bluuebunny/crossref_metadata_2025 huggingface dataset:
Caregiver’s Decision to Report Adverse Drug Reactions among Children Receiving Seasonal Malaria Chemoprevention in Ghana
Authors: Mohammed Abdul Gafaru , Dadzie Dora , Asumah George Adu , Adomako Isaac , Idun-Acquah Joel Jeffrey , Boateng Paul , Peprah Nana Yaw , Malm Keziah L.
Published: December 2024

Introduction

The antimalarial medicines used in Seasonal Malaria Chemoprevention (SMC) campaigns are generally well-tolerated but adverse drug reactions (ADRs) can occur. Monitoring, reporting, and prompt management of ADRs is essential to build and maintain trust in SMC campaigns in the implementing communities. The caregiver’s decision to report ADRs represents a critical issue at the intersection of public health, child welfare, and pharmacovigilance. As SMC campaigns continue to expand, it is imperative to understand and address the factors influencing caregivers’ decisions to report ADRs.

Methods

A mixed methods cross-sectional study involving questionnaire administration, focus group discussions, and review of children’s health records was employed to collect data from caregivers of children aged 3-59 months in the Northern, North-East, and Savanna regions of Ghana. A systematic random sample of 679 caregivers was recruited for the study across three regions. Data including ADR occurrence, maternal and child characteristics was collected from selected caregivers in their homes. Logistic regression was performed for associations between caregiver’s reports of ADRs and caregiver characteristics.

Results

About 49.5% (336/679) of caregivers mentioned the occurrence of ADRs in children after receiving SMC medication. The commonly cited ADR was diarrhea (34.7%, 116/336). Only 16.9% (57/336) of caregivers reported ADRs to the health workers at the time of occurrence. After adjusting for confounders, increasing age of child (aOR=1.04, 95%CI:1.008-1.065), receiving education on ADR reporting (aOR=4.03, 95%CI:4.366-6.119), education on management of mild ADRs (aOR=4.43, 95%CI:2.094-9.808) and having a means of reaching health personnel (aOR=1.56, 95%CI:1.202-2.037) increased the odds of ADR reporting while increasing age of caregivers (aOR=0.92, 95%CI:0.883-0.966) and being married (aOR=0.17, 95%CI:0.149-0.183) decreased the odds of reporting ADRs among the caregivers studied.

Conclusion

Less than 20% of caregivers whose children experienced ADRs after receiving SMC medication reported the incident. Caregiver education on ADRs and it’s management and means of reaching the health team were modifiable factors that influenced caregiver ADR reporting.
Risk stratification in hip and knee replacement using Artificial Intelligence: a dual centre study to support the utility of high-volume low-complexity hubs and ambulatory surgery centres
Authors: Woodward Christopher , Green Justin , Reed MR , Beard David J , Williams Paul R
Published: December 2024

The COVID-19 pandemic has resulted in a significant backlog of hip and knee replacement surgeries in the United Kingdom (UK).1,2To address this, surgical hubs have been proposed to enhance efficiency, particularly for high-volume, low-complexity cases.3,4These hubs and Ambulatory Surgery Centres often lack higher level care support such as intensive care facilities and are thus suited to patients with less co-morbidity and systemic illness. Pre-operative risk assessment is required to enable correct patient allocation to the appropriate site and reduce unwarranted risk.

This study explores the use of artificial intelligence (AI) for risk stratification in hip and knee arthroplasty. A polynomial regression model was developed using patient demographics, blood results, and comorbidities to assign risk scores for postoperative complications. The model was generated from 29,658 patient records from two UK National Health Service (NHS) healthcare organisations. It demonstrated an area under the receiver operating characteristic curve (AUROC) as the evaluation metric and was capable of categorising patients into high and low risk. Validation was performed using a retrospective analysis of 445 patients. Predicted versus actual complications and need for further care were used to examine agreement. The model’s sensitivity was 70% for identifying high-risk patients and had a negative predictive value of 96%. This AI risk prediction was comparable to consultant-led care in risk stratification.

These findings suggest that AI can support more streamlined and efficient preoperative risk stratification, potentially reducing the burden on preoperative assessment teams and optimising resource allocation. While not without limitations, the AI model offers a sophisticated adjunct to clinical decision-making around determining risk. This can support facilities like hubs in the UK NHS or Ambulatory Surgery Centres in the United States.
Native trees within plantations and surrounding forest cover are essential for bird conservation in cashew-dominated landscapes within a biodiversity hotspot
Authors: Madhu Nandita , Sadekar Vishal , Biswas Nayantara , Jayapal Rajah , Rege Anushka , Naniwadekar Rohit
Published: December 2024

Annually, agriculture is responsible for about 60% of tropical forest loss globally.

strategies in agricultural landscapes range from enhancing farm-level habitat diversity to retaining forest cover within landscapes. A critical question is determining the relative influence of native trees within farms and forest cover around them on avian diversity, trait responses and species persistence in tree-based systems in landscapes where protected areas are often absent, often the case in lowland tropical forest ecosystems.

By sampling birds across gradients of cashew plantation intensification and varying levels of surrounding cashew and forest cover, we examined the relative influence of site- and landscape-level factors on species composition, taxonomic, functional, and phylogenetic diversity, as well as species- and trait-specific responses, and whether phylogenetic relationships among bird species influenced these responses.

