bluuebunny/crossref_metadata_2025 huggingface dataset:
MappingPlasmodiumtransitions and interactions in theAnophelesfemale
Authors: Yan Yan , Cheung Elaine , Verzier Lisa H. , Appetecchia Federico , March Sandra , Craven Ailsa R. , Du Esrah , Probst Alexandra S. , Rinvee Tasneem A. , de Vries Laura E. , Kauffman Jamie , Bhatia Sangeeta N. , Nelson Elisabeth , Singh Naresh , Peng Duo , Shaw W. Robert , Catteruccia Flaminia
Published: November 2024

The human malaria parasite,Plasmodium falciparum, relies onAnophelesmosquitoes for transmission. Once ingested during blood feeding, most parasites die in the mosquito midgut lumen or during epithelium traversal. How surviving ookinetes interact with midgut cells and form oocysts is unknown, yet these steps are essential to initiate a remarkable, similarly uncharacterized growth process culminating in the production of thousands of infectious sporozoites. Here, using single-cell RNA sequencing of both parasites and mosquito cells across four time points and two metabolic conditions, we unveil key processes shaping developmental transitions and mosquito-parasite interactions occurring in the midgut. In depth functional analyses reveal processes regulating oocyst growth and identify the transcription factorPfSIP2 as essential for sporozoite infection of human hepatocytes. By combining the analysis of shared mosquito-parasite barcodes with confocal microscopy, we discover that parasites preferentially interact with midgut progenitor cells during epithelial crossing, potentially using their basal location as an exit landmark. Additionally, we unveil tight connections between extracellular late oocysts and surrounding muscle cells that may ensure parasites adhere to the midgut without damaging it. Ultimately, our study provides fundamental insight into the molecular events characterizing previously inaccessible biological transitions and mosquito-parasite interactions, and identifies candidates for transmission-blocking strategies.
Dynamic metabolic modeling of ATP allocation during viral infection
Authors: Lu Alvin , Dukovski Ilija , Segrè Daniel
Published: November 2024

Viral pathogens, like SARS-CoV-2, hijack the host’s macromolecular production machinery, imposing an energetic burden that is distributed across cellular metabolism. To explore the dynamic metabolic tension between the host’s survival and viral replication, we developed a computational framework that uses genome-scale models to perform dynamic Flux Balance Analysis of human cell metabolism during virus infections. Relative to previous models, our framework addresses the physiology of viral infections of non-proliferating host cells through two new features. First, by incorporating the lipid content of SARS-CoV-2 biomass, we discovered activation of previously overlooked pathways giving rise to new predictions of possible drug targets. Furthermore, we introduce a dynamic model that simulates the partitioning of resources between the virus and the host cell, capturing the extent to which the competition depletes the human cells from essential ATP. By incorporating viral dynamics into our COMETS framework for spatio-temporal modeling of metabolism, we provide a mechanistic, dynamic and generalizable starting point for bridging systems biology modeling with viral pathogenesis. This framework could be extended to broadly incorporate phage dynamics in microbial systems and ecosystems.
Structural basis of the catalytic and allosteric mechanism of bacterial acetyltransferase PatZ
Authors: Park Jun Bae , Lee Gwanwoo , Han Yu-Yeon , Kim Dongwook , Heo Kyoo , Kim Jeesoo , Park Juhee , Yun Hyosuk , Lee Chul Won , Cho Hyun-Soo , Kim Jong-Seo , Steinegger Martin , Seok Yeong-Jae , Roh Soung-Hun
Published: November 2024

GCN5-relatedN-Acetyltransferases (GNATs) play a crucial role in regulating bacterial metabolism by acetylating specific target proteins. Despite their importance in bacterial physiology, the mechanisms underlying GNATs’ enzymatic and regulatory functions remain poorly understood. In this study, we elucidated the structures ofEscherichia coliPatZ, a type I GNAT, and investigated its ligand interactions, catalytic processes, and allosterism. PatZ functions as a homotetramer, with each subunit comprising a catalytic domain and a regulatory domain. Our findings reveal that the regulatory domain is essential for acetyltransferase activity, as it not only induces cooperative conformational changes in the catalytic domain but also directly contributes to the formation of substrate binding pockets. Furthermore, a protein structure-based analysis on the evolution of bacterial GNAT types reveals a distinct pattern of the regulatory domain across phyla, underscoring the regulatory domain’s critical role in responding to cellular energy status.

SIGNIFICANCE STATEMENT

Post-translational modifications, particularly acetylation mediated by GCN5-related N-Acetyltransferases (GNATs), play a crucial role in bacterial physiology. Protein acetyltransferase Z (PatZ) is a key GNAT with diverse substrates, essential for understanding the bacterial acetylome. This study employs cryogenic electron microscopy, X-ray crystallography, and biochemical analyses to elucidate the mechanistic regulation ofEscherichia coliPatZ. Our high-resolution structures reveal PatZ’s homo-tetrameric architecture, with each subunit comprising regulatory and GNAT domains. We characterize ligand-PatZ interactions, demonstrating ligand-induced conformational changes that facilitate allosteric regulation of the catalytic domain. Furthermore, our analyses elucidate the regulatory domain’s contribution to substrate binding pocket formation, potentially enhancing substrate specificity. Structure-based phylogenetic analysis provides insights into the evolution of diverse regulatory domains in the GNAT superfamily across bacterial taxonomy. This first visualization of PatZ advances our mechanistic understanding of bacterial physiology, offering novel insights into GNAT-mediated bacterial adaptations.

