bluuebunny/crossref_metadata_2025_split huggingface dataset:
Most human DNA replication initiation is dispersed throughout the genome with only a minority within previously identified initiation zones
Authors: Carrington Jamie T. , Wilson Rosemary H C , Thiyagarajan Sathish , Barker Tom , Catchpole Leah , Durrant Alex , Knitlhoffer Vanda , Watkins Chris , Gharbi Karim , Nieduszynski Conrad A. 
Published: May 2024

AbstractThe identification of sites of DNA replication initiation in mammalian cells has been challenging. Here, we present unbiased detection of replication initiation events in human cells using BrdU incorporation and single-molecule nanopore sequencing. Increases in BrdU incorporation allow us to measure DNA replication dynamics, including identification of replication initiation, fork direction and termination on individual nanopore sequencing reads. Importantly, initiation and termination events are identified on single-molecules with high resolution, throughout S-phase and across the human genome. We find a significant enrichment of initiation sites within the broad initiation zones identified by population level studies. However, these focussed initiation sites only account for ∼20% of all identified replication initiation events. Most initiation events are dispersed throughout the genome and are missed by cell population approaches. This indicates that most initiation occurs at sites that, individually, are rarely used. These dispersed initiation sites contrast with the focused sites identified by population studies, in that they do not show a strong relationship to transcription or a particular epigenetic signature. Therefore, single-molecule sequencing enables unbiased detection and characterisation of DNA replication initiation events, including the numerous dispersed initiation events that replicate most of the human genome.
Activation of the proton-sensing GPCR, GPR65 on fibroblast-like synoviocytes contributes to inflammatory joint pain
Authors: Pattison Luke A. , Rickman Rebecca H. , Hilton Helen , Wijesinghe Susanne N. , Ladds Graham , Yang Li , Jones Simon W. , Smith Ewan St. John 
Published: May 2024

AbstractInflammation is associated with localised acidosis, however, attributing physiological and pathological roles to proton-sensitive receptors is challenging due to their diversity and widespread expression. Here, agonists of the proton-sensing GPCR, GPR65, were systematically characterised. The synthetic agonist BTB09089 (BTB) recapitulated many proton-induced signalling events and demonstrated selectivity for GPR65. BTB was used to show that GPR65 activation on fibroblast-like synoviocytes (FLS), cells that line synovial joints, results in the secretion of pro-inflammatory mediators capable of recruiting immune cells and sensitising sensory neurons. Intra-articular injection of BTB resulted in GPR65-dependent sensitisation of knee-innervating neurons and nocifensive behaviours in mice. Stimulation of GPR65 on human FLS also triggered the release of inflammatory mediators and synovial fluid samples from human osteoarthritis patients were shown to activate GPR65. These results suggest a role of GPR65 in mediating cell-cell interactions that drive inflammatory joint pain in both mice and humans.
Cell rearrangement progression along the apical-basal axis is linked with 3D epithelial tissue structure
Authors: Kusaka Erika M. , Ostvar Sassan , Wang Xun , Liu Xiaoyun , Kasza Karen E. 
Published: May 2024

AbstractEpithelial tissues undergo extensive structural remodeling during embryonic development. Tissue remodeling is often enabled by oriented cell rearrangements that are linked with patterns of mechanical stress in the tissue and with tissue mechanical properties. Cell rearrangements and their links to tissue structure have largely been studied at the apical side of tissues at the level of adherens junctions. Less is known about the involvement of basolateral domains in cell rearrangements. Here we use live confocal imaging to quantify cell rearrangements, cell packing structure, and cell morphology in 3D in the converging and extendingDrosophilagermband epithelium. We report gradients in cell shapes and tissue structure along the apical-basal axis of the germband, suggesting that the apical and basolateral domains display distinct behaviors. Cell rearrangements initiate at apical as well as basolateral positions, with initiation frequencies also displaying a gradient along the apical-basal axis. Following initiation, rearrangements propagate across the apical-basal axis and lateral cell contacts remodel; these events involve scutoids and other complex 3D cell shapes as intermediate states. These findings uncover novel aspects of the cell rearrangements that drive dynamic remodeling of epithelia and reveal links between rearrangements and gradients in tissue structure along the apical-basal axis.
Exploring the Transcriptomic Profile of Human Monkeypox Virus via CAGE and Native RNA Sequencing Approaches
Authors: Nagy Gergely Ármin , Tombácz Dóra , Prazsák István , Csabai Zsolt , Dörmő Ákos , Gulyás Gábor , Kemenesi Gábor , Tóth Gábor E. , Holoubek Jiří , Růžek Daniel , Kakuk Balázs , Boldogkői Zsolt 
Published: May 2024

