bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insights into the FOXE3 Transcriptional Network and Disease Mechanisms from the Investigation of a Regulatory Variant Driving Complex Microphthalmia
Authors: Plaisancié Julie , Angée Clémentine , Erjavec Elisa , Raymond-Letron Isabelle , Douet Jean-Yves , Goetz Mathilde , Vincent-Delorme Catherine , Karemaker Ino D. , Baltissen Marijke , Vermeulen Michiel , Valdivia Leonardo , Jabot-Hanin Fabienne , David Pierre , Hadjadj Djihad , Monsef Yanad Abou , Lyazrhi Faouzi , Calvas Patrick , Rozet Jean-Michel , Chassaing Nicolas , Fares-Taie Lucas 
Published: January 2025

ABSTRACTFOXE3encodes a conserved, lens-specific transcription factor essential for eye development. Biallelic mutations inFOXE3lead to a spectrum of ocular anomalies, from cataracts to complex microphthalmia (CM), with clinical severity correlating to genotype. In a CM case with a truncating mutation (p.Cys240*), we identified a regulatory variant (rv, rs745674596 G>A) 3 kb upstream ofFOXE3. Mouse models harboring either the rv or a frameshift mutation were generated in homozygosity (Foxe3rv/rv, Foxe3-/-) and compound heterozygosity (Foxe3rv/Foxe3-). Phenotypic analysis revealed progressive severity: Foxe3rv/rv mice exhibited cataracts and anterior segment dysgenesis, Foxe3rv/Foxe3-displayed more severe anomalies, andFoxe3-/-mice consistently developed CM. These findings align with human genotype-phenotype relationships. Notably, a direct correlation between protein levels and ocular phenotype was observed, with no association to mRNA levels. In Foxe3-/- mice, CM resulted from early disorganization of the anterior lens epithelium, leading to degeneration and ocular involution. Transcription factor binding assays identified USF2 as a key regulator ofFOXE3expression, positioning USF2 as a promising candidate in ocular development and disease, enhancing our understanding of the FOXE3-related network. This study underscores the importance of integrated approaches to identify genetic variants and cis-regulatory elements, revealing a novel mechanism for microphthalmia through degeneration and involution.
A V-ATPase complex, required for biogenesis of a lysosome-related organelle (LRO) inTetrahymena thermophila, disassembles during LRO maturation
Authors: Pradhan Ajay , Tadasare Niraj , Sarkar Debolina , Bansal Lavan K. , Turkewitz Aaron P. , Kumar Santosh 
Published: January 2025

AbstractIn the ciliateTetrahymena thermophila, a subset of proteins are exocytosed via lysosome-related organelles (LROs) called mucocysts. Formation of many LROs depends on modulation of pH by vacuolar-type ATPases (V-ATPases). Here, we used expression profiling to identify a V-ATPase a-subunit that is targeted to mucocysts. Cells lacking theV-ATPase-a1gene are defective in mucocyst biogenesis and exocytosis. However, the requirement for this subunit may not be limited to the canonical role of V-ATPases in proton pumping, since we find no evidence that mature mucocysts are acidified. Consistent with this, we find that while the a1-subunit is present in both immature and mature mucocysts, several other V-ATPase subunits are absent from the latter. These data suggest that the V-ATPase complex disassembles during mucocyst maturation, and that the a1-subunit performs roles independent of the holo-complex. Cells lacking the a1-subunit are defective in the targeting of both structural and enzymatic mucocyst proteins, and moreover appear deficient in fusion between vesicles from the secretory and endocytic pathways that is a feature of normal mucocyst maturation.
DUSP12 promotes cell cycle progression and protects cells from cell death by regulating ZPR9
Authors: Abdusamad Mai , Guo Xiao , Ramirez Ivan , Velasquez Erick F. , Cohn Whitaker , Gholkar Ankur A. , Whitelegge Julian P. , Torres Jorge Z. 
Published: January 2025

