Heterozygous BTNL8 variants in individuals with multisystem inflammatory syndrome in children (MIS-C).

Multisystem inflammatory syndrome in children (MIS-C) is a rare condition following SARS-CoV-2 infection associated with intestinal manifestations. Genetic predisposition, including inborn errors of the OAS-RNAseL pathway, has been reported. We sequenced 154 MIS-C patients and utilized a novel statistical framework of gene burden analysis, "burdenMC," which identified an enrichment for rare predicted-deleterious variants in BTNL8 (OR = 4.

Elongation of the nascent avian foregut requires coordination of intrinsic and extrinsic cell behaviors.

The foregut tube gives rise to the lungs and upper gastrointestinal tract, enabling vital functions of respiration and digestion. How the foregut tube forms during embryonic development has historically received considerable attention, but over the past few decades this question has primarily been addressed indirectly through studies on morphogenesis of the primitive heart tube, a closely related process. As a result, many aspects of foregut development remain unresolved.

Potential approaches to create ultimate genotypes in crops and livestock.

Many thousands and, in some cases, millions of individuals from the major crop and livestock species have been genotyped and phenotyped for the purpose of genomic selection. 'Ultimate genotypes', in which the marker allele haplotypes with the most favorable effects on a target trait or traits in the population are combined together in silico, can be constructed from these datasets. Ultimate genotypes display up to six times the performance of the current best individuals in the population, as demonstrated for net profit in dairy cattle (incorporating a range of economic traits), yield in wheat and 100-seed weight in chickpea.

Shared neutrophil and T cell dysfunction is accompanied by a distinct interferon signature during severe febrile illnesses in children.

Severe febrile illnesses in children encompass life-threatening organ dysfunction caused by diverse pathogens and other severe inflammatory syndromes. A comparative approach to these illnesses may identify shared and distinct features of host immune dysfunction amenable to immunomodulation. Here, using immunophenotyping with mass cytometry and cell stimulation experiments, we illustrate trajectories of immune dysfunction in 74 children with multi-system inflammatory syndrome in children (MIS-C) associated with SARS-CoV-2, 30 with bacterial infection, 16 with viral infection, 8 with Kawasaki disease, and 42 controls.

A quantum coherent spin in hexagonal boron nitride at ambient conditions.

Solid-state spin-photon interfaces that combine single-photon generation and long-lived spin coherence with scalable device integration-ideally under ambient conditions-hold great promise for the implementation of quantum networks and sensors. Despite rapid progress reported across several candidate systems, those possessing quantum coherent single spins at room temperature remain extremely rare. Here we report quantum coherent control under ambient conditions of a single-photon-emitting defect spin in a layered van der Waals material, namely, hexagonal boron nitride.

Genomic prediction for sugarcane diseases including hybrid Bayesian-machine learning approaches.

Sugarcane smut and Pachymetra root rots are two serious diseases of sugarcane, with susceptible infected crops losing over 30% of yield. A heritable component to both diseases has been demonstrated, suggesting selection could improve disease resistance. Genomic selection could accelerate gains even further, enabling early selection of resistant seedlings for breeding and clonal propagation.

Use of continuous genotypes for genomic prediction in sugarcane.

Genomic selection in sugarcane faces challenges due to limited genomic tools and high genomic complexity, particularly because of its high and variable ploidy. The classification of genotypes for single nucleotide polymorphisms (SNPs) becomes difficult due to the wide range of possible allele dosages. Previous genomic studies in sugarcane used pseudo-diploid genotyping, grouping all heterozygotes into a single class.

Optimising clonal performance in sugarcane: leveraging non-additive effects via mate-allocation strategies.

Mate-allocation strategies in breeding programs can improve progeny performance by harnessing non-additive genetic effects. These approaches prioritise predicted progeny merit over parental breeding value, making them particularly appealing for clonally propagated crops such as sugarcane. We conducted a comparative analysis of mate-allocation strategies, exploring utilising non-additive and heterozygosity effects to maximise clonal performance with schemes that solely consider additive effects to optimise breeding value.

Genomic prediction with machine learning in sugarcane, a complex highly polyploid clonally propagated crop with substantial non-additive variation for key traits.

Sugarcane has a complex, highly polyploid genome with multi-species ancestry. Additive models for genomic prediction of clonal performance might not capture interactions between genes and alleles from different ploidies and ancestral species. As such, genomic prediction in sugarcane presents an interesting case for machine learning (ML) methods, which are purportedly able to deal with high levels of complexity in prediction.

Diagnosis of Multisystem Inflammatory Syndrome in Children by a Whole-Blood Transcriptional Signature.

Background: To identify a diagnostic blood transcriptomic signature that distinguishes multisystem inflammatory syndrome in children (MIS-C) from Kawasaki disease (KD), bacterial infections, and viral infections.

Methods: Children presenting with MIS-C to participating hospitals in the United Kingdom and the European Union between April 2020 and April 2021 were prospectively recruited. Whole-blood RNA Sequencing was performed, contrasting the transcriptomes of children with MIS-C (n = 38) to those from children with KD (n = 136), definite bacterial (DB; n = 188) and viral infections (DV; n = 138).

Extending the breeder's equation to take aim at the target population of environments.

