bluuebunny/crossref_metadata_2025 huggingface dataset:
GEMS: A Generalizable GNN Framework For Protein-Ligand Binding Affinity Prediction Through Robust Data Filtering and Language Model Integration
Authors: Graber David , Stockinger Peter , Meyer Fabian , Mishra Siddhartha , Horn Claus , Buller Rebecca
Published: December 2024

The field of computational drug design requires accurate scoring functions to predict binding affinities for protein-ligand interactions. However, train-test data leakage between the PDBbind database and the CASF benchmark datasets has significantly inflated the performance metrics of currently available deep-learning-based binding affinity prediction models, leading to overestimation of their generalization capabilities. We address this issue by proposing PDBbind CleanSplit, a training dataset curated by a novel structure-based filtering algorithm that eliminates train-test data leakage as well as redundancies within the training set. Retraining the current best-performing model on CleanSplit caused its benchmark performance to drop to uncompetitive levels, indicating that the performance of existing models is largely driven by data leakage. In contrast, our graph neural network model for efficient molecular scoring (GEMS) maintains high benchmark performance when trained on CleanSplit. Leveraging a sparse graph modeling of protein-ligand interactions and transfer learning from language models, GEMS is able to generalize to strictly independent test datasets.
Chromosome engineering points to thecis-acting mechanism of chromosome arm-specific telomere length setting and robustness of plant phenotype, chromatin structure and gene expression
Authors: Helia Ondřej , Matúšová Barbora , Havlová Kateřina , Hýsková Anna , Lyčka Martin , Beying Natalja , Puchta Holger , Fajkus Jiří , Fojtová Miloslava
Published: December 2024

The study investigates the impact of targeted chromosome engineering on telomere dynamics, chromatin structure, gene expression, and phenotypic stability inArabidopsis thaliana. Using precise CRISPR/Cas-based engineering, reciprocal translocations of chromosome arms were introduced between non-homologous chromosomes. The subsequent homozygous generations of plants were assessed for phenotype, transcriptomic changes and chromatin modifications near translocation breakpoints, and telomere length maintenance. Phenotypically, translocated lines were indistinguishable from wild-type plants, as confirmed through morphological assessments and principal component analysis. Gene expression profiling detected minimal differential expression, with affected genes dispersed across the genome, indicating negligible transcriptional impact. Similarly, ChIPseq analysis showed no substantial alterations in the enrichment of key histone marks (H3K27me3, H3K4me1, H3K56ac) near junction sites or across the genome. Finally, bulk and arm-specific telomere lengths remained stable across multiple generations, except for minor variations in one translocation line. These findings highlight the remarkable genomic and phenotypic robustness ofA. thalianadespite large-scale chromosomal rearrangements. The study offers insights into thecis-acting mechanisms underlying chromosome arm-specific telomere length setting and establishes the feasibility of chromosome engineering for studies of plant genome evolution and crop improvement strategies.

Significance statement

This study demonstrates the robustness ofArabidopsis thalianain maintaining telomere stability, chromatin integrity, and wild-type phenotype despite large-scale chromosomal translocations. It underscores the potential of chromosome engineering in advancing genome evolution research and crop improvement, contributes to a deeper understanding of genome dynamics, and opens new avenues for precision breeding in plants.
Protein language model pseudolikelihoods capture features of in vivo B cell selection and evolution
Authors: van Ginneken Daphne , Samant Anamay , Daga-Krumins Karlis , Agrafiotis Andreas , Kladis Evgenios , Reddy Sai T. , Yermanos Alexander
Published: December 2024

B cell selection and evolution play crucial roles in dictating successful immune responses. Recent advancements in sequencing technologies and deep-learning strategies have paved the way for generating and exploiting an ever-growing wealth of antibody repertoire data. The self-supervised nature of protein language models (PLMs) has demonstrated the ability to learn complex representations of antibody sequences and has been leveraged for a wide range of applications including diagnostics, structural modeling, and antigen-specificity predictions. PLM-derived likelihoods have been used to improve antibody affinities in vitro, raising the question of whether PLMs can capture and predict features of B cell selection in vivo. Here, we explore how general and antibody-specific PLM-generated sequence pseudolikelihoods (SPs) relate to features of in vivo B cell selection such as expansion, isotype usage, and somatic hypermutation (SHM) at single-cell resolution. Our results demonstrate that the type of PLM and the region of the antibody input sequence significantly affect the generated SP. Contrary to previous in vitro reports, we observe a negative correlation between SPs and binding affinity, whereas repertoire features such as SHM, isotype usage, and antigen specificity were strongly correlated with SPs. By constructing evolutionary lineage trees of B cell clones from human and mouse repertoires, we observe that SHMs are routinely among the most likely mutations suggested by PLMs and that mutating residues have lower absolute likelihoods than conserved residues. Our findings highlight the potential of PLMs to predict features of antibody selection and further suggest their potential to assist in antibody discovery and engineering.

Key points

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In contrast to previous in vitro work (Hie et al., 2024), we observe a negative correlation between PLM-generated sequence pseudolikelihood (SP) and binding affinity. This contrast can be explained by the inherent antibody germline bias posed by PLM training data and the difference between in vivo and in vitro settings.

