bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel method for fine-scale retrospective isotope analysis in mammals using eye lenses
Authors: Miura Kazuki , Matsubayashi Jun , Yoshimizu Chikage , Takafumi Hino , Shirane Yuri , Mano Tsutomu , Tsuruga Hifumi , Tayasu Ichiro 
Published: March 2024

Abstract1. Investigating individual behavioural variations in mammals is essential for understanding their ecology and evolution, and plays a critical role in conservation and management practices. However, the reconstruction of long-term individual behaviour, such as via bio-logging, remains challenging owing to cost constraints and limitations of battery life and the impact of device size for smaller animals. This study proposed and tested a novel and cost-effective method for retrospective isotope analysis using mammalian eye lenses, specifically focusing on brown bears (Ursus arctos).2. Seven pairs of bear eye lenses were collected from southwestern Hokkaido, Japan. One or both lenses of each bear were segregated into small fragments from the outermost to the core tissues, and the nitrogen and carbon stable isotope ratios (δ15N and δ13C) of each eye lens fragment were measured. These isotope ratios in the eye lenses were compared with the δ15N and δ13C of potential brown bear diets in the study region (C3herbs, C3fruits, terrestrial animals, and corn). Additionally, we compared the isotopic patterns in both the right and left lenses of the same bear in two individuals to evaluate the consistency of our preparation protocol.3. In all eye lenses, high δ15N values were identified near the core, which gradually decreased towards the outer tissues, indicating ontogenetic dietary shifts related to lactation and weaning in the early life stage. Bears from study areas with high corn availability exhibited substantial increases in δ13C and δ15N in the outer lens tissues, suggesting a dietary shift toward corn consumption after weaning. Isotopic patterns between lens pairs from the same individual were similar, although discrepancies increased in tissues located 1.00 to 2.25 mm from the core, highlighting the need for standardisation in sample processing.4. This study demonstrates a novel and simple technique for retrospective isotope analysis in wild mammals using eye lenses, effectively reconstructing the feeding histories of brown bears. Our findings provide a new avenue for studying individual time-series behavioural patterns, with important implications for the fields of mammalian ecology, evolution, conservation, and management.
Regulation of immune signal integration and memory by inflammation-induced chromosome conformation
Authors: Daniel Bence , Chen Andy Y. , Sandor Katalin , Zhang Wenxi , Miao Zhuang , Lareau Caleb A. , Yost Kathryn E. , Chang Howard Y. , Satpathy Ansuman T. 
Published: March 2024

Abstract3-dimensional (3D) genome conformation is central to gene expression regulation, yet our understanding of its contribution to rapid transcriptional responses, signal integration, and memory in immune cells is limited. Here, we study the molecular regulation of the inflammatory response in primary macrophages using integrated transcriptomic, epigenomic, and chromosome conformation data, including base pair-resolution Micro-Capture C. We demonstrate that interleukin-4 (IL-4) primes the inflammatory response in macrophages by stably rewiring 3D genome conformation, juxtaposing endotoxin-, interferon-gamma-, and dexamethasone-responsive enhancers in close proximity to their cognate gene promoters. CRISPR-based perturbations of enhancer-promoter contacts or CCCTC-binding factor (CTCF) boundary elements demonstrated that IL-4-driven conformation changes are indispensable for enhanced and synergistic endotoxin-induced transcriptional responses, as well as transcriptional memory following stimulus removal. Moreover, transcriptional memory mediated by changes in chromosome conformation often occurred in the absence of changes in chromatin accessibility or histone modifications. Collectively, these findings demonstrate that rapid and memory transcriptional responses to immunological stimuli are encoded in the 3D genome.
Correlation measures in metagenomic data: the blessing of dimensionality
Authors: Fuschi Alessandro , Merlotti Alessandra , Binh Tran Thi Dong , Nguyen Hoan , Weinstock George M. , Remondini Daniel 
Published: March 2024

