariate GLM analyses were used to examine the determining factors of occurrence and horizontal extension of vegetation, occurrence of common reed (Phragmites australis) and water horsetail (Equisetum fluviatile) and the vegetation change in 474 sites. Despite differences in geography and water level regulation between the lakes, congruent trends were identified. The vegetation occurrence in both lakes had a positive response to clay soils and incoming nutrients and a negative response to housing and shore slope. Moraine soils, housing and shore slope had a negative effect on horizontal extension of vegetation in both lakes. The occurrence of P. australis was controlled by a negative response to moraine and the occurrence of E. fluviatile to slope in both lakes. The vegetation change in both lakes was characterized by a negative response to housing and slope.     

Soil water availability and rooting depth as determinants of hydraulic architecture of Patagonian woody species

Adaptations of species to capture limiting resources is central for understanding structure and function of ecosystems. We studied the water economy of nine woody species differing in rooting depth in a Patagonian shrub steppe from southern Argentina to understand how soil water availability and rooting depth determine their hydraulic architecture. Soil water content and potentials, leaf water potentials (Ψ_Leaf), hydraulic conductivity, wood density (ρ_w), rooting depth, and specific leaf area (SLA) were measured during two summers. Water potentials in the upper soil layers during a summer drought ranged from −2.3 to −3.6 MPa, increasing to −0.05 MPa below 150 cm. Predawn Ψ_Leaf was used as a surrogate of weighted mean soil water potential because no statistical differences in Ψ_Leaf were observed between exposed and covered leaves. Species-specific differences in predawn Ψ_Leaf were consistent with rooting depths. Predawn Ψ_Leaf ranged from −4.0 MPa for shallow rooted shrubs to −1.0 MPa for deep-rooted shrubs, suggesting that the roots of the latter have access to abundant moisture, whereas shallow-rooted shrubs are adapted to use water deposited mainly by small rainfall events. Wood density was a good predictor of hydraulic conductivity and SLA. Overall, we found that shallow rooted species had efficient water transport in terms of high specific and leaf specific hydraulic conductivity, low ρ_w, high SLA and a low minimum Ψ_Leaf that exhibited strong seasonal changes, whereas deeply rooted shrubs maintained similar minimum Ψ_Leaf throughout the year, had stems with high ρ_w and low hydraulic conductivity and leaves with low SLA. These two hydraulic syndromes were the extremes of a continuum with several species occupying different portions of a gradient in hydraulic characteristics. It appears that the marginal cost of having an extensive root system (e.g., high ρ_w and root hydraulic resistance) contributes to low growth rates of the deeply rooted species.     

Domain motions of hyaluronan lyase underlying processive hyaluronan translocation

Hyaluronan lyase (Hyal) is a surface enzyme occurring in many bacterial organisms including members of Streptococcus species. Streptococcal Hyal primarily degrades hyaluronan‐substrate (HA) of the extracellular matrix. This degradation appears to facilitate the spread of this bacterium throughout host tissues. Unlike purely endolytic degradation of its other substrates, unsulfated chondroitin or some chondroitin sulfates, the degradation of HA by Hyal proceeds by processive exolytic cleavage of one disaccharide at a time following an initial endolytic cut. Molecular dynamics (MD) studies of Hyal from Streptococcus pneumoniae are presented that address the enzyme's molecular mechanism of action and the role of domain motions for processive functionality. The analysis of extensive sub‐microsecond MD simulations of this enzyme action on HA‐substrates of different lengths and the connection between the domain dynamics of Hyal and the translocation of the HA‐substrate reveals that opening/closing and twisting domain motions of the Hyal are intimately linked to processive HA degradation. Enforced simulations confirmed this finding as the domain motions in SpnHyal were found to be induced by enforced substrate translocation. These results establish the dynamic interplay between Hyal flexibility and substrate translocation and provide insight into the processive mechanism of Hyal. Proteins 2009. © 2008 Wiley‐Liss, Inc.     

Elephant spatial use in wet and dry savannas of southern Africa

The influence of elephants on woody vegetation cover varies from place to place. In part this may be due to the way elephants utilize space across landscapes and within their home ranges in response to the availability and distribution of food. We used location data from 18 cows at six study sites across an east to west rainfall gradient in southern Africa to test whether wet- and dry-season home-range sizes, evenness of space use within seasonal home ranges and range overlap between seasons and between years, differed between wet and dry savannas. We then tested whether the quantity, distribution and seasonal stability in vegetation productivity, a coarse measure of food for elephants, explained differences. Elephants in wet savannas had smaller wet- and dry-season home ranges and also returned to a higher proportion of previously visited grid cells between seasons and between years than elephants living in dry savannas. Wet-season home-range sizes were explained by seasonal vegetation productivity while dry-season home-range sizes were explained by heterogeneity in the distribution of vegetation productivity. The influence of the latter on dry-season home ranges differed among structural vegetation classes. Range overlap between seasons and between years was related to inter-seasonal and inter-annual stability in vegetation productivity, respectively. Evenness of elephant spatial use within home ranges did not differ between savanna types, but it was explained by seasonal vegetation productivity and heterogeneity in the distribution of vegetation productivity during the wet season. Differences in elephant spatial use patterns between wet and dry savannas according to vegetation structure and season may need to be included in the development of site-specific objectives and management approaches for African elephants.