bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polyphosphate: The “Dark Matter” of Bacterial Chromatin Structure
Authors: Racki Lisa R. , Freddolino Lydia 
Published: February 2025

ABSTRACTPolyphosphate (polyP), broadly defined, consists of a chain of orthophosphate units connected by phosphoanhydride bonds. PolyP is the only universal inorganic biopolymer known to date and is present in all three domains of life. At a first approximation polyP appears to be a simple, featureless, and flexible polyanion. A growing body of evidence suggests that polyP is not as featureless as originally thought: it can form a wide variety of complexes and condensates through association with proteins, nucleic acids, and inorganic ions. It is becoming apparent that the emergent properties of the condensate superstructures it forms are both complex and dynamic. Importantly, growing evidence suggests that polyP can affect bacterial chromatin, both directly and by mediating interactions between DNA and proteins. In an increasing number of contexts, it is becoming apparent that polyP profoundly impacts both chromosomal structure and gene regulation in bacteria, thus serving as a rarely considered, but highly important, component in bacterial nucleoid biology.
CD8+ Regulatory T Cells Induced by Peptide Vaccination Ameliorates Experimental Model of Membranous Nephropathy
Authors: Chung Edmund Y. M. , Wang Yuan Min , Shaw Karli , Ronning Emily , Wang Ya , Zhang Geoff Yu , Hu Min , Keung Karen , McCarthy Hugh J. , Harris David C. H. , Stephen Alexander 
Published: February 2025

ABSTRACTAimCD8+ regulatory T cells (Tregs) are cross‐protective across multiple animal models of autoimmunity. Recently, specific peptides from a yeast‐peptide‐major histocompatibility complex library that expanded CD8+ Tregs in murine experimental multiple sclerosis were reported. Whether these peptides also expand CD8+ Tregs and protect against Heymann nephritis (HN), an experimental model of membranous nephropathy is unknown. We aimed to assess the efficacy of peptide vaccination to induce CD8+ Tregs in HN.MethodsLewis rats were immunised with Fx1A/complete Freund's adjuvant to induce HN and received peptide vaccination 1 week before (prevention vaccination) or 1 week after disease induction (treatment vaccination). To understand whether the effect of peptide vaccination was mediated by CD8+ Tregs, we adoptively transferred CD8+ T cells 1 week after peptide vaccination into HN rats.ResultsPrevention vaccination, but not treatment vaccination, significantly reduced anti‐Fx1A autoantibody levels and serum creatinine. Both prevention and treatment vaccination reduced histological kidney injury. mRNA expression of Helios, the major CD8+ Treg transcription factor, was upregulated in both the spleen and kidney with prevention vaccination and in the kidney with treatment vaccination. Adoptive transfer of CD8+ T cells after peptide vaccination significantly reduced serum creatinine, proteinuria, histological kidney injury, anti‐Fx1A autoantibody levels, germinal centre formation, and mRNA expression of markers of T follicular helper cells (Bcl6, interleukin‐21), T helper 1 cells (interferon‐γ, Tbet) and T helper 17 cells (interleukin‐6, interleukin‐17).ConclusionsPeptide vaccination induces CD8+ Tregs that ameliorate induction of experimental membranous nephropathy which may represent a further peripheral regulation of autoimmunity.
Polyploidization leads to salt stress resilience via ethylene signaling in citrus plants
Authors: Song Xin , Zhang Miao , Wang Ting‐Ting , Duan Yao‐Yuan , Ren Jie , Gao Hu , Fan Yan‐Jie , Xia Qiang‐Ming , Cao Hui‐Xiang , Xie Kai‐Dong , Wu Xiao‐Meng , Zhang Fei , Zhang Si‐Qi , Huang Ying , Boualem Adnane , Bendahmane Abdelhafid , Tan Feng‐Quan , Guo Wen‐Wu 
Published: February 2025

