Assessing different metrics of pedigree and genomic inbreeding and inbreeding effect on growth, fertility, and feed efficiency traits in a closed-herd Nellore cattle population.

BACKGROUND: The selection of individuals based on their predicted breeding values and mating of related individuals can increase the proportion of identical-by-descent alleles. In this context, the objectives of this study were to estimate inbreeding coefficients based on alternative metrics and data sources such as pedigree (FPED), hybrid genomic relationship matrix H (FH), and ROH of different length (FROH); and calculate Pearson correlations between the different metrics in a closed Nellore cattle population selected for body weight adjusted to 378 days of age (W378). In addition to total FROH (all classes) coefficients were also estimated based on the size class of the ROH segments: FROH1 (1-2 Mb), FROH2 (2-4 Mb), FROH3 (4-8 Mb), FROH4 (8-16 Mb), and FROH5 (> 16 Mb), and for each chromosome (FROH_CHR). Furthermore, we assessed the effect of each inbreeding metric on birth weight (BW), body weights adjusted to 210 (W210) and W378, scrotal circumference (SC), and residual feed intake (RFI). We also evaluated the chromosome-specific effects of inbreeding on growth traits. RESULTS: The correlation between FPED and FROH was 0.60 while between FH and FROH and FH and FPED were 0.69 and 0.61, respectively. The annual rate of inbreeding was 0.16% for FPED, 0.02% for FH, and 0.16% for FROH. A 1% increase in FROH5 resulted in a reduction of up to -1.327 ± 0.495 kg in W210 and W378. Four inbreeding coefficients (FPED, FH, FROH2, and FROH5) had a significant effect on W378, with reductions of up to -3.810 ± 1.753 kg per 1% increase in FROH2. There was an unfavorable effect of FPED on RFI (0.01 ± 0.0002 kg dry matter/day) and of FROH on SC (-0.056 ± 0.022 cm). The FROH_CHR coefficients calculated for BTA3, BTA5, and BTA8 significantly affected the growth traits. CONCLUSIONS: Inbreeding depression was observed for all traits evaluated. However, these effects were greater for the criterion used for selection of the animals (i.e., W378). The increase in the genomic inbreeding was associated with a higher inbreeding depression on the traits evaluated when compared to pedigree-based inbreeding. Genomic information should be used as a tool during mating to optimize control of inbreeding and, consequently, minimize inbreeding depression in Nellore cattle.

Assessing the best time interval between doses in a two-dose vaccination regimen to reduce the number of deaths in an ongoing epidemic of SARS-CoV-2.

The SARS-CoV-2 pandemic is a major concern all over the world and, as vaccines became available at the end of 2020, optimal vaccination strategies were subjected to intense investigation. Considering their critical role in reducing disease burden, the increasing demand outpacing production, and that most currently approved vaccines follow a two-dose regimen, the cost-effectiveness of delaying the second dose to increment the coverage of the population receiving the first dose is often debated. Finding the best solution is complex due to the trade-off between vaccinating more people with lower level of protection and guaranteeing higher protection to a fewer number of individuals. Here we present a novel extended age-structured SEIR mathematical model that includes a two-dose vaccination schedule with a between-doses delay modelled through delay differential equations and linear optimization of vaccination rates. By maintaining the minimum stock of vaccines under a given production rate, we evaluate the dose interval that minimizes the number of deaths. We found that the best strategy depends on an interplay between the vaccine production rate and the relative efficacy of the first dose. In the scenario of low first-dose efficacy, it is always better to vaccinate the second dose as soon as possible, while for high first-dose efficacy, the best strategy of time window depends on the production rate and also on second-dose efficacy provided by each type of vaccine. We also found that the rate of spread of the infection does not affect significantly the thresholds of the best window, but is an important factor in the absolute number of total deaths. These conclusions point to the need to carefully take into account both vaccine characteristics and roll-out speed to optimize the outcome of vaccination strategies.

Relationship between age, scrotal circumference, postweaning weight and semen quality in Nellore and Caracu bulls: a cross sectional study.

