On a probability Model for Classifying the Unknown Causes of Death Due to Two Competing Risks into Assignable Causes

A probability model to classify the otherwise unclassified causes of death due to two competing risks R₁ and R₂ has been evolved in this paper. A simple model based on Poisson inputs has been illustrated by numerical illustrations. Further generalization of the model with more than two competing risks is straightforward for the given model.     

The impact of under and over-recording of cancer on death certificates in a competing risks analysis: A simulation study

Background: With linked register and cause of death data becoming more accessible than ever, competing risks methodology is being increasingly used as a way of obtaining “real world” probabilities of death broken down by specific causes. It is important, in terms of the validity of these studies, to have accurate cause of death information. However, it is well documented that cause of death information taken from death certificates is often lacking in accuracy and completeness. Methods: We assess through use of a simulation study the effect of under and over-recording of cancer on death certificates in a competing risks analysis consisting of three competing causes of death: cancer, heart disease and other causes. Using realistic levels of misclassification, we consider 24 scenarios and examine the bias in the cause-specific hazard ratios and the cumulative incidence function. Results: The bias in the cumulative incidence function was highest in the oldest age group reaching values as high as 2.6 percentage units for the “good” cancer prognosis scenario and 9.7 percentage units for the “poor” prognosis scenario. Conclusion: The bias resulting from the chosen levels of misclassification in this study accentuate concerns that unreliable cause of death information may be providing misleading results. The results of this simulation study convey an important message to applied epidemiological researchers.     

Interspecific competition between Drosophila melanogaster and Drosophila simulans: Effects of adult density on adult viability

Survival (viability) of newly eclosed adults of D. simulans st and D. melanogaster Or R-C, which had excess quantities of dead yeast available throughout life, was measured daily for 7 days in an experiment where adult density (6 levels), species frequency (6 levels) and ³²P tissue content (2 levels) were varied factorially. A separate experiment comparing viability in different types of experimental unit also was done. Similar experiments were done for D. simulans st competing against D. melanogaster y w. The entire data were subjected to a least-squares (unbalanced, missing-plot) analysis of variance. D. melanogaster Or R-C had a higher average viability than D. melanogaster y w or D. simulans st, which were equal. The competing strain of D. melanogaster influenced D. simulans st viability — viability being higher when y w was the competitor. Viability decreased over the seven day period but at different rates for the three strains. Increasing density reduced viability for all three strains, but species frequency effects, although significant, were generally not consistent. Females had higher viability than males in both D. melanogaster strains, but the reverse was true in D. simulans st. ³²P lowered viability and experimental unit type altered viability. Numerous interactions were significant.Adult density was shown to have a delayed effect on viability — the delay before the appearance of the effect (an increase in death rate) being decreased as density rose. The term variably delayed density dependent has been adopted to describe the fitness component, adult viability. Some high density populations showed a readjustment (a decrease) in their death rate as a reaction to the effect of reduced density caused by high early mortality.     

The effects of chrysomelid beetle grazing and plant competition on the growth of Rumex obtusifolius

Summary The interaction between grazing by Gastrophysa viridula and interspecific plant competition was investigated for Rumex obtusifolius growing in the field. During an eight-month growing season non-competing R. obtusifolius grew larger than competing plants although herbivore loads (beetle productivity per unit leaf area) were similar for competing and non-competing plants. However, grazing significantly reduced the growth of R. obtusifolius only in competing plants thus demonstrating a synergism between plant competition and invertebrate herbivory. The relevance of these findings for the distribution of plant species is discussed.     

Host–parasitoid interaction as affected by interkingdom competition

Although still underrepresented in ecological research, competitive interactions between distantly related organisms (so-called “interkingdom competition”) are expected to be widespread in various ecosystems, with yet unknown consequences for, e.g. trophic interactions. In the model host–parasitoid system Drosophila melanogaster–Asobara tabida, toxic filamentous fungi have been shown to be serious competitors that critically affect the density-dependent survival of host Drosophila larvae. This study investigates the extent to which the competing mould Aspergillus niger affects key properties of the well-studied Drosophila–parasitoid system and how the host–parasitoid interaction influences the microbial competitor. In contrast to slightly positive density-dependent host mortality under mould-free conditions, competing A. niger mediated a strong Allee effect for parasitised larvae, i.e. mortality decreased with increasing larval density. It was found that the common toxic fungal metabolite kojic acid is not responsible for higher death rates in parasitised larvae. Single parasitised Drosophila larvae were less harmful to fungal reproduction than unparasitised larvae, but this effect vanished with an increase in larval density. As predicted from the negative effect of fungi on host survival and thus on parasitoid fitness at low larval densities, A. tabida females spent less time foraging in fungus-infested patches. Interestingly, even though high host larval densities increased host survival, parasitoids still reduced their search efforts in fungus-infested patches, indicating a benefit for host larvae from feeding in the presence of noxious mould. Thus, this experimental study provides evidence of the potentially important role of interkingdom competition in determining trophic interactions in saprophagous animal communities and the dynamics of both host–parasitoid and microbial populations.     

