bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell3DPositioning byOptical encoding(C3PO) and its application to spatial transcriptomics
Authors: Cotterell James , Swoger Jim , Robert-Moreno Alexandre , Cardona Heura , Musy Marco , Sharpe James 
Published: March 2024

AbstractCurrent state-of-the-art spatial omics approaches suffer from the drawback that they are tissue section-based and thus inherently 2-dimensional. A full understanding of biological processes will only be possible when such data is available in 3-dimensions (3D). Here, we introduce Cell 3D Positioning by Optical encoding (C3PO) - the first technique capable of reconstructing the 3D positions of cells in a tissue, after they have been fully dissociated for single-cell omics analysis. It imposes a Cartesian coordinate system of positions on the tissue and cells of interest, before dissociation. This is created by multiple orthogonal spatial gradients of active fluorophores, carefully shaped by a 3D bleaching method, such that each position in the tissue is encoded by a unique fluorescent address. Upon dissociation of the tissue the fluorescent addresses of the cells can be read via an appropriate device (such as a FACS machine) to computationally reconstruct the tissue in 3D, before omics are performed downstream. Here, we show two proof-of-principle results for C3PO. First, pure C3PO without omics, to reconstruct the 3D geometry of a developing mouse limb bud. Second, an application of C3PO to spatial transcriptomics, revealing the expression patterns of 73 genes with interesting gene expression patterns in the developing limb.. C3PO is a genuinely novel approach to reconstruct the original 3D positions of cells in a tissue after dissociation. Combined with transcriptomics, it can play a significant role in the study of any tissue or organ in which 3D structure and geometry is important, such as developmental biology, cancer biology and neuroscience. It is not an omics techniqueper se, and in the future could be combined with the growing family of other omics technologies.One sentence summaryC3PO is a novel optical technique that can preserve the 3D positional coordinates of cells after tissue dissociation, enabling a radically new approach to spatial transcriptomics.
Sex Hormones AlterPseudomonas aeruginosaIron Acquisition and Virulence Factors
Authors: Ebrahim H , Bryan N , Collette A , Armstrong S D , Bronowski C , Floyd R V , Fothergill J L 
Published: March 2024

AbstractUrinary Tract Infections (UTI) are one of the most widespread infections in healthcare and community settings worldwide.Pseudomonas aeruginosais the third most common pathogen associated with catheter-associated UTI (CAUTI).P. aeruginosainfections are highly resistant and difficult to treat and it is currently classified as priority 1 by the World Health Organisation.In vitrostudies of microbes typically employ laboratory media. The inadequacy of nutrient-rich media in simulating the physiological environment has led to the development of multiple media that mimic human body fluids, including Artificial Urine Medium (AUM). By studying growth andin vitrobiofilm assays along with proteomics, we sought to establish whether UTIP. aeruginosarespond differently in laboratory media, AUM and urine. To further probe the impact of environmental influences, sex hormones estradiol, progesterone and testosterone were added at physiologically relevant concentrations. The proteomic profiles were then compared between hormone supplemented AUM and urine.Our findings indicate that bacterial responses in standard laboratory media, AUM and urine were distinct. Increased proteins associated with iron acquisition mechanisms were similar in both AUM and urine. However, differences were observed in other virulence and iron pathways, such as phenazine production. Treatment with hormones decreased the abundance ofP. aeruginosaproteins involved in iron acquisition. Individual hormones exhibited specific bacterial alterations. The presence of estradiol increased protein abundance of the Pseudomonas Quinolone Signal (PQS) quorum sensing system. This study suggests thatP. aeruginosapathogenesis in UTI infections may be influenced by the presence of specific hormones in the host. Understanding the individual role of host factors could contribute to a personalised treatment approach based on the potential impact on infection susceptibility and outcome.
Cooperative colonization of the host and pathogen dissemination involves stochastic and spatially structured expression of virulence traits
Authors: López-Pagán Nieves , Rufián José S. , Luneau Julien , Sánchez-Romero María-Antonia , Aussel Laurent , van Vliet Simon , Ruiz-Albert Javier , Beuzón Carmen R. 
Published: March 2024

