bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analyzing the Involvement of Cholinesterases in the Immune Landscape of Lung Adenocarcinoma and Their Prognostic Values
Authors: Zhang Fengyu , Zhu Zhouhai , Guan Ying , Li Meng , Pan Zhenhua , Wang Ju 
Published: May 2024

AbstractLung adenocarcinoma (LUAD) is the most common subtype of lung cancer and its prognosis is poor. The cholinergic system is involved in the development of lung cancer but its role is still unclear. In this study, we collected 231 cholinergic-related genes, and examined their expression in LUAD samples and normal tissues, from which 37 differentially expressed genes were screened. Then, by survival analysis, we identified 7 genes related to the prognosis of LUAD, among which acetylcholinesterase (ACHE) and butyrylcholinesterase (BCHE) were included. The expression of AChE was upregulated in LUAD samples, and its expression had a significant positive correlation with the prognosis of male patients. But the expression of BChE was down-regulated in LUAD samples, and the elevated BChE expression was associated with a good prognosis in women and non-smoking patients. We also observed a close relationship between the two genes and immune landscape of LUAD. The AChE high expression patients had a higher ratio of tumor-infiltrating immune cells than the low expression patients, while the BChE high expression group had higher ratios of both tumor-infiltrating immune cells and stromal cells. We collected a total of 113 immunomodulatory genes associated with AChE and BChE to build an immunoregulatory network, which comprised several gene clusters. We also found that the expression of AChE and BChE was associated with immune escape in LUAD. Our results showed that AChE and BChE may play an important role in the development of LUAD, and could be promising biomarkers and targets for its diagnosis and treatment.
Imaging the extracellular matrix in live tissues and organisms with a glycan-binding fluorophore
Authors: Fiore Antonio , Yu Guoqiang , Northey Jason J. , Patel Ronak , Ravenscroft Thomas A. , Ikegami Richard , Kolkman Wiert , Kumar Pratik , Grimm Jonathan B. , Dilan Tanya L. , Ruetten Virginia M.S. , Ahrens Misha B. , Shroff Hari , Lavis Luke D. , Wang Shaohe , Weaver Valerie M. , Pedram Kayvon 
Published: May 2024

AbstractAll multicellular systems produce and dynamically regulate extracellular matrices (ECM) that play important roles in both biochemical and mechanical signaling. Though the spatial arrangement of these extracellular assemblies is critical to their biological functions, visualization of ECM structure is challenging, in part because the biomolecules that compose the ECM are difficult to fluorescently label individually and collectively. Here, we present a cell-impermeable small molecule fluorophore, termed Rhobo6, that turns on and red shifts upon reversible binding to glycans. Given that most ECM components are densely glycosylated, the dye enables wash-free visualization of ECM, in systems ranging fromin vitrosubstrates toin vivomouse mammary tumors. Relative to existing techniques, Rhobo6 provides a broad substrate profile, superior tissue penetration, nonperturbative labeling, and negligible photobleaching. This work establishes a straightforward method for imaging the distribution of ECM in live tissues and organisms, lowering barriers for investigation of extracellular biology.
Red Blood Cell-Derived Exosomal Oncogenic MicroRNA Promote Cancer Development and Progression
Authors: Li Jin , Dhilipkannah Pushpa , Holden Van K , Sachdeva Ashutosh , Jiang Feng 
Published: May 2024