ABSTRACTProtein phosphatases are critical for regulating cell signaling, cell cycle, and cell fate decisions, and their dysregulation leads to an array of human diseases like cancer. The dual specificity phosphatases (DUSPs) have emerged as important factors driving tumorigenesis and cancer therapy resistance. DUSP12 is a poorly characterized atypical DUSP widely conserved throughout evolution. Although no direct substrate has been firmly established, DUSP12 that has been implicated in protecting cells from stress, regulating ribosomal biogenesis, and modulating cellular DNA content. In this study, we used affinity- and proximity-based biochemical purification approaches coupled to mass spectrometry to identify the zinc finger protein ZPR9 as a novel DUSP12 interactor, which was validated by in-cell andin-vitroIP assays. Interestingly, ZPR9 binds to the unique zinc-binding domain of DUSP12, which previous reports indicated was important for many of DUSP12’s functions within the cell. Prior studies had implicated ZPR9 as a modulator of apoptosis, but it remained unclear if and how ZPR9 participated in the cell cycle and, more so, how it promoted cell death. Using mass spectrometry analyses, we found that overexpression of DUSP12 promoted de-phosphorylation of ZPR9 at Ser143. Overexpression of ZPR9, but not Ser143phosphomimetic and phosphorylation-deficient mutants, led to an increase in pre-metaphase mitotic defects while knockdown of DUSP12 also showed mitotic defects in metaphase. Furthermore, knockdown of DUSP12 promoted, while knockdown of ZPR9 suppressed, stress-induced apoptosis. Our results support a model where DUSP12 protects cells from stress-induced apoptosis by promoting de-phosphorylation of ZPR9.
Chloramphenicol-mobilizedBacillus subtilistransiently expresses resistance to multiple antibiotics, including the glycopeptides phleomycin and bleomycin
Authors: LaBonte Sandra , Liu Yongjin , Powers Morgan , Ford Evan De , Straight Paul D. 
Published: January 2025

ABSTRACTAntibiotic resistance is a global crisis that stems from the use of antibiotics as an essential part of modern medicine. Understanding how antibiotic resistance is controlled among cells in bacterial populations will provide insights into how antibiotics shape microbial communities. Here, we describe patterns ofB. subtilisgene expression that arise from growth on a surface either in isolation or under subinhibitory chloramphenicol exposure. We identified elevated expression of genes encoding five different antibiotic resistance functions. The expression of four of the five resistance functions is controlled by a combination of terminator attenuation and transcriptional regulation. Two of these,vmlRandtlrBprovide resistance to lincosamides and tylosin, respectively. We found thatbmrCDpromotes resistance to glycopeptides, including phleomycin and bleomycin. Promoter fusions to luciferase were used to follow expression ofbmrCD, vmlR,andtlrB. Subinhibitory chloramphenicol exposure induces sliding motility ofB. subtilis, wherein the three antibiotic resistance functions are expressed heterogeneously in spatiotemporally segregated pattern. We found that their expression is transiently elevated even in the absence of antibiotic exposure. The data suggest that for some antibiotics, intrinsic resistance genes are entrained to changes in growth and metabolism. Antibiotic exposure amplifies their expression, potentially providing a subpopulation of cells elevated protection to multiple classes of antibiotic.IMPORTANCEAntibiotics are a natural component of bacterial communities that are vital to modern medicine and to combatting antibiotic-resistant pathogens. Understanding the roles antibiotics play in microbial populations provides insights to the origins of antibiotic resistance. Many studies show that subinhibitory concentrations of antibiotics stimulate bacterial gene expression, including antibiotic resistance, and influence community dynamics. This study shows that bacteria on an agar surface transiently elevate expression of intrinsic resistance genes for multiple antibiotics. Subinhibitory chloramphenicol exposure stimulates the bacterial population both to expand across the surface and enhance expression of the resistance genes in a heterogeneous pattern.The results illustrate how exposure to some antibiotics substantially changes bacterial population dynamics that include the spatiotemporally controlled expression of endogenous antibiotic resistance.
A suite of pre-assembled, pET28b-based Golden Gate vectors for efficient protein engineering and expression
Authors: Gaur Deepika , Wohlever Matthew L. 
Published: January 2025

