bluuebunny/crossref_metadata_2025_split huggingface dataset:
A 3D endometrium-on-a-chip reveals the role of conceptus-derived factors CAPG and PDI in conceptus-endometrial communication
Authors: Tinning Haidee , Wang Dapeng , Forde Niamh 
Published: September 2024

ABSTRACTEarly embryo loss affects all mammalian species, including humans and agriculturally important food-producing mammals such as cattle. The developing conceptus (embryo and extra-embryonic membranes) secretes factors which modify the endometrium and can be critical for early pregnancy processes such maternal recognition of pregnancy (MRP) and enhancing uterine receptivity to implantation. For example, a competent bovine conceptus secretes IFNT to initiate MRP. The bovine conceptus also secretes other proteins at the time of MRP, including CAPG and PDI, which are highly conserved among placental mammals. We have previously shown that these proteins act upon the endometrium to modulate receptivity, embryo development, and implantation in species with different implantation strategies (humans and cattle). We hypothesise that developing a novel 3D bovine endometrium on a chip system will enhance our understanding of the role of conceptus-derived factors in altering the endometrium and/or ULF secretion. Here we have developed a 3D bovine endometrium on a chip system, comprising both stromal and epithelial cell culture combined with culture medium flow better mimics thein vivoendometrium and exposure to conceptus-derived factors than conventional 2D endometrial cell culture. We have demonstrated that the conceptus-derived proteins CAPG and PDI modulate the endometrial transcriptome and secretory response to promote pathways associated with early pregnancy and alter ULF composition. This work highlights the critical need for more robust andin vivo-like culture systems to study endometrial-conceptus interactionsin vitroto further investigate the role of conceptus derived factors for pregnancy success.SIGNIFICANCE STATEMENTWe have developed anin vitro3D bovine endometrium-on-a-chip system comprising both primary stromal cells under static conditions and epithelial cells under flow conditions to mimic thein vivoendometrial environment from the conceptuses perspective. The secretome of the 3D endometrium-on-a-chip was characterised, was found to contain proteins associated with cell adhesion and tissue development, and contained proteins previously identified inin vivouterine luminal fluid. PDI and CAPG (previously identified conceptus-derived factors) altered the transcriptome and secretome of cells within the system. Exposure to CAPG or PDI altered the secretome of proteins previously identified in pregnant uterine luminal fluid or associated with early pregnancy, and exposure to CAPG or PDI also altered the transcriptome to support processes such as immune response, secretion, proliferation, and adhesion related pathways. This data supports previously published works and highlights the need for the use of morein vivo-likein vitromodels to study conceptus-endometrial interactions.
A robustly rooted tree of eukaryotes reveals their excavate ancestry
Authors: Williamson Kelsey , Eme Laura , Baños Hector , McCarthy Charley , Susko Edward , Kamikawa Ryoma , Orr Russell J. S. , Muñoz-Gómez Sergio A. , Simpson Alastair G. B. , Roger Andrew J. 
Published: September 2024

SUMMARYThe eukaryote Tree of Life (eToL) depicts the relationships among all eukaryotic organisms; its root represents the last eukaryotic common ancestor (LECA) from which all extant complex lifeforms are descended. Locating this root is crucial for reconstructing the features of LECA, both as the endpoint of eukaryogenesis and the start-point for the evolution of the myriad complex traits underpinning the diversification of living eukaryotes. However, the position of the root remains contentious due to pervasive phylogenetic artefacts stemming from inadequate evolutionary models, poor taxon sampling, and limited phylogenetic signal. Here, we estimate the root of the eToL with unprecedented resolution based on a new, much larger, dataset of mitochondrial proteins which includes all known eukaryotic supergroups. Our comprehensive analyses with state-of-the-art phylogenetic models reveal that the eukaryotic root lies between two multi-supergroup assemblages: ‘Opimoda+’ and ‘Diphoda+’. Compellingly, this position is consistently supported across different models and robustness analyses. Notably, groups containing ‘typical excavates’ are placed on both sides of the root, suggesting the complex features of the ‘excavate’ cell architecture trace back to LECA. This study is the most comprehensive phylogenetic investigation of the eukaryote root to date, shedding light on the ancestral cells from which extant eukaryotes arose and providing a crucial framework for investigating the origin and evolution of canonical eukaryotic features.
Culture Conditions Differentially Regulate the Inflammatory Niche and Cellular Phenotype of Tracheo-Bronchial Basal Stem Cells
Authors: Murthy Shubha , Seabold Denise A. , Gautam Lalit K. , Caceres Adrian M. , Sease Rosemary , Calvert Ben A. , Busch Shana , Neely Aaron , Marconett Crystal N. , Ryan Amy L. 
Published: September 2024

