bluuebunny/crossref_metadata_2025_split huggingface dataset:
Self-reactive B cells traverse a perfect storm of somatic mutagenesis to cause a virus-induced autoimmune disease
Authors: Young Clara , Singh Mandeep , Jackson Katherine JL , Field Matt A , Peters Timothy J , Angioletti-Uberti Stefano , Frenkel Daan , Ravishankar Shyamsundar , Gupta Money , Wang Jing J , Agapiou David , Faulks Megan L , Al-Eryani Ghamdan , Luciani Fabio , Gordon Tom P , Reed Joanne H , Danta Mark , Carr Andrew , Kelleher Anthony D , Dore Gregory J , Matthews Gail , Brink Robert , Bull Rowena A , Suan Daniel , Goodnow Christopher C 
Published: January 2024

SummaryThe unexplained association between infection and autoimmune disease is strongest for hepatitis C virus-induced cryoglobulinemic vasculitis (HCV-CV). We traced the evolution of the pathogenic rheumatoid factor (RhF) autoantibodies in four HCV-CV patients by deep single cell multi-omic analysis, revealing three sources of B cell somatic mutation converged to drive accumulation of a large disease causing clone. A sensitive method for quantifying low affinity binding revealed three recurring heavy/light chain combinations created byV(D)Jrecombination bound self IgG but not viral E2 antigen. Whole genome sequencing revealed accumulation of thousands of somatic mutations, at levels comparable to CLL and normal memory B cells, but with 1-2 corresponding to driver mutations found recurrently in B cell leukemia/lymphoma.V(D)Jhypermutation created autoantibodies with compromised solubility. In this virus-induced autoimmune disease, infection promotes a perfect storm of somatic mutagenesis in the descendants of a single B cell.
Multiple DNA repair pathways prevent acetaldehyde-induced mutagenesis in yeast
Authors: Porcher Latarsha , Vijayraghavan Sriram , McCollum James , Mieczkowski Piotr A , Saini Natalie 
Published: January 2024

AbstractAcetaldehyde is the primary metabolite of alcohol and is present in many environmental sources including tobacco smoke. Acetaldehyde is genotoxic, whereby it can form DNA adducts and lead to mutagenesis. Individuals with defects in acetaldehyde clearance pathways have increased susceptibility to alcohol-associated cancers. Moreover, a mutation signature specific to acetaldehyde exposure is widespread in alcohol and smoking-associated cancers. However, the pathways that repair acetaldehyde-induced DNA damage and thus prevent mutagenesis are vaguely understood. Here, we usedSaccharomyces cerevisiaeto systematically delete genes in each of the major DNA repair pathways to identify those that alter acetaldehyde-induced mutagenesis. We found that deletion of the nucleotide excision repair (NER) genes,RAD1orRAD14, led to an increase in mutagenesis upon acetaldehyde exposure. Acetaldehyde-induced mutations were dependent on translesion synthesis as well as DNA inter-strand crosslink (ICL) repair inΔrad1strains. Moreover, whole genome sequencing of the mutated isolates demonstrated an increase in C→A changes coupled with an enrichment of gCn→A changes in the acetaldehyde-treatedΔrad1isolates. The gCn→A mutation signature has been shown to be diagnostic of acetaldehyde exposure in yeast and in human cancers. We also demonstrated that the deletion of the two DNA-protein crosslink (DPC) repair proteases,WSS1andDDI1, also led to increased acetaldehyde-induced mutagenesis. Defects in base excision repair (BER) led to a mild increase in mutagenesis, while defects in mismatch repair (MMR), homologous recombination repair (HR) and post replicative repair pathways did not impact mutagenesis upon acetaldehyde exposure. Our results in yeast were further corroborated upon analysis of whole exome sequenced liver cancers, wherein, tumors with defects in ERCC1 and ERCC4 (NER), FANCD2 (ICL repair) or SPRTN (DPC repair) carried a higher gCn→A mutation load than tumors with no deleterious mutations in these genes. Our findings demonstrate that multiple DNA repair pathways protect against acetaldehyde-induced mutagenesis.
Investigation of Zur-regulated metal transport systems reveals an unexpected role of pyochelin in zinc homeostasis
Authors: Secli Valerio , Michetti Emma , Pacello Francesca , Iacovelli Federico , Falconi Mattia , Astolfi Maria Luisa , Visaggio Daniela , Visca Paolo , Ammendola Serena , Battistoni Andrea 
Published: January 2024