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Our findings also reveal a considerable correlation between SPs and repertoire features such as the V-gene family, isotype, and the amount of somatic hypermutation (SHM). Moreover, labeled antigen-binding data suggested that SP is consistent with antigen-specificity and binding affinity.

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By reconstructing B cell lineage evolutionary trajectories, we detected predictable features of SHM using PLMs. We observe that SHMs are routinely among the most likely mutations suggested by PLMs and that mutating residues have lower absolute likelihoods than conserved residues.

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We demonstrate that the region of antibody sequence (CDR3 or full V(D)J) provided as input to the model, as well as the type of PLM used, influence the resulting SPs.
Effect of OASL on oxaliplatin-induced immunogenic cell death in gastric cancer via the cGAS-STING signaling pathway
Authors: Zhang Lingling , Liu Yi , Yang Haiying , Liu Luguang , Wang Longgang , Chai Jie , Zhao Weizhu , Sun Dong
Published: December 2024

This study investigates the role of 2’-5’ oligoadenylate synthetase-like (OASL) in Oxaliplatin (OXA)-induced immunogenic cell death (ICD) in Gastric cancer (GC) cells through the cGAS-STING signaling pathway. Knockdown of OASL enhanced ICD expression, while overexpression had the opposite effect. RNA sequencing of OASL-knockdown and control GC cells treated with OXA revealed significant enrichment of the second messenger signaling pathway (cGAMP). cGAMP could directly activate STING as a second messenger, and cGAS was a key synthetic enzyme upstream of cGAMP. Next, the role of OASL in OXA-induced ICD in GC cells was validated through the cGAS-STING signaling pathway. The Co-IP and immunofluorescence results confirmed that the OASL and cGAS proteins can bind directly. Further research validated these findings in vivo. Results show that OASL regulates OXA-induced ICD in GC cells via the cGAS-STING pathway, impacting chemosensitivity. The findings suggest new targets and strategies for improving GC therapy by modulating OASL expression to enhance OXA sensitivity through immunogenic mechanisms.
Discovery of molecular glues that bind FKBP12 and novel targets using DNA-barcoded libraries
Authors: Zandi Trevor A. , Romanowski Michael J. , Viscomi Jessica S. , Tan Zher Yin , Tong Bingqi , Bonazzi Simone , Zécri Frédéric J. , Schreiber Stuart L. , Michaud Gregory A.
Published: December 2024

Molecular glues are small molecules that engage their target and presenter proteins cooperatively. FKBP12 molecular glues (FK506 and rapamycin) were discovered several decades ago and have been used clinically, but our understanding of the breadth of FKBP12 molecular glues and targets has yet to be fully revealed. To identify novel targets of FKBP12 molecular glues, we constructed and screened a multi-million-member non-macrocyclic FKBP12-ligand DNA-encoded library using 25 structurally distinct proteins. Synthesis and validation of selected hits in biophysical and cell-based assays confirm FKBP12-dependent molecular-glue recruitment to bromodomain-containing protein 9 (BRD9) and quinoid dihydropteridine reductase (QDPR). One glue showed no measurable binding to QDPR alone but had appreciable binding in the presence of FKBP12 using either purified proteins or intact cells. The sites of recruitment were characterized with mutational analysis, competition-based methods and X-ray crystallography. The results of this study confirm that FKBP12-binding DELs can yield novel molecular glues generating highly selective FKBP12-target protein interactions.
Clonally expanded IgG antibody-secreting cells preferentially target influenza nucleoprotein following homologous and heterologous infections
Authors: Agrafiotis Andreas , Kuhn Raphael , Panetti Camilla , Venerito Marco , Phandee Hathaichanok , Stalder Lucas , Shlesinger Danielle , D’Arcy Vittoria Martinolli , Hong Kai-Lin , van Ginneken Daphne , Genovese Alessandro , Joller Nicole , Oxenius Annette , Reddy Sai T. , Yermanos Alexander
Published: December 2024

Infection with influenza virus remains a significant global health concern due to its ability to acquire mutations at key antigenic sites to escape antibody recognition. While germinal center (GC) and memory B cells have been well studied following influenza infection, the clonal dynamics of antibody secreting cells (ASCs), particularly those within the bone marrow (BM) niche that are responsible for serum immune protection, remain poorly understood. Here, we combine single-cell RNA (scRNA) and B cell receptor (BCR) sequencing to characterize individual ASCs following various Influenza exposure histories. We find that BM repertories are populated by highly expanded and class-switched ASCs following Influenza infection with similar transcriptional and repertoire characteristics regardless of homologous or heterologous infection histories. By combining single-cell analysis with monoclonal antibody expression and characterization, we find that a large proportion of the expanded IgG-, but not IgA-, ASC repertoire demonstrates specificity to influenza nucleoprotein (NP). Together, our data reveal the complex relationship between BM ASC repertoires, mucosal humoral immune responses, and BCR antigen specificity during influenza infection.
PathoFact 2.0: An Integrative Pipeline for Predicting Antimicrobial Resistance Genes, Virulence Factors, Toxins and Biosynthetic Gene Clusters in Metagenomes
Authors: Sunyer Júlia Ortís , Delgado Luis F. , Hickl Oskar , Laczny Cedric C. , May Patrick , Wilmes Paul
Published: December 2024