At the community level, forests, cashew agroforests, and cashew monocultures hosted compositionally different bird communities. Site-level variables, specifically the proportion of native trees, influenced taxonomic and phylogenetic diversity, while landscape-level variables had no effect. None of the predictor variables accounted for the variation in functional diversity.

At the species level, site-level variables, specifically the proportion of native trees, and landscape-level variables, particularly cashew cover around plantations, had positive and negative impacts on species responses, respectively. At the trait level, evergreen forest specialists were associated positively with the proportion of native trees and negatively associated with cashew cover. Resident species had a positive association with forest cover. We found a phylogenetic signal in species responses to predictor variables, indicating that closely-related species responded similarly to predictor variables.

Synthesis and applications: To retain taxonomic and phylogenetic diversity and ensure persistence of evergreen forest specialists, it is essential to retain native trees within cashew plantations and maintain surrounding forest cover. Future policies should incentivise the retention and restoration of forest patches and restrict the felling of native trees within cashew plantations.
Diagnostic Accuracy of the Daye Diagnostic Tampon Compared to Clinician-Collected and Self-Collected Vaginal Swabs for Detecting HPV: A Comparative Study
Authors: Milanova Valentina , Gomes Michelle , Mihaylova Kalina , Twelves John , Multmeier Jan , McMahon Hana , McCulloch Hannah , Cuschieri Kate
Published: December 2024

Introduction; Cervical cancer screening is vital for achieving global eradication of this preventable disease. Vaginal self-sampling (VSS) for human papillomavirus (HPV) increases screening uptake, particularly among individuals who dislike traditional methods. Expanding self-sampling options with accurate, acceptable collection devices is essential. The Daye Diagnostic Tampon (DDT) offers an innovative approach, utilising a menstrual tampon to collect vaginal and cervical fluid for HPV screening. This study assessed the diagnostic accuracy of the DDT in detecting high-risk HPV infections, using clinician-collected swabs (CCS) as the reference standard. Methods; In this UK-based study, 262 participants provided CCS, VSS, and DDT samples for HPV testing. Samples were analysed using a clinically validated assay for 14 high-risk HPV types. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the DDT were evaluated against CCS. Invalidity rates - HPV-negative results with negative internal controls were compared across sampling methods. Results; The DDT showed a sensitivity of 82.9% (95% CI: 72.4-89.9%), specificity of 91.6% (86.4-94.9%), and overall accuracy of 89.0% (84.4-92.4%) relative to CCS. McNemar's test showed no significant difference between CCS and DDT results (p = 0.845). Valid result rates were highest for DDT (99.2%), followed by VSS (94.7%) and CCS (90.8%). Conclusion; The DDT demonstrates comparable accuracy to CCS for detecting high-risk HPV and offers superior validity rates. This novel device shows promise as a transformative self-sampling method. Further, complementary research should focus on assessing DDT's clinical performance in detecting HPV associated with the cervical disease endpoints.
ClimateMind50+ a comprehensive short questionnaire to measure climate change knowledge, worries, preparedness, behaviours, and involvement of adults aged 50 and over
Authors: Zaninotto Paola , Wu Yu-Tzu , Prina Matthew
Published: December 2024

The ClimateMind50+ questionnaire is a tailored instrument to assess the knowledge, concerns, preparedness, behaviours, and involvement of individuals aged 50 and above. Older adults are particularly vulnerable to climate-related hazards such as extreme heat, flooding, and severe storms, yet their perspectives and contributions to climate resilience remain underrepresented in research. The systematic development of the ClimateMind50+ involved rigorous cognitive testing with diverse participants, ensuring clarity, accessibility, and relevance. The tool is designed for versatility in administration—face-to-face, via telephone, or self-completion—facilitating its integration across various research contexts.

Cognitive testing highlighted the need for clear wording, simplified response scales, and age-appropriate framing of questions. For instance, questions on climate preparedness and sustainable practices were refined to capture lifetime actions (“ever”) rather than limited timeframes, enhancing their relevance for older respondents. Additionally, the questionnaire effectively explores older adults’ engagement in climate actions, from individual behavioural changes to advocacy and activism, challenging stereotypes of passivity in this demographic.

By providing nuanced insights into the experiences of older adults and their potential contributions to climate mitigation and adaptation, the ClimateMind50+ offers a robust foundation for climate change research among older people. Its deployment can support policymaking and community initiatives aimed at reducing climate risks while promoting sustainable and healthy aging practices. This innovative tool underscores the importance of amplifying the voices of older adults in climate discourse and harnessing their capacities for fostering resilience.
Parent-of-Origin inference and its role in the genetic architecture of complex traits: evidence from ∼265,000 individuals
Authors: Hofmeister Robin J. , Cavinato Théo , Karimi Roya , van der Graaf Adriaan , Pajuste Fanny-Dhelia , Kronberg Jaanika , Taba Nele ,   Estonian Biobank research team, Mägi Reedik , Vaudel Marc , Rubinacci Simone , Johansson Stefan , Milani Lili , Delaneau Olivier , Kutalik Zoltán
Published: December 2024

Parent-of-origin effects (POEs) occur when the impact of a genetic variant depends on its parental origin. Traditionally linked to genomic imprinting, these effects are believed to have evolved from parental conflict over resource allocation to offspring, which results in opposing parental genetic influences. Despite their potential importance, POEs remain heavily understudied in complex traits, largely due to the lack of parental genomes.