The aim of this study was to investigate the relationship between age, scrotal circumference, postweaning weight and semen quality in Nellore and Caracu bulls selected for postweaning weight. Data from the andrological evaluation of 836 bulls born between 2000 and 2019, including 583 Nellore animals (Bos indicus) and 253 Caracu animals (Bos taurus), were used. The bulls were divided into categories of age at the time of assessment: category 1 consisted of animals aged 20 to 23 months (22 ± 0.76 months, 518 ± 94.17 kg), category 2 consisted of animals aged 24 to 35 months (30 ± 4.42 months, 679 ± 137.19 kg), and category 3 consisted of animals ≥ 36 months (60 ± 14.12 months, 907 ± 161.73 kg). The statistical model included the effects of breed, age category, date of semen collection, and breed x age category interaction. Heritability estimates for scrotal circumference at 13 months of age (SC1year) and semen quality traits were obtained for the sample of Nellore animals. Most semen quality traits improved with increasing age in both Nellore and Caracu animals. High heritability was observed for SC1year (0.45), while sperm motility, vigor, turbulence, and major, minor and total sperm defects exhibited low heritability (0.11, 0.019, 0.047, 0.017, 0.017 and 0.019, respectively). Spearman correlations of breeding values for postweaning weight (W378) and SC1year with the semen quality traits were low. Nellore and Caracu bulls have similar semen quality that improves with increasing age. In the Nellore breed, the heritability of SC is high, while semen quality traits exhibit low heritability. Selection for higher postweaning weight does not phenotypically affect the semen quality of bulls at breeding age.

Consumers' active choice behaviour promotes coevolutionary units in antagonistic networks.

Individual behaviour and local context can influence the evolution of ecological interactions and how they structure into networks. In trophic interactions, consumers can increase their fitness by actively choosing resources that they are more likely to explore successfully. Mathematical modelling is often employed in theoretical studies to understand the coevolutionary dynamics between consumers and resources. However, they often disregard the individual consumer behaviour since the complexity of these systems usually requires simplifying assumptions about interaction details. Using an individual-based model, we model a community of several species that interact antagonistically. Each individual has a trait (attack or defence) that is explicitly modelled and the probability of the interaction to occur successfully increases with increased trait-matching. In addition, consumers can actively choose resources that guarantee greater fitness. We show that active consumer choice can generate coevolutionary units over time. It means that the traits of both consumers and resources converge into multiple groups with similar traits and the species interactions stay restricted to these groups over time. We also observed that network structure is more dependent on the parameter that delimits active consumer choice than on the intensity of selective pressure. Thus, our results support the idea that consumer active choice behaviour plays an important role in the ecological and evolutionary processes that structure interacting communities.

Effect of Nellore (Bos indicus) donor age on in-vitro embryo production and pregnancy rate.

The aim of this study was to evaluate the effect of age of Nellore (Bos indicus) donors on the efficiency of in vitro embryo production (IVEP) and pregnancy rate. Thirty-six donors, including 11 female calves (13 ± 0.61 months), 17 prepubertal heifers (25 ± 0.78 months) and 8 cows (83 ± 28 months), were submitted to 3 procedures of ovum pickup (OPU) on random days of the estrous cycle at intervals of 21 days. Caspase-3 and IGFBP2 were quantified in oocytes and blastocysts for the evaluation of oocyte and embryo quality. The produced embryos were vitrified (n = 445) and transferred to synchronized recipients. Cows produced a larger number of follicles (cows: 54.5 ± 6.2; calves: 20.0 ± 0.57; prepubertal heifers: 20.8 ± 0.46), total oocytes (cows: 45.97 ± 7.22; calves: 28.93 ± 6.14; prepubertal heifers: 27.21 ± 4.94) and cleaved oocytes (cows: 21.14 ± 4.22; calves: 13.09 ± 3.72; prepubertal heifers: 12.4 ± 3.19). The cleavage rate was similar between age categories; however, cows tended (p < 0.07) to produce a larger number of blastocysts (9.74 ± 2.26) per OPU than calves (5.57 ± 1.99) and prepubertal heifers tended to have a higher blastocyst yield (35.4%) than calves (27.1%) (p < .07). The expression levels of IGFBP2 and caspase-3 were higher in oocytes derived from calves compared to the other two categories. The pregnancy rate was higher in calves (43.1%) and cows (40.4%) than in prepubertal heifers (33.8%) (p = .03). Despite the larger numbers of follicles and viable oocytes in cows, the blastocyst production results and pregnancy rates obtained indicate that the use of young females as oocyte donors in IVEP is feasible and may contribute to reduce the generation interval.

Gradual increase of temperature trigger metabolic and oxidative responses in plasma and body tissues in the Antarctic fish Notothenia rossii.

