Estimating protection afforded by prior infection in preventing reinfection: Applying the test-negative study design

Background: The Coronavirus Disease 2019 (COVID-19) pandemic has highlighted an urgent need to use infection testing databases to rapidly estimate effectiveness of prior infection in preventing reinfection (PES) by novel variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Methods: Mathematical modeling was used to demonstrate the applicability of the test-negative, case-control study design to derive PES. Modeling was also used to investigate effects of bias in PES estimation. The test-negative design was applied to national-level testing data in Qatar to estimate PES for SARS-CoV-2 infection and to validate this design. Results: Apart from the very early phase of an epidemic, the difference between the test-negative estimate for PES and the true value of PES was minimal and became negligible as the epidemic progressed. The test-negative design provided robust estimation of PES even when PES began to wane after prior infection. Assuming that only 25% of prior infections are documented, misclassification of prior infection status underestimated PES, but the underestimate was considerable only when >50% of the population was ever infected. Misclassification of latent infection, misclassification of current active infection, and scale-up of vaccination all resulted in negligible bias in estimated PES. PES against SARS-CoV-2 Alpha and Beta variants was estimated at 97.0% (95% CI: 93.6-98.6) and 85.5% (95% CI: 82.4-88.1), respectively. These estimates were validated using a cohort study design. Conclusions: The test-negative design offers a feasible, robust method to estimate protection from prior infection in preventing reinfection.

Educational Disparity in Drinking and Smoking in Japan for 2013–2019: a Cross-sectional Study

BackgroundIn Japan, studies of the relationship between drinking and educational background have not been as advanced as smoking studies, while Japan has extremely easy access to alcohol on a global level. We divided Japanese adults by drinking status, educational background, age, and gender, and analyzed the relationship, comparing to smokers’ data for reference.MethodsData were drawn from the Comprehensive Survey of Living Conditions (2013: 191,973 men, 214,815 women; 2016: 176,969 men, 196,181 women; 2019: 167,276 men, 183,963 women). We classified them as current drinkers, binge drinkers, current smokers, and heavy smokers. Drinking and smoking prevalence were analyzed by disparity indices, including rate difference, rate ratio, between-group variance, and slope index of inequality.ResultsWe found that higher positive estimates of educational disparity indices were among younger drinkers and got lower by aging. Surprisingly, among current drinkers, we also revealed women aged 45-94 had a negative estimate of an educational disparity index, while men aged 45-94 had negative one moving in a positive direction.ConclusionsEducation has a certain effect in preventing drinking, but the effect is so small among middle-aged and elderly people that other factors easily contribute to the phenomenon that those with a high education drink more than those with a low education. We estimated one of the factors is that many elderly women, who were high-educated and often forced to drink in accordance with women’s empowerment, are still alive and keep drinking. Further observation is needed to confirm it or reveal other factors.

PAN-INDIA 1000 SARS-CoV-2 RNA Genome Sequencing Reveals Important Insights into the Outbreak

The PAN-INDIA 1000 SARS-CoV-2 RNA Genome Sequencing Consortium has achieved its initial goal of completing the sequencing of 1000 SARS-CoV-2 genomes from nasopharyngeal and oropharyngeal swabs collected from individuals testing positive for COVID-19 by Real Time PCR. The samples were collected across 10 states covering different zones within India. Given the importance of this information for public health response initiatives investigating transmission of COVID-19, the sequence data is being released in GISAID database. This information will improve our understanding on how the virus is spreading, ultimately helping to interrupt the transmission chains, prevent new cases of infection, and provide impetus to research on intervention measures. This will also provide us with information on evolution of the virus, genetic predisposition (if any) and adaptation to human hosts.One thousand and fifty two sequences were used for phylodynamic, temporal and geographic mutation patterns and haplotype network analyses. Initial results indicate that multiple lineages of SARS-CoV-2 are circulating in India, probably introduced by travel from Europe, USA and East Asia. A2a (20A/B/C) was found to be predominant, along with few parental haplotypes 19A/B. In particular, there is a predominance of the D614G mutation, which is found to be emerging in almost all regions of the country. Additionally, mutations in important regions of the viral genome with significant geographical clustering have also been observed. The temporal haplotype diversities landscape in each region appears to be similar pan India, with haplotype diversities peaking between March-May, while by June A2a (20A/B/C) emerged as the predominant one. Within haplotypes, different states appear to have different proportions. Temporal and geographic patterns in the sequences obtained reveal interesting clustering of mutations. Some mutations are present at particularly high frequencies in one state as compared to others. The negative estimate Tajimas D (D = −2.26817) is consistent with the rapid expansion of SARS-CoV-2 population in India. Detailed mutational analysis across India to understand the gradual emergence of mutants at different regions of the country and its possible implication will help in better disease management.

