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Operational weather forecasts are routinely performed at convection-allowing resolutions, and thus these forecasts generate weather features that appear to be realistic. However, at times the comparison of the forecast to observations is less favorable, particularly at grid scales. This lack of skill is partly due to the chaotic system underlying the weather. Another problem is that it is impossible to evaluate the risk of making decisions based on deterministic forecasts. However, running global high-resolution ensembles involves substantial computational resources. A 555-m resolution WRF ensemble based on stochastic perturbations of a deterministic forecast of the North American Mesoscale model was created. Observations are used to constrain the ensemble and improve the skill. This method increases the skill for forecasting 60-h accumulated precipitation in five standard, statistical metrics: bias, false alarm ratio, threat score, probability of detection, and success ratio. Furthermore, the ensemble continuous ranked probability score (CRPS) will be compared to a poor man’s ensemble. The forecast error is generally smaller in more than 70% of the case studies performed when compared to nine deterministic model forecasts. The ensemble-enhanced mesoscale system presented can help to determine the most likely scenario without the significant computational requirement of global ensembles and is expected to be useful when global high-resolution ensembles are not available.

Chromatin is of major relevance for gene expression, cell division, and differentiation. Here, we determined the landscape of Arabidopsis thaliana chromatin states using 16 features, including DNA sequence, CG methylation, histone variants, and modifications. The combinatorial complexity of chromatin can be reduced to nine states that describe chromatin with high resolution and robustness. Each chromatin state has a strong propensity to associate with a subset of other states defining a discrete number of chromatin motifs. These topographical relationships revealed that an intergenic state, characterized by H3K27me3 and slightly enriched in activation marks, physically separates the canonical Polycomb chromatin and two heterochromatin states from the rest of the euchromatin domains. Genomic elements are distinguished by specific chromatin states: four states span genes from transcriptional start sites (TSS) to termination sites and two contain regulatory regions upstream of TSS. Polycomb regions and the rest of the euchromatin can be connected by two major chromatin paths. Sequential chromatin immunoprecipitation experiments demonstrated the occurrence of H3K27me3 and H3K4me3 in the same chromatin fiber, within a two to three nucleosome size range. Our data provide insight into the Arabidopsis genome topography and the establishment of gene expression patterns, specification of DNA replication origins, and definition of chromatin domains.

Background Common and complex traits are the consequence of the interaction and regulation of multiple genes simultaneously, therefore characterizing the interconnectivity of genes is essential to unravel the underlying biological networks. However, the focus of many studies is on the differential expression of individual genes or on co-expression analysis. Methods Going beyond analysis of one gene at a time, we systematically integrated transcriptomics, genotypes and Hi-C data to identify interconnectivities among individual genes as a causal network. We utilized different machine learning techniques to extract information from the network and identify differential regulatory pattern between cases and controls. We used data from the Allen Brain Atlas for replication. Results Employing the integrative systems approach on the data from CommonMind Consortium showed that gene transcription is controlled by genetic variants proximal to the gene (cis-regulatory factors), and transcribed distal genes (trans-regulatory factors). We identified differential gene regulatory patterns in SCZ-cases versus controls and novel SCZ-associated genes that may play roles in the disorder since some of them are primary expressed in human brain. In addition, we observed genes known associated with SCZ are not likely (OR = 0.59) to have high impacts (degree > 3) on the network. Conclusions Causal networks could reveal underlying patterns and the role of genes individually and as a group. Establishing principles that govern relationships between genes provides a mechanistic understanding of the dysregulated gene transcription patterns in SCZ and creates more efficient experimental designs for further studies. This information cannot be obtained by studying a single gene at the time.

