Enhanced long-range forecast skill in boreal winter following stratospheric strong vortex conditions

There has been a great deal of recent interest in producing weather forecasts on the 2–6 week sub-seasonal timescale, which bridges the gap between medium-range (0–10 day) and seasonal (3–6 month) forecasts. While much of this interest is focused on the potential applications of skilful forecasts on the sub-seasonal range, understanding the potential sources of sub-seasonal forecast skill is a challenging and interesting problem, particularly because of the likely state-dependence of this skill (Hudson et al 2011). One such potential source of state-dependent skill for the Northern Hemisphere in winter is the occurrence of stratospheric sudden warming (SSW) events (Sigmond et al 2013). Here we show, by analysing a set of sub-seasonal hindcasts, that there is enhanced predictability of surface circulation not only when the stratospheric vortex is anomalously weak following SSWs but also when the vortex is extremely strong. Sub-seasonal forecasts initialized during strong vortex events are able to successfully capture the associated surface temperature and circulation anomalies. This results in an enhancement of Northern annular mode forecast skill compared to forecasts initialized during the cases when the stratospheric state is close to climatology. We demonstrate that the enhancement of skill for forecasts initialized during periods of strong vortex conditions is comparable to that achieved for forecasts initialized during weak events. This result indicates that additional confidence can be placed in sub-seasonal forecasts when the stratospheric polar vortex is significantly disturbed from its normal state

Impact of the sea surface temperature forcing on hindcasts of Madden-Julian Oscillation events using the ECMWF model

This paper explores the sensitivity of hindcasts of the Madden Julian Oscillation (MJO) to the use of different sea surface temperture (SST) products as lower boundary conditions in the European Centre for Medium-range Weather Forecasts (ECMWF) atmospheric model. Three sets of monthly hindcast experiments are conducted, starting from initial conditions from the ERA interim reanalysis. First, as a reference, the atmosphere is forced by the SST used to produce ERA interim. In the second and third experiments, the SST is switched to the OSTIA (Operational Sea Surface Temperature and Sea-Ice Analysis) and the AVHRR-only (Advanced Very High Resolution Radiometer) reanalyses, respectively. Tests on the temporal resolution of the SST show that monthly fields are not optimal, while weekly and daily resolutions provide similar MJO scores. When using either OSTIA or AVHRR, the propagation of the MJO is degraded and the resulting scores are lower than in the reference experiment. Further experiments show that this loss of skill cannot be attributed to either the difference in mean state or temporal variability between the SST products. Additional diagnostics show that the phase relationship between either OSTIA or AVHRR SST and the MJO convection is distorted with respect to satellite observations and the ERA interim reanalysis. This distortion is expected to impact the MJO hindcasts, leading to a relative loss of forecast skill. A realistic representation of ocean–atmosphere interactions is thus needed for MJO hindcasts, but not all SST products – though accurate for other purposes – fulfill this requirement

Prioritization of Kidney Cell Types Highlights Myofibroblast Cells in Regulating Human Blood Pressure

INTRODUCTION: Blood pressure (BP) is a highly heritable trait with over 2000 underlying genomic loci identified to date. Although the kidney plays a key role, little is known about specific cell types involved in the genetic regulation of BP.METHODS: Here, we applied stratified linkage disequilibrium score (LDSC) regression to connect BP genome-wide association studies (GWAS) results to specific cell types of the mature human kidney. We used the largest single-stage BP genome-wide analysis to date, including up to 1,028,980 adults of European ancestry, and single-cell transcriptomic data from 14 mature human kidneys, with mean age of 41 years.RESULTS: Our analyses prioritized myofibroblasts and endothelial cells, among the total of 33 annotated cell type, as specifically involved in BP regulation (P &lt; 0.05/33, i.e., 0.001515). Enrichment of heritability for systolic BP (SBP) was observed in myofibroblast cells in mature human kidney cortex, and enrichment of heritability for diastolic BP (DBP) was observed in descending vasa recta and peritubular capillary endothelial cells as well as stromal myofibroblast cells. The new finding of myofibroblast, the significant cell type for both BP traits, was consistent in 8 replication efforts using 7 sets of independent data, including in human fetal kidney, in East-Asian (EAS) ancestry, using mouse single-cell RNA sequencing (scRNA-seq) data, and when using another prioritization method.CONCLUSION: Our findings provide a solid basis for follow-up studies to further identify genes and mechanisms in myofibroblast cells that underlie the regulation of BP.</p

