The one‐inflated positive Poisson mixture model for use in population size estimation

The one‐inflated positive Poisson mixture model (OIPPMM) is presented, for use as the truncated count model in Horvitz–Thompson estimation of an unknown population size. The OIPPMM offers a way to address two important features of some capture–recapture data: one‐inflation and unobserved heterogeneity. The OIPPMM provides markedly different results than some other popular estimators, and these other estimators can appear to be quite biased, or utterly fail due to the boundary problem, when the OIPPMM is the true data‐generating process. In addition, the OIPPMM provides a solution to the boundary problem, by labelling any mixture components on the boundary instead as one‐inflation.     

Evaluating faecal egg count reduction using a specifically designed package “eggCounts” in R and a user friendly web interface

The seemingly straightforward task of analysing faecal egg counts resulting from laboratory procedures such as the McMaster technique has, in reality, a number of complexities. These include Poisson errors in the counting technique which result from eggs being randomly distributed in well mixed faecal samples. In addition, counts between animals in a single experimental or observational group are nearly always over-dispersed. We describe the R package “eggCounts” that we have developed that incorporates both sampling error and over-dispersion between animals to calculate the true egg counts in samples of faeces, the probability distribution of the true counts and summary statistics such as the 95% uncertainty intervals. Based on a hierarchical Bayesian framework, the software will also rigorously estimate the percentage reduction of faecal egg counts and the 95% uncertainty intervals of data generated by a faecal egg count reduction test. We have also developed a user friendly web interface that can be used by those with limited knowledge of the R statistical computing environment. We illustrate the package with three simulated data sets of faecal egg count reduction experiments.     

Assessing and Addressing the Risk of Venous Thromboembolism Across the Spectrum of Gender Affirming Care: A Review

ObjectiveAccumulating evidence demonstrates that gender affirming hormone therapy (GAHT) improves mental health outcomes in transgender persons. Data specific to the risks associated with GAHT for transgender persons continue to emerge, allowing for improvements in understanding, predicting, and mitigating adverse outcomes while informing discussion about desired effects. Of particular concern is the risk of venous thromboembolism (VTE) in the context of both longitudinal GAHT and the perioperative setting. Combining what is known about the risk of VTE in cisgender individuals on hormone therapy (HT) with the evidence for transgender persons receiving HT allows for an informed approach to assess underlying risk and improve care in the transgender community.ObservationsHormone formulation, dosing, route, and duration of therapy can impact thromboembolic risk, with transdermal estrogen formulations having the lowest risk. There are no existing risk scores for VTE that consider HT as a possible risk factor. Risk assessment for recurrent VTE and bleeding tendencies using current scores may be helpful when assessing individual risk. Gender affirming surgeries present unique perioperative concerns, and certain procedures include a high likelihood that patients will be on exogenous estrogens at the time of surgery, potentially increasing thromboembolic risk.Conclusions and RelevanceWithholding GAHT due to potential adverse events may cause negative impacts for individual patients. Providers should be knowledgeable about the management of HT in transgender individuals of all ages, as well as in the perioperative setting, to avoid periods in which transgender individuals are off GAHT. Treatment decisions for both anticoagulation and HT should be individualized and tailored to patients’ overall goals and desired outcomes, given that the physical and mental health benefits of gender affirming care may outweigh the risk of VTE.     

A pseudolikelihood method for analyzing interval censored data

We introduce a method based on a pseudolikelihood ratio forestimating the distribution function of the survival time ina mixed-case interval censoring model. In a mixed-case model,an individual is observed a random number of times, and at eachtime it is recorded whether an event has happened or not. Oneseeks to estimate the distribution of time to event. We usea Poisson process as the basis of a likelihood function to constructa pseudolikelihood ratio statistic for testing the value ofthe distribution function at a fixed point, and show that thisconverges under the null hypothesis to a known limit distribution,that can be expressed as a functional of different convex minorantsof a two-sided Brownian motion process with parabolic drift.Construction of confidence sets then proceeds by standard inversion.The computation of the confidence sets is simple, requiringthe use of the pool-adjacent-violators algorithm or a standardisotonic regression algorithm. We also illustrate the superiorityof the proposed method over competitors based on resamplingtechniques or on the limit distribution of the maximum pseudolikelihoodestimator, through simulation studies, and illustrate the differentmethods on a dataset involving time to HIV seroconversion ina group of haemophiliacs.     

Relationship between somatic cell count and bacterial pathogens in goat milk

The study aimed at evaluation of total count and pattern of somatic cells, as well as lactose content in relation to the type of bacterial pathogens in goat milk. The study was conducted on 66 Polish White Improved and Polish Fawn Improved dairy goats. A total of 487 milk samples were taken from day 30th, 60th and 200th of lactation for three years. The milk samples were divided into four groups: group 1 – containing no pathogens, group 2 – with minor pathogens up to 1000 CFU/mL such as coagulase-negative staphylococci (CNS), alpha-haemolytic streptococci, Enterococcus spp., Corynebacterium spp., group 3 – with minor pathogens (CNS) above 1 × 10³ CFU/mL of milk and group 4 – with major pathogens such as Streptococcus agalactiae, Staphylococcus intermedius and Staphylococcus aureus.In the majority of milk samples (64.9%) no pathogens were observed. The CNS were isolated from 25.3%, while the major pathogens were from 9.8% of milk samples. Both the major pathogens and high numbers of minor pathogens influenced the total somatic cell count (SCC) and lactose content. The percentage of leukocytes in the total somatic cells amounted to about 50% in the milk samples, which contained a high number of CNS or major pathogens. In the remaining samples this value reached only about 35%. Close relationship occurred between the presence of bacterial pathogens and total SCC, percentage of all leukocytes and their subpopulations in milk. The percentage of eosinophils and neutrophils in the total SCC were dramatically higher (p ≤ 0.0016) in samples of group 4 as compared to groups 1, 2 and 3. The percentage of monocytes was the highest in milk samples containing large numbers of minor pathogens. No relationship was found between the type of isolated bacterial pathogen and the percentage of lymphocytes in milk. In most samples, the presence of bacterial pathogens in goat milk led to the increase of the total SCC. However, the microbiological analysis showed that the bacterial pathogens were presented in about 20% of milk samples containing low SCC (below 1 × 10⁶/mL).     

