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Abstract Pathogenic variants underlying Mendelian diseases often disrupt the normal physiology of a few tissues and organs. However, variant effect prediction tools that aim to identify pathogenic variants are typically oblivious to tissue contexts. Here we report a machine-learning framework, denoted “Tissue Risk Assessment of Causality by Expression for variants” (TRACEvar, https://netbio.bgu.ac.il/TRACEvar/ ), that offers two advancements. First, TRACEvar predicts pathogenic variants that disrupt the normal physiology of specific tissues. This was achieved by creating 14 tissue-specific models that were trained on over 14,000 variants and combined 84 attributes of genetic variants with 495 attributes derived from tissue omics. TRACEvar outperformed 10 well-established and tissue-oblivious variant effect prediction tools. Second, the resulting models are interpretable, thereby illuminating variants’ mode of action. Application of TRACEvar to variants of 52 rare-disease patients highlighted pathogenicity mechanisms and relevant disease processes. Lastly, the interpretation of all tissue models revealed that top-ranking determinants of pathogenicity included attributes of disease-affected tissues, particularly cellular process activities. Collectively, these results show that tissue contexts and interpretable machine-learning models can greatly enhance the etiology of rare diseases.

Abstract Bronchiolitis is the leading cause of infant hospitalization. However, the molecular networks driving bronchiolitis pathobiology remain unknown. Integrative molecular networks, including the transcriptome and metabolome, can identify functional and regulatory pathways contributing to disease severity. Here, we integrated nasopharyngeal transcriptome and metabolome data of 397 infants hospitalized with bronchiolitis in a 17-center prospective cohort study. Using an explainable deep network model, we identified an omics-cluster comprising 401 transcripts and 38 metabolites that distinguishes bronchiolitis severity (test-set AUC, 0.828). This omics-cluster derived a molecular network, where innate immunity-related metabolites (e.g., ceramides) centralized and were characterized by toll-like receptor (TLR) and NF-κB signaling pathways (both FDR

BackgroundPegozafermin is a long-acting glycopegylated (pegylated with the use of site-specific glycosyltransferases) fibroblast growth factor 21 (FGF21) analogue in development for the treatment of nonalcoholic steatohepatitis (NASH) and severe hypertriglyceridemia. The efficacy and safety of pegozafermin in patients with biopsy-proven noncirrhotic NASH are not well established.MethodsIn this phase 2b, multicenter, double-blind, 24-week, randomized, placebo-controlled trial, we randomly assigned patients with biopsy-confirmed NASH and stage F2 or F3 (moderate or severe) fibrosis to receive subcutaneous pegozafermin at a dose of 15 mg or 30 mg weekly or 44 mg once every 2 weeks or placebo weekly or every 2 weeks. The two primary end points were an improvement in fibrosis (defined as reduction by ≥1 stage, on a scale from 0 to 4, with higher stages indicating greater severity), with no worsening of NASH, at 24 weeks and NASH resolution without worsening of fibrosis at 24 weeks. Safety was also assessed.ResultsAmong the 222 patients who underwent randomization, 219 received pegozafermin or placebo. The percentage of patients who met the criteria for fibrosis improvement was 7% in the pooled placebo group, 22% in the 15-mg pegozafermin group (difference vs. placebo, 14 percentage points; 95% confidence interval [CI], -9 to 38), 26% in the 30-mg pegozafermin group (difference, 19 percentage points; 95% CI, 5 to 32; P = 0.009), and 27% in the 44-mg pegozafermin group (difference, 20 percentage points; 95% CI, 5 to 35; P = 0.008). The percentage of patients who met the criteria for NASH resolution was 2% in the placebo group, 37% in the 15-mg pegozafermin group (difference vs. placebo, 35 percentage points; 95% CI, 10 to 59), 23% in the 30-mg pegozafermin group (difference, 21 percentage points; 95% CI, 9 to 33), and 26% in the 44-mg pegozafermin group (difference, 24 percentage points; 95% CI, 10 to 37). The most common adverse events associated with pegozafermin therapy were nausea and diarrhea.ConclusionsIn this phase 2b trial, treatment with pegozafermin led to improvements in fibrosis. These results support the advancement of pegozafermin into phase 3 development. (Funded by 89bio; ENLIVEN ClinicalTrials.gov number, NCT04929483.).