Genome-wide association study identifies _FUT8_ and _ESR2_ as co-regulators of a bi-antennary N-linked glycan A2 (GlcNAc~2~Man~3~GlcNAc~2~) in human plasma proteins

HPLC analysis of N-glycans quantified levels of the biantennary glycan (A2) in plasma proteins of 924 individuals. Subsequent genome-wide association study (GWAS) using 317,503 single nucleotide polymorphysms (SNP) identified two genetic loci influencing variation in A2: FUT 8 and ESR2. We demonstrate that human glycans are amenable to GWAS and their genetic regulation shows sex-specific effects with _FUT 8_ variants explaining 17.3% of the variance in pre-menopausal women, while _ESR2_ variants explained 6.0% of the variance in post-menopausal women

Everything Hits at Once: How Remote Rainfall Matters for the Prediction of the 2021 North American Heat Wave

In June 2021, Western North America experienced an intense heat wave with unprecedented temperatures and far-reaching socio-economic consequences. Anomalous rainfall in the West Pacific triggers a cascade of weather events across the Pacific, which build up a high-amplitude ridge over Canada and ultimately lead to the heat wave. We show that the response of the jet stream to diabatically enhanced ascending motion in extratropical cyclones represents a predictability barrier with regard to the heat wave magnitude. Therefore, probabilistic weather forecasts are only able to predict the extremity of the heat wave once the complex cascade of weather events is captured. Our results highlight the key role of the sequence of individual weather events in limiting the predictability of this extreme event. We therefore conclude that it is not sufficient to consider such rare events in isolation but it is essential to account for the whole cascade over different spatiotemporal scales

Uncovering Networks from Genome-Wide Association Studies via Circular Genomic Permutation

Genome-wide association studies (GWAS) aim to detect single nucleotide polymorphisms (SNP) associated with trait variation. However, due to the large number of tests, standard analysis techniques impose highly stringent significance thresholds, leaving potentially associated SNPs undetected, and much of the trait genetic variation unexplained. Pathway- and network-based methodologies applied to GWAS aim to detect associations missed by standard single-marker approaches. The complex and non-random architecture of the genome makes it a challenge to derive an appropriate testing framework for such methodologies. We developed a rapid and simple permutation approach that uses GWAS SNP association results to establish the significance of pathway associations while accounting for the linkage disequilibrium structure of SNPs and the clustering of functionally related elements in the genome. All SNPs used in the GWAS are placed in a “circular genome” according to their location. Then the complete set of SNP association P values are permuted by rotation with respect to the genomic locations of the SNPs. Once these “simulated” P values are assigned, the joint gene P values are calculated using Fisher’s combination test, and the association of pathways is tested using the hypergeometric test. The circular genomic permutation approach was applied to a human genome-wide association dataset. The data consists of 719 individuals from the ORCADES study genotyped for ∼300,000 SNPs and measured for 51 traits ranging from physical to biochemical measurements. KEGG pathways (n = 225) were used as the sets of pathways to be tested. Our results demonstrate that the circular genomic permutations provide robust association P values. The non-permuted hypergeometric analysis generates ∼1400 pathway-trait combination results with an association P value more significant than P ≤ 0.05, whereas applying circular genomic permutation reduces the number of significant results to a more credible 40% of that value. The circular permutation software (“genomicper”) is available as an R package at http://cran.r-project.org/

Comparative assessment of methods for estimating individual genome-wide homozygosity-by-descent from human genomic data

<p>Abstract</p> <p>Background</p> <p>Genome-wide homozygosity estimation from genomic data is becoming an increasingly interesting research topic. The aim of this study was to compare different methods for estimating individual homozygosity-by-descent based on the information from human genome-wide scans rather than genealogies. We considered the four most commonly used methods and investigated their applicability to single-nucleotide polymorphism (SNP) data in both a simulation study and by using the human genotyped data. A total of 986 inhabitants from the isolated Island of Vis, Croatia (where inbreeding is present, but no pedigree-based inbreeding was observed at the level of F > 0.0625) were included in this study. All individuals were genotyped with the Illumina HumanHap300 array with 317,503 SNP markers.</p> <p>Results</p> <p>Simulation data suggested that multi-point FEstim is the method most strongly correlated to true homozygosity-by-descent. Correlation coefficients between the homozygosity-by-descent estimates were high but only for inbred individuals, with nearly absolute correlation between single-point measures.</p> <p>Conclusions</p> <p>Deciding who is really inbred is a methodological challenge where multi-point approaches can be very helpful once the set of SNP markers is filtered to remove linkage disequilibrium. The use of several different methodological approaches and hence different homozygosity measures can help to distinguish between homozygosity-by-state and homozygosity-by-descent in studies investigating the effects of genomic autozygosity on human health.</p

