bluuebunny/crossref_metadata_2025_split huggingface dataset:
Planning and developing an intervention to improve the psychological wellbeing of people living with persistent pain: De-StressPain
Authors: Hughes Stephanie , Pincus Tamar , Geraghty Adam W A , Chew-Graham Carolyn A. , Stuart Beth , Little Paul , Moore Michael , Birkinshaw Hollie 
Published: September 2024

AbstractBackgroundPeople with persistent musculoskeletal (MSK) pain often report depressive symptoms. Distress and depression have been found to predict the development of chronic pain conditions. Evidence suggests pain-related distress is qualitatively different from depressive illness, and current referral pathways and available interventions are sub-optimal for people with persistent MSK pain and distress. We aimed to develop and test the acceptability and proof of concept of an intervention to reduce pain-related distress in people with chronic MSK pain.MethodsThe Person-Based Approach (PBA)(1) informed the processes undertaken to inform intervention development. This included semi-structured interviews with people with persistent pain and with General Practitioners (GPs); and a stakeholder discussion with social prescribers. Patient and Public Involvement (PPI) representatives had input throughout all development work. Findings from these activities were triangulated to inform the development of a prototype intervention which was tested in a repeated-measures, mixed methods proof-of-concept study called De-StressPain.The De-StressPainintervention offered 4-6 social prescriber sessions over 12 weeks, and access to a study website. 16 participants were recruited from general practices, and 4 social prescribers were recruited from Primary Care Networks (PCNs) and charitable organisations. Both quantitative measures and qualitative interviews were completed by participants at baseline and 12 weeks post-baseline. Quantitative measures included questions about mood (DAPOS, WEMWBS, 4DSQ), pain chronicity, pain intensity and musculoskeletal health (MSK-HQ). Semi-structured interviews with participants explored the participants’ context, their experiences of pain related distress, and their experiences of the intervention. Social prescribers were interviewed to explore their experiences of delivering the intervention. Interviews were analysed using thematic analysis.ResultsThe De-StressPainintervention was acceptable both to patients and to social prescribers. Some participants experienced positive changes such as improved mood, increased hope and increased activity. The social prescribers (“De-Stress Coaches”) provided accountability and supported motivation. All measures of mood showed improvement. Limited time and money were identified as barriers to engagement, along with participants holding the view that increasing pleasurable activities was indulgent. Some participants were already socially engaged and busy at the point of entering the study.ConclusionsWe have confirmed the intervention is needed, acceptable and welcomed by people with pain. Social prescribers found the intervention acceptable to deliver. We identified the barriers that need to be addressed in future versions of the intervention.
Exploring MicroRNA Signatures in Pediatric Non-infectious Uveitis: Meta-Analysis and Molecular Profiling of Patient Samples
Authors: Wawrzyniak Olga , Wawrzyniak Dariusz , Smuszkiewicz Michał , Głodowicz Paweł , Gotz-Więckowska Anna , Rolle Katarzyna 
Published: September 2024

AbstractPurposeTo find a distinct non-coding RNA characteristic for idiopathic uveitis in the pediatric population. To explore the autoimmune-related miRNA expression profile in pediatric patients with idiopathic uveitis (IU) and juvenile idiopathic arthritis-associated uveitis (JIA-AU) and find a common molecular background for idiopathic uveitis and other autoimmune diseases.Materials and methodsThe expression levels of miRNAs were analyzed by quantitative real-time PCR using serum samples from patients with idiopathic uveitis (n=8), juvenile idiopathic arthritis-associated uveitis (n=7), and healthy controls. We selected the most promising miRNAs from the original research papers: miR-16-5p, miR-26a-5p, miR-145-5p, miR-451a as markers for juvenile idiopathic arthritis, miR-23a-3p, miR-29a-3p, miR-140-5p, miR-193a-5p and miR-491-5p for uveitis in the adult population, and miR-125a-5p, miR-146a-5p, miR-155-5p, miR-223-5p, miR-223-3p characteristic for both diseases and confirm their expression changes in serum from children with idiopathic uveitis. We comprehensively reviewed the literature enrolling the papers that met the inclusion criteria (miRNA and non-infectious uveitis/juvenile idiopathic arthritis) and performed target prediction analysis of appoint miRNAs. It additionally confirmed that altered miRNAs target the immunologically involved genes.ResultsImmunological involved miRNAs such as miR-146a-5p and miR-155-5p show diverse expression levels in different patients as they interact with multiple targets. miR-204-5p is downregulated in both patient groups compared to healthy controls.ConclusionmiR-204-5p and miR-155-5p are candidates for molecular markers of autoimmune uveitis. We did not identify the miRNAs specific only to idiopathic uveitis, but for the first time in the pediatric population, we confirmed that this disease entity shares a molecular basis with other autoimmune diseases. Further studies are required to elucidate the molecular interactions among miRNAs, cytokines, and transcription factors within the intricate immune response, particularly in the eye.
To FID or not to FID: Applying GANs for MRI Image Generation in HPC
Authors: Cepa Beatriz , Brito Cláudia , Sousa António 
Published: September 2024

