bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developmental rewiring of theNGAL/CUC/KLUnetwork associated with pleiotropic roles ofNGALgenes
Authors: Nicolas Antoine , Papadopoulos Panagiotis , Caroulle Mattéo , Adroher Bernard , Goussot Magali , Sarthou Anne-Sophie , Arnaud Nicolas , Maugarny Aude , Laufs Patrick 
Published: December 2024

AbstractGene Regulatory Networks (GRNs) play prominent roles in regulating developmental processes, and their modulation across species is a major source for evolutionary innovation. However, it remains poorly understood how GRNs are rewired between different organs within a single species. This question is particularly relevant for pleiotropic genes, which may exhibit organ-specific GRN modulations potentially reflecting their diverse functions. To address this, we investigated theNGATHA-like(NGAL) genes, as a model for pleiotropic genes that regulate growth or patterning in multiple Arabidopsis organs via two distinct pathways involving theCUP-SHAPED COTYLEDON(CUC) andKLUH(KLU) genes. By combining genetic analysis with gene expression characterization, we uncovered significant organ-specific rewiring of theNGAL/CUC/KLUregulatory module. Our findings highlight that changes in gene expression patterns, potentially arising from developmental constraints, play a pivotal role in the organ-specific modulation of GRNs. Furthermore, GRNs at the molecular and functional levels do not always align perfectly, potentially due to the influence of additional regulatory mechanisms. Altogether, our findings reveal significant modulation of the GRNs associated with pleiotropic genes. We propose that this flexibility in GRNs facilitates gene pleiotropy.
High-Accuracy RNA Integrity Definition for Unbiased Transcriptome Comparisons with INDEGRA
Authors: Cleynen Alice , Ravindran Agin , Sethi Aditya , Kumar Bhavika , Javaid Tanya , Mahmud Shafi , Woodward Katrina , Santos Vieira Helaine Graziele , Änkö Minna-Liisa , Weatheritt Robert , Eyras Eduardo , Robin Stéphane , Shirokikh Nikolay 
Published: December 2024

AbstractRNA sample integrity variability introduces biases and obscures natural RNA degradation, posing a significant challenge in transcriptomics. To address this, we developed the Direct Transcriptome Integrity (DTI) measure, a universal and robust RNA integrity metric based on nanopore sequencing. By accurately modeling RNA fragmentation, DTI provides a reliable assessment of sample quality. Integrated into the INDEGRA package (freely available athttps://github.com/Arnaroo/INDEGRA), we provide tools to correct false discoveries and enable precise differential expression and RNA degradation analyses, even for challenging sample types.INDEGRA software can be used to accurately measure RNA DTI stability metric, isolate biological component of RNA degradation from technical biases, compare biological RNA stability transcriptome-wide and suppress false degradation-induced differential gene expression hits to allow broad comparisons across samples of different qualityDTI offers a straightforward and accurate method for assessing RNA degradation, characterizing both overall sample integrity and transcript-specific degradation rates using direct RNA sequencing (DRS) data. Calculated through INDEGRA, DTI reveals inter- and intra-transcript variability in degradation, while INDEGRA separates RNA degradation from mapping inaccuracies, and connects degradation profiles to RNA fragmentation rates. By leveraging INDEGRA, researchers can minimize false differential transcript abundance findings caused by variations in overall sample integrity, while preserving genuine transcript-specific differences in stability and degradation.INDEGRA supports integration with widely used differential transcript abundance tools like DESeq2, limma-voom, and edgeR, enabling seamless analysis pipelines. INDEGRA enhances the accuracy and reliability of RNA quantification in high-throughput data and simplifies comparisons across diverse transcriptomic datasets, including those derived from different tissues, species, or experimental protocols.
A Distinct Autofluorescence Distribution Pattern Marks Enzymatic Deconstruction of Plant Cell Wall
Authors: Hossein Khani Solmaz , Ould Amer Khadidja , Remy Noah , Lebas Berangère , Habrant Anouck , Faraj Ali , Malandain Grégoire , Paës Gabriel , Refahi Yassin 
Published: December 2024