Antarctica is considered a thermally stable ecosystem; however, climate studies point to increases in water temperatures in this region. These thermal changes may affect the biological processes and promote metabolic changes in the adapted organisms that live in this region, rendering the animals more vulnerable to oxidative damage. This study assessed the effect of acclimation temperature on the levels of stress response markers in plasma, kidney, gill, liver, and brain tissues of Notothenia rossii subjected to gradual temperature changes of 0.5 °C/day until reaching temperatures of 2, 4, 6, and 8 °C. Under the effect of the 0.5 °C/day acclimation rate, gill tissue showed increased glutathione-S-transferase (GST) activity; kidney tissue showed increased H+-ATPase activity. In the liver, there was also an increase in GSH. In plasma, gradual decreases in the concentrations of total proteins and globulins were observed. These responses indicate a higher production of reactive oxygen species ROS, an imbalance in energy demand, and a lack in protein synthesis. Gradual increase in temperature may cause opposite responses to the thermal shock model in N. rossii.

Coevolutionary patterns caused by prey selection.

Many theoretical models have been formulated to better understand the coevolutionary patterns that emerge from antagonistic interactions. These models usually assume that the attacks by the exploiters are random, so the effect of victim selection by exploiters on coevolutionary patterns remains unexplored. Here we analytically studied the payoff for predators and prey under coevolution assuming that every individual predator can attack only a small number of prey any given time, considering two scenarios: (i) predation occurs at random; (ii) predators select prey according to phenotype matching. We also develop an individual based model to verify the robustness of our analytical prediction. We show that both scenarios result in well known similar coevolutionary patterns if population sizes are sufficiently high: symmetrical coevolutionary branching and symmetrical coevolutionary cycling (Red Queen dynamics). However, for small population sizes, prey selection can cause unexpected coevolutionary patterns. One is the breaking of symmetry of the coevolutionary pattern, where the phenotypes evolve towards one of two evolutionarily stable patterns. As population size increases, the phenotypes oscillate between these two values in a novel form of Red Queen dynamics, the episodic reversal between the two stable patterns. Thus, prey selection causes prey phenotypes to evolve towards more extreme values, which reduces the fitness of both predators and prey, increasing the likelihood of extinction.

Infrared thermography relationship between the temperature of the vulvar skin, ovarian activity, and pregnancy rates in Braford cows.

The objective of this study was to compare the presence of ovarian activity and pregnancy rates to temperature variation at the vulvar skin measured by infrared thermography (IRT). In addition, we also aimed to evaluate the IRT as a non-invasive method to evaluate animal breeding from fixed timed artificial insemination (FTAI). The study comprises 150 non-lactating beef Braford cows (5/8 Hereford × 3/8 Nellore) aged between 3 and 10 years. Data were collected along the FTAI protocol period during animal management. Animals were subjected to reproductive ultrasound evaluation and thermal images were performed by an infrared camera. Mean skin vulvar temperature (°C) and ovarian structures data were compared using Tukey's t test used as follow-up test to ANOVA. We observed a statistical difference in the mean vulvar skin temperature between animals that had the presence of ovarian follicles (34.2 ± 1.8) compared to no activity (35.4 ± 1.0; P < 0.05). However, vulvar skin temperature were similar between pregnant (34.5 ± 1.5) compared to non-pregnant (34.3 ± 1.9) animals (P > 0.05). In conclusion, the IRT technique was efficient to detect changes on vulvar skin temperature observed during FTAI protocol in Braford cows. Therefore, the use of IRT as an indirectly diagnostic tool to detect ovarian activity seems promising and further studies are required to validate their potential in beef cattle production.

[Eating habit and metabolic syndrome in a sample of Brazilian adults]. / Hábito alimentar e síndrome metabólica em uma amostra de adultos brasileiros.

