Sampling Optimization and Crop Interface Effects on Lygus lineolaris Populations in Southeastern USA Cotton

Tarnished plant bug, Lygus lineolaris (Hemiptera: Miridae), is an economically damaging pest in cotton production systems across the southern United States. We systematically scouted 120 commercial cotton fields across five southeastern states during susceptible growth stages in 2019 and 2020 to investigate sampling optimization and the effect of interface crop and landscape composition on L. lineolaris abundance. Variance component analysis determined field and within-field spatial scales, compared with agricultural district and state, accounted for more variation in L. lineolaris density using sweep net and drop cloth sampling. This result highlights the importance of field-level scouting efforts. Using within-field samples, a fixed-precision sampling plan determined 8 and 23 sampling units were needed to determine L. lineolaris population estimates with 0.25 precision for sweep net (100 sweeps per unit) and drop cloth (1.5 row-m per unit) sampling, respectively. A spatial Bayesian hierarchical model was developed to determine local landscape (<0.5 km from field edges) effects on L. lineolaris in cotton. The proportion of agricultural area and double-crop wheat and soybeans were positively associated with L. lineolaris density, and fields with more contiguous cotton areas negatively predicted L. lineolaris populations. These results will improve L. lineolaris monitoring programs and treatment management decisions in southeastern USA cotton.

Influence of genetic and environmental factors on the contents of carotenoids and phenolic acids in red pepper fruits (Capsicum annuum L.)

Red pepper is enriched in antioxidant components, such as carotenoids, phenolic compounds, and vitamins. In this study, we investigated the natural variability in the content of carotenoids and phenolic acids in 11 red pepper cultivars grown in two locations in South Korea during 2016, 2017, and 2018. Seven carotenoids and six phenolic acids, including soluble and insoluble forms, were detected in the red fruit pericarps. The major carotenoids were β-carotene (40%) and capsanthin (20%). The content of insoluble phenolic acids was higher than that of soluble phenolic acids because of the large amount of insoluble p-coumaric acid. The statistical analysis of combined data showed significant differences among varieties, locations, and years for most of the measured components. The results from variance component analysis indicated that the effects of location, year and the interaction of location and year mainly accounted for the variation in carotenoids, whereas variations in phenolic acid content were attributed to year and variety. In addition, the results of principal component analysis and orthogonal partial least-squares discriminant showed that carotenoids were well discriminated by location and year, whereas phenolic acids were distinctively separated only by year. The data from this study could explain the natural variation in the content of carotenoids and phenolic acids in red pepper fruits by genotype and environment.

SpatialDE2: Fast and localized variance component analysis of spatial transcriptomics

Spatial transcriptomics is now a mature technology, allowing to assay gene expression changes in the histological context of complex tissues. A canonical analysis workflow starts with the identification of tissue zones that share similar expression profiles, followed by the detection of highly variable or spatially variable genes. Rapid increases in the scale and complexity of spatial transcriptomic datasets demand that these analysis steps are conducted in a consistent and integrated manner, a requirement that is not met by current methods. To address this, we here present SpatialDE2, which unifies the mapping of tissue zones and spatial variable gene detection as integrated software framework, while at the same time advancing current algorithms for both of these steps. Formulated in a Bayesian framework, the model accounts for the Poisson count noise, while simultaneously offering superior computational speed compared to previous methods. We validate SpatialDE2 using simulated data and illustrate its utility in the context of two real-world applications to the spatial transcriptomics profiles of the mouse brain and human endometrium.

A variance component analysis of the moral circle

People’s treatment of others—humans, animals, or other targets—often depends on whether they think the entity is worthy of moral consideration. Recent work has begun to examine which factors determine whether an entity is included in people’s moral circle. Here, we rely on multilevel modeling to map the variance components of the moral circle. We examine how much variance in moral concern is explained by who is being judged (i.e., between-target differences), by who is making the judgment (i.e., between-judge differences), and by their interaction. Two studies with participants from the Netherlands, the United States, the United Kingdom, and Australia (N = 836) show that all three components explain substantial amounts of variance in judgments of moral concern. Few cross-country differences emerged. Thus, to accurately predict when people grant moral standing to a target, characteristics of the target, characteristics of the judge, and their interaction need to be considered.