AbstractAchieving an economically viable transformation of plant cell walls into bioproducts requires a comprehensive understanding of enzymatic deconstruction. Microscale quantitative analysis offers a relevant approach to enhance our understanding of cell wall hydrolysis, but becomes challenging under high deconstruction conditions. This study comprehensively addresses the challenges of quantifying the impact of extensive enzymatic deconstruction on plant cell wall at microscale. Investigation of highly deconstructed spruce wood provided spatial profiles of cell walls during hydrolysis with a remarkable precision. A distinct cell wall autofluorescence distribution pattern marking enzymatic hydrolysis along with an asynchronous impact of hydrolysis on cell wall structure, with cell wall volume reduction preceding cell wall accessible surface area decrease, were revealed. This study provides novel insights into enzymatic deconstruction of cell wall at under-investigated cell scale, and a robust computational pipeline applicable to diverse biomass species and pretreatment types for assessing hydrolysis impact and efficiency.
Replication of treatment effects and differences among populations during experimental evolution of sex allocation in an annual plant
Authors: Villamil Nora , Li Xinji , Pannell John R. 
Published: December 2024

ABSTRACTVariation among replicates of experimental evolution studies that begin by sampling from a single source population can be attributed to measurement error or to random differences in the environment experienced by measured individuals. On the basis of measurements in a large common garden, Cossard et al. (2021:Current Biology7, 1-7) reported rapid evolution of enhanced ‘leaky’ sex allocation by females (which produced male flowers) in experimental populations of the dioecious herbMercurialis annuafrom which males had been removed. Their study thus demonstrated the rapid dissolution of dioecy via changes in sex allocation in response to mate limitation and strong competition for siring success. But their study also found substantial variation among replicate populations. Here, we replicated their common garden, growing plants from the same populations but under different conditions and assaying the measured variables differently. The effects (significance, magnitude and direction) of selection treatment and generation on the sex expression of females with inconstant sex expression met five definitions for successful replication. Importantly, comparisons between the two studies revealed relatively consistent differences among the replicate populations, suggesting that the among-population variation reported by Cossard et al. cannot be attributed to random noise or local differences in growing conditions in the common garden. Our study represents a rare example of the replication of a common garden study and raises interesting questions about the nature of interpopulation divergence within treatment groups of studies using experimental evolution.
Dynamic cell fate plasticity and tissue integration drive functional synovial joint regeneration
Authors: Blumenkrantz Maria , Woron Felicia , Gagarin Ernesto , Weinstein Everett , Kamel Maryam H. , Campos Leonardo , Geras Agnieszka , Anderson Troy , Mo Julia , Sherwood Desmarie , Gwin Maya , Dumitrascu Bianca , Chahine Nadeen O. , Smeeton Joanna 
Published: December 2024

AbstractAdult mammalian synovial joints have limited regenerative capacity, where injuries heal with mechanically inferior fibrotic tissues. Here we developed a unilateral whole-joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using a combination of microCT, histological, live imaging, and single-cell RNA sequencing (scRNAseq) approaches after complete removal of all joint tissues, we find de novo regeneration of articular cartilage, ligament, and synovium into a functional joint. Clonal lineage tracing and scRNAseq implicate a multipotent, neural crest-derived population in the adult skeleton as a cell source for these regenerating tissues. Together, our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage.
Deep homology of abrachyuryregulatory syntax and origin of the notochord
Authors: Fan Tzu-Pei , Lee Jun-Ru , Lin Che-Yi , Chen Yi-Chih , Cutting Ann E. , Cameron R. Andrew , Yu Jr-Kai , Su Yi-Hsien 
Published: December 2024

AbstractThebrachyurygene encodes a T-box transcription factor (TF) that is crucial for the development of the notochord, a novel trait of chordates1.Brachyuryexpression in axial mesodermal cells (notochord progenitors) is regarded as a chordate innovation2, yet it remains unclear how the chordate ancestor acquired this expression domain. By examining the sequences of previously identified notochord enhancers of several chordatebrachyurygenes3–5, we uncovered a regulatory syntax consisting of binding sites for four TFs (Su(H), Foxh1, Zic, and Ets) with a strict order and orientation. We also identified this syntax, here named SFZE, in potentialcis-regulatory modules (CRMs) ofbrachyuryorthologs in various non-chordate animals and even inCapsaspora, a close unicellular relative to animals. Reporter assays demonstrated that SFZE-containing CRMs from non-chordate organisms exhibited regulatory activity in the zebrafish notochord, and mutagenesis of the TF sites reduced the activity. Furthermore, the SFZE syntax in sea urchin confers its endoderm activity, with the TF sites functionally decoupled during gastrulation. These findings indicate that the association of the SFZE syntax withbrachyuryis ancient, likely predating the origin of animals. The emergence of axialbrachyuryexpression is therefore probably not the result of a newly acquired notochord enhancer, but is instead likely attributed to co-option of upstream signals acting on the conserved SFZE syntax, which facilitates the origin of the notochord from rudimentary endodermal cells.
Social constructs, male prejudices, tradition and culture: are these undermining female-headed farming households’ fundamental right to food security?
Authors: Reddy Mahendra 
Published: December 2024