Summary
Polyploidization is a common occurrence in the evolutionary history of flowering plants, significantly contributing to their adaptability and diversity. However, the molecular mechanisms behind these adaptive advantages are not well understood.
Through comprehensive phenotyping of diploid and tetraploid clones from Citrus and Poncirus genera, we discovered that genome doubling significantly enhances salt stress resilience. Epigenetic and transcriptomic analyses revealed that increased ethylene production in the roots of tetraploid plants was associated with hypomethylation and enhanced chromatin accessibility of the ACO1 gene. This increased ethylene production activates the transcription of reactive oxygen species scavenging genes and stress‐related hormone biosynthesis genes. Consequently, tetraploid plants exhibited superior root functionality under salt stress, maintaining improved cytosolic K+/Na+ homeostasis.
To genetically validate the link between salt stress resilience and ACO1 expression, we generated overexpression and knockout lines, confirming the central role of ACO1 expression regulation following genome doubling in salt stress resilience.
Our work elucidates the molecular mechanisms underlying the role of genome doubling in stress resilience. We also highlight the importance of chromatin dynamics in fine‐tuning ethylene gene expression and activating salt stress resilience pathways, offering valuable insights into plant adaptation and crop genome evolution.
Factor Models With Sparse Vector Autoregressive Idiosyncratic Components
Authors: Krampe Jonas , Margaritella Luca 
Published: February 2025

ABSTRACTWe reconcile dense and sparse modelling by exploiting the positive aspects of both. We employ a high‐dimensional, approximate static factor model and assume the idiosyncratic term follows a sparse vector autoregressive model (VAR). The estimation is articulated in two steps: (i) factors and loadings are estimated via principal component analysis (PCA); (ii) a sparse VAR is estimated via the lasso on the estimated idiosyncratic components from (i). Step (ii) allows to model cross‐sectional and time dependence left after the factors estimation. We prove the consistency of this approach as the time and cross‐sectional dimensions diverge. In (ii), sparsity is allowed to be very general: approximate, row‐wise, and growing with the sample size. However, the estimation error of (i) needs to be accounted for. Instead of simply plugging‐in the standard rates derived for the PCA estimation of the factors in (i), we derive a refined expression of the error, which enables us to derive tighter rates for the lasso in (ii). We discuss applications on forecasting & factor‐augmented regression and present an empirical application on macroeconomic forecasting using the Federal Reserve Economic Data ‐ Monthly Database (FRED‐MD).
Generation of suspension cell cultures with high syringin content and anti‐inflammatory activity through overexpressing glycotransferase SiUGT72BZ2 in Saussurea involucrata
Authors: Xu Yue , Cao Yingping , Tie Fangfang , Kong Xiuya , Liu Yuchen , Zhang Yaru , Guan Wenna , Hu Na , Wang Honglun , Qin Xiaochun , Wu Zhenying , Fu Chunxiang 
Published: February 2025

SummaryThe snow lotus species Saussurea involucrata (Kar. & Kir.) Sch.Bip., an endangered traditional Chinese herb, belongs to a genus of the Asteraceae family. Syringin present in S. involucrata stands as one of the predominant bioactive compounds. However, the biosynthetic pathway of syringin remains largely elusive. Here, S. involucrata suspension cell culture was subjected to methyl jasmonate (MeJA) treatment, which stimulated the synthesis of syringin, increasing its content by up to 3.9‐fold. Comparative transcriptome analysis revealed that genes involved in syringin biosynthesis were generally upregulated in response to MeJA. Furthermore, two candidate UDP‐glycosyltransferase genes, SiUGT72BZ2 and SiUGT72CY1, were identified through phylogenetic tree and expression profiling analyses. Overexpression of SiUGT72BZ2 (BZ2_OE) and SiUGT72CY1 (CY1_OE) in S. involucrata suspension cell cultures led to 15.2‐ and 5.9‐fold higher syringin levels than empty vector control cultures, respectively. Notably, upregulation of SiUGT72BZ2 enhanced the biosynthesis of coniferin as well. In contrast, only trace amounts of coniferin were present in control and CY1_OE cell cultures. Subsequent anti‐inflammatory assays using lipopolysaccharide (LPS)‐stimulated RAW264.7 cells demonstrated that the extracts from these cell cultures possessed remarkable anti‐inflammatory properties. Most strikingly, the BZ2_OE cultures exhibited superior anti‐inflammatory effects compared to the control and CY1_OE. In conclusion, our research has not only identified the key enzymes in syringin synthesis but also, through genetic engineering, has generated novel cell culture resources enriched with syringin and coniferin, and enhanced anti‐inflammatory activities, highlighting the potential of S. involucrata cell culture as an alternative for wild snow lotus resources.
Impact of Dietary Habits, Physical Activity, and Perceived Health Status on Health‐Related Quality of Life by Household Characteristics of Patients With Chronic Diseases: The Korea Community Health Survey (KCHS)
Authors: Kang Soyean , Sagong Hae , Lee Juyoung 
Published: February 2025

