K29-linked free polyubiquitin chains affect ribosome biogenesis and direct ribosomal proteins to the intranuclear quality control compartment.

Ribosome assembly requires precise coordination between the production and assembly of ribosomal components. Mutations in ribosomal proteins that inhibit the assembly process or ribosome function are often associated with ribosomopathies, some of which are linked to defects in proteostasis. In this study, we examine the interplay between several yeast proteostasis enzymes, including deubiquitylases (DUBs) Ubp2 and Ubp14, and E3 ligases Ufd4 and Hul5, and we explore their roles in the regulation of the cellular levels of K29-linked unanchored polyubiquitin (polyUb) chains. Accumulating K29-linked unanchored polyUb chains associate with maturing ribosomes to disrupt their assembly, activate the ribosome assembly stress response (RASTR), and lead to the sequestration of ribosomal proteins at the intranuclear quality control compartment (INQ). These findings reveal the physiological relevance of INQ and provide insights into mechanisms of cellular toxicity associated with ribosomopathies.

Characterization of the zebrafish gabra1sa43718/sa43718 germline loss of function allele confirms a function for Gabra1 in motility and nervous system development.

Mutation of the GABRA1 gene is associated with neurodevelopmental defects and epilepsy. GABRA1 encodes for the α1 subunit of the γ-aminobutyric acid type A receptor (GABAAR), which regulates the fast inhibitory impulses of the nervous system. Multiple model systems have been developed to understand the function of GABRA1, but these models have produced complex and, at times, incongruent data. Thus, additional model systems are required to validate and substantiate previous results. We sought to provide initial phenotypic analysis of a novel germline mutant allele. Our analysis provides a solid foundation for the future use of this allele to characterize gabra1 functionally and pharmacologically using zebrafish. We investigated the behavioral swim patterns associated with a nonsense mutation of the zebrafish gabra1 (sa43718 allele) gene. The sa43718 allele causes a decrease in gabra1 mRNA expression, which is associated with light induced hypermotility, one phenotype previously associated with seizure like behavior in zebrafish. Mutation of gabra1 was accompanied by decreased mRNA expression of gabra2, gabra3, and gabra5, indicating a reduction in the expression of additional α sub-units of the GABAAR. Although multiple sub-units were decreased, larvae continued to respond to pentylenetetrazole (PTZ), indicating that a residual GABAAR exists in the sa43718 allele. Proteomics analysis demonstrated that mutation of gabra1 is associated with abnormal expression of proteins that regulate synaptic vesicle fusion, vesicle transport, synapse development, and mitochondrial protein complexes. These data support previous studies performed in a zebrafish nonsense allele created by CRISPR/Cas9 and validate that loss of function mutations in the gabra1 gene result in seizure-like phenotypes with abnormal development of the GABA synapse. Our results add to the existing body of knowledge as to the function of GABRA1 during development and validate that zebrafish can be used to provide complete functional characterization of the gene.

Nocardia Infection in Patients With Anti-Granulocyte-Macrophage Colony-Stimulating Factor Autoantibodies: A Prospective Multicenter French Study.

Background: Nocardiosis, a bacterial opportunistic infection caused by Nocardia spp, has recently been reported in patients with anti-granulocyte-macrophage colony-stimulating factor (GM-CSF) autoantibodies, but insufficient data are available about disease presentation, outcomes, and occurrence of autoimmune pulmonary alveolar proteinosis (aPAP) in this population. Methods: We performed a prospective, multicenter, nationwide study in France and included patients with a Nocardia infection who had anti-GM-CSF autoantibodies. We describe their clinical, microbiological, and radiological characteristics, and their outcome at 1 year of follow-up. Results: Twenty patients (18 [90%] male) were included, with a median age of 69 (interquartile range, 44-75) years. The organs most frequently involved were the brain (14/20 [70%]) and the lung (12/20 [60%]). Half of the infections were disseminated (10/20 [50%]). Nocardia identification was predominantly made in abscess fluid (17/20 [85%]), among which 10 (59%) were brain abscesses. The 1-year all-cause mortality was 5% (1/20), and only 1 case of aPAP (1/20 [5%]) occurred during the follow-up period. Conclusions: Nocardiosis with anti-GM-CSF autoantibodies is associated with a low mortality rate despite a high incidence of brain involvement. Although the occurrence of aPAP was infrequent during the 1-year follow-up period, long-term clinical data are needed to fully understand the potential relationship between nocardiosis, anti-GM-CSF autoantibodies, and aPAP.