HIGHLIGHTS

-E. coliPatZ forms a homotetramer, with each subunit possessing a GNAT catalytic domain and a regulatory domain.

- Cooperative binding of acetyl-CoA to the regulatory domains is a prerequisite for inducing the structural compatibility of the catalytic domain with a substrate.

- Diverse regulatory domains in GNATs evolved to adapt to varied metabolic conditions across bacterial taxonomy.
Cryo-EM structures of human ClpXP reveal mechanisms of assembly and proteolytic activation
Authors: Chen Wenqian , Yang Jie , Lander Gabriel C.
Published: November 2024

The human ClpXP complex (hClpXP) plays a central role in mitochondrial protein quality control by degrading misfolded or unneeded proteins. While bacterial ClpXP complexes have been extensively characterized, the molecular determinants underlying hClpXP assembly and regulation are not as well understood. We determined cryo-electron microscopy (cryo-EM) structures of hClpP in isolation and in complex with hClpX, revealing how hClpX binding promotes rearrangement of an asymmetric hClpP heptamer to assemble as a symmetric tetradecamer. Our hClpXP structure also highlights the stabilizing role of a previously uncharacterized eukaryotic ClpX sequence, referred to as the E-loop, and its importance in ATPase activity and hexamer assembly. We further show that peptide interaction with the hClpP proteolytic active site promotes the complex to adopt a proteolytically competent conformation. Together, these findings advance our understanding of the molecular mechanisms defining hClpXP activation and function.
Peripheral immune profiles in individuals at genetic risk for amyotrophic lateral sclerosis and Alzheimer’s disease
Authors: Deecke Laura , Ohlei Olena , Goldeck David , Homann Jan , Toepfer Sarah , Demuth Ilja , Bertram Lars , Pawelec Graham , Lill Christina M.
Published: November 2024

The immune system plays a crucial role in the pathogenesis of neurodegenerative diseases. Here, we explored whether blood immune cell profiles are already altered in healthy individuals with a genetic predisposition to amyotrophic lateral sclerosis (ALS) or Alzheimer’s disease (AD).

Using multicolor flow cytometry, we analyzed 92 immune cell phenotypes in the blood of 448 healthy participants from the Berlin Aging Study II. We calculated polygenic risk scores (PGS) using genome-wide significant SNPs from recent large genome-wide association studies on ALS and AD. Linear regression analyses were then performed of the immune cell types on the PGS in both the overall sample and a subgroup of older participants (>60 years).

While we did not find any significant associations between immune cell subtypes and ALS and AD PGS when controlling for the false discovery rate (FDR=0.05), we observed several nominally significant results (p<0.05) with consistent effect directions across strata. The strongest association was observed with CD57+ CD8+ early-memory T cells and ALS risk (p=0.006). Other immune cell subtypes associated with ALS risk included PD-1+ CD8+ and CD57+ CD4+ early-memory T cells, non-classical monocytes, and myeloid dendritic cells. For AD, naïve CD57+ CD8+ T cells, and mature NKG2A+ natural killer cells showed nominally significant associations.

We did not observe immune cell changes in individuals with high genetic risk for ALS or AD, suggesting immune alterations may arise later in disease progression. Additional studies are required to validate our nominally significant findings.
Environmental and social impact assessment in healthcare business planning: a national survey of NHS trusts in England
Authors: Takahashi Haruna , Kudsk-Iversen Søren
Published: November 2024

Background

Decision-making in healthcare should include considerations for its environmental and social consequences as well as clinical and financial. Business cases represent projects which are likely to have particularly high impact, in which performing an Environmental and Social Impact Assessment may reduce negative effects. The practice of assessing these impacts is not mandatory, therefore our aim was to determine to what extent environmental and social considerations are incorporated into business planning across NHS trusts in England. We also set out to identify examples of good practice, common challenges and possible solutions to overcome these.

Methods

We conducted a cross-sectional survey across trusts in NHS England to capture current practice. This was carried out online between April and July 2024.

Results

Ninety seven out of 210 trusts (46%) responded to the survey. Thirty two currently assess the environmental and/or social impact of their business cases and 25 are in the process of doing so, illustrating a growing practice. There is significant variation between trusts in terms of content, format and process of the assessment.

