bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design, infectability, and transcriptomic analysis of transregionally differentiated and scalable lung organoids derived from adult bronchial cells
Authors: Valenzuela Alicia Reyes , Turner Mark , Markarian Nathan , Lachance-Brais Christophe , Hanrahan John , Vali Hojatollah , Vidal Silvia , Mongeau Luc 
Published: July 2024

AbstractThe lung is a primary target for many lethal respiratory viruses, leading to significant global mortality. Current organoid models fail to completely mimic the cellular diversity and intricate tubular and branching structures of the human lung. Lung organoids derived from adult primary cells have so far only included cells from the input cell region, proximal or distal. Existing models are expensive. They often require cells from invasive deep lung tissue biopsies. The present study aimed to address these limitations. The lung organoids obtained using an original protocol exhibited transregional differentiation and were derived from relatively more accessible primary cells from the trachea/bronchi. Immortal bronchial cell lines were also used to simplify organoid fabrication and improve its scalability. The lung organoids are formed starting from bronchial cells with fibroblasts feeder cells in an alginate hydrogel coated with base membrane zone proteins. Characterizations were performed using bulk RNA sequencing and tandem mass tags. The resulting organoids express markers of different lung regions and mimic to some extent the tubular and branching morphology of the lung. The proteomic profile of organoid from primary cells and from cell lines was found to evolve towards that of mature lung tissue. Upregulated genes were mostly related to the respiratory system, tube development, and various aspects of respiratory viral infections. Infection with SARS-CoV-2 and influenza H1N1 was successful and did not require organoid disassembly. The organoids matured within 21 days and did not require complex or expensive culture methods. Transregionally differentiated lung organoid may find applications for the study of emerging or re-emerging viral infections and fostering the development of novel in-vitro therapeutic strategies.
Sensorimotor awareness requires intention: Evidence from minuscule eye movements
Authors: Klanke Jan-Nikolas , Ohl Sven , Rolfs Martin 
Published: July 2024

AbstractMicrosaccades are tiny eye movements that are thought to occur spontaneously and without awareness but can also be intentionally controlled with high precision. We used these tiny visual actions to investigate how intention modulates sensorimotor awareness by directly comparing intended, unintended, and spontaneous microsaccades. In addition, we dissociated the effects of action intention and the actions’ visual consequences on awareness. In 80% of all trials, we presented a stimulus at high temporal frequency rendering it invisible during stable fixation. Critically, the stimulus became visible when a microsaccade in the same direction caused it to slow down on the retina (generated microsaccade condition; 40% of trials) or when the microsaccades’ visual consequence was replayed (replayed microsaccade condition; 40% of trials). Participants reported whether they perceived the stimulus (visual sensitivity), whether they believed they had made a microsaccade (microsaccade sensitivity), and their level of confidence that their eye movement behavior was linked to their perception (causality assignment). Visual sensitivity was high for both, generated and replayed microsaccades and comparable for intended, unintended, and spontaneous eye movements. Microsaccade sensitivity, however, was low for spontaneous microsaccades, but heightened for both intended and unintended eye movements, showing that the intention to saccade or fixate enhances awareness of otherwise undetected eye movements. Visual consequences failed to aid eye movement awareness, and confidence ratings revealed a poor understanding of a causal relationship between eye movement and sensory consequence. These findings highlight the functional relevance of intention in sensorimotor awareness at the smallest scale of visual actions.Significance statementWhile eye movements are among the most frequent human actions, they are rarely perceived consciously, despite causing sweeping changes in retinal inputs. Here investigate how intention can modulate awareness of even the smallest human actions: microsaccades. We developed a novel paradigm that allowed us to dissociate the role of action intention and an action’s sensory consequence for awareness, two factors that previous research has typically confounded. Our data provide strong evidence that observers can detect small eye movements reliably and demonstrates that sensitivity towards microsaccades was neither driven by an eye movement’s motor component nor its visual consequences alone. Instead, we find that intention opens a gate to sensorimotor awareness, even for actions typically too small to be perceived.
Myoferlin is an essential component of late-stage vRNP trafficking vesicles for enveloped RNA viruses
Authors: Bonazza Stefano , Turkington Hannah L , Coutts Hannah L , Sukumar Swathi , Hawthorn Courtney , Getty Erin M P E , Touzelet Olivier , Barabas Judit , Power Ultan F , Courtney David G 
Published: July 2024