Efficacy and safety of antibiotics targeting Gram-negative bacteria in nosocomial pneumonia: a systematic review and Bayesian network meta-analysis.

BACKGROUND: Multiple randomized controlled studies have compared numerous antibiotic regimens, including new, recently commercialized antibiotics in the treatment of nosocomial pneumonia (NP). The objective of this Bayesian network meta-analysis (NMA) was to compare the efficacy and the safety of different antibiotic treatments for NP. METHODS: We conducted a systematic search of PubMed, Medline, Web of Science, EMBASE and the Cochrane Library databases from 2000 through 2021. The study selection included studies comparing antibiotics targeting Gram-negative bacilli in the setting of NP. The primary endpoint was 28 day mortality. Secondary outcomes were clinical cure, microbiological cure and adverse events. RESULTS: Sixteen studies encompassing 4993 patients were included in this analysis comparing 13 antibiotic regimens. The level of evidence for mortality comparisons ranged from very low to moderate. No significant difference in 28 day mortality was found among all beta-lactam regimens. Only the combination of meropenem plus aerosolized colistin was associated with a significant decrease of mortality compared to using intravenous colistin alone (OR = 0.43; 95% credible interval [0.17-0.94]), based on the results of the smallest trial included. The clinical failure rate of ceftazidime was higher than meropenem with (OR = 1.97; 95% CrI [1.19-3.45]) or without aerosolized colistin (OR = 1.40; 95% CrI [1.00-2.01]), imipemen/cilastatin/relebactam (OR = 1.74; 95% CrI [1.03-2.90]) and ceftazidime/avibactam (OR = 1.48; 95% CrI [1.02-2.20]). For microbiological cure, no substantial difference between regimens was found, but ceftolozane/tazobactam had the highest probability of being superior to comparators. In safety analyses, there was no significant difference between treatments for the occurrence of adverse events, but acute kidney failure was more common in patients receiving intravenous colistin. CONCLUSIONS: This network meta-analysis suggests that most antibiotic regimens, including new combinations and cefiderocol, have similar efficacy and safety in treating susceptible Gram-negative bacilli in NP. Further studies are necessary for NP caused by multidrug-resistant bacteria. Registration PROSPERO CRD42021226603.

Treatment of infections caused by multidrug-resistant Gram-negative bacilli: A practical approach by the Italian (SIMIT) and French (SPILF) Societies of Infectious Diseases.