The objective was to analyze indicators related to eating habits and their association with metabolic syndrome (MetS) in a representative sample of adults in a community from State of São Paulo, Brazil. The sample was comprised of 1,112 participants aged ≥ 20 years. Data from sociodemographic issues, indicators regarding eating habits, anthropometric measures, resting arterial pressure, blood glucose and plasma lipids were registered. MetS was assessed according to the NCEP-ATP III criteria. The results showed that adequate consumption of fruits and vegetables was reported by less than 10% of the individuals. Regular consumption of fatty foods (5 days/week) was reported by 54.2% and sugar-added products and soft drinks by 3 8.6% of the interviewees. Gender, age, schooling, socioeconomic level and nutritional status influenced significantly the eating habits. Prevalence of MetS was approximately 24%, significantly higher in men (27.8% vs 20.3%; p = 0.005). Risk to identify MetS in individuals who reported not consuming regularly fruits and vegetables was approximately two times higher than their peers who reported adequate intake (women: OR = 1.93; 95% CI 1.51 - 2.38; men: OR = 2.04; 95% CI 1.63 - 2.40). Exposure risk for MetS was progressively higher according to reported higher consumption of fatty foods, sugar-added products and soft drinks. The findings suggest interventions in order to emphasize healthy eating habits, which could help to minimize risk of MetS.

Correction: The Brazilian vaccine divide: How some municipalities were left behind in the Covid-19 vaccine coverage.

[This corrects the article DOI: 10.1371/journal.pgph.0002493.].

Spatial clusters and social inequities in COVID-19 vaccine coverage among children in Brazil.

This study examined the spatial distribution and social inequalities in COVID-19 vaccine coverage among children aged 5-11 in Brazil. First and second dose vaccine coverage was calculated for all Brazilian municipalities and analyzed by geographic region and deciles based on human development index (HDI-M) and expected years of schooling at 18 years of age. Multilevel models were used to determine the variance partition coefficient, and bivariate local Moran's I statistic was used to assess spatial association. Results showed significant differences in vaccine coverage rates among Brazilian municipalities, with lower coverage in the North and Midwest regions. Municipalities with lower HDI and expected years of schooling had consistently lower vaccine coverage rates. Bivariate clustering analysis identified extensive concentrations of municipalities in the Northern and Northeastern regions with low vaccine coverage and low human development, while some clusters of municipalities in the Southeast and South regions with low coverage were located in areas with high HDI-M. These findings highlight the persistent municipal-level inequalities in vaccine coverage among children in Brazil and the need for targeted interventions to improve vaccine access and coverage in underserved areas.

Functional and morphological adaptations to aging in knee extensor muscles of physically active men.

It is not known if a physically active lifestyle, without systematic training, is sufficient to combat age-related muscle and strength loss. Therefore, the purpose of this study was to evaluate if the maintenance of a physically active lifestyle prevents muscle impairments due to aging. To address this issue, we evaluated 33 healthy men with similar physical activity levels (IPAQ = 2) across a large range of ages. Functional (torque-angle and torque-velocity relations) and morphological (vastus lateralis muscle architecture) properties of the knee extensor muscles were assessed and compared between three age groups: young adults (30 ± 6 y), middle-aged subjects (50 ± 7 y) and elderly subjects (69 ± 5 y). Isometric peak torques were significantly lower (30% to 36%) in elderly group subjects compared with the young adults. Concentric peak torques were significantly lower in the middle aged (18% to 32%) and elderly group (40% to 53%) compared with the young adults. Vastus lateralis thickness and fascicles lengths were significantly smaller in the elderly group subjects (15.8 ± 3.9 mm; 99.1 ± 25.8 mm) compared with the young adults (19.8 ± 3.6 mm; 152.1 ± 42.0 mm). These findings suggest that a physically active lifestyle, without systematic training, is not sufficient to avoid loss of strength and muscle mass with aging.

The Brazilian vaccine divide: How some municipalities were left behind in the Covid-19 vaccine coverage.

This study aims to assess the progress of geographic, socioeconomic, and demographic disparities in Covid-19 vaccination coverage in Brazil over the first two years of the vaccination campaign. Data from the National Immunization Program Information System were used to estimate covid-19 vaccine coverage. Brazilian municipalities were divided into two groups based on their vaccine coverage for the booster dose. The first group comprised 20% of municipalities with the lowest coverage, while the second group (80% of municipalities) had higher coverage. The analysis was conducted separately for four age groups: 5-11, 12-17, 18-59, and 60+. Explanatory variables included socioeconomic and health services indicators. Crude and adjusted logistic regression models were used to estimate the probability of a municipality being among those with the worst vaccination coverage according to the categories of exploratory variables. Between January/2021 and December/2022, Brazil administered 448.2 million doses of the covid-19 vaccine. The booster vaccination coverage varied from 24.8% among adolescents to 79.7% among the elderly. The difference between the group with the highest and lowest coverage increased during the national vaccination campaign. Municipalities with lower education levels, higher proportion of Black population, higher Gini index, and worse health service indicators had a greater likelihood of having lower vaccination coverage. High and increasing levels of inequality in Covid-19 vaccination were observed in Brazil across all age groups during the vaccination campaign in 2021-2022.

