Survival analysis of time-to-event data in respiratory health research studies

This article provides a review of techniques for the analysis of survival data arising from respiratory health studies. Popular techniques such as the Kaplan–Meier survival plot and the Cox proportional hazards model are presented and illustrated using data from a lung cancer study. Advanced issues are also discussed, including parametric proportional hazards models, accelerated failure time models, time-varying explanatory variables, simultaneous analysis of multiple types of outcome events and the restricted mean survival time, a novel measure of the effect of treatment.

Bias and precision of measures of survival gain from right-censored data

In cost-effectiveness analyses of drugs or health technologies, estimates of life years saved or quality-adjusted life years saved are required. Randomised controlled trials can provide an estimate of the average treatment effect; for survival data, the treatment effect is the difference in mean survival. However, typically not all patients will have reached the endpoint of interest at the close-out of a trial, making it difficult to estimate the difference in mean survival. In this situation, it is common to report the more readily estimable difference in median survival. Alternative approaches to estimating the mean have also been proposed. We conducted a simulation study to investigate the bias and precision of the three most commonly used sample measures of absolute survival gain - difference in median, restricted mean and extended mean survival - when used as estimates of the true mean difference, under different censoring proportions, while assuming a range of survival patterns, represented by Weibull survival distributions with constant, increasing and decreasing hazards. Our study showed that the three commonly used methods tended to underestimate the true treatment effect; consequently, the incremental cost-effectiveness ratio (ICER) would be overestimated. Of the three methods, the least biased is the extended mean survival, which perhaps should be used as the point estimate of the treatment effect to be inputted into the ICER, while the other two approaches could be used in sensitivity analyses. More work on the trade-offs between simple extrapolation using the exponential distribution and more complicated extrapolation using other methods would be valuable.

Determining the sensitivity of the Antarctic amphipod Orchomenella pinguides to metals using a joint model of survival response to exposure concentration and duration

Developing water quality guidelines for Antarctic marine environments requires understanding the sensitivity of local biota to contaminant exposure. Antarctic invertebrates have shown slower contaminant responses in previous experiments compared to temperate and tropical species in standard toxicity tests. Consequently, test methods which take into account environmental conditions and biological characteristics of cold climate species need to be developed. This study investigated the effects of five metals on the survival of a common Antarctic amphipod, Orchomenella pinguides. Multiple observations assessing mortality to metal exposure were made over the 30 days exposure period. Traditional toxicity tests with quantal data sets are analysed using methods such as maximum likelihood regression (probit analysis) and Spearman–Kärber which treat individual time period endpoints independently. A new statistical model was developed to integrate the time-series concentration–response data obtained in this study. Grouped survival data were modelled using a generalized additive mixed model (GAMM) which incorporates all the data obtained from multiple observation times to derive time integrated point estimates. The sensitivity of the amphipod, O. pinguides, to metals increased with increasing exposure time. Response times varied for different metals with amphipods responding faster to copper than to cadmium, lead or zinc. As indicated by 30 days lethal concentration (LC50) estimates, copper was the most toxic metal (31 µg/L), followed by cadmium (168 µg/L), lead (256 µg/L) and zinc (822 µg/L). Nickel exposure (up to 1.12 mg/L) did not affect amphipod survival. Using longer exposure durations and utilising the GAMM model provides an improved methodology for assessing sensitivities of slow responding Antarctic marine invertebrates to contaminants.

Pro-oxidative synergic bactericidal effect of NO: kinetics and inhibition by nitroxides

NO plays diverse roles in physiological and pathological processes, occasionally resulting in opposing effects, particularly in cells subjected to oxidative stress. NO mostly protects eukaryotes against oxidative injury, but was demonstrated to kill prokaryotes synergistically with H2O2. This could be a promising therapeutic avenue. However, recent conflicting findings were reported describing dramatic protective activity of NO. The previous studies of NO effects on prokaryotes applied a transient oxidative stress while arbitrarily checking the residual bacterial viability after 30 or 60min and ignoring the process kinetics. If NO-induced synergy and the oxidative stress are time-dependent, the elucidation of the cell killing kinetics is essential, particularly for survival curves exhibiting a "shoulder" sometimes reflecting sublethal damage as in the linear-quadratic survival models. We studied the kinetics of NO synergic effects on H2O2-induced killing of microbial pathogens. A synergic pro-oxidative activity toward gram-negative and gram-positive cells is demonstrated even at sub-μM/min flux of NO. For certain strains, the synergic effect progressively increased with the duration of cell exposure, and the linear-quadratic survival model best fit the observed survival data. In contrast to the failure of SOD to affect the bactericidal process, nitroxide SOD mimics abrogated the pro-oxidative synergy of NO/H2O2. These cell-permeative antioxidants, which hardly react with diamagnetic species and react neither with NO nor with H2O2, can detoxify redox-active transition metals and catalytically remove intracellular superoxide and nitrogen-derived reactive species such as (•)NO2 or peroxynitrite. The possible mechanism underlying the bactericidal NO synergy under oxidative stress and the potential therapeutic gain are discussed.