INTRODUCTION: The emergence of multidrug-resistant Gram-negative bacilli and the development of new antibiotics have complicated the selection of optimal regimens. International guidelines are valuable tools, but are limited by the scarcity of high-quality randomized trials in many situations. METHODS: A panel of experts from the French and Italian Societies of Infectious Diseases aimed to address unresolved issues in clinical practice based on their experience, an updated literature review and open discussions. RESULTS: The panel reached consensus for the following 'first choices': (i) cefepime for ventilator-acquired pneumonia due to AmpC ß-lactamase-producing Enterobacterales; (ii) the ß-lactam/ß-lactamase inhibitor combination most active in vitro, or cefiderocol combined with fosfomycin, and aerosolized colistin or aminoglycosides, for severe pneumonia due to Pseudomonas aeruginosa resistant to ceftolozane-tazobactam; (iii) high-dose piperacillin-tazobactam (including loading dose and continuous infusion) for complicated urinary tract infections (cUTIs) caused by extended-spectrum ß-lactamase-producing Enterobacterales with piperacillin-tazobactam minimum inhibitory concentration (MIC) ≤8 mg/L; (iv) high-dose cefepime for cUTIs due to AmpC ß-lactamase-producing Enterobacterales other than Enterobacter spp. if cefepime MIC ≤2 mg/L; (v) ceftolozane-tazobactam or ceftazidime-avibactam plus metronidazole for intra-abdominal infections (IAIs) due to third-generation cephalosporin-resistant Enterobacterales; (vi) ceftazidime-avibactam plus aztreonam plus metronidazole for IAIs due to metallo-ß-lactamase-producing Enterobacterales; (vii) ampicillin-sulbactam plus colistin for bloodstream infections (BSIs) caused by carbapenem-resistant Acinetobacter baumannii; (viii) meropenem-vaborbactam for BSIs caused by Klebsiella pneumoniae carbapenemase-producing Enterobacterales; and (ix) ceftazidime-avibactam plus fosfomycin for neurological infections caused by carbapenem-resistant P. aeruginosa. CONCLUSIONS: These expert choices were based on the necessary balance between antimicrobial stewardship principles and the need to provide optimal treatment for individual patients in each situation.

Expanding TheCellVision.org: a central repository for visualizing and mining high-content cell imaging projects.

We previously constructed TheCellVision.org, a central repository for visualizing and mining data from yeast high-content imaging projects. At its inception, TheCellVision.org housed two high-content screening (HCS) projects providing genome-scale protein abundance and localization information for the budding yeast Saccharomyces cerevisiae, as well as a comprehensive analysis of the morphology of its endocytic compartments upon systematic genetic perturbation of each yeast gene. Here, we report on the expansion of TheCellVision.org by the addition of two new HCS projects and the incorporation of new global functionalities. Specifically, TheCellVision.org now hosts images from the Cell Cycle Omics project, which describes genome-scale cell cycle-resolved dynamics in protein localization, protein concentration, gene expression, and translational efficiency in budding yeast. Moreover, it hosts PIFiA, a computational tool for image-based predictions of protein functional annotations. Across all its projects, TheCellVision.org now houses >800,000 microscopy images along with computational tools for exploring both the images and their associated datasets. Together with the newly added global functionalities, which include the ability to query genes in any of the hosted projects using either yeast or human gene names, TheCellVision.org provides an expanding resource for single-cell eukaryotic biology.

PIFiA: self-supervised approach for protein functional annotation from single-cell imaging data.

Fluorescence microscopy data describe protein localization patterns at single-cell resolution and have the potential to reveal whole-proteome functional information with remarkable precision. Yet, extracting biologically meaningful representations from cell micrographs remains a major challenge. Existing approaches often fail to learn robust and noise-invariant features or rely on supervised labels for accurate annotations. We developed PIFiA (Protein Image-based Functional Annotation), a self-supervised approach for protein functional annotation from single-cell imaging data. We imaged the global yeast ORF-GFP collection and applied PIFiA to generate protein feature profiles from single-cell images of fluorescently tagged proteins. We show that PIFiA outperforms existing approaches for molecular representation learning and describe a range of downstream analysis tasks to explore the information content of the feature profiles. Specifically, we cluster extracted features into a hierarchy of functional organization, study cell population heterogeneity, and develop techniques to distinguish multi-localizing proteins and identify functional modules. Finally, we confirm new PIFiA predictions using a colocalization assay, suggesting previously unappreciated biological roles for several proteins. Paired with a fully interactive website ( https://thecellvision.org/pifia/ ), PIFiA is a resource for the quantitative analysis of protein organization within the cell.

Proteome-scale movements and compartment connectivity during the eukaryotic cell cycle.

