Survival analyses

Survival analyses are a key tool for demographers, ecologists, and evolutionary biologists. This chapter presents the most common methods and illustrates their use for species across the Tree of Life. It discusses the challenges associated with various types of survival data, how to model species with a complex life cycle, and includes the impact of environmental factors and individual heterogeneity. It covers the analysis of ‘known-fate’ data collected in lab conditions, using the Kaplan–Meier estimator and Cox’s proportional hazard regression analysis. Alternatively, survival data collected on free-ranging populations usually involve individuals missing at certain monitoring occasions and unknown time at death. The chapter provides an overview of capture–mark–recapture (CMR) models, from single-state to multi-state and multi-event models, and their use in animal and plant demography to estimate demographic parameters while correcting for imperfect detection of individuals. It discusses various inference frameworks available to implement CMR models using a frequentist or Bayesian approach. Only humans are an exception among free-ranging populations, with the existence of several consequent databases with perfect knowledge of age and cause of death for all individuals. The chapter presents an overview of the most common models used to describe mortality patterns over age and time using human mortality data. Throughout, focus is placed on eight case studies, which involve lab organisms, free-ranging animal populations, plant populations, and human populations. Each example includes data and codes, together with step-by-step guidance to run the survival analysis.

Download Full-text

Experimentally increased noise levels change spatial and singing behaviour

Biology Letters ◽

10.1098/rsbl.2012.0771 ◽

2013 ◽

Vol 9 (1) ◽

pp. 20120771 ◽

Cited By ~ 26

Author(s):

Kirsty Elizabeth McLaughlin ◽

Hansjoerg P. Kunc

Keyword(s):

Noise Source ◽

Noise Pollution ◽

Erithacus Rubecula ◽

Noise Levels ◽

Acoustic Environment ◽

Animal Populations ◽

Suitable Habitats ◽

Free Ranging ◽

The Impact ◽

New Infrastructure

The reasons why animal populations decline in response to anthropogenic noise are still poorly understood. To understand how populations are affected by noise, we must understand how individuals are affected by noise. By modifying the acoustic environment experimentally, we studied the potential relationship between noise levels and both spatial and singing behaviour in the European robin ( Erithacus rubecula ). We found that with increasing noise levels, males were more likely to move away from the noise source and changed their singing behaviour. Our results provide the first experimental evidence in a free ranging species, that not merely the presence of noise causes changes in behaviour and distribution, but that the level of noise pollution plays a crucial role as well. Our results have important implications for estimating the impact of infrastructure which differs in the level of noise produced. Thus, governmental planning bodies should not only consider the physical effect on the landscape when assessing the impact of new infrastructure, but also the noise levels emitted, which may reduce the loss of suitable habitats available for animals.

Download Full-text

The impact of novel lyssavirus discovery

Microbiology Australia ◽

10.1071/ma17006 ◽

2017 ◽

Vol 38 (1) ◽

pp. 17 ◽

Cited By ~ 18

Author(s):

Ashley C Banyard ◽

Anthony R Fooks

Keyword(s):

Rabies Virus ◽

Human Exposure ◽

Animal Health ◽

Potential Effect ◽

Human Populations ◽

Human Society ◽

Scientific Interest ◽

Animal Populations ◽

Potential Impact ◽

The Impact

The global discovery of novel lyssaviruses is of continued scientific interest through its importance to both public and animal health. Lyssaviruses cause an invariably fatal encephalitis that is more commonly known as rabies. The term rabies has a long history in human society, as rabies virus (RABV) is the only pathogen that is associated with 100% fatality once the onset of clinical disease has started. Although predominantly associated across the globe with domestic and feral dog populations, the association of bats is clear. Whilst evolutionarily associated with bats, RABV is most commonly transmitted to human populations through the bite of an infected dog and dogs are considered the primary reservoir of disease. Indeed, RABV does cause more than an estimated 70000 deaths every year globally in human populations and whilst this is largely in areas where the disease is endemic, areas that remain free of rabies must remain vigilant to the risk of re-incursion of disease. Characterisation of novel lyssaviruses is of importance on several levels. Not least to investigate the pathogenesis and potential transmission routes of different lyssavirus species but also to assess the potential effect of post-exposure treatments and vaccination should human exposure occur. Bat lyssaviruses and the problems associated with novel discoveries and the potential impact they have on both human and animal populations are discussed.

