bluuebunny/crossref_metadata_2025_split huggingface dataset:
The incidence and prevalence of juvenile idiopathic arthritis differs between ethnic groups in England
Authors: Beesley Richard P , Hyrich Kimme L , Humphreys Jenny H 
Published: December 2023

Abstract

Objectives
JIA is a heterogeneous group of rare autoimmune disorders characterized by chronic joint inflammation of unknown aetiology with onset under 16 years. Accurate estimates of disease rates help understand impacts on individuals and society, and provide evidence for health service planning and delivery. This study aimed to produce the first national estimates of incidence and prevalence by ethnic group using electronic health records.

Methods
Data from the Clinical Practice Research Datalink Aurum, a primary care electronic health record database in England, were used to estimate the incidence and prevalence of JIA by ethnic group amongst children and young people aged under 16 years between 2003 and 2018, with cases validated using Hospital Episode Statistics. χ2 was used to test the difference in proportions compared with the ethnic distribution of England.

Results
A total of 424 incident cases of JIA were identified, 389 validated using Hospital Episode Statistics records. Incidence of JIA was higher amongst those of white ethnic group (6.2 per 100 000 population) compared with mixed (3.0 per 100 000), Asian (2.7 per 100 000) and Black (2.9 per 100 000) communities. The ethnic group distribution of cases differed significantly compared with the general population (P &lt; 0.0001).

Conclusion
The incidence and prevalence of JIA differs between ethnic groups, and is different from the general population. This is likely to be due to a combination of genetic and equity factors. Further research to understand the underlying cause of these differences is important to enable targeted interventions and appropriate service provision.
Protective impacts of Artemisia annua against hepatic toxicity induced by gentamicin
Authors: Althobaiti Saed A , Qahl Safa H , Toufig Hind , Almalki Daklallah A , Nasir Omaima , Soliman Mohamed Mohamed 
Published: December 2023

Abstract
The current study aimed to investigate the ameliorative effects of Artemisia annua (RA) extract on hepatic toxicity induced by gentamicin injection mice. Sixteen mice were divided into four groups; the control group received saline, the second group received 1% A. annua (RA) extract, third group injected 80 mg/kg gentamicin (GEN) intraperitoneally. The protective group treated with a combination of GEN and A. annua. All mice were treated for consecutive 15 days. Results confirmed that hepatic biomarkers (GPT, GCT, GOT, IL-6 and IL-1β), all were altered after gentamycin injection. The histological analysis confirmed that gentamycin injected mice showed portal vein congestion, micro and macro steatosis, and nuclear pyknosis of hepatocytes. The protective group showed intact central vein with less microsteatosis of some hepatocytes. Immunochemistry analysis confirmed that the immunoreactivity of COX-2 gene showed negative impact in examined groups. Unlike, NF-κB gene exhibited diffuse positive expression in the gentamicin group. TGF-β1 immunoreactivity was mild positive in control and highly upregulated in gentamicin treated mice, all were normalized after RA administration. In conclusion, RA showed a beneficial impact against gentamycin induced hepatic toxicity at cellular and biochemical levels by regulating proteins and inflammatory markers associated with liver activity.
A systematic review of the Iberian springsnail subgenus Alzoniella (Navarriella) (Caenogastropoda: Hydrobiidae), with the description of a new potentially relict subfamily
Authors: García-Guerrero Fernando , Miller Jonathan P , Delicado Diana , Novo Marta , Ramos Marian A 
Published: December 2023