Uncovering inequities in Covid-19 vaccine coverage for adults and elderly in Brazil: A multilevel study of 2021-2022 data.

Vaccination is crucial for reducing severe COVID-19 cases, hospitalizations, and deaths. However, vaccine access disparities within countries, particularly in low- and middle-income nations, may leave disadvantaged regions and populations behind. This study aimed to investigate potential inequalities in vaccine coverage among Brazilian aged 18 years and older based on demographic, geographic, and socioeconomic characteristics at the municipal level. A total of 389 million vaccination records from the National Immunization Program Information System were analyzed to calculate vaccine coverage rates for the first, second, and booster doses among adults (18-59 years) and elderly (60 + years) vaccinated between January 2021 and December 2022. We analyzed the data by gender and used a three-level (municipalities, states, regions) multilevel regression analysis to assess the association between vaccine coverage and municipal characteristics. Vaccination coverage was higher among the elderly than among adults, particularly for the second and booster doses. Adult women showed higher coverage rates than men (ranging from 118 % to 25 % higher along the analyzed period). Significant inequalities were observed when analyzing the evolution of vaccination coverage by sociodemographic characteristics of municipalities. In the early stages of the vaccination campaign, municipalities with higher per capita Gross Domestic Product (pGDP), educational level, and fewer Black residents reached higher population coverages earlier. In December 2022, adult and elderly booster vaccine coverage was 43 % and 19 %, respectively, higher in municipalities in the highest quintile of educational level. Higher vaccine uptake was also observed in municipalities with fewer Black residents and higher pGDP. Municipalities accounted for most of the variance in vaccine coverage (59.7 %-90.4 % depending on the dose and age group). This study emphasizes the inadequate booster coverage and the presence of socioeconomic and demographic disparities in COVID-19 vaccination rates. These issues must be addressed through equitable interventions to avoid potential disparities in morbidity and mortality.

Estimating the impact of implementation and timing of the COVID-19 vaccination programme in Brazil: a counterfactual analysis.

Background: Vaccines developed between 2020 and 2021 against the SARS-CoV-2 virus were designed to diminish the severity and prevent deaths due to COVID-19. However, estimates of the effectiveness of vaccination campaigns in achieving these goals remain a methodological challenge. In this work, we developed a Bayesian statistical model to estimate the number of deaths and hospitalisations averted by vaccination of older adults (above 60 years old) in Brazil. Methods: We fit a linear model to predict the number of deaths and hospitalisations of older adults as a function of vaccination coverage in this group and casualties in younger adults. We used this model in a counterfactual analysis, simulating alternative scenarios without vaccination or with faster vaccination roll-out. We estimated the direct effects of COVID-19 vaccination by computing the difference between hypothetical and realised scenarios. Findings: We estimated that more than 165,000 individuals above 60 years of age were not hospitalised due to COVID-19 in the first seven months of the vaccination campaign. An additional contingent of 104,000 hospitalisations could have been averted if vaccination had started earlier. We also estimated that more than 58 thousand lives were saved by vaccinations in the period analysed for the same age group and that an additional 47 thousand lives could have been saved had the Brazilian government started the vaccination programme earlier. Interpretation: Our estimates provided a lower bound for vaccination impacts in Brazil, demonstrating the importance of preventing the suffering and loss of older Brazilian adults. Once vaccines were approved, an early vaccination roll-out could have saved many more lives, especially when facing a pandemic. Funding: The Coordenação de Aperfeiçoamento de Pessoal de Nível Superior-Brazil (Finance Code 001 to F.M.D.M. and L.S.F.), Conselho Nacional de Desenvolvimento Científico e Tecnológico - Brazil (grant number: 315854/2020-0 to M.E.B., 141698/2018-7 to R.L.P.d.S., 313055/2020-3 to P.I.P., 311832/2017-2 to R.A.K.), Fundação de Amparo à Pesquisa do Estado de São Paulo - Brazil (contract number: 2016/01343-7 to R.A.K.), Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro - Brazil (grant number: E-26/201.277/2021 to L.S.B.) and Inova Fiocruz/Fundação Oswaldo Cruz - Brazil (grant number: 48401485034116) to L.S.B., O.G.C. and M.G.d.F.C. The funding agencies had no role in the conceptualization of the study.