Cell cycle progression relies on coordinated changes in the composition and subcellular localization of the proteome. By applying two distinct convolutional neural networks on images of millions of live yeast cells, we resolved proteome-level dynamics in both concentration and localization during the cell cycle, with resolution of ∼20 subcellular localization classes. We show that a quarter of the proteome displays cell cycle periodicity, with proteins tending to be controlled either at the level of localization or concentration, but not both. Distinct levels of protein regulation are preferentially utilized for different aspects of the cell cycle, with changes in protein concentration being mostly involved in cell cycle control and changes in protein localization in the biophysical implementation of the cell cycle program. We present a resource for exploring global proteome dynamics during the cell cycle, which will aid in understanding a fundamental biological process at a systems level.

Antioxidant Activity of an Aqueous Extract of Cuttlefish Ink during Fish Muscle Heating.

The antioxidant effect of cuttlefish (Sepia officinalis) ink (CFI) was analysed in the present study. A model system consisting of minced seabream (Sparus aurata) muscle and different concentrations of an aqueous extract of CFI was subjected to a heat (50 °C) treatment for 12 days. The effects of the CFI content and the heating time on lipid oxidation (conjugated diene (CD), conjugated triene (CT), and peroxide values and fluorescent compound formation), hydrolysis (free fatty acid content) development, and changes in the fatty acid (FA) profile (polyene index (PI), unsaturated FA content, ω3/ω6 ratio) were determined. The addition of the aqueous extract of CFI led to a lower (p < 0.05) development of lipid oxidation (CD, CT, and fluorescent compound determination) and to a higher (p < 0.05) retention of unsaturated FAs (PI determination). More important effects were found with increased CFI concentrations and at advanced heating times. However, a definite effect on lipid hydrolysis development (FFA value) could not be inferred. A new approach for the beneficial use of cuttlefish ink is presented. According to the direct relationship between rancidity stability and nutritional and sensory values, the present study provides a new strategy for the quality enhancement of thermally treated seafood.

Cardiac arrest in an emergency department in Colombia during 2011-2020: A descriptive study.

Background: Cardiac arrest is a public health problem related to high morbidity and mortality. In Colombia, objective data characterize in our population has been not available. The aim of this study has been to determined the epidemiological characteristics of patients with cardiorespiratory arrest treated in an emergency room. Methods: A retrospective observational cross-sectional cohort study was performed. We included adult patients admitted with a diagnostic of out-of-hospital cardiac arrest (OHCA) or who presented with in-hospital cardiac arrest while in the emergency department (ED). Results: A total of 415 patients were included 232 were men, and the median age was 67 years. OHCA was presented in 383 patients. In this group, 80.2% required orotracheal intubation, 90.1% received Epinephrine, and and 52.6% received immediate resuscitation. Survival after discharge was 43.1% in patients with non-shockable rhythm registered. Return of spontaneous circulation was achieved in 49.6%. The survival after hospital discharge was 22.2%. Cerebral performance category score <=2 was 20.4%. Conclusion: In our study, the epidemiological characteristics and outcomes of patients seen in the ED with cardiac arrest are similar to those described in the literature.

Prognostic value of serum Krebs von den Lungen-6 (KL-6) levels in COVID-19 pneumonia.

