Faculty Bibliography

Hepatic encephalopathy (HE) is a common complication of decompensated cirrhosis that can be reversed with treatment. Frequent episodes of recurrence are common, impacting patients, caregivers and healthcare systems, increasing morbidity and mortality statistics and resulting in grave financial consequences. Uptake and adherence to formal recommendations for HE diagnosis and management are low. There is an unmet need to advocate for the use of these recommendations in a more pragmatic form. Clinicians from multiple disciplines, dedicated to raising liver disease awareness, convened in a roundtable format to review and discuss the latest HE guidelines and relevant peer-reviewed literature on HE. The result was this clinical care publication on the screening, diagnosis and management of HE which seeks to facilitate clinicians' recognition and diagnosis of HE, apply a pathway of care for HE that addresses steps for initial management, long-term maintenance and prevention; it also addresses practical recommendations concerning situations encountered in HE. Resources are provided to address the different needs of the three key players in HE: patients, caregivers, and healthcare professionals.

The immune system is tasked with mounting effective responses to pathogens while preventing inflammation triggered by innocuous antigens, including those derived from self, food, and commensal microbes. This balance is especially critical in the intestine, where dietary and microbial antigens are constantly encountered. Peripherally induced regulatory T cells (pTreg or iTreg) play a key role in suppressing inappropriate immune activation and maintaining gut homeostasis. Elucidating how pTreg cells are generated along the gastrointestinal tract is therefore critical to understanding peripheral tolerance. Recent studies have revealed that intestinal antigen-specific pTreg cell differentiation is induced by a distinct lineage of antigen-presenting cells (APCs) requiring expression of the transcription factors RORγt and PRDM16. Genetic perturbation of these APCs results not only in microbiota-specific proinflammatory T cell responses but also in the breakdown of oral tolerance, which in turn predisposes to allergic inflammation. In this review, we summarize the discovery of these tolerance-inducing APCs, highlight their role in instructing pTreg cell differentiation in response to microbiota and dietary antigens, and discuss the regulatory networks that support their function during intestinal immune tolerance.

Therapeutic targeting of mutant KRAS pathways driving cancers is being actively investigated to identify feedback mechanisms responsible for the development of adaptive resistance to mutant KRAS inhibitors undergoing clinical trials. Here we report RASH3D19 as a mediator of RAS pathway activation through a positive feedback loop involving the KRAS-microRNA signalling axis. KRAS-induced miR-222 represses ETS1 expression and downstream transactivation of miR-301a leading to elevation of its target RASH3D19. RASH3D19 facilitates activation of RAS pathways by promoting dimerization and interaction of EGFR with the SOS2, GRB2, SHP2 and GAB1 complex. Genetic deletion of RASH3D19 in mutant KRAS-expressing cancer cells exhibits growth retardation in vitro, in vivo and sensitized pancreatic ductal adenocarcinoma and colorectal cancer cells, organoids and xenografts to mutant KRAS inhibitors, suppressing feedback reactivation of RAS pathways. Therapeutic targeting of RASH3D19 is expected to lead to tumour debulking and alleviating resistance to KRAS inhibitors in mutant KRAS-expressing cancers.

Monitoring intracellular calcium is central to understanding cell signaling across nearly all cell types and organisms. Fluorescent genetically encoded calcium indicators (GECIs) remain the standard tools for in vivo calcium imaging, but require intense excitation light, leading to photobleaching, background autofluorescence and phototoxicity. Bioluminescent GECIs, which generate light enzymatically, eliminate these artifacts but have been constrained by low dynamic range and suboptimal calcium affinities. Here we show that CaBLAM ('calcium bioluminescence activity monitor'), an engineered bioluminescent calcium indicator, achieves an order-of-magnitude improvement in signal contrast and a tunable affinity matched to physiological cytosolic calcium. CaBLAM enables single-cell and subcellular activity imaging at video frame rates in cultured neurons and sustained imaging over hours in awake, behaving animals. These capabilities establish CaBLAM as a robust and general alternative to fluorescent GECIs, extending calcium imaging to regimes where excitation light is undesirable or infeasible.

PURPOSE/OBJECTIVE:To introduce mtrk, a new open-source tool based on modern software-engineering principles that simplifies pulse-sequence design, implementation, and dissemination. METHODS:The mtrk framework is vendor-agnostic and relies on a compact and human-readable descriptive language. Users can design pulse sequences using either a Python-based programming interface or an intuitive graphical interface. The graphical interface also allows for visualizing pulse-sequence diagrams. A driver sequence was developed to run mtrk sequences on MR scanners. A spin-echo sequence was designed with mtrk and converted to Pulseq for comparison. Both versions were compared to an equivalent vendor sequence in phantom and in vivo experiments. RESULTS:Images from the mtrk and Pulseq versions were nearly identical and showed over 90% similarity compared to the vendor sequence, despite minor unavoidable design differences. Phantom images matched corresponding synthetic images simulated using the same pulse sequences. CONCLUSION/CONCLUSIONS:The mtrk framework simplifies the development of pulse sequences by providing an intuitive descriptive language and compatibility with the Pulseq format. Users can design and simulate pulse sequences using the graphical interface without any programming experience.