AbstractThe role of red blood cells (RBCs) in tumorigenesis is poorly understood. We previously identified RBC-microRNAs with aberrations linked to lung cancer, including miR-93-5p. Here we find that miR-93-5p levels are elevated in RBC-derived exosomes among lung cancer patients and are associated with their shorter survivals. RBC-derived miR-93-5p transfers to cancer cells primarily through the exosomal pathway. The transferred RBC-miR-93-5p can target PTEN in cancer cells, and hence increase cell proliferation, invasion, and migration. RBC-derived miR-93-5p accelerates, whereas targeting miR-93-5p diminishes tumor growth in xenograft models. These findings reveal a novel biological function of RBCs in tumorigenesis, where they facilitate cancer progression by transferring the oncomiR via exosomes, thereby offering new diagnostic and treatment strategies for lung cancer.
Neuron Derived Cytokine Interleukin-34 Controls Developmental Microglia Function
Authors: Devlin Benjamin A. , Nguyen Dang M. , Grullon Gabriel , Clark Madeline J. , Ceasrine Alexis M. , Deja Martha , Shah Ashka , Ati Shomik , Finn Amelie , Ribeiro Diogo , Schaefer Anne , Bilbo Staci D. 
Published: May 2024

AbstractNeuron-microglia interactions dictate the development of neuronal circuits in the brain. However, the factors that support and broadly regulate these processes across developmental stages are largely unknown. Here, we find that IL34, a neuron-derived cytokine, is upregulated in development and plays a critical role in supporting and maintaining neuroprotective, mature microglia in the anterior cingulate cortex (ACC) of mice. We show that IL34 mRNA and protein is upregulated in neurons in the second week of postnatal life and that this increase coincides with increases in microglia number and expression of mature, homeostatic markers, e.g., TMEM119. We also found that IL34 mRNA is higher in more active neurons, and higher in excitatory (compared to inhibitory) neurons. Genetic KO of IL34 prevents the functional maturation of microglia and results in an anxiolytic phenotype in these mice by adulthood. Acute, low dose blocking of IL34 at postnatal day (P)15 in mice decreased microglial TMEM119 expression and increased aberrant microglial phagocytosis of thalamocortical synapses within the ACC. In contrast, viral overexpression of IL34 early in life (P1-P8) caused early maturation of microglia and prevented microglial phagocytosis of thalamocortical synapses during the appropriate neurodevelopmental refinement window. Taken together, these findings establish IL34 as a key regulator of neuron-microglia crosstalk in postnatal brain development, controlling both microglial maturation and synapse engulfment.
UPF1 is required for gene expression in mitochondria and paternal mtDNA clearance during spermatogenesis
Authors: Wright Matthew T , Singh Anand K , Dixon Hannah L , Price Emily M , Connolly Elizabeth , Maio Alessandro Di , Barlow Jonathon , Catoni Marco , Fan Yun , Brogna Saverio 
Published: May 2024

AbstractUPF1 is a conserved RNA helicase in eukaryotes which is crucial for the correct expression of nuclear genes. This study presents ChIP-seq evidence indicating its RNA-dependent interaction with mtDNA transcription sites inDrosophilaS2 cells. Mitochondrial and frequent co-localisation with nucleoids were validated by immunostaining and GFP-tagging of UPF1 in various fly tissues and cell types. Depletion of UPF1, but not other NMD factors, during spermatogenesis, causes severe meiosis and cytokinesis defects, leading to sterility. RNA-seq indicates that these phenotypes could be primarily due to the reduced expression of genes essential for chromosome segregation. Yet also shows that spermatids depleted of UPF1 exhibit a widespread downregulation of mtDNA transcription and, unlike in wild type, fail to eliminate their mtDNA at the elongation stage. Cumulatively, this study indicates a crucial requirement of UPF1 in the expression of both nuclear and mtDNA genes during spermatogenesis.
Task-specific topographical maps of neural activity in the primate lateral prefrontal cortex
Authors: Xiang Jinkang Derrick , Roussy Megan , Corrigan Benjamin , Gulli Roberto A. , Luna Rogelio , Mofrad Maryam Hasanzadeh , Muller Lyle , Diedrichsen Jörn , Schmitz Taylor W. , Martinez-Trujillo Julio , Mur Marieke 
Published: May 2024