Identification of a novel large intragenic deletion in a family with Fanconi anemia: First molecular report from India and review of literature

We report here an Indian case with Fanconi anemia (FA) presented with fever, pallor, short stature, hyperpigmentation and upper limb anomaly. Chromosome breakage analysis together with FANCD2 Western blot monoubiquitination assay confirmed the diagnosis as FA. Multiplex ligation-dependent probe amplification (MLPA) revealed a novel homozygous large intragenic deletion (exons 8–27 del) in the FANCA gene in the proband. His sib and parents were also analyzed and found to be heterozygous for the same mutation. We also reviewed the literature of FANCA large intragenic deletions found in FA patients from different countries and the mechanism involved in the formation of these deletions. To the best of our knowledge, this is the first molecular report from India on FA. The finding expands the mutation spectrum of the FANCA gene. Identification of the mutation confirms the diagnosis of FA at DNA level and helps in providing proper genetic counseling to the family.     

Relationships among somatic cell count, California mastitis test, impedance and bacteriological status of milk in goats and sheep in early lactation

The objectives of this trial were to evaluate and compare the test characteristics of a number of indirect tests of bacteriological status of the milk from goats and sheep and to assess the affect of varying levels of prevalence of infection on the performance of those tests.The somatic cell count, California mastitis test (CMT) score, electrical impedance and the bacteriological status of 220 and 262 milk samples from the glands of lactating dairy goats and sheep, respectively, were determined. The sensitivity and specificity of indirect tests in predicting the bacteriological status were compared by analyzing the areas under the receiver operating characteristic curve and calculating the likelihood ratio at various cut-off values.Bacteria were isolated from 17.7 and 4.6% of glands from goats and sheep, respectively. Somatic cell count was a better predictor of bacteriological status than either the CMT score or impedance in both goats and sheep. However, knowledge of the CMT score in both sheep and goats and the impedance in goats increases the likelihood of predicting the presence of a bacterial pathogen compared to no testing at all (P<0.05). Knowledge of the age and days postpartum of the animals at the time of testing did not increase the probability that infection status could be predicted. Variation in cut-off levels to predict infection status reported in the literature may be due to variation in the prevalence of infection in the populations studied. Use of likelihood ratio allows comparison of tests over a range of prevalence’s as likelihood ratios are independent of prevalence. The prevalence of infection within a herd should be considered when selecting a cut-off value for indirect testing for the presence of bacteria in milk of small ruminants.     

Do male secondary sexual characters signal ejaculate quality? A meta‐analysis

There are two reasons why researchers are interested in the phenotypic relationship between the expression of male secondary sexual characters (SSCs) and ‘ejaculate quality’ (defined as sperm/ejaculate traits that are widely assumed to increase female fertility and/or sperm competitiveness). First, if the relationship is positive then females could gain a direct benefit by choosing more attractive males for fertility assurance reasons (‘the phenotype‐linked fertility’ hypothesis). Second, there is much interest in the direction of the correlation between traits favoured by pre‐copulatory sexual selection (i.e. affecting mating success) and those favoured by post‐copulatory sexual selection (i.e. increasing sperm competitiveness). If the relationship is negative this could lead to the two forms of selection counteracting each other. Theory predicts that the direction of the relationship could be either positive or negative depending on the underlying genetic variance and covariance in each trait, the extent of variation among males in condition (resources available to allocate to reproductive traits), and variation among males in the cost or rate of mating. We conducted a meta‐analysis to determine the average relationship between the expression of behavioural and morphological male secondary sexual characters and four assays of ejaculate quality (sperm number, viability, swimming speed and size). Regardless of how the data were partitioned the mean relationship was consistently positive, but always statistically non‐significant. The only exception was that secondary sexual character expression was weakly but significantly positively correlated with sperm viability (r = 0.07, P < 0.05). There was no significant difference in the strength or direction of the relationship between behavioural and morphological SSCs, nor among relationships using the four ejaculate quality assays. The implications of our findings are discussed.     

No fever and leucocytosis in response to a lipopolysaccharide challenge in an insectivorous bat

Bat immune systems may allow them to respond to zoonotic agents more efficiently than other mammals. As the first line of defence, the taxonomically conserved acute phase immune reaction of leucocytosis and fever is crucial for coping with infections, but it is unknown if this response is a key constituent to bat immunological success. We investigated the acute phase reaction to a standard lipopolysaccharide (LPS) challenge in Pallas''s mastiff bats (Molossus molossus). Challenged bats lost mass, but in contrast to other mammals showed no leucocytosis or fever. There also was no influence on body temperature reduction during torpor. When compared to recent genome-wide assays for constituent immune genes, this lack of a conserved fever response to LPS contributes to a clearer understanding of the innate immune system in bat species and of the coevolution of bats with a wide diversity of pathogens.