Discussion

This was the first study to portray not only whether and how environmental and social impacts are assessed in NHS business planning, but also the barriers and potential solutions in embedding this assessment. The variation in practice signifies heterogeneity of NHS trusts and there is unlikely to be a single tool that would suit every organisation. An impact assessment process with a clear purpose, that reflects organisational values, and is supported by multidisciplinary expertise is likely to be more meaningful. We include an Environmental and Social Impact Assessment tool for our trust, which has been developed based on the learning points from this study and modified to our trust’s needs, as an example.
Explainable machine learning to identify patients at risk of developing hospital acquired infections
Authors: Creagh Andrew P. , Pease Tom , Ashworth Philip , Bradley Lloyd , Duport Sophie
Published: November 2024

Hospital-acquired infections (HAIs) contribute to increased mortality rates and extended hospital stays. Patients with complex neurological impairments, secondary to conditions such as acquired brain injury or progressive degenerative conditions are particularly prone to HAIs and often have the worst resulting clinical outcomes and highest associated cost of care. Research indicates that the prompt identification of such infections can significantly mitigate mortality rates and reduce hospitalisation duration. The current standard of care for timely detection of HAIs for inpatient acute and post-acute care settings in the UK is the National Early Warning Score v02 (NEWS2). NEWS2, despite its strengths, has been shown to have poor prognostic accuracy for specific indications, such as infections. This study developed a machine learning (ML) based risk stratification tool, utilising routinely collected patient electronic health record (EHR) data, encompassing over 800+ patients and 400k+ observations collected across 4-years, aimed at predicting the likelihood of infection in patients within an inpatient care setting for patients with complex acquired neurological conditions. Built with a combination of historical patient data, clinical coding, observations, clinician reported outcomes, and textual data, we evaluated our framework to identify individuals with an elevated risk of infection within a 7-day time-frame, retrospectively over a 1-year “silent-mode” evaluation. We investigated several time-to-event model configurations, including manual feature-based and data-driven deep generative techniques, to jointly estimate the timing and risk of infection onset. We observed strong performance of the models developed in this study, achieving high prognostic accuracy and robust calibration from 72–6 hours prior to clinical suspicion of infection, with AUROC values ranging from 0.776–0.889 and well-calibrated risk estimates exhibited across those time intervals (IBS<0.178). Furthermore, by assigning model-generated risk scores into distinct categories (low, moderate, high, severe), we effectively stratified patients with a higher susceptibility to infections from those with lower risk profiles. Post-hoc explainability analysis provided valuable insights into key risk factors, such as vital signs, recent infection history, and patient age, which aligned well with prior clinical knowledge. Our findings highlight our framework’s potential for accurate and explainable insights, facilitating clinician trust and supporting integration into real-world patient care workflows. Given the heterogeneous and complex patient population, and our under-utilisation of the data recorded in routine clinical notes and lab reports, there are considerable opportunities for performance improvement in future research by expanding our model’s multimodal capabilities, generalisability, and additional model personalisation steps.
Feasibility Study on the Application of Transcranial Focused Ultrasound Stimulation in Ischemic Stroke Rehabilitation
Authors: Jung JeYoung , Cho Minjae , Lee Sekwang , Yoo Hyun-Joon , Lambon Ralph Matthew A. , Pyun Sung-Bom
Published: November 2024

Stroke is a leading cause of long-term neurological disability and death worldwide. Traditional neurorehabilitation methods result in full recovery for less than 15% of stroke patients, highlighting the need for innovative approaches. Low-intensity transcranial focused ultrasound stimulation (tFUS) has emerged as a promising non-invasive neuromodulation technique with high focality and deep tissue penetration. This study evaluates the feasibility, safety and efficacy of tFUS for motor rehabilitation in ischemic stroke patients. We conducted a single-group prospective pilot study involving two stroke patients who received tFUS targeting the motor cortex contralateral to the lesion site three times a week. Patients were evaluated using multiple clinical measures of motor function. Both patients showed improvements in the Fugl-Meyer Assessment upper extremity score, kinesthetic sensation, stereognosis score from the Nottingham Sensory Assessment, and the Modified Barthel Index score. Follow-up evaluations immediately and three weeks after stimulation indicated sustained motor function improvements. The results suggest that tFUS can effectively enhance motor recovery in stroke patients without adverse events. This study provides robust evidence supporting the potential of tFUS in stroke rehabilitation, opening new avenues for clinical application and research.
Botulinum Toxin Application for Treatment of Graft Vasospasm: A Reverse Translational Study
Authors: Atai Nadia A , Ravina Kristine , Sizdahkhani Saman , Rennert Robert C , Abedi Aidin , Kress Gavin , Fabris Federico , Nguyen Vincent , Louie Stan , Shin Laura , Asante Isaac , Hawes Debra A , Rossetto Ornella , Carey Jospeh , Russin Jonathan J
Published: November 2024

Vascular graft vasospasm is a lethal risk when using grafts for revascularization and reconstructive surgery. Revascularization is a treatment modality for ischemic diseases including Moyamoya disease that requires bypass surgery. Cerebrovascular graft transplantation carries a 5-10% risk of vasospasm, which can lead to devastating neurological sequelae. Here we report clinical outcomes associated with ex vivo botulinum toxin A (BoNT/A) treatment of arterial graft and provide reverse translational studies investigating the potential mechanisms of action of BoNT/A to reduce vasospasm. A retrospective review of the maintained database of patients undergoing surgery was performed for 63 patients. We used paired human vascular graft tissue for ex vivo BoNT/A studies to assess for spasmolytic downstream effectors; cleaved SNAP25, pMLC, pMYPT, ROCK1/2, and levels of catecholamines. We found that low-dose BoNT/A graft treatment is associated with 1) a reduction in clinical vasospasm (13.3%, p<0.05) without any identified safety concerns in patients, 2) an increase in arterial cleaved SNAP25, 3) reduced levels of pMLC and pMYPT, and 4) reduced levels of catecholamines. The mechanism of action leading to vascular relaxation is likely through pleiotropic vasodilatory pathways. The application of BoNT/A as a spasmolytic has potentially safe and broad applications across multiple surgical and scientific subspecialties.
Clinical Sentiment Analysis by Large Language Models Enhances the Prediction of Hepatorenal Syndrome in Decompensated Cirrhosis
Authors: Lai Mason , Fenton Cynthia , Rubin Jessica , Huang Chiung-Yu , Pletcher Mark , Lai Jennifer C. , Cullaro Giuseppe , Ge Jin
Published: November 2024

