The BayesLCA package for R provides tools for performing latent class analysis within a Bayesian setting. Three methods for fitting the model are provided, incorporating an expectation-maximization ...algorithm, Gibbs sampling and a variational Bayes approximation. The article briefly outlines the methodology behind each of these techniques and discusses some of the technical difficulties associated with them. Methods to remedy these problems are also described. Visualization methods for each of these techniques are included, as well as criteria to aid model selection.
Biological invasions expand not only as a continuous front, but also via translocation of small numbers of individuals to sites far from the main distribution. Detecting and eradicating such ...satellite populations is critical to curtailing the invasion. Cane toads (
Rhinella marina
) have been spreading through Australia since 1935, and in 2010 were reported in suburban Sydney, 500 km from the main invasion. The amphibians arrived as stowaways in trucks, and bred successfully in at least 3 years. Local residents noted the toads’ presence long before management authorities. As soon as they recognised the population’s establishment, however, the authorities surveyed locations of toads, assessed toad demography, and culled toads. Radio-tracking revealed the locations of spawning sites, which were then fenced to exclude access. As a result of reproduction, growth, and sex-specific culling (due to sex differences in distribution and catchability), successive years saw major changes in toad abundance, body-size distributions and sex ratios. Rates of infection of toads by parasites (lungworms) increased through time also. Adult male toads were collected primarily from the initial introduction site, whereas adult females were collected from a broader area. A total of > 900 post-metamorphic cane toads and > 5000 earlier life stages were collected, and those efforts (plus predation by rats and birds) exterminated the population (no sightings for the past 3 years). Cane toads will continue to be translocated to sites far outside their main invaded range, but the successful eradication effort suggests that well-integrated programs, with close collaboration among stakeholders, can prevent such populations from establishing.
Abstract
Data surrounding sex-specific differences in ANCA-associated vasculitis glomerulonephritis (ANCA-GN) outcomes is sparse. We hypothesised that the previously observed increased risk of ...end-stage kidney disease (ESKD) in males is driven by sex-specific variation in immunosuppression dosing. Patients were recruited to the Irish Rare Kidney Disease Registry or followed by the Royal Free Hospital vasculitis team (2012–2020). Inclusion criteria: prior diagnosis of ANCA-GN (biopsy proven pauci-immune glomerulonephritis) and positive serology for anti-MPO or -PR3 antibodies. Renal and patient survival, stratified by sex and Berden histological class, was analysed. The cumulative- and starting dose/kilogram of induction agents and prednisolone, respectively, was compared between sexes. 332 patients were included. Median follow-up was time 40.2 months (IQR 17.3–69.2). 73 (22%) reached ESKD and 47 (14.2%) died. Overall 1- and 5-year renal survival was 82.2% and 76.7% in males and 87.1% and 82.0% in females, respectively (
p
0.13). The hazard ratio for ESKD in males versus females, after adjustment for age, ANCA serology, baseline creatinine and histological class was 1.07 (95% CI 0.59–1.93). There was no difference between sexes in the dose/kilogram of any induction agent. We did not observe a strong impact of sex on renal outcome in ANCA-GN. Treatment intensity does not vary by sex.
Meiolaniid or horned turtles are members of the extinct Pleistocene megafauna of Australia and the southwest Pacific. The timing and causes of their extinction have remained elusive. Here we report ...the remains of meiolaniid turtles from cemetery and midden layers dating 3,100/3,000 calibrated years before present to approximately 2,900/2,800 calibrated years before present in the Teouma Lapita archaeological site on Efate in Vanuatu. The remains are mainly leg bones; shell fragments are scant and there are no cranial or caudal elements, attesting to off-site butchering of the turtles. The new taxon differs markedly from other named insular terrestrial horned turtles. It is the only member of the family demonstrated to have survived into the Holocene and the first known to have become extinct after encountering humans.
Identification of those who are most at risk of developing specific patterns of disease across different populations is required for directing public health policy. Here, we contrast prevalence and ...patterns of cross-national disease incidence, co-occurrence and related risk factors across population samples from the U.S., Canada, England and Ireland.
Participants (n = 62,111) were drawn from the US Health and Retirement Study (n = 10,858); the Canadian Longitudinal Study on Ageing (n = 36,647); the English Longitudinal Study of Ageing (n = 7938) and The Irish Longitudinal Study on Ageing (n = 6668). Self-reported lifetime prevalence of 10 medical conditions, predominant clusters of multimorbidity and their specific risk factors were compared across countries using latent class analysis.
The U.S. had significantly higher prevalence of multimorbid disease patterns and nearly all diseases when compared to the three other countries, even after adjusting for age, sex, BMI, income, employment status, education, alcohol consumption and smoking history. For the U.S. the most at-risk group were younger on average compared to Canada, England and Ireland. Socioeconomic gradients for specific disease combinations were more pronounced for the U.S., Canada and England than they were for Ireland. The rates of obesity trends over the last 50 years align with the prevalence of eight of the 10 diseases examined. While patterns of disease clusters and the risk factors related to each of the disease clusters were similar, the probabilities of the diseases within each cluster differed across countries.
This information can be used to better understand the complex nature of multimorbidity and identify appropriate prevention and management strategies for treating multimorbidity across countries.