Abstract
The threatened springsnail subgenus Alzoniella (Navarriella) in the Iberian Peninsula has been suggested to be an old and relict lineage of the family Hydrobiidae. The subgenus is represented by two morphological species, both endemic to the Pyrenees and their southern foothills. We conducted phylogenetic analyses based on mitochondrial and nuclear gene fragments of topotypes and other populations, four molecular species delimitation methods, and morphological examinations to clarify the uncertain systematic position of the subgenus within the family, assess its species diversity, and understand the population genetic structure of the two geographically restricted species. Our phylogenetic results revealed that Alzoniella (Navarriella) is distantly related to all other species of Alzoniella, even belonging to an independent subfamily-level clade, for which we introduce the new genus Navarriella and the new subfamily Navarriellinae subfam. nov. Molecular methods and geometric morphometric analysis of shell shape identified a single species in the new genus. The significant phylogenetic distance from other hydrobiid taxa, narrow distribution, and limited gene flow among its populations (estimated from mitochondrial cytochrome c oxidase subunit I sequences) highlight Navarriella as an isolated lineage within the family that requires urgent conservation attention. Furthermore, our results cast a new light on the northern Iberian Mountains as a dispersal barrier for ancient spring lineages.
Decreases in Employer Referrals to First-Time Substance Use Treatment for Adults From 2004 to 2020
Authors: Ware Orrin D. , Hussong Andrea , Frey Jodi J. , Daughters Stacey , Cloeren Marianne , Gryczynski Jan , Lister Jamey J. , Jordan Robyn 
Published: December 2023

Objective
The aim of the study is to examine trends of employer/employee assistance program referred admissions to outpatient substance use disorder (SUD) treatment in the United States.

Methods
The publicly available Treatment Episode Data Set was used. Full-time employed adults with no history of SUD treatment referred to outpatient treatment by an employer/employee assistance program from 2004 to 2020 were included (N = 36,142). Joinpoint regression examined admission trends.

Results
Employer/employee assistance program referred admissions to outpatient treatment decreased annually by 6.4% from 2004 to 2020 (P < 0.001). Joinpoint analyses identified 2 linear segments from 2004 to 2008 (increased but not significant) and from 2008 to 2020. From 2008 to 2020, an average annual percent decrease of 8.7% (P < 0.001) was identified.

Conclusions
Findings from this repeated cross-sectional study suggest a missed opportunity for workplaces to serve as a potential SUD treatment access point.
The science of joy: happiness among healthcare workers
Authors: Caraballo-Arias Yohama , Feola Daniela , Milani Simona 
Published: December 2023

Purpose of review
Understanding the impact of healthcare workers’ (HCW) happiness on patient care is crucial.
The aim of this review is to provide an update on recent advances in the field.

Recent findings
The article depicts the importance of HCW's happiness; the factors, the psychometric tests, tools and methods to measure their happiness and wellbeing, as well as interventions that organizations can implement to improve it, summarizing what have been published from January 2022 up to August 2023.

Summary
HCW often face demanding work environments, long working hours, and emotional challenges when dealing with patients’ suffering. The constant exposure to such stressors can lead to physical and mental health issues. Factors like job satisfaction, work-life balance, and support from colleagues and supervisors play a significant role in their happiness. Tools such as the Shorted Happiness at Work Scale (SHAW) and Eudemonic and Hedonic happiness investigation, and other surveys and qualitative methods have been used to assess overall well being. Organizational strategies have been implemented to promote a positive work culture, recognize and reward efforts, and create a supportive environment to improve happiness. Mindfulness-based techniques, web-based interventions, practice gratitude, peer support programs, and stress management training seem to be effective measures to enhance the wellbeing of HCW.
Altered defense patterns upon retrotransposition highlights the potential for rapid adaptation by transposable elements
Authors: Aller Emma S.T. , Kanstrup Christa , Hunziker Pascal , Kliebenstein Daniel J. , Burow Meike 
Published: December 2023