Background and Aims

Hepatorenal syndrome – Acute Kidney Injury (HRS-AKI) is a severe complication of decompensated cirrhosis that is challenging to predict. Sentiment analysis, a computational process of identifying and categorizing opinions and judgment expressed in text, may enhance traditional prediction methodologies based on structured variables. Large language models (LLMs), such as generative pretrained transformers (GPTs), have demonstrated abilities to perform sentiment analyses on non-clinical texts. We sought to determine if GPT-performed sentiment analysis could improve upon predictions using clinical covariates alone in the prediction of HRS-AKI.

Methods

Adult patients admitted to a single academic medical center with decompensated cirrhosis and AKI. We used a protected health information (PHI) compliant version of Microsoft Azure OpenAI GPT-4o to derive a sentiment score ranging from 0 to 1 for HRS-AKI, and conduct natural language processing (NLP) extraction of clinical terms associated with HRS-AKI in clinical notes. The area under the receiver operator curve (AUROC) was compared in logistic regression models incorporating structured variables (socio-demographics, MELD 3.0, hemodynamic parameters) with compared to without sentiment scores and NLP-extracted clinical terms.

Results

In our cohort of 314 participants, higher sentiment score was associated with the diagnosis of HRS-AKI (OR 1.33 per 0.1, 95% CI 1.02-1.79) in multivariate models. AUROC of the baseline model using structured clinical covariates alone was 0.639. With the addition of the GPT-4o derived sentiment score and clinical terms to structured covariates, the final model yielded an improved AUROC of 0.758 (p= 0.03).

Conclusions

Clinical texts contain large amounts of data that are currently difficult to extract using standard methodologies. Sentiment analysis and NLP-based variable derivation with GPT-4o in clinical application is feasible and can improve the prediction of HRS-AKI over traditional modeling methodologies alone.
Age of menopause and dementia risk in 10,832 women from the Swedish Twin Registry
Authors: Saelzler Ursula G. , Sundermann Erin E. , Foret Janelle T. , Gatz Margaret , Karlsson Ida K. , Panizzon Matthew S.
Published: November 2024

INTRODUCTION

An earlier age of menopause (AOM) is hypothesized to increase vulnerability to the neuropathological processes of dementia which begin in midlife.

METHODS

We tested this hypothesis in a sample of 10,832 women from the Swedish Twin Registry, stratified by menopause etiology. Survival models showed that a U-shaped association was present for women whose menopause occurred spontaneously. Sensitivity analyses conducted in hormone naïve,APOEε4+ and AOM restricted subsamples showed largely analogous patterns of results.

DISCUSSION

Supporting conclusions from basic research, our results suggest that estrogens (proxied here by AOM) interact with several biological pathways mediating dementia disease processes. In line with trends in hormone research across the past century, our findings challenge the oversimplified ’more-is-better’ perspective on hormone exposure. Specifically, the non-linear association we observed between AOM and dementia risk points to the involvement of distinct and interacting biological mechanisms beyond just estrogen levels.
HELMET: A Hybrid Machine Learning Framework for Real-Time Prediction of Edema Trajectory in Large Middle Cerebral Artery Stroke
Authors: Phillips Ethan , O’Donoghue Odhran , Zhang Yumeng , Tsimpos Panos , Mallinger Leigh Ann , Chatzidakis Stefanos , Pohlmann Jack , Du Yili , Kim Ivy , Song Jonathan , Brush Benjamin , Smirnakis Stelios , Ong Charlene J , Orfanoudaki Agni
Published: November 2024