Unraveling the Relationship between Milk Yield and Quality at the Test Day with Rumination Time Recorded by a PLF Technology

The study aimed to estimate the components of rumination time (RT) variability recorded by a neck collar sensor and the relationship between RT and milk composition. Milk test day (TD) and RT data were collected from 691 cows in three farms. Daily RT data of each animal were averaged for 3, 7, and 10 days preceding the TD date (RTD). Variance component analysis of RTD, considering the effects of farm, cow, parity, TD date, and lactation phase, showed that a farm, followed by a cow, had major contributions to the total variability. The RT10 variable best performed on TD milk yield and quality records across models by a multi-model inference approach and was adopted to study its relationship with milk traits, by linear mixed models, through a 3-level stratification: low (LRT10 ≤ 8 h/day), medium (8 h/day < MRT10 ≤ 9 h/day), and high (HRT10 > 9 h/day) RT. Cows with HRT10 had greater milk, fat, protein, casein, and lactose daily yield, and lower fat, protein, casein contents, and fat to protein ratio compared to MRT10 and LRT10. Higher percentages of saturated fatty acid and lower unsaturated and monounsaturated fatty acid were found in HRT10, with respect to LRT10 and MRT10 observations.

Genetic and Genome-Wide Association Analysis of Yearling Weight Gain in Israel Holstein Dairy Calves

Yearling weight gain in male and female Israeli Holstein calves, defined as 365 × ((weight − 35)/age at weight) + 35, was analyzed from 814,729 records on 368,255 animals from 740 herds recorded between 1994 and 2021. The variance components were calculated based on valid records from 2008 through 2017 for each sex separately and both sexes jointly by a single-trait individual animal model analysis, which accounted for repeat records on animals. The analysis model also included the square root, linear, and quadratic effects of age at weight. Heritability and repeatability were 0.35 and 0.71 in the analysis of both sexes and similar in the single sex analyses. The regression of yearling weight gain on birth date in the complete data set was −0.96 kg/year. The complete data set was also analyzed by the same model as the variance component analysis, including both sexes and accounting for differing variance components for each sex. The genetic trend for yearling weight gain, including both sexes, was 1.02 kg/year. Genetic evaluations for yearling weight gain was positively correlated with genetic evaluations for milk, fat, protein production, and cow survival but negatively correlated with female fertility. Yearling weight gain was also correlated with the direct effect on dystocia, and increased yearling weight gain resulted in greater frequency of dystocia. Of the 1749 Israeli Holstein bulls genotyped with reliabilities >50%, 1445 had genetic evaluations. As genotyping of these bulls was performed using several single nucleotide polymorhphism (SNP) chip platforms, we included only those markers that were genotyped in >90% of the tested cohort. A total of 40,498 SNPs were retained. More than 400 markers had significant effects after permutation and correction for multiple testing (pnominal < 1 × 10−8). Considering all SNPs simultaneously, 0.69 of variance among the sires’ transmitting ability was explained. There were 24 markers with coefficients of determination for yearling weight gain >0.04. One marker, BTA-75458-no-rs on chromosome 5, explained ≈6% of the variance among the estimated breeding values for yearling weight gain. ARS-BFGL-NGS-39379 had the fifth largest coefficient of determination in the current study and was also found to have a significant effect on weight at an age of 13–14 months in a previous study on Holsteins. Significant genomic effects on yearling weight gain were mainly associated with milk production quantitative trait loci, specifically with kappa casein metabolism.

Genetic and environmental effects on weaning weight in crossbred beef cattle (Bos taurus × Bos indicus)

This work aimed to evaluate the effects of sire's and dam's biological type, dam's age class at calving and individual heterozygosis, and to estimate variance components for weaning weight adjusted to 210 days (WW210) in beef cattle of different breed groups. Records of 13 687 animals, obtained from 2000 to 2007, were used. Bulls from the biological types Zebu (N), Adapted (A), British (B), Continental (C) and ¼N|¼A|¼B|¼C were mated with purebred zebu (N) and crossbred females (½C|½N and ½B|½N). Dam age at calving was 3–12 years. The influence of several effects on WW210 was tested using the least square method. Variance component analysis was performed using a Bayesian approach. The model included contemporary group, dam's age class at calving, sire's and dam's biological types as systematic effects, animal's age and individual heterozygosis as linear covariates, and direct and maternal additive genetic, maternal permanent environmental and residual effects as random effects. The progeny of bulls from biological type B and the crossbred cows showed higher WW210 means. Cows at 6–7 years old weaned heavier calves. Direct and maternal heritability estimates for WW210 were 0.5 ± 0.04 and 0.1 ± 0.02, respectively. Calves with 100% individual heterozygosis weighed on average 25.98 kg more at weaning compared to progenies from pure breeds. Sire's and dam's biological types influence the WW210 of the crossed progenies. Crossbred cows produce heavier calves compared to biological type N cows. These results and the obtained direct and maternal heritabilities suggest it is possible to choose the lines of sires and dams that could be used to make the crosses to obtain progenies with better performance for WW210.