AbstractNeurons in the primate lateral prefrontal cortex (LPFC) flexibly adapt their activity to support a wide range of cognitive tasks. Whether and how the topography of LPFC neural activity changes as a function of task is unclear. In the present study, we address this issue by characterizing the functional topography of LPFC neural activity in awake behaving macaques performing three distinct cognitive tasks. We recorded from chronically implanted multi-electrode arrays and show that the topography of LPFC activity is stable within a task, but adaptive across tasks. The topography of neural activity exhibits a spatial scale compatible with that of cortical columns and prior anatomical tracing work on afferent LPFC inputs. Our findings show that LPFC maps of neural population activity are stable for a specific task, providing robust neural codes that support task specialization. Moreover, the variability in functional topographies across tasks indicates activity landscapes can adapt, providing flexibility to LPFC neural codes.
Unraveling Morphogenesis, Starvation, and Light Responses in a Mushroom-Forming Fungus,Coprinopsis cinerea, Using Long Read Sequencing and Extensive Expression Profiling
Authors: Hegedüs Botond , Sahu Neha , Bálint Balázs , Haridas Sajeet , Bense Viktória , Merényi Zsolt , Virágh Máté , Wu Hongli , Liu Xiao-Bin , Riley Robert , Lipzen Anna , Koriabine Maxim , Savage Emily , Guo Jie , Barry Kerrie , Ng Vivian , Urbán Péter , Gyenesei Attila , Freitag Michael , Grigoriev Igor V. , Nagy László G. 
Published: May 2024

AbstractMushroom-forming fungi (Agaricomycetes) are emerging as pivotal players in several fields, as drivers of nutrient cycling, sources of novel applications, and the group includes some of the most morphologically complex multicellular fungi. Genomic data for Agaricomycetes are accumulating at a steady pace, however, this is not paralleled by improvements in the quality of genome sequence and associated functional gene annotations, which leaves gene function notoriously poorly understood in comparison with other fungi and model eukaryotes. We set out to improve our functional understanding of the model mushroomCoprinopsis cinereaby integrating a new, chromosome-level assembly with high-quality gene predictions and functional information derived from gene-expression profiling data across 67 developmental, stress, and light conditions. The new annotation has considerably improved quality metrics and includes 5’- and 3’-untranslated regions (UTRs), polyadenylation sites (PAS), upstream ORFs (uORFs), splicing isoforms, conserved sequence motifs (e.g., TATA and Kozak boxes) and microexons. We found that alternative polyadenylation is widespread inC. cinerea, but that it is not specifically regulated across the various conditions used here. Transcriptome profiling allowed us to delineate core gene sets corresponding to carbon starvation, light-response, and hyphal differentiation, and uncover new aspects of the light-regulated phases of life cycle. As a result, the genome ofC. cinereahas now become the most comprehensively annotated genome among mushroom-forming fungi, which will contribute to multiple rapidly expanding fields, including research on their life history, light and stress responses, as well as multicellular development.
Human Substantia Nigra Neurons Encode Reward Expectations
Authors: Imtiaz Zarghona , Kato Ayaka , Kopell Brian H. , Qasim Salman E. , Davis Arianna Neal , Martinez Lizbeth Nunez , Heflin Matt , Kulkarni Kaustubh , Morsi Amr , Gu Xiaosi , Saez Ignacio 
Published: May 2024

AbstractDopamine (DA) signals originating from substantia nigra (SN) neurons are centrally involved in the regulation of motor and reward processing. DA signals behaviorally relevant events where reward outcomes differ from expectations (reward prediction errors, RPEs). RPEs play a crucial role in learning optimal courses of action and in determining response vigor when an agent expects rewards. Nevertheless, how reward expectations, crucial for RPE calculations, are conveyed to and represented in the dopaminergic system is not fully understood, especially in the human brain where the activity of DA neurons is difficult to study. One possibility, suggested by evidence from animal models, is that DA neurons explicitly encode reward expectations. Alternatively, they may receive RPE information directly from upstream brain regions. To address whether SN neuron activity directly reflects reward expectation information, we directly examined the encoding of reward expectation signals in human putative DA neurons by performing single-unit recordings from the SN of patients undergoing neurosurgery. Patients played a two-armed bandit decision- making task in which they attempted to maximize reward. We show that neuronal firing rates (FR) of putative DA neurons during the reward expectation period explicitly encode reward expectations. First, activity in these neurons was modulated by previous trial outcomes, such that FR were greater after positive outcomes than after neutral or negative outcome trials. Second, this increase in FR was associated with shorter reaction times, consistent with an invigorating effect of DA neuron activity during expectation. These results suggest that human DA neurons explicitly encode reward expectations, providing a neurophysiological substrate for a signal critical for reward learning.
Polyamines promote disordered protein phase separation
Authors: Percival Matthew , Pantoja Christian F. , Cima-Omori Maria-Sol , Becker Stefan , Zweckstetter Markus 
Published: May 2024