ABSTRACTHuman bronchial epithelial cells (HBECs) derived from the tracheo-bronchial regions of human airways provide an excellentin vitromodel for studying pathological mechanisms and evaluating therapeutics in human airway cells. This cell population comprises a mixed population of basal cells (BCs), the predominant stem cell in airways capable of both self-renewal and functional differentiation. Despite their potential for regenerative medicine, BCs exhibit significant phenotypic variability in culture. To investigate how culture conditions influence BC phenotype and function, we expanded three independent BC isolates in three media, airway epithelial cell growth medium (AECGM), dual-SMAD inhibitor (DSI)-enriched AECGM, and Pneumacult Ex plus (PEx+). Extensive RNA sequencing, immune assays and electrical measurements revealed that PEx+ media significantly drove cell proliferation and a broad pro-inflammatory phenotype in BCs. In contrast, BCs expanded in AECGM, displayed increased expression of structural and extracellular matrix components at high passage. Whereas culture in AECGM increased expression of some cytokines at high passage, DSI suppressed inflammation altogether thus implicating TGF-β in BC inflammatory processes. Differentiation capacity declined with time in culture irrespective of expansion media except for PLUNC expressing secretory cells that were elevated at high passage in AECGM and PEx+ suggestive of an immune modulatory role of PLUNC in BCs. These findings underscore the profound impact of media conditions on inflammatory niche and function ofin vitroexpanded BCs. The broad pro-inflammatory phenotype driven by PEx+ media, in particular, should be considered in the development of cell-based models for airway diseases and therapeutic application.NEW & NOTEWORTHYAirway basal cells, vital for airway regeneration and potential therapies, show significant changes based on culture conditions. Our study reveals that media composition and culture duration greatly affect basal cell properties with profound changes in the pro-inflammatory phenotype and extracellular matrix deposition driven by changes in growth conditions. These results underscore the critical impact of culture conditions on BC phenotype, influencing cell-based models for airway disease research and therapy.
Correlative Imaging for Comprehensive Molecular Mapping of Individual Cell Types in Biological Tissues
Authors: Yang Manxi , Iqfath Mushfeqa , Meke Frederick Nguele , Qu Zihan , Hernly Emerson L. , Su Pei , Zhang Zhong-Yin , Laskin Julia 
Published: September 2024

AbstractMass spectrometry imaging (MSI) is a powerful technique for label-free spatial mapping of multiple classes of biomolecules in tissue sections. However, differences in desorption and ionization efficiency of different classes of molecules make it challenging to simultaneously map biomolecules at each omics layer in the same tissue sample. Herein, we present a correlative imaging method using nanospray desorption electrospray ionization (nano-DESI) MSI, which enables the spatial mapping of lipids, metabolites, peptides, and proteins with cellular-level spatial resolution in a single tissue section. We demonstrate the molecular profiling of specific cell types and identify truncated peptides in mouse pancreatic tissue. Distinct chemical gradients of peptides and lipids extending from endocrine cells to exocrine cells indicate their different roles in endocrine-exocrine crosstalk and intracellular signaling. The results underscore the power of the developed imaging approach for spatial multi-omics analysis that provides deep insights into cellular diversity and the intricate molecular interactions that occur within heterogenous biological tissues.
Proteomic Investigation of Neurotrophictrans-Banglene Reveals Potential Link to Iron Homeostasis
Authors: Gunawardana Piyumi B. Wijesiri , Gohil Khyati , Moon Kyung-Mee , Foster Leonard J. , Williams Florence J. 
Published: September 2024

