Bidirectionally Tolerating Inconsistency: Partial Transformations

Abstract. A foundational property of bidirectional transformations is that they should be correct: that is, the transformation should succeed in restoring consistency between any models it is given. In practice, how-ever, transformation engines sometimes fail to restore consistency, e.g. because there is no consistent model to return, or because the tool is unable to select a best model to return from among equally good candi-dates. In this paper, we formalise properties that may nevertheless hold in such circumstances and discuss relationships and implications.

Germline 16p11.2 Microdeletion Predisposes to Neuroblastoma

Neuroblastoma is a cancer of the developing sympathetic nervous system. It is diagnosed in 600–700 children per year in the United States and accounts for 12% of pediatric cancer deaths. Despite recent advances in our understanding of this malignancy's complex genetic architecture, the contribution of rare germline variants remains undefined. Here, we conducted a genome-wide analysis of large (>500 kb), rare (<1%) germline copy number variants (CNVs) in two independent, multi-ethnic cohorts totaling 5,585 children with neuroblastoma and 23,505 cancer-free control children. We identified a 550-kb deletion on chromosome 16p11.2 significantly enriched in neuroblastoma cases (0.39% of cases and 0.03% of controls; p = 3.34 × 10−9). Notably, this CNV corresponds to a known microdeletion syndrome that affects approximately one in 3,000 children and confers risk for diverse developmental phenotypes including autism spectrum disorder and other neurodevelopmental disorders. The CNV had a substantial impact on neuroblastoma risk, with an odds ratio of 13.9 (95% confidence interval = 5.8–33.4). The association remained significant when we restricted our analysis to individuals of European ancestry in order to mitigate potential confounding by population stratification (0.42% of cases and 0.03% of controls; p = 4.10 × 10−8). We used whole-genome sequencing (WGS) to validate the deletion in paired germline and tumor DNA from 12 cases. Finally, WGS of four parent-child trios revealed that the deletion primarily arose de novo without maternal or paternal bias. This finding expands the clinical phenotypes associated with 16p11.2 microdeletion syndrome to include cancer, and it suggests that disruption of the 16p11.2 region may dysregulate neurodevelopmental pathways that influence both neurological phenotypes and neuroblastoma

Neuroblastoma in relation to joint effects of vitamin A and maternal and offspring variants in vitamin A-related genes: A report of the Children's Oncology Group

Background: There is evidence vitamin A plays a role in neuroblastoma. Not only is 13-cis-retinoic acid used as maintenance therapy for high-risk cases, but prenatal vitamin intake use may decrease neuroblastoma risk. We hypothesized that single nucleotide polymorphisms (SNPs) in vitamin A-related genes are may be associated with neuroblastoma risk and potentially be modified by vitamin A intake. Methods: The Neuroblastoma Epidemiology in North America (NENA) study recruited 563 case-parent sets through the Children's Oncology Group's Childhood Cancer Research Network. We ascertained dietary nutrient intake through questionnaires and genotyped 463 SNPs in vitamin A-related genes from saliva DNA. Offspring and maternal log-additive risk ratios (RR) and stratum-specific RR for gene-environment interaction were estimated with a log-linear model. We avoided false positives due to multiple testing by using the false discovery rate (FDR). Results: When all neuroblastoma cases were considered together, no offspring variants met the significance criteria (FDR Q-value < 0.2). One maternal SNP (rs12442054) was associated with decreased risk of neuroblastoma (RR: 0.61; 95% Confidence Interval (CI): 0.47–0.79, Q = 0.076). When the cases were categorized according to prognostic risk category and age at onset, nine offspring SNPs were significantly associated with intermediate-risk neuroblastoma. Maternal rs6776706 was associated with (RR: 0.49; 95% CI: 0.33–0.72, Q = 0.161) high-risk neuroblastoma and maternal rs11103603 (RR: 0.60; 95% CI: 0.45–0.79, Q = 0.127) was associated with neuroblastoma aged <1 year. For gene-environment interaction, maternal rs729147 was associated with decreased risk of neuroblastoma among mothers with vitamin A consumption above the recommendation. Conclusions: Although there is biologic plausibility for the role of vitamin A in neuroblastoma, we found weak evidence of a relationship between vitamin A related genes and neuroblastoma

The Pediatric Cell Atlas: defining the growth phase of human development at single-cell resolution

Single-cell gene expression analyses of mammalian tissues have uncovered profound stage-specific molecular regulatory phenomena that have changed the understanding of unique cell types and signaling pathways critical for lineage determination, morphogenesis, and growth. We discuss here the case for a Pediatric Cell Atlas as part of the Human Cell Atlas consortium to provide single-cell profiles and spatial characterization of gene expression across human tissues and organs. Such data will complement adult and developmentally focused HCA projects to provide a rich cytogenomic framework for understanding not only pediatric health and disease but also environmental and genetic impacts across the human lifespan

Svpluscnv: Analysis and visualization of complex structural variation data

Motivation: Despite widespread prevalence of somatic structural variations (SVs) across most tumor types, understanding of their molecular implications often remains poor. SVs are extremely heterogeneous in size and complexity, hindering the interpretation of their pathogenic role. Tools integrating large SV datasets across platforms are required to fully characterize the cancer's somatic landscape. Results: svpluscnv R package is a swiss army knife for the integration and interpretation of orthogonal datasets including copy number variant segmentation profiles and sequencing-based structural variant calls. The package implements analysis and visualization tools to evaluate chromosomal instability and ploidy, identify genes harboring recurrent SVs and detects complex rearrangements such as chromothripsis and chromoplexia. Further, it allows systematic identification of hot-spot shattered genomic regions, showing reproducibility across alternative detection methods and datasets

Characterizing summertime chemical boundary conditions for airmasses entering the US West Coast

