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.     

Towards automation: Radiata pine shoot hedges in vitro

A novel system for in vitro shoot production has been developed whereby shoot hedges are maintained in one vessel. Monthly crops of shoots are produced for rooting. Radiata pine shoot hedges were maintained on Lepoivre (LP) nutrient agar medium for 18 months using a weekly liquid-nutrient replenishment system. In a separate experiment liquid-LP-nutrient replenishment of shoots twice weekly without transfers (D) resulted in better shoot growth and health than monthly transfers to fresh agar medium (B), monthly transfers to fresh agar medium plus aeration twice weekly (C), or no transfers and no liquid nutrient addition (A). Liquid nutrient replenishment twice weekly was better than 2 weekly or 4 weekly replenishment. The percentage of normal waxy (abundant tubular epicuticular wax) shoots harvested monthly increased significantly over the culture period from 41% at the first harvest to 93% at the eight harvest, and remained high at 97% from the ninth to twelfth harvest. The percentage of wet (no tubular epicuticular wax, small amounts of globular epicuticular wax) shoots harvested showed a corresponding decline—from 59%, to 7% at the eighth harvest. Shoots were harvested at a rate of 672/h (1.19 cents/shoot at a labour cost of NZ$8.00/h) and approximately 1100 shoots were produced per square metre of agar surface per month. Initial problems of contamination and crowding were overcome. These results will greatly facilitate progress towards automation of shoot production and reduction of costs of micropropagated trees. An automated system used in combination with other cost-saving techniques or robotics could potentially result in a substantial reduction in costs. This is the first report of a method of culturing shoots as hedges for a period of up to 18 months without manual subculturing.     

Novel Form of ClpB/HSP100 Protein in the Cyanobacterium Synechococcus

Synechococcus sp. strain PCC 7942 has a second clpB gene that encodes a 97-kDa protein with novel features. ClpBII is the first ClpB not induced by heat shock or other stresses; it is instead an essential, constitutive protein. ClpBII is unable to complement ClpBI function for acquired thermotolerance. No truncated ClpBII version is normally produced, unlike other bacterial forms, while ectopic synthesis of a putative truncated ClpBII dramatically decreased cell viability.     

Does Height Off the Ground Affect Bird Visitation and Fruit Set in the Pollen‐Limited Mistletoe Peraxilla tetrapetala (Loranthaceae)?

For pollination studies of forest species it is sometimes only possible to work on those flowers nearest to the ground. We test whether using low flowers introduces bias, by measuring height effects on bird visitation and fruit set in one mistletoe species pollinated by bellbirds in New Zealand. At this site, previous studies have shown fruit set near the ground to be pollen limited. We measured fruit set on 32 mistletoes at different heights in 11 host trees. Mistletoe fruit set varied significantly among host trees but did not vary with height. Although bellbirds generally forage preferentially in the upper part of the forest, mistletoe flowers appear to be attractive enough to ensure adequate visitation and fruit set at all heights.     

Cystatin C Is Downregulated in Prostate Cancer and Modulates Invasion of Prostate Cancer Cells via MAPK/Erk and Androgen Receptor Pathways

Cystatin C is believed to prevent tumor progression by inhibiting the activities of a family of lysosomal cysteine proteases. However, little is known about the precise mechanism of cystatin C function in prostate cancer. In the present study, we examined the expression of cystatin C and its association with matrix metalloproteinases 2 (MMP2) and androgen receptor (AR) in a tissue microarray comparing benign and malignant specimens from 448 patients who underwent radical prostatectomy for localized prostate cancer. Cystatin C expression was significantly lower in cancer specimens than in benign tissues (p<0.001) and there was a statistically significant inverse correlation between expression of cystatin C and MMP2 (r_s ² = −0.056, p = 0.05). There was a clear trend that patients with decreased level of cystatin C had lower overall survival. Targeted inhibition of cystatin C using specific siRNA resulted in an increased invasiveness of PC3 cells, whereas induction of cystatin C overexpression greatly reduced invasion rate of PC3 in vitro. The effect of cystatin C on modulating the PC3 cell invasion was provoked by Erk2 inhibitor that specifically inhibited MAPK/Erk2 activity. This suggests that cystatin C may mediate tumor cell invasion by modulating the activity of MAPK/Erk cascades. Consistent with our immunohistochemical findings that patients with low expression of cystatin C and high expression of androgen receptor (AR) tend to have worse overall survival than patients with high expression of cystatin C and high AR expression, induced overexpression of AR in PC3 cells expressing cystatin C siRNA greatly enhanced the invasiveness of PC3 cells. This suggests that there may be a crosstalk between cystatin C and AR-mediated pathways. Our study uncovers a novel role for cystatin C and its associated cellular pathways in prostate cancer invasion and metastasis.     

Opinions of UK Rescue Shelter and Rehoming Center Workers on the Problems Facing Their Industry

Animal shelters exist worldwide to care for and rehome unwanted or straying pets. Previous studies have examined why owners breed unwanted animals, or relinquish their pets to shelters. However, the views of shelter workers, who receive and care for these animals, have previously been largely unexplored. The aim of this study was to investigate the perceptions of animal shelter workers on the problems facing their industry. A sampling frame was constructed, consisting of every identified shelter in the UK, and a postal questionnaire sent to each. This included two open questions, soliciting respondents’ views on their biggest problems, and inviting further comments. A total of 661 respondents replied to at least one question. Thematic analysis on the free text content was carried out, and basic and global themes identified. Respondents’ main concerns centered on a mismatch between the continuous demand for their services and their limited resources, which has worsened during the recent financial crisis. Respondents perceived a need for increased public awareness of the commitment involved in keeping a pet, and of controlling breeding by neutering. Points of intervention, such as education programs, were suggested. Coordinating efforts with others, including local authorities, landlords, and housing associations, and a potential role for veterinary professionals working in shelter medicine were all explored by respondents. Rehoming organizations play an important role in the management of pet overpopulation, and the views and beliefs of their workers form an important contribution to the dialogue surrounding this issue. Consideration of these perspectives may suggest alternative routes to address underlying causes and management of pet overpopulation.