bluuebunny/crossref_metadata_2025 huggingface dataset:
Fresh Human Retinal scRNA-seq Atlas Reveals a Novel Cone Subtype and Cellular Diversity
Authors: Yang Luning , Tao Yiwen , Pan Qi , Cai Tengda , Ye Yunyan , Liu Jianhui , Zhou Yang , Shao Yongqing , Yi Quanyong , Lu Zen Haut , Chen Lie , McKay Gareth , Rankin Richard , Meng Weihua
Published: September 2024

The human retina has a remarkable diversity of cell types, which is crucial for understanding the mechanisms underpinning visual development and function. While single-cell RNA sequencing (scRNA-seq) has advanced our understanding of retinal biology, most studies have relied on postmortem or frozen samples, potentially missing important transcriptional information. The aim of this study was to create the first comprehensive scRNA-seq atlas of fresh human retinal samples from living donors and recently deceased individuals using scRNA-seq technology. A total of 106,829 cells were analyzed, which were collected from nine retinal samples using standardized scRNA-seq workflow. Our findings identified several novel subtypes of known retinal cells, including new subgroups of cones and amacrine cells (ACs), each characterized by distinct gene expression profiles. Notably, we discovered a novel cone subtype, the ELF1-Cone, which shows a clear developmental trajectory from mlCone precursors. This subtype exhibits unique functional properties and metabolic profiles, regulated by key transcription factors ELF1 and PRKAA1. We also identified five distinct AC subtypes, including three GABAergic ACs, each with unique gene expression profiles and functional characteristics. Our study highlights the critical importance of using fresh human retinal tissue for accurate cellular mapping and trajectory inference. Significant differences were observed between fresh and postmortem retinal samples in terms of pseudo time analysis such as RNA velocity. We also performed a comparative analysis of diabetic without retinopathy, diabetic retinopathy, and non-diabetic samples, suggesting diabetes-related transcriptional variation. In conclusion, we present a comprehensive human retina atlas using fresh samples that contribute to existing knowledge of retinal cell diversity, function, and transcriptional profiles. Our study is a milestone for future studies that will improve understanding of retinal biology and disease mechanisms.
A thiol–ene click-based strategy to customize injectable polymer–nanoparticle hydrogel properties for therapeutic delivery
Authors: Bailey Sophia J. , Eckman Noah , Brunel Elisa S. , Jons Carolyn K. , Sen Samya , Appel Eric A.
Published: September 2024

Polymer–nanoparticle (PNP) hydrogels are a promising injectable biomaterial platform that has been used for a wide range of biomedical applications including adhesion prevention, adoptive cell delivery, and controlled drug release. By tuning the chemical, mechanical, and erosion properties of injected hydrogel depots, additional control over cell compatibility and pharmaceutical release kinetics may be realized. Here, we employ thiol–ene click chemistry to prepare a library of modified hydroxypropylmethylcellulose (HPMC) derivatives for subsequent use in PNP hydrogel applications. When combined with poly(ethylene glycol)-b-poly(lactic acid) nanoparticles, we demonstrate that systematically altering the hydrophobic, steric, or pi stacking character of HPMC modifications can readily tailor the mechanical properties of PNP hydrogels. Additionally, we highlight the compatibility of the synthetic platform for the incorporation of cysteine-bearing peptides to access PNP hydrogels with improved bioactivity. Finally, through leveraging the tunable physical properties afforded by this method, we show hydrogel retention timein vivocan be dramatically altered without sacrificing mesh size or cargo diffusion rates. This work offers a route to optimize PNP hydrogels for a variety of translational applications and holds promise in the highly tunable delivery of pharmaceuticals and adoptive cells.
Biocontrol of bacterial wilt disease using plant-associated bacterial communities in tomato
Authors: Tanaka Eriko , Umeki Daisuke , Kido Shota , Makishima Rikako , Tamaki Yuko , Murakami Takumi , Fujiwara Masayuki , Saijo Yusuke
Published: September 2024

Host-protective or disease-suppressive microorganisms are anticipated as sustainable controls for crop diseases, such as bacterial wilt. However, the efficacy of biocontrol strategies is often limited by a lack of resilience under varying environmental conditions and interactions with native microbial communities in the field. In this study, we assembled a bacterial wilt-suppressive synthetic community (SynCom) in tomato, consisting of bacterial isolates derived from co-cultured microbial complexes associated with the plant. This SynCom demonstrates significant disease-suppressive effects againstRalstonia solanacearumin tomato seedlings under both axenic and soil conditions. Additionally, our findings suggest the existence of an optimal level of SynCom colonization in plants, which is critical for effective disease control. Furthermore, the SynCom exhibits direct antibiotic activity and immunogenic properties that enhance the production of defense-related secondary metabolites, thereby influencing the plant-associated microbiome. Our results provide an effective approach to constructing SynComs that exert disease-suppressive effects within microbial community contexts.
Genetic associations between SGLT2 inhibition, DPP4 inhibition or GLP1R agonism and prostate cancer risk: a two-sample Mendelian randomisation study
Authors: Shen Lin , Yang Yifan , Lu Lei , Chou Oscar Hou In , Lee Quinncy , Liu Tong , Li Guoliang , Cheng Shuk Han , Tse Gary , Zhou Jiandong
Published: September 2024

Background

Epidemiological studies have linked the use of the anti-diabetic medications, sodium-glucose co-transporter-2 inhibitors (SGLT2I), dipeptidyl peptidase-4 inhibitors (DPP4I) and glucagon-like peptide-1 receptor agonists (GLP1RA), with prostate cancer risk. However, these studies cannot infer causality.