Interspecific interference and the functional response of four species of carnivorous stoneflies

1. A previous study compared the functional responses to their prey and intraspecific interference in mature larvae of Perlodes microcephalus, Isoperla grammatica, Dinocras cephalotes and Perla bipunctata. The present study extends this work by assessing interspecific interference between pairs of these species in equal numbers (one, two or three larvae per species) to provide total predator densities of two, four or six larvae. Baetis larvae as prey were replaced as they were eaten, and their density per predator was varied between 20 and 200 larvae. 2. The number of prey eaten by each competing species increased curvilinearly with prey density, the relationship being well described by a Type II model. Of the two constants in the model, handling time varied considerably between species, mean values being shortest for Perlodes, slightly higher for Isoperla, and much higher for Dinocras and Perla. It was not affected significantly either by predator density or the identity of the competing species. 3. Attack rate also varied between species and decreased with predator density. This decrease was slight for Perlodes, and also for Dinocras and Perla in competition with Isoperla. The decrease in Dinocras and Perla was similar to that for intraspecific interference. 4. The decrease in attack rate was described by a convex curve for Perlodes with the other three species and for Dinocras/Perla with Isoperla, but by a concave curve (negative power function) for Isoperla competing with the other three species, and for both Dinocras and Perla in competition with Perlodes. Prey consumption also decreased with predator density, the severity of competition with different species reflecting that for attack rate. 5. A comparison with previous results for intraspecific interference showed that the latter was dominant for Perlodes in all contests and for Dinocras or Perla competing with Isoperla, whilst interspecific interference dominated for Isoperla in all contests and for Dinocras and Perla competing with Perlodes. Both types of interference were applicable to competition between Dinocras and Perla. Isoperla was the least, and Perlodes the most, aggressive of the four species with Dinocras and Perla intermediate.     

Temporal trends in net and crude probability of death from cancer and other causes in the Australian population, 1984–2013

BackgroundWhile net probabilities of death in the relative survival framework ignore competing causes of death, crude probabilities allow estimation of the real risk of cancer deaths. This study quantifies temporal trends in net and crude probabilities of death.MethodsAustralian population-based cohort of 2,015,903 people aged 15-89 years, diagnosed with a single primary invasive cancer from 1984 to 2013 with mortality follow-up to 31 December 2014. Survival was analyzed with the cohort method. Flexible parametric relative survival models were used to estimate both probability measures by diagnosis year for all cancers and selected leading sites.ResultsFor each site, excess mortality rates reduced over time, especially for prostate cancer. While both the 10-year net and crude probability of cancer deaths decreased over time, specific patterns varied. For example, the crude probability of lung cancer deaths for males aged 50 years decreased from 0.90 (1984) to 0.79 (2013); whereas the corresponding probabilities for kidney cancer were 0.64 and 0.18 respectively. Patterns for crude probabilities of competing deaths were relatively constant. Although for younger patients, both net and crude measures were similar, crude probability of competing deaths increased with age, hence for older ages net and crude measures were different except for lung and pancreas cancers.ConclusionsThe observed reductions in probabilities of death over three decades for Australian cancer patients are encouraging. However, this study also highlights the ongoing mortality burden following a cancer diagnosis, and the need for continuing efforts to improve cancer prevention, diagnosis and treatment.     

Dynamic clinical prediction models for discrete time‐to‐event data with competing risks—A case study on the OUTCOMEREA database

The development of clinical prediction models requires the selection of suitable predictor variables. Techniques to perform objective Bayesian variable selection in the linear model are well developed and have been extended to the generalized linear model setting as well as to the Cox proportional hazards model. Here, we consider discrete time‐to‐event data with competing risks and propose methodology to develop a clinical prediction model for the daily risk of acquiring a ventilator‐associated pneumonia (VAP) attributed to P. aeruginosa (PA) in intensive care units. The competing events for a PA VAP are extubation, death, and VAP due to other bacteria. Baseline variables are potentially important to predict the outcome at the start of ventilation, but may lose some of their predictive power after a certain time. Therefore, we use a landmark approach for dynamic Bayesian variable selection where the set of relevant predictors depends on the time already spent at risk. We finally determine the direct impact of a variable on each competing event through cause‐specific variable selection.     

