bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probing mechanical selection in diverse eukaryotic genomes through accurate prediction of 3D DNA mechanics
Authors: Park Jonghan , Prokopchuk Galina , Popchock Andrew R. , Hao Jingzhou , Liao Ting-Wei , Yan Sophia , Hedman Dylan J. , Larson Joshua D. , Walther Brandon K. , Becker Nicole A. , Basu Aakash , Maher L. James , Wheeler Richard J. , Asbury Charles L. , Biggins Sue , Lukeš Julius , Ha Taekjip 
Published: December 2024

AbstractConnections between the mechanical properties of DNA and biological functions have been speculative due to the lack of methods to measure or predict DNA mechanics at scale. Recently, a proxy for DNA mechanics, cyclizability, was measured by loop-seq and enabled genome-scale investigation of DNA mechanics. Here, we use this dataset to build a computational model predicting bias-corrected intrinsic cyclizability, with near-perfect accuracy, solely based on DNA sequence. Further, the model predicts intrinsic bending direction in 3D space. Using this tool, we aimed to probe mechanical selection - that is, the evolutionary selection of DNA sequence based on its mechanical properties - in diverse circumstances. First, we found that the intrinsic bend direction of DNA sequences correlated with the observed bending in known protein-DNA complex structures, suggesting that many proteins co-evolved with their DNA partners to capture DNA in its intrinsically preferred bent conformation. We then applied our model to large-scale yeast population genetics data and showed that centromere DNA element II, whose consensus sequence is unknown, leaving its sequence-specific role unclear, is under mechanical selection to increase the stability of inner-kinetochore structure and to facilitate centromeric histone recruitment. Finally,in silicoevolution under strong mechanical selection discovered hallucinated sequences with cyclizability values so extreme that they required experimental validation, yet, found in nature in the densely packed mitochondrial(mt) DNA ofNamystynia karyoxenos, an ocean-dwelling protist with extreme mitochondrial gene fragmentation. The need to transmit an extraordinarily large amount of mtDNA, estimated to be > 600 Mb, in combination with the absence of mtDNA compaction proteins may have pushed mechanical selection to the extreme. Similarly extreme DNA mechanics are observed in bird microchromosomes, although the functional consequence is not yet clear. The discovery of eccentric DNA mechanics in unrelated unicellular and multicellular eukaryotes suggests that we can predict extreme natural biology which can arise through strong selection. Our methods offer a way to study the biological functions of DNA mechanics in any genome and to engineer DNA sequences with desired mechanical properties.
In vivomultiplex imaging of dynamic neurochemical networks with designed far-red dopamine sensors
Authors: Zheng Yu , Cai Ruyi , Wang Kui , Zhang Junwei , Zhuo Yizhou , Dong Hui , Zhang Yuqi , Wang Yifan , Deng Fei , Ji En , Cui Yiwen , Fang Shilin , Zhang Xinxin , Zhang Kecheng , Wang Jinxu , Li Guochuan , Miao Xiaolei , Wang Zhenghua , Yang Yuqing , Li Shaochuang , Grimm Jonathan , Johnsson Kai , Schreiter Eric , Lavis Luke , Chen Zhixing , Mu Yu , Li Yulong 
Published: December 2024

ABSTRACTNeurochemical signals like dopamine (DA) play a crucial role in a variety of brain functions through intricate interactions with other neuromodulators and intracellular signaling pathways. However, studying these complex networks has been hindered by the challenge of detecting multiple neurochemicalsin vivosimultaneously. To overcome this limitation, we developed a single-protein chemigenetic DA sensor, HaloDA1.0, which combines a cpHaloTag-chemical dye approach with the G protein-coupled receptor activation-based (GRAB) strategy, providing high sensitivity for DA, sub-second response kinetics, and an extensive spectral range from far-red to near-infrared. When used together with existing green and red fluorescent neuromodulator sensors, Ca2+indicators, cAMP sensors, and optogenetic tools, HaloDA1.0 provides high versatility for multiplex imaging in cultured neurons, brain slices, and behaving animals, facilitating in-depth studies of dynamic neurochemical networks.
Introgression and divergence in a young species group
Authors: Satokangas I. , Martin SH. , Seifert B. , Puukko T. , Helanterä H. , Kulmuni J. 
Published: December 2024