Malignant cerebral edema occurs when brain swelling displaces and compresses vital midline structures within the first week of a large middle cerebral artery stroke. Early interventions such as hyperosmolar therapy or surgical decompression may reverse secondary injury but must be administered judiciously. To optimize treatment and reduce secondary damage, clinicians need strategies to frequently and quantitatively assess the trajectory of edema using updated, relevant information. However, existing risk assessment tools are limited by the absence of structured records capturing the evolution of edema and typically estimate risk at a single time point early in the admission, therefore failing to account for changes in variables over the following hours or days. To address this, we developed and validated dynamic machine learning models capable of accurately predicting the severity of midline structure displacement, an established indicator of malignant edema, in real-time. Our models can provide updated estimations as frequently as every hour, using data from structured time-varying patient records, radiographic text, and human-curated neurological characteristics. Our work resulted in two novel multi-class classification models, collectively named Hybrid Ensemble Learning Models for Edema Trajectory (HELMET), predicting the progression of midline shift over 8-hour (HELMET-8) and 24-hour windows (HELMET-24), respectively. HELMET combines transformer-based large language models with supervised ensemble learning, demonstrating the value of merging human expertise and multimodal health records in developing clinical risk scores. Both models were trained on a retrospective cohort of 15,696 observations from 623 patients hospitalized with large middle cerebral artery ischemic stroke and were externally validated using 3,713 observations from 60 patients at a separate hospital system. Our HELMET models are accurate and generalize effectively to diverse populations, achieving a cross-validated mean area under the receiver operating characteristic score of 96.6% in the derivation cohort and 92.5% in the external validation cohort. Moreover, our approach provides a framework for developing hybrid risk prediction models that integrate both human-extracted and algorithm-derived multi-modal inputs. Our work enables accurate estimation of complex, dynamic, and highly specific clinical targets, such as midline shift, in real-time, even when relevant structured information is limited in electronic health record databases.
Genome-wide association study of varenicline-aided smoking cessation
Authors: Coley Kayesha , Wang Qingning , Packer Richard , John Catherine , Abner Erik , Reis Kadri ,   Estonian Biobank Research Team, Bedair Khaled F. , Srinivasan Sundararajan , Paciga Sara , Hyde Craig , Free Robert C. , Reeve Nicola F. , Shepherd David J. , Esko Tõnu , Palmer Colin , Pearson Ewan , Malarstig Anders , Tobin Martin D. , Batini Chiara
Published: November 2024

Introduction

Varenicline is an α4β2nicotinic acetylcholine receptor partial agonist with the highest therapeutic efficacy of any pharmacological smoking cessation aid and a 12-month cessation rate of 26%. Genetic variation may be associated with varenicline response, but to date no genome-wide association studies of varenicline response have been published.

Methods

In this study, we investigated the genetic contribution to varenicline effectiveness using two electronic health record-derived phenotypes. We defined short-term varenicline effectiveness (SVE) and long-term varenicline effectiveness (LVE) by assessing smoking status at 3 and 12 months, respectively, after initiating varenicline treatment. In Stage 1, comprising five European cohort studies, we tested genome-wide associations with SVE (1,405 cases, 2,074 controls) and LVE (1,576 cases, 2,555 controls), defining sentinel variants (the most strongly associated variant within 1 megabase) withp-value <5×10−6to follow up in Stage 2. In Stage 2, we tested association between sentinel variants and comparable smoking cessation endpoints in varenicline randomised controlled trials. We subsequently meta-analysed Stages 1 and 2.

Results

No variants reached genome-wide significance in the meta-analysis. In Stage 1, 10 sentinel variants were associated with SVE and five with LVE at a suggestive significance threshold (p-value <5×10−6). None of these sentinels were previously implicated in varenicline-aided smoking cessation or in genetic studies of smoking behaviour.

Conclusions

We provide initial insights into the biological underpinnings of varenicline-aided smoking cessation, through implicating genes involved in various processes, including gene expression, cilium assembly and early-stage development.

Implications

Leveraging electronic health records, we undertook the largest genetic study of varenicline-aided smoking cessation to date, and the only such study to test genome-wide associations. We showed distinct genetic variants associated (p-value <5×10−6) with varenicline-aided smoking cessation which implicate diverse cellular functions, including transcriptional regulation, RNA modification and cilium assembly. These provide insights which, if independently corroborated, will improve understanding of varenicline response. The growing availability of biobank resources with genetic and varenicline response data will provide future opportunities for larger studies using the approach we developed.
Parental and individual socioeconomic position show distinct associations with trajectories of diet quality across adolescence and early adulthood
Authors: Rousham Oscar , Braune Tanya , Mori Trevor A , Beilin Lawrence J , Winpenny Eleanor M
Published: November 2024

Background

Adolescence and early adulthood is an important period for the development of health behaviours and diet quality, which may persist through adult life. Socioeconomic position (SEP) during early adulthood shows associations with inequalities in diet quality and cardiometabolic health later in adulthood, yet little is known about how dietary inequalities develop during adolescence and early adulthood. This study aimed to identify distinct diet quality trajectories observed across adolescence and early adulthood; and explore the association between parental and individual SEP and these trajectories.

Methods

The Raine Study is a large multigenerational cohort (n=1984) based in Western Australia. Dietary data was self-reported at five time points from ages 14 to 27 years. Growth mixture modelling was used to identify distinct diet quality trajectories based on Dietary Approaches to Stop Hypertension (DASH) diet scores. Multinomial logistic regression was used to determine the associations of parental SEP (maternal education level; and household income at age 14) and individual SEP (school leaving age) with diet quality trajectory membership.

Results

Three diet quality trajectories were identified: consistently low quality (41%), low-to-high quality (42%), and consistently high quality (16%). The ‘low-to-high’ diet quality trajectory showed a steep increase in diet quality from ages 14 to 20 years. Higher parental SEP was associated with a higher diet quality trajectory. After adjusting for parental SEP, leaving school before year 11 remained strongly associated with the low diet quality trajectory.