Download Full-text

Impact of gender on the survival of patients with glioblastoma

Bioscience Reports ◽

10.1042/bsr20180752 ◽

2018 ◽

Vol 38 (6) ◽

Cited By ~ 21

Author(s):

Minjie Tian ◽

Wenying Ma ◽

Yueqiu Chen ◽

Yue Yu ◽

Donglin Zhu ◽

...

Keyword(s):

Sex Hormones ◽

Survival Data ◽

Cox Regression ◽

Population Based ◽

Cancer Specific Survival ◽

Term Survival ◽

Kaplan Meier ◽

Male Patients ◽

Stratified Analysis ◽

The Impact

Background: Preclinical models have suggested a role for sex hormones in the development of glioblastoma multiforme (GBM). However, the impact of gender on the survival time of patients with GBM has not been fully understood. The objective of the present study was to clarify the association between gender and survival of patients with GBM by analyzing population-based data. Methods: We searched the Surveillance, Epidemiology, and End-Results database who were diagnosed with GBM between 2000 and 2008 and were treated with surgery. Five-year cancer specific survival data were obtained. Kaplan–Meier methods and multivariable Cox regression models were used to analyze long-term survival outcomes and risk factors. Results: A total of 6586 patients were identified; 61.5% were men and 38.5% were women. The 5-year cancer-specific survival (CSS) rates in the male and female groups were 6.8% and 8.3%, respectively (P=0.002 by univariate and P<0.001 by multivariate analysis). A stratified analysis showed that male patients always had the lowest CSS rate across localized cancer stage and different age subgroups. Conclusions: Gender has prognostic value for determining GBM risk. The role of sex hormones in the development of GBM warrants further investigation.

Download Full-text

Early Pseudoprogression following Chemoradiotherapy in Glioblastoma Patients: The Value of RANO Evaluation

Journal of Oncology ◽

10.1155/2013/690585 ◽

2013 ◽

Vol 2013 ◽

pp. 1-9 ◽

Cited By ~ 33

Author(s):

Paulo Linhares ◽

Bruno Carvalho ◽

Rita Figueiredo ◽

Rui M. Reis ◽

Rui Vaz

Keyword(s):

Survival Data ◽

Response Assessment ◽

Rank Analysis ◽

Rano Criteria ◽

Macdonald Criteria ◽

Kaplan Meier ◽

Early Progression ◽

Radiological Response ◽

The Impact ◽

True Progression

Introduction. The aim of this study was to determine the frequency of pseudoprogression in a cohort of glioblastoma (GBM) patients following radiotherapy/temozolomide (RT/TMZ) by comparing Macdonald criterial to Response Assessment in Neuro-Oncology (RANO) criteria. The impact on prognosis and survival analysis was also studied.Materials and Methods. All patients receiving RT/TMZ for newly diagnosed GBM from January 2005 to December 2009 were retrospectively evaluated, and demographic, clinical, radiographic, treatment, and survival data were reviewed. Updated RANO criteria were used for the evaluation of the pre-RT and post-RT MRI and compared to classic Macdonald criteria. Survival data was evaluated using the Kaplan-Meier and log-rank analysis.Results and Discussion. 70 patients were available for full radiological response assessment. Early progression was confirmed in 42 patients (60%) according to Macdonald criteria and 15 patients (21%) according to RANO criteria. Pseudoprogression was identified in 10 (23.8%) or 2 (13.3%) patients in Macdonald and RANO groups, respectively. Cumulative survival of pseudoprogression group was higher than that of true progression group and not statistically different from the non-progressive disease group.Conclusion. In this cohort, the frequency of pseudoprogression varied between 13% and 24%, being overdiagnosed by older Macdonald criteria, which emphasizes the importance of RANO criteria and new radiological biomarkers for correct response evaluation.