SUMMARYBacteria respond to changing environments by altering gene expression. Some responses display probabilistic cell-to-cell variation within isogenic populations. A few paradigmatic examples in animal pathogens have demonstrated that this phenotypic heterogeneity has biological relevance for virulence.We investigate single-cell flagellar expression in relation to type III secretion expression in the plant pathogenPseudomonas syringaeand describe that both systems undergo phenotypic heterogeneity throughout plant colonization. We establish that high expression of these system carries growth penalties. Stochastic, spatial and time factors shape dynamics of a phenotypically diverse population which displays division of labor during colonization: T3SSONbacteria effectors act as ‘common goods’ to suppress immunity, allowing the increase of motile bacteria that actively leave the infected tissue before necrosis. This study provides a comprehensive view of how processes underlying bacterial specialization play out in the context of complex and changing environments of biological and applied relevance such as host colonization.
Growth arrest is a DNA damage protection strategy in plants
Authors: Serrano-Mislata Antonio , Hernández-García Jorge , de Ollas Carlos , Blanco-Touriñán Noel , Gómez-Cadenas Aurelio , Sablowski Robert , Alabadí David , Blázquez Miguel A. 
Published: March 2024

AbstractWhen exposed to stress, plants slow down their growth while activating defensive mechanisms. This behaviour has been proposed to help plants reallocate resources and meet the energy demands required for survival. In this study, we show instead that plants can grow under limited water availability without compromising their tolerance to the stress. However, cells that continue to divide under stress accumulate DNA damage, which frequently leads to cell death. Given that the DNA lesions are observed in the apical stem cells that give rise to all plant organs, including flowers, we propose that systemic growth arrest is used as a defense strategy that plants employ not only to maximize individual fitness, but also to ensure the accurate transmission of genetic information to their progeny.
Resolved Genomes of Wastewater ESBL-ProducingEscherichia coliand Metagenomic Analysis of Source Wastewater Samples
Authors: Cheney Clinton , Johnson Jared D. , Marie John P. Ste. , Gacosta Kayla Y.M. , Denlinger Drumm Natalie B. , Jones Gerrad , Waite-Cusic Joy , Navab-Daneshmand Tala 
Published: March 2024

ABSTRACTExtended-spectrum beta-lactamase (ESBL) producingEscherichia colipose a serious threat to human health because of their resistance to the most commonly prescribed antibiotics: penicillins and cephalosporins. In this study, we provide a genomic and metagenomic context for the determinant ESBL genes ofE. coliisolated from various wastewater treatment utilities in Oregon, USA. Class A beta-lactamase genes on chromosomes (blaCTX-M,blaTEM)were clustered with antibiotic resistance genes associated with other classes of antibiotics (sulfonamides and aminoglycosides) along with insertional elements. ESBL genes such asblaCTX-M,blaTEM, andblaSHV were also detected on conjugable plasmids of IncF and IncI incompatibility types. One novel IncF plasmid (pSHV2A_ESBLF) was identified in which carried a multi-drug resistance genotype (blaSHV-2A,aadA22, aac(3), aph(6),tetA, andsul1) in addition to amer(mercury resistance) operon, colicin, and aerobactin genes. Shotgun metagenomic analysis of theE. coli-originating wastewater samples showed the presence of class A beta-lactamases; however, the ESBL genes identified in theE. coligenomes were below the detection limits. Other ESBL-associated genes (i.e.,blaOXA.11,blaFOX.7, andblaGES.17) were identified in the wastewater samples and their occurrences were correlated with the core microbial genera (e.g.,Paraprevotella). In both theE. coligenomes and the wastewater samples, tetracycline, aminoglycoside, and beta-lactam resistance determinants frequently co-occurred. The unique combination of whole-genome and metagenomic analysis provides a holistic description of ESBL-producing organisms and genes in the Oregonian wastewater system.
Autophagosome turnover requires Arp2/3 complex-mediated maintenance of lysosomal integrity
Authors: Theodore Corey J. , Wagner Lianna H. , Campellone Kenneth G. 
Published: March 2024