Conclusion

Our study demonstrates the development of dietary inequalities across adolescence and early adulthood, highlighting the importance of emerging individual SEP, in addition to parental SEP in shaping this. Interventions to improve diet quality in early adulthood are particularly needed among those who leave education at a young age.
Distinct rates of VUS reclassification are observed when subclassifying VUS by evidence level
Authors: Bennett Gwendolyn , Karbassi Izabela , Chen Wenjie , Harrison Steven M. , Lebo Matthew S. , Meng Linyan , Nagan Narasimhan , Rigobello Robert , Rehm Heidi L.
Published: November 2024

Purpose

Genetic testing commonly yields a plethora of variants of uncertain significance (VUS) that can lead to ongoing uncertainty for patients and their caregivers. While all VUS hold uncertainty, some VUS have more evidence in support of pathogenicity while others have more evidence of a benign role. Sharing these nuances can help guide the investment in follow-up clinical and research investigations and may, at times, influence medical decision-making despite appreciated uncertainty.

Methods

Four clinical laboratories have been subclassifying VUS to help prioritize investigation and guide reporting decisions. Each laboratory developed a distinct approach for how these subclasses are used in their laboratories and, in some cases, displayed on reports. We examined the composition of each laboratory’s VUS subclasses and the likelihood variants from each subclass were reclassified towards pathogenic or benign.

Results

We found that variants in the lowest subclass of VUS were never reclassified as likely pathogenic (LP) or pathogenic (P), while those in the highest subclass were much more likely to be reclassified as P/LP.

Conclusion

Given that forthcoming professional guidance in variant classification will advise the use of VUS subclasses, the experience of our laboratories in using VUS subclasses can inform future practices.
Product Features Used to Promote Top-selling Cannabis Vape Products in An Online Retail Environment
Authors: Chen-Sankey Julia , Capria Kathryn La , Meng Siyan , Mazzeo Rosanna , Vijayakumar Neha , Padon Alisa A. , Wagoner Kimberly G. , Moran Meghan B. , Rossheim Matthew , Berg Carla , Jackson Kristina M.
Published: November 2024

Introduction

Exposure to commercial marketing of cannabis vape products (CVPs) may encourage CVP use, yet little is known about how these products are marketed. This study examined marketing descriptions of CVPs’ functions and benefits in an online retail environment.

Methods

Product descriptions from a sample of 343 CVPs from 78 top-selling cannabis brands in 2023 were obtained from a large cannabis e-commerce website. Each description was thematically coded based on the promoted product features.

Results

The most frequently mentioned product feature was flavor profile and sensation (74.1%), including general and specific flavor descriptors (e.g., fruit flavors) and sensory experiences (e.g., sweet, spicy). Psychoactive effects were noted in 47.5% of the descriptions, detailing potency or effects such as feeling “high,” “stoned,” or “buzzed.” Product quality, such as “purity,” “natural,” or “organic,” was mentioned in 42.3% of the descriptions. Other product benefits described included mood enhancement (33.8%), reduced harm (24.2%), relaxation/tension reduction (23.9%), therapeutic effects (18.4%), focus/creativity (16.6%), convenience/discreetness (11.1%), socialization enhancement (6.7%), and physical performance enhancement (6.1%).

Discussion

Some frequently promoted product features of CVPs, such as flavor and sensation and psychoactive effects, may particularly appeal to younger consumers for non-medical use. Meanwhile, attributes surrounding high product quality and reduced harm may reduce individuals’ perceived risks of CVP use and may violate state restrictions on therapeutic claims. Additional research assessing the influence of exposure to marketed product features on product perceptions and use behaviors among priority populations is needed to inform regulations and enforcement.
Vaccination coverage trends in European Union from 1980 to 2020: A joinpoint Regression Analysis
Authors: Causio FA , Villani L , Mariani M , Pastorino R , De Waure C , Ricciardi W , Boccia S
Published: November 2024

Vaccination coverage trends across European Union (EU) countries have shown concerning variations in recent years. This study aims to analyze vaccination coverage trends for seven key vaccinations across all EU member states from 1980 to 2020. Data from the WHO/UNICEF Estimates of National Immunization Coverage (WUENIC) dataset were analyzed using joinpoint regression models to identify significant changes in vaccination coverage trends. Seven vaccination indicators were examined: DTP-3, HEPB-3, HIB-3, MCV-1, PCV-3, POL-3, and RCV-1. Trends were categorized as positive or negative and significant or not significant, based on Annual Percent Change (APC) calculations. Analysis of 180 joinpoint regressions revealed a predominantly downward trend in vaccination coverage across the EU. 51.7% showed negative performance, while only 37.8% showed positive performance. Only 8 countries (29.6%) demonstrated increased coverage in at least four indicators, while 14 countries (51.8%) showed reduced coverage. The study reveals a concerning decline in vaccination coverage across most EU countries. The findings suggest that mandatory vaccination policies may contribute to maintaining higher coverage rates, though multiple factors influence vaccination uptake, including political, social, and educational determinants.
Prevalence and Determinants of Academic Bullying Among Junior Doctors in Sierra Leone
Authors: Jalloh Fatima , Bah Ahmed Tejan , Kanu Alieu , Jalloh Mohamed Jan , Agboola Kehinde , Faulkner Monalisa M.J. , Foray Foray M. , Abiri Onome T. , Sillah Arthur , Lebbie Aiah , Jalloh Mohamed B.
Published: November 2024

Background

Academic bullying among junior doctors—characterized by repeated actions that undermine confidence, reputation, and career progression—is associated with adverse consequences for mental health and professional development. We aimed to investigate the prevalence and determinants of academic bullying among junior doctors in Sierra Leone.