Gramene (gramene.org) is a comprehensive reference database for comparative plant genomics and pathway analysis, integrating functional annotations, evidence-based curated pathways and their projections, and multi-omics datasets. Since our last report, Gramene has added crop-specific pan-genome portals for maize, sorghum, rice, and grapevine. These pan-genome portals host population-scale datasets and multiple assembled genomes per species, all anchored by shared reference genomes. Importantly, these portals now adopt standardized rsIDs for genetic variants, advancing FAIR data principles and enabling cross-database interoperability. The main site is now Gramene Plants, emphasizing its broad genome coverage. Release 69 features 233 reference genomes, curated pathways for 139 species, expression data from 1026 studies across 27 species, and genetic variation data mapped to 27 genomes from 19 species. Key updates to the integrated search functionality include embedded expression viewers from the Bio-Analytic Resource for Plant Biology and EMBL-EBI Expression Atlas, a literature-curated catalog of gene functions, and a new Germplasm tab linking accessions with loss-of-function alleles to seed repositories. These advances reinforce Gramene as a comprehensive platform for exploring plant genomic diversity, gene function, and evolutionary conservation across the Green Tree of Life and within key agricultural species.

OBJECTIVES/UNASSIGNED:To examine how structural factors, such as child protective services (CPS) involvement, prehospital interactions with police or emergency medical services (EMS), and clinical factors, such as autism diagnosis, contribute to physical restraint use among pediatric patients presenting to the emergency department (ED) for behavioral health concerns. METHODS/UNASSIGNED:In this retrospective cohort study, we reviewed pediatric ED encounters from January 1, 2021, to October 31, 2023, at a tertiary care children's hospital. Multivariable logistic regression was used to assess associations among autism diagnosis, CPS involvement, and arrival mode (police/EMS) and physical restraint use, adjusted for demographic variables. RESULTS/UNASSIGNED:Among 6288 behavioral health encounters, physical restraints were used in 124 (1.97%; 95% CI, 1.69, 2.58) encounters. Children arriving by police or EMS were 3 times more likely to be restrained than those arriving by car or walk-in (adjusted odds ratio, aOR = 3.07, 95% CI, 2.01-4.69). Children with CPS involvement were almost twice as likely to be restrained (aOR = 1.91; 95% CI, 1.26-2.88). Children diagnosed with autism were 7 times more likely to be restrained (aOR = 7.25, 95% CI, 3.61-14.55). Black children were more likely to be restrained than White children (aOR = 1.78, 95% CI, 1.12-2.84). CONCLUSION/UNASSIGNED:CPS involvement, transport by police or EMS, autism diagnosis, and Black race were independently associated with increased physical restraint use in pediatric ED patients. These findings emphasize the role of both structural and child-level factors in contributing to physical restraint in emergency behavioral health care, highlighting the need for a multifactorial approach to reduce restraint use.

BACKGROUND/UNASSIGNED:Autism spectrum disorder (ASD) shows significant clinical variability, likely due to a combination of genetic and environmental factors. Preterm birth is a known risk factor for ASD, occurring in approximately 13% of diagnosed individuals. While genetic factors contribute to preterm birth in the general population, the relationship between genetic variation, preterm birth, and ASD heterogeneity remains unclear. METHODS/UNASSIGNED:We investigated the genetic factors associated with preterm birth in 31,947 autistic individuals using data from the SPARK (Simons Foundation Powering Autism Research for Knowledge) sample. We conducted 3 ancestry-specific genome-wide association studies for African/African American, admixed American, and non-Finnish European ancestries, followed by a meta-analysis of 3308 preterm cases and 28,639 controls using METAL. Functional mapping and gene-based analyses were performed using FUMA, and genetic correlations were estimated using LDSC and Popcorn. Polygenic risk scores (PRSs) were computed with BridgePRS, using PRS of preterm birth in the general population. RESULTS/UNASSIGNED:Our study identified ancestry-specific genetic loci associated with preterm birth in ASD cases. Although the meta-analysis results were not statistically significant, the estimated single nucleotide polymorphism heritability was 14%, indicating a meaningful contribution of common genetic variants. Across ancestry groups, preterm birth status was not significantly associated with PRSs for any psychiatric or medical conditions analyzed. However, polygenic liability to preterm birth in the general population was linked to several congenital anomalies after multiple testing adjustments. CONCLUSIONS/UNASSIGNED:These findings highlight the importance of diverse ancestries and early-life exposures in understanding ASD heterogeneity. Future research should replicate these findings in larger samples and explore rare variants associated with preterm birth to better understand the relationship between gestational duration and clinical and genetic differences in ASD.