AbstractMicrobiome analysis has revolutionized our understanding of various biological processes, spanning human health, epidemiology (including antimicrobial resistance and horizontal gene transfer), as well as environmental and agricultural studies. At the heart of microbiome analysis lies the characterization of microbial communities through the quantification of microbial taxa and their dynamics. In the study of bacterial abundances, it is becoming more relevant to consider their relationship, to embed these data in the framework of network theory, allowing characterization of features like node relevance, pathway and community structure. In this study, we address the primary biases encountered in reconstructing networks through correlation measures, particularly in light of the compositional nature of the data, within-sample diversity, and the presence of a high number of unobserved species. These factors can lead to inaccurate correlation estimates. To tackle these challenges, we employ simulated data to demonstrate how many of these issues can be mitigated by applying typical transformations designed for compositional data. These transformations enable the use of straightforward measures like Pearson’s correlation to correctly identify positive and negative relationships among relative abundances, especially in high-dimensional data, without having any need for further corrections. However, some challenges persist, such as addressing data sparsity, as neglecting this aspect can result in an underestimation of negative correlations.
Stabilization of AMPK/PFKL/RPIA in the Glycolytic Bodies Transduces IL6/STAT3 Signal in Hepatocarcinogenesis
Authors: Hsiao He-Yun , Cheng Chun-Chia , Chou Yu-Ting , Kuo Cheng-Chin , Wang Wen-Ching , Sampurna Bonifasius Putera , Wang Yi-Wen , Hsiao Chun-Ling , Wu Jing-Yiing , Lin Kuan-Hao , Yang Wan-Yu , Lin Yu-Hsuan , Gwee Kong-Huai , Wang Horng-Dar , Yuh Chiou-Hwa 
Published: March 2024

AbstractMetabolic reprogramming is a pivotal characteristic of cancer, yet the intricate interplay between glycolysis and the pentose phosphate pathway (PPP) remains elusive. This study unveils the pivotal role of 6-phosphofructokinase liver type (PFKL) in glycolysis and ribose 5-phosphate isomerase A (RPIA) in PPP, orchestrating liver tumorigenesis. PFKL, the rate-limiting enzyme in glycolysis, stabilizes RPIA by impeding ubiquitination/proteasome activity. The pro-inflammatory and tumor cytokine interleukin 6 activates pSTAT3 which binds to the promoter region and activates AMPK and PFKL transcription. Furthermore, pAMPK stabilizes PFKL protein by preventing proteasome degradation in hepatoma cells. Inhibiting PFKL, AMPK, and STAT3 genetically or pharmacologically can reduce glycolysis, ATP production, resulting in reduction of hepatoma cell proliferation and migration. Intriguingly, the PFKL, AMPK, RPIA, and PKM2 are co-localized in the Glycolytic body (G-body) which starts forming at chronic hepatitis, dramatically increases during active hepatitis, and the size of G-bodies becomes bigger from cirrhosis to hepatocellular carcinoma. Furthermore, using Bimolecular fluorescence complementation (BiFC) assay, we demonstrated that PFKL and RPIA direct interacts. Targeting AMPK or STAT3 significantly reduced tumor formation and lipid accumulation in zebrafish models, suggesting the STAT3/AMPK/PFKL axis as a potential therapeutic avenue for liver cancer treatment.
Student Cognitive Enhancement with Non-Prescribed Modafinil. Is it Cheating?
Authors: Kesta Alexia , Newton Philip M. 
Published: March 2024

AbstractModafinil, a prescription-only drug, it is mainly used to treat narcolepsy and sleep disorders, but it is also used, without a prescription, as a cognitive enhancer by ∼10% of UK University students. Previous research has focused on the prevalence of, and motivations for, these behaviours. Here we focused specifically on determining whether students view this behaviour as cheating. We used a scenario-based approach to quantify, and qualitatively understand, student views on this topic. Most students did not view this behaviour as cheating, in part due to similarities with freely available stimulants such as caffeine, and a view that cognitive enhancement does not confer new knowledge or understanding. Although a minority of students did view it as cheating, they also expressed strong views, based in part on basic questions of fairness and access. Few students did not have a view either way. These views remained largely unchanged even when presented with considerations of other moderators of the ethics of cognitive enhancement with modafinil.
Assessment of Stiffness-Dependent Autophagosome Formation and Apoptosis in Embryonal Rhabdomyosarcoma Tumor Cells
Authors: Sezen Serap , Adiguzel Sevin , Zareour Atefeh , Khosravi Arezoo , Gordon Joseph W , Ghavami Saeid , Zarrabi Ali 
Published: March 2024