PSIII-13 Genetic parameters and the purebred–crossbred genetic correlation for growth, carcass, and meat quality traits in pigs

Growth, meat quality, and carcass traits are of economic importance in swine breeding. Understanding their genetic basis in commercial crossbred pigs and purebred-crossbred genetic correlations are necessary for a successful breeding program. The objectives of this study were to 1) estimate genetic parameters for growth, meat quality and carcass traits in a purebred sire line and related commercial crossbred pigs and 2) estimate the corresponding genetic correlations between purebreds and crossbreds (rpc). We analyzed 115266, 10927 and 43057 purebred records for growth, meat quality (n = 4) and carcass traits (n = 7), respectively. For crossbreds, there were 2000 pigs with growth records, with 900 of them having meat quality and carcass data. A series of univariate and bivariate analyses were used to estimate genetic parameters and rpc. Growth showed moderate heritability (0.20 ± 0.10 to 0.25 ± 0.01) in both purebreds and crossbreds. Heritability estimates for meat quality traits ranged from 0.21 ± 0.03 to 0.42 ± 0.04 in purebreds and from 0.17 ± 0.14 to 0.47 ± 0.15 in crossbreds. Carcass traits had higher heritability estimates in purebreds compared to crossbreds, except for hot carcass weight (0.10 ± 0.02 vs. 0.24 ± 0.16). Genetic correlations among meat quality traits were variable in both populations, whereas genetic correlations among carcass traits were similar in purebreds and crossbreds. Estimates of rpc were high for growth (0.99 ± 0.5) and for meat quality traits (0.94 ± 0.39 to 0.99 ± 0.2), except for Minolta color (-0.48 ± 0.56). Carcass traits had moderate to high estimates of rpc (0.64 ± 0.4 to 0.92 ± 0.3). Carcass fat had a negative estimate of rpc (-0.1 ± 0.5). However, ultrasound fat as an indicator trait for carcass fat had a high positive estimate of rpc (0.88 ± 0.14). Our results indicate that selection in purebreds can be efficient to improve these traits in both purebreds and crossbreds but for some traits, genetic gain can be improved by applying combined crossbred and purebred selection. Funding provided by Genome Canada and the National Research Council.

Safety aspects of the bicycle traffic and the needs of cyclists in the City of Zagreb and its surrounding

The goals of this study were: to determine the possibility of forecasting for the preferences of cycling on the basis of all relevant factors Zagreb cycling (1) and to determine the differences between the participants in all the relevant factors in Zagreb cycling, by gender, in relation to membership in the Association "Trad Union of bicyclists", type of cycling and part of the city where cyclists live (2). Over 3000 members of the Association and cyclists who are not members of the Association ("average" cyclist) are tested, using conveniently assembled questionnaire. It turned out that latent dimensions of the sub-questionnaires well represented themes: barriers to cycling, the role of the City in bicycle traffic, the purpose of using bicycle accident during bicycle traffic. People who are more inclined to participate in city traffic riding, often believe that the City should significantly improve conditions for cycling, tend to safer driving and more negative estimate lack of road cycling conditions in Zagreb. Women and members of the Union of cyclists often feel that the City should improve conditions for cycling and negatively evaluate the existing conditions of cycling, more often use the bike for different purposes and had frequent accidents bicycle. In the northern part of the city, Samobor, Zapresic and Sesvete, Dugo Selo and Ivanja Reka participants were assessed to have the most adverse road conditions for cycling, while the wider center of Zagreb currently has the most favorable conditions for cycling. The results provide the guidance for improving the safety of the cycling in Zagreb and its surrounding, for taking constructive social actions at the state level and on the local-community level, as well as in the broader context of sustainable development.