AbstractThe Rab11a endosomal recycling pathway is exploited by important respiratory RNA viruses such as IAV and RSV, aiding viral egress from the apical surface of polarized epithelial cells. Late in infection, Rab11a-containing vesicles specifically transport viral ribonucleoprotein (vRNP) complexes towards the cell surface before packaging and budding. Rather than employing traditional Rab11a-positive recycling endosomes, virus-infected cells generate remodelled Rab11a-containing vesicles, as observed during IAV infection. Besides Rab11a, no other conserved host co-factors have been identified among these various vRNP trafficking vesicles. Here we discovered and confirmed myoferlin’s association with IAV vRNPs in the cytoplasm and colocalisation with Rab11a during late stages of infection. We also found that this role was conserved in late-stage vRNP trafficking of other viruses, including RSV and SeV. Myoferlin likely recruits the EHD family of proteins, which are involved in endosomal biogenesis, to these unique vRNP trafficking endosomes, highlighting myoferlin’s pivotal role in viral replication.
Neural correlates of nightmares revisited: findings from large-scale fMRI cohorts
Authors: Pereira Mariana , Terpstra Noëlle , Rutiku Renate , Sandberg Kristian , Dresler Martin , Krause Florian 
Published: July 2024

AbstractStudy ObjectivesNightmares are linked to daytime distress and psychiatric and neurological disorders. However, knowledge about the brain regions involved in nightmare production is sparse. This study aimed to examine the relationship between nightmare frequency and the functional connectivity of the amygdala with the prefrontal cortex, which is central to emotional regulation. Additionally, the study sought to replicate previous findings on the neural correlates of nightmares using two large cohorts.Methods464 participants underwent functional and structural MRI recordings and answered questions assessing nightmare and dream recall frequency. A general linear model assessed the voxelwise correlation between the amygdala-prefrontal cortex connectivity with nightmare frequency. Additionally, regional homogeneity (ReHo) maps were calculated, high and low nightmare frequency and the entire nightmare frequency spectrum contrasts were determined while controlling for age, sex, and dream recall frequency.ResultsThe study did not find a significant correlation between nightmare frequency and amygdala-prefrontal cortex connectivity. Previous ReHo findings of group differences between high and low nightmare frequency could not be replicated. However, parametric analysis revealed an association between nightmare frequency and ReHo differences in the cerebellum.ConclusionsThis failure to confirm hypothesized and previously reported results, especially with a larger sample size, suggests a need to reevaluate the existing knowledge of the neural correlates of nightmares and consider individual differences such as personality, trauma history, and cognitive processes. Overall, our findings highlight the complexities of interpreting neuroimaging data in sleep research.
TORC1-containing signaling endosomes source membrane from vacuoles
Authors: Muneshige Kenji , Hatakeyama Riko 
Published: July 2024