Key Points The regulated translation of messenger RNAs is crucial for many developmental processes, including oocyte maturation, establishment of the embryonic axes, and regulation of 'synaptic memory' in the central nervous system. The initiation complex is a key target for both positive and negative regulators of translation. Particular features of an mRNA also affect its translational efficiency, including sequences that lie in its 3′ and 5′ untranslated regions (UTRs). During oocyte maturation, there is an intricate network of translational activation and repression of stored maternal mRNAs. One crucial factor for this is the serine/threonine kinase Mos, one of whose functions is to induce translational activation of cyclin B1 mRNA. Intriguingly, the translation of Mos itself must first be activated during maturation. Many dormant mRNAs, including Mos and cyclin B1, contain short poly(A) tails, which must be elongated for translational initiation to occur. Polyadenylation requires two elements in the 3′ UTR: the hexanucleotide AAUAAA and the cytoplasmic polyadenylation element (CPE), the latter of which varies in copy number and distance from the hexanucleotide. The CPE is bound by CPEB, which, through an interaction with the AAUAAA-binding factor (CPSF), recruits poly(A) polymerase to the mRNA, and thus triggers polyadenylation. CPEB is also proposed to act indirectly as a masking factor, but the main protein that mediates translational repression is maskin, an eIF4E-associated factor. An attractive model is that polyadenylation relieves repression by triggering dissociation of maskin from the eIF4E, the cap binding protein. After oocyte maturation, most CPEB is destroyed, apart from that associating with spindles and centrosomes. Maskin also localizes to those structures, and both proteins are proposed to regulate translation initiation during embryonic cell divisions. One crucial target is thought to be cyclin B1 mRNA. A possible role for CPEB-mediated translational activation in neuronal synapses is indicated by the localization of CPEB in postsynaptic densities of hippocampal neurons. At this locale, synaptic plasticity may be controlled, as least in part, by the polyadenylation and translation of CPE-containing mRNAs. The regulated translation of messenger RNA is essential for cell-cycle progression, establishment of the body plan during early development, and modulation of key activities in the central nervous system. Cytoplasmic polyadenylation, which is one mechanism of controlling translation, is driven by CPEB — a highly conserved, sequence-specific RNA-binding protein that binds to the cytoplasmic polyadenylation element, and modulates translational repression and mRNA localization. What are the features and functions of this multifaceted protein?

CPEB (Cytoplasmic Polyadenylation Element Binding) proteins are a family of four RNA-binding proteins that regulate the translation of maternal mRNAs controlling meiotic cell cycle progression. But CPEBs are not limited to the transcriptionally silent germline; they are also expressed, in various combinations, in somatic cells, yet their role in regulation of mitosis-related gene expression is largely unknown. Deregulation of CPEB1 and CPEB4 have been linked to tumor development. However, a systematic analysis addressing their requirements for the temporal regulation of mitotic gene expression has yet to be performed. This study addresses the requirements of each of the four CPEBs for mitotic phase transitions, with a particular focus on cytoplasmic polyadenylation and translational regulation. We demonstrate that CPEB3 is the only member dispensable for mitotic cell division, whereas the other three members, CPEB1, 2, and 4, are essential to successful mitotic cell division. Thus, CPEB1 is required for prophase entry, CPEB2 for metaphase and CPEB4 for cytokinesis. These three CPEBs have sequential non-redundant functions that promote the phase-specific polyadenylation and translational activation of CPE-regulated transcripts in the mitotic cell cycle.

The Sepsis-3 Task Force updated the clinical criteria for sepsis, excluding the need for systemic inflammatory response syndrome (SIRS) criteria. The clinical implications of the proposed flowchart including the quick Sequential (Sepsis-related) Organ Failure Assessment (qSOFA) and SOFA scores are unknown. To perform a clinical decision-making analysis of Sepsis-3 in patients with community-acquired pneumonia. This was a cohort study including adult patients with community-acquired pneumonia from two Spanish university hospitals. SIRS, qSOFA, the Confusion, Respiratory Rate and Blood Pressure (CRB) score, modified SOFA (mSOFA), the Confusion, Urea, Respiratory Rate, Blood Pressure and Age (CURB-65) score, and Pneumonia Severity Index (PSI) were calculated with data from the emergency department. We used decision-curve analysis to evaluate the clinical usefulness of each score and the primary outcome was in-hospital mortality. Of 6,874 patients, 442 (6.4%) died in-hospital. SIRS presented the worst discrimination, followed by qSOFA, CRB, mSOFA, CURB-65, and PSI. Overall, overestimation of in-hospital mortality and miscalibration was more evident for qSOFA and mSOFA. SIRS had lower net benefit than qSOFA and CRB, significantly increasing the risk of over-treatment and being comparable with the \"treat-all\" strategy. PSI had higher net benefit than mSOFA and CURB-65 for mortality, whereas mSOFA seemed more applicable when considering mortality/intensive care unit admission. Sepsis-3 flowchart resulted in better identification of patients at high risk of mortality. qSOFA and CRB outperformed SIRS and presented better clinical usefulness as prompt tools for patients with community-acquired pneumonia in the emergency department. Among the tools for a comprehensive patient assessment, PSI had the best decision-aid tool profile.

One of the objectives of road infrastructure sustainability is to ensure that users are treated equally and their quality of life is improved by providing better mobility and traffic safety. When designing roads, it is important to evaluate different design criteria alternatives - in this case, we look at traffic safety principles. For this, we used the Safety Performance Functions (SPF) tool to obtain the expected crash frequency. The data used were Medellín’s crash records from 2012 to 2016, as well as the geometric features and traffic conditions at signalized intersections. A negative binomial model was fitted to estimate the SPF. Exposure, geometry, and traffic volume were found to be statistically significant in determining the expected crash frequency for collisions where there was property damage only (PDO) and fatal or injury (FI). It was found that accidents were less likely on T-junctions compared to four-leg junctions, one-way approaches were found to be safer whereas right turns were found to increase collisions causing FI. 

