Activity-based epidemic propagation and contact network scaling in auto-dependent metropolitan areas

We build on recent work to develop a fully mechanistic, activity-based and highly spatio-temporally resolved epidemiological model which leverages person-trajectories obtained from an activity-based model calibrated for two full-scale prototype cities, consisting of representative synthetic populations and mobility networks for two contrasting auto-dependent city typologies. We simulate the propagation of the COVID-19 epidemic in both cities to analyze spreading patterns in urban networks across various activity types. Investigating the impact of the transit network, we find that its removal dampens disease propagation significantly, suggesting that transit restriction is more critical for mitigating post-peak disease spreading in transit dense cities. In the latter stages of disease spread, we find that the greatest share of infections occur at work locations. A statistical analysis of the resulting activity-based contact networks indicates that transit contacts are scale-free, work contacts are Weibull distributed, and shopping or leisure contacts are exponentially distributed. We validate our simulation results against existing case and mortality data across multiple cities in their respective typologies. Our framework demonstrates the potential for tracking epidemic propagation in urban networks, analyzing socio-demographic impacts and assessing activity- and mobility-specific implications of both non-pharmaceutical and pharmaceutical intervention strategies.

Impact of the Geographic Resolution on Population Synthesis Quality

Microsimulation-based models, increasingly used in the transportation domain, require richer datasets than traditional models. Precisely enumerated population data being usually unavailable, transportation researchers generate their statistical equivalent through population synthesis. While various synthesizers are proposed to optimize the accuracy of synthetic populations, no insight is given regarding the impact of the geographic resolution on population synthesis quality. In this paper, we synthesize populations for the Census Metropolitan Areas of Montreal, Toronto, and Vancouver at various geographic resolutions using the enhanced iterative proportional updating algorithm. We define accuracy (representativeness of the sociodemographic characteristics of the entire population) and precision (representativeness of the real population’s spatial heterogeneity) as metrics of synthetic populations’ quality and measure the impact of the reference resolution on them. Moreover, we assess census targets’ harmonization and double geographic resolution control as means of quality improvement. We find that with a less aggregate reference resolution, the gain in precision is higher than the loss in accuracy. The most disaggregate resolution is thus found to be the best choice. Harmonization proves to further optimize synthetic populations while double control harms their quality. Hence, synthesizing at the Dissemination Area resolution using harmonized census targets is found to yield optimal synthetic populations.

Crossing design shapes patterns of genetic variation in synthetic recombinant populations of Saccharomyces cerevisiae

Abstract“Synthetic recombinant” populations have emerged as a useful tool for dissecting the genetics of complex traits. They can be used to derive inbred lines for fine QTL mapping, or the populations themselves can be sampled for experimental evolution. In the latter application, investigators generally value maximizing genetic variation in constructed populations. This is because in evolution experiments initiated from such populations, adaptation is primarily fueled by standing genetic variation. Despite this reality, little has been done to systematically evaluate how different methods of constructing synthetic populations shape initial patterns of variation. Here we seek to address this issue by comparing outcomes in synthetic recombinant Saccharomyces cerevisiae populations created using one of two strategies: pairwise crossing of isogenic strains or simple mixing of strains in equal proportion. We also explore the impact of the varying the number of parental strains. We find that more genetic variation is initially present and maintained when population construction includes a round of pairwise crossing. As perhaps expected, we also observe that increasing the number of parental strains typically increases genetic diversity. In summary, we suggest that when constructing populations for use in evolution experiments, simply mixing founder strains in equal proportion may limit the adaptive potential.

Genotype screening of Cannabis sativa L. based on the specifics of minor cannabinoids manifestation

Analysis of hemp collection samples based on the content of minor (rare) non-psychotropic cannabinoids, such as cannabichromene (CBC), cannabidivarin (CBDV), and cannabinol (CBN); determination of correlation relationships between them and common compounds; selection of valuable breeding genotypes. Methods. Field, biochemical (gas chromatography of cannabinoid compounds), and statistical (pair, partial, and multiple linear correlations). Results. Quantitative analysis of 210 samp­les of various ecological-geographical and genetic origin (local and wild forms, self-filing lines, hybrids, varieties, synthetic populations, polyploids) with a tetrahydrocannabinol (THC) content of less than 0.08% in dried plants showed the level of manifestation of the trait from its absence within the sensitivity of the gas chromatograph up to 0.6838% CBC, 0.1719% CBC and 0.3274% CBN. In the studied hemp samples, a medium negative relationship was found between the signs of the CBC and cannabidiol (CBD) contents (r = –0.53), a weak negative relationship between CBC and CBDV contents (r = –0.35), medium positive relationships between the signs of CBC and THC contents (r = 0.57) and CBC and CBN contents (r = 0.59). A medium positive correlation (r = 0.57) was found between the signs of CBDV and CBD contents, while CBN had a strong positive relationship with THC (r = 0.82). There is almost no correlation between cannabigerol (CBG) and the minor cannabinoids under study. The biosynthesis of minor cannabinoid compounds is quite complex. Signs manifestation is affected by many genetic and external factors. Partial correlation coefficients (given that one of the three signs is eliminated) and multiple correlation coefficients (given that the relationship of one sign is determined and two other signs are combined) give grounds to state that the gene for CBCA-synthase affects the production of CBD and, in particular THC. Conclusions. The closeness of the linear relationships between minor cannabinoids and common components allows selecting valuable hemp samples with a high content of one or several compounds under the absence or low content of psychotropic THC.