Antimicrobial resistance genes (ARGs) and virulence factors (VFs) are central contributors to the global health crisis surrounding drug-resistant infections. PathoFact, a bioinformatics pipeline introduced in 2021, provides insights into ARGs, VFs, and bacterial toxins from metagenomic data. However, recent advancements in bioinformatics highlight the need for an updated version of PathoFact. We introduce PathoFact 2.0, an enhanced pipeline for improved ARG, VF, and toxin prediction. Key updates include an updated machine learning (ML) model for VF identification, a new ML model for toxin identification, expanded hidden Markov model profiles, and the antiSMASH 7.0 integration for predicting biosynthetic gene clusters. These upgrades make PathoFact 2.0 a more powerful, user-friendly platform for predicting microbiome-based pathogenicity and resistance, offering a crucial tool for better understanding and addressing the challenges posed by antimicrobial resistance and infectious diseases.

Availability and Implementation

PathoFact 2.0 is available for download athttps://gitlab.lcsb.uni.lu/ESB/PathoFact2/.
Apocarotenoid signaling regulates meristem activity and shapes shoot and root lateral organ formation inArabidopsis
Authors: Sierra Julio , Escobar-Tovar Lina , Napsucialy-Mendivil Selene , Oltehua-López Omar , Dubrovsky Joseph G. , McQuinn Ryan P. , Leon Patricia
Published: December 2024

Plant carotenoids are precursors to phytohormones and signaling molecules, playing critical roles in plant development, an emerging area of research. This study investigates the function of the undefined apocarotenoid ACS1 signal in modulating plant development, particularly its impact on the morphologenesis of lateral organs and apical meristems. By modulating ACS1 levels under varying light conditions, we demonstrate its dynamic role in leaf and root development. Notably the characteristic radial leaf morphology of theclb5mutant reverts to normal even days post-germination, demonstrating that ACS1 is not a toxic signal but rather a key component of a biogenic retrograde signaling pathway.

Transcriptomic analysis ofclb5seedlings at different post-germination stages underscores the critical role of ACS1 during specific developmental window. The expression profile of this mutant correlates with a proplastid stage, where even the expression of most of the genes involved in plastid biogenesis are downregulated. Furthermore, ACS1 disrupts the expression of diverse developmentally important genes, including those participating in auxin transport and signaling, leading to impaired meristem maintenance and inhibiting leaf expansion.

The effects of ACS1 extends beyond photosynthetic tissues, impacting shoot and apical root meristem organization. In particular, ACS1 affects columella cell pattering, disrupting normal gravitropic responses. These findings demonstrate that ACS1 dynamically regulates both leaf and root development, as well as meristem activity.

This study provides new insights into the role ofcis-carotenoids as retrograde signals, functioning very early in the plastid differentiation and emphasizes the significance of plastid retrograde signaling in plant growth and development.
Targeted neural stimulation congruent with immersive reality decreases neuropathic pain – a Randomized Controlled Trial
Authors: Aurucci Giuseppe Valerio , Gozzi Noemi , Wagner Markus , Preatoni Greta , Brunello Nicola , Secerovic Natalija , Zipser Carl Moritz , Raspopovic Stanisa
Published: December 2024

Background

Chronic neuropathic pain is a complex experience, posing a major challenge in personalizing its treatment. Present treatments consist of non-specific, standardized drugs that are often addictive, leaving many patients non-respondent and with significant side effects. Designing individualized therapies requires targeting the multidimensionality of pain and developing objective endpoints to demonstrate their effectiveness. Currently, non-pharmacological alternatives are emerging, such as neurostimulation and Virtual Reality (VR), activating pain relief via peripheral neuromodulation and attention modulation. Similarly to drugs, many neurostimulation approaches are unspecific, targeting areas near the pain site and disregarding the neural pathway of pain. Above all, neurostimulation and VR are yet to be evaluated as a combined synergistic intervention, particularly in a randomized controlled trial (RCT).

Methods and Findings

To this aim, we developed a targeted neurostimulation congruent with immersive VR platform providing a multisensory pain intervention through the synergistic application of somatotopic electro-tactile and visual stimuli. The endpoints included measuring sensory, neurophysiological (EEG), and self-reported indicators of pain. We tested the efficacy of the multisensory intervention against the control consisting of VR-only intervention on four consecutive intervention days in an RCT (N=18 neuropathic patients). The multisensory intervention resulted in a clinically significant reduction of pain (>50%), lasting up to one-week follow-up. The provided analgesic effect was statistically stronger compared to the VR-only control across treatment days and at follow-up. The clinically relevant pain decrease was accompanied with objective improvements in tactile acuity, proprioceptive measures, and changes in EEG pain biomarkers for the multisensory intervention group only.

Conclusions

The developed multisensory treatment showed a clinically significant reductions in self-reported pain, supported by improvements in objective sensory and neurophysiological measures. These results represent a significant advancement in the treatment and assessment of pain, offering a non-invasive, accessible, and cost-effective solution for neuropathic pain, a major societal burden and one of the most prevalent neurological conditions worldwide.