AbstractThe process of speciation concerns often not only pairs of species but rather groups of diverging and interacting taxa, as highlighted by recent research. Hence, to understand the evolution of species’ diversity and their persistence, it is crucial to understand how gene flow and evolution of reproductive isolation shape groups of closely related species. Using resequencing data, we disentangle here genomic patterns of divergence and introgression in fiveFormica rufagroup wood ant species that are at the early stage of speciation. We first revise earlier mitochondrial phylogenies with a nuclear genomic tree, and demonstrate then introgression that is in line with observations of their current day natural hybridisation. Investigating the genome-wide differentiation and divergence we find correlations between population genetic parameters of divergence, differentiation, and diversity, that are in line with theoretical expectations for young species. Despite previously found evidence for polygenic species barriers, our data lacks the genome-wide correlation between differentiation and divergence that would be expected under a model of polygenic barriers. The likely explanation for this lack is the dominating effect of ancestral diversity at these early stages of speciation. As hybridisation has led to both deleterious and adaptive consequences within the group, we examined the signatures of introgression. We find no strong positive correlation between introgression and recombination, suggesting introgression does not have a predominantly deleterious effect. We also infer low diversity in the genomic regions with high proportions of introgression, consistent with the idea that selection has locally favoured introgression. This could be due to sharing of adaptive alleles or reduction of genetic load in the receiving species. Interestingly, gene flow in this group could potentially cross multiple species boundaries even in the absence of direct interbreeding between all the species. We discuss the long-term benefits and costs of introgression in young species, including the effect of environmental fluctuations and multi-species introgression.
Proteostasis Signatures in Human Diseases
Authors: Lim Christine M , Vendruscolo Michele 
Published: December 2024

AbstractThe protein homeostasis (proteostasis) system maintains the proteome in a healthy state. Although this system has been comprehensively mapped, its perturbations in disease remain incompletely characterised. To address this problem, here we define the proteostasis signatures, which represent the characteristic patterns of change in the proteostasis system associated with disease. We performed a large-scale, pandisease analysis across 32 human diseases spanning 7 disease types. We first identified unique proteostasis perturbations in specific disease states. We then uncovered distinctive signatures differentiating disease types, pointing to a range of proteostasis mechanisms in disease development. Next, we tracked the temporal evolution of proteostasis signatures, revealing shifts in proteostasis disruption over the course of disease progression. Finally, we demonstrated how smoking, a major risk factor of many diseases, impairs proteostasis in a manner similar to disease, potentially creating a predisposed environment for disease onset. These results illustrate the opportunities offered by the study of human diseases from the perspective of proteostasis signatures.
Tryptophan metabolite atlas uncovers organ, age, and sex-specific variations
Authors: Perez-Castro Lizbeth , Nawas Afshan F. , Kilgore Jessica A. , Garcia Roy , Lafita-Navarro M.Carmen , Acosta Paul H. , Nogueira Pedro A. S. , Williams Noelle S. , Conacci-Sorrell Maralice 
Published: December 2024

ABSTRACTAlthough tryptophan (Trp) is the largest and most structurally complex amino acid, it is the least abundant in the proteome. Its distinct indole ring and high carbon content enable it to generate various biologically active metabolites such as serotonin, kynurenine (Kyn), and indole-3-pyruvate (I3P). Dysregulation of Trp metabolism has been implicated in diseases ranging from depression to cancer. Investigating Trp and its metabolites in healthy tissues offers pathways to target disease-associated disruptions selectively, while preserving essential functions. In this study, we comprehensively mapped Trp metabolites across the Kyn, serotonin, and I3P pathways, as well as the microbiome-derived metabolite tryptamine, in C57BL/6 mice. Our comprehensive analysis covered 12 peripheral organs, the central nervous system, and serum in both male and female mice at three life stages: young (3 weeks), adult (54 weeks), and aged (74 weeks). We found significant tissue-, sex-, and age-specific variations in Trp metabolism, with notably higher levels of the oncometabolites I3P and Kyn in aging males. These findings emphasize the value of organ-specific analysis of Trp metabolism for understanding its role in disease progression and identifying targeted therapeutic opportunities.AUTHOR SUMMARYTrp metabolism has primarily been studied in cell lines, often leading to generalized assumptions about its role in health and disease. However, how Trp and its metabolites are allocated across tissues, sexes, and life stages has remained poorly understood. This gap is critical, as Trp is the largest amino acid, minimally used for protein synthesis, and largely metabolized in the liver, yet its distribution and metabolism in other tissues are unknown. Misconceptions, such as the idea that all cancers universally increase Kyn production, have contributed to therapeutic failures, highlighting the need for rigorous, tissue-specific studies. Our study systematically quantifies Trp metabolites across organs and tissues in vivo, revealing significant organ-, sex-, and age-specific variations. These findings provide a foundational resource for understanding Trp metabolism in normal physiology and disease, with potential applications in cancer, neurodegeneration, and other metabolic disorders.
Perception of AI tool adoption and training: initial validation using GSEM method
Authors: Vázquez-Parra José Carlos , Henao-Rodríguez Carolina , Lis-Gutiérrez Jenny Paola , Palomino-Gámez Sergio , Suárez-Brito Paloma 
Published: December 2024