Methods

This was a two-sample Mendelian randomization (MR) using genome-wide association study data designed to identify causal relationships between SGLT2I, DPP4I or GLP1RA and prostate cancer. Genetic associations with HbA1c and risk of prostate cancer were extracted from IEU Open-GWAS Project database with GWAS id ukb-d-30750_irnt (UK Biobank cohort) and ebi-a-GCST006085 (European Molecular Biology Laboratory’s European Bioinformatics Institute cohort), respectively. The two GWAS datasets chosen were obtained from individuals of European ancestry to minimise potential bias from population stratification. The encoding genes targeted by SGLT2I, DPP4I and GLP1RA were SGC5A2, DPP4 and GLP1R, located in Chr16: 31494323-31502181, Chr2: 162848755-162930904 and Chr6: 39016557-39059079, respectively.

Results

A total of 31, 2 and 5 single nucleotide variants (SNVs) were used for SGC5A2, DPP4 and GLP1R. Our MR analysis results supported a causal relationship between genetic variation in SLC5A2 and DPP4 and reduced risk of prostate cancer at the Bonferroni-corrected threshold, with odds ratios (OR) [95% confidence intervals] of 0.47 [0.38-0.58] and 0.35 [0.24-0.53], but not for GLP1R (OR: 1.39 [0.93-2.07]). Sensitivity analyses by the leave-one-out method did not significantly alter the OR for SGLT2I.

Conclusions

The two-sample MR analysis found that SGLT2 and DPP4 inhibition, but not GLP1R agonism, was associated with lower risks of developing prostate cancer.
Comparing Client and Provider Preferences for HIV Care Coordination Program Features using Discrete Choice Experiments
Authors: Zimba Rebecca , Fong Chunki , Conte Madellena , Guarino Honoria , Avoundjian Tigran , Carmona Jennifer , Herndon Grace , Gambone Gina , Irvine Mary , Nash Denis
Published: September 2024

Introduction

The New York City (NYC) HIV Care Coordination Program (CCP) is designed to promote care engagement and treatment adherence among the people with HIV (PWH) who struggle the most with these key components of managing their health. We assessed preferences for CCP components among PWH enrolled in the program (“clients”) and among providers of CCP services. In this report we compare the preferences between clients and providers, previously analyzed separately.

Methods

We used a discrete choice experiment to assess preferences for four CCP features (“attributes”): Help with Adherence to Antiretroviral Therapy (ART), Help with Primary Care Appointments, Help with Issues other than Primary Care, and Where Program Visits Happen. Each of these attributes had three to four variants (“levels”). In the original surveys, levels within Where Program Visits Happen varied by participant type (client versus provider). We re-coded the levels by visit location (VL) or by travel time (TT) to make them comparable, and report results from both approaches. Preferences were quantified using the relative importance of the attributes and utility of the levels.

Results

January 2020 to March 2021, 152 providers and 181 clients completed the survey. In both the VL and TT analyses, clients were most influenced by Help with Adherence to ART, preferring medication reminders via phone or text, and Where Program Visits Happen, preferring visits via phone or video chat. In the VL analysis, providers were most influenced by Help with Adherence to ART, valuing directly observed therapy most highly, and Help with Issues other than Primary Care, valuing helping clients with connections to specialty medical care. In the TT analysis, providers were most influenced by Where Program Visits Happen, preferring to meet at clients’ homes, and Help with Issues other than Primary Care, again preferring helping clients make connections to specialty medical care.

Conclusions

Client and provider preferences clearly diverged with regard to CCP service intensity: in the aggregate, clients tended to prefer lower-intensity services, whereas providers endorsed higher-intensity services. These results highlight the importance of engaging clients as partners in decisions about program services so that they are aligned with client values.
Efficacy and Safety of Nicorandil for Prevention of Contrast-Induced Nephropathy in Patients Undergoing Coronary Procedures: A Systematic Review and Meta-Analysis
Authors: Butt Ayesha Imran , Afzal Fazila , Raza Sukaina , Namal FNU , Ahmed Dawood , Abid Hassaan , Hudaib Muhammad , Sarwar Zainab Safdar Ali , Bashir Soha , Khalid Asadullah , Hassan Umer , Ebad Ur Rehman Mohammad , Cheema Huzaifa Ahmad , Husnain Ali , Anwar Usama , Tahir Muhammad Mohid , Ahmad Adeel , Rehman Wajeeh Ur , Ahmed Raheel
Published: September 2024

Background

Contrast-induced nephropathy (CIN) is a potentially serious complication of intravenous or intra-arterial contrast administration during angiographic procedures that results in renal dysfunction. This meta-analysis assesses the efficacy and safety of nicorandil for the prevention of CIN in patients undergoing percutaneous coronary intervention (PCI) or coronary angiography (CAG).

Methods

Cochrane Central Register of Controlled Trials, MEDLINE, Embase, andClinicalTrials.govwere used to perform a thorough literature search from their inception to July 2024. A random-effects meta-analysis was performed on RevMan and pooled estimates were presented as forest plots. The Mantel-Haenszel method was used for dichotomous outcomes and risk ratios (RRs) were calculated along with 95% confidence intervals (95% CI).

