Statistical power in COVID-19 case-control host genomic study design

The identification of genetic variation that directly impacts infection susceptibility to SARS-CoV-2 and disease severity of COVID-19 is an important step towards risk stratification, personalized treatment plans, therapeutic, and vaccine development and deployment. Given the importance of study design in infectious disease genetic epidemiology, we use simulation and draw on current estimates of exposure, infectivity, and test accuracy of COVID-19 to demonstrate the feasibility of detecting host genetic factors associated with susceptibility and severity in published COVID-19 study designs. We demonstrate that limited phenotypic data and exposure/infection information in the early stages of the pandemic significantly impact the ability to detect most genetic variants with moderate effect sizes, especially when studying susceptibility to SARS-CoV-2 infection. Our insights can aid in the interpretation of genetic findings emerging in the literature and guide the design of future host genetic studies.

Alternative time scales and failure time models

In many reliability applications, there may not be a unique plausible scale in which to measure time to failure or assess performance. This is especially the case when several measures of usage are available on each unit. For example, the age, the total number of flight hours, and the number of landings are usage measures that are often considered important in aircraft reliability. Similarly, in medical or biological applications of survival analysis there are often alternative scales (e.g., Oakes, 1995). This paper considers the definition of a "good" time scale, along with methods of determining a time scale.

Risk factors for repeated cerebrospinal shunt failures in pediatric patients with hydrocephalus

OBJECT

Repeated cerebrospinal fluid (CSF) shunt failures in pediatric patients are common, and they are a significant cause of morbidity and, occasionally, of death. To date, the risk factors for repeated failure have not been established. By performing survival analysis for repeated events, the authors examined the effects of patient characteristics, shunt hardware, and surgical details in a large cohort of patients.

METHODS

During a 10-year period all pediatric patients with hydrocephalus requiring CSF diversion procedures were included in a prospective single-institution observational study. Patient characteristics were defined as age, gender, weight, head circumference, American Society of Anesthesiology class, and cause of hydrocephalus. Surgical details included whether the procedure was performed on an emergency or nonemergency basis, use of antibiotic agents, concurrent surgical procedures, and duration of the surgical procedure. Details on shunt hardware included: the type of shunt, the valve system, whether the shunt system included multiple or complex components, the type of distal catheter, the site of the shunt, and the side on which the shunt was placed. Repeated shunt failures were assessed using multivariable time-to-event analysis (by using the Cox regression model). Conditional models (as established by Prentice, et al.) were formulated for gap times (that is, times between successive shunt failures). There were 1183 shunt failures in 839 patients. Failure time from the first shunt procedure was an important predictor for the second and third episodes of failure, thus establishing an association between the times to failure within individual patients. An age younger than 40 weeks gestation at the time of the first shunt implantation carried a hazard ratio (HR) of 2.49 (95% confidence interval [CI] 1.68-3.68) for the first failure, which remained high for subsequent episodes of failure. An age from 40 weeks gestation to 1 year (at the time of the initial surgery) also proved to be an important predictor of first shunt malfunctions (HR 1.77, 95% CI 1.29-2.44). The cause of hydrocephalus was significantly associated with the risk of initial failure and, to a lesser extent, later failures. Concurrent other surgical procedures were associated with an increased risk of failure.

CONCLUSIONS

The patient's age at the time of initial shunt placement and the time interval since previous surgical revision are important predictors of repeated shunt failures in the multivariable model. Even after adjusting for age at first shunt insertion as well as the cause of hydrocephalus, there is significant association between repeated failure times for individual patients.

Methods for the estimation of failure distributions and rates from automobile warranty data

We consider the occurrence of warranty claims for automobiles when both age and mileage accumulation may affect failure. The presence of both age and mileage limits on warranties creates interesting problems for the analysis of failures. We propose a family of models that relates failure to time and mileage accumulation. Methods for fitting the models based on warranty data and supplementary information about mileage accumulation are presented and illustrated on some real data. The general problem of modelling failures in equipment when both time and usage are factors is discussed.

Corpora lutea of pregnancy and elevated serum progesterone during pregnancy and postpartum anestrus in woodchucks (Marmota monax)

Serum samples (n = 62) were collected from wild-caught woodchucks (n = 45) that were nonpregnant (n = 3), pregnant (n = 25) or postpartum (n = 34) when bled at the time of capture and/or necropsy, or following maintenance and observation for variable periods of time. Progesterone concentrations were determined by radioimmunoassay and related to the actual or estimated time from parturition which occurs at 31 days postcoitum in this species. Mean serum progesterone levels during the initial, middle and last third of pregnancy were 6.5 +/- 1.7, 22.5 +/- 3.7 and 16.8 +/- 3.2 ng/ml, respectively. Postpartum progesterone levels were elevated above basal values (less than or equal to 0.3 ng/ml) in both lactating and nonlactating animals for 2-3 months postpartum and were not consistently basal until more than 90 days postpartum. Mean progesterone levels at less than 30, 30-60, 61-90, and greater than 90 days postpartum were 25.1 +/- 6.2, 60.6 +/- 18.5, 22.8 +/- 8.7 and 0.4 +/- 0.2 ng/ml, respectively, and those at 30-60 days postpartum were greater than those at midpregnancy (P less than 0.05). Mean corpus luteum diameters were also greater (P less than 0.05) postpartum (2.9 +/- 0.3 mm) than during pregnancy (1.5 +/- 0.3 mm). The correlation between placental scars and ipsilateral corpora lutea indicated that the corpora lutea observed postpartum were the corpora lutea of the recent pregnancy. The termination of each uterine horn in a separate external cervical os precluded the occurrence of transcornual migration.(ABSTRACT TRUNCATED AT 250 WORDS)

GGDMLE: a computer program which finds maximum likelihood estimates for the generalized log gamma distribution

A FORTRAN program is described which finds maximum likelihood estimates for the generalized log gamma model for survival time data. The model includes regression variables which are assumed to be linearly related to log survival time and handles censored data. The shape parameter is treated as fixed in the optimization procedure (a modification of Powell's hybrid method), but the program can find maximum likelihood estimates (MLE) for several different values of the shape parameter in one run. The other parameters can be optionally fixed so special cases of the generalized log gamma (GLG) model, such as the log exponential, extreme value and normal models, can be studied. A subroutine is included which calculates initial parameter estimates for a given shape parameter value which can be used to start the optimization procedure. After some background mathematics, a description of how to use the program is given, including input/output features, a description of the subroutines and an explanation of the flow of control. An application, using data from Princess Margaret Hospital, Toronto, is presented to illustrate the program's use.

Carbon, Carbides, and Methane in an Apollo 12 Sample

Total carbon in the Apollo 12 sample 12023 fines was 110 micrograms per gram of sample with a carbon isotopic abundance delta(13)C (relative to the Pee Dee belemnite standard) of +12 per mil. Hydrolysis of the fines with deuterium chloride yielded undeuterated methane along with deuterated hydrocarbons, thus confirming the presence of 7 to 21 micrograms of carbon per gram of sample as carbide and about 2 micrograms of carbon per gram of sample as indigenous methane. After vacuum pyrolysis of the fines to 1100 degrees C the following gases were detected in the relative abundance: carbon monoxide carbon dioxide methane. Variations of the delta(13)C value with the pyrolysis temperature indicated the presence of carbon with more than one range of isotopic values. The observed delta(13)C value of +14 per mil for lunar carbide is much higher than that of carbide in meteorites. These results suggest that lunar carbide is either indigenous to the moon or a meteoritic contribution that has been highly fractionated isotopically.