ABSTRACTAutophagy is an intracellular degradation process that maintains homeostasis, responds to stress, and plays key roles in the prevention of aging and disease. Autophagosome biogenesis, vesicle rocketing, and autolysosome tubulation are controlled by multiple actin nucleation factors, but the impact of actin assembly on completion of the autophagic pathway is not well understood. Here we studied autophagosome and lysosome remodeling in fibroblasts harboring an inducible knockout (iKO) of the Arp2/3 complex, an essential actin nucleator. Arp2/3 complex ablation resulted in increased basal levels of autophagy receptors and lipidated membrane proteins from the LC3 and GABARAP families. Under both steady-state and starvation conditions, Arp2/3 iKO cells accumulated abnormally high numbers of autolysosomes, suggesting a defect in autophagic flux. The inability of Arp2/3 complex-deficient cells to complete autolysosome degradation and turnover is explained by the presence of damaged, leaky lysosomes. In cells treated with an acute lysosomal membrane-damaging agent, the Arp2/3-activating protein WHAMM is recruited to lysosomes, where Arp2/3 complex-dependent actin assembly is crucial for restoring intact lysosomal structure. These results establish the Arp2/3 complex as a central player late in the canonical autophagy pathway and reveal a new role for the actin nucleation machinery in maintaining lysosomal integrity.
A metastasis-associated Pannexin1 mutant (Panx11-89) forms a minimalist ATP release channel
Authors: Wang Junjie , Mim Carsten , Dahll Gerhard , Barro-Soria Rene 
Published: March 2024

AbstractA truncated form of the ATP release channel pannexin 1 (Panx1), Panx11–89, is enriched in metastatic breast cancer cells and has been proposed to mediate metastatic cell survival by increasing ATP release through mechanosensitive Panx1 channels. However, whether Panx11–89on its own (without the presence of wtPanx1) mediates ATP release has not been tested. Here, we show that Panx11–89by itself can form a constitutively active membrane channel, capable of releasing ATP even in the absence of wild type Panx1. Our biophysical characterization reveals that most basic structure-function features of the channel pore are conserved in the truncated Panx11–89peptide. Thus, augmenting extracellular potassium ion concentrations enhances Panx11–89-mediated conductance. Moreover, despite the severe truncation, Panx11–89retains the sensitivity to most of wtPanx1 channel inhibitors and can thus be targeted. Therefore, Panx1 blockers have the potential to be of therapeutic value to combat metastatic cell survival. Our study not only elucidates a mechanism for ATP release from cancer cells, but it also supports that the Panx11–89mutant should facilitate structure-function analysis of Panx1 channels.
Toward generalizable phenotype prediction from single-cell morphology representations
Authors: Tomkinson Jenna , Kern Roshan , Mattson Cameron , Way Gregory P. 
Published: March 2024

AbstractFunctional cell processes (e.g., molecular signaling, response to environmental stimuli, mitosis, etc.) impact cell phenotypes, which scientists can easily and robustly measure with cell morphology. However, linking these morphology measurements with phenotypes remains challenging because biologically interpretable phenotypes require manually annotated labels. Automatic phenotype annotation from cell morphology would link biological processes with their phenotypic outcomes and deepen understanding of cell function. We propose that nuclear morphology can be a predictive marker for cell phenotypes that is generalizable across cell types. Nucleus morphology is commonly and easily accessible with microscopy, but annotating specific phenotypic information requires labels. Therefore, we reanalyzed a pre-labeled, publicly-available nucleus microscopy dataset from the MitoCheck consortium to predict single-cell phenotypes. We extracted single-cell morphology features using CellProfiler and DeepProfiler, which provide fast, robust, and generalizable data processing pipelines. We trained multinomial, multi-class elastic net logistic regression models to classify nuclei into one of 15 phenotypes such as ‘Anaphase,’ ‘Apoptosis’, and ‘Binuclear’. In a held-out test set, we observed an overall F1 score of 0.84, where individual phenotype scores ranged from 0.64 (indicating moderate performance) to 0.99 (indicating high performance). Notably, phenotypes such as ‘Elongated’, ‘Metaphase’, and ‘Apoptosis’ showed high performance. While CellProfiler and DeepProfiler morphology features were generally equally effective, combining feature spaces yielded the best results for 9 of the 15 phenotypes. However, leave-one-image-out (LOIO) cross-validation analysis showed a significant performance decline, indicating our model could not reliably predict phenotype in new single images. Poor performance, which we show was unrelated to factors like illumination correction or model selection, limits generalizability to new datasets and highlights the challenges of morphology to phenotype annotation. Nevertheless, we modified and applied our approach to the JUMP Cell Painting pilot data. Our modified approach improved dataset alignment and highlighted many perturbations that are known to be associated with specific phenotypes. We propose several strategies that could pave the way for more generalizable methods in single-cell phenotype prediction, which is a step toward morphology representation ontologies that would aid in cross-dataset interpretability.
Searching for
H→hh→bb¯ττ
in the 2HDM type-I at the LHC
Authors: Arhrib A. , Moretti S. , Semlali S. , Shepherd-Themistocleous C. H. , Wang Y. , Yan Q. S. 
Published: March 2024