ERA-Interim/Land: a global land surface reanalysis data set

ERA-Interim/Land is a global land surface reanalysis data set covering the period 1979–2010. It describes the evolution of soil moisture, soil temperature and snowpack. ERA-Interim/Land is the result of a single 32-year simulation with the latest ECMWF (European Centre for Medium-Range Weather Forecasts) land surface model driven by meteorological forcing from the ERA-Interim atmospheric reanalysis and precipitation adjustments based on monthly GPCP v2.1 (Global Precipitation Climatology Project). The horizontal resolution is about 80 km and the time frequency is 3-hourly. ERA-Interim/Land includes a number of parameterization improvements in the land surface scheme with respect to the original ERA-Interim data set, which makes it more suitable for climate studies involving land water resources. The quality of ERA-Interim/Land is assessed by comparing with ground-based and remote sensing observations. In particular, estimates of soil moisture, snow depth, surface albedo, turbulent latent and sensible fluxes, and river discharges are verified against a large number of site measurements. ERA-Interim/Land provides a global integrated and coherent estimate of soil moisture and snow water equivalent, which can also be used for the initialization of numerical weather prediction and climate models

Enrichment of pathogenic alleles in the brittle cornea gene, ZNF469, in keratoconus

Keratoconus, a common inherited ocular disorder resulting in progressive corneal thinning, is the leading indication for corneal transplantation in the developed world. Genome-wide association studies have identified common SNPs 100 kb upstream of ZNF469 strongly associated with corneal thickness. Homozygous mutations in ZNF469 and PR domain-containing protein 5 (PRDM5) genes result in brittle cornea syndrome (BCS) Types 1 and 2, respectively. BCS is an autosomal recessive generalized connective tissue disorder associated with extreme corneal thinning and a high risk of corneal rupture. Some individuals with heterozygous PRDM5 mutations demonstrate a carrier ocular phenotype, which includes a mildly reduced corneal thickness, keratoconus and blue sclera. We hypothesized that heterozygous variants in PRDM5 and ZNF469 predispose to the development of isolated keratoconus. We found a significant enrichment of potentially pathologic heterozygous alleles in ZNF469 associated with the development of keratoconus (P = 0.00102) resulting in a relative risk of 12.0. This enrichment of rare potentially pathogenic alleles in ZNF469 in 12.5% of keratoconus patients represents a significant mutational load and highlights ZNF469 as the most significant genetic factor responsible for keratoconus identified to date

Seasonal forecasts of North Atlantic tropical cyclone activity in the North American Multi-Model Ensemble

The North American Multi-Model Ensemble (NMME)-Phase II models are evaluated in terms of their retrospective seasonal forecast skill of the North Atlantic (NA) tropical cyclone (TC) activity, with a focus on TC frequency. The TC identification and tracking algorithm is modified to accommodate model data at daily resolution. It is also applied to three reanalysis products at the spatial and temporal resolution of the NMME-Phase II ensemble to allow for a more objective estimation of forecast skill. When used with the reanalysis data, the TC tracking generates realistic climatological distributions of the NA TC formation and tracks, and represents the interannual variability of the NA TC frequency quite well. Forecasts with the multi-model ensemble (MME) when initialized in April and later tend to have skill in predicting the NA seasonal TC counts (and TC days). At longer leads, the skill is low or marginal, although one of the models produces skillful forecasts when initialized as early as January and February. At short lead times, while demonstrating the highest skill levels the MME also tends to significantly outperform the individual models and attain skill comparable to the reanalysis. In addition, the short-lead MME forecasts are quite reliable. At regional scales, the skill is rather limited and mostly present in the western tropical NA and the Caribbean Sea. It is found that the overall MME forecast skill is limited by poor representation of the low-frequency variability in the predicted TC frequency, and large fluctuations in skill on decadal time scales. Addressing these deficiencies is thought to increase the value of the NMME ensemble in providing operational guidance