A simulation approach for power calculation in large cohort studies based on multistate models

Realistic power calculations for large cohort studies and nested case control studies are essential for successfully answering important and complex research questions in epidemiology and clinical medicine. For this, we provide a methodical framework for general realistic power calculations via simulations that we put into practice by means of an R‐based template. We consider staggered recruitment and individual hazard rates, competing risks, interaction effects, and the misclassification of covariates. The study cohort is assembled with respect to given age‐, gender‐, and community distributions. Nested case‐control analyses with a varying number of controls enable comparisons of power with a full cohort analysis. Time‐to‐event generation under competing risks, including delayed study‐entry times, is realized on the basis of a six‐state Markov model. Incidence rates, prevalence of risk factors and prefixed hazard ratios allow for the assignment of age‐dependent transition rates given in the form of Cox models. These provide the basis for a central simulation‐algorithm, which is used for the generation of sample paths of the underlying time‐inhomogeneous Markov processes. With the inclusion of frailty terms into the Cox models the Markov property is specifically biased. An “individual Markov process given frailty” creates some unobserved heterogeneity between individuals. Different left‐truncation‐ and right‐censoring patterns call for the use of Cox models for data analysis. p‐values are recorded over repeated simulation runs to allow for the desired power calculations. For illustration, we consider scenarios with a “testing” character as well as realistic scenarios. This enables the validation of a correct implementation of theoretical concepts and concrete sample size recommendations against an actual epidemiological background, here given with possible substudy designs within the German National Cohort.     

Multipotent Cancer Stem Cells Derived from Human Malignant Peritoneal Mesothelioma Promote Tumorigenesis

During the progression of malignant peritoneal mesothelioma (MPeM), tumor nodules propagate diffusely within the abdomen and tumors are characterized by distinct phenotypic sub-types. Recent studies in solid organ cancers have shown that cancer stem cells (CSCs) play a pivotal role in the initiation and progression of tumors. However, it is not known whether tumorigenic stem cells exist and whether they promote tumor growth in MPeM. In this study, we developed and characterized a CSC model for MPeM using stably expandable tumorigenic stem cells derived from patient tumors. We found morphologically distinct populations of CSCs that divide asymmetrically or symmetrically in MPeM in vitro cell culture. The MPeM stem cells (MPeMSCs) express stem cell markers c-MYC, NES and VEGFR2 and in the presence of matrix components cells form colony spheres. MPeMSCs are multipotent, differentiate into neuronal, vascular and adipose progeny upon defined induction and the differentiating cells express lineage-specific markers such as TUBB3, an early neuronal marker; vWF, VEGFA, VEGFC and IL-8, endothelial markers; and PPARγ and FABP4, adipose markers. Xenotransplantation experiments using MPeMSCs demonstrated early tumor growth compared with parental cells. Limiting dilution experiments using MPeMSCs and endothelial lineage-induced cells derived from a single MPeMSC resulted in early tumor growth in the latter group indicating that endothelial differentiation of MPeMSCs is important for MPeM tumor initiation. Our observation that the MPeM tumors contain stem cells with tumorigenic potential has important implications for understanding the cells of origin and tumor progression in MPeM and hence targeting CSCs may be a useful strategy to inhibit malignant progression.     

Impact of Non-Native Birds on Native Ecosystems: A Global Analysis

Introduction and naturalization of non-native species is one of the most important threats to global biodiversity. Birds have been widely introduced worldwide, but their impacts on populations, communities, and ecosystems have not received as much attention as those of other groups. This work is a global synthesis of the impact of nonnative birds on native ecosystems to determine (1) what groups, impacts, and locations have been best studied; (2) which taxonomic groups and which impacts have greatest effects on ecosystems, (3) how important are bird impacts at the community and ecosystem levels, and (4) what are the known benefits of nonnative birds to natural ecosystems. We conducted an extensive literature search that yielded 148 articles covering 39 species belonging to 18 families -18% of all known naturalized species. Studies were classified according to where they were conducted: Africa, Asia, Australasia, Europe, North America, South America, Islands of the Indian, of the Pacific, and of the Atlantic Ocean. Seven types of impact on native ecosystems were evaluated: competition, disease transmission, chemical, physical, or structural impact on ecosystem, grazing/ herbivory/ browsing, hybridization, predation, and interaction with other non-native species. Hybridization and disease transmission were the most important impacts, affecting the population and community levels. Ecosystem-level impacts, such as structural and chemical impacts were detected. Seven species were found to have positive impacts aside from negative ones. We provide suggestions for future studies focused on mechanisms of impact, regions, and understudied taxonomic groups.     

Gene flow between populations of two invertebrates in springs

1. Using allozymes, we analysed genetic structure of the freshwater gastropod Bythinella dunkeri and the freshwater flatworm Crenobia alpina. The two species are habitat specialists, living almost exclusively in springs. The sampled area in Hesse (Germany) covers a spatial scale of 20 km and includes two river drainages. From the biology of the two species we expected little dispersal along rivers. However, the possibility exists that groundwater provide suitable pathways for dispersal. 2. In B. dunkeri heterozygosity decreased from west to east. For some alleles we found clines in this geographic direction. These clines generated a positive correlation between geographic distance and genetic differentiation. Furthermore patterns of genetic variation within populations suggested that populations may have been faced with bottlenecks and founder effects. If populations are not in population genetic equilibrium, such founder effects would also explain the rather high amount of genetic differentiation between populations (10%). 3. For C. alpina the mean number of alleles decreased with increasing isolation of populations. Genetic differentiation between populations contributed 19% to the total genetic variation. Genetic differentiation was not correlated to geographic distance, but compared with B. dunkeri variability of pairwise differentiation between pairs of populations was higher in C. alpina. 4. Overall B. dunkeri appears to be a fairly good disperser, which may use groundwater as dispersal pathway. Furthermore populations seem to be not in equilibrium. In contrast C. alpina forms rather isolated populations with little dispersal between springs and groundwater seems to play no important role for dispersal.     

Use of EDTA to prevent spontaneous cell-to-cell transformation provides a more accurate estimation of gene transfer frequencies

Summary Spontaneous cell-to-cell transformation between naturally competent bacteria on selective media resulted in an overestimation of the transferability of genetic information. EDTA effectively prevented transformation on selective media whereas DNaseI did not reliably inhibit cell-to-cell transformation. An improved method to estimate gene transfer frequencies is described.