AbstractIn this study, we employed short- and long-read sequencing technologies to delineate the transcriptional architecture of the human monkeypox virus and to identify key regulatory elements that govern its gene expression. Specifically, we conducted a transcriptomic analysis to annotate the transcription start sites (TSSs) and transcription end sites (TESs) of the virus by utilizing cap analysis of gene expression sequencing on the Illumina platform and direct RNA sequencing on the Oxford Nanopore technology device. Our investigations uncovered significant complexity in the use of alternative TSSs and TESs in viral genes. In this research, we also detected the promoter elements and poly(A) signals associated with the viral genes. Additionally, we identified novel genes in both the left and right variable regions of the viral genome.ImportanceGenerally, gaining insight into how the transcription of a virus is regulated offers insights into the key mechanisms that control its life cycle. The recent outbreak of the human monkeypox virus has underscored the necessity of understanding the basic biology of its causative agent. Our results are pivotal for constructing a comprehensive transcriptomic atlas of the human monkeypox virus, providing valuable resources for future studies.
Performance of the BD Phoenix CPO detect assay for the detection and classification of OXA-48 producing-Escherichia colithat do not coproduce ESBL/pAmpC
Authors: Galán-Sánchez Fátima , Portillo-Calderón Inés , Rodriguez-Iglesias Manuel , Pascual Álvaro , López-Cerero Lorena 
Published: May 2024

ABSTRACTReliable detection of OXA-48-like enzymes in routine antimicrobial susceptibility testing is difficult, especially if the isolate does not coproduce other beta-lactamases. The BD Phoenix™ Emerge panel includes the CPO Detect Test (CPO-T), which allows simultaneous antimicrobial susceptibility testing and carbapenemase detection and characterization. We evaluated the accuracy of detection and classification of carbapenemases determined by CPO-T against a characterized set of OXA-48-producingEscherichia coliisolates that do not co-produce ESBL/pAmpC, and BD Phoenix™ for rapid antimicrobial susceptibility testing. A total of 51E. coliisolates were included All the isolates were sequenced using Illumina and analyzed using Resfinder and CARD for resistance determinants, MLSTfinder for typing and Clermont Phylotyper for phylotypes. CPO-T was performed within the BD Phoenix™ NMIC-502 panel. Disk diffusion, with readings at 4, 6, 8 and 24 hours, was performed as reference method (RDD). The CPO-T detected carbapenemase activity in 100% of the isolates within 7 hours of incubation and 42 (82.4%) isolates were correctly assigned to the class D Ambler. For all isolates and antibiotics, BD Phoenix™ provided definitive susceptibility results in less than 8 hours in 64.6% of cases compared to 58.2% with RDD. Overall categorical agreement was 90.7% and 5.9% very major, 6.2% major and 3.2% minor errors were observed. Our results demonstrate that CPO-T is a reliable tool for the detection of OXA-48 inE. coliisolates that do not co-produce ESBL/pAmpCwithout the need for additional testing, and that BD Phoenix™ provides rapid results for the antibiotics most commonly used in empirical treatment.IMPORTANCEDetection of OXA-48-like enzymes in isolates that do not co-produce other beta-lactamases in routine antimicrobial susceptibility testing is difficult, and studies on these types of isolates are scarce. Our study analyzes the performance of the BD Phoenix™ Emerge panel, which includes the CPO detection test (CPO-T), in a characterized set of OXA-48-producingEscherichia coliisolates that do not co-produce ESBL/pAmpC, and also provide information about time to results of this system.
How light at night sets the circalunar clock in the marine midgeClunio marinus
Authors: Peralta Carolina M. , Feunteun Eric , Guillaudeau Julien , Briševac Dušica , Kaiser Tobias S. 
Published: May 2024