Here, we present a multi-step approach to infer the parent-of-origin of alleles without parental genomes, leveraging inter-chromosomal phasing, mitochondrial and chromosome X data, and sibling-based crossover inference. Applied to the UK Biobank (discovery cohort) and Estonian Biobank (replication cohort), this scalable approach enabled parent-of-origin inference for up to 221,062 individuals, representing the largest dataset of its kind.

GWAS scans in the UK Biobank for more than 60 complex traits and over 2,400 protein levels contrasting maternal and paternal effects identified over 30 novel POEs and confirmed more than 50% of testable known associations. Notably, approximately half of our POEs exhibited a bi-polar pattern, where maternal and paternal alleles exert conflicting effects. These effects were particularly prevalent for traits related to growth (e.g., IGF-1, height, fat-free mass) and metabolism (e.g., type 2 diabetes, triglycerides, glucose). Replication in the Estonian Biobank and in 45,402 offspring from the Norwegian Mother, Father and Child Cohort Study validated over 75% of testable associations.

Overall, our findings shed new light on the influence of POEs on diverse complex traits and align with the parental conflict hypothesis, providing compelling evidence for this understudied evolutionary phenomenon.
Dnmt3a-dependentde novoDNA methylation enforces lineage commitment and preserves functionality of memory Th1 and Tfh cells
Authors: Perkins Bryant , Novis Camille L. , Baessler Andrew , Sircy Linda M. , Thomas Monyca M. , Harrison-Chau Malia , Richens Andrew W. , Fuchs Bryce , Nguyen Nguyen X. , Flint Kaitlyn , Strobelt Brittany M. , Varley Katherine E. , Hale J. Scott
Published: December 2024

Following acute viral infection, naïve CD4+ T cells differentiate into T follicular helper (Tfh) and T helper 1 (Th1) cells that generate long-lived memory cells. However, it is unclear how memory Tfh and Th1 cells maintain their lineage commitment. We demonstrate that Tfh and Th1 lineages acquire distinct Dnmt3a-dependentde novoDNA methylation programs that are preserved into memory.Dnmt3adeletion impairs lineage commitment and functionality of memory Th1 and Tfh cells, resulting in aberrantRunx1upregulation that represses germinal center Tfh cell differentiation. In contrast, transient pharmacological DNA methyltransferase inhibition during priming impairs repression of Tfh-associated genes while properly silencingRunx1, and results in enhanced Tfh cell functionality in primary and secondary responses to viral infections. Together, these findings demonstrate that Dnmt3a-mediated epigenetic programing is required to enforce T helper lineage commitment and preserve Tfh and Th1-specific functions during the recall response to infection, and reveal novel strategies to improve long-lived adaptive immunity against infectious diseases.

This article demonstrates that Dnmt3a-dependent epigenetic programing regulates functionality and plasticity of Th1 and Tfh memory cells. Furthermore, early pharmacological inhibition of such programing enhances GC Tfh cell differentiation, suggesting novel strategies for modulating the immune response to viral infections.
The R-loop Grammar predicts R-loop formation under different topological constraints
Authors: Ferrari Margherita Maria , Poznanović Svetlana , Riehl Manda , Lusk Jacob , Hartono Stella , González Georgina , Chédin Frédéric , Vázquez Mariel , Jonoska Nataša
Published: December 2024

R-loops are transient three-stranded nucleic acids that form during transcription when the nascent RNA hybridizes with the template DNA, freeing the DNA non-template strand. There is growing evidence that R-loops play important roles in physiological processes such as control of gene expression, and that they contribute to chromosomal instability and disease. It is known that R-loop formation is influenced by both the sequence and the topology of the DNA substrate, but many questions remain about how R-loops form and the 3-dimensional structures that they adopt. Here we represent an R-loop as a word in a formal grammar called theR-loop grammarand predict R-loop formation. We train the R-loop grammar on experimental data obtained by single-molecule R-loop footprinting and sequencing (SMRF-seq). Despite not containing explicit topological information, the R-loop grammar accurately predicts R-loop formation on plasmids with varying starting topologies and outperforms previous methods in R-loop prediction.

Author summary

R-loops are prevalent triple helices that play regulatory roles in gene expression and are involved in various diseases. Our work improves the understanding of the relationship between the nucleotide sequence and DNA topology in R-loop formation. We use a mathematical approach from formal language theory to define an R-loop language and a set of rules to model R-loops as words in that language. We train the resulting R-loop grammar on experimental data of co-transcriptional R-loops formed on different DNA plasmids of varying topology. The model accurately predicts R-loop formation and outperforms prior methods. The R-loop grammar distills the effect of topology versus sequence, thus advancing our understanding of R-loop structure and formation.
Microvalve-based devices for flow-free gradient generators
Authors: Bohec Pierre , Dupuy Florian , Tishkova Victoria , de Noray Valentine Seveau , Valignat Marie-Pierre , Theodoly Olivier
Published: December 2024