BACKGROUND AND OBJECTIVES: Krebs von den Lungen-6 (KL-6), expressed by damaged type II pneumocytes, is useful in the diagnosis and severity assessment of many diffuse interstitial lung diseases. The objective of our study was to determine the prognostic value of the initial KL-6 plasma level in COVID-19 pneumonia. METHODS: All patients hospitalized for a suspected COVID-19 pneumonia between March and May 2020 in our Chest department of a French university hospital were included. KL-6 serum concentrations were measured within 72 h of diagnostic suspicion by chemiluminescence enzyme immunoassay Survival analysis was performed using a Cox regression and modeled by a Kaplan-Meier curve. RESULTS: Sixty-six COVID-19 patients (average age = 64 ± 14 years, 71.2 % males) with KL-6 serum measurement were included. Median KL-6 serum concentration was 409 ± 312 U/mL. KL-6 was significantly higher in men (p = 0.003), elders (p = 0.0001) and in patients with greater Charlson's score (p = 0.002). Higher KL-6 concentration was significantly associated with in-hospital mortality (HR: 8.66; 95 % CI:1.1-69.2, p = 0.014), radiological extension of lesions on chest CT scan (p = 0.004) and higher WHO severity score (p = 0.042), but not with admission in intensive care unit. In 9 (14 %) non-surviving COVID-19 patients, KL-6 serum concentration increased whereas it remained stable or decreased in survivors. At 3 months follow-up (n = 48), DLCO was negatively correlated with the initial KL-6 value (r = 0.47, p = 0.001), while FVC, FEV1 and MRC score were not. CONCLUSION: Initial KL-6 serum concentration is significantly associated with in-hospital mortality, unfavorable outcome, and persistent impairment of DLCO at 3 months. Initial KL-6 plasma determination appears as a prognostic biomarker in COVID-19 pneumonia.

Pleural penetration of amoxicillin and metronidazole during pleural infection: An ambispective cohort study.

OBJECTIVES: The pharmacokinetics of antibiotics in pleural fluid during pleural infections has been poorly described. This study aimed to explore amoxicillin and metronidazole diffusion into the pleural space. METHODS: This was an ambispective, single-centre study that included patients with complicated parapneumonic effusion or pleural empyema managed with repeated therapeutic thoracentesis as first-line treatment between 2014 and 2022. Pleural steady-state or trough concentrations of amoxicillin and metronidazole were measured, with a lower limit of quantification of 5 mg/L. RESULTS: Seventy paired blood and pleural samples were analysed from 40 patients. The median (interquartile range) patient age was 55 years (45-67 years) and 88% were male. The median patient weight was 65.8 kg (57.3-82 kg) and median plasma albumin concentration was 29.7 g/L (23.7-33.9 g/L). Median creatinine clearance was 106 mL/min (95-117 mL/min). Median amoxicillin pleural concentrations in patients treated with oral, bolus and continuous intravenous administrations (6 g/day) were, respectively, 5.2 (<5-6.4), 9.4 (8-13.1) and 10.8 (7.1-13.1) mg/L. Pleural concentrations were <5 mg/L in 5/11 samples (45%) with oral treatment and 6/59 (10%) with intravenous treatment. Median metronidazole pleural concentrations were 18.4 (15.7-22.8) mg/L, with all patients being treated orally (1.5 g/day). CONCLUSIONS: Oral metronidazole (1.5 g/day) and intravenous amoxicillin (6 g/day) achieved therapeutic targets in pleural fluid in most cases, but oral amoxicillin did not.

Infections in autoimmune pulmonary alveolar proteinosis: a large retrospective cohort.

BACKGROUND: Autoimmune pulmonary alveolar proteinosis (aPAP) is a rare disease, predisposing to an increased risk of infection. A complete picture of these infections is lacking. RESEARCH QUESTION: Describe the characteristics and clinical outcomes of patients diagnosed with aPAP, and to identify risk factors associated with opportunistic infections. METHODS: We conducted a retrospective cohort including all patients diagnosed with aPAP between 2008 and 2018 in France and Belgium. Data were collected using a standardised questionnaire including demographics, comorbidities, imaging features, outcomes and microbiological data. RESULTS: We included 104 patients, 2/3 were men and median age at diagnosis was 45 years. With a median follow-up of 3.4 years (IQR 1.7-6.6 years), 60 patients (58%), developed at least one infection, including 23 (22%) with opportunistic infections. Nocardia spp was the main pathogen identified (n=10). Thirty-five (34%) patients were hospitalised due to infection. In univariate analysis, male gender was associated with opportunistic infections (p=0.04, OR=3.88; 95% CI (1.02 to 22.06)). Anti-granulocyte macrophage colony-stimulating factor antibody titre at diagnosis was significantly higher among patients who developed nocardiosis (1058 (316-1591) vs 580 (200-1190), p=0.01). Nine patients had died (9%), but only one death was related to infection. INTERPRETATION: Patients with aPAP often presented with opportunistic infections, especially nocardiosis, which highlights the importance of systematic search for slow-growing bacteria in bronchoalveolar lavage or whole lung lavage.