ABSTRACTIn an effort to gain insight into cellular systems impacted by neurotrophictrans-banglene (t-BG), global proteomic profiling and Western blot analyses were employed. Expression level changes in response tot-BG treatment were compared to those observed with nerve growth factor (NGF), a natural neurotrophic protein and functional analog tot-BG. Findings from these studies did not point to direct interception of NGF/TrkA signaling byt-BG. Instead, significant alterations in iron-binding and iron-regulating proteins were observed. Intracellular iron measurements by FerroOrange indicate lower ferrous (Fe2+) iron levels int-BG treated cells but not in NGF treated cells. These results highlight a potential connection between iron regulation and neurotrophic activity.
Microbial Metabolic Enzymes, Pathways and Microbial Hosts for Co-Metabolic Degradation of Organic Micropollutants in Wastewater
Authors: Lyu Boyu , Manna Bharat , Zhou Xueyang , Leung Ivanhoe K. H. , Singhal Naresh 
Published: September 2024

AbstractOrganic micropollutants (OMPs) in wastewater present significant environmental challenges, but effective removal strategies are hindered by our limited understanding of their co-metabolic biodegradation. We aim to elucidate the microbial enzymes, metabolic pathways, and community members involved in OMP co-metabolic degradation, thereby paving the way for more effective wastewater treatment strategies. We integrated multi-omics (metagenomics, metaproteomics, and metabolomics) and functional group analysis to investigate 24 OMPs under three aeration conditions. Our findings reveal that oxidoreductases, particularly cytochrome P450s and peroxidases, are crucial for recalcitrant OMPs containing halogen groups (-Cl, -F) like fluoxetine and diuron. Hydrolases, including amidases, are instrumental in targeting amide-containing (-CONH₂) OMPs such as bezafibrate and carbamazepine. Regarding microbial metabolism involved in OMP co-metabolic degradation, we found that amino acid metabolism is crucial for degrading amine-containing (-NH₂) OMPs like metoprolol and citalopram. Lipid metabolism, particularly for fatty acids, contributes to the degradation of carboxylic acid (-COOH) containing OMPs such as bezafibrate and naproxen. Finally, withActinobacteria,Bacteroidetes, andProteobacteriaemerging as primary contributors to these functionalities, we established connections between OMP functional groups, degradation enzymes, metabolic pathways, and microbial phyla. Our findings provide generalized insights into structure-function relationships in OMP co-metabolic degradation, offering the potential for improved wastewater treatment strategies.Graphical abstract
Zbtb38 inhibits apoptosis by transcriptionally regulatingXIAPexpression
Authors: Matsuda Eishou , Shigeoka Toshiaki , Nagaoka Hiroyuki , Nurulita Nunuk Aries , Tada Shogo , Ishida Yasumasa , Bessho Yasumasa 
Published: September 2024

AbstractX-linked inhibitor of apoptosis protein (XIAP) is a key suppressor of apoptosis, a major form of programmed cell death critical for cellular differentiation, embryogenesis, and cancer development. Despite its importance, the upstream regulators and regulatory elements ofXIAPare not well understood. This study provides evidence that the zinc finger transcription factor Zbtb38, a negative regulator of apoptosis, regulatesXIAPexpression in Zbtb38 loss- and gain-of-function experiments. Notably, XIAP overexpression rescued the apoptosis induced byZbtb38knockdown, indicating that Zbtb38-mediated apoptosis is at least partially dependent on XIAP. Chromatin immunoprecipitation and luciferase assays revealed that Zbtb38 binds to and activates E-boxes within theXIAPenhancer, underscoring the critical role of these E-boxes inXIAPexpression. Additionally, Zbtb38 loss during embryonic stem (ES) cell differentiation and embryogenesis resulted in increased apoptosis and decreased expression of XIAP and Bcl-2, highlighting their importance in these processes. Furthermore, Zbtb38 downregulation induced apoptosis in cancer cells lacking p53 expression, suggesting that Zbtb38 could be a potential therapeutic target in cancer.
Electric Field of DNA in Solution: Who Is in Charge?
Authors: Hedley Jonathan G. , Coshic Kush , Aksimentiev Aleksei , Kornyshev Alexei A. 
Published: September 2024