Experiments with gradients of soluble bioactive species have significantly advanced with microfluidic developments that enable cell observation and stringent control of environmental conditions. While some methodologies rely on flow to establish gradients, other opt for flow-free conditions, which is particularly beneficial for studying non-adherent and/or shear-sensitive cells. In flow-free devices, bioactive species diffuse either through resistive microchannels in “microchannel-based” devices, a porous membrane in “membrane-based” devices, or a hydrogel in “gel-based” devices. However, despite significant advancements over traditional methods such as “Boyden chambers”, these technologies have not widely disseminated in biological laboratories, arguably due to entrenched practices and the intricate skills required for conducting microfluidic assays. Here, we integrated Quake-type pneumatic microvalves in place of microgrooves, membranes, or gels, and developed devices with precise control over residual flow, establishment initial gradient, and long-term stability of gradients. The “Microvalve-based” approach enables the generation of the automatization of delicate microfluidic manipulations, which paves the way for routine applications of controlled and tunable flow-free gradients in academic laboratories and biomedical units.
Fingerprinting and chemotyping approaches reveal a wide genetic and metabolic diversity among wild hops (Humulus lupulusL.)
Authors: Ducrocq Florent , Piutti Séverine , Henychová Alena , Villerd Jean , Laflotte Alexandre , Girardeau Loïc , Grosjean Jérémy , Patzak Josef , Hehn Alain
Published: December 2024

Hop (Humulus lupulusL.) is an emblematic industrial crop in the French North East region that developed at the same time as the brewing activity. Presently, this sector, especially microbreweries, are interested in endemic wild hops, which give beer production a local signature. In this study, we investigated the genetic and metabolic diversity of thirty-six wild hops sampled in various ecological environments. These wild accessions were propagated aeroponically and cultivated under uniform conditions (the same soil and the same environmental factors). Our phytochemical approach based on UHPLC-ESI-MS/MS analysis led to the identification of three metabolic clusters based on leaf content and characterized by variations in the contents of twelve specialized metabolites that were identified (including xanthohumol, bitter acids, and their oxidized derivatives). Furthermore, molecular characterization was carried out using sixteen EST-SSR microsatellites, allowing a genetic affiliation of our wild hops with hop varieties cultivated worldwide and wild hops genotyped to date using this method. Genetic proximity was observed for both European wild and hop varieties, especially for Strisselspalt, the historical variety of our region. Finally, our findings collectively assessed the impact of the hop genotype on the chemical phenotype through multivariate regression tree (MRT) analysis. Our results highlighted the ‘WRKY 224’ allele as a key discriminator between high– and low-metabolite producers. Moreover, the model based on genetic information explained 40% of the variance in the metabolic data. However, despite this strong association, the model lacked predictive power, suggesting that its applicability may be confined to the datasets analyzed.
Characterization and whole genome sequencing ofSaccharomyces cerevisiaestrains lacking several amino acid transporters: tools for studying amino acid transport
Authors: Sonawala Unnati , Busidan Aymeric , Haak David , Pilot Guillaume
Published: December 2024

Saccharomyces cerevisiaemutants have been used since the early 1980s as a tool to characterize genes from other organisms by functional complementation. This approach has been extremely successful in cloning and studying transporters, for instance, plant amino acid, sugar, urea, ammonium, peptide, sodium, and potassium were characterized using yeast mutants lacking these functions. Over the years, new strains lacking even more endogenous transporters have been developed, enabling the characterization of transport properties of heterologous proteins in a more precise way. Furthermore, these strains provide the added advantage of characterization of a transporter belonging to a family of proteins in isolation, and thus can be used to study the relative contribution of redundant transporters to the whole function. We focused on amino acid transport; starting with the yeast strain 22Δ8AA, developed to clone plant amino acid transporters in the early 2000s. We recently deleted two additional amino acid permeases, Gnp1 and Agp1, creating 22Δ10α. In the present work, five additional permeases (Bap3, Tat1, Tat2, Agp3, Bap2) were deleted from 22Δ10α genome in up to a combination of three at a time. Unexpectedly, the amino acid transport properties of the new strains were not very different from the parent, suggesting that these amino acid permeases play a minor role in amino acid uptake in our conditions. The inability to grow on a few amino acids as the sole nitrogen sources did not correlate with lower uptake activity, questioning the well-accepted relationship between lack of growth and loss of transport properties. Finally, in order to verify the mutations and the integrity of 22Δ10α genome, we performed whole-genome sequencing of 22Δ10α using long-read PacBio sequencing technology. We successfully assembled 22Δ10α’s genomede novo, identified all expected mutations and precisely characterized the nature of the deletions of the ten amino acid transporters. The sequencing data and genome will serve as a resource to researchers interested in using these strains as a tool for amino acid transport study.
Association between the use of levodopa/carbidopa and the disease outcomes included in the National Alzheimer’s Coordinating Center Uniform Data Set
Authors: Sárkány Zsuzsa , Damásio Joana , Macedo-Ribeiro Sandra , Martins Pedro M.
Published: December 2024

INTRODUCTION

This retrospective study investigates whether exposition to levodopa/carbidopa (LA/CA) medication is associated with modified Alzheimer’s disease (AD) trajectories.

METHODS

Multivariate analysis used cerebrospinal fluid (CSF) biomarker information included in the National Alzheimer’s Coordinating Center Uniform Data Set for subjects with normal cognition (NC), mild cognitive impairment (MCI) and dementia (DE). Survival analyses examined the progression to MCI/DE and death events.

RESULTS

LA/CA use is associated with lower levels of CSF amyloid beta, phosphorylated tau (P-tau) and total Tau. After adjusting for age, sex and APOE ε4 allele presence, that effect was quantified by negative coefficients of the fitted linear mixed models − P values <0.01 in all cases except for P-tau in the MCI subgroup (P=0.02). No similar effects were identified for other antiparkinsonian drugs. Exposition to LA/CA decreased the progression from MCI to DE (P=0.03).