AbstractTransposable elements can be activated in response to environmental changes and lead to changes in DNA sequence. Their target sites of insertions have previously been thought to be random, but this theory has lately been contradicted. For instance, mobilization is favored towards genes involved in regulatory processes. This makes them interesting as potential players in rapid responses required under stressful environmental conditions. In this paper, we report the in-depth characterization of anArabidopsis thalianaCol-0-based line whose altered DNA methylation pattern made it vulnerable for transposable element movement. We identified a transposable element retrotransposition into a transporter of glucosinolate defense compounds. As a consequence of this transposable element movement, the plants showed tissue-specific changes in glucosinolate profiles and levels accompanied by rewiring of glucosinolate- and defense-related transcriptional changes. As this single transposable element had strong impact on the plants’ resistance to insect herbivory, our findings highlight the potential for transposable elements to play a role in plant adaptation.
Oblique Line Scan Illumination Enables Expansive, Accurate and Sensitive Single Protein Measurements in Solution and in Living Cells
Authors: Driouchi Amine , Bretan Mason , Davis Brynmor J. , Heckert Alec , Seeger Markus , Bradley Silva Maité , Forrest William SR. , Hsiung Jessica , Tan Jiongyi , Yang Hongli , McSwiggen David T. , Song Linda , Sule Askhay , Abaie Behnam , Conroy Brianna , Elliott Liam A. , Gonzalez Eric , Ilkov Fedor , Isaacs Joshua , Labaria George , Lagana Michelle , Larsen Delaine D. , Margolin Brian , Nguyen Mai K. , Rine Jeremy , Tang Yangzhong , Vana Martin , Wilkey Andrew , Zhang Zhengjian , Basham Stephen , Ho Jaclyn J. , Johnson Stephanie , Klammer Aaron A. , Lin Kevin , Darzacq Xavier , Betzig Eric , Berman Russell T. , Anderson Daniel J. 
Published: December 2023

AbstractSingle-molecule localization microscopy (SMLM) techniques, such as single-molecule tracking (SMT), enablein situmeasurements in cells from which data-rich metrics can be extracted. SMT has been successfully applied to a variety of biological questions and model systems, aiming to unravel the spatiotemporal regulation of molecular mechanisms that govern protein function, downstream pathway effects, and cellular function. While powerful, SMLM often suffers from low throughput and illumination inhomogeneity, along with microscope and user-induced technical biases. Due to technical limitations in scaling SMLM techniques, a tradeoff between spatiotemporal resolution and throughput has been made historically, restricting broad application of these technologies. Here we address these limitations using Oblique Line Scan (OLS), a robust single-objective light-sheet based illumination and detection modality that achieves nanoscale spatial resolution and sub-millisecond temporal resolution across a 250 × 190 μm field of view. We demonstrate OLS-enabled SMT on Halo-Tagged proteins in living cells capturing protein motion up to 14 μm2/s. By exploiting the adaptability of the acquisition frame rate and the improved rejection of out of focus light, we extend the utility of OLS beyond cellular compartments with in-solution SMT (isSMT) for single-molecule measurement of ligand-protein interactions and disruption of protein-protein interactions (PPI). We illustrate the versatility of OLS by showcasing two-color SMT, STORM, and single molecule fluorescence recovery after photobleaching (FRAP). OLS expands the range of SMLM applications and paves the way for robust, high-throughput single-molecule investigations of protein dynamics required for drug screening and systems biology studies, both in cells and in solution.
Cytosolic acetyl-CoA synthetase (ACSS2) does not generate butyryl- and crotonyl-CoA
Authors: Zeaiter Nour , Belot Laura , Cunin Valérie , Nahed Roland Abi , Tokarska-Schlattner Malgorzata , Le Gouellec Audrey , Petosa Carlo , Khochbin Saadi , Schlattner Uwe 
Published: December 2023

AbstractAcetyl and other acyl groups from different short-chain fatty acids (SCFA) competitively modify histones at various lysine sites. To fully understand the functional significance of such histone acylation, a key epigenetic mechanism, it is crucial to characterize the cellular sources of the corresponding acyl-CoA molecules required for the lysine modification. Like acetate, SCFAs such as propionate, butyrate and crotonate are thought to be the substrates used to generate the corresponding acyl-CoAs by enzymes known as acyl-CoA synthetases. The acetyl-CoA synthetase, ACSS2, which produces acetyl-CoA from acetate in the nucleocytoplasmic compartment, has been proposed to also mediate the synthesis of acyl-CoAs such as butyryl- and crotonyl-CoA from the corresponding SCFAs. This idea is now widely accepted and is sparking new research projects. However, based on our directin vitroexperiments with purified or recombinant enzymes and structural considerations, we demonstrate that ACSS2 is unable to mediate the generation of non-acetyl acyl-CoAs like butyryl- and crotonyl-CoA. It is therefore essential to re-examine published data and corresponding discussions in the light of this new finding.
Anhedonia severity mediates the relationship between attentional networks recruitment and emotional blunting during music listening
Authors: Cahart Marie-Stephanie , Giampietro Vincent , Naysmith Laura , Zelaya Fernando , Williams Steven , O’Daly Owen 
Published: December 2023