Results

This meta-analysis included 12 RCTs consisting of 2787 participants (nicorandil: 1418, control: 1394). The use of nicorandil was protective against CIN (RR 0.38, 95% CI 0.29-0.50). The incidence of major adverse events was comparable in both groups (RR 0.77, 95% CI 0.52-1.13, p=0.18). Similarly, the use of nicorandil did not affect the risk of developing stroke (RR 1.05), myocardial infarction (RR 0.90), heart failure (RR 0.81), cardiac death (RR 0.90), and dialysis (RR 0.70).

Conclusion

This study revealed that nicorandil effectively reduced the risk of developing CIN in patients undergoing angiographic procedures like PCI or coronary angiography. However, more RCTs should be conducted for a more definitive conclusion.
The lack of trade-off between conformational stability and binding affinity in a nanobody with therapeutic potential for a misfolding disease
Authors: Gómez-Mulas Atanasio , Naganathan Athi N. , Pey Angel L.
Published: September 2024

To improve protein pharmaceuticals, we need to balance protein stability and binding affinity within vivoefficiency. We have recently developed a nanobody (NB-AGT-2) against the alanine:glyoxylate aminotransferase with high stability (Tm∼85°C) that may be useful to treat a misfolding disease called primary hyperoxaluria type 1. In this work, we characterize the relationships between protein stability and binding affinity in NB-AGT-2 by generating single and double cavity-creating mutants in its hydrophobic core. These mutations decrease thermal stability by 10-20 °C, reflecting changes in thermodynamic stability of up to 8 kcal·mol-1, hardly affecting their binding affinity for its target. Our results thus show that NB stability can be challenged without an effect on its binding.
Leveraging weighted quartet distributions for enhanced species tree inference from genome-wide data
Authors: Hasan Navid Bin , Biswas Avijit , Wahab Zahin , Mahbub Mahim , Reaz Rezwana , Bayzid Md Shamsuzzoha
Published: September 2024

Species tree estimation from genes sampled from throughout the whole genome is challeng-ing in the presence of gene tree discordance, often caused by incomplete lineage sorting (ILS), where alleles can coexist in populations for periods that may span several speciation events. Quartet-based summary methods for estimating species trees from a collection of gene trees are becoming popular due to their high accuracy and theoretical guarantees of robustness to arbitrarily high amounts of ILS. ASTRAL, the most widely used quartet-based method, aims to infer species trees by maximizing the number of quartets in the gene trees that are consistent with the species tree. An alternative approach (as in wQFM) is to infer quartets for all subsets of four species and amalgamate them into a coherent species tree. While summary methods can be highly sensitive to gene tree estimation errors–especially when gene trees are derived from short alignments–quartet amalgamation offers an advantage by potentially bypassing the need for gene tree estimation. However, greatly understudied is the choice of weighted quar-tet inference method and downstream effects on species tree estimations under realistic model conditions. In this study, we investigated a broad range of methods for generating weighted quartets and critically assessed their impact on species tree inference. Our results on a collec-tion of simulated and empirical datasets suggest that amalgamating quartets weighted based on gene tree frequencies (GTF) typically produces more accurate trees than leading quartet-based methods like ASTRAL and SVDquartets. Further enhancements in GTF-based weighted quar-tet estimation were achieved by accounting for gene tree uncertainty, through the utilization of a distribution of trees for each gene (instead of a single tree), by employing traditional nonpara-metric bootstrapping methods or Bayesian MCMC sampling. Our study provides evidence that the careful generation and amalgamation of weighted quartets, as implemented in methods like wQFM, can lead to significantly more accurate trees compared to widely employed methods like ASTRAL, especially in the face of gene tree estimation errors.
De novoassembly of the selfishtsupergene reveals a deleterious evolutionary trajectory
Authors: Runge Jan-Niklas , Ullrich Kristian , Lindholm Anna K.
Published: September 2024

Supergenes are linked clusters of DNA that are transmitted together due to rare or absent recombination. They undergo co-adaptation, allowing evolution to work on several genes to refine complex phenotypes, giving supergenes a competitive edge. Yet, due to their lack of recombination, supergenes are susceptible to deterioration as they cannot efficiently purge deleterious DNA. Few examples outside of sex chromosomes have been available for study. Here, we present the first assembly of thethaplotype, a 33.4 Mb supergene in house mice that ‘selfishly’ transmits itself at non-Mendelian frequencies. We characterize the four large non-overlapping inversions that make up thethaplotype. We compare in at/tindividual two differenttvariants with different recessive lethal phenotypes (age at death). Despite that difference, they differ much less from each other than the rest of the chromosome. However, the differences that they have were much more likely to be deleterious than the differences between the two variants of the rest of the chromosome. We interpret this marked difference as evidence of the accumulation of deleterious variants, a hallmark of deterioration. Thetregion of chromosome 17 is more distant to the reference than the rest of the chromosome, and has a higher fraction of impactful differences here as well. Thus, we conclude that thetappears as a quickly spreading and deteriorating selfish supergene, a rare example of Muller’s ratchet outside of sex chromosomes. Furthermore, we aim for our assembly to provide a resource for comparative work on thethaplotype, such as its evolutionary history.
Ecotype formation in the European anchovy fuelled by structural variants of different origins and genetic interactions with a southern lineage
Authors: Meyer Laura , Barry Pierre , Arbiol Christine , Castilho Rita , Van der Lingen Carl , Chlaïda Malika , McKeown Niall J , Ernande Bruno , Le Moan Alan , Bonhomme François , Gagnaire Pierre-Alexandre , Guinand Bruno
Published: September 2024