Download Full-text

Food and fitness: associations between crop yields and life-history traits in a longitudinally monitored pre-industrial human population

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2012.1190 ◽

2012 ◽

Vol 279 (1745) ◽

pp. 4165-4173 ◽

Cited By ~ 22

Author(s):

Adam D. Hayward ◽

Jari Holopainen ◽

Jenni E. Pettay ◽

Virpi Lummaa

Keyword(s):

Natural Selection ◽

Crop Yields ◽

Economic Status ◽

Food Shortage ◽

Human Populations ◽

Fitness Traits ◽

Animal Populations ◽

Specific Mortality ◽

Selection For ◽

The Impact

Severe food shortage is associated with increased mortality and reduced reproductive success in contemporary and historical human populations. Studies of wild animal populations have shown that subtle variation in environmental conditions can influence patterns of mortality, fecundity and natural selection, but the fitness implications of such subtle variation on human populations are unclear. Here, we use longitudinal data on local grain production, births, marriages and mortality so as to assess the impact of crop yield variation on individual age-specific mortality and fecundity in two pre-industrial Finnish populations. Although crop yields and fitness traits showed profound year-to-year variation across the 70-year study period, associations between crop yields and mortality or fecundity were generally weak. However, post-reproductive individuals of both sexes, and individuals of lower socio-economic status experienced higher mortality when crop yields were low. This is the first longitudinal, individual-based study of the associations between environmental variation and fitness traits in pre-industrial humans, which emphasizes the importance of a portfolio of mechanisms for coping with low food availability in such populations. The results are consistent with evolutionary ecological predictions that natural selection for resilience to food shortage is likely to weaken with age and be most severe on those with the fewest resources.

Download Full-text

Comparative survival of cancer patients requiring Israeli permits to exit the Gaza Strip for health care: A retrospective cohort study from 2008 to 2017

PLoS ONE ◽

10.1371/journal.pone.0251058 ◽

2021 ◽

Vol 16 (6) ◽

pp. e0251058

Author(s):

Benjamin Bouquet ◽

Francesco Barone-Adesi ◽

Mohamed Lafi ◽

Kathryn Quanstrom ◽

Federica Riccardi ◽

...

Keyword(s):

Cancer Patients ◽

Cox Regression ◽

Gaza Strip ◽

Mortality Data ◽

Primary Analysis ◽

Kaplan Meier ◽

Significant Difference ◽

The Difference ◽

The Gaza Strip ◽

The Impact

Background Gaza has been under land, sea, and aerial closure for 13 years, during which time Palestinian patients from Gaza have been required to obtain Israeli-issued permits to access health facilities in the West Bank (including east Jerusalem), as well as in Israel and Jordan. Specific groups, like cancer patients, have a high need for permits due to lack of services in Gaza. The approval rate for patient permits to exit Gaza dropped from 94% in 2012 to 54% in 2017. We aimed to assess the impact of access restrictions due to permit denials/delays on all-cause mortality for cancer patients from Gaza referred for chemotherapy and/or radiotherapy. Methods This study matched 17,072 permit applications for 3,816 cancer patients referred for chemotherapy and/or radiotherapy from 1 January 2008 to 31 December 2017 with referrals data for the same period and mortality data from 1 January 2008 to 30 June 2018. We carried out separate analyses by period of first application (2008–14; 2015–17), in light of varying access to Egypt during these times. Primary analysis compared survival of patients according to their first referral decision (approved versus denied/delayed) using Kaplan-Meier method and Cox regression. Findings Mortality in patients unsuccessful in permit applications from 2015–17 was significantly higher than mortality among successful patients, with a hazard ratio of 1·45 (95% CI: 1·19–1·78, p<0.001), after adjusting for age, sex, type of procedure, and type of cancer. There was no significant difference in mortality risk for the two groups in the 2008–2014 period. Interpretation Limitations to patient access due to unsuccessful applications for permits to exit the Gaza Strip had a significant impact on mortality for cancer patients applying for chemotherapy and/or radiotherapy in the period 2015–17. The substantially higher number of annual unsuccessful permit applications from 2015, combined with severely limited alternatives to access chemotherapy and radiotherapy during these years, may be important factors to explain the difference in the impact of permits delays/denials between the two study periods.

