bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioimaging with fluorescent nucleic-acid aptamers for the specific detection and quantification ofPseudomonas aeruginosaalone and in heterogeneous bacterial populations
Authors: Mezouarhi Chaimae , Vauchelles Romain , Abdallah Basma , Régine Janel , Ouadghiri Mouna , Ait Benhassou Hassan , Fechter Pierre , Choulier Laurence 
Published: February 2025

ABSTRACTThe rising prevalence of bacterial infections, antibiotic resistance, and emerging pathogens underscores the urgent need for innovative diagnostic approaches. Aptamers, short nucleic acid sequences with high specificity and affinity for their targets, are promising candidates for diagnostic applications due to their ability to detect a wide range of pathogens. In this study, we present a fluorescent aptamer-based bioimaging approach for detectingPseudomonas aeruginosa, a multidrug-resistant pathogen of significant clinical concern. Conjugated with fluorescent dye, the detection efficacy of the F23 aptamer was evaluated on 15 different Gram-negative and Gram-positive bacteria, including fixed and lived cells, as well as homogeneous and heterogeneous population. To quantify microscopy images, we developed an automated, open-access identification software using ImageJ. Its high sensitivity provides a robust platform for accurately quantifying bacteria labeled with aptamers and potentially other fluorescent ligands. For instance, it successfully detected 1122P. aeruginosacells labeled with aptamer F23 out of a total of 1123P. aeruginosacells in a single image. With almost 200,000 analyzed bacteria and an exceptionally clear signal-to-noise ratio, we demonstrated that the F23 aptamer effectively detects various reference and clinical strains ofPseudomonas aeruginosa, while failing to detect Gram-positiveStaphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus epidermidisandCorynebacterium striatum, as well as Gram-negativeKlebsiella pneumonia, Acinetobacter baumannii, andEscherichia coli. The F23 aptamer is therefore a promising tool to distinguishPseudomonas aeruginosafrom different strains of the skin microbiota. However, our quantitative method also revealed partial labeling to other bacterial cells, highlighting the issue of refining aptamer selection to improve selectivity.
Stable states in an unstable landscape: microbial resistance at the front line of climate change
Authors: Cronin Dylan , Holland-Moritz Hannah , Smith Derek , Aroney Samuel T. N. , Hodgkins Suzanne , Borton Mikayla , Li Yueh-Fen , Healy Kieran ,   IsoGenie Field & Analytic Teams 2010-2017,   EMERGE Institute Coordinators, Tfaily Malak M. , Crill Patrick , McCalley Carmody K. , Wrighton Kelly , Varner Ruth , Tyson Gene W. , Woodcroft Ben , Bagby Sarah C. , Ernakovich Jessica , Rich Virginia I. 
Published: February 2025

AbstractMicrobiome responses to warming may amplify or ameliorate terrestrial carbon loss and thus are a critical unknown in predicting climate outcomes. We quantified microbial warming response over seven years in a thawing permafrost peatland, using large-scale multi-omics data. We integrated analyses of organisms (via taxonomy), functions (via metabolic pathways and proteins), and community organization (via network structure and ecological assembly) to deeply characterize response mechanisms. This revealed unexpected and comprehensive microbiome stability. This resistance to change appeared bolstered by habitat-specific dispersal and community-level functional redundancy, particularly via versatile carbon generalists. Our findings challenge widespread assumptions of significant soil microbiome alteration with climate change, and reveal key genome-inferred processes that underlie microbiome stability. This suggests that future research should reorient towards critical habitat transitions.One Sentence SummaryIn a warming permafrost peatland, microbiome shifts are concerted and correspond to habitat change, rather than proceeding gradually with rising temperature, with multiple lines of evidence indicating that this microbiome ecological resistance is linked to functional redundancy and high dispersal.
Verification of emerging genomic mutations inMycobacterium tuberculosisallows transmission chains to be distinguished in an epidemiological typing cluster extending over thirty years
Authors: de Zwaan Rina , de Vries Gerard , Ubbelohde Ella , Mulder Arnout , Kamst Miranda , Rebel Karin , Kautz Saskia , Kremer Kristin , Anthony Richard M , van Soolingen Dick 
Published: February 2025