Clinical trial registration

The trial was registered withClinicalTrial.gov(NCT05483816).
Harnessing methods, data analysis, and near-real-time wastewater monitoring for enhanced public health response using high throughput sequencing
Authors: Ramachandran Padmini , Kayikcioglu Tunc , Walsky Tamara , Judy Kathryn , Amirzadegan Jasmine , Bias Candace Hope , Tesfaldet Bereket , Balkey Maria , EppSchmidt Dietrich , Rand Hugh , Pettengill James , Tallent Sandra , Brown Eric , Pfefer Tina , Timme Ruth , Windsor Amanda , Grim Christopher , Hoffmann Maria
Published: December 2024

Wastewater-based analysis has emerged as a pivotal method for monitoring SARS-CoV-2 (SC2). Leveraging high-throughput sequencing on wastewater samples facilitates a comprehensive, population-level assessment of circulating and emerging SC2 variants within a community. This study meticulously evaluates the detection performance, variant calling accuracy, and the time taken from sample collection to public data release for wastewater SC2 monitoring. We employed two different SC2 target enrichment panels on Illumina MiSeq and Oxford Nanopore Technologies (ONT) GridION sequencing platforms for a robust analysis. Daily collection of routine raw grab and composite samples took place at a wastewater treatment plant (WWTP) site in Maryland, USA (MD) from mid-January 2022 to the end of June 2022. Total Nucleic Acid (TNA) was extracted from samples and target enrichment was executed using QIAseq DIRECT and NEBNext VarSkip Short amplicon kits, with subsequent sequencing on MiSeq or ONT GridION platforms, respectively. Obtained sequences was analyzed using our custom CFSAN Wastewater Analysis Pipeline (C-WAP). Raw sequence data and detailed metadata were submitted to NCBI (BioProject PRJNA757291) as it became available. Our wastewater data successfully detected the onset of new variants BA.2, BA.2.12, BA.4.6, and BA.5 to the observed population. Notably, Omicron sub-variants were identified approximately a week ahead of publicly available clinical data at the MD ZIP-code level. Variation in quality metrics paralleled the rise and fall of BA waves, underscoring the impact of viral load on sequencing quality. Regular updates of estimated variant proportions were made available on the FDA-CFSAN “Wastewater Surveillance for SARS-CoV-2 Variants” website. In contrast to the median 28-day turnaround for our samples, the lead time from sample collection to public release of raw sequence data via NCBI was remarkably swift, accomplished within a mere 57 hours in this specific exercise. Our processing, sequencing, and analysis methods empowered the swift and accurate detection of SC2 trends and circulating variants within a community, offering insights for public health decision-making.
A Cohort Study of Urinary Tract Infections in People Living with Dementia: Epidemiology and Diagnostic Challenges
Authors: Jackson Raphaella , Tran Martin , Jensen Kirsten , Crone Michael A. , Webb Alexander J. , Cameron Loren P. , Nilforooshan Ramin , Wingfield David , Sharp David J. , Freemont Paul S.
Published: December 2024

Background

Urinary tract infections (UTIs) are a leading cause of hospitalization in people living with dementia, making accurate detection and prompt treatment critical in this vulnerable population.

Methods

This retrospective, longitudinal cohort study evaluated the diagnostic accuracy of self-reported symptoms and urine dipstick test results for identifying UTIs in people with dementia. Participants included 78 community-dwelling individuals over the age of 50 with a confirmed dementia diagnosis. These participants were recruited from cohorts established by the Surrey and Borders Partnership NHS Foundation Trust and the Hammersmith & Fulham Partnership Primary Care Network between late 2019 and 2023.

Results

The frequency of UTIs in people living with dementia (PLWD) is highly variable, some individuals having nearly chronic infections and others not acquiring a single UTI during their enrolment in the study. The taxonomy of the microbes associated with the urinary tract infections in this cohort were consistent with those that have been observed in other demographics. When we modelled the relationship between self-reported symptoms, dipstick results, and the presence of UTIs we found that there was no significant relationship between UTI and symptoms. However, there was a highly significant correlation between dipstick test results positive for leucocytes and nitrites with the presence of a UTI.

Conclusions

Urine dipstick tests for nitrites and leucocytes should be incorporated into diagnostic protocols and should also be considered for ongoing surveillance of UTIs in people living with dementia.

Study Registration Numbers

Research Ethics Committee (REC) reference: 19/LO/0102

Integrated Research Application System (IRAS) project ID: 257561
Evolution of child acute malnutrition during war in the Gaza Strip, 2023-2024: retrospective estimates and scenario-based projections
Authors: Checchi Francesco , Jamaluddine Zeina
Published: December 2024

Background

Nutritional status has been compromised by ongoing war and restrictions on food deliveries in the Gaza Strip. We developed a mathematical model that outputs retrospective estimates and scenario-based projections of acute malnutrition prevalence among children given caloric intake and other factors. We present here the model and its application to the crisis in Gaza.

Methods

We extended an existing mechanistic model for weight change as a function of energy balance, calibrating it to represent variability in growth curves observed in pre-war Gaza. We simulated open cohorts of children exposed to time-varying caloric intake, infant exclusive breastfeeding prevalence, incidence of infectious disease and coverage of malnutrition treatment, while allowing for adult caloric sacrifice to supplement child intake in times of food scarcity.

