Recent turbidite deposition in the eastern Atlantic: Early diagenesis and biotic recovery

An interface core taken in Capbreton canyon shows a succession of sedimentary facies interpreted as classical Bouma turbiditic sequences. Activities of 234Th and 210Pb suggest that the deposition of the most recent turbidite was triggered by the violent storm that affected the Atlantic coast of southern France on the 27th of December 1999, about four months before the sampling of the core. This turbidite allows us to study the ongoing diagenesis of the new sediment layer and of the previous sediment-water interface, which has been buried and only slightly eroded. A study of benthic foraminiferal populations informs us about the rate of benthic ecosystem recovery after such a major ecosystem disturbance event. The composition of the benthic foraminiferal fauna suggests that the benthic ecosystem in Capbreton canyon remains in an early stage of colonization. The rare agglutinant taxon Technitella melo appears to be the first colonizing species. It is suggested that Technitella melo is advantaged by the food-impoverished conditions in the days following turbidite deposition. Almost all of the turbidite layer and the previous oxic sediment-water interface contain reduced dissolved metal species and were anoxic. The buried interface contains Fe- and Mn-oxides inherited from its recent oxic past. The reduction of manganese oxides was in progress at the time of core collection. The reduced Mn remained trapped in the sediment as Mn-containing carbonates. Iron-oxides did not undergo significant reductive dissolution. The top of the newly deposited turbidite formed an oxic layer, which was rapidly enriched in metal-oxides. The enrichment of manganese oxides was mostly due to the oxidation of dissolved Mn2+, which diffused from below. The enrichment of iron oxides is explained both by the oxidation of the upward flux of dissolved Fe2+, and by the input of detrital iron oxide after, or as a result of the turbidite deposition

Influence of substrate density and cropping conditions on the cultivation of sun mushroom

Aim of the study: To evaluate agronomical features demanded by the sun mushroom (Agaricus subrufescens) in order to optimise the commercial cultivation of this worldwide demanded medicinal mushroom.Area of study: The study was carried out in Castilla-La Mancha (Spain), the second most productive region of cultivated mushrooms in Spain.Material and methods: In this work we summarise the results obtained while evaluating the performance of sun mushroom crops (A. subrufescens). Two agronomical traits have been evaluated, the effect on the productive outputs of applying five different compost filling rates of high N substrate (yield and BE of the compost), and the influence of implementing two different conditions for the induction to fructification on the analytical properties of the harvested mushrooms. Besides, two commercial compost formulations (CM and VC) obtained from local providers have been used.Main results: The number of sporophores harvested and the yield per unit area increased with rising density of compost load, although the biological efficiency was not significantly modified. Compost fill rate of 70 kg m-2 provided an average yield of 13.33 kg m-2 and BE=55.45 kg dt-1, generally higher than those values reported in the literature. The proposed moderate slow induction provides better yields, particularly in the last flushes, and larger sporophores. Proximate analysis of harvested sporophores has not shown significant differences between treatments or factors.Research highlights: As guidance for growers, compost fill weight between 65 and 70 kg per m2 of productive area with a moderate slow induction to fructification is presented as the best option for commercial production under controlled environmental conditions

Improving medium-range ensemble weather forecasts with hierarchical ensemble transformers

Statistical post-processing of global ensemble weather forecasts is revisited by leveraging recent developments in machine learning. Verification of past forecasts is exploited to learn systematic deficiencies of numerical weather predictions in order to boost post-processed forecast performance. Here, we introduce PoET, a post-processing approach based on hierarchical transformers. PoET has 2 major characteristics: 1) the post-processing is applied directly to the ensemble members rather than to a predictive distribution or a functional of it, and 2) the method is ensemble-size agnostic in the sense that the number of ensemble members in training and inference mode can differ. The PoET output is a set of calibrated members that has the same size as the original ensemble but with improved reliability. Performance assessments show that PoET can bring up to 20% improvement in skill globally for 2m temperature and 2% for precipitation forecasts and outperforms the simpler statistical member-by-member method, used here as a competitive benchmark. PoET is also applied to the ENS10 benchmark dataset for ensemble post-processing and provides better results when compared to other deep learning solutions that are evaluated for most parameters. Furthermore, because each ensemble member is calibrated separately, downstream applications should directly benefit from the improvement made on the ensemble forecast with post-processing