Summary/AbstractRemodeling of the extracellular matrix (ECM) eventually causes the stiffening of tumors and changes to the microenvironment. The stiffening alters the biological processes in cancer cells due to altered signaling through cell surface receptors. Autophagy, a key catabolic process in normal and cancer cells, is thought to be involved in mechano-transduction and the level of autophagy is probably stiffness-dependent. Here, we provide a methodology to study the effect of matrix stiffness on autophagy in embryonal rhabdomyosarcoma cells. To mimic stiffness, we seeded cells on GelMA hydrogel matrices with defined stiffness and evaluated autophagy-related endpoints. We also evaluated autophagy dependent pathways, apoptosis, and cell viability. Specifically, we utilized immunocytochemistry and confocal microscopy to track autophagosome formation through LC3 lipidation. This approach suggests that the use GelMA hydrogels with defined stiffness represent a novel method to evaluate the role of autophagy in embryonal rhabdomyosarcoma and other cancer cells.Workflow
LHP1 and INO80 cooperate with ethylene signaling for warm ambient temperature response by activating specific bivalent genes
Authors: Shao Zhengyao , Bai Yanan , Huq Enamul , Qiao Hong 
Published: March 2024

AbstractEthylene signaling has been indicated as a potential positive regulator of plant warm ambient temperature response but its underlying molecular mechanisms are largely unknown. Here, we show that LHP1 and INO80 cooperate with ethylene signaling for warm ambient temperature response by activating specific bivalent genes. We found that the presence of warm ambient temperature activates ethylene signaling through EIN2 and EIN3, leading to an interaction between LHP1 and accumulated EIN2-C to co-regulate a subset of LHP1-bound genes marked by H3K27me3 and H3K4me3 bivalency. Furthermore, we demonstrate that INO80 is recruited to bivalent genes by interacting with EIN2-C and EIN3, promoting H3K4me3 enrichment and facilitating transcriptional activation in response to warm ambient temperature. Together, our findings illustrate a novel mechanism wherein ethylene signaling orchestrates LHP1 and INO80 to regulate warm ambient temperature response through activating specific bivalent genes in Arabidopsis.
Time-course transcriptome data of silk glands in day 0–7 last-instar larvae ofBombyx mori(w1 pndstrain)
Authors: Masuoka Yudai , Jouraku Akiya , Tsubota Takuya , Ono Hiromasa , Chiba Hirokazu , Sezutsu Hideki , Bono Hidemasa , Yokoi Kakeru 
Published: March 2024

AbstractTime-course transcriptome expression data were constructed for four parts of the silk gland (anterior, middle, and posterior parts of the middle silk gland, along with the posterior silk gland) in the domestic silkworm,Bombyx mori, from days 0 to 7 of the last-instar larvae. For sample preparation, silk glands were extracted from one female and one male larva every 24 hours accurately after the fourth ecdysis. The reliability of these transcriptome data was confirmed by comparing the transcripts per million (TPM) values of the silk gene and quantitative reverse transcription PCR results. Hierarchical cluster analysis results supported the reliability of transcriptome data. These data are likely to contribute to the progress in molecular biology and genetic research usingB. mori, such as elucidating the mechanism underlying the massive production of silk proteins, conducting entomological research using a meta-analysis as a model for lepidopteran insect species, and exploring medical research usingB. morias a model for disease species by utilising transcriptome data.
Toxic eburicol accumulation drives the antifungal activity of azoles againstAspergillus fumigatus
Authors: Elsaman Hesham , Golubtsov Evgeny , Brazil Sean , Ng Natanya , Klugherz Isabel , Dichtl Karl , Müller Christoph , Wagener Johannes 
Published: March 2024