DISCUSSION

The identified effects of LA/CA exposition on AD biomarkers and progression deserve further investigation in controlled clinical trials.
Genome-wide Association Study of Complex Lipid Species: Results from the Population-based Rhineland Study
Authors: Landstra Elvire N. , Imtiaz Mohammed A. , Talevi Valentina , Eichelmann Fabian , Schulze Matthias B. , Aziz N. Ahmad , Breteler Monique M.B.
Published: December 2024

The human lipidome comprises numerous complex lipids, dysregulation of which can contribute to the pathogenesis of a wide range of diseases. Despite the high heritability of parts of the lipidome, the genetic architecture of many circulating lipid species and their structure remains mostly unknown. Thus, we performed genome-wide association studies on 970 lipid species and 267 fatty acid composite measures using samples from the population-based Rhineland Study (n=6,096). We validated our findings using corresponding data from two other independent cohorts, including FinnGen (n=7,266) and EPIC-Potsdam (n=1,188). Out of 217 lead genomic loci, we found 135 to be novel, such asFDFT1. Using mendelian randomization and individual-level gene expression data, we identified five possible causal associations between candidate genes and corresponding lipid species, includingFDFT1-diacylglycerol (16:0/18:0). Our findings provide new insights into the intricate genetic underpinnings of lipid metabolism, which may facilitate risk stratification and discovery of new therapeutic targets.
A 2-year calorie restriction intervention reduces glycomic biological age biomarkers
Authors: Pribić Tea , Das Jayanta K , Đerek Lovorka , Belsky Daniel W. , Orenduff Melissa , Huffman Kim M , Kraus William E , Deriš Helena , Šimunović Jelena , Štambuk Tamara , Hodžić Azra Frkatović , Kraus Virginia B , Das Sai Krupa , Racette Susan B. , Banskota Nirad , Ferruci Luigi , Pieper Carl , Lewis Nathan E , Lauc Gordan , Krishnan Sridevi
Published: December 2024

Background/Objective

In a subset of participants from the CALERIE™ Phase 2 study we evaluated the effects of 2y of ∼25% Calorie Restriction (CR) diet on IgG N-glycosylation (GlycAge), plasma and complement C3 N-glycome as markers of aging and inflammaging.

Methods

Plasma samples from 26 participants in the CR group who completed the CALERIE2 trial and were deemed adherent to the intervention (∼>10 % CR at 12 mo) were obtained from the NIA AgingResearchBiobank. Glycomic investigations using UPLC or LC-MS analyses were conducted on samples from baseline (BL), mid-intervention (12 mo) and post-intervention (24 mo), and changes resulting from the 2y CR intervention were examined. In addition, anthropometric, clinical, metabolic, DNA methylation (epigenetic) and skeletal muscle transcriptomic data were analyzed to identify aging-related changes that occurred in tandem with the N-glycome changes.

Results

Following the 2y CR intervention, IgG galactosylation was higher at 24mo compared to BL (p = 0.051), digalactosylation and GlycAge (the IgG-based surrogate for biological age) were not different between BL and 12mo or BL and 24mo, but increased between 12mo and 24mo (p = 0.016, 0.027 respectively). GlycAge was also positively associated with TNF-α and ICAM-1 (p=0.030, p=0.017 respectively). Plasma highly branched glycans were decreased by the 2y intervention (BL vs 24 mo: p=0.013), but both plasma and IgG bisecting GlcNAcs were increased (BL vs 24mo: p<0.001, p = 0.01 respectively). Furthermore, total complement C3 protein concentrations were reduced (BL vs 24mo: p <0.001), as were Man9 glycoforms (BL vs 24mo: p<0.001), and Man10 (which is glucosylated) C3 glycoforms (BL vs 24mo: p = 0.046).

Conclusions

24-mos of CR was associated with several favorable, anti-aging, anti- inflammatory changes in the glycome: increased galactosylation, reduced branching glycans, and reduced GlycAge. These promising CR effects were accompanied by an increase in bisecting GlcNAc, a known pro-inflammatory biomarker. These intriguing findings linking CR, clinical, and glycomic changes may be anti-aging and inflammatory, and merit additional investigation.
Real-World Evidence on Dose-Reduction and Treatment Outcomes in Small Cell Lung Cancer; A Bayesian mixed effects and Competitive Risk Approach
Authors: Marzano Luca , Dan Asaf , Darwich Adam S. , De Petris Luigi , Tendler Salomon , Lewensohn Rolf , Raghothama Jayanth , Meijer Sebastiaan
Published: December 2024

Background

Small cell lung cancer (SCLC) is a challenging disease to treat due to rapid progression, development of chemo-resistance, and discrepancies in outcomes between real-world data and clinical trials. Previous studies lack comprehensive analyses of intermediate events and the treatment process, such as treatment decisions, progression of disease, and the occurrence of adverse events (AEs) over time. The aim of this study was to apply advanced statistical methods on a longitudinal SCLC data set in order to identify factors of importance for the risk of AEs and for survival.