Partner status and survival after cancer: A competing risks analysis

ObjectiveThe survival benefits of having a partner for all cancers combined is well recognized, however its prognostic importance for individual cancer types, including competing mortality causes, is less clear. This study was undertaken to quantify the impact of partner status on survival due to cancer-specific and competing mortality causes.MethodsData were obtained from the population-based Queensland Cancer Registry on 176,050 incident cases of ten leading cancers diagnosed in Queensland (Australia) from 1996 to 2012. Flexible parametric competing-risks models were used to estimate cause-specific hazards and cumulative probabilities of death, adjusting for age, stage (breast, colorectal and melanoma only) and stratifying by sex.ResultsBoth unpartnered males and females had higher total cumulative probability of death than their partnered counterparts for each site. For example, the survival disadvantage for unpartnered males ranged from 3% to 30% with higher mortality burden from both the primary cancer and competing mortality causes. The cause-specific age-adjusted hazard ratios were also consistent with patients without a partner having increased mortality risk although the specific effect varied by site, sex and cause of death. For all combined sites, unpartnered males had a 46%, 18% and 44% higher risk of cancer-specific, other cancer and non-cancer mortality respectively with similar patterns for females. The higher mortality risk persisted after adjustment for stage.ConclusionsIt is important to better understand the mechanisms by which having a partner is beneficial following a cancer diagnosis, so that this can inform improvements in cancer management for all people with cancer.     

On the competitive exclusion principle

The Competitive Exclusion Principle, formulated by V. Volterra (Memorie del R. Comitato Talassografico Italiano,131, 1–142, 1927) for a number of species competing for a common ecological niche, is extended to a number of species competing for many ecological niches. Supported by an N.I.H. training grant.     

Competition between Lolium perenne and Digitaria sanguinalis: Ecological consequences for harbouring an endosymbiotic fungus

Abstract. This study examined the influence of the fungal endophyte Neotyphodium lolii on the competitive interactions between its perennial, cool season host, Lolium perenne (perennial ryegrass), and a warm season, annual grass, Digitaria sanguinalis (large crabgrass), in densely planted stands (>1000 plant.m^?2) in the glasshouse. Endophyte infection had little or no effect on L. perenne tiller production, above‐ or below‐ground biomass or root: shoot ratio in monoculture. However, endophyte infection significantly reduced L. perenne tiller production and above‐ground biomass in mixtures with D. sanguinalis. Conversely, D. sanguinalis had significantly higher above‐ground biomass and yielded more seed (g) when competing with endophyte infected L. perenne. An apparent trade‐off between allocation of resources to reproductive vs root tissues was observed in D. sanguinalis– root: shoot ratio was significantly lower when competing with endophyte infected L. perenne. Results indicate negative ecological consequences for harbouring the fungal endophyte when competing with the fast growing annual grass in newly established stands. These findings underscore the existence of a physiological cost of harbouring the fungal endophyte which is often overlooked.     

Asymptotic Interval Estimation of Some Cause-Specific Mortality Risk Measures in Epidemiologic Studies

The present paper describes the algebraic and statistical relationships between the population-based mortality risk measures, the Standardized Mortality Ratio (SMR) and the Standardized Risk Ratio (SRR), and their respective proportional mortality-based counterparts, the internally and externally Standardized Proportional Mortality Ratios (SPMR, S_ePMR). The paper shows, how under some reasonable assumptions, asymptotically precise inferences about population-based risk measures can be made from studies of proportional mortality. Through application of the asymptotic multivariate normal approximation to the multinomial distribution, shortest confidence intervals for the relative SMR (RSMR) involving the corresponding SPMR are constructed for any cause of death. This same technique is also used to construct asymptotic prediction intervals about the cause-specific S_ePMR which, with high probability, contains the corresponding relative SRR (RSRR). The utility of the proportional mortality measures SPMR and S_ePMR as estimators of the corresponding cause-specific risks RSMR and RSRR in occupational epidemiologic research is empirically evaluated using data from two recent occupational cohort studies. Asymptotic Bonferroni type simultaneous inferential techniques are also developed for these measures which facilitate the assessment of overall risk in the presence of several competing factors.     