Methods

We conducted a cross-sectional survey of 126 junior doctors at the University of Sierra Leone Teaching Hospitals Complex (USLTHC) in Freetown between January 1 and March 30, 2024. Participants were selected through random sampling. Data were collected using a semi-structured, self-administered questionnaire and analyzed with descriptive statistics and multivariable logistic regression.

Results

Of the 126 participants (61.1% male; mean age 31.9 years), 86 (68.3%) reported experiencing academic bullying. Among those, 54.6% experienced it occasionally and 35.2% very frequently. The most common forms were unfair criticism (73.3%), verbal aggression (66.3%), and derogatory remarks (47.7%). Consultants and senior doctors were the main perpetrators, with incidents primarily occurring during ward rounds, clinical meetings, and academic seminars. No statistically significant predictors of bullying were found for gender (odds ratio [OR] 2.07, 95% CI 0.92–4.64; p=0.08) or less than two years of practice (OR 0.30, 95% CI 0.05–1.79; p=0.19).

Conclusion

Academic bullying is pervasive among junior doctors at USLTHC, with significant implications for their mental health and professional development. Urgent implementation of comprehensive strategies—including culturally sensitive policies, targeted training programs, confidential reporting mechanisms, and leadership development—is essential to address this issue. Promoting ethical leadership and fostering a culture of respect may mitigate incivility and burnout, enhancing the work environment for junior doctors.
Development of the Kunonga Framework for Extending Approaches in Health Inequality and Inequity Evidence Syntheses
Authors: Kunonga Tafadzwa Patience , Addis Pauline , Johnson Eugenie Evelynne , Bower Peter , Hanratty Barbara , Craig Dawn
Published: November 2024

Health inequalities and inequities are shaped by intersecting factors and life-course experiences, yet current evidence synthesis methods often lack the depth to capture these dimensions. The Kunonga Framework was developed through a three-phase approach to address these gaps, enhancing methodologies to better focus on health inequality and inequity in research. In the first phase, a systematic review identified key gaps in current inequality/inequity considerations. The second phase involved expert Key Informant Interviews, refining the frameworks design. Finally, findings from both phases informed the proposed framework, offering practical recommendations for integrating inequality and inequity considerations across evidence synthesis processes. At the protocol stage, reviewers are advised to explicitly define health inequality and inequity, select frameworks like PROGRESS-Plus, and develop a logic model to map pathways between social determinants, life-course factors, and health outcomes. During data extraction, organising data by demographic, socioeconomic, and healthcare factors is recommended to detect patterns of inequality and inequity. In analysis, an intersectionality matrix and life-course analysis will help reveal overlapping social determinants and cumulative effects on health outcomes. The Kunonga Framework offers a structured approach to embedding intersectional, life-course perspectives in evidence synthesis, supporting policymakers and researchers in designing more effective, inequality/inequity-focused interventions.
Risk-averse optimization of genetic circuits under uncertainty
Authors: Kobiela Michal , Oyarzún Diego A. , Gutmann Michael U.
Published: November 2024

Synthetic biology aims to engineer biological systems with specified functions. This requires navigating an extensive design space, which is challenging to achieve with wet lab experiments alone. To expedite the design process, mathematical modelling is typically employed to predict circuit functionin silicoahead of implementation, which when coupled with computational optimization can be used to automatically identify promising designs. However, circuit models are inherently inaccurate which can result in sub-optimal or non-functionalin vivoperformance. To mitigate this issue, here we propose to combine Bayesian inference, Thompson sampling, and risk management to find optimal circuit designs. Our approach employs data from non-functional designs to estimate the distribution of the model parameters and then employs risk-averse optimization to select design parameters that are expected to perform well given parameter uncertainty and biomolecular noise. We illustrate the approach by designing robust adaptation circuits and genetic oscillators with a prescribed frequency. The proposed approach provides a novel methodology for the design of robust genetic circuitry.
A Chaperonin Complex Regulates Organelle Proteostasis in Malaria Parasites
Authors: Tissawak Amanda , Rosin Yarden , Shahar Michal , Trabelsi Nirit , Furman-Schueler Ora , Johnson Steven M , Florentin Anat
Published: November 2024