ABSTRACTAzole antifungals inhibit the sterol C14-demethylase (CYP51/Erg11), a key enzyme in the ergosterol biosynthesis pathway. They have fungistatic effects against yeasts but fungicidal effects against molds. The molecular basis for this difference remained unknown. The sequence of enzymatic steps required for ergosterol biosynthesis is different in yeasts and molds. Here we show that the azole-induced synthesis of fungicidal cell wall carbohydrate patches in the pathogenic moldAspergillus fumigatusstrictly correlates with the accumulation of the CYP51 substrate eburicol. A lack of other essential ergosterol biosynthesis enzymes, such as sterol C24-methyltransferase (Erg6A), squalene synthase (Erg9) or squalene epoxidase (Erg1) does not result in comparable cell wall alterations. Partial repression of Erg6A, which converts lanosterol into eburicol, increases azole resistance. The sterol C5-desaturase (ERG3)-dependent conversion of eburicol into 14-methylergosta-8,24(28)-dien-3β,6α-diol, the “toxic diol” responsible for the antifungal effects of azoles in yeasts, is not required for the fungicidal effects inA. fumigatus. In contrast to yeast, where a lack of ERG3 functionality causes azole resistance,A. fumigatuslacking ERG3 becomes more azole susceptible. Mutants lacking mitochondrial complex III functionality, which are less susceptible to the fungicidal effects of azoles, but get strongly inhibited in growth, convert eburicol much more efficiently into the supposedly “toxic diol”. Our results support a mechanistic model where the mode of action of azoles against the pathogenic moldA. fumigatus, other than in yeast, relies on the accumulation of eburicol which exerts fungicidal effects by triggering the formation of cell wall carbohydrate patches.
Trabectedin Enhances Oncolytic Virotherapy by Reducing Barriers to Virus Spread and Cytotoxic Immunity in Preclinical Pediatric Bone Sarcoma
Authors: Ringwalt Emily M. , Currier Mark A. , Glaspell Andrea M. , Chen Chun-Yu , Cannon Matthew V. , Cam Maren , Gross Amy C. , Gust Matthew , Wang Pin-Yi , Boon Louis , Biederman Laura E. , Schwarz Emily , Rajappa Prajwal , Lee Dean A. , Mardis Elaine R. , Carson William E. , Roberts Ryan D. , Cripe Timothy P. 
Published: March 2024

AbstractWe previously reported that the DNA alkylator and transcriptional-blocking chemotherapeutic agent trabectedin enhances oncolytic herpes simplex viroimmunotherapy in human sarcoma xenograft models, though the mechanism remained to be elucidated. Here we report trabectedin disrupts the intrinsic cellular anti-viral response which increases viral transcript spread throughout the human tumor cells. We also extended our synergy findings to syngeneic murine sarcoma models, which are poorly susceptible to virus infection. In the absence of robust virus replication, we found trabectedin enhanced viroimmunotherapy efficacy by reducing immunosuppressive macrophages and stimulating granzyme expression in infiltrating T and NK cells to cause immune-mediated tumor regressions. Thus, trabectedin enhances both the direct virus-mediated killing of tumor cells and the viral-induced activation of cytotoxic effector lymphocytes to cause tumor regressions across models. Our data provide a strong rationale for clinical translation as both mechanisms should be simultaneously active in human patients.
Two PYRIDOXAL PHOSPHATE HOMEOSTASIS PROTEINs are essential for management of the coenzyme in plants
Authors: Farkas Peter , Fitzpatrick Teresa B. 
Published: March 2024

ABSTRACTCoenzyme management is believed to be important for the required pool of active enzymes driving metabolic routes to facilitate homeostasis and match environmental circumstance. The coenzyme pyridoxal 5’-phosphate (PLP) (a vitamin B6derivative) is involved in a diverse array of enzyme reactions spanning amino acid to hormone metabolism. However, dedicated proteins that contribute to PLP homeostasis have not yet been studied in plants. Here we demonstrate the importance of proteins annotated PLP HOMEOSTASIS PROTEINs (PLPHPs) for control of PLP in Arabidopsis. A systematic analysis indicates that while most kingdoms have a singlePLPHPhomolog, Angiosperms within the plant kingdom have two. PLPHPs from Arabidopsis bind PLP and exist as monomers in solution in contrast to reported PLP-dependent enzymes from all kingdoms. Disrupting functionality of both homologs perturbs vitamin B6content including a PLP deficit accompanied by impaired and light hypersensitive root growth, unlike biosynthesis mutants. Micrografting studies show that the PLP deficit can be relieved distally between shoots and roots. Yet, supplementation experiments do not restore vitamin B6homeostasis in the absence of PLPHP. A series of chemical treatments probing PLP-dependent reactions, notably those for auxin and ethylene, provide evidence that the physiological role of PLPHPs is dynamic management of PLP. Assays in vitro show that Arabidopsis PLPHP can coordinate both PLP transfer and withdrawal. This study expands our broader knowledge of vitamin B6biology and highlights the importance of PLP coenzyme homeostasis in plants, providing a platform for further investigations in boosting adaptive responses.One sentence summaryPLPHPs contribute to surveillance of vitamin B6homeostasis, likely acting as a rheostat in adaptive responses as a function of the use of the coenzyme PLP.
Yellow Fever Emergence: Role of Heterologous Flavivirus Immunity in Preventing Urban Transmission
Authors: Shinde Divya P. , Plante Jessica A. , Scharton Dionna , Mitchell Brooke , Walker Jordyn , Azar Sasha R. , Campos Rafael K. , Sacchetto Lívia , Drumond Betânia P. , Vasilakis Nikos , Plante Kenneth S. , Weaver Scott C. 
Published: March 2024