Validation of discrete time-to-event prediction models in the presence of competing risks

Clinical prediction models play a key role in risk stratification, therapy assignment and many other fields of medical decision making. Before they can enter clinical practice, their usefulness has to be demonstrated using systematic validation. Methods to assess their predictive performance have been proposed for continuous, binary, and time-to-event outcomes, but the literature on validation methods for discrete time-to-event models with competing risks is sparse. The present paper tries to fill this gap and proposes new methodology to quantify discrimination, calibration, and prediction error (PE) for discrete time-to-event outcomes in the presence of competing risks. In our case study, the goal was to predict the risk of ventilator-associated pneumonia (VAP) attributed to Pseudomonas aeruginosa in intensive care units (ICUs). Competing events are extubation, death, and VAP due to other bacteria. The aim of this application is to validate complex prediction models developed in previous work on more recently available validation data.     

When seasnake meets seabird: Ecosystem engineering,facilitation and competition

Ecosystem engineers such as burrowing seabirds can increase habitat availability for sympatric taxa – but only if the burrow's owner allows other species to use the newly created shelter site. Our studies on a small Pacific island suggest that an avian burrower (the wedge‐tailed shearwater Puffinus pacificus) is both a facilitator and a competitor for amphibious seasnakes. Video camera inspection of 102 burrows revealed frequent usage of these burrows as retreat sites by the snakes, with Laticauda laticaudata restricted to burrows <4 m from the water's edge, whereas Laticauda saintgironsi often used burrows further inland. Snakes never occupied burrows that contained adult shearwaters, suggesting active burrow defence by the birds. Model snakes that we inserted into burrows were attacked, especially on the head and upper body, and we found one snake pecked to death outside a burrow. Wedge‐tailed shearwaters act as facilitators, creating a thermally favourable microhabitat and substantially enhancing habitat suitability for snakes; but they are also competitors, aggressively competing with snakes for occupancy of the resource that has been created.     

Why we should take care of the competing risk bias in survival analysis: A phase II trial on the toxicity profile of radiotherapy for prostate cancer

AimThe aim of the present study is to evaluate and quantify the bias of competing risks in an Italian oncologic cohort comparing results from different statistical analysis methods.BackgroundCompeting risks are very common in randomized clinical trials and observational studies, in particular oncology and radiotherapy ones, and their inappropriate management causes results distortions widely present in clinical scientific articles.Materials and methodsThis is a single-institution phase II trial including 41 patients affected by prostate cancer and undergoing radiotherapy (IMRT-SIB) at the University Hospital of Udine.Different outcomes were considered: late toxicities, relapse, death.Death in the absence of relapse or late toxicity was considered as a competing event.ResultsThe Kaplan Meier method, compared to cumulative incidence function method, overestimated the probability of the event of interest (toxicity and biochemical relapse) and of the competing event (death without toxicity/relapse) by 9.36%. The log-rank test, compared to Gray's test, overestimated the probability of the event of interest by 5.26%.The Hazard Ratio's and cause specific hazard's Cox regression are not directly comparable to subdistribution hazard's Fine and Gray's modified Cox regression; nonetheless, the FG model, the best choice for prognostic studies with competing risks, found significant associations not emerging with Cox regression.ConclusionsThis study confirms that using inappropriate statistical methods produces a 10% overestimation in results, as described in the literature, and highlights the importance of taking into account the competing risks bias.     

The fate of an internal parasitoid,Nemeritis canescens,in a variety of insects

• 1 The fate of Nemeritis canescens has been studied in 36 species or, counting different stages, in 51 kinds of insects, in order to discover the causes of its success or failure in each.
• 2 The parasitoid was able to develop to the adult stage in 14 of the species studied.
• 3 A defence reaction of the host, cellular encapsulation, was by far the most frequent cause of the death of canescens in species in which it could not develop.
• 4 Deposition of melanin over its mouth probably caused the death of canescens in two species; in other species the role of melanisation was subordinate to encapsulation.
• 5 Very few species, if any, were unsuitable as food; larvae of the parasitoid ingested and assimilated the blood of a wide variety of insects.
• 6 Some individuals of a few species were unsuitable as a habitat for the parasitoid larva.
• 7 The survival of canescens in suitable hosts is discussed with reference to the means by which this parasitoid resists defence reactions.
• 8 Attention is drawn to incidental results of the research: (i) a state of diapause in some hosts was transmitted to first-instar larvae of canescens and delayed their development; (ii) evidence was found that the teratocytes formed by braconid parasitoids function as a means of preventing cellular defence reactions, that they act by attrition of the host, and that they protect a larva of canescens present in the same host; (iii) observations concerning the behaviour of adult canescens in attacking some species, and the survival of supernumerary larvae after competing for the host, are mentioned.