Download Full-text

Food Safety Considerations Related to the Consumption and Handling of Game Meat in North America

Veterinary Sciences ◽

10.3390/vetsci7040188 ◽

2020 ◽

Vol 7 (4) ◽

pp. 188

Author(s):

Hayden D. Hedman ◽

Csaba Varga ◽

Jared Duquette ◽

Jan Novakofski ◽

Nohra E. Mateus-Pinilla

Keyword(s):

Food Safety ◽

North America ◽

Foodborne Pathogens ◽

Foodborne Diseases ◽

Human Populations ◽

Foodborne Disease ◽

Game Meat ◽

Animal Populations ◽

Increased Risk ◽

Free Ranging

Emerging foodborne pathogens present a threat to public health. It is now recognized that several foodborne pathogens originate from wildlife as demonstrated by recent global disease outbreaks. Zoonotic spillover events are closely related to the ubiquity of parasitic, bacterial, and viral pathogens present within human and animal populations and their surrounding environment. Foodborne diseases have economic and international trade impacts, incentivizing effective wildlife disease management. In North America, there are no food safety standards for handling and consumption of free-ranging game meat. Game meat consumption continues to rise in North America; however, this growing practice could place recreational hunters and game meat consumers at increased risk of foodborne diseases. Recreational hunters should follow effective game meat food hygiene practices from harvest to storage and consumption. Here, we provide a synthesis review that evaluates the ecological and epidemiological drivers of foodborne disease risk in North American hunter populations that are associated with the harvest and consumption of terrestrial mammal game meat. We anticipate this work could serve as a foundation of preventive measures that mitigate foodborne disease transmission between free-ranging mammalian and human populations.

Download Full-text

EP.TU.142Impact of PC-CRC on curative intent and survival of patients

British Journal of Surgery ◽

10.1093/bjs/znab311.015 ◽

2021 ◽

Vol 108 (Supplement_7) ◽

Author(s):

Karim Elsayeh ◽

Alexander Brown ◽

Srinivas Chintapatla ◽

Michael Lim

Keyword(s):

Median Survival ◽

Metastatic Disease ◽

Survival Data ◽

Delayed Diagnosis ◽

Rank Test ◽

P Value ◽

Curative Intent ◽

Kaplan Meier ◽

Diagnosis Of Cancer ◽

The Impact

Abstract Introduction PC-CRC is an important benchmark of endoscopy performance and results in a delayed diagnosis of cancer for patients. Little is known of the impact of PC-CRC on survival; we chose to study this in a cohort of patient at our institution. Methods A retrospective analysis was performed on all PC-CRC from 2015 to 2020. Electronic endoscopic records and case-note review were performed to identify cases. Suitable patients underwent surgery in the absence of widespread metastatic disease after MDT discussion. Survival data were recorded, Kaplan-Meier curves were constructed; the log rank test was used to compare groups, a p-value of < 0.05 was deemed significant. Results There were 32 (24 male) patients with a PC-CRC out of 1207 patients during this interval. The 5-year PC-CRC rate was 2.6%. Median age was 72 (IQR 63-79) years. 10 patients had metastatic disease, 9 with large volume disease that was not resectable. All 9 were palliated with a median survival of 3 (IQR 2-23) months. Twenty-three had potentially curative disease and all underwent surgery. On follow-up a further seven patients died with recurrent disease at a median of 19 (IQR 13-35) months. Sixteen are alive with a median survival of 38 (IQR 27-52) months. The survival curves for the 3 groups are significantly divergent, p-value <0.001. Conclusion The impact of PC-CRC on individual patients is significant as a quarter die within 3 months of diagnosis. A further quarter die within 24 months despite a potentially curative operation due to metastatic disease.

Download Full-text

The influence of variant histology on survival outcomes of radical cystectomy for bladder cancer.

Journal of Clinical Oncology ◽

10.1200/jco.2012.30.5_suppl.278 ◽

2012 ◽

Vol 30 (5_suppl) ◽

pp. 278-278

Author(s):

Adrian Stuart Fairey ◽

Eila C. Skinner ◽

Anne Schuckman ◽

Gary Leiskovsky ◽

Jie Cai ◽

...