In solution, DNA, the “most important molecule of life,” is a highly charged macromolecule that bears a unit of negative charge on each phosphate of its sugar-phosphate backbone. Although partially compensated by counterions (cations of the solution) adsorbed at or condensed near it, DNA still produces a substantial electric field in its vicinity, which is screened by buffer electrolytes at longer distances from the DNA. This electric field is experienced by any charged or dipolar species approaching and interacting with the DNA. So far, such a field has been explored predominantly within the scope of a primitive model of the electrolytic solution, not considering more complicated structural effects of the water solvent. In this paper, we investigate the distribution of electric field around DNA using linear response nonlocal electrostatic theory, applied here for helix-specific charge distributions, and compare the predictions of such a theory with specially performed, fully atomistic, large-scale, molecular dynamics simulations. Both approaches are applied to unravel the role of the structure of water at close distances to and within the grooves of a DNA molecule in the formation of the electric field. As predicted by the theory and reported by the simulations, the main finding of this study is that oscillations in the electrostatic potential distribution are present around DNA, caused by the overscreening effect of structured water. Surprisingly, electrolyte ions at physiological concentrations do not strongly disrupt these oscillations and are rather distributed according to these oscillating patterns, indicating that water structural effects dominate the short-range electrostatics. We also show that (i) structured water adsorbed in the grooves of DNA leads to a positive electrostatic potential core relative to the bulk, (ii) the Debye length some 10 Å away from the DNA surface is reduced, effectively renormalized by the helical pitch of the DNA molecule, and (iii) Lorentzian contributions to the nonlocal dielectric function of water, effectively reducing the dielectric constant close to the DNA surface, enhance the overall electric field. The impressive agreement between the atomistic simulations and the developed theory substantiates the use of nonlocal electrostatics when considering solvent effects in molecular processes in biology.

Published by the American Physical Society
2024
Psychometric evaluation of technology adoption propensity (TAP) index within independent samples of Turkish individuals
Authors: Celik Hakan , Aybas Meryem 
Published: September 2024

PurposeThe technology adoption propensity (TAP) index is a parsimonious yet robust tool for measuring an individual’s willingness to accept new technologies. However, further investigation is still needed to evaluate its merits in non-Western countries. With this task in mind, this study assesses the psychometric properties and predictive capabilities of TAP in Turkey.Design/methodology/approachThe researchers utilized an iterative process of forward-backward translation and three rounds of piloting to ensure the cross-cultural, conceptual and linguistic equivalence for the chosen tool. The final survey was conducted online on a convenience sample of 352 academics and in person for 2 other convenience samples that comprised a total of 259 municipal officers and 300 individuals.FindingsTAP’s four-subscale structure was confirmed by a principal component analysis (PCA), and A confirmatory factor analysis (CFA) showed an acceptable fit across all samples. The total composition of the optimism, proficiency, dependence and vulnerability subscales was found to have adequate internal consistency and discriminant validity. Measurement invariance testing further demonstrated that TAP’s factorial organization was invariant across gender, age and income at configural, metric, scalar and strict levels. Finally, logistic and ordinary leas squares (OLS) regression analyses revealed that the TAP scores were predictive of prior technology adoption and use frequency.Originality/valueAlthough these results are still preliminary, the confirmation and replication of TAP in Turkey clearly suggest that TAP is a dependable tool for assessing technology readiness that can be utilized well across different cultures.
Development and validation of social entrepreneurship career decisions scale among higher education students
Authors: Viswanath Parvathy , Kumar Aneesh 
Published: September 2024