One piece of the puzzle: Modeling vector presence and environment reveals seasonality, distribution, and prevalence of sandflies and Leishmania in an expansion area.

The recent geographic spread of Leishmania infantum along the borders of Argentina, Brazil and Paraguay has been highlighted. In our previous study, Lutzomyia longipalpis was found in 55 of 123 patches surveyed, and in some patches, sandflies were found at higher densities, forming hotspots. Based on the One Health approach, we investigated the seasonality of the vector, the presence of parasite DNA, and the environmental factors that contribute to vector and parasite dispersal in these previously described hotspots in Foz do Iguaçu, Brazil. Entomological surveys were conducted monthly for one year. Fourteen hotspots peridomicile and six intradomicile were sampled. PCR was used to assess the prevalence of Leishmania DNA in sandflies. Zero-inflated negative binomial regression was used to determine the association of micro- and mesoscale environmental variables with the occurrence and abundance of the three most abundant sandfly species sampled. A total of 3543 species were captured, with Lutzomyia longipalpis being the predominant species (71.78%) of the 13 species found. Evandromyia edwardsi, Expapillata firmatoi, Micropygomyia ferreirana and Pintomyia christenseni were reported for the first time in the region. NDVI, distance to water, precipitation, west-to-east wind, wind speed, maximum and minimum relative humidity, and sex were significant variables associated with vector presence/abundance in the environment. Vector presence/abundance in the peridomicile was associated with precipitation, altitude, maximum temperature, minimum and maximum relative humidity, west-to-east wind, wind speed, and sex. Leishmania DNA was detected in an average of 21% of Lu. longipalpis throughout the year. Vector abundance is concentrated in urban and peri-urban areas, with some specimens present in different parts of the city and some sites with high vector abundance. This distribution suggests that the risk of actual contact between humans and parasite vectors in urban areas during the epidemic period is associated with patches of peri-urban vegetation and then extends into urban areas.

Modeling the impact of child vaccination (5-11 y) on overall COVID-19 related hospitalizations and mortality in a context of omicron variant predominance and different vaccination coverage paces in Brazil.

Background: Developing countries have experienced significant COVID-19 disease burden. With the emergence of new variants, particularly omicron, the disease burden in children has increased. When the first COVID-19 vaccine was approved for use in children aged 5-11 years of age, very few countries recommended vaccination due to limited risk-benefit evidence for vaccination of this population. In Brazil, ranking second in the global COVID-19 death toll, the childhood COVID-19 disease burden increased significantly in early 2022. This prompted a risk-benefit assessment of the introduction and scaling-up of COVID-19 vaccination of children. Methods: To estimate the potential impact of vaccinating children aged 5-11 years with mRNA-based COVID-19 vaccine in the context of omicron dominance, we developed a discrete-time SEIR-like model stratified in age groups, considering a three-month time horizon. We considered three scenarios: No vaccination, slow, and maximum vaccination paces. In each scenario, we estimated the potential reduction in total COVID-19 cases, hospitalizations, deaths, hospitalization costs, and potential years of life lost, considering the absence of vaccination as the base-case scenario. Findings: We estimated that vaccinating at a maximum pace could prevent, between mid-January and April 2022, about 26,000 COVID-19 hospitalizations, and 4200 deaths in all age groups; of which 5400 hospitalizations and 410 deaths in children aged 5-11 years. Continuing vaccination at a slow/current pace would prevent 1450 deaths and 9700 COVID-19 hospitalizations in all age groups in this same time period; of which 180 deaths and 2390 hospitalizations in children only. Interpretation: Maximum vaccination of children results in a significant reduction of COVID-19 hospitalizations and deaths and should be enforced in developing countries with significant disease incidence in children. Funding: This manuscript was funded by the Brazilian Council for Scientific and Technology Development (CNPq - Process # 402834/2020-8).

Dynamic transmission modeling of COVID-19 to support decision-making in Brazil: A scoping review in the pre-vaccine era.