Unlike other realizations of the 2-Higgs doublet model (2HDM), the so-called type-I allows for a very light Higgs boson spectrum. Specifically, herein, the heaviest of the two CP-even neutral Higgs states, H, can be the one discovered at the Large Hadron Collider (LHC) in 2012, with a mass of ≈125  GeV and couplings consistent with those predicted by the Standard Model (SM). In such a condition of the model, referred to as “inverted mass hierarchy,” the decay of the SM-like Higgs state into pairs of the lightest CP-even neutral Higgs boson, h, is possible, for masses of the latter ranging from MH/2≈65  GeV down to 15 GeV or so, all compatible with experimental constraints. In this paper, we investigate the scope of the LHC in accessing the process gg→H→hh→bb¯ττ by performing a Monte Carlo (MC) analysis aimed at extracting this signal from the SM backgrounds, in presence of a dedicated trigger choice and kinematic selection. We prove that some sensitivity to such a channel exists already at run 3 of the LHC while the High-Luminosity LHC (HL-LHC) will be able to either confirm or disprove this theoretical scenario over sizable regions of its parameter space.

Published by the American Physical Society
2024
Do social investment policies promote employment among the vulnerable? A case of single mothers
Authors: Sakamoto Takayuki 
Published: March 2024

PurposeThis study aims to investigate whether social investment (SI) policies improve employment among single mothers.Design/methodology/approachThis paper analyzes the potential effects of SI policies on vulnerable individuals and workers at the macro level by using the employment position of single mothers as a dependent variable. Time-series cross-national data from 18 OECD countries between 1998 and 2017 are analyzed. Multilevel model analysis is also used for robustness check.FindingsI find that public spending on education and family support is positively associated with the employment rates of single mothers. In contrast, active labor market policy (ALMP) spending is negatively associated. ALMP’s negative effects stand out particularly with public spending on job training. Of all family support policies, family allowances are positively associated with single mothers’ employment, which runs counter to the conventional argument that family allowances are a disincentive for women’s or mothers’ employment. Paid leave (length and generosity) is also associated with higher employment for single mothers. There is also some tentative evidence that public spending on maternity leave benefits (spending level) may raise the odds of single mothers being employed, when individual-level factors are controlled for in multilevel analysis we implement for robustness check.Research limitations/implicationsThis paper does not analyze the effects of the qualitative properties of SI policies. Future research is necessary in this respect.Originality/valueThe effects of SI policies on employment among single mothers have not yet been examined in the literature. This paper seeks to be a first cut at measuring the effects.
Knowledge trajectory of eSports as an emerging field of research
Authors: Zhu Jiantao , Cao Chuhan , Liu Hefu , Lim Eric Tze Kuan , Tan Chee-Wee 
Published: March 2024