The apicoplast ofPlasmodiumparasites serves as a metabolic hub that synthesize essential biomolecules. Like other endosymbiotic organelles, 90% of the apicoplast proteome is encoded by the cell nucleus and transported to the organelle. Evidence suggests that the apicoplast has minimal control over the synthesis of its proteome and therefore it is unclear how organelle proteostasis is regulated. Here, we identified and investigated a large and conserved chaperonin (CPN) complex with a previously unknown function. Using genetic tools, we demonstrated that its main subunit, CPN60, localizes to the apicoplast and is essential for parasite’s asexual replication due to its organellar functions. Unlike its close orthologues in other prokaryotic and eukaryotic cells, CPN60 is not upregulated during heat shock (HS) and does not affect HS response in the parasite. Instead, we found that it is directly involved in proteostasis through interaction with a proteolytic complex called Clp (caseinolytic protease) that degrades organellar proteins in a regulated manner. We showed that CPN60 physically binds both the active and inactive forms of the Clp complex, and manipulates its stability. Using computational prediction tools, we modeled the interaction between these two large complexes to understand how a stable interface is attained. Finally, we screened a library of inhibitors for the bacterial CPN60 orthologue GroEL, in order to test the potential of chaperonin inhibition as antimalarial. These inhibitors demonstrated an anti-Plasmodialactivity that was not restricted to apicoplast function. Taken together, this work reveals how balanced activities of proteolysis and refolding safeguard the apicoplast proteome.

Significance Statement

The cell of the human malaria parasite,Plasmodium falciparum, has a unique organelle called the apicoplast that produces essential metabolites. Most apicoplast proteins are encoded by the nucleus and it is unclear how the organelle maintains a stable proteome. Here, we address the question of organelle proteostasis by investigating the function of a large chaperonin complex. We show that it is essential for parasite’s viability due to its role in apicoplast functions. We demonstrate that it binds and stabilizes another large proteolytic complex, and further explore its potential as a drug target. This study reveals how balanced refolding and proteolysis safeguard the apicoplast proteome and opens a new avenue for antimalarial drug discovery.
ConsolidatingUlvafunctional genomics: Gene editing and new selection systems
Authors: Blomme Jonas , Arraiza Ribera Júlia , Clerck Olivier De , Jacobs Thomas B.
Published: November 2024

The green seaweedUlva compressais a promising model for functional biology. In addition to historical research on growth and development, -omics data and molecular tools for stable transformation are available. However, more efficient tools are needed to study gene function. Here, we expand the molecular toolkit forUlva. We screened the survival ofUlvaand its mutualistic bacteria on 14 selective agents and establish that Blasticidin deaminases (BSD or bsr) can be used as selectable markers to generate stable transgenic lines. We show that Cas9 and Cas12a RNPs are suitable for targeted mutagenesis and can generate genomic deletions up to 20 kb using the marker gene ADENINE PHOSPHORIBOSYLTRANSFERASE (APT). We demonstrate that targeted insertion of a selectable marker via homology-directed repair or co-editing with APT is possible for non- marker genes. We evaluated 31 vector configurations and found that bicistronic fusion of Cas9 to a resistance marker or incorporation of introns in Cas9 led to the most mutants. We used this to generate mutants in three non-marker genes using a co-editing strategy. This expanded molecular toolkit now enables us to reliably make gain- and loss-of-function mutants, additional optimizations will be necessary to allow for vector-based multiplex genome editing inUlva.
Small molecule inhibitor combination treatment effectively represses global B-cell signaling in diffuse large B-cell lymphoma
Authors: Witmond Melde , Bollen Babet , Heijmans Pam , van Spriel Annemiek , van Buggenum Jessie A.L.G. , Huck Wilhelm
Published: November 2024

Cells sense their environment via signaling networks and malignant cells often hijack signaling pathways for their growth, which complicates defining the effects of drugs. Here, we map the state of the signaling network of B-cell lymphoma cells via simultaneous quantification of 111 (phospho-)proteins. We demonstrate that the B-cell signaling network can be disrupted with specific clinical small molecule inhibitors (iBTK, iSYK, iNFκB), thereby inducing a repressed state of the network. Principal component analysis identifies how the three inhibitors work along subtly different repression axes through the signaling state landscape. Finally, we observe that 1 μM combination treatment with all three inhibitors is more effective in inducing the repressed state than 10 μM of the single inhibitors. These results emphasize that cellular signaling occurs in complex networks, and underscore how quantification of the signaling state landscape provides insights into how combination drug treatments can bring cells in a desired network state.
A blueprint for biomolecular condensation driven by bacterial microcompartment encapsulation peptides
Authors: Trettel Daniel S. , López Cesar A. , Rodriguez Eliana , Marrone Babetta L. , Gonzalez-Esquer Cesar Raul
Published: November 2024

Bacterial microcompartments (BMC) are protein organelles with diverse metabolic capabilities. Their functional diversity is determined by an enzymatic core that is sequestered within a structurally conserved protein shell architecture. Segregation of protein cargo into the BMC is enabled by encapsulation peptides (EPs), which are short helical domains fused to core proteins through a disordered linker. Here, we investigate how EPs drive multicomponent cargo assembly into biomolecular condensates.In vitroexperiments supported by molecular dynamics simulations demonstrate the importance of both conserved hydrophobic packing and electrostatic interactions in stabilizing trimeric EP bundles. Topological rearrangements of EP domains can drive programmable liquid-or gel-like partitioningin vitroandin vivo. This partitioning is found to be EP-specific, modular and can co-assemble at least three fluorescent reporters. In summary, we describe the molecular features necessary to drive biomolecular condensation using a widespread peptide tag. This work can serve as a blueprint for implementing EP biotechnology across diverse applications.