The speciation of ecotypes can unfold in diverse ways and likely depends on multiple processes. The variants involved in ecotype divergence can include new mutations as well as older allelic variation that evolved in different contexts. Among the different types of variants that can contribute to reproductive isolation between ecotypes, structural variants (SVs) represent likely candidates due to their ability to protect divergent haplotypes from recombination and gene flow. The European anchovy (Engraulis encrasicolus) is known to be subdivided into marine and coastal ecotypes, and their divergence shows patterns that are consistent with SVs. Here, we present the first genome-scale study investigating genetic structure in theE. encrasicolusspecies complex. We generated a reference genome and produced whole-genome resequencing data for anchovies from the North-East Atlantic and Mediterranean Sea, as well as from South Africa. We complemented this approach with the analysis of RAD-seq data in order to study ecotypic structure across the entire distribution range. We found that genetic diversity is not only characterised by the presence of two genetic clusters, namely the marine and coastal ecotypes, but also by a third ancestry which corresponds to a southern Atlantic lineage. This lineage occurs off South Africa but also in southern Morocco and the Canary Islands, and shows a gradient of admixture with northern populations nearing the Atlantic-Mediterranean transition zone. Genomic landscapes of differentiation showed evidence for large regions of high linkage disequilibrium, likely representing SVs that differentiate the three anchovy lineages. We found evidence that three of the SVs contributing to the gene flow barrier between ecotypes originated in the southern lineage, suggesting that the coastal and southern lineages have a partly shared evolutionary history. In addition to these barriers, three other SVs contributing to ecotype differentiation appear to have evolvedin situ. Anchovies thus present an interesting case for the study of ecotype speciation, since the barriers involved in reproductive isolation have different origins and have partly diverged in geographic isolation.
Sex-, development-, and nutrition-dependent expression of a major age-at-maturity gene in Atlantic salmon
Authors: Åsheim Eirik Ryvoll , Debes Paul Vincent , House Andrew , Liljeström Petra , Ruokolainen Annukka , Frapin Morgane , Donner Iikki , Ahi Ehsan Pashay , Erkinaro Jaakko , Verta Jukka-Pekka , Primmer Craig R
Published: September 2024

Sexual maturation is a key process in the life history of an organism and is influenced by both genetic and environmental factors. In Atlantic salmon (Salmo salar), alternative alleles at the gene vgll3 have been found to associate with a large proportion of the variation in maturation age, yet the molecular and physiological mechanisms of this association are still largely unknown. Here, we investigated the mechanisms by which genetic variation in this major age-at-maturity gene translated into phenotypic variation. We established a time series of gonadal vgll3 mRNA expression in male and female Atlantic salmon in a common garden setting, starting at the prepubertal stage and spanning multiple spawning seasons. We found that vgll3 mRNA expression is reduced in early-maturing males and females. However, for the second spawning season, vgll3 expression increased with gonadal development in males, but eventually decreased in females. Expression of vgll3 had context-dependent correlations with expression of amh and lhr. We also found signs of reduced testicular vgll3 expression in a low-fat feed treatment. By significantly widening the scope of our knowledge on temporal vgll3 expression dynamics, our results exemplify that major-effect genes may use different pathways in sexes but achieve similar outcomes.
Molecular Magnetic Resonance Imaging of Dysregulated Zinc Secretion Detects Early Pancreatic Ductal Adenocarcinoma Lesions and Response to KRASG12D Inhibitor Treatment
Authors: Jordan Veronica Clavijo , Sojoodi Mozhdeh , Moloudi Farzad , Gonzalez-Pagan Patricia , Jin Manyu , Pantazopoulos Pamela , French Ethan , Whittier Jonah Weigand , Rotile Nicholas , Tavallai Mehrad , Hallin Jill , Ramsay Ian , Gale Eric M , Barrett Stephen C. , El-Bardeesy Nabeel , Qadan Motaz , Tanabe Kenneth K. , Caravan Peter
Published: September 2024

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer, primarily due to late-stage diagnosis and limited treatment options. Zinc homeostasis is markedly dysregulated in PDAC and this dysregulation can be probed by administering a secretagogue to stimulate zinc secretion (SSZS) in the exocrine pancreas and imaging this secretion with a zinc sensitive MRI probe. This study demonstrates the potential of SSZS MRI for early detection, monitoring treatment response, and assessing recurrence after treatment withdrawal in PDAC. Our approach relies on interrogating the pancreas, circumventing the challenge of locating small, elusive tumors. By SSZS MRI, we detected PDAC by observing the unique zinc hypersecretory activity of the pancreas when malignancy is present. We observed dysregulation of zinc transporters in both human and mouse pancreas containing PDAC and confirmed secretagogue-stimulated zinc secretion in vitro and in vivo. We found that combining secretagogues such as secretin and caerulein maximized zinc secretion and as such MRI signal in the pancreas. Notably, SSZS MRI detected treatment responses to KRAS G12D inhibition within 3-5 days and identified cancer recurrence as early as one day post-treatment withdrawal. Additionally, secretagogue stimulation improved treatment responses and delayed recurrence in both treatment models. These findings suggest that SSZS MRI could significantly enhance PDAC diagnosis and management, providing a novel, non-invasive imaging modality to improve patient outcomes.