AbstractLimiting the availability of transition metals at infection sites serves as a critical defense mechanism employed by the innate immune system to combat microbial infections.Pseudomonas aeruginosaexhibits a remarkable ability to thrive in zinc-deficient environments, which is facilitated by intricate cellular responses governed by numerous genes regulated by the zinc-responsive transcription factor Zur. Many of these genes have unknown functions, including those within the predictedPA2911-PA2914andPA4063-PA4066operons. A bioinformatic analysis revealed thatPA2911-PA2914comprises a TonB-dependent outer membrane receptor and an inner membrane ABC-permease responsible for importing metal-chelating molecules, whereasPA4063-PA4066contains genes encoding a MacB transporter, likely involved in the export of large molecules. Molecular genetics and biochemical experiments, feeding assays, and intracellular metal content measurements demonstrated thatPA2911-PA2914andPA4063-PA4066are engaged in the import and export of the pyochelin-cobalt complex, respectively. Notably, cobalt can reduce zinc demand and promote the growth ofP. aeruginosastrains unable to import zinc, highlighting pyochelin-mediated cobalt import as a novel bacterial strategy to counteract zinc deficiency. These results unveil an unexpected role for pyochelin in zinc homeostasis and challenge the traditional view of this metallophore exclusively as an iron transporter.
K48- and K63-linked ubiquitin chain interactome reveals branch- and chain length-specific ubiquitin interactors
Authors: Waltho Anita , Popp Oliver , Lenz Christopher , Pluska Lukas , Dötsch Volker , Mertins Phillip , Sommer Thomas 
Published: January 2024

AbstractThe ubiquitin (Ub) code denotes the complex Ub architectures, including Ub chains of different length, linkage-type and linkage combinations, which enable ubiquitination to control a wide range of protein fates. Although many linkage-specific interactors have been described, how interactors are able to decode more complex architectures is not fully understood. We conducted a Ub interactor screen, in humans and yeast, using Ub chains of varying length, as well as, homotypic and heterotypic branched chains of the two most abundant linkage types – K48- and K63-linked Ub. We identified some of the first K48/K63 branch-specific Ub interactors, including histone ADP-ribosyltransferase PARP10/ARTD10, E3 ligase UBR4 and huntingtin-interacting protein HIP1. Furthermore, we revealed the importance of chain length by identifying interactors with a preference for Ub3 over Ub2 chains, including Ub-directed endoprotease DDI2, autophagy receptor CCDC50 and p97-adaptor FAF1. Crucially, we compared datasets collected using two common DUB inhibitors – Chloroacetamide and N-ethylmaleimide. This revealed inhibitor-dependent interactors, highlighting the importance of inhibitor consideration during pulldown studies. This dataset is a key resource for understanding how the Ub code is read.
The suprapyramidal and infrapyramidal blades of the dentate gyrus exhibit different GluN subunit content and dissimilar frequency-dependent synaptic plasticity in vivo
Authors: Strauch Christina , Böge Juliane , Shchyglo Olena , Dubovyk Valentyna , Manahan-Vaughan Denise 
Published: January 2024