PurposeThis study develops and validates the “Perception of the Adoption and Training in the Use of Artificial Intelligence Tools in the Profession” instrument, designed to measure Latin American university students' attitudes and perceptions regarding AI training in their professional education across diverse fields.Design/methodology/approachThe instrument was administered to 238 students from various disciplines at a Mexican university. Structural validity and reliability were assessed using a generalized structural equation model (GSEM) with quasi-maximum likelihood (QML) to handle data non-normality and analyze latent construct relationships.FindingsResults show high internal consistency and validity, with strong correlations between items and constructs of “attitude” and “perception of AI training value.” The study found significant relationships between understanding AI tools and the perceived value of AI training, as well as between this perception and attitudes toward incorporating AI in professional training.Practical implicationsThe instrument helps institutions identify student attitudes and training needs related to AI, enabling tailored curricula and training programs that foster positive AI acceptance, thus preparing students for modern technological challenges.Originality/valueThis study offers a validated instrument tailored to the Latin American context, addressing a gap in measuring student perceptions of AI in professional training. It serves as a diagnostic tool for educators and policymakers in designing AI-integrated pedagogical strategies that align with student needs.
Digital leadership and its impact on agility, innovation and resilience: a qualitative study of the UAE media industry
Authors: Albannai Najla Abdullah Ahmed , Raziq Muhammad Mustafa , Malik Mehreen , Abrar Ayesha 
Published: December 2024

PurposeTo explore the role of digital leadership in fostering strategic agility, innovation adaptivity, organizational agility and resilience in the context of digital transformation.Design/methodology/approachFollowing an interpretive case study approach and using a thematic data analysis technique, we conducted 20 in-depth interviews with digital leaders from five different media firms across the UAE.FindingsThe findings reveal that digital leaders are central to developing and executing digital strategies that enhance organizational agility and competitive edge, particularly in firms’ digital transformation. Digital leaders catalyze innovation and adaptability, ensuring the organization’s readiness for technological and market shifts. Moreover, digital leaders are instrumental in fostering an environment that promotes continuous learning, technological integration and a culture of change, which drives organizational agility and resilience.Originality/valueThe originality of this study lies in its focused examination of digital leadership within the UAE’s media sector, offering new insights into how digital leadership drives strategic agility, innovation adaptivity, organizational agility and resilience in a regionally specific digital transformation context. Our findings contribute to the broader academic and practical understanding of digital transformation in the media industry.
Promoting water accounting implementation processes: an argumentation-based Fuzzy-DEMATEL approach
Authors: Behzadian Fatah , Abdoli Mohammadreza 
Published: December 2024

PurposeThis paper’s purpose is to contribute to the financial management knowledge literature by presenting the framework of water accounting factors and evaluation of its identified factors through an argumentation-based Fuzzy-DEMATEL approach.Design/methodology/approachThis study adopted mixed, inductive and deductive approaches to develop a water accounting framework, validate its practicability and verify its effectiveness in selected firms listed on the Tehran Stock Exchange (TSE). In developing the framework and implementation procedure, the study employed an exploratory data collection (qualitative) approach to review the phenomenon of water accounting factors. Then, in this study’s second phase, Fuzzy-DEMATEL is used to evaluate the areas identified in the presented framework. In this study, Fuzzy-Delphi is also used to verify the reliability of the core components so that it is possible to generalize the factors to the Fuzzy-DEMATEL process.FindingsThe results obtained from the process of ground theory indicate the identification of 3 categories, 6 core components and 29 propositional themes, which are considered to constitute the framework of water accounting. Besides was determined in the quantitative phase that the optimal water consumption efficiency is considered the most effective component of implementing water accounting in capital market firms.Originality/valueThis research is one of the few studies in the field of water accounting framework and Fuzzy evaluation of its functions in the capital market. Because prior research has only described the importance of financial functions and sustainability in the form of a case study, this study seeks to achieve a framework for the implementation of water accounting. Also, through the evaluation of Fuzzy-DEMATEL, this study tries to develop the strategic functions of firms in managing water consumption. The originality of this study is, firstly, the identification of the driving fields of the water accounting, and secondly, the study follows the Fuzzy-Delphi and Fuzzy-DEMATEL of the factors identified in the TSE. Both implications raised in this section show the knowledge-enhancing and practical capacities of the study.
Marketing contracts and technical efficiency of citrus production
Authors: Zhang Hepei , Ma Wanglin 
Published: December 2024