AbstractRecent studies have reported atypical emotional processing in individuals with greater levels of anhedonic depressive symptoms. However, the relationship between brain networks dynamics and moment-to-moment affective responses to naturalistic paradigms, as emotions are unfolding, remains unclear. In this study, we used the unique temporal characteristics of music to investigate behavioural and brain network dynamics as a function of anhedonic depressive symptoms severity in healthy adults during an emotionally provocative music listening task. Thirty-one neurotypical participants aged 18-30 years were required to continuously rate happy, neutral and sad pieces of music whilst undergoing MRI scanning. They were also asked to fill in questionnaires assessing their levels of anhedonic depressive symptoms. Using a novel fMRI analysis method called Leading Eigenvector Dynamics Analysis (LEiDA), we found an increased probability of occurrence of attentional networks and a blunted emotional response to both happy and sad pieces of music in participants with greater levels of anhedonic depressive symptoms. More specifically, anhedonic depressive symptoms mediated the relationship between attentional networks recruitment and emotional blunting. Furthermore, the elevated recruitment of attentional networks during emotional pieces of music carried over into subsequent neutral music. Future studies are needed to investigate whether these findings could be generalised to a clinical population (i.e., Major Depressive Disorder).
Rab3 mediates cyclic AMP-dependent presynaptic plasticity and olfactory learning
Authors: Sachidanandan Divya , Aravamudhan Aishwarya , Mrestani Achmed , Nerlich Jana , Lamberty Marius , Hasenauer Natalie , Ehmann Nadine , Pauls Dennis , Seubert Teresa , Maiellaro Isabella , Selcho Mareike , Heckmann Manfred , Hallermann Stefan , Kittel Robert J. 
Published: December 2023

SUMMARYPresynaptic forms of plasticity occur throughout the nervous system and play an important role in learning and memory but the underlying molecular mechanisms are insufficiently understood. Here we show that the small GTPase Rab3 is a key mediator of cyclic AMP (cAMP)-induced presynaptic plasticity inDrosophila. Pharmacological and optogenetic cAMP production triggered concentration-dependent alterations of synaptic transmission, including potentiation and depression of evoked neurotransmitter release, as well as strongly facilitated spontaneous release. These changes correlated with a nanoscopic rearrangement of the active zone protein Unc13A and required Rab3. To link these results to animal behaviour, we turned to the established role of cAMP signalling in memory formation and demonstrate that Rab3 is necessary for olfactory learning. As Rab3 is dispensable for basal synaptic transmission, these findings highlight a molecular pathway specifically dedicated to tuning neuronal communication and adaptive behaviour.
ChimericFragments: Computation, analysis, and visualization of global RNA networks
Authors: Siemers Malte , Lippegaus Anne , Papenfort Kai 
Published: December 2023

ABSTRACTRNA-RNA interactions are key for post-transcriptional gene regulation in all domains of life. While ever more experimental protocols are being developed to study RNA-RNA interactions on a genome-wide scale, computational methods to analyze the underlying data are lagging behind. Here, we present ChimericFragments, an analysis and visualization framework for RNA-seq experiments producing chimeric RNA molecules. ChimericFragments implements a novel statistical method based on the complementarity of the base-pairing RNAs around their ligation site and is compatible with several widely used experimental procedures. We demonstrate that ChimericFragments enables the systematic identification of RNA regulators and RNA-RNA pairs and outperforms existing approaches.
SOAPy: a Python package to dissect spatial architecture, dynamics and communication
Authors: Wang Heqi , Li Jiarong , Jing Siyu , Lin Ping , Li Yu , Zhang Haibing , Chen Yujie , Wang Zhen , Li Hong 
Published: December 2023