Objective: Circadian Sleep Disorders Network has created a registry of circadian rhythm sleep-wake disorder (CRSWD) patients, and a survey of their experiences. The purpose of the registry is to provide volunteers willing to participate in research; the purpose of the survey is to fill some of the knowledge gaps on these disorders, including information on subjective patient experience and the efficacy and durability of treatments.Researchers are invited to contact Circadian Sleep Disorders Network for permission to use the registry to find potential research participants, and to further analyze the survey data. Patients: Over 1627 patients have participated; 1298 have completed the entire survey. Here we present results based on the 479 clinically diagnosed CRSWD patients. Methods: The survey covers a variety of topics relating to CRSWDs, including diagnosis, comorbidities, treatments, and work/educational accommodations. Conclusions: Results of this survey diverged from much of the literature. More than half the participants reported tiredness even when sleeping on their preferred schedule. While depression may cause sleep problems, our data suggests that sleep/circadian problems often precede depression.There were more people suffering from sighted non-24-hour sleep-wake rhythm disorder than some of the literature would lead us to expect.Current treatments did not appear to be helpful to a large percentage of our participants. Most of them did not find light therapy helpful and nearly all participants who tried phase-delay chronotherapy reported at best only short-term improvement. A sizable proportion of people who tried phase-delay chronotherapy subsequently developed non-24-hour sleep-wake rhythm disorder.

Abstract The Perseverance rover has collected seven oriented samples of sedimentary rocks, all likely older than the oldest signs of widespread life on Earth, at the exposed base of the western fan in Jezero crater, Mars. The samples include a sulfate‐ and clay‐bearing mudstone and sandstone, a fluvial sandstone from a stratigraphically low position at the fan front, and a carbonate‐bearing sandstone deposited above the sulfate‐bearing strata. All samples contain aqueously precipitated materials and most or all were aqueously deposited. Although the rover instruments have not confidently detected organic matter in the rocks from the fan front, the much more sensitive terrestrial instruments will still be able to search for remnants of prebiotic chemistries and past life, and study Mars's past habitability in the samples returned to Earth. The hydrated, sulfate‐bearing mudstone has the highest potential to preserve organic matter and biosignatures, whereas the carbonate‐bearing sandstones can be used to constrain when and for how long Jezero crater contained liquid water. Returned sample science analyses of sulfate, carbonate, clay, phosphate and igneous minerals as well as trace metals and volatiles that are present in the samples acquired at the fan front would provide transformative insights into past habitable environments on Mars, the evolution of its magnetic field, atmosphere and climate and the past and present cycling of atmospheric and crustal water, sulfur and carbon.

Background Respiratory syncytial virus (RSV) bronchiolitis contributes to a large morbidity and mortality burden globally. While emerging evidence suggests that airway microRNA (miRNA) is involved in the pathobiology of RSV infection, its role in the disease severity remains unclear.Methods In this multicentre prospective study of infants (aged

Abstract A key objective of the Perseverance rover mission is to acquire samples of Martian rocks for future return to Earth. Eventual laboratory analyses of these samples would address key questions about the evolution of the Martian climate, interior, and habitability. Many such investigations would benefit greatly from samples of Martian bedrock that are oriented in absolute Martian geographic coordinates. However, the Mars 2020 mission was designed without a requirement for orienting the samples. Here we describe a methodology that we developed for orienting rover drill cores in the Martian geographic frame and its application to Perseverance's first 20 rock samples. To orient the cores, three angles were measured: the azimuth and hade of the core pointing vector (i.e., vector oriented along the core axis) and the core roll (i.e., the solid body angle of rotation around the pointing vector). We estimated the core pointing vector from the attitude of the rover's Coring Drill during drilling. To orient the core roll, we used oriented images of asymmetric markings on the bedrock surface acquired with the rover's Wide Angle Topographic Sensor for Operations and eNgineering (WATSON) camera. For most samples, these markings were in the form of natural features on the outcrop, while for four samples they were artificial ablation pits produced by the rover's SuperCam laser. These cores are the first geographically‐oriented (