AbstractWhole genome sequencing (WGS) is able to identify epidemiological links betweenMycobacterium tuberculosisisolates. Recent clustering can be ruled out using a pre-defined single nucleotide polymorphism (SNP) threshold. If WGS clusters grow significantly over time limited genetic variability hampers epidemiological investigations.Newly emerging (informative) SNPs in isolates of an extended cluster growing for more than 30 years to >150 cases in the Netherlands were analysed. WGS data was analyzed from 61 sequencing files from 54 patients. Genomic positions that varied within the cluster isolates were carefully screened for minority populations in other isolates from the cluster. A transmission scheme was generated on the basis of WGS data alone then compared to the epidemiological information available.Fifty-two informative SNPs were identified, eight of which were also detected as mixed variants. One emerging SNP indnaA(1199G>A R400H) has been observed in other transmitted strains and may be under selection. There was high concordance between the transmission chains suggested on basis of the newly emerging SNPs and scenario’s identified using classical epidemiological cluster investigations.Analysis of filtered SNPs accumulating in the genome ofM. tuberculosisin large clusters contains information on transmission dynamics and can be used to support epidemiological investigations.
Drosophilalarval gut transcriptome reveals a microbe-mediated intestinal tissue growthviaEcdysone during adaptive growth
Authors: Bai Longwei , Bellemin Stéphanie , Drelon Coralie , Joncour Pauline , Guillemot Elodie , Strigini Maura , Gillet Benjamin , Leulier François , Ramos Cathy Isaura 
Published: February 2025

AbstractJuvenile growth is an adaptive trait since chronic undernutrition leads to reduced growth rate and delayed maturation. UsingDrosophilaand mouse gnotobiotic models, we previously established the evolutionarily conserved influence of the intestinal microbiota and selectedLactobacillistrains on juvenile growth. Here we aimed to identify the molecular mechanisms underlying microbe-mediatedDrosophilaadaptive growth. Since the intestine is the interface of host-microbe interactions, we conducted an analysis of the larval midgut transcriptome in presence or absence of an intestinalLactobacillistrain representative of theDrosophilamicrobiota. Among the different biological processes identified, Ecdysone signaling has emerged as a newLactobacilli-mediated signature. Through functional and morphometrical approaches, we show that, upon bacteria association, intestinal Ecdysone is not rate limiting for the larval systemic plastic growth but required for the adaptation of midgut growth toLactobacilli. Our results reveal a tissue-specific contribution of the pleiotropic hormone Ecdysone in the control of midgut adaptive growth and maturation.
Kinetic characterization of three human DExD/H-box RNA helicases
Authors: Li Fengling , Chan U Hang , Perez Julia Garcia , Zeng Hong , Chau Irene , Li Yanjun , Seitova Alma , Halabelian Levon 
Published: February 2025

AbstractHuman DExD/H-box RNA helicases are ubiquitous molecular motors that unwind and rearrange RNA secondary structures in an ATP-dependent manner. These enzymes play essential roles in nearly all aspects of RNA metabolism. While their biological functions are well-characterized, the kinetic mechanisms remain relatively understudiedin vitro. In this study, we describe the development and optimization of a bioluminescence-based assay to kinetically characterize three human RNA helicases: MDA5, LGP2, and DDX1. The assays were conducted using annealed 24-mer RNA (blunt-ended double-stranded RNA) or double-stranded RNA (ds-RNA) with a 25- nt 3ʹ overhang. These findings establish a robust and high-throughputin vitroassay suitable for a 384-well format, enabling the discovery and characterization of inhibitors targeting MDA5, LGP2, and DDX1. This work provides a valuable resource for advancing our understanding of these helicases and their therapeutic potential in Alzheimer’s disease.
A silicon rhodamine-fused glibenclamide to label and detect malaria-infected red blood cells
Authors: Bastl Claudia , Close Cindy M. , Holtz Ingo , Gatin-Fraudet Blaise , Eis Mareike , Werum Michelle , Konrad Smilla , Roßmann Kilian , Huhn Christiane , Ghosh Souvik , Ast Julia , Roosen Dorien A. , Lehmann Martin , Haucke Volker , Reymond Luc , Hodson David J. , Tinnefeld Philip , Johnsson Kai , Glembockyte Viktorija , Kilian Nicole , Broichhagen Johannes 
Published: February 2025