STATEMENT OF SIGNIFICANCE

This study demonstrates the utility of secretagogue-stimulated zinc secretion (SSZS) MRI in detecting pancreatic ductal adenocarcinoma (PDAC) at early stages, monitoring treatment responses, and assessing cancer recurrence, thereby offering a promising non-invasive imaging modality to improve PDAC patient management and outcomes.
Multi-task benchmarking of single-cell multimodal omics integration methods
Authors: Liu Chunlei , Ding Sichang , Kim Hani Jieun , Long Siqu , Xiao Di , Ghazanfar Shila , Yang Pengyi
Published: September 2024

Single-cell multimodal omics technologies have empowered the profiling of complex biological systems at a resolution and scale that were previously unattainable. These biotechnologies have propelled the fast-paced innovation and development of data integration methods, leading to a critical need for their systematic categorisation, evaluation, and benchmark. Navigating and selecting the most pertinent integration approach poses a significant challenge, contingent upon the tasks relevant to the study goals and the combination of modalities and batches present in the data at hand. Understanding how well each method performs multiple tasks, including dimension reduction, batch correction, cell type classification and clustering, imputation, feature selection, and spatial registration, and at which combinations will help guide this decision. This study aims to develop a much-needed guideline on choosing the most appropriate method for single-cell multimodal omics data analysis through a systematic categorisation and comprehensive benchmarking of current methods.
PGR5 promotes energy-dependent non-photochemical quenching to enable efficient C4photosynthesis under fluctuating light
Authors: Woodford Russell , Watkins Jacinta , Moore Marten , Nix Samuel J. , Yee Suyan , Chan Kai Xun , Pogson Barry , von Caemmerer Susanne , Furbank Robert T. , Ermakova Maria
Published: September 2024

PROTON GRADIENT REGULATION 5 (PGR5) is essential for generating proton motive force across thylakoid membranes in C3plants and supporting photoprotection under fluctuating light conditions. It is proposed that this function is achieved by regulating cyclic electron flow around Photosystem I. During the evolutionary transition from C3to C4photosynthesis, the leaf abundance of PGR5 has increased, coinciding with a rise in the cyclic electron flow rate. To investigate the contribution of PGR5 to photoprotection in C4photosynthesis, we generated model C4monocotSetaria viridiswith nullpgr5alleles. We show that plants lacking PGR5 struggle to establish proton motive force and energy-dependent non-photochemical quenching (qE) at higher irradiances during instantaneous measurements. This leads to a progressive decline in maximum Photosystem I activity when leaves are exposed to repeated cycles of high irradiance. Additionally, plants without PGR5 exhibit severely reduced growth and photosynthesis compared to wild type plants when grown under fluctuating daylight but not under constant daylight. In the absence of PGR5, a slower-relaxing, zeaxanthin-dependent form of non-photochemical quenching supports growth under fluctuating light, albeit at the cost of reduced photochemical efficiency and assimilation rate. Our findings underscore the role of PGR5 in enabling efficient C4photosynthesis under fluctuating light by establishing proton motive force for the rapid upregulation of qE and preventing photodamage to the electron transport machinery. This study highlights the importance of various non-photochemical quenching mechanisms for C4photosynthesis and emphasises the role of PGR5 in the evolution of C4plants.
Integration of Group A Streptococcus Rapid Tests with the Open Fluidic CandyCollect Device
Authors: Sanchez J. Carlos , Robertson Ingrid H. , Shinkawa Victoria A. M. , Su Xiaojing , Tu Wan-chen , Robinson Timothy R. , Chang Megan M. , Blom Andrea , Alfaro Elena , Hatchett Daniel B. , Olanrewaju Ayokunle O. , Wald Ellen R. , DeMuri Gregory P. , Berthier Erwin , Thongpang Sanitta , Theberge Ashleigh B.
Published: September 2024

The CandyCollect device is a lollipop-inspired open fluidic oral sampling device designed to provide a comfortable user sampling experience. We demonstrate that the CandyCollect device can be coupled with a rapid antigen detection test (RADT) kit designed for Group A Streptococcus (GAS). Throughin vitroexperiments with pooled saliva spiked withStreptococcus pyogeneswe tested various reagents and elution volumes to optimize the RADT readout from CandyCollect device samples. The resulting optimized protocol uses the kit-provided reagents and lateral flow assay (LFA) while replacing the kit’s pharyngeal swab with the CandyCollect device, reducing the elution solution volume, and substituting the tube used for elution to accommodate the CandyCollect device. Positive test results were detected by eye with bacterial concentrations as low as the manufacturer’s “minimal detection limit” - 1.5×105CFU/mL. LFA strips were also scanned and quantified with image analysis software to determine the signal-to-baseline ratio (SBR) and categorize positive test results without human bias. We tested our optimized protocol for integrating CandyCollect and RADT using CandyCollect clinical samples from pediatric patients (n=6) who were previously diagnosed with GAS pharyngitis via pharyngeal swabs tested with RADT as part of their clinical care. The LFA results of these CandyCollect devices and interspersed negative controls were determined by independent observers, with positive results obtained in four of the six participants on at least one LFA replicate. Taken together, our results show that CandyCollect devices from children with GAS pharyngitis can be tested using LFA rapid tests.