AbstractOrganelle biogenesis is fundamental to eukaryotic cell biology. Yeast signaling endosomes were recently identified as a signaling platform for the evolutionarily conserved Target of Rapamycin Complex 1 (TORC1) kinase complex. Despite the importance of signaling endosomes for TORC1-mediated control of cellular metabolism, how this organelle is generated has been a mystery. Here, we developed a system to induce synchronizedde novoformation of signaling endosomes, enabling real-time monitoring of their biogenesis. Using this system, we identify vacuoles as a membrane source for newly formed signaling endosomes. Membrane supply from vacuoles is mediated by the CROP membrane-cutting complex, consisting of Atg18 PROPPIN and retromer subunits. The formation of signaling endosomes requires TORC1 activity, suggestive of a tightly regulated process. This study unveiled the first mechanistic principles and molecular participants of signaling endosome biogenesis.SummaryMembrane is supplied by vacuoles during biogenesis of yeast signaling endosomes, in a process mediated by the membrane-cutting CROP complex and promoted by TORC1 kinase activity.
Transdiagnostic Neurobiology of Social Cognition and Individual Variability as Measured by Fractional Amplitude of Low-Frequency Fluctuation in Schizophrenia and Autism Spectrum Disorders
Authors: Bagheri Soroush , Yu Ju-Chi , Gallucci Julia , Tan Vinh , Oliver Lindsay D. , Dickie Erin W. , Rashidi Ayesha G. , Foussias George , Lai Meng-Chuan , Buchanan Robert W. , Malhotra Anil K. , Voineskos Aristotle N. , Ameis Stephanie H. , Hawco Colin 
Published: July 2024

AbstractFractional amplitude of low-frequency fluctuation (fALFF) is a validated measure of resting-state spontaneous brain activity. Previous fALFF findings in autism and schizophrenia spectrum disorders (ASDs and SSDs) have been highly heterogeneous. We aimed to use fALFF in a large sample of typically developing control (TDC), ASD and SSD participants to explore group differences and relationships with inter-individual variability of fALFF maps and social cognition. fALFF from 495 participants (185 TDC, 68 ASD, and 242 SSD) was computed using functional magnetic resonance imaging as signal power within two frequency bands (i.e., slow-4 and slow-5), normalized by the power in the remaining frequency spectrum. Permutation analysis of linear models was employed to investigate the relationship of fALFF with diagnostic groups, higher-level social cognition, and lower-level social cognition. Each participant’s average distance of fALFF map to all others was defined as a variability score, with higher scores indicating less typical maps. Lower fALFF in the visual and higher fALFF in the frontal regions were found in both SSD and ASD participants compared with TDCs. Limited differences were observed between ASD and SSD participants in the cuneus regions only. Associations between slow-4 fALFF and higher-level social cognitive scores across the whole sample were observed in the lateral occipitotemporal and temporoparietal junction. Individual variability within the ASD and SSD groups was also significantly higher compared with TDC. Similar patterns of fALFF and individual variability in ASD and SSD suggest some common neurobiological deficits across these related heterogeneous conditions.
An HERV-WENVtranscription in atypical memory B cells linked to COVID-19 evolution and risk for long COVID can express the encoded protein from a ribosome readthrough of mRNA from chromosome X
Authors: Brunel Joanna , Paganini Julien , Galloux Melissa , Charvet Benjamin , Perron Hervé 
Published: July 2024

ABSTRACTThe human genome comprises 8% of endogenous retroviruses (HERVs). Though HERVS contribute to physiological functions, copies retained pathogenic potential. The HERV-W ENV protein was shown expressed in patients with worse COVID-19 symptoms and post-COVID syndrome. A significant detection of the mRNA encoding HERV-W ENV from patients with COVID-19 in B cells from RNAseq reads obtained from peripheral blond mononuclear cells. This data stratified with increased COVID-19 symptoms or with post-acute sequelae of COVID-19 (long COVID) after 3 months. The HERV-WENV-U3RRNA was confirmed to display the best alignment with chromosome X ERVWE2 locus. However, a stop codon precluding its translation was re-addressed after recent understandings of ribosome readthrough mechanisms. Experimental results evidenced that this HERV gene can effectively express a full-length protein in the presence of molecules allowing translation via a readthrough mechanism at the ribosome level. Results not only confirm HERV-WENVRNA origin in these patients, but show for the first time how a defective HERV copy can be translated into a complete protein when specific factors make it possible at the ribosome level. The present proof of concept now requires further studies to identify the factors involved in this newly understood mechanism, following SARS-CoV-2 exposure.
A spatially resolved multiomic single-cell atlas of soybean development
Authors: Zhang Xuan , Luo Ziliang , Marand Alexandre P. , Yan Haidong , Jang Hosung , Bang Sohyun , Mendieta John P. , Minow Mark A.A. , Schmitz Robert J. 
Published: July 2024