Methods

Information was collected on the treatment pathways of 421 SCLC patients treated at the Karolinska University Hospital between 2016-2022 (Stockholm, Sweden). Analysis focused on the impact of dose-adjustment on adverse events (AEs), including neutropenia, by estimating odds ratios (OR) using Bayesian mixed-effects modelling. Covariate’s effects on ECOG performance status (PS) deterioration and early discontinuation of chemotherapy with cause-specific hazard ratios (csHR) were explored using competitive risk models. This approach was applied to cohorts of patients receiving first line platinum etoposide, and second line platinum etoposide or platinum irinotecan.

Results

At the end of the first line treatment, most patients exhibited tumour regression (n=167). Patients with neutropenia had longer overall survival (HR: 0.70 [0.53, 0.92]). Higher etoposide dose levels were associated with subsequent occurrences of AEs (OR: 5.97 [1.41, 30.5]) and neutropenia (OR: 3.55 [1.03, 13.3]). Dose adjustment did not affect overall survival as long as the patient completed the four-dose regimen treatment. For the second-line, fewer patients completed four treatment cycles and the most common reason of early discontinuation was tumour progression (n=72). Male patients experienced fewer AEs and better first line treatment response compared to females (csHR: 0.51 [0.25, 0.90]). High-risk patients (here defined as ECOG PS 2-3, or age over 75 years) with early discontinuation of therapy had survival outcomes similar to those who did not receive therapy.

Conclusions

Our results indicate that SCLC therapies may benefit from more individualized dosing strategies. These strategies would aim to balance improved survival with reduced risk of AEs, particularly neutropenia. It would also be beneficial to assess the risk-benefit of treating specific subgroups, including patients receiving second line therapy. Real-world data are crucial for studying therapy response and risk-benefit of treating patient groups that are underrepresented in clinical trials.
Evolution in response to prophage activation attenuates the virulence of culturableSerratia symbioticarelatives of aphid endosymbionts
Authors: VanDieren Anthony J. , Barrick Jeffrey E.
Published: December 2024

Serratia symbioticabacteria exhibit a range of relationships with aphids. They may be co-obligate mutualists, commensals, or even pathogens depending on the strain, aphid host species, and environment.Serratia symbioticaCWBI-2.3T(CWBI), a culturable member of this group, is transmitted to embryos transovarially when it is injected into pea aphids (Acyrthosiphon pisum), the same route used byS. symbioticastrains that are vertically inherited endosymbionts. Yet, aphids colonized with CWBI die before they give birth to infected offspring. We evolved laboratory populations of CWBI through 15-30 serial passages at two different temperatures in rich media. These conditions mimic aspects of the nutritional environment in aphid hosts that lead to the evolution of reduced endosymbiont genomes. Unexpectedly, allS. symbioticapopulations propagated at one temperature appeared to evolve slower growth after only a few days due to reactivation of a lytic prophage from the CWBI genome. Though these populations continued to reach saturating cell densities slower than cultures of the ancestor throughout the experiment, most bacteria in them had mutations affecting lipopolysaccharide biosynthesis and were resistant to the phage. Some evolved strains exhibited less virulence when injected into aphids, and we observed instances of gene inactivation and loss mediated by insertion elements. Our results illustrate how transposons and prophages can dominate laboratory evolution of newly cultured bacteria, particularly those that are host-associated in nature and have genomes rife with selfish DNA elements. They also suggest that bacteria-phage coevolution can catalyze evolutionary paths that contribute to converting pathogens into stably inherited endosymbionts.

IMPORTANCE

Laboratory experiments can be used to explore evolutionary innovations in how microbes associate with animal hosts.Serratia symbioticabacteria exhibit a variety of interactions with aphids. Some strains are obligate endosymbionts. Others have facultative associations with benefits or costs depending on the environmental context.S. symbioticaCWBI-2.3T(CWBI) resembles aphid endosymbionts in how it can be transovarially transmitted to aphid embryos. However, adults injected with CWBI do not survive long enough to give birth to infected offspring. We evolved this aphid protosymbiont in rich media to see if this would attenuate its virulence and recapitulate genome reduction observed in endosymbionts. We observed large deletions and gene inactivation, but reactivation of a prophage from the CWBI genome and then evolution of phage resistance dominated. Some evolved strains became less virulent to aphids, suggesting that evolution driven by selfish DNA elements can contribute to the emergence of new endosymbionts from pathogen ancestors.
Unusually Rapid Isomerization of Aspartic Acid in Tau
Authors: Shoff Thomas A. , Van Orman Brielle , Onwudiwe Vivian C. , Genereux Joseph C. , Julian Ryan R.
Published: December 2024

Spontaneous chemical modifications in long-lived proteins can potentially change protein structure in ways that impact proteostasis and cellular health. For example, isomerization of aspartic acid interferes with protein turnover and is anticorrelated with cognitive acuity in Alzheimer’s disease. However, few isomerization rates have been determined for Asp residues in intact proteins. To remedy this deficiency, we used protein extracts from SH-SY5Y neuroblastoma cells as a source of a complex, brain-relevant proteome with no baseline isomerization. Cell lysates were agedin vitroto generate isomers, and extracted proteins were analyzed by data-independent acquisition (DIA) liquid chromatography-mass spectrometry (LC-MS). Although no Asp isomers were detected at Day 0, isomerization increased across time and was quantifiable for 105 proteins by Day 50. Data analysis revealed that isomerization rate is influenced by both primary sequence and secondary structure, suggesting that steric hindrance and backbone rigidity modulate isomerization. Additionally, we examined lysates extracted under gentle conditions to preserve protein complexes and found that protein-protein interactions often slow isomerization. Base catalysis was explored as a means to accelerate Asp isomerization due to findings of accelerated asparagine deamidation. However, no substantial rate enhancement was found for isomerization, suggesting fundamental differences in acid-base chemistry. With an enhanced understanding of Asp isomerization in proteins in general, we next sought to better understand Asp isomerization in tau.In vitroaging of monomeric and aggregated recombinant tau revealed that tau isomerizes significantly faster than any similar protein within our dataset, which is likely related to its correlation with cognition in Alzheimer’s disease.