AbstractWith the rapid growth of Deep Learning models and neural networks, the medical data available for training – which is already significantly less than other types of data – is becoming scarce. For that purpose, Generative Adversarial Networks (GANs) have received increased attention due to their ability to synthesize new realistic images. Our preliminary work shows promising results for brain MRI images; however, there is a need to distribute the workload, which can be supported by High-Performance Computing (HPC) environments. In this paper, we generate 256×256 MRI images of the brain in a distributed setting. We obtained an FIDRadImageNetof 10.67 for the DCGAN and 23.54 for the WGAN-GP, which are consistent with results reported in several works published in this scope. This allows us to conclude that distributing the GAN generation process is a viable option to overcome the computational constraints imposed by these models and, therefore, facilitate the generation of new data for training purposes.
Identifying similar populations across independent single cell studies without data integration
Authors: González-Velasco Óscar , Simon Malte , Yilmaz Rüstem , Parlato Rosanna , Weishaupt Jochen , Imbusch Charles D. , Brors Benedikt 
Published: September 2024

AbstractSupervised and unsupervised methods have emerged to address the complexity of single cell data analysis in the context of large pools of independent studies. Here, we present ClusterFoldSimilarity (CFS), a novel statistical method design to quantify the similarity between cell groups acroos any number of independent datasets, without the need for data correction or integration. By bypassing these processes, CFS avoids the introduction of artifacts and loss of information, offering a simple, efficient, and scalable solution. This method match groups of cells that exhibit conserved phenotypes across datasets, including different tissues and species, and in a multimodal scenario, including single-cell RNA-Seq, ATAC-Seq, single-cell proteomics, or, more broadly, data exhibiting differential abundance effects among groups of cells. Additionally, CFS performs feature selection, obtaining cross-dataset markers of the similar phenotypes observed, providing an inherent interpretability of relationships between cell populations. To showcase the effectiveness of our methodology we generated single-nuclei RNA-Seq data from the motor cortex and spinal cord of adult mice. By using CFS, we identified three distinct sub-populations of astrocytes conserved on both tissues. CFS includes various visualization methods for the interpretation of the similarity scores and similar cell populations.
Whole blood transcriptome profile identifies motor neurone disease (MND) RNA biomarker signatures
Authors: Kõks Sulev , Rallmann Karin , Muldmaa Mari , Price Jack , Pfaff Abigail L , Taba Pille 
Published: September 2024