Oxidation capacity changes in the atmosphere of large urban areas in Europe: Modelling and experimental campaigns in atmospheric simulation chambers.

Air pollution is a major concern for human health and the environment. Consequently, environmental standards have become stricter to improve air quality. Thanks to this, the ambient levels of O3 precursors such as VOCs and NOX have decreased. However, O3 levels in Europe, especially during winter, have increased, potentially impacting on atmospheric oxidation capacity and the associated chemistry of tropospheric oxidants. In this work, we focus on recent changes in the oxidation capacity of urban atmospheres. The study is conducted with the results of the CMAQ modelling system with a regional resolution with 12 × 12 km2 across the entire European continent for the winter (January) and summer (July) of 2007 and 2015. The 2015 meteorological data is used for both years to emphasise emission changes during the studied period. We scrutinise the changes in ambient concentration levels of the main tropospheric oxidants (O3 and HOX radicals) in five representative cities, Valencia, Madrid, Milan, Berlin, and The Hague. The enhanced O3 formation in winter seems to be due to the low VOC/NOX ratio, while the opposite trend in summer may be related to a relatively high ratio. Additionally, photooxidation experiments are carried out in the EUPHORE chambers to study the effect of changes in NOX concentration and NO/NO2 ratio on the variation of the given oxidants at constant VOCs concentrations. For the baseline experiments, two scenarios are selected based on the model results of 2015: two representative winter and summer days of low and high pollution in Berlin and Madrid, respectively. The role of VOC/NOX and NO/NO2 ratios on atmospheric reactivity is discussed. As a result, it is first suggested that further decreases in ambient NOX levels are required to reduce ambient O3 levels. Moreover, additional factors should be considered when designing local-specific emission abatement strategies.

Conditional Generative Models for Dynamic Trajectory Generation and Urban Driving.

This work explores methodologies for dynamic trajectory generation for urban driving environments by utilizing coarse global plan representations. In contrast to state-of-the-art architectures for autonomous driving that often leverage lane-level high-definition (HD) maps, we focus on minimizing required map priors that are needed to navigate in dynamic environments that may change over time. To incorporate high-level instructions (i.e., turn right vs. turn left at intersections), we compare various representations provided by lightweight and open-source OpenStreetMaps (OSM) and formulate a conditional generative model strategy to explicitly capture the multimodal characteristics of urban driving. To evaluate the performance of the models introduced, a data collection phase is performed using multiple full-scale vehicles with ground truth labels. Our results show potential use cases in dynamic urban driving scenarios with real-time constraints. The dataset is released publicly as part of this work in combination with code and benchmarks.

Probabilistic Semantic Mapping for Autonomous Driving in Urban Environments.

Statistical learning techniques and increased computational power have facilitated the development of self-driving car technology. However, a limiting factor has been the high expense of scaling and maintaining high-definition (HD) maps. These maps are a crucial backbone for many approaches to self-driving technology. In response to this challenge, we present an approach that fuses pre-built point cloud map data with images to automatically and accurately identify static landmarks such as roads, sidewalks, and crosswalks. Our pipeline utilizes semantic segmentation of 2D images, associates semantic labels with points in point cloud maps to pinpoint locations in the physical world, and employs a confusion matrix formulation to generate a probabilistic bird's-eye view semantic map from semantic point clouds. The approach has been tested in an urban area with different segmentation networks to generate a semantic map with road features. The resulting map provides a rich context of the environment that is valuable for downstream tasks such as trajectory generation and intent prediction. Moreover, it has the potential to be extended to the automatic generation of HD maps for semantic features. The entire software pipeline is implemented in the robot operating system (ROS), a widely used robotics framework, and made available.