Modelling spin evolution of magnetars

The origin and fate of magnetars (young, extremely magnetized neutron stars, NSs) remains unsolved. Probing their evolution is therefore crucial for investigating possible links to other species of isolated NSs, such as the X-ray dim NSs (XDINSs) and rotating radio transients (RRATs). Here we investigate the spin evolution of magnetars. Two avenues of evolution are considered: one with exponentially decaying B-fields, the other with sub- and super-exponential decay. Using Monte Carlo methods, we synthesize magnetar populations using different input distributions and physical parameters, such as for the initial spin period, its time derivative and the B-field decay timescale. Additionally, we introduce a fade-away procedure that can account for the fading of old magnetars, and we briefly discuss the effect of alignment of the B-field and spin axes. Imposing the Galactic core-collapse supernova rate of ∼20 kyr−1 as a strict upper limit on the magnetar birthrate and comparing the synthetic populations to the observed one using both manual and automatic optimization algorithms for our input parameter study, we find that the B-field must decay exponentially or super-exponentially with a characteristic decay timescale of 0.5 − 10 kyr (with a best value of ∼4 kyr). In addition, the initial spin period must be less than 2 sec. If these constraints are kept, we conclude that there are multiple choices of input physics that can reproduce the observed magnetar population reasonably well. We also conclude that magnetars may well be evolutionary linked to the population of XDINSs, whereas they are in general unlikely to evolve into RRATs.

PEMBENTUKAN POPULASI SINTETIS UNTUK PENINGKATAN KUALITAS GENETIK IKAN MAS

Benih ikan mas telah mengalami penurunan kualitas genetik yang menyebabkan penurunan performa fenotipik di lingkungan budidaya. Salah satu upaya perbaikan genetik adalah melalui pembentukan populasi sintetis yang merupakan penggabungan potensi genetik beberapa populasi plasma nutfah ikan mas. Penelitian ini bertujuan membentuk dan mengevaluasi performa genotipik dan fenotipik populasi sintetis ikan mas, yang merupakan penggabungan dari strain Rajadanu, Majalaya, Sutisna, Wildan, dan Sinyonya. Performa genotipik dievaluasi menggunakan metode mikrosatelit DNA, sedangkan performa fenotipik dievaluasi menggunakan analisis biometrik terkait kegiatan budidaya. Hasil penelitian menunjukkan bahwa nilai keragaman genetik populasi sintetis lebih tinggi 55,0%-287,5% dengan tingkat inbreeding 40,0%-77,14% lebih rendah dibanding populasi-populasi pembentuknya. Hal ini berdampak terhadap performa fenotipik populasi sintetis yang lebih baik, diindikasikan dengan peningkatan panjang, bobot akhir, dan tingkat produktivitas, masing-masing sebesar 2,5%-20,6%; 9,4%-61,8%; dan 18,2%-66,0% lebih baik dibanding populasi-populasi pembentuknya. Peningkatan kualitas genetik dan performa fenotipik populasi sintetis ini memberikan peluang untuk memperbaiki kualitas benih ikan mas pada kegiatan budidaya.Common carp in Indonesia has experienced a decline in genetic quality. The progressive decline leads to a significant decrease in carp performance in the farming environment. One of the efforts to genetically improve carp growth performance is through developing synthetic carp populations, which is a blend of the genetic potentials from several germplasm populations. This study aimed to form and evaluate the performance of genotypic and phenotypic of synthetic populations of common carp, blended from five strains of common carp, i.e., Rajadanu, Majalaya, Sutisna, Wildan, and Sinyonya. The genotypic performance was evaluated using the DNA microsatellite method. The phenotypic performance was assessed using biometric analysis, especially in terms of culture performance. The results showed that the genotypic performance of the synthetic populations of common carp was better than that of the founder strains. This performance was indicated by higher genetic diversity values, about 55.0%-287.5% and lower levels of inbreeding, about 40.0%-77.1%, compared with their founder populations. Phenotypic performance of the synthetic populations is also better than their founder populations, indicated by higher body length, weight, and productivity, about 2.5%-20.6%, 9.4%-61.8%, and 18.2%-66.0%, respectively. The improvement on genetic quality and phenotypic performance of the synthetic population provide opportunities to improve the quality of common carp fry in aquaculture activity.