Table of Contents/Abstract Figure
Serum, Cell-Free, HPV-Human DNA Junction Detection and HPV Typing for Predicting and Monitoring Cervical Cancer Recurrence
Authors: Van Arsdale Anne , Mescheryakova Olga , Gallego Sonia , Maggi Elaine C. , Harmon Bryan , Kuo Dennis Y.S. , Van Doorslaer Koenraad , Einstein Mark H. , Haas Brian J. , Montagna Cristina , Lenz Jack
Published: September 2024

Almost all cervical cancers are caused by human papillomaviruses (HPVs). In most cases, HPV DNA is integrated into the human genome. We found that tumor-specific, HPV-human DNA junctions are detectable in serum cell-free DNA of a fraction of cervical cancer patients at the time of initial treatment and/or at six months following treatment. Retrospective analysis revealed these junctions were more frequently detectable in women in whom the cancer later recurred. We also found that cervical cancers caused by HPV types outside of phylogenetic clade α9 had a higher recurrence frequency than those caused by α9 types in both our study and The Cancer Genome Atlas cervical cancer database, despite the higher prevalence of α9 types including HPV16 in cervical cancer. Thus, HPV-human DNA junction detection in serum cell-free DNA and HPV type determination in tumor tissue may help predict recurrence risk. Screening serum cell-free DNA for junctions may also offer an unambiguous, non-invasive means to monitor absence of recurrence following treatment.
Performance of Deep Learning Models in Predicting the Nugent Score to Diagnose Bacterial Vaginosis
Authors: Watanabe Naoki , Watari Tomohisa , Akamatsu Kenji , Miyatsuka Isao , Otsuka Yoshihito
Published: September 2024

The Nugent score is a commonly used tool for diagnosing bacterial vaginosis; however, its accuracy depends on the skills of laboratory technicians. We aimed to evaluate the performance of deep learning models in predicting the Nugent score, with the goal of improving diagnostic consistency and accuracy. A total of 1,510 vaginal images collected from a hospital in Japan between 2021 and 2023 were assessed. Each image was annotated by laboratory technicians into one of four categories based on the Nugent score—normal vaginal flora, absence of vaginal flora, altered vaginal flora, or bacterial vaginosis. Deep learning models were developed to predict these categories, and their performance was evaluated by comparing the predicted scores with technician annotations. A high magnification model was further optimized and evaluated using an independent test set of 106 images to assess its performance relative to that of the technicians. The deep learning models demonstrated an accuracy of 84% at low magnification and 89% at high magnification in predicting the Nugent score categories. After optimization, the high magnification model achieved 94% accuracy, surpassing the average 92% accuracy of the technicians. The agreement between deep learning model predictions and technician annotations was 92% for normal vaginal flora, 100% for absence of vaginal flora, 91% for altered vaginal flora, and 100% for bacterial vaginosis. The deep learning models demonstrated accuracy comparable to that of laboratory technicians, which indicates their potential utility in improving the diagnostic accuracy of bacterial vaginosis.

IMPORTANCE

Bacterial vaginosis is a global health issue affecting women, causing symptoms such as abnormal vaginal discharge and discomfort. The Nugent score is the standard method for diagnosing bacterial vaginosis and is based on manual interpretation of Gram-stained vaginal smears. However, this method relies on the skill and experience of trained professionals, leading to variability in results and challenges in facilities with limited access to such experts. This poses significant challenges for settings with limited access to experienced technicians. The deep learning models developed in this study predict the Nugent score with high accuracy; thus, they can be used to standardize the diagnosis of bacterial vaginosis, reduce observer variability, and enable reliable diagnosis even in settings without experienced personnel. Although larger scale validation is needed, our results suggest that deep learning models may represent a new approach for the diagnosis of bacterial vaginosis.
Randomized dose-response trial of n-3 fatty acids in hormone receptor negative breast cancer survivors—impact on breast adipose oxylipin and DNA methylation patterns
Authors: Frankhouser David E. , DeWess Todd , Snodgrass Isabel F. , Cole Rachel M. , Steck Sarah , Thomas Danielle , Kalu Chidimma , Belury Martha A. , Clinton Steven K. , Newman John W. , Yee Lisa D.
Published: September 2024

Background

Increasing evidence suggests the unique susceptibility of estrogen receptor and progesterone receptor negative (ERPR-) breast cancer to dietary fat amount and type. Dietary n-3 polyunsaturated fatty acids (PUFAs), such as docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), may modulate breast adipose fatty acid profiles and downstream bioactive metabolites to counteract pro-inflammatory, pro-carcinogenic signaling in the mammary microenvironment.

Objective

To determine effects of ∼1 to 5 g/d EPA+DHA over 12 months on breast adipose fatty acid and oxylipin profiles in women with ERPR(−) breast cancer, a high-risk molecular subtype.

Methods

We conducted a 12-month randomized controlled, double-blind clinical trial of ∼5g/d vs ∼1g/d DHA+EPA supplementation in women within 5 years of completing standard therapy for ERPR(−) breast cancer Stages 0-III. Blood and breast adipose tissue specimens were collected every 3 months for biomarker analyses including fatty acids by gas chromatography, oxylipins by LC-MS/MS, and DNA methylation by reduced-representation bisulfite sequencing (RRBS).

Results

A total of 51 participants completed the 12-month intervention. Study treatments were generally well-tolerated. While both doses increased n-3 PUFAs from baseline in breast adipose, erythrocytes, and plasma, the 5g/d supplement was more potent (n =51, p <0.001). The 5g/d dose also reduced plasma triglycerides from baseline (p =0.008). Breast adipose oxylipins at 0, 6, and 12 months showed dose-dependent increases in unesterified and esterified DHA and EPA metabolites (n =28). Distinct DNA methylation patterns in adipose tissue after 12 months were identified, with effects unique to the 5g/d dose group (n =17).