A major focus for genomic prediction has been on improving trait prediction accuracy using combinations of algorithms and the training data sets available from plant breeding multi-environment trials (METs). Any improvements in prediction accuracy are viewed as pathways to improve traits in the reference population of genotypes and product performance in the target population of environments (TPE). To realize these breeding outcomes there must be a positive MET-TPE relationship that provides consistency between the trait variation expressed within the MET data sets that are used to train the genome-to-phenome () model for applications of genomic prediction and the realized trait and performance differences in the TPE for the genotypes that are the prediction targets.

Two pathogen loci determine Blumeria graminis f. sp. tritici virulence to wheat resistance gene Pm1a.

Blumeria graminis f. sp. tritici (Bgt) is a globally important fungal pathogen of wheat that can rapidly evolve to defeat wheat powdery mildew (Pm) resistance genes.

Understanding the Intensive Care Unit Experience of Patients and Relatives at the End-of-Life During the Coronavirus Disease 2019 Pandemic.

The coronavirus disease 2019 (COVID-19) pandemic has had a significant impact on patients and relatives' experiences of end-of-life care, as well as changing the provision of these services in intensive care units (ICUs) across the world. Established methods for assisting relatives through the grieving process have required modification due to the unique features and circumstances surrounding deaths from this disease. This mixed-methods study from the United Kingdom (UK) aims to review data from patients who died in a large ICU (the unit had a capacity for more than 100 ventilated patients), over the course of approximately 1 year.

A linkage disequilibrium-based approach to position unmapped SNPs in crop species.

Background: High-density SNP arrays are now available for a wide range of crop species. Despite the development of many tools for generating genetic maps, the genome position of many SNPs from these arrays is unknown. Here we propose a linkage disequilibrium (LD)-based algorithm to allocate unassigned SNPs to chromosome regions from sparse genetic maps.

RAPD PCR detects co-colonisation of multiple group B streptococcus genotypes: A practical molecular technique for screening multiple colonies.

Group B Streptococcus (GBS) is a leading cause of neonatal meningitis, pneumonia, and sepsis. The biggest contributing factor of neonatal infections is due to vertical transmission from maternal colonisation of GBS in the genitourinary tract. Multiple serotype colonisation is often not investigated in epidemiological studies, but it is an important consideration for serotype-based vaccine development and implementation to ensure less abundant serotypes are not under-represented.

Genomic evaluations using data recorded on smallholder dairy farms in low- to middle-income countries.

Breeding has increased genetic gain for dairy cattle in advanced economies but has had limited success in improving dairy cattle in low- to middle-income countries (LMIC). Genetic evaluations are a central component of delivering genetic gain, because they separate the genetic and environmental effects of animals' phenotypes. Genetic evaluations have been successful in advanced economies because of large data sets and strong genetic connectedness, provided by the widespread use of artificial insemination (AI) and accurate recording of pedigree information.

Perspectives on Applications of Hierarchical Gene-To-Phenotype (G2P) Maps to Capture Non-stationary Effects of Alleles in Genomic Prediction.

Genomic prediction of complex traits across environments, breeding cycles, and populations remains a challenge for plant breeding. A potential explanation for this is that underlying non-additive genetic (GxG) and genotype-by-environment (GxE) interactions generate allele substitution effects that are non-stationary across different contexts. Such non-stationary effects of alleles are either ignored or assumed to be implicitly captured by most gene-to-phenotype (G2P) maps used in genomic prediction.

Spatial modelling improves genetic evaluation in smallholder breeding programs.

Background: Breeders and geneticists use statistical models to separate genetic and environmental effects on phenotype. A common way to separate these effects is to model a descriptor of an environment, a contemporary group or herd, and account for genetic relationship between animals across environments. However, separating the genetic and environmental effects in smallholder systems is challenging due to small herd sizes and weak genetic connectedness across herds.

In silico simulation of future hybrid performance to evaluate heterotic pool formation in a self-pollinating crop.

Hybrid vigour has the potential to substantially increase the yield of self-pollinating crops such as wheat and rice, but future hybrid performance may depend on the initial strategy to form heterotic pools. We used in silico stochastic simulation of future hybrid performance in a self-pollinating crop to evaluate three strategies of forming heterotic pools in the founder population. The model included either 500, 2000 or 8000 quantitative trait nucleotides (QTN) across 10 chromosomes that contributed to a quantitative trait with population mean 100 and variance 10.

Determining patient risk factors associated with accelerated growth of popliteal artery aneurysms.

Objective: The objective of this study was to determine the natural progression of popliteal artery aneurysms (PAAs) and clinical variables associated with their accelerated growth.

Methods: Retrospective chart review of 224 patients with encounters between January 2008 and May 2016 and with at least one PAA was conducted. From this group, 65 asymptomatic patients had either unilateral (n = 43) or bilateral (n = 22) PAAs that were observed for at least 1 year of medical management before intervention.

Left subclavian artery revascularization in zone 2 thoracic endovascular aortic repair is associated with lower stroke risk across all aortic diseases.

Background: The best management strategy for the left subclavian artery (LSA) in pathologic processes of the aorta requiring zone 2 thoracic endovascular aortic repair (TEVAR) remains controversial. We compared LSA coverage with or without revascularization as well as the different means of LSA revascularization.

Methods: A retrospective chart review was conducted of patients with any aortic diseases who underwent zone 2 TEVAR deployment from 2007 to 2014.

In Search of Lost Springs: A Protocol for Locating Active and Inactive Springs.

Groundwater springs are significant landscape features for humans and the biota that occupies their habitat. Many springs become inactive where groundwater exploitation by humans has lowered the water table or artesian pressure. In order to assess this impact, it is important to identify and locate active, and with more difficulty, inactive springs.