AbstractExpression and purification of recombinant proteins inE. coliis a bedrock technique in biochemistry and molecular biology. Expression optimization requires testing different combinations of solubility tags, affinity purification techniques, and site-specific proteases. This optimization is laborious and time consuming as these features are spread across different vector series and require different cloning strategies with varying efficiencies. Modular cloning kits based on the Golden Gate system exist, but are overly complicated for many applications, such as undergraduate research or simple screening of protein purification features. An ideal solution is for a single gene synthesis or PCR product to be compatible with a large series of pre-assembled Golden Gate vectors containing a broad array of purification features at either the N or C-terminus. To our knowledge, no such system exists. To fulfill this unmet need, we Golden Gate domesticated the pET28b vector and developed a suite of 21 vectors with different combinations of purification tags, solubility domains, visualization/labeling tags, and protease sites. We also developed a completely scarless vector series with 9 different N-terminal tags. The system is modular, allowing users to easily customize the vectors with their preferred combinations of features. To allow for easy visual screening of cloned vectors, we optimized constitutive expression of the fluorescent protein mScarlet3 in the reverse strand, resulting in a red to white color change upon successful cloning. Testing with the model protein sfGFP shows the ease of visual screening, high efficiency of cloning, and robust protein expression. These vectors provide versatile, high-throughput solutions for protein engineering and functional studies inE. coli.
Mixed positive and negative feedback loops drive diverse single-cell gene expression dynamics
Authors: Loman Torkel E. , Schwall Christian P. , Saez Teresa , Liu Yujia , Locke James C. W. 
Published: January 2025

AbstractGenetic circuits with only a few components can generate complex gene regulatory dynamics. Here, we combine stochastic modelling and single-cell time-lapse microscopy to reveal the possible dynamics generated by a key gene circuit motif: the mixed positive/negative feedback loop. Our minimal stochastic model of this motif reveals ten distinct classes of dynamic output, including stochastic pulsing, oscillations, and bistability. These dynamics are influenced by only a few important biological parameters, such as the strength of the positive and negative feedbacks. Experimental validation in two different mixed feedback circuits in the bacteriumB. subtilis, σBand σV, confirms our model’s predictive power. Guided by our simulations, we are able to transition between dynamic behaviours by modulatingin vivoparameters. Together, these results demonstrate how mixed feedback loops generate diverse single-cell behaviours, improving our understanding of this common biological network motif and informing our efforts to engineer them for synthetic biology applications.
A synthetic cell with integrated DNA self-replication and membrane biosynthesis
Authors: Sierra Ana María Restrepo , Gomez Federico Ramirez , van Tongeren Mats , Heras Laura Sierra , Danelon Christophe 
Published: January 2025

AbstractThe emergence, organization, and persistence of cellular life are the result of the functional integration of metabolic and genetic networks. Here, we engineer phospholipid vesicles that can operate three essential functions, namely transcription-translation of a partial genome, self-replication of this DNA program, and membrane synthesis. The synthetic genome encodes six proteins and its compartmentalized expression produces active liposomes with distinct phenotypes demonstrating successful module integration. Our results reveal that genetic factors exert a stronger control over DNA replication and membrane synthesis than metabolic crosstalk or module co-activity. By showing how genetically encoded functions derived from different species can be integrated in liposome compartments, our work opens new avenues for the construction of autonomous and evolving synthetic cells.
First Direct Search for Light Dark Matter Using the NEON Experiment at a Nuclear Reactor
Authors: Choi J. J. , Ha C. , Jeon E. J. , Kim J. Y. , Kim K. W. , Kim S. H. , Kim S. K. , Kim Y. D. , Ko Y. J. , Koh B. C. , Lee S. H. , Lee I. S. , Lee H. , Lee H. S. , Lee J. S. , Oh Y. M. , Park B. J. ,   NEON Collaboration
Published: January 2025