AbstractMany organisms inhabiting the interface between land and sea have evolved biological clocks corresponding to the period of the semilunar (14.77d) or the lunar (29.53d) cycle. Since tidal amplitude is modulated across the lunar cycle, these circasemilunar or circalunar clocks allow organisms to adapt to the tides. Biological clocks are synchronized to external cycles via environmental cues calledzeitgebers. Here, we explore how light at night sets the circalunar and circasemilunar clocks ofClunio marinus, a marine insect that relies on these clocks to control timing of emergence. We first characterized how moonlight intensity is modulated by the tides by measuring light intensity in the natural habitat ofC. marinus. In laboratory experiments, we then explored how different moonlight treatments set the phase of the clocks of twoC. marinusstrains, one with a lunar rhythm and one with a semilunar rhythm. Light intensity alone does not affect the phase or strength of the lunar rhythm. Presenting moonlight during different 2-hour or 4-hour windows during the subjective night shows that (1) the required duration of moonlight is strain-specific, (2) there are strain-specific moonlight sensitivity windows and (3) timing of moonlight can shift the phase of the lunar rhythm to stay synchronized with the lowest low tides. Experiments simulating natural moonlight patterns with moonrise and moonset confirm that the phase is set by the timing of moonlight. Light intensity within the ranges observed in the field leads to the best synchronization. Taken together, we show that there is a complex and strain-specific integration of intensity, duration and timing of light at night to precisely entrain the lunar and semilunar rhythms. The observed fine-tuning of the rhythms under the most natural moonlight regimes lays the foundation for a better chronobiological and genetic dissection of the circa(semi)lunar clock inC. marinus.
WITHDRAWN: Revealing Mechanism of Allostery in RIPK2 kinase
Authors: Bhakat Soumendranath , Siokas Ioannis , Covitz Rachel Mei-Lian , Degterev Alexei 
Published: May 2024

Withdrawal StatementThe authors have withdrawn their manuscript owing to a conflict of interest. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author, Soumendranath Bhakat.
Convergent evolution of noncoding elements associated with short tarsus length in birds
Authors: Shakya Subir B. , Edwards Scott V. , Sackton Timothy B. 
Published: May 2024

AbstractConvergent evolution is the independent evolution of similar traits in unrelated lineages across the Tree of Life. Various factors underlie convergent evolution including convergent rate changes through consistent shifts in substitution rate in the same genes or gene networks. In this study, we use comprehensive phenotypic data to identify seven bird clades with independent shortening in tarsus length and use both comparative genomic and population genetic data to identify convergent evolutionary changes among four target clades with shifts to shorter optimal tarsus length. Using a newly generated, comprehensive set of avian conserved non-exonic elements (CNEEs), we find strong evidence for convergent acceleration in short-tarsi clades among CNEEs, but not protein-coding genes. Accelerated CNEEs in short-tarsi clades are preferentially located near genes with functions in development, with the strongest enrichment associated with skeletal system development. Further analysis of gene networks highlighted this larger role of changes in regulation of broadly homologous developmental genes and pathways as being an integral aspect of limb size variability in birds.
Flexibility in the face of climate change? A rapid and dramatic shift toward later spring migration in Hudsonian Godwits (Limosa haemastica)
Authors: Puleo Lauren , Huang Feipeng , Stager Maria , Senner Nathan R. 
Published: May 2024