Abstract Figure
Optimized navigator-based correction of breathing-induced B0field fluctuations in multi-echo gradient-echo imaging of the spinal cord
Authors: Beghini Laura , Büeler Silvan , Liechti Martina D. , Jaffray Alexander , David Gergely , Vannesjo S. Johanna
Published: December 2024

Purpose

Multi-echo gradient-echo (ME-GRE) imaging in the spinal cord is susceptible to breathing-induced B0field fluctuations due to the proximity of the lungs, leading to ghosting artifacts. A navigator readout can be used to monitor the fluctuations; however, standard navigator processing often fails in the spinal cord. Here, we introduce navigator processing tailored specifically for spinal cord imaging.

Methods

ME-GRE data covering all spinal cord regions were acquired in six healthy volunteers during free breathing at 3T. Centerline navigator readouts and respiratory belt recordings were collected during the acquisitions. The navigator processing included a Fast Fourier Transform and subsequent interval selection targeting the spinal cord, as well as SNR-weighted averaging over samples and coils on the complex data. Furthermore, a phase unwrapping algorithm making use of the belt recordings was developed. Imaging data were corrected by phase demodulation before image reconstruction.

Results

B0field fluctuations and ghosting artifacts were largest in the lower cervical and upper lumbosacral cord (∼5 Hz std), close to the edges of the lungs. Image reconstruction based on optimized navigator correction improved visual image quality and quantitative metrics (SNR, CNR, ghosting) in all regions of the spinal cord. The improvement was largest in regions with large field fluctuations (group-averaged increase in SNR/CNR of up to 29%/37% in single-echo images).

Conclusions

Optimized navigator-based correction can reduce ghosting artifacts and increase SNR/CNR in anatomical ME-GRE of the spinal cord. The enhanced image quality and ease of implementation across sites makes the technique attractive for clinical and scientific applications.
Scalable emulation of protein equilibrium ensembles with generative deep learning
Authors: Lewis Sarah , Hempel Tim , Jiménez Luna José , Gastegger Michael , Xie Yu , Foong Andrew Y. K. , García Satorras Victor , Abdin Osama , Veeling Bastiaan S. , Zaporozhets Iryna , Chen Yaoyi , Yang Soojung , Schneuing Arne , Nigam Jigyasa , Barbero Federico , Stimper Vincent , Campbell Andrew , Yim Jason , Lienen Marten , Shi Yu , Zheng Shuxin , Schulz Hannes , Munir Usman , Tomioka Ryota , Clementi Cecilia , Noé Frank
Published: December 2024

Following the sequence and structure revolutions, predicting the dynamical mechanisms of proteins that implement biological function remains an outstanding scientific challenge. Several experimental techniques and molecular dynamics (MD) simulations can, in principle, determine conformational states, binding configurations and their probabilities, but suffer from low throughput. Here we develop a Biomolecular Emulator (BioEmu), a generative deep learning system that can generate thousands of statistically independent samples from the protein structure ensemble per hour on a single graphics processing unit. By leveraging novel training methods and vast data of protein structures, over 200 milliseconds of MD simulation, and experimental protein stabilities, BioEmu's protein ensembles represent equilibrium in a range of challenging and practically relevant metrics. Qualitatively, BioEmu samples many functionally relevant conformational changes, ranging from formation of cryptic pockets, over unfolding of specific protein regions, to large-scale domain rearrangements. Quantitatively, BioEmu samples protein conformations with relative free energy errors around 1 kcal/mol, as validated against millisecond-timescale MD simulation and experimentally-measured protein stabilities. By simultaneously emulating structural ensembles and thermodynamic properties, BioEmu reveals mechanistic insights, such as the causes for fold destabilization of mutants, and can efficiently provide experimentally-testable hypotheses.
De novodesign of potent CRISPR-Cas13 inhibitors
Authors: Taveneau Cyntia , Chai Her Xiang , D’Silva Jovita , Bamert Rebecca S. , Hayes Brooke K. , Calvert Roland W. , Curwen Daniel J. , Munder Fabian , Martin Lisandra L. , Barr Jeremy J. , Grinter Rhys , Knott Gavin J.
Published: December 2024

CRISPR-Cas systems are transformative tools for gene editing which can be tuned or controlled by anti-CRISPRs (Acrs) - phage derived inhibitors that regulate CRISPR-Cas activity. However, Acrs that are capable of inhibiting biotechnologically relevant CRISPR systems are relatively rare and challenging to discover. To overcome this limitation, we describe a highly successful, rapid, and generalisable approach that leveragesde novoprotein design to develop new-to-nature proteins for controlling CRISPR-Cas activity. Using CRISPR-Cas13 as a representative example, we demonstrate that AI-designed anti-CRISPRs (AIcrs) are capable of highly potent and specific inhibition of CRISPR-Cas13 proteins. We present a comprehensive workflow for design validation and demonstrate AIcrs functionality in controlling CRISPR-Cas13 activity in bacteria. The ability to design bespoke inhibitors of Cas effectors will contribute to the ongoing development of CRISPR-Cas tools in diverse applications across research, medicine, agriculture, and microbiology.
Unambiguous assignment of kinked beta sheets leads to insights into molecular grammar of reversibility in biomolecular condensates
Authors: Roy Irawati , Appadurai Rajeswari , Srivastavava Anand
Published: December 2024