Summary: Background: Bronchiolitis is a leading cause of infant hospitalization. Recent research suggests the heterogeneity within bronchiolitis and the relationship of airway viruses and bacteria with bronchiolitis severity. However, little is known about the pathobiological role of fungi. We aimed to identify bronchiolitis mycotypes by integrating fungus and virus data, and determine their association with bronchiolitis severity and biological characteristics. Methods: In a multicentre prospective cohort study of 398 infants (age

ObjectiveTo investigate the efficacy and safety of aceneuramic acid extended-release (Ace-ER), a treatment intended to replace deficient sialic acid, in patients with GNE myopathy.MethodsUX001-CL301 was a phase 3, double-blind, placebo-controlled, randomized, international study evaluating the efficacy and safety of Ace-ER in patients with GNE myopathy. Participants who could walk ≥200 meters in a 6-minute walk test at screening were randomized 1:1, and stratified by sex, to receive Ace-ER 6 g/d or placebo for 48 weeks and assessed every 8 weeks. The primary endpoint was change in muscle strength over 48 weeks measured by upper extremity composite (UEC) score. Key secondary endpoints included change in lower extremity composite (LEC) score, knee extensor strength, and GNE myopathy-Functional Activity Scale (GNEM-FAS) mobility domain score. Safety assessments included adverse events (AEs), vital signs, and clinical laboratory results.ResultsEighty-nine patients were randomized (Ace-ER n = 45; placebo n = 44). Change from baseline to week 48 for UEC score between treatments did not differ (least square mean [LSM] Ace-ER -2.25 kg vs placebo -2.99 kg; LSM difference confidence interval [CI] 0.74 [-1.61 to 3.09]; p = 0.5387). At week 48, there was no significant difference between treatments for the change in key secondary endpoints: LEC LSM difference (CI) -1.49 (-5.83 to 2.86); knee extension strength -0.40 (-2.38 to 1.58); and GNEM-FAS mobility domain score -0.72 (-2.01 to 0.57). Gastrointestinal events were the most common AEs.ConclusionsAce-ER was not superior to placebo in improving muscle strength and function in patients with GNE myopathy.Classification of evidenceThis study provides Class I evidence that for patients with GNE myopathy, Ace-ER does not improve muscle strength compared to placebo.

Bronchiolitis is major cause of infection, morbidity and hospitalisation. Here the authors apply transcriptomic based assessment of the host response, microbiome composition and function, and associate this to bronchiolitis severity.

Abstract Objective Bronchiolitis within the first 3 months of life is a risk factor for more severe illness. We aimed to identify characteristics associated with mild bronchiolitis in infants ≤90 days old presenting to the emergency department (ED). Methods We conducted a secondary analysis of infants ≤90 days old with clinically diagnosed bronchiolitis using data from the 25th Multicenter Airway Research Collaboration prospective cohort study. We excluded infants with direct intensive care unit admissions. Mild bronchiolitis was defined as (1) sent home after the index ED visit and did not have a return ED visit or had a return ED visit without hospitalization, or (2) were hospitalized from the index ED visit to the inpatient floor for

BackgroundBronchiolitis is the leading cause of infant hospitalization in U.S. and is associated with increased risk for childhood asthma. Immunoglobulin E (IgE) not only plays major roles in antiviral immune responses and atopic predisposition, but also offers a potential therapeutic target.ObjectiveWe aimed to identify phenotypes of infant bronchiolitis by using total IgE (tIgE) and virus data, to determine their association with asthma development, and examine their biological characteristics.MethodsIn a multicenter prospective cohort study of 1,016 infants (age