AbstractBlood-based biomarkers for motor neuron disease are needed for better diagnosis, progression prediction, and clinical trial monitoring. We used whole blood-derived total RNA and performed whole transcriptome analysis to compare the gene expression profiles in (motor neurone disease) MND patients to the control subjects. We compared 42 MND patients to 42 aged and sex-matched healthy controls and described the whole transcriptome profile characteristic for MND. In addition to the formal differential analysis, we performed functional annotation of the genomics data and identified the molecular pathways that are differentially regulated in MND patients. We identified 12,972 genes differentially expressed in the blood of MND patients compared to age and sex-matched controls. Functional genomic annotation identified activation of the pathways related to neurodegeneration, RNA transcription, RNA splicing and extracellular matrix reorganisation. Blood-based whole transcriptomic analysis can reliably differentiate MND patients from controls and can provide useful information for the clinical management of the disease and clinical trials.
Myocardial Endoglin Regulates Cardiomyocyte Proliferation and Cardiac Regeneration
Authors: Sorensen Daniel W. , Tan Philip M. , Garay Bayardo I. , Solinsky Jacob , Yücel Doğacan , Zhang Michael J. , Galvin Conor , Elsenpeter Henry , Mikkila Jennifer , Jerdee Kendra , O’Connell Timothy D. , Molkentin Jeffery D. , Perlingeiro Rita C.R. , Kawakami Yasuhiko , Saucerman Jeffrey J. , van Berlo Jop H. 
Published: September 2024

AbstractThe mammalian heart loses almost all its regenerative potential in the first week of life due to the cessation of the ability of cardiomyocytes to proliferate. In recent years, a number of regulators of cardiomyocyte proliferation have been identified. Despite this, a clear understanding of the regulatory pathways that control cardiomyocyte proliferation and cardiac regeneration is lacking, and there are likely additional regulators to be discovered. Here, we performed a genome-wide screen on fetal murine cardiomyocytes to identify potential novel regulators of cardiomyocyte proliferation. Endoglin was identified as an inhibitor of cardiomyocyte proliferation in vitro. Endoglin knock-down resulted in enhanced DNA synthesis, cardiomyocyte mitosis and cytokinesis in mouse, rat and human cardiomyocytes. Using gene-targeted mice, we confirmed myocardial Endoglin to be important in cardiomyocyte proliferation and cardiac regeneration using gene-targeted mice. Mechanistically, we show that Smad signaling is required for the endoglin-mediated anti-proliferative effects. Our results identify the TGF-β coreceptor Endoglin as a regulator of cardiac regeneration and cardiomyocyte proliferation.SummaryHigh-content function screening is used to identify a novel inhibitor of cardiomyocyte proliferation which can promote mammalian cardiac regeneration.
Identifying Agronomic, Nutrition and Leaf Vein Quantitative Trait Loci in the Orphan CropGynandropsis gynandra
Authors: Simpson Conor J. C. , Sogbohossou Dêêdi E. O. , Reeves Gregory , Schranz M. Eric , Singh Pallavi , Hibberd Julian M. 
Published: September 2024

AbstractA sustainable food supply is vital for addressing the challenges of a growing global population and climate change.Gynandropsis gynandra, a nutritious C4orphan crop native to Africa and Asia, thrives in low-input agricultural systems, making it a valuable candidate for future food security. This crop also serves as a model for studying C4photosynthesis. However, research on its genetic improvement is limited. In this study, two mapping populations from diverse parental lines were used to identify Quantitative Trait Loci (QTL) linked to agronomically relevant traits like plant height, leaf area, flowering time, nutritional content, and photosynthesis. Fifteen QTL were identified, with two affecting both leaf size and flowering time across populations, which can be applied for marker assisted selection for crop improvement. Additionally, QTL linked to C4photosynthesis provide insights into the genetic mechanisms behind this pathway. Overall, this research enhances the potential ofG. gynandraas a climate-resilient crop.One sentence summaryLeveraging natural variation inGynandropsis gynandrato identify QTL associated with important traits.
Sirtuin 6 is a histone delactylase
Authors: Nickel Garrison A. , Pederson Nicholas J. , Faheem  , Yang Zhenyu , Bulf Jack , Diehl Katharine L. 
Published: September 2024