We report new results from the neutrino elastic scattering observation with NaI (NEON) experiment in the search for light dark matter (LDM) using 2636  kg·days of NaI(Tl) exposure. The experiment employs an array of NaI(Tl) crystals with a total mass of 16.7 kg, located 23.7 m away from a 2.8 GW thermal power nuclear reactor. We investigated LDM produced by the of dark photons, a well-motivated mechanism generated by high-flux photons during reactor operation. The energy spectra collected during reactor-on and reactor-off periods were compared within the LDM signal region of 1–10 keV. No signal consistent with LDM interaction with electrons was observed, allowing us to set 90% confidence level exclusion limits on the dark matter-electron scattering cross section (σe) across dark matter masses ranging from 1 to 1000  keV/c2. Our results set a 90% confidence level upper limit of σe=3.17×10−35  cm2 for a dark matter mass of 100  keV/c2, marking the best laboratory result in this mass range. Additionally, our search extends the coverage of LDM below 100  keV/c2 for the first time, assuming the specific of dark photons.

Published by the American Physical Society
2025
Unpacking the power of trust: how relative advantage, compatibility, ease of use and usefulness drive hotel self-directed bookings
Authors: Azhar Nur Batrisyia Aza , Zahari Mohd Salehuddin Mohd , Ferdian Feri , Hanafiah Mohd Hafiz 
Published: January 2025

Purpose
This paper aims to explore how relative advantages, compatibility, perceived ease of use and perceived usefulness affect hotel room self-directed booking (SDB) behavior, specifically focusing on the mediating role of trust.

Design/methodology/approach
The research utilized the responses of 432 hotel guests, applying an extended technology acceptance model (TAM)− innovation diffusion theory (IDT)−trust framework and using partial least squares structural equation modeling to conduct both direct and indirect path analyses to confirm the study hypotheses.

Findings
Results show that perceived relative advantages, compatibility, usefulness and ease of use of the online booking platform significantly impact guests’ SDB behavior, with trust significantly mediating each of the proposed relationships, highlighting its crucial role in promoting online booking behavior.

Research limitations/implications
This study underscores the importance of SDB providers’ showcasing the benefits and efficiency of online booking systems in influencing consumer decisions, offering new insights into how technological advancements affect SDB behavior in the hotel industry.

Originality/value
By integrating TAM, IDT and trust into an integrated framework, this study provides a comprehensive understanding of the diverse factors influencing hotel guest engagement with SDB, offering practical insights to enhance guest satisfaction with the SDB platform.
Peanut oil price change forecasts through the neural network
Authors: Jin Bingzi , Xu Xiaojie , Zhang Yun 
Published: January 2025

Purpose
For a wide range of market actors, including policymakers, forecasting changes in commodity prices is crucial. As one of essential edible oil, peanut oil’s price swings are certainly important to predict. In this paper, the weekly wholesale price index for the period of January 1, 2010 to January 10, 2020 is used to address this specific forecasting challenge for the Chinese market.

Design/methodology/approach
The nonlinear auto-regressive neural network (NAR-NN) model is the forecasting method used. Forecasting performance based on various settings, such as training techniques, delay counts, hidden neuron counts and data segmentation ratios, are assessed to build the final specification.

Findings
With training, validation and testing root mean square errors of 5.89, 4.96 and 5.57, respectively, the final model produces reliable and accurate forecasts. Here, this paper demonstrates the applicability of the NAR-NN approach for commodity price predictions.

Originality/value
On the one hand, the findings may be used as independent technical price movement predictions. Conversely, they may be included in forecast combinations with forecasts derived from other models to form viewpoints of commodity price patterns for policy research.
Numerical research on two typical flow structures and aerodynamic drag characteristics of blunt-nosed trains
Authors: Zhong Sha , Yang Mingzhi , Qian Bosen , Zhang Lei , He Dongqing , Lin Tongtong , Lien Fue-Sang 
Published: January 2025

Purpose
This study aims to provide new insights into aerodynamic drag reduction for increasingly faster blunt-nosed trains, such as urban and freight trains. Specifically, this work investigates two distinctly different wake structures and associated aerodynamic drag of blunt-nosed trains.

Design/methodology/approach
Three typical cases of blunt-nosed trains with 1-, 2- and 3-m nose lengths are selected. The time-averaged and unsteady flow structures around the trains are analyzed using the improved delayed detached eddy simulation model and proper orthogonal decomposition method.