AbstractThe malaria parasitePlasmodium falciparumaffects the lives of millions of people worldwide every year. The detection of replicating parasites within human red blood cells is of paramount importance, requiring appropriate diagnostic tools. Herein, we design and apply a silicon rhodamine-fused glibenclamide (SiR-glib). We first test this far-red fluorescent, fluorogenic and endoplasmic reticulum-targeting sulfonylurea in mammalian cells and pancreatic tissues, before characterizing its labeling performance in red blood cells infected with the asexual developmental stages ofPlasmodium falciparum. We further combineSiR-glibwith a portable smartphone-based microscope to easily and rapidly identify parasitized red blood cells, providing proof of principle for diagnostic use in rural endemic areas without major healthcare facilities.
Spatial transcriptomics reveals heterogeneous cell–cell interactions among brain regions in a cuprizone model consistent with multiple sclerosis lesions
Authors: Tsai Hui-Hsin , Piya Sarbottam , Wang Jing , Zhu Jing , Hu Wenxing , Gehrke Andrew R. , Cao Shaolong , Guise Amanda J. , Chan Su Jing , Sheehan Mark , Chu Jenhwa , Ouyang Zhengyu , Ryals Matthew , Lee Michelle , Wang Wanli , Zhao Edward , Cullen Patrick , Challa Ravi , Marshall Eric , Zeng Wanyong , Kaeser-Woo Yea Jin , Ehrenfels Chris , Jandreski Luke , McLaughlin Helen , Carlile Thomas M. , Gagnon Jake , Reynolds Taylor L. , Li Mingyao , Li Kejie , Zhang Baohong 
Published: February 2025

AbstractThe cuprizone (CPZ) model is widely used for modeling demyelination in multiple sclerosis (MS) and for testing potential remyelination therapies. We integrated single-cell and spatial transcriptomics (ST) to fine map the spatial cellular and molecular responses during de and remyelination. ST revealed global demyelination and neuroinflammation in the brain beyond the corpus callosum, with region-specific differences. We identified oligodendroglia and microglia as two major cell types with significant transcriptomic changes in the model. Ligand receptor pairing analyses predicted growth factor and phagocytic pathway enrichment during demyelination, which is consistent with changes in MS lesions. During remyelination, while mature oligodendrocytes nearly reversed their phenotype back to the control state, microglia remained associated with the demyelination phenotype. Finally, astrocytes in the CPZ model had the greatest preservation of disease-associated modules to MS lesions, while the MOL, OPC, and microglia showed moderate to low preservation, which overall suggested that the CPZ model had moderate translatability to chronically active MS lesions.
Natural Variation in Photoprotection: Rapid NPQ Kinetics in Ferns
Authors: Maryn Nina M. , Chaparro Antonio , Short Audrey , Fleming Graham R. , Niyogi Krishna K. 
Published: February 2025

AbstractLand plants perform oxygenic photosynthesis but are unable to use all of the solar radiation that they absorb on a daily basis. To minimize the production of reactive oxygen species in excess light, photosynthetic organisms use non-photochemical quenching (NPQ) mechanisms to dissipate excess excitation energy. However, the on-off transition of these mechanisms is slower than the light fluctuations themselves. In high-to-low light transitions, this can be costly to the overall productivity and carbon gain of the organism across its lifetime, because useful light energy is wasted. Here, we characterize the rapid kinetics of NPQ found in species across the fern lineage. Most of the 23 examined fern species showed faster NPQ induction and faster and more complete NPQ relaxation. Curve fitting suggested that energy-dependent quenching was the dominant contributor to the kinetics. The xerophytic fernAstrolepis windhamiiexhibited rapid, dithiothreitol-resistant accumulation of zeaxanthin during NPQ induction, and it maintained low residual NPQ after NPQ relaxation, which however was not associated with rapid re-epoxidation of zeaxanthin. Rapid NPQ kinetics might have been an adaptive trait as ferns radiated in sunflecked forest understories during angiosperm diversification and expansion during the Cretaceous.
Single-Cell Transcriptomics Reveals Dynamic Microglial States and Neural-Immune Networks in Human Diabetic Retinopathy
Authors: Yang Luning , Lin Sen , Tao Yiwen , Pan Qi , Cai Tengda , Ye Yunyan , Liu Jianhui , Zhou Yang , Yi Quanyong , Lu Zen Haut , Chen Lie , McKay Gareth , Rankin Richard , Shao Yongqing , Meng Weihua 
Published: February 2025