AbstractThe entorhinal cortex sends afferent information to the hippocampus by means of the perforant path(PP), whereby the medial PP (MPP) is believed to convey information about spatial context and the lateral PP (LPP) may convey information about item identity. This information is encoded by means of synaptic plasticity. The PP input to the dentate gyrus(DG) terminates in the suprapyramidal (upper/inner) and infrapyramidal (lower/outer) blades. To what extent frequency-dependent synaptic plasticity in these blades differs is unclear. Here, we compared MPP-DG responses in the supra- (sDG) and infrapyramidal blades (iDG) of freely behaving adult rats and found that synaptic plasticity in the sDG is broadly frequency-dependent whereby long-term depression (LTD, >24h) is induced with stimulation at 1Hz, short-term depression (<2h) is triggered by 5 or 10Hz and long-term potentiation (LTP) of increasing magnitudes is induced by 200 and 400 Hz stimulation, respectively. By contrast, although the iDG expresses STD following 5 or 10Hz stimulation, LTD induced by 1Hz is weaker, LTP is not induced by 200Hz and LTP induced by 400Hz stimulation is significantly smaller in magnitude and is less persistent (<4h) compared to LTP in sDG. Furthermore, the stimulus-response relationship of the iDG is suppressed compared to sDG. Patch clamp recordings, in vitro, revealed reduced firing frequencies in response to high currents, and different action potential thresholds in iDG compared to sDG. Assessment of the expression of GluN subunits revealed significantly lower expression levels of GluN1, GluN2A and GluN2B in iDG compared to sDG. Taken together, these data indicate that synaptic plasticity in the infrapyramidal blade of the dentate gyrus is weaker, less persistent and less responsive to afferent frequencies than synaptic plasticity in sDG. Effects may be mediated by weaker NMDA receptor expression in iDG. These characteristics may explain reported differences in experience-dependent information processing in sDG versus iDG.
The role of conscious attention in statistical learning: evidence from patients with impaired consciousness
Authors: Benjamin Lucas , Zang Di , Fló Ana , Qi Zengxin , Su Pengpeng , Zhou Wenya , Wang Liping , Wu Xuehai , Gui Peng , Dehaene-Lambertz Ghislaine 
Published: January 2024

AbstractThe debate over whether conscious attention is necessary for statistical learning has produced mixed and conflicting results. Testing individuals with impaired consciousness may provide some insight, but very few studies have been conducted due to the difficulties associated with testing such patients. In this study, we examined the ability of patients with varying levels of consciousness disorders (DOC), including coma, unresponsive wakefulness syndrome, minimally conscious patients, and emergence from minimally conscious state patients, to extract statistical regularities from an artificial language composed of four randomly concatenated pseudowords. We used a methodology based on frequency tagging in EEG, which was developed in our previous studies on speech segmentation in sleeping neonates. Our study had two main objectives: firstly, to assess the automaticity of the segmentation process and explore correlations between the level of covert consciousness and the abilities to extract statistical regularities, second, to explore a potential new diagnostic indicator to aid in patient management by examining the correlation between successful statistical learning markers and consciousness level. We observed that segmentation abilities were preserved in some minimally conscious patients, suggesting that statistical learning is an inherently automatic low-level process. Due to significant inter-individual variability, word segmentation may not be a sufficiently robust candidate for clinical use, unlike temporal accuracy of auditory syllable responses, which correlates strongly with coma severity. Therefore, we propose that frequency tagging of an auditory stimulus train, a simple and robust measure, should be further investigated as a possible metric candidate for DOC diagnosis.
Effect of RNA m6A methyltransferase activation by a low molecular weight compound on anxiety- and depression-related behaviours, monoamine neurochemistry and striatal gene expression in the rat
Authors: Kanarik Margus , Liiver Kristi , Školnaja Marianna , Teino Indrek , Org Tõnis , Laugus Karita , Shimmo Ruth , Karelson Mati , Saarma Mart , Harro Jaanus 
Published: January 2024

AbstractModification of mRNA by methylation is involved in post-transcriptional regulation of gene expression by affecting the splicing, transport, stability and translation of mRNA. Methylation of adenosine at N6(m6A) is the most common and most important cellular modification occurring in the mRNA of eukaryotes. Evidence that m6A mRNA methylation is involved in regulation of stress response and that its dysregulation may contribute to the pathogenesis of neuropsychiatric disorders is accumulating. We have examined the acute and subchronic (up to 18 days once per day intraperitoneally) effect of the first METTL3/METTL14 activator compound CHMA1004 (methyl-piperazine-2-carboxylate) at two doses (1 and 5 mg/kg) in male and female rats. CHMA1004 had a profound locomotor activating and anxiolytic-like profile in open field and elevated zero-maze tests. In female rats sucrose consumption and swimming in Porsolt’s test were increased. Nevertheless, CHMA1004 did not exhibit strong psychostimulant-like properties: CHMA1004 had no effect on 50-kHz ultrasonic vocalizations except that it reduced the baseline difference between male and female animals, and acute drug treatment had no effect on extracellular dopamine levels in striatum. Subchronic CHMA1004 alteredex vivocatecholamine levels in several brain regions. RNA sequencing of female rat striata after subchronic CHMA1004 treatment revealed changes in the expression of a number of genes linked to dopamine neuron viability, neurodegeneration, depression, anxiety and stress response. Conclusively, the first-in-class METTL3/METTL14 activator compound CHMA1004 increased locomotor activity and elicited anxiolytic-like effects after systemic administration, demonstrating tha pharmacological activation of RNA m6A methylation has potential for neuropsychiatric drug development.
Development of a 3D vascular network visualization platform for one-dimensional hemodynamic simulation
Authors: Chen Yan , Kobayashi Masaharu , Yuhn Changyoung , Oshima Marie 
Published: January 2024