SummaryCis-regulatory elements (CREs) precisely control spatiotemporal gene expression in cells. Using a spatially resolved single-cell atlas of gene expression with chromatin accessibility across ten soybean tissues, we identified 103 distinct cell types and 303,199 accessible chromatin regions (ACRs). Nearly 40% of the ACRs showed cell-type-specific patterns and were enriched for transcription factor (TF) motifs defining diverse cell identities. We identifiedde novoenriched TF motifs and explored conservation of gene regulatory networks underpinning legume symbiotic nitrogen fixation. With comprehensive developmental trajectories for endosperm and embryo, we uncovered the functional transition of the three sub-cell types of endosperm, identified 13 sucrose transporters sharing the DOF11 motif that were co-up-regulated in late peripheral endosperm and identified key embryo cell-type specification regulators during embryogenesis, including a homeobox TF that promotes cotyledon parenchyma identity. This resource provides a valuable foundation for analyzing gene regulatory programs in soybean cell types across tissues and life stages.
Molecular control of dormancy transitions throughout the year in the monoecious cork oak
Authors: Silva Helena Gomes , Sobral Rómulo , Alhinho Ana Teresa , Afonso Hugo Ricardo , Ribeiro Teresa , Silva Patrícia M. A. , Bousbaa Hassan , Morais-Cecílio Leonor , Costa Maria Manuela Ribeiro 
Published: July 2024

AbstractBud dormancy plays a vital role in flowering regulation and fruit production, being highly regulated by endogenous and environmental cues. Deployment of epigenetic modifications and differential gene expression control bud dormancy/break cycles. Information on how these genetic and epigenetic mechanisms are regulated throughout the year is still scarce for temperate trees, such asQuercus suber. Here, the expression levels ofQsCENLandQsDYL1during different seasonal cycles of bud development suggest thatQsCENLmay be implicated in the establishment of growth cessation inQ. suberand thatQsDYL1is a good dormancy marker. Moreover, the analysis of the profiles of epigenetic marks and the expression of modifiers, in dormant versus non-dormant bud meristems, indicate that epigenetic regulation is implicated in how bud development progresses inQ. suber. The identification of bud specific mechanisms opens new possibilities to understand how trees respond to challenging environmental signals derived from climate change.
DWARF14 and KARRIKIN INSENSITIVE2 mediate signaling of the apocarotenoid zaxinone in Arabidopsis
Authors: Moreno Juan C. , Hameed Umar Shahul , Balakrishna Aparna , Ablazov Abdugaffor , Liew Kit Xi , Jamil Muhamad , Mi Jianing , Alashoor Kawthar , de Saint Germain Alexandre , Arold Stefan T. , Al-Babili Salim 
Published: July 2024

AbstractThe natural growth regulator zaxinone increases the levels of the phytohormones strigolactone (SL) and abscisic acid in Arabidopsis (Arabidopsis thaliana) via unknown mechanisms. We demonstrate that parts of the effects of zaxinone in Arabidopsis depend on the SL receptor DWARF14 (AtD14), the karrikin receptor KARRIKIN INSENSITIVE2 (AtKAI2), and the F-Box protein MORE AXILLARY BRANCHING2 (AtMAX2) that mediates the signaling of SLs and karrikins. Binding assays and co-crystallization revealed zaxinone as an additional ligand ofAtD14 and an SL antagonist that interrupts the interaction ofAtD14 withAtMAX2. Zaxinone also bound toAtKAI2. These findings unveil a perception mechanism for zaxinone in Arabidopsis and demonstrate the capability ofAtD14 andAtKAI2 to bind signaling molecules, other than strigolactones or karrikins, and mediate their transduction.
Unpacking the financial attributes of blue-chip non-fungible tokens (NFTs) against traditional and digital assets
Authors: Havidz Shinta Amalina Hazrati , Santoso Maria Divina , Alexander Theodore , Caroline Caroline 
Published: July 2024