Background Vertebrate CPEB proteins bind mRNAs at cytoplasmic polyadenylation elements (CPEs) in their 3′ UTRs, leading to cytoplasmic changes in their poly(A) tail lengths; this can promote translational repression or activation of the mRNA. However, neither the regulation nor the mechanisms of action of the CPEB family per se have been systematically addressed to date. Results Based on a comparative analysis of the four vertebrate CPEBs, we determine their differential regulation by phosphorylation, the composition and properties of their supramolecular assemblies, and their target mRNAs. We show that all four CPEBs are able to recruit the CCR4-NOT deadenylation complex to repress the translation. However, their regulation, mechanism of action, and target mRNAs define two subfamilies. Thus, CPEB1 forms ribonucleoprotein complexes that are remodeled upon a single phosphorylation event and are associated with mRNAs containing canonical CPEs. CPEB2–4 are regulated by multiple proline-directed phosphorylations that control their liquid–liquid phase separation. CPEB2–4 mRNA targets include CPEB1-bound transcripts, with canonical CPEs, but also a specific subset of mRNAs with non-canonical CPEs. Conclusions Altogether, these results show how, globally, the CPEB family of proteins is able to integrate cellular cues to generate a fine-tuned adaptive response in gene expression regulation through the coordinated actions of all four members.

Mutation bias in prokaryotes varies from extreme adenine and thymine (AT) in obligatory endosymbiotic or parasitic bacteria to extreme guanine and cytosine (GC), for instance in actinobacteria. GC mutation bias deeply influences the folding stability of proteins, making proteins on the average less hydrophobic and therefore less stable with respect to unfolding but also less susceptible to misfolding and aggregation. We study a model where proteins evolve subject to selection for folding stability under given mutation bias, population size, and neutrality. We find a non-neutral regime where, for any given population size, there is an optimal mutation bias that maximizes fitness. Interestingly, this optimal GC usage is small for small populations, large for intermediate populations and around 50% for large populations. This result is robust with respect to the definition of the fitness function and to the protein structures studied. Our model suggests that small populations evolving with small GC usage eventually accumulate a significant selective advantage over populations evolving without this bias. This provides a possible explanation to the observation that most species adopting obligatory intracellular lifestyles with a consequent reduction of effective population size shifted their mutation spectrum towards AT. The model also predicts that large GC usage is optimal for intermediate population size. To test these predictions we estimated the effective population sizes of bacterial species using the optimal codon usage coefficients computed by dos Reis et al. and the synonymous to non-synonymous substitution ratio computed by Daubin and Moran. We found that the population sizes estimated in these ways are significantly smaller for species with small and large GC usage compared to species with no bias, which supports our prediction.

Background: Ceftobiprole is a fifth-generation cephalosporin that has been approved in Europe solely for the treatment of community-acquired and nosocomial pneumonia. The objective was to analyze the use of ceftobiprole medocaril (Cefto-M) in Spanish clinical practice in patients with infections in hospital or outpatient parenteral antimicrobial therapy (OPAT). Methods: This retrospective, observational, multicenter study included patients treated from 1 September 2021 to 31 December 2022. Results: A total of 249 individuals were enrolled, aged 66.6 ± 15.4 years, of whom 59.4% were male with a Charlson index of four (IQR 2–6), 13.7% had COVID-19, and 4.8% were in an intensive care unit (ICU). The most frequent type of infection was respiratory (55.8%), followed by skin and soft tissue infection (21.7%). Cefto-M was administered to 67.9% of the patients as an empirical treatment, in which was administered as monotherapy for 7 days (5–10) in 53.8% of cases. The infection-related mortality was 11.2%. The highest mortality rates were identified for ventilator-associated pneumonia (40%) and infections due to methicillin-resistant Staphylococus aureus (20.8%) and Pseudomonas aeruginosa (16.1%). The mortality-related factors were age (OR: 1.1, 95%CI (1.04–1.16)), ICU admission (OR: 42.02, 95%CI (4.49–393.4)), and sepsis/septic shock (OR: 2.94, 95%CI (1.01–8.54)). Conclusions: In real life, Cefto-M is a safe antibiotic, comprising only half of prescriptions for respiratory infections, that is mainly administered as rescue therapy in pluripathological patients with severe infectious diseases.