Brazil was one of the countries most affected during the first year of the COVID-19 pandemic, in a pre-vaccine era, and mathematical and statistical models were used in decision-making and public policies to mitigate and suppress SARS-CoV-2 dispersion. In this article, we intend to overview the modeling for COVID-19 in Brazil, focusing on the first 18 months of the pandemic. We conducted a scoping review and searched for studies on infectious disease modeling methods in peer-reviewed journals and gray literature, published between January 01, 2020, and June 2, 2021, reporting real-world or scenario-based COVID-19 modeling for Brazil. We included 81 studies, most corresponding to published articles produced in Brazilian institutions. The models were dynamic and deterministic in the majority. The predominant model type was compartmental, but other models were also found. The main modeling objectives were to analyze epidemiological scenarios (testing interventions' effectiveness) and to project short and long-term predictions, while few articles performed economic impact analysis. Estimations of the R0 and transmission rates or projections regarding the course of the epidemic figured as major, especially at the beginning of the crisis. However, several other outputs were forecasted, such as the isolation/quarantine effect on transmission, hospital facilities required, secondary cases caused by infected children, and the economic effects of the pandemic. This study reveals numerous articles with shared objectives and similar methods and data sources. We observed a deficiency in addressing social inequities in the Brazilian context within the utilized models, which may also be expected in several low- and middle-income countries with significant social disparities. We conclude that the models were of great relevance in the pandemic scenario of COVID-19. Nevertheless, efforts could be better planned and executed with improved institutional organization, dialogue among research groups, increased interaction between modelers and epidemiologists, and establishment of a sustainable cooperation network.

Use of auxiliary techniques for assessing the reproductive capacity of natural service Nellore bulls.

The aim of this study was to investigate whether parameters obtained by computer-assisted sperm analysis (CASA), infrared thermography (IRT), and testicular B-mode and Doppler ultrasound can be used as indicators of fertility in natural service Nellore bulls. Twenty-nine Nellore bulls were evaluated on days 66 (-D66), 38 (-D38), and 10 (-D10) before the beginning of natural service mating. In all assessments, semen samples were collected and sperm kinetics were evaluated by CASA, thermographic imaging of the scrotal and ocular region, testicular B-mode ultrasound, and Doppler ultrasound of the spermatic cord. At the end of natural service, the bulls were classified based on the pregnancy rate of individual batches into low fertility (pregnancy rate 66.57 ± 0.62 %), medium fertility (76.47 ± 0.51 %), and high fertility (84.80 ± 0.60 %) groups. No difference in the IRT parameters was observed between groups. High fertility animals exhibited higher average path velocity (VAP = 110.98 µm/s), straight line velocity (VSL = 87.05 µm/s), curvilinear velocity (VCL = 190.78 µm/s), pulsatility index (PI = 0.93), and resistive index (RI = 0.57) than low fertility animals (VAP = 100.02 µm/s; VSL = 79.84 µm/s; VCL = 173.22 µm/s; PI = 0.69; RI = 0.48). Positive correlations were observed between pregnancy rate and VSL (0.21), PI (0.28) and RI (0.32). In conclusion, IRT does not provide fertility indicators in Nellore bulls. The VAP, VSL and VCL obtained by CASA and PI and RI obtained by Doppler ultrasound can be used as indicators of fertility in Nellore bulls.

Percolation across households in mechanistic models of non-pharmaceutical interventions in SARS-CoV-2 disease dynamics.

Since the emergence of the novel coronavirus disease 2019 (COVID-19), mathematical modelling has become an important tool for planning strategies to combat the pandemic by supporting decision-making and public policies, as well as allowing an assessment of the effect of different intervention scenarios. A proliferation of compartmental models were developed by the mathematical modelling community in order to understand and make predictions about the spread of COVID-19. While compartmental models are suitable for simulating large populations, the underlying assumption of a well-mixed population might be problematic when considering non-pharmaceutical interventions (NPIs) which have a major impact on the connectivity between individuals in a population. Here we propose a modification to an extended age-structured SEIR (susceptible-exposed-infected-recovered) framework, with dynamic transmission modelled using contact matrices for various settings in Brazil. By assuming that the mitigation strategies for COVID-19 affect the connections among different households, network percolation theory predicts that the connectivity among all households decreases drastically above a certain threshold of removed connections. We incorporated this emergent effect at population level by modulating home contact matrices through a percolation correction function, with the few additional parameters fitted to hospitalisation and mortality data from the city of São Paulo. Our model with percolation effects was better supported by the data than the same model without such effects. By allowing a more reliable assessment of the impact of NPIs, our improved model provides a better description of the epidemiological dynamics and, consequently, better policy recommendations.