PurposeAmidst a substantial body of research investigating gender discrimination within formal employment sectors, this study concentrates on a critical yet frequently overlooked dimension: the non-formal agriculture sector. It aims to elucidate how prevailing male prejudices and entrenched social constructs systematically disadvantage female household heads in their quest for household food security.Design/methodology/approachThis study investigates food security status and statistical disparities between female-headed and male-headed households utilizing data from 63,601 farming households. By identifying the factors contributing to gender-based discrimination, we empirically evaluate their impact on households’ food security by applying the discrete choice ordered logit model.FindingsThe results demonstrate significantly higher levels of food insecurity among female-headed households than their male counterparts (p < 0.05). It empirically establishes that factors contributing to discrimination adversely affect female farmers’ ability to secure food. These factors include challenges in accessing markets, smaller farm sizes and receiving less government assistance than male farmers.Originality/valueWhile previous studies have acknowledged gender discrimination, this research is the first to systematically demonstrate how various factors directly impact food security in female-headed households in Fiji, thereby addressing a critical gap in the literature. Focusing specifically on the intersection of gender discrimination and food security, this study provides robust empirical evidence of the profound influence of gender discrimination and male biases on the food security of these households, thereby making a significant and original contribution to the field and underlining the importance of this research.
Distinctive capabilities system in MSME’s business model adaptation: evidence of the moderating and mediating effect of adaptive capability
Authors: Arraya Marco 
Published: December 2024

PurposeThis study aims to enhance the understanding of adaptive capability (ADC) as a moderating and mediating factor in the relationship between a distinctive capabilities system (DCS) and the nonfinancial and financial performance of Portuguese micro-, small- and medium-sized enterprises (MSMEs) within the context of business model adaptation in response to exogenous shocks.Design/methodology/approachIn this study, I utilized an exploratory and quantitative methodology. Moreover, I administered a structured questionnaire to collect data from 223 Portuguese MSME respondents. To ensure the variables’ validity and reliability, I conducted a confirmatory factor analysis and employed structural equation modeling to test the proposed hypotheses.FindingsThe results demonstrate a significant direct impact of DCS on both nonfinancial and financial performance, with the former mediated by ADC. These findings suggest that MSME management practices during an exogenous shock have the potential to generate superior performance by reconfiguring DCS with ADC support. This enables MSMEs to leverage existing resources and capabilities to continuously improve and adapt their business models, defend their market share and adjust their exploitation and exploration strategies in response to exogenous shocks. Moreover, the development of proactive managerial capabilities can contribute to this combination of factors and potentially lead to superior MSME performance.Originality/valueLiterature lacks studies on strategy and management regarding the role of DCS as a predictor of MSME’s business model adaptation and the mediating effect of ADC in this relationship. The current study sought to address this deficiency by investigating the crucial role of ADC in facilitating the reconfiguration, renewal or creation of resources, capabilities, processes and routines that foster adaptation while confirming DCS’s role as a critical component of the business model. My research extends and builds on earlier findings by demonstrating how these capabilities enable MSMEs to respond effectively to exogenous shocks while maintaining their superior performance.
Cryptocurrencies as a new trigger for credit card misuse during economic downturns
Authors: Bai Zefeng , Wang Pengcheng , Jia Miaoqing 
Published: December 2024

PurposeIn this paper, we empirically investigate how crypto investments in times of economic downturn would affect credit card usage, a widely used payment method that has a significant impact on individual financial well-being.Design/methodology/approachWe carry out an ordinary least squares regression analysis and an instrumental variable design on data from the most recent National Financial Capability Study 2021 (NFCS2021). The NFCS2021 collects information about various demographic and financial backgrounds of US adults.FindingsWe find that crypto investments are associated with a significantly higher likelihood of credit card misuse, as indicated by making only the minim um payments, late payments and using credit cards for cash advances. Meanwhile, social media use is a strong predictor of crypto investments. Results from our analysis are robust after accounting for endogeneity concerns using an instrumental variable design.Originality/valueOur findings provide new insights into the influence of emerging financial instruments on delinquent credit card behaviors, which can further intensify individual and household financial instability during periods of market stress. Furthermore, our findings underscore the necessity of improving individual awareness of the high-risk characteristics of cryptocurrencies, despite their increasing popularity in the financial marketplace in the current financial marketplace.
EU climate countdown: economic risks, adaptation and smart policies
Authors: Varadi Ana-Elena , Lobont Oana-Ramona , Vatavu Sorana 
Published: December 2024

Purpose
This paper aims to analyse the impact of various climate change indicators on economic growth while further scrutinising the overall efficiency of environmental policies adopted at the European Union (EU) level. The paper considers the European Green Deal policy framework as a prism for assessing whether an increase in environmental expenditure mitigates climate change.