Breeding biology, adult survival and territoriality of the white-browed treecreeper (climacteris affinis) in north-west Victoria, Australia

This is the first study to present empirical data describing the social organisation and breeding biology of the White-browed Treecreeper (Climacteris affinis). The species is typical of many small Australian passerines in that it has high annual survival (~80%), small clutches (mean = 1.95 ± 0.05), long breeding seasons (eggs laid August to November) and long incubation (17–18 days) and nestling periods (25–26 days), corrected for body weight. Reproductive effort is modified in response to variation in climatic conditions by adjusting the commencement of breeding and number of clutches laid per season, which is facilitated by an extended breeding season. White-browed Treecreepers occupied relatively large (mean = 8.4 ± 0.8 ha), all-purpose territories throughout the year. However, unlike many group territorial birds, territory size was not related to the number of occupants. The role of food limitation and climatic variability in relation to territory dispersion and life-history traits is explored. Facultative cooperative breeding was confirmed. Cooperative groups were formed through male philopatry, with usually only one, but up to three, male helpers present in a moderate fraction (35%) of breeding units. Thus, all species of Climacteris are now confirmed as facultative cooperatively breeding species, which provides further evidence for the aggregation of cooperative breeders at the generic level in mixed (i.e. cooperative and pair breeders) phylogenetic clades. In C. affinis, males may attain breeding positions through inheritance of their natal territory or by filling vacancies in nearby territories. Females obtained breeding positions by ‘floating’ as non-breeding residents in established territories, waiting for a vacancy to arise.

Survival of relatives of patients with hepatocellular carcinoma

Background:Families of patients with hepatocellular carcinoma (HCC) carry a high risk of developing HCC. We determine the number of fatalities in relatives of HCC patients during an 8-year period to understand the risk and cause of HCC in relatives of patients with HCC.
Methods:From 1992 to 1997, 15 410 relatives of HCC patients in three generations were screened prospectively for HCC by ultrasonography, α-fetoprotein, liver biochemistry and viral markers. By using national citizen identification numbers, we searched the total fatalities in relatives of HCC patients between 1992 and 1999 from the national mortality data bank. The results were compared among different viral infection groups.
Results:Of the relatives studied, 37.8% were hepatitis B s antigen (HBsAg) positive (+), 4.3% were anti-hepatitis C virus (HCV) (+) and 1.7% were both HBsAg (+) and anti-HCV (+). A total of 399 fatalities, including 139 because of HCC (34.8%), 37 because of liver diseases (9.3%), 88 because of other cancers (22.1%) and 135 because of other diseases (33.8%), were found. Relatives who were HBsAg (+) or anti-HCV (+)showed a lower cumulative survival than did relatives who were negative for both HBsAg and anti-HCV. Relatives with dual infection of hepatitis B and C virus showed the highest mortality due to HCC or terminal liver diseases.
Conclusions:Chronic viral infection rather than a hereditary factor is the main cause of a familial tendency for HCC. Dual infection of hepatitis B and C virus increases the risk of HCC or decompensated liver diseases.
Background:Families of patients with hepatocellular carcinoma (HCC) carry a high risk of developing HCC. We determine the number of fatalities in relatives of HCC patients during an 8-year period to understand the risk and cause of HCC in relatives of patients with HCC.
Methods:From 1992 to 1997, 15 410 relatives of HCC patients in three generations were screened prospectively for HCC by ultrasonography, α-fetoprotein, liver biochemistry and viral markers. By using national citizen identification numbers, we searched the total fatalities in relatives of HCC patients between 1992 and 1999 from the national mortality data bank. The results were compared among different viral infection groups.
Results:Of the relatives studied, 37.8% were hepatitis B s antigen (HBsAg) positive (+), 4.3% were anti-hepatitis C virus (HCV) (+) and 1.7% were both HBsAg (+) and anti-HCV (+). A total of 399 fatalities, including 139 because of HCC (34.8%), 37 because of liver diseases (9.3%), 88 because of other cancers (22.1%) and 135 because of other diseases (33.8%), were found. Relatives who were HBsAg (+) or anti-HCV (+)showed a lower cumulative survival than did relatives who were negative for both HBsAg and anti-HCV. Relatives with dual infection of hepatitis B and C virus showed the highest mortality due to HCC or terminal liver diseases.
Conclusions:Chronic viral infection rather than a hereditary factor is the main cause of a familial tendency for HCC. Dual infection of hepatitis B and C virus increases the risk of HCC or decompensated liver diseases.