     

Birth,death and horizontal transfer of the fumonisin biosynthetic gene cluster during the evolutionary diversification of Fusarium

Fumonisins are a family of carcinogenic secondary metabolites produced by members of the Fusarium fujikuroi species complex (FFSC) and rare strains of Fusarium oxysporum. In Fusarium, fumonisin biosynthetic genes (FUM) are clustered, and the cluster is uniform in gene organization. Here, sequence analyses indicated that the cluster exists in five different genomic contexts, defining five cluster types. In FUM gene genealogies, evolutionary relationships between fusaria with different cluster types were largely incongruent with species relationships inferred from primary‐metabolism (PM) gene genealogies, and FUM cluster types are not trans‐specific. In addition, synonymous site divergence analyses indicated that three FUM cluster types predate diversification of FFSC. The data are not consistent with balancing selection or interspecific hybridization, but they are consistent with two competing hypotheses: (i) multiple horizontal transfers of the cluster from unknown donors to FFSC recipients and (ii) cluster duplication and loss (birth and death). Furthermore, low levels of FUM gene divergence in F. bulbicola, an FFSC species, and F. oxysporum provide evidence for horizontal transfer of the cluster from the former, or a closely related species, to the latter. Thus, uniform gene organization within the FUM cluster belies a complex evolutionary history that has not always paralleled the evolution of Fusarium.     

A novel F420‐dependent anti‐oxidant mechanism protects Mycobacterium tuberculosis against oxidative stress and bactericidal agents

Mycobacterium tuberculosis (Mtb) is an aerobic bacterium that persists intracellularly in host macrophages and has evolved diverse mechanisms to combat and survive oxidative stress. Here we show a novel F₄₂₀‐dependent anti‐oxidant mechanism that protects Mtb against oxidative stress. Inactivation of the fbiC gene in Mtb results in a cofactor F₄₂₀‐deficient mutant that is hypersensitive to oxidative stress and exhibits a reduction in NADH/NAD⁺ ratios upon treatment with menadione. In agreement with the recent hypothesis on oxidative stress being an important component of the pathway resulting in cell death by bactericidal agents, F₄₂₀^? mutants are hypersensitive to mycobactericidal agents such as isoniazid, moxifloxacin and clofazimine that elevate oxidative stress. The Mtb deazaflavin‐dependent nitroreductase (Ddn) and its two homologues Rv1261c and Rv1558 encode for an F₄₂₀H₂‐dependent quinone reductase (Fqr) function leading to dihydroquinones. We hypothesize that Fqr proteins catalyse an F₄₂₀H₂‐specific obligate two‐electron reduction of endogenous quinones, thereby competing with the one‐electron reduction pathway and preventing the formation of harmful cytotoxic semiquinones, thus protecting mycobacteria against oxidative stress and bactericidal agents. These findings open up an avenue for the inhibition of the F₄₂₀ biosynthesis pathway or Fqr‐class proteins as a mechanism to potentiate the action of bactericidal agents.     

Towards a one-step Enterobacter sakazakii enrichment

Aims: The current international standard method for detection of Enterobacter sakazakii from milk products is by the International Organization for Standardization and the International Dairy Federation documented method, a procedure involving two-step enrichment. This study aimed to assess enrichment of E. sakazakii using a one-step enrichment. Methods and Results: Enrichment of four strains of E. sakazakii was compared using five different media, with stressed or unstressed cells, and at three levels of competing microflora, which were included to assess their effects on the positive isolation of E. sakazakii. Enrichment of milk powders, prepared by spray-drying milk seeded with E. sakazakii, was assessed using one-step enrichment for detection of E. sakazakii, followed by confirmation of positive isolates by real-time PCR. Conclusions: Current media are unsuitable for enrichment and detection of all E. sakazakii isolates, in particular, when high levels of background microflora are present in the sample matrix, and new defined media are needed for successful one-step enrichment. Significance and Impact of the Study: These findings provide further analysis of one-step enrichment processes for E. sakazakii in the presence of competing microflora, and show that further formulation is needed for a universal E. sakazakii enrichment medium, with careful selection of both nutrients and selective agents.