PurposeThis study examines the impacts of marketing contracts (written contracts, verbal contracts and no contracts) on technical efficiency, taking citrus production in Jiangxi Province, China, as an example.Design/methodology/approachWe first use a stochastic production frontier (SPF) model to calculate the technical efficiency scores of citrus production at the individual level. Then, we use a multinomial endogenous switching regression (MESR) model, which mitigates selection bias issues arising from observed and unobserved factors, to estimate the treatment effects of marketing contract choices on technical efficiency. Data used in this study were collected from a survey of citrus farmers conducted between October and November 2022 in Jiangxi Province, China.FindingsThe SPF model estimates show that the mean technical efficiency score of citrus production is 0.616, ranging between 0.021 and 0.894. The MESR model estimates reveal that the technical efficiency scores for written and oral contract users are 18.3 and 10.5% higher, respectively, compared to citrus farmers with no marketing contracts. Additionally, the average technical efficiency score for written contract users exceeds that of oral contract users by 2.5%. We also find that farmers with higher household incomes and less farming experience were more likely to use written contracts. At the same time, those endowed with better education, larger farm sizes and better production conditions were more likely to use verbal contracts.Originality/valueFarmers seeking marketing contracts for product sales need to adjust their production behaviour in advance to meet the product attributes required by market buyers. However, little is known about whether marketing contract users are more efficient in farm production than non-users. This study provides the first attempt to investigate the associations between different types of marketing contracts and technical efficiency.
Classification and fault diagnosis of power transformers with dissolved gas analysis using improved clustering methods
Authors: Kianimehr Nasser , Zeinoddini-Meymand Hamed , Shahnia Farhad 
Published: December 2024

Purpose
Power transformers are vital components of an electrical network. A defective transformer can cause instability and blackouts in parts of the network. An accurate classification of different transformer faults results in a relatively accurate fault diagnosis and timely corrective actions. It is possible to increase productivity and reduce costs by using fault detection of power transformers through the analysis of gases dissolved in oil. The proposed technique is a suitable tool to help the utilities and engineers in charge of preventive maintenance by reducing the costs of different fault diagnosis tests for power transformers.

Design/methodology/approach
In this paper, the IEC 60599 standard along with clustering and classification methods are used to classify power transformer’s fault types. K-means and Fuzzy C-means clustering methods are used for clustering, and the support vector machine (SVM) method is used for classification of different types of faults in ‎power ‎transformers. The performance of K-means and SVM methods is improved by using the Grasshopper Optimization Algorithm (GOA). The efficiency of the proposed methods is evaluated using real field data of power transformers. The purpose of this study is to propose hybrid methods including K-means-GOA clustering and SVM-GOA classification for accurate fault diagnosis. These methods have been used for the first time in fault diagnosis determination of power transformers through gas analysis. The Silhouette criteria is used in this paper to compare the efficiency of different clustering methods.

Findings
Simulation results of the paper are based on the gas chromatography data related to 266 different real power transformers. They show the high accuracy and high-performance speed of intelligent clustering and classification methods compared to conventional ones. This analysis would be helpful in performing the required maintenance check and plan for repairs.

Originality/value
The applicability and efficiency of the proposed hybrid K-means-GOA and SVM-GOA models are verified for transformer fault detection using the experimental diverse data set including 266 set of real field test parameters of power transformers.
A reflection on governance, ethics and intellectual boundary enforcement in academic journals
Authors: Ozkazanc-Pan Banu 
Published: December 2024

PurposeThis paper critiques practices related to governance, ethics and intellectual boundary enforcement in critically oriented academic journals in the aftermath of mass resignations from the leading feminist journal, Gender, Work & Organization. In doing so, the paper highlights problematic issues that undermine inclusive academic publishing in regard to non-White, non-Western and/or early-career academics. It calls upon scholars to address the lack of inclusion and transparency in these journals and offers suggestions to be undertaken by all academic editors to remedy the situation.Design/methodology/approachBased on the author’s experiences as joint editor-in-chief at Gender, Work & Organization, the paper offers a viewpoint of exclusion issues and problematic behaviors within academic publishing through a first-hand perspective and critical analysis of practices.FindingsThree issues are found to impact inclusion in academic publishing. First, there is a lack of transparency in how editorships and board seats are allocated in many critically oriented academic journals. Alongside these governance issues, potential conflicts of interest related to prolific “cartel” or networked publishing among scholars create ethical challenges. Finally, boundary enforcement of intellectual contributions results in narrowly defined academic communities that replicate racialized exclusionary practices.Originality/valueThis paper is a reflexive praxis that calls out the need for academics to engage in good governance practices in journal management and foster ethical approaches in the publishing process. It also calls upon scholars and editors to reflect upon their practices in enforcing intellectual boundaries for the purpose of keeping particular ideas and people out of networks and consequently, out of academic communities.