Results and conclusions

The model accurately replicates growth standards, pre-war growth patterns and expected parameter dependencies. It suggests that a considerable increase in acute malnutrition occurred in northern Gaza during early 2024. Projections for late 2024 include a serious nutritional emergency if relatively pessimistic assumptions are made about food availability. The model may hold considerable promise for informing decisions in humanitarian response but requires further validation and development.
Unseen Yet Overcounted: The Paradox of Seizure Frequency Reporting
Authors: Wong Victoria , Hannon Timothy , Fernandes Kiran M. , Cook Mark J. , Nurse Ewan S.
Published: December 2024

Objective

Seizure control is often assessed using patient-reported seizure frequencies. Despite its subjectivity, self-reporting remains essential for guiding anti-seizure medication (ASM) decisions and ongoing patient investigations. Additionally, clinical trials frequently rely on self-reported seizure rates for participant selection and outcome measures. This study aims to compare patient-reported seizure frequencies with electrographic frequencies captured via ambulatory video EEG (avEEG).

Methods

Data from intake forms and seizure diaries were collected from patients undergoing home-based avEEG in Australia (April 2020–April 2022). Intake forms included monthly seizure frequency estimates. Only avEEG-confirmed epilepsy cases were analyzed. Univariate and multivariate analyses compared seizure frequencies reported via EEG, diaries, and surveys.

Results

Of 3,407 reports, 853 identified epilepsy cases, with 234 studies analyzed after excluding outliers. Diary-reported frequencies correlated with EEG frequency (p<0.00001), but survey-reported frequencies did not (p>0.05). Surveys significantly overestimated seizure frequency (median = 3.98 seizures/month, p<0.0001), while diaries showed substantially smaller differences (median = 0.01 seizures/month, p<0.0001). Carer presence was associated with higher diary-reported frequencies (p=0.047). Age negatively correlated with survey frequency estimation error (p=0.016). Multivariate analysis identified age and carer status as significant predictors of residuals.

Conclusions

Most patients overestimate their seizure frequency, influencing therapeutic decisions and raising concerns about the reliability of self-reported data in clinical trials.

Significance

An “over-reporting, over-prescribing” cascade may affect epilepsy treatment and highlights the issue of clinical drug trials relying on self-reported seizure rates.

Key points

Self-reported seizure frequencies often differ from electrographic seizure frequencies captured by avEEG.

Survey reports tend to overestimate seizure frequency compared to EEG, while diary reports show smaller discrepancies.

Carer presence is associated with higher reported seizure frequencies in diaries.

Older age is weakly negatively correlated with the overestimation of seizures in surveys.

Over-reporting of seizures may influence clinical decision-making and the reliability of clinical trial outcomes using self-reported data.
Acute psychosis and the risk of motor vehicle crash
Authors: Staples John A , Daly-Grafstein Daniel , Khan Mayesha , Erdelyi Shannon , Chan Herbert , Honer William G. , Brubacher Jeffrey R
Published: December 2024

Importance

Limited empirical evidence guides fitness-to-drive decision-making following an episode of acute psychosis.

Objective

To evaluate the association between acute psychosis and subsequent crash risk.

Design

Retrospective observational analyses using 20 years of population-based administrative health and driving data. We first assessed the association between psychosis and collisions using a case-crossover design, which controls for relatively fixed individual characteristics like personality, driving experience and routine driving habits. Next, we conducted a responsibility analysis which accounts for the changes in road exposure (miles of driving per month) that might occur after recent hospitalization.

Setting

British Columbia, Canada.

Participants

Drivers with a police-attended motor vehicle crash, 2000-2016.

Exposure

A hospital stay for acute psychosis ending in the 6-week interval prior to crash.

Main Outcomes and Measures

The case-crossover analysis examined crash involvement as a driver. The responsibility analysis examined driver responsibility for contributing to their crash. We used logistic regression with adjustment for potential confounders to evaluate associations between outcomes and recent acute psychosis.

Results

Among 9842 crashes in the case-crossover analysis, a hospital stay for acute psychosis ended in 199 pre-crash intervals and in 147 control intervals, suggesting acute psychosis was temporally associated with subsequent crash (2.0% vs 1.5% of intervals; adjusted odds ratio (aOR), 1.32; 95%CI, 1.05-1.66; p=0.02). Among 819,348 drivers with a police-attended crash and determinate crash responsibility, 178 of 235 drivers with a recent hospitalization for acute psychosis and 440,543 of 819,113 drivers without recent psychosis were deemed responsible for their crash (75.7% vs 53.8%; aOR, 2.38; 95%CI, 1.75-3.24; p<0.001).

Conclusions

The 6-week interval following a hospitalization for acute psychosis is associated with increased odds of crash and increased likelihood of a driver being deemed responsible for contributing to their crash. More stringent temporary driving restrictions after an episode of acute psychosis might reduce crash risk.

KEY POINTS

Questions

Does a recent episode of acute psychosis increase a driver’s likelihood of being involved in a motor vehicle crash?

Findings

Using population-based administrative health and driving data, investigators found that the odds of crash were higher in the first 6 weeks after a hospital stay for acute psychosis than during control periods. A responsibility analysis accounting for changes in road exposure found drivers were also more likely to be deemed responsible for contributing to their crash during this period.