AbstractDiabetic retinopathy (DR) is a major cause of vision loss worldwide. Here, we perform single-cell RNA sequencing of thirteen human retina samples (from living and post-mortem donors) across non-diabetic, diabetic, and DR states to create a comprehensive transcriptomic atlas. We uncover three distinct microglial states—homeostatic, stress-response, and inflammatory—along a functional continuum, rather than discrete activation states, with dynamic transitions occurring throughout disease progression. Trajectory analysis indicates bifurcating paths starting from the homeostatic state branching toward stress-response and inflammatory states. Three major functional modules: ribosomal/translation, coordinated immune cell function, and inflammatory/transcriptional regulation, showing disease-specific activation patterns were identified. Cell communication analysis further highlights sophisticated neural-immune interactions, particularly between photoreceptors and microglia. Our findings provide insights into the complex cellular dynamics of DR progression and suggest potential therapeutic targets for early intervention.
Igf2regulates early postnatal DPP4+preadipocyte pool expansion
Authors: Altun Irem , Walia Safal , Yan Xiaocheng , Singh Inderjeet , Karlina Ruth , Miok Viktorian , Kang Lingru , Ho Diep Vo Khanh , Lutter Dominik , Perrochi Fabiana , Ussar Siegfried 
Published: February 2025

AbstractAdipose tissue is rapidly expanding early in life. Identifying the queues facilitating this process will advance our understanding of metabolically healthy obesity. Single-cell RNA sequencing revealed compositional differences between pre-wean and adult murine subcutaneous adipose tissue. We identify a dipeptidyl peptidase-4 (Dpp4) positive precursor population in pre-wean mice residing at the reticular interstitium of subcutaneous adipose tissue expressing insulin growth factor 2 (Igf2). We show that IGF2 drives proliferation rather than differentiation in these cells. Moreover, loss ofIgf2inDpp4+progenitor cells promotes adipogenesis. We show that expression ofIgf2at a limited timeframe during development promotes preadipocyte expansion.
How does effective internal communication impact employees’ external whistleblowing intention? The mediating role of the relational psychological contract
Authors: Jin Jie , You Leping 
Published: February 2025

PurposeAs less is known about how internal communication can influence employees’ whistleblowing intention, this study aims to explore how participatory communication, organizational listening and organizational responsiveness influence employees’ external whistleblowing intention.Design/methodology/approachAn online survey was conducted with 657 employees across various industries in the United States.FindingsThe results revealed that participatory communication, organizational listening and organizational responsiveness can fulfill the organization’s relational contract with their employees. As a communication-charged outcome, the fulfillment of employees’ relational psychological contract is associated with a lower intention to blow the whistle externally.Originality/valueThis study is among the first to examine internal communication strategies, namely, participatory communication, organizational listening and organizational responsiveness, as the antecedents of employees’ relational psychological contract and external whistleblowing intention.
Measuring the impact of leadership attributes on employee engagement through psychological empowerment: a study from the pharmaceutical industry
Authors: Rasheed Rizwana , Rashid Aamir , Tunio Muhammad Nawaz , Amirah Noor Aina 
Published: February 2025