AbstactMembrane-less organelles are spatially heterogenous deposits of interacting macromolecules, often intrinsically disordered proteins and RNA, that form and dissolve in response to cellular stimuli. How membraneless organelles control composition while maintaining stimuli-responsiveness in an environment with competitive interactions is not well understood. Here we demonstrate that natural polyamines, which are found in all living organisms and help in many biological processes, promote protein phase separation via attractive interactions with acidic disordered domains. We show that the abundant polyamine spermine promotes phase separation of the stress-granule associated protein G3BP1 and modulates together with RNA the phase separation and amyloid formation of the Parkinson’s disease-related protein α-synuclein. Polyamine-promoted phase separation is controllable via polyamine acetylation and RNA-mediated competitive interactions. The results suggest that cellular polyamines may serve diverse roles in biomolecular condensation and the regulation of membraneless organelles.
Laboratoryin vitroreplication of Ostreid Herpes Virus (OsHV-1) using Pacific oyster tissue explants
Authors: Potts Robert W.A. , Regan Tim , Ross Stuart , Bateman Kelly , Hooper Chantelle , Paley Richard , Houston Ross D. , Bean Tim P. 
Published: May 2024

AbstractPacific oysters (CrassostreaorMagallana gigas) are one of the most economically important aquaculture species globally. Over the past two decades, ostreid herpesvirus (OsHV-1), has become a major pathogen of cultured Pacific oysters resulting in widespread mortality with a global distribution. Experimental use of OsHV-1 is challenging for many reasons, including both complexity and relative obscurity of host pathogen dynamics, and a lack of functioning model systems. The goal of this study was to improve the tools available for working with OsHV-1 in both whole animals and in tissue explants establishedex vivofrom oysters and maintained in controlled laboratory conditions. Tissue explants were taken from oysters originating from two different sources that have different levels of mortality in OsHV-1 challenges and were used in disease challenges alongside whole animals for comparison. Quantitative PCR, histology and electron microscopy were used to confirm that the explants were capable of replicating OsHV-1. Furthermore, the quantitative PCR results suggests that the source of the oysters was significant in determining the outcome of infection in the explants, supporting the validity of the explant model for OsHV-1 infection. This approach for studying OsHV-1 allows for the control of confounding factors in disease outcome that is not possible in whole animal challenges, providing a new tool for studying OsHV-1 in Pacific oysters.
Encoding of interdependent features of head direction and angular head velocity in navigation
Authors: Cai Dongqin , Liu Tao , Liu Jia 
Published: May 2024