Conclusions

Over the course of 1 year, EPA+DHA dose-dependently increased concentrations of these fatty acids and their derivative oxylipin metabolites, producing differential DNA methylation profiles of gene promoters involved in metabolism-related pathways critical to ERPR(−) breast cancer development and progression. These data provide evidence of both metabolic and epigenetic effects of n-3 PUFAs in breast adipose tissue, elucidating novel mechanisms of action for high-dose EPA+DHA-mediated prevention of ERPR(−) breast cancer.

Clinicaltrials.gov identifierNCT02295059
Prevalence and real-world effectiveness of popular smoking cessation aids in England: a population-based study
Authors: Jackson Sarah E. , Brown Jamie , Buss Vera , Shahab Lion
Published: September 2024

Importance

A wide range of medications, non-combustible nicotine products, behavioural support, and alternative treatments are available in England to help people stop smoking. Understanding their effectiveness in the real world can support informed decision-making.

Objectives

To provide up-to-date estimates of the prevalence and real-world effectiveness of different smoking cessation aids and explore moderation of effectiveness by socioeconomic position.

Design

Population-based survey, 2006-2024.

Setting

England.

Participants

25,094 adults (≥16y) who reported having tried to quit smoking in the past year.

Main outcomes and measures

The outcome variable was self-reported continuous abstinence from the start of the most recent quit attempt up to the time of survey. Independent variables were use (yes/no) of the following aids in the most recent attempt: nicotine replacement therapy (NRT) obtained on prescription or over-the-counter; varenicline; bupropion; e-cigarettes; face-to-face behavioural support; telephone support; written self-help materials; websites; smartphone apps; hypnotherapy; Allen Carr’s Easyway method; heated tobacco products (HTPs); nicotine pouches. Covariates included sociodemographic characteristics and features of the quit attempt.

Results

We analysed data from 25,094 participants (mean [SD] age = 38.7y [15.3]; 48.5% women). In 2023/24, the most used aids were e-cigarettes (40.2%) and over-the-counter NRT (17.3%); 40.8% of quit attempts were unaided. While e-cigarette use was associated with higher odds of abstinence after adjustment for use of other aids and covariates (OR=1.95 [1.74-2.17]), use of over-the-counter NRT was not (OR=1.03 [0.93-1.15]). Other aids positively associated with abstinence were websites (used by 4.6% in 2023/24; OR=1.43 [1.03-1.98]), prescription NRT (4.5%; OR=1.33 [1.12-1.58]), varenicline (1.1%; OR=1.80 [1.50-2.18]), and HTPs (0.7%; OR=2.37 [1.24-4.51]). Face-to-face behavioural support (used by 2.2% in 2023/24) was also associated with higher odds of abstinence among those from less advantaged (OR=1.59 [1.19-2.14]) but not more advantaged social grades (OR=0.91 [0.65-1.29]). There was not clear evidence of a benefit of any other aid, although some analyses were inconclusive.

Conclusions and relevance

A range of effective smoking cessation aids are available in England, but many people try to quit using less effective forms of support or none at all. Quit success rates could be improved by encouraging people to use more effective methods.
Allelic effects onKLHL17expression likely mediated by JunB/D underlie a PDAC GWAS signal at chr1p36.33
Authors: Connelly Katelyn E. , Hullin Katherine , Abdolalizadeh Ehssan , Zhong Jun , Eiser Daina , O’Brien Aidan , Collins Irene , Das Sudipto , Duncan Gerard ,   Pancreatic Cancer Cohort Consortium,   Pancreatic Cancer Case-Control Consortium, Chanock Stephen J. , Stolzenberg-Solomon Rachael Z. , Klein Alison P. , Wolpin Brian M. , Hoskins Jason W. , Andresson Thorkell , Smith Jill P. , Amundadottir Laufey T.
Published: September 2024

Pancreatic Ductal Adenocarcinoma (PDAC) is the third leading cause of cancer-related deaths in the U.S. Both rare and common germline variants contribute to PDAC risk. Here, we fine-map and functionally characterize a common PDAC risk signal at 1p36.33 (tagged by rs13303010) identified through a genome wide association study (GWAS). One of the fine-mapped SNPs, rs13303160 (r2=0.93 in 1000G EUR samples, OR=1.23,Pvalue=2.74×10−9) demonstrated allele-preferential gene regulatory activityin vitroand allele-preferential binding of JunB and JunDin vitroandin vivo. Expression Quantitative Trait Locus (eQTL) analysis identifiedKLHL17as a likely target gene underlying the signal. Proteomic analysis identified KLHL17 as a member of the Cullin-E3 ubiquitin ligase complex in PDAC-derived cells.In silicodifferential gene expression analysis of the GTExv8 pancreas data suggested an association between lower KLHL17 (risk associated) and pro-inflammatory pathways. We hypothesize that KLHL17 may mitigate inflammation by recruiting pro-inflammatory proteins for ubiquitination and degradation thereby influencing PDAC risk.
Statin uses and skeletal muscle-related phenotypes: insights from epidemiological and Mendelian randomization analyses
Authors: Tang Fan , Chen Zhanchao , Qiu Hongbing , Liu Yige , Shen Yanjiao , Zhang Yiying , Wang Shanjie , Yu Bo
Published: September 2024

Background

The association between statin use and skeletal muscle-related side effects is always controversial. This study aimed to comprehensively investigate the associations between statin use and muscle-related phenotypes including sarcopenia, sarcopenic obesity, serum lactate dehydrogenase (LDH), and musculoskeletal pain symptoms among adults with indications for statin use for secondary prevention (cardiovascular disease, diabetes, or hyperlipidemia).