PurposeManagers are continuously worried about the engagement of employees in the organization. This research aimed to investigate the employees’ perceptions regarding leadership attributes, which enhance the workers’ psychological empowerment and engagement.Design/methodology/approachA sample of 296 employees from three pharmaceutical companies based in Karachi was selected. For hypothesis testing, IBM SPSS AMOS version 24 was used to perform a confirmatory factor analysis and structural equation modelling.FindingsThe outcomes of multiple regression analysis expressed that the attributes of a leader positively influence psychological empowerment and employee engagement. The study found that psychological empowerment partially mediates the relationship between leadership attributes (feedback and delegation) and employee retention. Furthermore, psychological empowerment has no mediation between leadership attributes (empathy) and employee retention.Originality/valueThis study offers a unique contribution by focusing on the relationship between leadership attributes (empathy, delegation and feedback) and employee engagement within the pharmaceutical industry in Karachi, a relatively underexplored context. Psychological empowerment as a partial mediator between leadership attributes and employee retention adds a novel perspective, particularly by revealing that it mediates the impact of delegation and feedback but not empathy. Moreover, this research provides actionable insights for policymakers and operational managers in industries beyond pharmaceuticals, making it valuable for enhancing employee engagement across sectors. Advanced statistical techniques like structural equation modelling and confirmatory factor analysis further reinforce the study’s methodological rigour.
Developing global leadership competence: redefining higher education for interconnected economies
Authors: Bilderback Stephanie , Thompson Chelsae B. 
Published: February 2025

PurposeThis paper explores how higher education institutions can redesign curricula to produce globally competitive graduates equipped with critical skills for success in an interconnected workforce. It emphasizes the integration of interdisciplinary learning, global competence and experiential education while positioning leadership development as a central pillar of career readiness.Design/methodology/approachThe study synthesizes human capital theory, social cognitive career theory and global competence theory to create a framework for equipping students with emotional intelligence, technological proficiency and a global mindset. Using a structured literature review, the paper analyzes stakeholder collaboration strategies and provides actionable recommendations for curriculum redesign and workforce alignment.FindingsHigher education institutions must move beyond traditional academic models by adopting interdisciplinary approaches, fostering experiential learning and building global partnerships. These strategies help students adapt to dynamic international settings. Stakeholder collaboration and curriculum innovation are critical for ensuring that graduates are prepared to meet the demands of an evolving global economy.Originality/valueThis paper offers a unique contribution by integrating three foundational theories into practical framework that aligns academic preparation with global workforce needs. The proposed framework highlights leadership competence as essential for global adaptability and provides actionable insights for educators, policymakers and industry leaders to bridge academic preparation and workforce demands.
Examining the link between narcissism and perceived inequity: the mediating role of sense of entitlement
Authors: Queiri Abdelbaset , Alhejji Hussain 
Published: February 2025

Purpose
This study aims, firstly, to investigate the relationship between narcissism and perceived inequity, and secondly, to explore the mediating role of the sense of entitlement in this relationship.

Design/methodology/approach
A total of 150 local employees in Oman completed self-report questionnaires assessing narcissism, sense of entitlement and perceived inequity. A two-step structural equation modelling approach was used to examine the proposed model. Both procedural and statistical remedies were used to account for common method bias.

Findings
The results of the study indicate a positive relationship between narcissism and the sense of entitlement, both of which contribute to a negative impact on the perception of equity. The study suggests that narcissistic individuals perceive inequity due to an overestimation of their contributions (i.e. entitlement).

Research limitations/implications
This study is limited by its cross-sectional design and self-reported data, which could introduce bias. Additionally, the use of convenience sampling may restrict the generalizability of the findings to the broader population.

Practical implications
Organizations should consider individual personality differences, especially in dealing with narcissistic individuals. It is advisable for organizations to implement structured and formal policies, procedures and processes to improve the perception of equity. This may involve revising reward and promotion systems with clearly defined and transparent criteria. Additionally, managers can engage narcissistic employees through team-based activities and promote collaboration to enhance team dynamics.

Originality/value
This study adds to the existing literature on narcissism by shedding light on the complex relationship between narcissism, sense of entitlement and perceived inequity. It is particularly noteworthy for focusing on the Middle East context, an area that has been understudied in the realm of narcissism research within work environments.