Commercial sex work, survival sex, sexual violence and HIV/AIDS prevention in Arumeru District, Arusha region Of Tanzania

Objective: To examine the knowledge and practices about HIV/AIDS among female Tanzanian commercial sex workers (CSWs) and assess the contextual dynamics that prevent safer sexual behaviours.

Method: The study used mixed methods and was implemented in two phases. Phase one assessed the knowledge and practices about HIV/AIDS among CSWs. Data were obtained with 54 CSWs, who were selected by using a snowball sampling approach. Semi-structured, face-to-face interviews with the CSWs were undertaken to allow the research participants to describe and discuss their lived realities as they perceive and experience them. In phase two, three discrete focus group discussions, each comprising 6-10 women, were carried out with 26 of the 54 CSWs who were interviewed in phase one.

Results: There was exploitation and inequity in the women's lives due to the multiple and overlapping oppressions of poverty and patriarchy. Sexual violence was framed, legitimised and reinforced by structural and cultural inequities. Such exploitation impacted not only on CSWs' lives as sex workers, but on their previous and/or simultaneous lives as mothers, wives, girlfriends and daughters. The women practised ‘survival sex’ as CSWs and/or sexual partners of men, and experienced sexual violence from their clients/partners. This violence was either culturally legitimised within a patriarchal framework or manifested itself as ‘displaced aggressive sex’ by men experiencing marginalisation in socio-economic spheres.

Estimating survival and movements using both live and dead recoveries : a case study of oystercatchers confronted with habitat change

1. Animals facing partial habitat loss can try to survive in the remaining habitat or emigrate. Effects on survival and movements should be studied simultaneously since survival rates may be underestimated if emigrants are not considered, and since emigrants may experience reduced survival.

2. We analysed movements and survival of adult wintering oystercatcher Haematopus ostralegus in response to the 1986–1987 partial closure of the Oosterschelde in the Dutch Delta. This reduced by one-third the tidal area of this major European wintering area for waders.

3. We developed a novel variant of a multistate capture–recapture model allowing simultaneous estimation of survival and movement between sites using a mixture of data (live recaptures and dead recoveries). We used a two-step process, first estimating movements between sites followed by site-specific survival rates.

4. Most birds were faithful to their ringing site. Winter survival was negatively affected by winter severity and was lowest among birds changing wintering site (i.e. moving outside of the Oosterschelde).

5. During mild winters, survival rates were very high, and similar to before the closure in both changed and unchanged sectors of the Oosterschelde. However, the combined effect of habitat loss with severe winters decreased the survival of birds from changed sectors and induced emigration.

6. The coastal engineering project coincided with three severe winters and high food stock, making assessment of its effects difficult. However, the habitat loss seems to have had less impact on adult survival and movements than did winter severity.

7. Synthesis and applications. Human-induced habitat change may result in population decline through costly emigration or reduced survival or reproduction of individuals that stay. Long-term monitoring of marked individuals helps to understand how populations respond to environmental change, but site-specific survival and movement rates should be integrated in the same model in order to maximize the information yield. Our modelling approach facilitates this because it allows the inclusion of recoveries from outside the study area.

Introgression of domesticated alleles into a wild trout genotype and the impact on seasonal survival in natural lakes

We tested the fitness consequences of introgression of fast-growing domesticated fish into a wild population. Fry from wild and domesticated rainbow trout (Oncorhynchus mykiss) crosses, F1 hybrids, and first- and second-generation backcrosses were released into two natural lakes. Parentage analysis using microsatellite loci facilitated the identification of survivors, so fitness was estimated in nature from the first-feeding stage. Results indicated that under certain conditions, domesticated fish survived at least as well as wild fish within the same environment. Relative growth and survival of the crosses, however, were highly dependent on environment. During the first summer, fastest-growing crosses had the highest survival, but this trend was reversed after one winter and another summer. Although the F1 hybrids showed evidence of outbreeding depression because of the disruption of local adaptation, there was little evidence of outbreeding depression in the backcrosses, and the second-generation backcrosses exhibited a wild-type phenotype. This information is relevant for assessing the multigenerational risk of escaped or released domesticated fish should they successfully interbreed with wild populations and provides information on how to minimize detrimental impacts of a conservation breeding and/or management programme. These data also further understanding of the selection pressures in nature that maintain submaximal rates of growth.