Meaning

More stringent driving restrictions in the first 6 weeks after an episode of acute psychosis might reduce crash risk.
Impact of the Covid-19 pandemic on elective and trauma orthopaedic surgery in a tertiary referral hospital in Kenya: A retrospective cross-sectional study
Authors: Baraza Njalalle , Odari Ian , Lomole Emmanuel Marsuk , Karanja Sarah , Ating’a Mordicai
Published: December 2024

The impact of the COVID-19 pandemic is still being felt in multiple spheres of life. In healthcare, COVID-19 noticeably affected surgical practice in sub-Saharan Africa indicated by a reduction in elective cases with prioritisation of cancer and emergency cases. This study sought to describe the impact of COVID-19 on orthopaedic surgery volumes in a private tertiary referral hospital.

Ethical approval was obtained for this retrospective cross-sectional study carried out at the Aga Khan University Hospital, Nairobi. The orthopaedic data was collected using the Electronic Healthcare Record (EHR) system in the hospital. Elective and trauma caseloads recorded during COVID-19 were compared with similar quarters in the pre and post COVID-19 periods.

In the third quarter before the COVID-19 pandemic, there were 15 arthroplasty, 53 arthroscopy and 31 implant removal cases. During the pandemic, there was an expected fall in the numbers of procedures by 33%, 30% and 13% respectively compared to the previous (pre pandemic) year. There was also the expected drop in the number of adult trauma cases, however, there was an increase in paediatric fracture fixation with k-wires. In spinal surgery, there was a 71% increase in the number of laminectomies and anterior cervical decompression and fusions (ACDF) from the pre pandemic 21 cases recorded.

The COVID-19 pandemic had an impact on elective and emergency orthopaedic procedure volumes. There was a reduction in the number of elective arthroplasty, arthroscopy, nailing and orthopaedic implant removal procedures. On the other hand there was a significant increase in the number of paediatric fracture fixation and with K-wires and ACDF/laminectomy volumes.
Wnt target IQGAP3 promotes Wnt signaling via disrupting Axin1-CK1α interaction
Authors: Rahmat Muhammad Bakhait , Hussain Aashiq , Xuan Teh Yu , Dutta Bibek , Pundrik Sumedha , Kappei Dennis , Ito Yoshiaki
Published: December 2024

The scaffold protein IQGAP3 is highly upregulated in most epithelial cancers. While recent studies have highlighted its pivotal roles in cancer cell proliferation and metastasis, a deeper mechanistic understanding of IQGAP3 is currently lacking. We have here used TurboID to map IQGAP3 proximity partners and identified the Wnt signaling members Axin1 and CK1α as IQGAP3-interacting proteins. Our functional studies demonstrated that overexpression of IQGAP3 increases β-catenin levels, while IQGAP3 depletion reduces β-catenin levels in gastric cancer cells. Mechanistically, IQGAP3 disrupts Axin1-CK1α interaction, thereby inhibiting β- catenin phosphorylation and ultimately leading to its accumulation. Importantly, we discovered that IQGAP3 itself is regulated by Wnt signaling, suggesting its involvement in a positive feedback loop in Wnt/β-catenin signaling through interactions with Axin1 and CK1α. These findings identify IQGAP3 as a novel mediator of β-catenin stabilization and underscore its potential as a target for cancer therapy.
Cytoplasmic calcium influx mediated by Lr14a regulates stomatal immunity against leaf rust in wheat
Authors: Yue Lili , Wang Limin , Neuhäuser Benjamin , Zhang Songyuan , Herren Gerhard , Heuberger Matthias , Jung Esther , Ludewig Uwe , Zipfel Cyril , Keller Beat
Published: December 2024

The race-specific resistance geneLr14ain wheat confers a unique type of heterogenous resistance reaction. It encodes an ankyrin-repeat transmembrane domain protein that confers immunity against the fungal pathogenPuccinia triticina. Here, we show that Lr14a functions as a calcium-permeable channel, mediating cytoplasmic Ca²⁺ influx that is crucial for leaf rust resistance in wheat. Infection with avirulent isolates inducedLr14aexpression predominantly in mesophyll cells while triggering cell death in guard cells in wheat. This study revealed a mechanism by which the product of anRgene regulates stomatal immunity non-cell autonomously through the mediation of calcium signaling.
Microglia from patients with multiple sclerosis display a cell-autonomous immune activation state
Authors: Hyvärinen Tanja , Lotila Johanna , Giudice Luca , Tujula Iisa , Nylund Marjo , Ohtonen Sohvi , Scoyni Flavia , Jäntti Henna , Pihlava Sara , Skottman Heli , Narkilahti Susanna , Airas Laura , Malm Tarja , Hagman Sanna
Published: December 2024

Aberrant and sustained activation of microglia is implicated in the progression and severity of multiple sclerosis (MS). However, whether intrinsic alterations in microglial function impact the pathogenesis of this disease remains unclear.

We conducted transcriptomic and functional analyses of microglia-like cells (iMGLs) differentiated from induced pluripotent stem cells (iPSCs) from patients with MS (pwMS) to answer this question.