Purpose
The importance of sustainable development has become increasingly significant in today’s fast-paced world. The 17 sustainable development goals (SDGs) aim to solve a range of environmental, economic and social challenges, which requires global collaboration among governments and private organisations. In light of this, social entrepreneurship has garnered significant attention as it combines the social purpose of non-profits with the market-driven approach of for-profits to address SDG goals. Yet the cognitive processes underpinning the career decisions of social entrepreneurs remain underexplored. This study aims to develop and validate a scale to measure social entrepreneurial career decisions based on the appraisal of perceived challenges.

Design/methodology/approach
The study followed the steps of tool development and was carried out in three phases: item analysis, exploratory factor analysis (EFA) and confirmatory factor analysis (CFA).

Findings
The final 20-item scale focuses on the appraisal components in pre-entry social entrepreneurial career decision-making and has four factors, which are relevance, coping potential, knowledge and resources and normative significance.

Research limitations/implications
The study contributes to the literature on entrepreneurial cognition, specifically focusing on social entrepreneurship. The scale could guide model testing and quantitative research in social entrepreneurial cognition. The four-dimensional structure identified in the study may also have implications for researchers interested in the antecedents and effects of social entrepreneurial decision-making.

Practical implications
Accurate measurement of cognitive appraisal is necessary to understand the perceived challenges and thought processes of potential social entrepreneurs. The scale could be used to examine the cognitive appraisal patterns among students. Social entrepreneurship educators and policymakers can use the scale to design and assess educational programs.

Originality/value
Distinct from existing studies, this scale offers a multidimensional approach that captures the stages of career decision-making, providing a robust tool to enhance our understanding of the decision-making dynamics in social entrepreneurship.
Factors influencing consumers’ loyalty in the use of mobile telecommunication services: the case study in Vietnam
Authors: Nguyen Van Khoa , Pham Thi Huyen , Phan Thuy Anh 
Published: September 2024

PurposeThe research aimed to identify factors influencing customer loyalty in the use of mobile telecommunication services in Vietnam, focusing on two dimensions “attitudinal loyalty” and “behavioral loyalty.”Design/methodology/approachBased on survey data collected from 820 in two of Vietnam’s major cities users, Hanoi and Ho Chi Minh City, the data were processed using SPSS and AMOS software.FindingsThe study identified four factors affecting customer loyalty to mobile telecommunication services, with perceived service quality directly impacting both attitudinal and behavioral loyalty. Corporate image and perceived switching costs influenced attitudinal loyalty, while trust affected behavioral loyalty. Moreover, perceived service quality indirectly influenced attitudinal loyalty through corporate image and perceived switching costs.Research limitations/implicationsThe study only focuses on a limited number of factors influencing mobile telecommunications service user loyalty, its restricted geographical sample from only Hanoi and Ho Chi Minh City, and the simplification of perceived switching costs without considering their various components, such as psychological, financial and procedural costs, which could provide more comprehensive experimental and theoretical insights.Practical implicationsThe study reveals that customer loyalty in Vietnam’s mobile telecommunications sector is linked to the relationship between attitude toward the service provider and continued usage behavior, categorizing customer groups into genuine loyalty, latent loyalty, feigned loyalty and disloyalty. It suggests that service providers should focus on improving service quality and cultivating a positive, transparent corporate image to bolster customer trust, foster stable relationships and remain competitive in the market.Originality/valueThe research model combines Oliver’s (1999) theory of loyalty with Aydin and Özer’s (2005) research model, focusing on perceived service quality, corporate image, trust and perceived switching costs, examining their relationships with both behavioral and attitudinal loyalty simultaneously.