SUMMARYWith rapid environmental change, shifts in migration timing are vitally important for maintaining population stability and have been widely documented. However, little remains known abouthowmigrants are driving these shifts and what factors may influence the effective utilization of these strategies, limiting our ability to accurately assess species- and population-level vulnerability to climate change. The Hudsonian godwit (Limosa haemastica) is an extreme long-distance migratory shorebird that has (1) previously shifted its population-level migration timing and (2) exhibits sex-specific morphological differences. Therefore, we combined over a decade of light-level geolocator tracking data from a single breeding population with a historical predictive model to assess on-going shifts in migration timing while determining the time-shifting strategies utilized by each sex. Surprisingly, we found that godwit departure and arrival timing rapidly shifted 6 days later from 2010-2023 with no differences in timing between the sexes. Despite this change in migration timing, the population has maintained an average migratory duration of 24 days, suggesting that godwits are driving shifts in arrival timing entirely by shifting their nonbreeding ground departure, something rarely documented in long-distance migrants. Yet, we also found that godwits are not shifting their migration timing in the direction predicted by our model, providing evidence that this response may not be adaptive. These results emphasize the urgent need for a more holistic approach to assessing the relative vulnerability of migratory species and the adaptiveness of changes in migration timing.
Hunting for hypercharge anapole dark matter in all spin scenarios
Authors: Choi Seong Youl , Jeong Jaehoon , Kang Dong Woo , Shin Seodong 
Published: May 2024

We conduct a combined analysis to investigate dark matter (DM) with hypercharge anapole moments, focusing on scenarios where Majorana DM particles with spin 1/2, 1, 3/2, and 2 interact exclusively with Standard Model particles through U(1)Y hypercharge anapole terms for the first time. For completeness, we construct general effective U(1) gauge-invariant three-point vertices. These enable the generation of hypercharge gauge-invariant interaction vertices for both a virtual photon γ and a virtual Z boson with two identical massive Majorana particles of any nonzero spin s, after the spontaneous breaking of electroweak gauge symmetry. For complementarity, we adopt effective operators tailored to each dark matter spin allowing crossing symmetry. We calculate the relic abundance, analyze current constraints and future sensitivities from dark matter direct detection and collider experiments, and apply the conceptual naive perturbativity bound. Our estimations based on a generalized vertex calculation demonstrate that the scenario with a higher-spin DM is more stringently constrained than a lower-spin DM, primarily due to the reduced annihilation cross section and/or the enhanced rate of LHC monojet events. As a remarkable outcome, the spin-2 anapole DM scenario is almost entirely excluded, while the high-luminosity LHC exhibits high sensitivities in probing spin-1 and -3/2 scenarios, except for a tiny parameter range of DM mass around 1 TeV. A significant portion of the remaining parameter space in the spin-1/2 DM scenario can be explored through upcoming Xenon experiments, with more than 20 ton-yr exposure equivalent to approximately 5 years of running the XENONnT experiment.

Published by the American Physical Society
2024
Supervisor incivility and service employee creativity: a moderated mediation model of negative affect state and core self-evaluation
Authors: A. Anjaly , S. Nemat Sheereen 
Published: May 2024

PurposeThe present study examines the effect of supervisor incivility on service employee creativity and the mediating mechanism of negative affect state on the said relationship with the aid of Affective Events Theory (AET) and Social Power Theory. Additionally, the study explores the mitigating role of core self-evaluation in the dual stage of the moderated mediation model.Design/methodology/approachSurvey data were collected from 420 frontline employees working in four-star and five-star hotels across India and PROCESS macro in SPSS 23.0 was employed to test the hypotheses proposed in the study.FindingsThe study findings observe that frontline employees experiencing supervisor incivility face a negative affect state and it further diminishes service employee creativity. Also, the indirect effect gets attenuated at dual stages when frontline employees are equipped with a high level of core self-evaluation.Practical implicationsThe study findings provide various insights to the managers to understand the deleterious effect of supervisor incivility at work and to develop interventions to manage supervisor incivility and the negative affect state among frontline hotel employees.Originality/valueThe present study is the first and unique attempt to investigate the role of supervisor incivility experienced by frontline hotel employees in India with reference to their creativity towards customers and mediating mechanism of negative affect state. The study adds value to the literature by establishing the role of core self-evaluation in the moderated mediation model. Further, the study also provides a unique contribution to the management of frontline hospitality employees.
The effects of servant leadership and despotic leadership on employees’ happiness at work (HAW): the role of job crafting
Authors: Hamid Zeeshan 
Published: May 2024