ABSTRACTTo comprehend the complex world around us, our brains are tasked with the remarkable job of integrating multiple features into a cohesive whole. While previous studies have primarily focused on the processing and integration of independent features, here we investigated the simultaneous encoding of the interdependent features, specifically head direction (HD) and its temporal derivative, angular head velocity (AHV), by first employing computational modeling on HD systems to explore emergent algorithms and then validated its biological plausibility with empirical data from mice’s HD systems. Our analysis revealed two distinct neuron populations: those with multiphasic tuning curves for HD compromised their HD encoding capacity to better capture AHV dynamics, while those with monophasic tuning curves primarily encoded HD. This pattern of functional dissociation was observed in both artificial HD systems and the cortical and subcortical regions upstream of biological HD systems, suggesting a general principle for encoding interdependent features. Further, exploration of the underlying mechanisms involved examining neural manifolds embedded within the representational space constructed by these neurons. We found that the manifold by neurons with multiphasic tuning curves was locally jagged and complex, which effectively expanded the dimensionality of the neural representation space and in turn facilitated a high-precision representation of AHV. Therefore, the encoding strategy for HD and AHV likely integrates characteristics of both dense and sparse coding schemes to achieve a balance between preserving specificity for individual features and maintaining their interdependency nature, marking a significant departure from the encoding of independent features and thus advocating future research delving into the encoding strategies of interdependent features.
Architectural learning networks: a study on eliciting the learning agendas of architectural schools
Authors: Baloğlu Melis , Demir Yüksel 
Published: May 2024

PurposeThe purpose of this paper is to demonstrate how network theory and methods can provide insights into the forces shaping architectural learning agendas and knowledge construction in architectural schools.Design/methodology/approachThe methodology involves conceptualising learning as a constructivist process and the agenda as an interconnected network of actors, concepts and relations. Network analysis techniques, including centrality and brokerage metrics, are used to identify roles and knowledge flows using the data locally collected from Turkish universities as well as from the OpenSyllabus open-source database.FindingsThe analysis reveals the enduring influence of early modernists, signalling imbalanced canon formation in the architectural learning system. However, marginal voices highlight struggles in integrating unconventional perspectives. Limited integration of local figures indicates a consolidation of Eurocentric epistemes. Identifying these hidden forces is vital for reimagining learning agendas and socio-culturally engaged forms of learning. Pioneering figures demonstrate potential for synthesis when situated as brokers, not bifurcated schools.Research limitations/implicationsThe outcomes are limited by the geographical and temporal boundaries of the data and the analysis method employed. Despite limitations, the diagnostic network framework reveals architectural learning as an open, contested ecosystem demanding pluralistic pedagogies concerning not only the global but the local, both canonical and marginal. Further research covering more data could enrich the understanding of qualitative complexities.Practical implicationsThe network perspective prompts critical reflexivity about power, ideology and exclusion in knowledge construction. Strategic inclusion and diversification of voices provide pathways to bridge divides and ground learning locally.Originality/valueThis research offers a methodology model to examine forces and influences shaping architectural education by elucidating hidden and remote roles and knowledge gaps in learning agendas. Extending the techniques more widely can enable strategic interventions toward inclusive, impactful learning across disciplines, time and geographies.
Hotel booking intentions in the TikTok era: the role of online celebrity brand equity
Authors: Tran Phuong Kim Thi , Ho-Mai Nhi Thao , Nguyen Vien Ky , Do Uyen Thu Thi , Truong Thanh Ba , Tran Vinh Trung 
Published: May 2024

Purpose
This study aims to explore the pathway of increasing hotel booking intentions by mapping the linkage mechanism between the antecedents and components of brand equity to ultimately drive followers’ hotel booking intention. In addition, the role of over-endorsement as a moderating variable is also evaluated.

Design/methodology/approach
The conceptual model and research hypotheses were each assessed using covariance-based structural equation modeling. Paper-based and online surveys were used to collect data from 443 respondents who are TikTok users and follow at least one TikTok online celebrity, while that online celebrity must have reviewed at least one type of accommodation.

Findings
Except for the relationship between virtual interactivity and online celebrity brand image, the results confirmed the relationships between research concepts.

Research limitations/implications
Further studies are needed to validate the results in other cultural contexts, generalize findings and broaden the range of target respondents.

Originality/value
This study contributes to the hotel literature by illustrating how online celebrity brand equity (OCBE) drives hotel booking intentions. The study highlights the importance of antecedent factors – follower-centered drivers (e.g. lifestyle congruence, friendship) and online celebrity-led drivers (e.g. virtual interactivity, expertise) – to achieve a hierarchical relationship between OCBE components and followers’ booking intentions.