A comparative analysis of decision trees vis-à-vis other computational data mining techniques in automotive insurance fraud detection

The development and application of computational data mining techniques in financial fraud detection and business failure prediction has become a popular cross-disciplinary research area in recent times involving financial economists, forensic accountants and computational modellers. Some of the computational techniques popularly used in the context of - financial fraud detection and business failure prediction can also be effectively applied in the detection of fraudulent insurance claims and therefore, can be of immense practical value to the insurance industry. We provide a comparative analysis of prediction performance of a battery of data mining techniques using real-life automotive insurance fraud data. While the data we have used in our paper is US-based, the computational techniques we have tested can be adapted and generally applied to detect similar insurance frauds in other countries as well where an organized automotive insurance industry exists.

Early diagnosis and treatment of necrotizing fasciitis can improve survival : an observational intensive care unit cohort study

Background
The aim of this study was to describe the clinical characteristics, causative pathogens, clinical management and outcomes of patients presenting to a tertiary adult Australian intensive care unit (ICU) with a diagnosis of necrotizing fasciitis (NF).
Methods
This retrospective observational study was conducted in a 19-bed, level III, adult ICU in a 450-bed tertiary, regional hospital. Clinical databases were accessed for patients diagnosed with NF and admitted to The Geelong Hospital ICU between 1 February 2000 and 1 June 2011. Information on severity of sepsis, surgical procedures and microbiological results were collected.
Results
Twenty patients with NF were identified. The median age was 52.5 years and 38% were female. The overall mortality rate was 8.3%. Common co-morbidities were diabetes (21%) and heart failure (17%), although 50% of patients had no co-morbidities. Group A Streptococcus was the identified pathogen in 11 (46%) patients, and Streptococcus milleri group in 5 (21%) patients. Hyperbaric oxygen therapy was not used in the majority of patients. The initial antibiotics administered were active against subsequently cultured bacteria in 83% of patients. Median time to surgical debridement was 20 h. Diagnosis and management was delayed in the nosocomial group.
Conclusions
This study reports physiological data, aetiology and therapeutic interventions in NF for an adult tertiary hospital. We demonstrate one of the lowest reported mortality rates, with early surgical debridement being achieved in the majority of patients. The main delay was found to be in the diagnosis of NF.

Death or survival from invasive pneumococcal disease in Scotland: associations with serogroups and multilocus sequence types

We describe associations between death from invasive pneumococcal disease (IPD) and particular serogroups and sequence types (STs) determined by multilocus sequence typing (MLST) using data from Scotland. All IPD episodes where blood or cerebrospinal fluid (CSF) culture isolates were referred to the Scottish Haemophilus, Legionella, Meningococcal and Pneumococcal Reference Laboratory (SHLMPRL) from January 1992 to February 2007 were matched to death certification records by the General Register Office for Scotland. This represented 5959 patients. The median number of IPD cases in Scotland each year was 292. Deaths, from any cause, within 30 days of pneumococcal culture from blood or CSF were considered to have IPD as a contributing factor. Eight hundred and thirty-three patients died within 30 days of culture of Streptococcus pneumoniae from blood or CSF [13.95 %; 95 % confidence interval (13.10, 14.80)]. The highest death rates were in patients over the age of 75. Serotyping data exist for all years but MLST data were only available from 2001 onward. The risk ratio of dying from infection due to particular serogroups or STs compared to dying from IPD due to all other serogroups or STs was calculated. Fisher’s exact test with Bonferroni adjustment for multiple testing was used. Age adjustment was accomplished using the Cochran–Mantel–Haenszel test and 95 % confidence intervals were reported. Serogroups 3, 11 and 16 have increased probability of causing fatal IPD in Scotland while serogroup 1 IPD has a reduced probability of causing death. None of the 20 most common STs were significantly associated with death within 30 days of pneumococcal culture, after age adjustment. We conclude that there is a stronger association between a fatal outcome and pneumococcal capsular serogroup than there is between a fatal outcome and ST.