PurposeResearch on electric sports (eSports) has experienced significant growth in recent years as a consequence of increasing connectivity, institutionalization, and technological advances. However, the interdisciplinary nature of the eSports as a field and the burgeoning growth in eSports articles have rendered it necessary to conduct a systematic review of extant literature to take stock of the knowledge accumulated. To this end, we aim to undertake a comprehensive review of extant literature that takes stock of published research to derive opportunities for future research in the realm of eSports. In so doing, we contribute to the advancement of the field by mapping out the knowledge trajectory of eSports research and elucidating areas that have remained underexplored thus far.Design/methodology/approachTo conduct systematic review of the eSports literature, we employed a framework that included six essential steps: protocol, search, appraisal, synthesis, analysis, and report. This comprehensive approach enables us to meticulously investigate the existing body of literature on eSports and identify key trends and topics addressed within the field. By conducting the multidisciplinary systematic literature review, we thoroughly assess the current state of eSports literature and subsequently outline potential research avenues that can contribute to eSports fields.FindingsThis study draws on a six-phase framework – member preparation, team formation, character selection, team coordination, team performance, and team reflection – to illustrate the roles played by different levels of analysis unit (i.e. characters, players, and teams) and three distinct yet interconnected stages (i.e. inputs, process, and outputs) within eSports games as well as the research opportunities it brings.Originality/valueWe conducted a rigorous systematic review of the eSports literature by using quantitative citation analysis and qualitative content analysis. Furthermore, we adopted team dynamic view of eSports to identify potential research avenues for future research that contribute to advancing our understanding of the eSports tournaments.
Transforming metaverse marketing into strategic agility in SMEs through mediating roles of IMT and CI: theoretical framework and research propositions
Authors: Abrokwah-Larbi Kwabena 
Published: March 2024

PurposeThis study aims to explore the conversion of metaverse marketing (MVM) into strategic agility among SMEs based on dynamic capabilities (DC) and dynamic management capabilities (DMC) theories. This paper discusses how constructs such as immersive marketing technologies (IMT), customer immersion (CI) and managerial capabilities (MC) play critical role in the transformation of MVM into strategic agility (SA).Design/methodology/approachA theoretical framework based on DC and DMC theories, and a comprehensive review of the literature on MVM, IMT, CI, MC and SA, was developed in order to theoretically investigate the relationships between MVM and SA. In this theoretical framework, MVM is the independent variable, while the dependent variable is SA. Also, IMT and CI both mediate the association between MVM and SA, while MC moderate the association between MVM and SA in one stream; and CI and SA in another stream.FindingsThis research study develops a theoretical framework that recommends nine set of important research propositions in MVM. An extensive literature review was conducted to examine the theoretical framework on the effect of MVM on SA. The proposed theoretical framework suggests that brand community development and communication, experiential marketing and personalisation in MVM, once accessed through IMT (i.e. VR, AR, MR) and CI (i.e. customer engagement, customer absorption-customer acquisition and assimilation of knowledge, presence) can produce significant SA through customer experience management, value co-creation and process innovation.Originality/valueThis current study develops a theoretical framework that theorise the relationship between MVM and SA rooted in literature on MVM and SA, and also based on DC and DMC perspective. The moderating effect of MC on the relationship between IMT and SA on one hand, and CI and SA on the other, provides support to IMT and CI as mediators in the transformation of MVM into SA. This study also provides insight into SME adoption of MVM and how it generates SA. Lastly, the current study contributes to the body of knowledge on MVM, IMT, CI, MC and SA.
Research on the evolution law of dynamic performance of CR400BF EMU train based on stochastic dynamics simulation
Authors: Cheng Di , Wen Yuqing , Guo Zhiqiang , Hu Xiaoyi , Wang Pengsong , Song Zhikun 
Published: March 2024

PurposeThis paper aims to obtain the evolution law of dynamic performance of CR400BF electric multiple unit (EMU).Design/methodology/approachUsing the dynamic simulation based on field test, stiffness of rotary arm nodes and damping coefficient of anti-hunting dampers were tested. Stiffness, damping coefficient, friction coefficient, track gauge were taken as random variables, the stochastic dynamics simulation method was constructed and applied to research the evolution law with running mileage of dynamic index of CR400BF EMU.FindingsThe results showed that stiffness and damping coefficient subjected to normal distribution, the mean and variance were computed and the evolution law of stiffness and damping coefficient with running mileage was obtained.Originality/valueFirstly, based on the field test we found that stiffness of rotary arm nodes and damping coefficient of anti-hunting dampers subjected to normal distribution, and the evolution law of stiffness and damping coefficient with running mileage was proposed. Secondly stiffness, damping coefficient, friction coefficient, track gauge were taken as random variables, the stochastic dynamics simulation method was constructed and applied to the research to the evolution law with running mileage of dynamic index of CR400BF EMU.