Malignant melanotic nerve sheath tumor with PRKAR1A, KMT2C and GNAQ mutations

Malignant melanotic nerve sheath tumor (MMNST) is a rare and potentially aggressive lesion defined in the 2021 WHO Classification of Tumors of the Central Nervous System. MMNST demonstrate overlapping histologic and clinical features of schwannoma and melanoma. MMNST often harbor PRKAR1A mutations, especially within the Carney Complex. We present a case of aggressive MMNST of the sacral region in a 48-year-old woman. The tumor contained PRKAR1A frameshift pR352Hfs*89, KMT2C splice site c.7443-1G>T and GNAQ p.R183L missense mutations, as well as BRAF and MYC gains. Genomic DNA methylation analysis using the Illumina 850K EpicBead chip revealed that the lesion did not match an established methylation class; however, uniform manifold approximation and projection (UMAP) placed the tumor very near, or with, schwannomas. The tumor expressed PD-L1, and the patient was treated with radiation and immune checkpoint inhibitors following en bloc resection. Although she had symptomatic improvement, she suffered early disease progression with local recurrence, and distant metastases, and died 18 months after resection. It has been suggested that the presence of GNAQ mutations can differentiate leptomeningeal melanocytic neoplasms and uveal melanoma from MMNST. This case and others demonstrate that GNAQ mutations may exist in malignant nerve sheath tumors; that GNAQ and PRKAR1A mutations are not always mutually exclusive and that neither can be used to differentiate MMNST or MPNST from all melanocytic lesions

Reintegrating informal settlements into the Greater Cairo Region of Egypt through the regional highway network

This study analyses informal settlements and the regional highway network in the Greater Cairo Region of Egypt to propose alternatives to reduce regional spatial fragmentation that may lead to spatial segregation. Findings indicate that the street structure of informal settlements provides a configuration that supports social interaction for their residents. While the regional highway network can act to physically disconnect the wider region by isolating or splitting neighbourhoods, some highways can act as an integrator. Analysis at the urban scale can identify points in the settlements’ street networks where they can be connected to the regional transport network, which could have an impact on regional consolidation

Beyond Shielding: The Roles of Glycans in the SARS-CoV‑2 Spike Protein

The ongoing COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in more than 28,000,000 infections and 900,000 deaths worldwide to date. Antibody development efforts mainly revolve around the extensively glycosylated SARS-CoV-2 spike (S) protein, which mediates host cell entry by binding to the angiotensin-converting enzyme 2 (ACE2). Similar to many other viral fusion proteins, the SARS-CoV-2 spike utilizes a glycan shield to thwart the host immune response. Here, we built a full-length model of the glycosylated SARS-CoV-2 S protein, both in the open and closed states, augmenting the available structural and biological data. Multiple microsecond-long, all-atom molecular dynamics simulations were used to provide an atomistic perspective on the roles of glycans and on the protein structure and dynamics. We reveal an essential structural role of N-glycans at sites N165 and N234 in modulating the conformational dynamics of the spike’s receptor binding domain (RBD), which is responsible for ACE2 recognition. This finding is corroborated by biolayer interferometry experiments, which show that deletion of these glycans through N165A and N234A mutations significantly reduces binding to ACE2 as a result of the RBD conformational shift toward the “down” state. Additionally, end-to-end accessibility analyses outline a complete overview of the vulnerabilities of the glycan shield of the SARS-CoV-2 S protein, which may be exploited in the therapeutic efforts targeting this molecular machine. Overall, this work presents hitherto unseen functional and structural insights into the SARS-CoV-2 S protein and its glycan coat, providing a strategy to control the conformational plasticity of the RBD that could be harnessed for vaccine development

Glioneuronal tumor with ATRX alteration, kinase fusion and anaplastic features (GTAKA): a molecularly distinct brain tumor type with recurrent NTRK gene fusions

Glioneuronal tumors are a heterogenous group of CNS neoplasms that can be challenging to accurately diagnose. Molecular methods are highly useful in classifying these tumors-distinguishing precise classes from their histological mimics and identifying previously unrecognized types of tumors. Using an unsupervised visualization approach of DNA methylation data, we identified a novel group of tumors (n = 20) that formed a cluster separate from all established CNS tumor types. Molecular analyses revealed ATRX alterations (in 16/16 cases by DNA sequencing and/or immunohistochemistry) as well as potentially targetable gene fusions involving receptor tyrosine-kinases (RTK; mostly NTRK1-3) in all of these tumors (16/16; 100%). In addition, copy number profiling showed homozygous deletions of CDKN2A/B in 55% of cases. Histological and immunohistochemical investigations revealed glioneuronal tumors with isomorphic, round and often condensed nuclei, perinuclear clearing, high mitotic activity and microvascular proliferation. Tumors were mainly located supratentorially (84%) and occurred in patients with a median age of 19 years. Survival data were limited (n = 18) but point towards a more aggressive biology as compared to other glioneuronal tumors (median progression-free survival 12.5 months). Given their molecular characteristics in addition to anaplastic features, we suggest the term glioneuronal tumor with ATRX alteration, kinase fusion and anaplastic features (GTAKA) to describe these tumors. In summary, our findings highlight a novel type of glioneuronal tumor driven by different RTK fusions accompanied by recurrent alterations in ATRX and homozygous deletions of CDKN2A/B. Targeted approaches such as NTRK inhibition might represent a therapeutic option for patients suffering from these tumors