PurposeDrawing on the conservation of resources (COR) theory, this study aims to examine the effects of servant leadership and despotic leadership on employees’ happiness at work (HAW) through job crafting.Design/methodology/approachTo test the hypothesized relationships, the data were collected from 309 Pakistani employees. Structural equation modeling was used to analyze the data.FindingsThe findings showed that servant leadership is an optimal leadership style for creating employees’ HAW. In addition, job crafting was found to mediate the effects of servant leadership on employees’ broad-based positive attitudinal outcome (HAW). Moreover, results showed that despotic leadership negatively influences employees’ HAW through job crafting.Originality/valueThis study is novel as it investigates how newer forms of positive (servant) and negative (despotic) leadership styles influence employees’ multidimensional attitudinal outcome (HAW) via job crafting. By doing so, this research extends the nomological network of servant leadership, despotic leadership, job crafting and HAW.
How compulsive and impulsive buying affect consumer emotional regulation. Is anxiety a differential element?
Authors: Cachón-Rodríguez Gabriel , Blanco-González Alicia , Prado-Román Camilo , Fernández-Portillo Antonio 
Published: May 2024

PurposeAcademic literature calls for research on the impact of psychological states derived from mental illness on detrimental consumer behaviour. The purpose of this study is to assess the impact of anxiety on the consumer’s buying processes (compulsive and impulsive) and emotional regulation.Design/methodology/approachTo carry out the statistical analysis, the data were obtained through an online survey (n = 726) of supermarket consumers. The treatment of the data was using partial least squares structural equation modelling (PLS-SEM).FindingsThe results obtained show that anxiety influences the generation of harmful behaviour, as it has a positive impact on compulsive and impulsive buying. In addition, compulsive and impulsive buying generate higher levels of consumers’ emotional regulation.Originality/valueThis study contributes to the management of anxiety as a priority element to reduce harmful behaviour. Therefore, it provides useful information for marketing managers and professionals in psychological and healthy consumer processes.
Determinants and spatial spillover effects of inbound tourism in Chinese cities
Authors: Li Guangqin , Pu Kangyun 
Published: May 2024

Purpose
By using a wide range of macro and micro factors, this paper aims to provide a new assessment of the recent literature on inbound tourism demand models.

Design/methodology/approach
This study examines the determinants and spatial effects of inbound tourism using Hausman–Taylor and spatial econometric models.

Findings
Several important factors were identified, including local economic growth, openness to the outside world, regional size, geographic distance, foreign direct investment, level of innovation and average annual temperature. In addition, the study found strong cross-city competition effects on tourism resource endowment and hotel infrastructure.

Originality/value
Inbound tourism is a crucial link in achieving high-quality economic development. However, previous studies have mainly focused on the analysis of single influencing factors, ignoring the spatial spillover effects of factors.
The implications of handwritten text recognition for accessing the past at scale
Authors: Nockels Joseph , Gooding Paul , Terras Melissa 
Published: May 2024

PurposeThis paper focuses on image-to-text manuscript processing through Handwritten Text Recognition (HTR), a Machine Learning (ML) approach enabled by Artificial Intelligence (AI). With HTR now achieving high levels of accuracy, we consider its potential impact on our near-future information environment and knowledge of the past.Design/methodology/approachIn undertaking a more constructivist analysis, we identified gaps in the current literature through a Grounded Theory Method (GTM). This guided an iterative process of concept mapping through writing sprints in workshop settings. We identified, explored and confirmed themes through group discussion and a further interrogation of relevant literature, until reaching saturation.FindingsCatalogued as part of our GTM, 120 published texts underpin this paper. We found that HTR facilitates accurate transcription and dataset cleaning, while facilitating access to a variety of historical material. HTR contributes to a virtuous cycle of dataset production and can inform the development of online cataloguing. However, current limitations include dependency on digitisation pipelines, potential archival history omission and entrenchment of bias. We also cite near-future HTR considerations. These include encouraging open access, integrating advanced AI processes and metadata extraction; legal and moral issues surrounding copyright and data ethics; crediting individuals’ transcription contributions and HTR’s environmental costs.Originality/valueOur research produces a set of best practice recommendations for researchers, data providers and memory institutions, surrounding HTR use. This forms an initial, though not comprehensive, blueprint for directing future HTR research. In pursuing this, the narrative that HTR’s speed and efficiency will simply transform scholarship in archives is deconstructed.