Kinked-βsheets are short peptide motifs that appear as distortions inβ-strands and often mediate formation of reversible amyloid fibrils in prion-like proteins. Standard methods for assigning secondary structures cannot distinguish these esoteric motifs. Here, we provide a supervised machine learning based structural quantification map to unambiguously characterize Kinked-βsheets from coordinate data. We find that these motifs, although deviating from standardβ-strand region of the Ramachandran plot, scatter around the allowed regions. We also demonstrate the applicability of our technique in wresting out LARKS, which are kinkedβ-strands with designated sequence. Additionally, from our exhaustive simulation generated conformations, we create a repository of potential kinked peptide-segments that can be used as a screening-library for assigning beta-kinks in unresolved coordinate dataset. Overall, our map for Kinked-βprovides a robust framework for detailed structural and kinetics investigation of these important motifs in prion-like proteins that lead to formation of amyloid fibrils.
Rad52 Acts as an Assembly Chaperone to Form and Stabilize Rad51 Filaments Through a Large C-Terminus 85-Residue Segment
Authors: Ma Emilie , Lakhal Fadma , Litsardaki Eleni , Ruault Myriam , Audin Maxime , Levrier Natacha , Navarro Emilie , Garnier Mickaël , Maloisel Laurent , Depagne Jordane , Brocas Clémentine , Thureau Aurelien , Busso Didier , Veaute Xavier , Guerois Raphaël , Taddei Angela , Ochsenbein Françoise , Coïc Eric
Published: December 2024

Homologous recombination (HR) is essential for the repair of DNA double-strand breaks and the restart of stalled replication forks. A critical step in HR is the formation of Rad51 nucleofilaments, which perform homology search and strand invasion of a homologous DNA sequence required for repair synthesis. In the yeastSaccharomyces cerevisiae, Rad52 facilitates Rad51 nucleofilament formation by mediating Rad51 loading onto ssDNA and counteracting the dissociation of Rad51 filaments by the DNA translocase Srs2. The molecular basis of these two Rad52 functions remains unclear. Our integrative structural analyses of the Rad51-Rad52 interaction, combining NMR, SAXS, and modeling, reveal that an 85-residue segment of Rad52, conserved in fungi, folds upon binding to a broad surface of a Rad51 monomer. Notably, it includes an FxxA motif conserved in the BRC repeats of BRCA2 and at the Rad51-Rad51 interface. This binding mode was validated through an extensive set of mutations. Usingin vivoassays and a functional fluorescent GFP-Rad51 fusion protein, we demonstrated that this entire segment is critical for Rad51 filament formation. These findings highlight how Rad52 functions as an assembly chaperone, preventing Rad51 oligomerization, promoting nucleation of Rad51 nucleofilaments on ssDNA, and protecting Rad51 filaments from destabilization by Srs2.
Leucine zipper-based SAIM imaging identifies therapeutic agents to disrupt the cancer cell glycocalyx for enhanced immunotherapy
Authors: Park Sangwoo , Paek Justin H. , Colville Marshall J. , Huang Ling-Ting , Struzyk Audrey P. , Womack Sydney J. , Neelamegham Sriram , Reesink Heidi L. , Paszek Matthew J.
Published: December 2024

The abnormally thick glycocalyx of cancer cells can provide a physical barrier to immune cell recognition and effective immunotherapy. Here, we demonstrate an optical method based on Scanning Angle Interference Microscopy (SAIM) for the screening of therapeutic agents that can disrupt the glycocalyx layer as a strategy to improve anti-cancer immune responses. We developed a new membrane labeling strategy utilizing leucine zipper pairs to fluorescently mark the glycocalyx layer boundary for precise and robust measurement of glycocalyx thickness with SAIM. Using this platform, we evaluated the effects of glycosylation inhibitors and targeted enzymatic degraders of the glycocalyx, with particular focus on strategies for cholangiocarcinoma (CCA), a highly lethal malignancy with limited therapeutic options. We found that CCA had the highest mean expression of the cancer-associated mucin, MUC1, across all cancers represented in the cancer cell line encyclopedia. Pharmacological inhibitors of mucin-type O-glycosylation and mucin-specific proteases, such as StcE, could dramatically reduce the glycocalyx layer in the YSCCC model of intrahepatic CCA. Motivated by these findings, we engineered Natural Killer (NK) cells tethered with StcE to enhance NK cell-mediated cytotoxicity against CCA. In a CCA xenograft model, these engineered NK cells demonstrated superior anti-tumor efficacy compared to wild-type NK cells, with no observable adverse effects. Our findings not only provide a reliable imaging-based screening platform for evaluating glycocalyx-targeting pharmacological interventions but also offer mechanistic insights into how CCA may avoid immune elimination through fortification of the glycocalyx layer with mucins. Additionally, this work presents a novel therapeutic strategy for mucin-overexpressing cancers, potentially improving immunotherapy efficacy across various cancer types.