Appropriate margin for planning target volume for breast radiotherapy during deep inspiration breath-hold by variance component analysis

Background This study aimed to quantify errors by using a cine electronic portal imaging device (cine EPID) during deep inspiration breath-hold (DIBH) for left-sided breast cancer and to estimate the planning target volume (PTV) by variance component analysis. Methods This study included 25 consecutive left-sided breast cancer patients treated with whole-breast irradiation (WBI) using DIBH. Breath-holding was performed while monitoring abdominal anterior–posterior (AP) motion using the Real-time Position Management (RPM) system. Cine EPID was used to evaluate the chest wall displacements in patients. Cine EPID images of the patients (309,609 frames) were analyzed to detect the edges of the chest wall using a Canny filter. The errors that occurred during DIBH included differences between the chest wall position detected by digitally reconstructed radiographs and that of all cine EPID images. The inter-patient, inter-fraction, and intra-fractional standard deviations (SDs) in the DIBH were calculated, and the PTV margin was estimated by variance component analysis. Results The median patient age was 55 (35–79) years, and the mean irradiation time was 20.4 ± 1.7 s. The abdominal AP motion was 1.36 ± 0.94 (0.14–5.28) mm. The overall mean of the errors was 0.30 mm (95% confidence interval: − 0.05–0.65). The inter-patient, inter-fraction, and intra-fractional SDs in the DIBH were 0.82 mm, 1.19 mm, and 1.63 mm, respectively, and the PTV margin was calculated as 3.59 mm. Conclusions Errors during DIBH for breast radiotherapy were monitored using EPID images and appropriate PTV margins were estimated by variance component analysis.

Intrinsic hospital factors: overlooked cause for variations in delay to transfer for endovascular thrombectomy

BackgroundIntrinsic hospital factors leading to time delay to inter-hospital transfer for endovascular thrombectomy (EVT) have not been adequately investigated, leading to uncertainty in generalizability of hub and spoke EVT services. We investigated the contribution of intrinsic hospital factors to variations in time delay in a multicenter, retrospective study.MethodsThe setting was a hub and spoke EVT state-wide system for a population of 6.3 million and 34 spoke hospitals. We collected data on acute large vessel occlusion strokes transferred from spoke to hub for consideration of EVT between January 2016 and December 2018. The primary endpoint was the proportion of variability in delay-time in transfer cases contributed to by intrinsic hospital factors estimated through variance component analysis implemented as a mixed-effect linear regression model with hospitals as random effects.ResultsWe included 434 patients. The median age was 72 years (IQR 62–79), 44% were female, and the median baseline National Institutes of Health Stroke Scale (NIHSS) was 16 (IQR 11–20). The median onset to CT time was 100 mins (IQR 69–157) at the spoke hospitals and CT acquisition at the spoke hospital to time of transfer was 93 min (IQR 70–132). 53% of the observed variability in time from CT acquisition at the spoke hospital to transfer to the EVT center was explained by intrinsic hospital factors, as opposed to patient-related factors.ConclusionsIntrinsic hospital factors explained more than half of the observed variability in time from CT acquisition at the spoke hospital to departure for transfer. We recommend that the design of hub and spoke EVT services should account for intrinsic hospital factors to minimize hospital transfer delay.

Phenotypic yield and its structure variability of moderately late and late potato cultivars

The breeding of new potato cultivars of a given earliness group is closely related to the knowledge of the range of variability and interdependence of traits in a given year and between years. The research results were based on the field experience conducted in 2010–2012, in Central-Eastern Poland (51°34'N, 23°02'E), on lessive, slightly acidic soil. The experiment was carried out in a randomized block design in triplicate. Seventeen medium late and late potato cultivars were tested. Agronomic and plant protection treatments were carried out following the principles of good agricultural practice. The variability of potato economic characteristics was assessed through variance analysis, variance component analysis, cluster analysis, and principal component analysis (PCA). The years of research (52.5–94.6%) have played a dominant role in the phenotypic variability of general yield, commercial and seed yield, and their structure. The genetic factor was from 1.3 to 24.1%, and the interaction of the cultivar × years – from 3.1 to 61.7% of the variance share in the total variance. The analysis of the main components has identified four groups of cultivars with specific properties. They can be used in the decision-making system of breeding the new potato creations.