AbstractHistone lactylation (Kla) is a post translational modification (PTM) that is derived from metabolic lactate. Histone Kla has been extensively studied in the field of inflammation resolution and macrophage polarization but has also been implicated in diverse cellular processes including differentiation, various wound repair phenotypes, and oncogenesis in several cancer models. While mechanistic connections between histone Kla and transcriptional changes have been studied in very limited contexts, general mechanistic details describing how regulation of gene expression by histone Kla occurs are scarce. It is hypothesized that histone Kla may be installed either through nonenzymatic means or by the p300 histone acyltransferase complex, and it is known that Class I HDACs and Sirtuins 1-3 can remove histone Kla. Here, we identified histone delactylase activity of the deacylase enzyme Sirtuin 6 (Sirt6), a member of the Class III HDAC family known to have roles in regulating metabolic homeostasis. We characterized the ability of Sirt6 to delactylate histonesin vitroand in mammalian cell culture. We identified H3K9 and H3K18, canonical histone sites of Sirt6-catalyzed deacetylase activity, as sites of its delactylase activity. We also demonstrated that the delactylase activity of Sirt6 and the Class I HDACs are additive, suggesting that they represent different cellular axes of regulating gene expression via controlling levels of histone Kla.
Periodontal health in a French cohort of people with Parkinson’s disease
Authors: Samot J , Courtin E , Guehl D , Damon-Perriere N , Branchard O , Saint-Jean M , Chuy V , Ella B , Badet MC 
Published: September 2024

ABSTRACTThe deterioration of motor skills and fine hand movement impairment associated with Parkinson’s disease (PD) hinders the performance of daily oral hygiene procedures. This study examined the periodontal health of people with PD using clinical and microbiological periodontal parameters measured at two time points during their medical follow-up.This prospective cohort study included participants with PD. Clinical oral health data, including oral hygiene and periodontal status, as well as microbiological samples were collected at baseline and after follow-up for at least 3 months.Forty people with PD were recruited (35% female; median [Q1–Q3] age: 65.3 [57.9– 72.8] years) and 35 were followed up. The participants had good hygiene habits, and the proportion of participants with a “good” plaque index improved during follow-up (+21 points,p= 0.239). The proportion of patients with periodontal pockets > 6 mm decreased from 20% to 3% (p= 0.131). This improvement was associated with a reduction in theTreponema denticolabacterial load (p= 0.003).The oral hygiene of people with PD improved during this study. Although these promising results require confirmation, they are an important step toward enhancing oral care support for PD patients.ClinicalTrials.gov Identifier:NCT03827551, registered on January 31, 2019, (https://clinicaltrials.gov/study/NCT03827551)
Nitroxoline evidence Amoebicidal Activity againstAcanthamoeba castellaniithrough DNA damage and the stress response pathways
Authors: Chen Lijun , Han Wei , Feng Meng , Jing Wenwen , Zhou Qingtong , Cheng Xunjia 
Published: September 2024

AbstractAcanthamoeba castellaniiis a widespread unicellular eukaryote found in diverse environments, including tap water, soil, and swimming pools. It is responsible for severe infections, such asAcanthamoebakeratitis and granulomatous amebic encephalitis, particularly in individuals with immunocompromisation. The ability of protozoans to form dormant cysts complicates treatment, as current therapies are ineffective against cyst stages and suffer from poor specificity and side effects. Nitroxoline, a quinoline derivative with well-established antibacterial, antifungal, and antiviral properties, is a promising therapeutic candidate. This study aimed to elucidate cellular signalling events that counteract the effects of nitroxoline. In this study, nitroxoline significantly reduced the viability ofA. castellaniitrophozoites in a dose- and time-dependent manner, inducing morphological changes and apoptosis. Transcriptomic analysis revealed substantial alterations in gene expression, including enrichment of metabolic pathways, DNA damage responses, and iron ion binding. Nitroxoline treatment upregulated genes involved in DNA repair and oxidative stress response while regulating genes in the methionine and cysteine cycles. It also decreased the mitochondrial membrane potential, H₂S production, and total iron amount inA. castellanii. Bioinformatics analyses and molecular docking studies suggest direct interactions between nitroxoline andA. castellaniiproteins. Our research provides a comprehensive molecular map of the response ofA. castellaniito nitroxoline, revealing significant changes in gene expression related to the stress response and metabolic pathways. These findings underscore the potential of nitroxoline as a potent anti-Acanthamoebaagent, offering new insights into its mechanism of action and paving the way for effective therapeutic strategies.
Pulvinar perturbation causes functional reorganization of visual attentional information in posterior parietal cortex
Authors: Yang Fang-Chi , Chiang Feng-Kuei , Rich Erin L. , Burwell Rebecca D. 
Published: September 2024