AbstractAdvances in spatial omics technologies have brought opportunities to dissect tissue microenvironment, while also posing more requirements and challenges for computational methods. Here we developed a package SOAPy to systematically dissect spatial architecture, dynamics and communication from spatial omics data. Specifically, it provides analysis methods for multiple spatial-related tasks, including spatial domain, spatial expression tendency, spatiotemporal expression pattern, cellular co-localization, multi-cellular niches, and ligand-receptor-mediated and spatial-constrained cell communication. Applying SOAPy on different spatial omics technologies and diverse biological fields has demonstrated its power on elucidation of biological questions about tumors, embryonic development, and normal physiological structures. Overall, SOAPy is a universal tool for spatial omics analysis, providing a foundation for continued investigation of the microenvironment.
An integrated analysis of the structural changes and gene expression of spleen in human visceral leishmaniasis with and without HIV coinfection
Authors: Fontes Jonathan L. M. , Khouri Ricardo , Reinaldo Luis Gustavo C. , Hassegawa Erina M. A. , Filho Antônio José Meneses , de Melo Caroline V. B. , Ramos Pablo Ivan P. , de Deus Moura Rafael , Pagliari Carla , Santos Marta , Araújo Raimundo José C. , Van Weyenbergh Johan , de Freitas Luiz A. R. , Costa Carlos Henrique N. , dos-Santos Washington L. C. 
Published: December 2023

AbstractThe spleen plays a pivotal role in the pathogenesis of visceral leishmaniasis. In severe forms of the disease, the spleen undergoes changes that can compromise its function in surveilling blood-circulating pathogens. In this study, we present an integrated analysis of the structural and gene expression alterations in the spleens of three patients with relapsing visceral leishmaniasis, two of whom were coinfected with HIV. Our findings reveal that the IL6 signaling pathway plays a significant role in the disorganization of the white pulp, whileBCL10andICOSLGare associated with spleen organization. Patients coinfected with HIV and visceral leishmaniasis exhibited lower splenic CD4+ cell density and reduced expression of genes such asIL15. These effects may contribute to a compromised immune response againstL. infantumin coinfected individuals, further impacting the structural organization of the spleen.
CSF plasma cell expansion in LGI1-/CASPR2-autoimmune encephalitis is associated with loss of regulatory MAIT cells
Authors: Esser Daniela , Müller-Miny Louisa , Heming Michael , Paunovic Manuela , van Duijn Martijn , Cabrera Ligia Abrante , Mair Katharina , Strippel Christine , Räuber Saskia , Bindels Eric , Dargvainiene Justina , Wiendl Heinz , Meuth Sven G. , Bauer Jan , Melzer Nico , Titulaer Maarten J. , Leypoldt Frank , Meyer zu Hörste Gerd ,   EMC-AIE Study group
Published: December 2023

AbstractAnti-Leucine-rich glioma inactivated-1 (LGI1) and anti-contactin-associated-protein-2 (CASPR2) associated autoimmune encephalitis (AIE) variants are characterized by directly pathogenic autoantibodies present in serum and CSF. The dynamics and drivers of intrathecal and systemic autoantibody production are incompletely understood. We aimed to elucidate the immunologic basis of the LGI1-/CASPR2-associated AIE variants by performing multi-omic profiling of CSF/blood in untreated patients. We validated findings by flow cytometry in independent cohorts and confirmed functionality using rodent immunization.We identified clonal IgG2 and IgG4 plasma cell expansion and affinity maturation in the CSF together with clonally restricted, activated, antigen-experienced CD8 and CD4 T cells as a hallmark of these encephalitis variants. Using recombinant cloning, we confirmed that expanded CSF plasma cell clones almost exclusively bound the respective neuronal autoantigen. In addition, we found a loss of regulatory mucosa-associated invariant T (MAIT) cells and gamma delta T cells in the CSF and – to a lesser degree – in blood. We validated the functional role of these invariant T cells using a novel murine active immunization paradigm using both autoantigens: MAIT cells suppressed systemic formation of LGI1 and CASPR2-specific anti-neuronal antibodies.We propose that loss of systemic and intrathecal regulatory mechanisms mediated by innate-like T cells promote plasma cell expansion and autoantibody production as a shared mechanism in AIE.One sentence summaryCerebrospinal fluid (CSF) and peripheral blood (PB) single cell transcriptomics of patients with untreated anti-LGI1 and anti-CASPR2 autoimmune encephalitis demonstrated CSF specific expansion of autoantigen-specific plasma cell clones and systemic loss of invariant mucosa-associated T-cells (MAIT).