International audienceThe objective of this study is to analyze the pollution inflow into California during summertime and how it impacts surface air quality through combined analysis of a suite of observations and global and regional models. The focus is on the transpacific pollution transport investigated by the NASA Arctic Research of the Composition of the Troposphere from Aircraft and Satellites (ARCTAS) mission in June 2008. Additional observations include satellite retrievals of carbon monoxide and ozone by the EOS Aura Tropospheric Emissions Spectrometer (TES), aircraft measurements from the MOZAIC program and ozonesondes. We compare chemical boundary conditions (BC) from the MOZART-4 global model, which are commonly used in regional simulations, with measured concentrations to quantify both the accuracy of the model results and the variability in pollution inflow. Both observations and model reflect a large variability in pollution inflow on temporal and spatial scales, but the global model captures only about half of the observed free tropospheric variability. Model tracer contributions show a large contribution from Asian emissions in the inflow. Recirculation of local US pollution can impact chemical BC, emphasizing the importance of consistency between the global model simulations used for BC and the regional model in terms of emissions, chemistry and transport. Aircraft measurements in the free troposphere over California show similar concentration ranges, variability and source contributions as free tropospheric air masses over ocean, but caution has to be taken that local pollution aloft is not misinterpreted as inflow. A flight route specifically designed to sample boundary conditions during ARCTAS-CARB showed a prevalence of plumes transported from Asia and thus may not be fully representative for average inflow conditions. Sensitivity simulations with a regional model with altered BCs show that the temporal variability in the pollution inflow does impact modeled surface concentrations in California. We suggest that time and space varying chemical boundary conditions from global models provide useful input to regional models, but likely still lead to an underestimate of peak surface concentrations and the variability associated with long-range pollution transport

Concentrações séricas hormonais em vacas azebuadas submetidas à baixa e alta ingestão alimentar Serum hormone concentrations of zebu cows under low and high feed intake

O objetivo deste trabalho foi avaliar a influência da ingestão alimentar nas concentrações séricas de hormônios reprodutivos e metabólicos em vacas azebuadas. Dezoito vacas foram divididas em dois grupos: 170% (alta ingestão = A) e 66% (baixa ingestão = B) da dieta de manutenção. Com 21 dias nas dietas experimentais, as vacas tiveram o estro sincronizado. Posteriormente, os ovários foram avaliados por ultra-sonografia transretal e sangue foi coletado diariamente até o dia 7 do ciclo (ovulação = dia 1). Na análise estatística, utilizou-se o teste t. As vacas ganharam 1,1 kg por dia no grupo A e perderam 1,5 kg por dia de PV no grupo B. Apesar de não ter havido diferença entre os grupos no diâmetro máximo do folículo ovulatório, o grupo A apresentou pico pré-ovulatório de estradiol sérico menor. Não foi observada diferença entre os grupos quanto ao volume luteal e concentração sérica de progesterona no dia 7 do ciclo e de FSH, IGF-I e insulina séricos no período peri-ovulatório. As dietas experimentais não alteraram a função ovariana e as concentrações séricas de hormônios reprodutivos e metabólicos, com exceção do estradiol, sugerindo que, no grupo de alta ingestão, ocorreu maior metabolismo desse hormônio.<br>The objective of this work was to evaluate the influence of feed intake on serum concentrations of reproductive and metabolic hormones in zebu cows. Eighteen cows were divided into two groups: 170% (high feed intake = H) and 66% (low feed intake = L) of the maintenance diet. Within 21 days on the experimental diets, cows had estrus synchronized. Subsequently, ovaries were scanned by trans-rectal ultrasonography and blood samples were collected daily until day 7 of the cycle (ovulation = day 1). For statistical analysis, t test was utilized. Cows from group H gained 1.1 kg per day and from group L lost 1.5 kg per day of body weight. Although there was no difference between groups regarding maximum diameter of the ovulatory follicle, a lower preovulatory estradiol surge was observed in group H cows. There was no difference between groups for luteal tissue volume and serum progesterone concentration on day 7 and serum FSH, IGF-I and insulin concentrations during the periovulatory period. Experimental diets did not alter ovarian function and serum concentrations of reproductive and metabolic hormones, except for estradiol, suggesting that greater metabolism of this hormone has occurred on the cows under high feed intake

A g316a polymorphism in the ornithine decarboxylase gene promoter modulates mycn\u2010driven childhood neuroblastoma

Ornithine decarboxylase (ODC1), a critical regulatory enzyme in polyamine biosynthesis, is a direct transcriptional target of MYCN, amplification of which is a powerful marker of aggressive neuroblastoma. A single nucleotide polymorphism (SNP), G316A, within the first intron of ODC1, results in genotypes wildtype GG, and variants AG/AA. CRISPR\u2010cas9 technology was used to investigate the effects of AG clones from wildtype MYCN\u2010amplified SK\u2010N\u2010BE(2)\u2010C cells and the effect of the SNP on MYCN binding, and promoter activity was investigated using EMSA and luciferase assays. AG clones exhibited decreased ODC1 expression, growth rates, and histone acetylation and increased sensitivity to ODC1 inhibition. MYCN was a stronger transcriptional regulator of the ODC1 promoter containing the G allele, and preferentially bound the G allele over the A. Two neu-roblastoma cohorts were used to investigate the clinical impact of the SNP. In the study cohort, the minor AA genotype was associated with improved survival, while poor prognosis was associated with the GG genotype and AG/GG genotypes in MYCN\u2010amplified and non\u2010amplified patients, re-spectively. These effects were lost in the GWAS cohort. We have demonstrated that the ODC1 G316A polymorphism has functional significance in neuroblastoma and is subject to allele\u2010specific regulation by the MYCN oncoprotein