AbstractRecent advancements in computational performance and medical simulation technology, have made significant strides, particularly in predictive diagnosis. This study focuses on the blood flow simulation reduced-order models, which provide swift and cost-effective solutions for complex vascular systems, positioning them as practical alternatives to 3D simulations in resource-limited medical settings. The paper introduces a visualization platform for patient-specific and image-based 1D-0D simulations. This platform covers the entire workflow, from modeling to dynamic 3D visualization of simulation results. Two case studies on respectively carotid stenosis and arterial remodeling demonstrate its utility in surgical planning and preventing complications like cerebral hyperperfusion syndrome.
Changes in enclosure use and basking behaviour associated with pair housing in Tokay geckos (Gekko gecko)
Authors: Szabo Birgit 
Published: January 2024

AbstractDue to often insufficient information reptiles suffer welfare issues and increased mortality in captivity. In particular, the impact of the social environment remains poorly understood, despite evidence suggesting its’ importance for welfare in a wide range social animals. The current study investigated how pair housing changes enclosure use, basking and hiding behaviour in tokay geckos (Gekko gecko). While the captive conditions and husbandry procedures employed in this study align with existing literature recommendations, they have not been previously evaluated for their suitability for this particular species. The results show that, when socially deprived, lizards were more likely to move and hide before feeding. Furthermore, males were more likely to be found at the front than females during pair housing but not during single housing. Finally, contrary to single housing, enclosure temperature had no effect on the probability to move and hide behind a shelter during pair housing. Consistently, however, lizards were more likely to bask after feeding across housing conditions and females were more likely to bask before their first clutch. Together, pair housing decreases movement and hiding in relation to human presence (feeding) which might indicate that pair housing improves tokay gecko welfare and suggest that the presence of a conspecific should be considered to improve welfare policies in social reptiles. This study serves as a baseline for future research into how enclosure furnishings, husbandry techniques, and enrichment practices impact the welfare of tokay geckos which will be crucial for refining our understanding of and improving on the welfare of reptiles in captivity.
Bioinformatic analysis of sulfotransferases from an unexplored gut microbe,Sutterella wadsworthensis 3_1_45B: Possible roles towards detoxification via sulfation by the members of the human gut microbiome
Authors: Langford Lauryn , Shah Dhara D. 
Published: January 2024

AbstractSulfation, primarily facilitated by sulfotransferases, plays a crucial role in the detoxification pathways of both endogenous substances and xenobiotics, enhancing their water solubility and promoting metabolism and elimination. Traditionally, this bioconversion has been attributed to a family of human cytosolic sulfotransferases (hSULTs) known for their high sequence similarity and dependence on 3’-phosphoadenosine 5’-phosphosulfate (PAPS) as a sulfate donor. However, recent studies have revealed the presence of PAPS-dependent sulfotransferases within gut commensals, indicating that the gut microbiome may harbor a diverse array of sulfotransferase enzymes and may contribute to detoxification processes via sulfation. In this study, we investigated the prevalence of sulfotransferases in the members of the human gut microbiome. Interestingly, we stumbled upon a different class of sulfotransferases, known as aryl-sulfate sulfotransferases (ASSTs). ASSTs have been characterized from a few different prokaryotes includingE. coli. ASSTs do not utilize PAPS which is the default sulfate donor for the human sulfotransferases. Our bioinformatics analyses revealed that the gut microbial genusSutterellapossesses a significant number ofasstgenes, possibly encoding multiple ASST enzymes. Fluctuations in the microbes of the genusSutterellahave been associated with various health conditions. For this reason, we characterized 17 different ASSTs fromSutterella wadsworthensis 3_1_45Bwith bioinformatics. Our findings reveal thatSwASSTs share similarities withE. coliASST but also exhibit significant structural variations and sequence diversity. These differences might drive potential functional diversification and likely reflect an evolutionary divergence from their PAPS-dependent counterparts.
Charmless
B→PPP
decays: The fully antisymmetric final state
Authors: Bhattacharya Bhubanjyoti , Fines-Neuschild Mirjam , Houck Andrea , Imbeault Maxime , Jean Alexandre , London David 
Published: January 2024