We generated iPSCs from six pwMS showing increased microglial activity via translocator protein (TSPO)-PET imaging. We demonstrated that the differentiated iMGL transcriptional profile resembled the microglial signature found in MS lesions. Importantly, compared with healthy controls, MS iMGLs presented cell-autonomous differences in their regulation of inflammation, both in the basal state and following inflammatory lipopolysaccharide challenge. Through transcriptomic profiling, we showed that MS iMGLs display increased expression of genes known to be upregulated in MS microglia. Furthermore, upregulated genes in MS iMGLs were associated with immune receptor activation, antigen presentation, and the complement system, with known MS implications. Finally, functional analyses indicated that the transcriptional changes in MS iMGLs corresponded with alterations in the secretion of inflammatory cytokines and chemokines and increased phagocytosis.

Together, our results provide evidence of putative cell-autonomous microglial activation in pwMS and identify transcriptomic and functional changes that recapitulate the phenotypes observedin vivoin microglia from pwMS. These findings indicate that MS disease-specific iPSCs are valuable tools for studying disease-specific microglial activationin vitroand highlight microglia as potential therapeutic targets in MS.
Engineering a Biosynthetic Pathway for the Production of (+)-Brevianamides A and B inEscherichia coli
Authors: Sandoval Hurtado Casandra P , Kelly Samantha P , Shende Vikram , Perez Makayla , Curtis Brian J , Newmister Sean A , Ott Kaleb , Pereira Filipa , Sherman David H
Published: December 2024

The privileged fused-ring system comprising the bicyclo[2.2.2]diazaoctane (BDO) core is prevalent in diketopiperazine (DKP) natural products with potent and diverse biological activities, with some being explored as drug candidates. Typically, only low yields of these compounds can be extracted from native fungal producing strains and the available synthetic routes remain challenging due to their structural complexity. BDO-containing DKPs including (+)-brevianamides A and B are assembled via multi-component biosynthetic pathways incorporating non-ribosomal peptide synthetases, prenyltransferases, flavin monooxygenases, cytochrome P450s and semi-pinacolases. To simplify access to this class of alkaloids, we designed an engineered biosynthetic pathway inEscherichia coli, composed of six enzymes sourced from different kingdoms of life. The pathway includes a cyclodipeptide synthase (NascA), a cyclodipeptide oxidase (DmtD2/DmtE2), a prenyltransferase (NotF), a flavin-dependent monooxygenase (BvnB), and kinases (PhoN and IPK). Cultivated in glycerol supplemented with prenol, the engineeredE. colistrain produces 5.3 mg/L of (-)-dehydrobrevianamide E (4), which undergoes a terminal,ex vivolithium hydroxide catalyzed rearrangement reaction to yield (+)-brevianamides A and B with a 46% yield and a 92:8 diastereomeric ratio. Additionally, titers of4were increased eight-fold by enhancing NADPH pools in the engineeredE. colistrain. Our study combines synthetic biology, biocatalysis and synthetic chemistry approaches to provide a five-step engineered biosynthetic pathway for producing complex indole alkaloids inE. coli.

Abstract Figure
Mechanisms of synergistic Mediator recruitment in RNA polymerase II transcription activation revealed by single-molecule fluorescence
Authors: Zhou Daniel H. , Jeon Jongcheol , Farheen Nida , Friedman Larry J. , Kondev Jane , Buratowski Stephen , Gelles Jeff
Published: December 2024

Transcription activators trigger transcript production by RNA Polymerase II (RNApII) via the Mediator coactivator complex. Here the dynamics of activator, Mediator, and RNApII binding at promoter DNA were analyzed using multi-wavelength single-molecule microscopy of fluorescently labeled proteins in budding yeast nuclear extract. Binding of Mediator and RNApII to the template required activator and an upstream activator sequence (UAS), but not a core promoter. While Mediator and RNApII sometimes bind as a pre-formed complex, more commonly Mediator binds first and subsequently recruits RNApII to form a preinitiation complex precursor (pre-PIC) tethered to activators on the UAS. Interestingly, Mediator occupancy has a highly non-linear response to activator concentration, and fluorescence intensity measurements show Mediator preferentially associates with templates having at least two activators bound. Statistical mechanical modeling suggests this “synergy” is not due to cooperative binding between activators, but instead occurs when multiple DNA-bound activator molecules simultaneously interact with a single Mediator.
Enhancing RNA Delivery: Practical Insights into NeoLNP™ Transfection Reagent
Authors: Chen Xiaobao , Wu Yan , Liu Li , Wang Wei
Published: December 2024

The rapid advancement of RNA-based therapeutics, particularly in the wake of COVID-19 vaccine success, has prompted significant research into optimizing RNA delivery mechanisms. This study evaluates the NeoLNP™ RNA Transfection Kit developed by Scindy Pharmaceutical, which utilizes lipid nanoparticles (LNPs) for efficient RNA encapsulation and delivery. We systematically investigate various parameters affecting transfection efficiency, including RNA concentration, RNA/LNP volume ratios, mixing techniques, LNP stability, and culture media. Our results demonstrate that the optimal RNA concentration for transfection efficiency is around 40-60 ng/µL, with a 1:0.75-1:1 RNA-to-LNP ratio yielding the highest protein expression. Additionally, we find that gentle mixing techniques outperform harsher methods, and the stability of LNP-RNA complexes significantly influences transfection outcomes. This research provides practical guidelines for enhancing RNA transfection efficiency, paving the way for more effective RNA therapeutics.
In silico biophysics and rheology of blood and red blood cells in Gaucher Disease
Authors: Chai Zhaojie , Li Guansheng , Ndour Papa Alioune , Connes Philippe , Buffet Pierre A. , Franco Melanie , Karniadakis George Em
Published: December 2024