Findings
The simulation results indicate that for 2- and 3-m nose lengths, the flow separates at first and then reattaches to the slanted surface of the tail, with a pair of longitudinal vortices dominating the wake. In contrast, for the 1-m nose length case, the wake structure is characterized by complete separation, attributed to the larger curvature of the slanted tail surface. Consequently, the total time-averaged drag coefficient is reduced by 27.2% and 19.2% for the 1-m nose length case compared to the 2- and 3-m cases, respectively. Moreover, the predominant unsteady structures with Strouhal numbers St = 0.30 and St = 0.28 are detected in the near-wake of the 2- and 3-m nose length cases, respectively. These structures result from periodic vortex shedding at the lower slanted tail surface. In contrast, for the 1-m nose length case, the predominant unsteady structure with St = 0.19 is induced by the nearly periodic expansion and contraction of the upper bubbles.

Originality/value
Two distinctly different wake structures in blunt-nosed trains are identified. Unlike high-speed trains with longer, streamlined noses, for blunt-nosed trains, shorter nose lengths result in lower aerodynamic drag. Insights for reducing energy consumption in blunt-nosed trains are provided.
Corporate misconduct and corporate social responsibility: the roles of CEO incentives and institutional ownership
Authors: Thosuwanchot Nongnapat , Lee Min Suk 
Published: January 2025

Purpose
This study aims to examine why executives increase investments in corporate social responsibility (CSR) as a strategic action to protect their firms’ reputation from the possibility of a contagion effect following CSR-related corporate misconduct in the industry by drawing on an impression management perspective. This study also examines internal and external governance mechanisms as boundary conditions.

Design/methodology/approach
The sample includes panel data of firms listed in the S&P 500 index from 2009 to 2013. The authors used firm fixed-effects models to test the hypotheses.

Findings
The results show that recent CSR-related corporate misconduct occurred in other firms, inducing executives to increase investments in CSR. Moreover, internal and external governance mechanisms, which are CEO incentives and institutional ownership, moderated the relationship.

Originality/value
This study contributes to prior literature on the factors influencing CSR at the multilevel of analysis by examining how recent CSR-related corporate misconduct in the industry interacts with corporate governance mechanisms as boundary conditions to influence firm commitment to CSR.
Assembly Graph as the Rosetta Stone of Ecological Assembly
Authors: Song Chuliang 
Published: January 2025

ABSTRACTEcological assembly—the process of ecological community formation through species introductions—has recently seen exciting theoretical advancements across dynamical, informational, and probabilistic approaches. However, these theories often remain inaccessible to non‐theoreticians, and they lack a unifying lens. Here, I introduce the assembly graph as an integrative tool to connect these emerging theories. The assembly graph visually represents assembly dynamics, where nodes symbolise species combinations and edges represent transitions driven by species introductions. Through the lens of assembly graphs, I review how ecological processes reduce uncertainty in random species arrivals (informational approach), identify graphical properties that guarantee species coexistence and examine how the class of dynamical models constrain the topology of assembly graphs (dynamical approach), and quantify transition probabilities with incomplete information (probabilistic approach). To facilitate empirical testing, I also review methods to decompose complex assembly graphs into smaller, measurable components, as well as computational tools for deriving empirical assembly graphs. In sum, this math‐light review of theoretical progress aims to catalyse empirical research towards a predictive understanding of ecological assembly.
Broke and Broken: The Crises Facing Local Government in England
Authors: Jeffery David 
Published: January 2025

AbstractEnglish local government faces a perilous position owing to insufficient funding, structural issues and capacity challenges. Fourteen years of austerity have significantly reduced council budgets, while increased demand for services—particularly adult social care—has strained resources. The current funding system is regressive and fails to incentivise economic growth, and the structure of local government is not fit for purpose due to a focus on unitary authorities, which are sub‐optimal for service delivery. To address these issues, this article proposes a four‐tier system of local government, a more robust funding mechanism and electoral reforms to ensure effective governance and representation.