Under flavor SU(3) symmetry (SU(3)F), the final-state particles in B→PPP decays (P is a pseudoscalar meson) are treated as identical, and the PPP must be in a fully-symmetric (FS) state, a fully-antisymmetric (FA) state, or in one of four mixed states. In this paper, we present the formalism for the FA states. We write the amplitudes for the 22B→PPP decays that can be in an FA state in terms of both the SU(3)F reduced matrix elements and diagrams. This shows the equivalence of diagrams and SU(3)F. We also give 15 relations among the amplitudes in the SU(3)F limit as well as the additional four that appear when the diagrams E/A/PA are neglected. We present sets of B→PPP decays that can be used to extract γ using the FA amplitudes. The value(s) of γ found in this way can be compared with the value(s) found using the FS states.

Published by the American Physical Society
2024
Investigation on laser absorption and x-ray radiation in microstructured titanium targets heated by short-pulse relativistic laser pulses
Authors: Pan X. , Šmíd M. , Huang L. G. , Kluge T. , Bagnoud V. , Brambrink E. , Cowan T. E. , Colgan J. , Ebert T. , Hartnagel D. , Hesse M. , Hornung J. , Kleinschmidt A. , Perez-Martin P. , Neukirch A. , Philipp K. , Sander S. , Schaumann G. , Tebartz A. , Zielbauer B. , Roth M. , Falk K. 
Published: January 2024

The enhancement effect of a microstructured surface on laser absorption and characteristic Kα emission has been investigated by measuring K-shell emission from titanium (Ti) targets irradiated with high-intensity (∼1020Wcm−2), subpicosecond (500 fs) laser pulses. The experimental results indicate a modest enhancement (1.6×) of Kα emission from microstructured targets compared to flat foils, but with a similar intensity and profile of Heα and Li-like satellites. Particle-in-cell (PIC) simulations are implemented to further understand the underlying physical processes in the laser interaction with both targets, interpreting the mechanisms responsible for the Kα enhancement. The reasons for the lower-than-expected enhancement of Kα emission are discussed. The rapid heating of the bulk plasma might result in the premature shutdown of Kα emission before the thermalization of hot electrons or even the end of laser pulses, suggesting that the use of Kα emission as a diagnostic of the hot-electron yield or relaxation could lead to a misinterpretation.

Published by the American Physical Society
2024
Telecom Networking with a Diamond Quantum Memory
Authors: Bersin Eric , Sutula Madison , Huan Yan Qi , Suleymanzade Aziza , Assumpcao Daniel R. , Wei Yan-Cheng , Stas Pieter-Jan , Knaut Can M. , Knall Erik N. , Langrock Carsten , Sinclair Neil , Murphy Ryan , Riedinger Ralf , Yeh Matthew , Xin C.J. , Bandyopadhyay Saumil , Sukachev Denis D. , Machielse Bartholomeus , Levonian David S. , Bhaskar Mihir K. , Hamilton Scott , Park Hongkun , Lončar Marko , Fejer Martin M. , Dixon P. Benjamin , Englund Dirk R. , Lukin Mikhail D. 
Published: January 2024

Practical quantum networks require interfacing quantum memories with existing channels and systems that operate in the telecom band. Here we demonstrate low-noise, bidirectional quantum frequency conversion that enables a solid-state quantum memory to directly interface with telecom-band systems. In particular, we demonstrate conversion of visible-band single photons emitted from a silicon-vacancy (SiV) center in diamond to the telecom O band, maintaining low noise (g2(0)<0.1) and high indistinguishability (V=89±8%). We further demonstrate the utility of this system for quantum networking by converting telecom-band time-bin pulses, sent across a lossy and noisy 50-km deployed fiber link, to the visible band and entangling them with a diamond quantum memory with fidelity F≥87±2.5%. These results demonstrate the viability of SiV quantum memories integrated with telecom-band systems for scalable quantum networking applications.

Published by the American Physical Society
2024