Gaucher Disease (GD) is a rare genetic disorder characterized by a deficiency in the enzyme glucocerebrosidase, leading to the accumulation of glucosylceramide in various cells, including red blood cells (RBCs). This accumulation results in altered biomechanical properties and rheological behavior of RBCs, which may play an important role in blood rheology and the development of bone infarcts, avascular necrosis (AVN) and other bone diseases associated with GD. In this study, dissipative particle dynamics (DPD) simulations are employed to investigate the biomechanics and rheology of blood and RBCs in GD under various flow conditions. The model incorporates the unique characteristics of GD RBCs, such as decreased deformability and increased aggregation properties, and aims to capture the resulting changes in RBC biophysics and blood viscosity. This study is the first to explore the Young's modulus and aggregation parameters of GD RBCs by validating simulations with confocal imaging and experimental RBC disaggregation thresholds. Throughin silicosimulations, we examine the impact of hematocrit, RBC disaggregation threshold, and cell stiffness on blood viscosity in GD. The results reveal three distinct domains of GD blood viscosity based on shear rate: the aggregation domain, where the RBC disaggregation threshold predominantly influences blood viscosity; the transition area, where both RBC aggregation and stiffness impact on blood viscosity; and the stiffness domain, where the stiffness of RBCs emerges as the primary determinant of blood viscosity. By quantitatively assessing RBC deformability, RBC disaggregation threshold, and blood viscosity in relation to bone disease, we find that the RBC aggregation properties, as well as their deformability and blood viscosity, may contribute to its onset. These findings enhance our understanding of how changes in RBC properties impact on blood viscosity and may affect bone health, offering a partial explanation for the bone complications observed in GD patients.
A transcription factor toggle switch determines differentiated epidermal cell identities inHydra
Authors: Ferenc Jaroslav , Bonvin Marylène , Papasaikas Panagiotis , Ferralli Jacqueline , Nuninger Clara , Tsiairis Charisios D.
Published: December 2024

InHydra, a simple cnidarian model, epithelio-muscular cells play a crucial role in shaping and maintaining the body architecture. These cells are continuously renewed as undifferentiated cells from the body’s mid-region get displaced toward the extremities, replacing shed, differentiated cells and adopting specific identities. This ongoing differentiation, coupled with the maintenance of distinct anatomical regions, provides an ideal system to explore the relationship between cell type specification and axial patterning. However, the molecular mechanisms governing epithelial cell identity inHydraremain largely unknown. In this study, we describe a double-negative feedback loop between the transcription factors Zic4 and Gata3 that functions as a toggle switch to control epidermal cell fate. Zic4 is activated by Wnt signaling from the mouth organizer and triggers battery cell specification in tentacles. In contrast, Gata3 promotes basal disk cell identity at the aboral end. Functional analyses demonstrate that Zic4 and Gata3 are mutually antagonistic; suppression of one leads to the dominance of the other, andvice versa, resulting in ectopic cell specification. Notably, simultaneous knockdown of both factors rescues the phenotype, indicating that it is the balance between these transcription factors, rather than their absolute levels, that dictates cell identity. This study highlights the mechanisms by which distinct cellular identities are established atHydrabody termini and reveals how cell fate decisions are coordinated with axial patterning.
5’ HOXD GENES DIFFERENTIALLY REGULATE GENE EXPRESSION OF SYNOVIAL FIBROBLASTS IN HAND JOINTS
Authors: Mirrahimi Masoumeh , Klein Kerstin , Cebrián Camino Calvo , Khmelevskaya Alexandra , Houtman Miranda , Camarillo Retamosa Eva , Saadat Mohammd Hossein , Ezen Ege , Vogetseder Alexander , Rothenfluh Esin , Berli Martin , Rauer Thomas , Catanzaro Sabrina , Jingyi Wang , Andersson Johan , Distler Oliver , Ospelt Caroline
Published: December 2024

We previously demonstrated that Homeobox (HOX) transcription factors are differentially expressed between joint locations and can accurately assign synovial fibroblasts (SFs) to their correct joint location. We show here that the expression of the 5’HOXD transcription factors HOXD10, HOXD11, and HOXD13 in SFs strikingly overlaps with predilection sites for the development of rheumatoid arthritis (RA). Changes in SFs gene expression after silencing 5’HOXDs aligned with joint-specific differences of RA SFs. In particular, we identify HOXD13 as regulator or primary cilia function in SFs modulating cell cycle, DNA damage and proteasome activity. Accordingly, we show joint specific differences in primary cilia morphology, DNA damage repair and proteasome activity. We thus propose that HOXD13 and primary cilia play a role in shaping joint-specific SFs functions that might underlie the pathognomic pattern of joint involvement in RA.