PurposeThis study aims to identify the financial attributes of non-fungible tokens (NFTs) as safe havens, hedges or diversifiers against traditional (stock indices, foreign exchange, gold and government bonds) and digital (Bitcoin and Ethereum) assets.Design/methodology/approachThe quantile via moments was utilized, and the data spanned from 20 September 2021 to 31 January 2022. The authors incorporated feasible generalized least squares (FGLS) and difference-generalized method of moments (diff-GMM) as the robustness check.FindingsOverall, NFTs offer strongly safe havens, hedging and diversifier attributes against cryptocurrencies, while weak properties for traditional assets. The specific findings are: (1) Bored Ape Yacht Club (BAYC) serves as a strong hedge for Bitcoin during market rise; (2) Mutant Ape Yacht Club (MAYC) serves as a strong safe haven against Bitcoin during market bull; (3) Crypto punk (CP) provides strong safe havens properties for gold during market turmoil while serving as a strong hedge against gold and Bitcoin on average and (4) the three blue-chip NFTs are powered by Ethereum blockchain, thus serving as a diversifier against Ethereum.Practical implicationsBitcoin investors are suggested to include NFTs in their investment portfolio to mitigate the losses when Bitcoin falls. Meanwhile, the inclusion of crypto punk is advised for risk-averse investors who invest in gold. NFTs are powered by the Ethereum blockchain, indicating co-movement among them and thus, serve as diversifiers. Policymakers and regulators are suggested to watch closely over NFTs' great development and restructure the existing policies and thus, stabilization of asset markets can be achieved.Originality/valueThe originality aspects are: (1) focusing on the three blue-chip NFTs (i.e. BAYC, MAYC and CP) that are categorized as the largest NFTs by floor market capitalization; (2) testing the NFT attributes (safe havens, hedges or diversifiers) against traditional and digital assets, a.k.a., cryptocurrencies and (3) panel setting on 14 countries with the highest NFT users.
Mediating impact of integrated reporting on audit quality and market reactions in Africa: evidence from South Africa
Authors: Bagonza Amon , Chen Yan , Rech Frederik 
Published: July 2024

Purpose
The purpose of this study is to investigate the mediating impact of integrated reporting on the relationship between audit quality and market reactions in Africa using South Africa as a sample.

Design/methodology/approach
The study sample size consists of 119 firms listed on the Johannesburg Stock Exchange. The study was carried out for the period 2011–2019. Market reactions were proxy by share price and adjusted market returns. The authors controlled for the effects of market reactions by using other firm specifics like operating income, assets, leverage and return on assets and thereafter carried out robustness checks included under additional analysis.

Findings
Results from the study showed that integrated reporting partially mediates the relationship between audit quality and market reactions. Moreover, audit quality has a positive significant impact on market reactions in the form of the share price. The results were obtained in addition to a robustness check using adjusted market returns as a proxy for market reactions.

Practical implications
Regulators and standard setters in other countries should make integrated reporting mandatory. This study not only informs the public and investors about the organization’s business performance but also reveals auditor assurances that enchase market confidence in the company.

Social implications
Exploring the mediating impact of integrated reporting on the relationship between audit quality and market reactions yields valuable insights. Integrated reporting, which combines financial and non-financial information, influences how investors perceive and react to audit quality. Understanding this interplay could shed light on the broader implications for corporate transparency and accountability.

Originality/value
The authors are the first to conduct such a study in an emerging economy. Hence, the authors used integrated reporting as a new variable in the study of audit quality and market reactions. Furthermore, the authors used adjusted market returns under robustness checks to check if audit quality has an impact on market reactions.