AbstractThe pulvinar nucleus of the thalamus (PUL) is a higher-order thalamic relay and the main visual extrageniculate thalamic nucleus. Evidence suggests the PUL coordinates information processing across cortical areas involved in visual perception and attention. Other findings suggest the PUL may also influence higher-order cognitive processes, such as attentional control, through interactions with connected neocortical areas like the posterior parietal cortex (PPC). We hypothesized that PUL input to the dorsal and caudal PPC (DPPC and CPPC) enhances visuospatial processing and attention. To test this hypothesis, we recorded neuronal activity in the PUL, DPPC, and CPPC of freely behaving rats performing the visuospatial attention (VSA) task while optogenetically suppressing PUL neurons on some trials. We found that PUL manipulation did not affect behavioral performance, but reorganized neural codes in DPPC and CPPC as well as PUL itself.
Spin Exchange-Enabled Quantum Simulator for Large-Scale Non-Abelian Gauge Theories
Authors: Halimeh Jad C. , Homeier Lukas , Bohrdt Annabelle , Grusdt Fabian 
Published: September 2024

A central requirement for the faithful implementation of large-scale lattice gauge theories (LGTs) on quantum simulators is the protection of the underlying gauge symmetry. Recent advancements in the experimental realizations of large-scale LGTs have been impressive, albeit mostly restricted to Abelian gauge groups. Guided by this requirement for gauge protection, we propose an experimentally feasible approach to implement large-scale non-Abelian SU(N) and U(N) LGTs with dynamical matter in d+1D, enabled by two-body spin-exchange interactions realizing local emergent gauge-symmetry stabilizer terms. We present two concrete proposals for 2+1DSU(2) and U(2) LGTs, including dynamical bosonic matter and induced plaquette terms, that can be readily implemented in current ultracold-molecule and next-generation ultracold-atom platforms. We provide numerical benchmarks showcasing experimentally accessible dynamics, and demonstrate the stability of the underlying non-Abelian gauge invariance. We develop a method to obtain the effective gauge-invariant model featuring the relevant magnetic plaquette and minimal gauge-matter coupling terms. Our approach paves the way towards near-term realizations of large-scale non-Abelian quantum link models in analog quantum simulators.

Published by the American Physical Society
2024
Comparative analysis of data protection regulations in East African countries
Authors: Shao Deo , Ishengoma Fredrick , Nikiforova Anastasija , Swetu Mrisho 
Published: September 2024

Purpose
Protection of personal data is integral to the digital economy, ensuring trust and privacy as its foundational elements. The purpose of this study is to analyze data protection laws in Tanzania, Kenya, Uganda and Rwanda to understand their legal frameworks and identify challenges hindering their effective implementation.

Design/methodology/approach
This study uses a comparative exploratory case study approach, analyzing legal frameworks of four East African (EA) countries through examination of legal documents, official reports and academic articles. The dimensions of analysis include registration, supervisory authority, data subject rights and cross-border data transfer regulations.

Findings
While all four EA countries are in the process of enacting data protection acts, they differ in scope, provisions and enforcement; more needs to be done to ensure mature data protection in these countries. The commonalities and distinctions in the legal frameworks are underscored, providing a mapping of data protection regulations in the EA region. Moreover, this study reports implementation constraints and areas for improvement.

Practical implications
The findings of this study provide valuable insights for policymakers, highlighting areas where data protection regulations can be improved. The results of this study can guide harmonizing regional data protection laws, ensuring consistent and effective enforcement. This study offers a foundation for future policy development and regional cooperation on data protection issues.

Social implications
The social implications of this research lie in its potential to shape public attitudes on data protection and privacy rights. By highlighting these concerns, this study may influence societal norms and values, encouraging a more informed and conscientious public discourse on inclusive policies that consider the diverse needs of different regional populations.

Originality/value
This study provides a pioneering comparative analysis of data protection regulations across four EA countries, offering unique insights into the regional variations and commonalities in legal frameworks. Its value lies in informing future policy development, enhancing regional cooperation and contributing to the harmonization of data protection practices in the selected EA countries, which remains an under-explored area in existing literature.