AbstractDuring major, recent yellow fever (YF) epidemics in Brazil, human cases were attributed only to spillover infections from sylvatic transmission with no evidence of human amplification. Furthermore, the historic absence of YF in Asia, despite abundant peridomesticAedes aegyptiand naive human populations, represents a longstanding enigma. We tested the hypothesis that immunity from dengue (DENV) and Zika (ZIKV) flaviviruses limits YF virus (YFV) viremia and transmission byAe. aegypti. Prior DENV and ZIKV immunity consistently suppressed YFV viremia in experimentally infected macaques, leading to reductions inAe. aegyptiinfection when mosquitoes were fed on infected animals. These results indicate that, in DENV- and ZIKV-endemic regions such as South America and Asia, flavivirus immunity suppresses YFV human amplification potential, reducing the risk of urban outbreaks.One-Sentence SummaryImmunity from dengue and Zika viruses suppresses yellow fever viremia, preventing infection of mosquitoes and reducing the risk of epidemics.
“I can almost recognize its voice”: AI and its impact on ethical teacher-centaur labor
Authors: Fassbender William Joseph 
Published: March 2024

Purpose
This study builds on previous theoretical work that considered artificial intelligence (AI) and its potential for creating “teacher-centaurs” whose labor could be accelerated through the use of generative AI (Fassbender, in review). The purpose of this paper is to use empirical methods to study centaur teachers and the division of labor (Durkheim, 1893/2013) that arise from outsourcing teaching tasks to AI.

Design/methodology/approach
Multiple case study (Stake, 2006) was used to collect data on two secondary English teachers who were early adopters of generative AI. Data included semi-structured interviews as well as ChatGPT chat logs, which helped in describing how teaching approaches evolved using AI technology.

Findings
Results showed that teachers used AI for planning, instruction and assessment. AI-augmented teaching practices allowed teachers to complete tasks with greater speed, which in turn increased stamina and short-term work–life balance. Given the novelty of AI, concerns about data privacy and academic integrity raised ethical questions.

Originality/value
ChatGPT’s rise to popularity in 2023 brought with it significant discussions about education, specifically how students would use AI primarily as a tool for plagiarism. This study takes a different focus, considering how early adoption of AI has begun changing teacher labor, offering implications for the future of the teaching profession.
The impact of environmental, social and governance (ESG) reporting on corporate profitability: evidence from Thailand
Authors: Treepongkaruna Sirimon , Suttipun Muttanachai 
Published: March 2024

Purpose
The United Nations' sustainable development goals (SDGs) put together a global framework in an attempt to address environmental, social and governance (ESG) concerns. Measuring a company’s contribution to the SDGs relies heavily on ESG reporting. This paper aims to examine the impact of ESG reporting on the corporate profitability of listed companies in Thailand over the period of 2019–2021.

Design/methodology/approach
Using 147 listed firms in the ESG group, content analysis was used to quantify the ESG reporting (within 11 themes), while corporate profitability was measured by return on asset and return on equity. Descriptive analysis, correlation matrix and panel regression are used to analyze the data of this study.

Findings
Consistent with the legitimacy, stakeholder and signaling theories, the authors found a statistically significant and positive impact of ESG reporting on corporate profitability in Thailand.

Originality/value
The findings highlight the importance of incorporating ESG considerations into companies’ reporting and decision-making processes, as these can enhance firm profitability and performance, attract stakeholders, improve their competitive advantage and step toward sustainability.