Design/methodology/approach
Given the duality of the study, this paper examines the immediate impact of climate change on economic growth by using multiple linear regression and evaluates the effectiveness of environmental policies through a multiple indicators multiple cause (MIMIC) Model. As the paper assesses the policy efficiency in EU countries, this paper has used various climate and economic-related indicators from all 27 EU member states for a period of 12 years (2010–2021).

Findings
The results suggest that the macroeconomic environment is indeed impacted by climate change mechanisms, particularly through industrial activity that leads to pollution and resource depletion. Furthermore, through the MIMIC model approach, the results display that environmental expenditures have also diminished the risks associated with climate change indicators, especially in reducing greenhouse gas emissions.

Originality/value
This paper provides a clear overview of the manner in which climate change risks affect economic growth and, in turn, how EU countries are mitigating such risks. It proposes a traditional yet controversial method for assessing the correlation between indicators and corresponding causes whilst also considering various indicators to explain the means through which the EU Commission had applied its adopted environmental policies to mitigate environmental risks.
What makes an AI-themed hotel successful? New evidence from a sequential research design
Authors: Yi Bowen , Shi Da , Li Gang 
Published: December 2024

Purpose
Although artificial intelligence (AI) is an essential component of hospitality in the technological empowerment era, AI’s effectiveness as an attraction in this context remains unclear. Grounded in Herzberg’s motivation theory and complexity theory, this study aims to explore configurational paths whereby combinations of qualities lead to success for different types of AI-themed hotels.

Design/methodology/approach
This study innovatively blends topic modeling and fuzzy-set qualitative comparative analysis (fsQCA) to investigate configurational paths whereby combined qualities produce positive guest evaluations of 12 AI-themed hotels as evidenced by 7,431 customer reviews.

Findings
The results indicate that AI could serve as a “theme” to attract customers under certain circumstances. First, “attractive” and “must-be” qualities are first identified for different types of AI-themed hotels. Furthermore, 6, 15 and 15 configurational paths inspiring favorable guest evaluations of luxury-independent, budget-independent and chain AI-themed hotels, respectively. Technology-related qualities are found to be especially attractive for luxury-independent AI-themed hotels, whereas the role of technology is minimal for budget AI-themed hotels. The impact of technology is salient for chain AI-themed hotels when combined with other factors. In addition, the effect of price differs among the configurational paths for the three hotel types.

Research limitations/implications
This study expands the understanding of AI applications within the hospitality context by exploring the role of AI in AI-themed hotels and comparing its effectiveness in attracting customers across various hotel types. It also provides operational strategies for adopting AI for different types of hotels and for other hospitality and tourism sectors.

Originality/value
This study represents an early attempt to integrate topic modeling and fsQCA to clarify customers’ perceptions of AI-themed hotels and the combined impacts of various qualities. The findings expand on Kano’s model by classifying technology-related qualities into attractive qualities within AI-themed hotels.
Comparative analysis of multi-platform e-commerce online reviews based LDA and sentiment dictionary
Authors: Xie Wanying , Zhao Wei , Xu Zeshui 
Published: December 2024

PurposeThis study aims to investigate the differences in consumer reviews across multiple e-commerce platforms to better assist consumers in making informed decisions. By examining the specific content of these differentiated reviews, the study seeks to provide insights that can enhance e-commerce services and improve consumer satisfaction.Design/methodology/approachThe research utilizes the latent Dirichlet allocation (LDA) method for text analysis to identify the varying concerns of consumers across different e-commerce platforms for the same product. Additionally, the study expands the sentiment dictionary to address polysemy issues, allowing for a more precise capture of sentiment differences among consumers. A non-parametric test is employed to compare reviews across multiple platforms, providing a comprehensive analysis of review disparities.FindingsThe findings reveal that consumer concerns and sentiments vary significantly across different e-commerce platforms, even for the same product. The combination of text analysis and non-parametric testing highlights the objectivity of the research, offering valuable evidence and recommendations for improving e-commerce services and enhancing the shopping experience.Originality/valueThis study is original in its approach to combining text analysis with non-parametric testing to examine multi-platform review differences. The research not only contributes to the understanding of consumer behavior in the context of e-commerce but also provides practical suggestions for platforms and consumers, aiming to optimize service quality and consumer satisfaction.