Disagreement exists on the taxonomic identity of the extant populations of the Australian
Elseya
referred to in 1992 as the gulf
Elseya
(= Elseya sp. aff. dentata Nicholson). The extant form has ...since 1997 been considered conspecific with the late Pleistocene fossil
Elseya lavarackorum
(White and Archer, 1994). Recently it has been considered a new species,
Elseya oneiros
Joseph-Ouni et al., 2020, conspecific with another fossil found in the same site and stratum as
Elseya lavarackorum
. Here we re-examine the fossil material and reassess the characters used by previous authors in an attempt to decide the issue. We find that the anterior bridge suture with the carapace of the fossil
Elseya lavarackorum
is associated with extensive and prominent plastral elements, which has led to misinterpretation of characters associated with this structure. We furthermore show that interindividual variation in sulci patterns is so great as to render them of little taxonomic value. On the basis of (a) deviation of the anterior shape of the carapace from ovoid such that, in aged individuals, the most anterior point of the carapace occurs at marginal scutes M2 (a resultant nuchal bay occurs in such individuals); (b) the typical absence of a cervical scute; (c) no evidence of a medial constriction in the anterior bridge strut suture; and (d) absence of evidence of any other informative variation of taxonomic value; we conclude that the decision to consider the late Pleistocene (ca 23 kyr old) fossil and the extant Elseya sp. aff. dentata Nicholson as
Elseya lavarackorum
(White and Archer, 1994) as conspecific should stand.
Plague and Pleasure is a lively popular history that introduces a new hypothesis about the impetus behind the cultural change in Renaissance Italy. The Renaissance coincided with a period of chronic, ...constantly recurring plague, unremitting warfare and pervasive insecurity. Consequently, people felt a need for mental escape to alternative, idealized realities, distant in time or space from the unendurable present but made vivid to the imagination through literature, art, and spectacle.
The geochemistry of the earth’s surface is controlled by chemical equilibrium, and the kinetics of the approach toward equilibrium. Many low temperature processes, such as weathering, do not reach ...equilibrium except over geologically long time periods. The approach to equilibrium can be described by kinetic theory and the application of kinetic theory to geochemical systems has made vast advances in the last several decades. Geochemical kinetics as a topic is now of importance to a wide range of geochemists in academia, industry, and government, and all geochemists need a rudimentary knowledge of the field. This book will summarize the fundamentals of geochemical kinetics with examples drawn especially from mineral dissolution and precipitation, but will also encompass discussion of high temperature processes and global geochemical cycle modeling. Analysis of textures of rocks, sediments, and mineral surfaces will be incorporated throughout and will be a subtheme of the book.
Type I interferon (IFN) dysregulation is a major contributory factor in the development of several autoimmune diseases, termed type I interferonopathies, and is thought to be the pathogenic link with ...chronic inflammation in these conditions. Anti-neutrophil cytoplasmic antibody (ANCA)-Associated Vasculitis (AAV) is an autoimmune disease characterised by necrotising inflammation of small blood vessels. The underlying biology of AAV is not well understood, however several studies have noted abnormalities in type I IFN responses. We hypothesised that type I IFN responses are systemically dysregulated in AAV, consistent with features of a type I interferonopathy. To investigate this, we measured the expression of seven interferon regulated genes (IRGs) (ISG15, SIGLEC1, STAT1, RSAD2, IFI27, IFI44L and IFIT1) in peripheral blood samples, as well as three type I IFN regulated proteins (CXCL10, MCP-1 and CCL19) in serum samples from AAV patients, healthy controls and disease controls. We found no difference in type I IFN regulated gene or protein expression between AAV patients and healthy controls. Furthermore, IRG and IFN regulated protein expression did not correlate with clinical measurements of disease activity in AAV patients. Thus, we conclude that systemic type I IFN responses are not key drivers of AAV pathogenesis and AAV should not be considered a type I interferonopathy.
Background
In decision modeling with time-to-event data, there are a variety of parametric models that can be used to extrapolate the survival function. Each model implies a different hazard ...function, and in situations in which there is moderate censoring, this can result in quite different survival projections. External information such as expert opinion on long-term survival can more accurately characterize the uncertainty in these extrapolations.
Objective
We present a general and easily implementable approach to incorporate various types of expert opinions into parametric survival models, focusing on opinions about survival at various landmark time points.
Methods
Expert opinion is incorporated into parametric survival models using Bayesian and frequentist approaches. In the Bayesian method, expert opinion is included through a loss function and in the frequentist approach by penalizing the likelihood function, although in both cases the core approach is the same. The issue of aggregating multiple expert opinions is also considered.
Results
We apply this method to data from a leukemia trial and use previously elicited expert opinion on survival probabilities for that particular trial population at years 4 and 5 to inform our analysis. We take a robust approach to modeling expert opinion by using pooled distributions and fit a broad class of parametric models to the data. We also assess statistical goodness of fit of the models to both the observed data and expert opinion.
Conclusions
Expert opinions can be implemented in a straightforward manner using this novel approach; however, more work is required on the correct elicitation of these quantities.
Highlights
Presentation of a novel and open-source method to incorporate expert opinion into decision modeling.
Extends upon earlier work in that expert opinion can be incorporated into a wide range of parametric models.
Provides methodological guidance for directly including expert opinion in decision modeling, which is a research focus area in NICE TSD 21.1
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