Keyword(s):

Bladder Cancer ◽

Urothelial Carcinoma ◽

Radical Cystectomy ◽

Survival Data ◽

Multivariable Analysis ◽

High Risk Group ◽

Kaplan Meier ◽

Variant Histology ◽

Primary Bladder ◽

The Impact

278 Background: The role of variant histology bladder cancer as an independent prognostic factor for survival after radical cystectomy is poorly defined. Our aim was to examine the impact of variant histology on survival. Methods: A retrospective analysis of prospectively collected data from the University of Southern California Bladder Cancer Database was performed. Between 1971 and 2008, 2098 patients underwent radical cystectomy and extended pelvic lymph node dissection for primary bladder cancer. All surgical specimens underwent centralized pathologic review by dedicated genitourinary pathologists. Histologic type was categorized according to the WHO/ISUP 1998 classification as urothelial carcinoma (UC; n=1595), UC + variant (n=380), or non-urothelial carcinoma (Non-UC; n=123). The outcomes were overall survival (OS) and recurrence-free survival (RFS). The Kaplan-Meier method and Cox proportional regression models were used to analyze survival data. Results: The median follow-up duration was 12.8 years (range, 0 to 36.6 years). The predicted 5-year OS (61%, 53%, and 47%, Log rank p=0.005) and RFS (68%, 59%, and 58%, Log rank p=0.001) rates differed between patients with UC, UC + variant, and Non-UC histology. Multivariable analysis showed that Non-UC (but not UC + variant) histology was independently associated with OS (Non-UC versus UC: HR 1.26, 95% CI 1.01 to 1.57, p=0.040; UC + variant versus UC: HR 0.97, 95% CI 0.85 to 1.12, p=0.697) but not RFS (Non-UC versus UC: HR 1.14, 95% CI 0.83 to 1.56, p=0.411; UC + variant versus UC: HR 1.06, 95% CI 0.88 to 1.28, p=0.551). Conclusions: Non-UC histology was independently associated with poorer OS after radical cystectomy for bladder cancer. Clinical trials are needed to determine whether this high risk group will benefit from multimodal therapy.

Download Full-text

Efficacy of Chemotherapy for Malignant Pleural Mesothelioma According to Histology

10.21203/rs.3.rs-677246/v1 ◽

2021 ◽

Author(s):

Susana Cedres ◽

Juan David Assaf ◽

Patricia Iranzo ◽

Ana Callejo ◽

Nuria Pardo ◽

...

Keyword(s):

Survival Data ◽

Cox Regression ◽

Progression Free Survival ◽

University Hospital ◽

First Line ◽

Kaplan Meier ◽

Platinum Agent ◽

Clinical Records ◽

The Impact ◽

Line Chemotherapy

Abstract PurposeCheckMate 743 trial demonstrated survival benefit of immunotherapy in first line in MPM with some differences in the efficacy of chemotherapy according to histology. The objective of this study is to characterize the impact of chemotherapy according to histology in patients diagnosed with MPM at our institution. MethodsClinical records of all MPM patients diagnosed at Vall d´Hebron University Hospital between November 2002 and April 2020 were reviewed. Associations between clinical variables and outcomes were assessed with Cox regression models. Survival data were calculated by the Kaplan-Meier method. Results189 patients were included with 76% of tumors classified as epithelioid subtype. First line chemotherapy was offered to 85% of patients. Median survival in overall population was 21.3 months (95%CI17.2-24.3). We found that patients with epithelioid tumors had better overall survival (OS) and progression free survival (PFS). Median OS of epithelioid patients treated with first line chemotherapy was 26.7 months versus 15.0 months in nonepithelioid patients (HR2.25 CI95% 1.4-3.4; p<0.001). Median PFS for patients with epithelioid tumors treated with chemotherapy was 4.8 months versus 3.6 months in nonepithelioid (HR1.5 CI95% 1.0-2.3; p=0.03). The improvement of outcomes in patients with epithelioid histology was detected in patients treated with cisplatin or carboplatin. Histology was not a predictive factor for the platinum agent sensitivity (p of interaction PFS=0.09, p of interaction OS=0.65). Conclusions In our series, patients with nonepithelioid tumors presented worse prognosis. Although epithelioid tumors exposed to cisplatin had higher PFS, histology was not a clear predictor of chemotherapy efficacy.

Download Full-text