Aristotle on the Impossibility of Anaximander’s apeiron: On Generation and Corruption, 332a20-25

In On Generation and Corruption, Aristotle rejects the very possibility of such a thing as Anaximander’s apeiron. Characterized as a kind of intermediate stuff, the apeiron turns out to consist of contraries and as such is impossible. Commentators have rightly noted this point and some have also indicated that Aristotle offers an argument of sorts for his negative estimate. However, the argument has received scant attention, and it is fair to say that it remains unclear exactly why Aristotle rejects Anaximander’s intermediate stuff. Indeed, it is unclear how Aristotle’s argument is supposed to run in the first place. This paper offers a reconstruction of Aristotle’s argument for the impossibility of the apeiron, and on this basis offers to explain Aristotle’s grounds for rejecting Anaximander’s intermediate stuff. This is especially called for in light of the fact that Aristotle himself thinks that there can be intermediate stuffs. Finally, some attention is given to the parallel between the apeiron and Aristotle’s prime matter.

The Term Structure of Variance Swap Rates and Optimal Variance Swap Investments

This paper performs specification analysis on the term structure of variance swap rates on the S&P 500 index and studies the optimal investment decision on the variance swaps and the stock index. The analysis identifies 2 stochastic variance risk factors, which govern the short and long end of the variance swap term structure variation, respectively. The highly negative estimate for the market price of variance risk makes it optimal for an investor to take short positions in a short-term variance swap contract, long positions in a long-term variance swap contract, and short positions in the stock index.

Structure of the clinical and geriatric depression: Similarities and differences

Studies demonstrating the uniqueness of depression in old age are numerous, but conclusions on the fact if the problems of the elderly people cause depression or if they are a part of depression are not unique. The aim of this paper is to compare the structure of depression of old people without the history of mental illness and middle-aged people treated for depression. The sample consists of 82 healthy inmates of different Homes for the Aged and 78 patients diagnosed with some sort of affective disorder. A depression has been assessed with the shorten version of the MMPI D-scale. The structure of the geriatric and clinical depression has been compared with the method of maximum likelihood, over the matrix of co-variances of answers on the items on the depression scale. The results point out to the statistically significant difference in the structure of depression of the old and clinically depressed individuals. However, half of the items of the D-scale have significant loadings on the factor of depression in both groups. The essence of the depression in both samples is made of cognitive subject matters, depressive affect, decline of motivation and a negative estimate of one's basic abilities. Symptoms concerning low self-esteem, experiencing cognitive deficit, energy and impaired physical health have been significant in describing the clinical depression, while a feeling of reduced positive stimulation and the affective liability is typical for the depression of geriatric sample. The conclusion is that, despite the differences, there is a common core of symptoms that makes the essence of depression, apart from the samples.

Influence of sire by year interactions on the direct-maternal genetic correlation for weaning weight of Western Australian Merino sheep

The relationship between the direct-maternal genetic (co)variance σam and sire by year (SY) interactions for weaning weight in Merino sheep was examined through simulation and real data analyses. Weaning weight was simulated using models containing interaction and σam = 0 (S1), interaction and σam < 0 (S2), interaction and σam >�0 (S3), and without interaction and σam < 0 (S4). When S1 data were analysed ignoring interaction, a negative (co)variance was observed and direct and maternal variances were inflated. Analysis of S2 data ignoring σam resulted in deflated direct and maternal variances, inflated residual and interaction variances, and no change for the permanent environmental component. Ignoring the interaction effect in S3 data resulted again in a negative (co)variance component and highly biased genetic parameters. On application to weaning weight of Merino sheep, the model ignoring SY resulted in a direct-maternal genetic correlation of –0.43. The model using both (co)variance and interaction effects fit the data better (P < 0.001). The interaction variance represented 9.2% of the phenotypic variance but explained 86% of the (co)variance between direct and maternal genetic effects estimated ignoring SY.�A small (–0.096) but still negative estimate of the genetic correlation was obtained. The implication of these findings in the context of Central Test Sire Evaluation and Maternal Sire Central Progeny Test Schemes is discussed.