Methods

This cross-sectional study included 22,549 patients aged ≥20 years with cardiovascular disease, diabetes, or hyperlipidemia. Weighted generalized linear regression analysis and propensity score matching methods were used to estimate the associations between the use of statins or other lipid-lowering agents and skeletal muscle-related phenotypes. Mendelian randomization (MR) analysis was additionally used to verify the causal relationship between statin use and skeletal muscle-related phenotypes.

Results

The weighted mean age was 59 years, 50.3% were male, and 37.6% (n=8,481) received statin treatment. In the unadjusted model, compared with adults without any lipid-lowering drugs, statin use was associated with a higher likelihood of sarcopenia (appendicular skeletal muscle mass [ASM]/Body mass index [BMI] OR 1.35 (95%CI 1.12 to 1.62, p < 0.001), ASM/weight [Wt] OR 1.86 (95%CI 1.62 to 2.13, p < 0.001), max HGS β -3.01 (95% CI -3.97 to -2.06, p < 0.001), relative HGS β -0.23 (95% CI -0.30 to -0.17, p < 0.001) and combined HGS β -5.90 (95% CI -7.86 to -3.93, p < 0.001)), sarcopenic obesity (ASM/height squared [Ht2] and body fat percentage definition [OR 1.36 (95% CI 1.13 to 1.63, p < 0.001]). After multivariable adjustment or propensity score match, the independent associations of statin use with sarcopenia, sarcopenic obesity, HGS, LDH, and musculoskeletal pain became nonsignificant. Stepwise regression suggested that age was the predominant confounding factor for the associations. MR analysis also revealed no significant causality between statin use and skeletal muscle-related phenotypes.

Conclusions

Our epidemiological and MR analyses did not support the causality between statin use and skeletal muscle-related phenotypes. A higher likelihood of skeletal muscle-related adverse phenotypes in statin users may be attributed to age. Future studies should further explore the biological factors that may affect statin-related muscle phenotypes to provide evidence for the safety of statins.
Effects of a Cardiac and Psychosocial Rehabilitation Program on Anxiety, Depression, Self-Efficacy, Quality of Life, and Exercise Capacity in Young Adults With Fontan Circulation: A Randomized Controlled Trial
Authors: Moon Ju Ryoung , Huh June , Song Jinyoung , Kang I-Seok , Park Goeun , Kim Kyunga , Sung Jidong , Chang Sung-A , Park Seung Woo , Yang Ji-Hyuk , Jun Tae-Gook
Published: September 2024

BACKGROUND

Young adults with Fontan circulation (FC) face psychosocial, physical, and environmental challenges and are vulnerable to emotional distress. They need holistic intervention programs to face these problems and enhance their quality of life. This study developed and evaluated a cardiac and psychosocial rehabilitation (CPR) program for young adults with FC.

METHODS AND RESULTS

Thirty-eight young adults with FC aged 18–23 years were prospectively recruited from an outpatient clinic and randomized into a CPR group (n = 12) that underwent eight weekly group-based sessions combining a psychosocial program based on cognitive behavioral therapy with home-based cardiac rehabilitation (CR), a CR group (n = 12) that received only home-based CR, and a usual care control group (n = 12). The study assessed CPR program effectiveness based on the Hospital Anxiety and Depression Scale, self-efficacy, quality of life, and exercise capacity testing at three time points: pre-intervention, post-intervention, and four weeks post-intervention. Participants’ average ages were 19.75 (2.28), 19.65 (1.79), and 20.38 (1.85) years in the CPR, CR, and control groups, respectively; 50% (CPR group) to 53.8% (CR and control groups) of the participants were male. After eight weeks, depression and anxiety decreased, whereas self-efficacy and quality of life increased in the CPR group compared with the CR and control groups. The groups showed no differences in exercise capacity.

CONCLUSION

CPR can be part of an intervention for alleviating psychological distress and improving self-efficacy in young adults with FC. Efforts should be made to increase the efficacy of home-based CR.
The role of disease state in confined migration
Authors: Meid Annika
Published: September 2024

Cell migration is a fundamental process in both normal and cancerous tissues, playing a crucial role in development, immune responses, and, in the case of cancer cells, metastasis- a leading cause of cancer-related mortality. Understanding the differences between healthy and cancerous cell migration is essential for uncovering potential therapeutic targets. This study aims to elucidate these differences by comparing the migratory behaviors of healthy cells (nHDF cells) and cancer cells (MDA-MB-231 cells). Our findings reveal that cancer cells significantly reduce their stiffness during migration through narrow channels, a phenomenon not observed in healthy cells. Additionally, DNA and membrane repair mechanisms are more active in healthy cells during migration compared to tumor cells. Notably, the use of MDA-MB-231 FUCCI cells demonstrates that the cell cycle profoundly influences cell migration under confined conditions. These insights provide a deeper understanding of the cellular mechanisms driving migration in both healthy and cancerous cells.