ABSTRACTBackgroundModern societies are seeing a steady rise in individuals living alone. This study examines the impact of dietary habits, physical activity, and perceived health status on the health‐related quality of life (QoL) of adults aged 40 and older with chronic diseases, comparing living‐alone households to multi‐person households.MethodsData from the 2022 Korean Community Health Survey, including 65,861 respondents, were analyzed. The analysis utilized the Rao‐Scott χ2 test, independent t‐test, and multiple logistic regression with a complex sample design to assess differences in variables affecting QoL by household type.ResultsIndividuals living alone were more likely to be female, older, less educated, economically inactive, divorced or separated, and have lower household incomes compared to those in multi‐person households. Physical activity, perceived health status, and QoL were higher in multi‐person households. Although all variables influenced QoL in multi‐person households, nutritional labeling awareness and frequency of physical activity showed no significant association with QoL in living‐alone households.ConclusionLiving‐alone households with chronic diseases face notable demographic disparities. Additional research is needed to understand why nutritional labeling awareness and physical activity frequency do not significantly affect QoL in this group. The influence of mental health warrants further investigation to guide targeted interventions.
Nitrogen Deficiency Accelerates Rice Leaf Senescence Through ABA Signaling and Sugar Metabolic Shifts
Authors: Asad Muhmmad Asad Ullah , Guan Xianyue , Zhang Yan , Zhou Lujian , Bartas Martin , Ullah Najeeb , Zhou Weijun , Cheng Fangmin 
Published: February 2025

AbstractNitrogen (N) deficiency is one of the critical factors that induce leaf senescence by integrating with abscisic acid (ABA) metabolism, which results in a shortened leaf photosynthetic period and markedly lowered grain yield. However, the metabolic pathway by which ABA signaling participates in the regulation of senescence‐associated change in sugar metabolism and its relationship with N allocation in plant tissues are not well understood. In this paper, the effect of supply level on leaf C/N allocation and its relation to ABA signalling, sugar metabolism, and N assimilation were investigated by using two rice genotypes subjected to four N treatments. Results indicated that N‐deficiency markedly induced PYR1‐like (PYL) expression and ABA biosynthesis, consequently leading to the activation of ABA signaling. The increased ABA concentration in leaf tissues triggered the catabolic pathways of sugar and N metabolisms, resulting in the reduced photosynthetic pigments and intensified oxidative damage in N‐deficient leaves. ABA signaling induced by N‐deficiency upregulates the expression of senescence‐associated genes (SAGs) and C/N allocation by mediating several senescence‐promoting factors, such as NAC, bZIP, and WRKY TFs, along with the suppression of PP2Cs. Therefore, N‐deficiency impairs chlorophyll biosynthesis and triggers chlorophyll degradation to accelerate the timing and rate of leaf senescence. This metabolic network could provide helpful information for understanding the regulatory mechanism of leaf senescence in relation to sugar signaling, N‐assimilation and N‐use efficiency.
ECT8, an mRNA m6A reader, enhances salt stress tolerance by modulating mRNA stability in Arabidopsis
Authors: Nguyen Thi Kim Hang , Amara Umme , Kang Hunseung 
Published: February 2025

AbstractN6‐methyladenosine (m6A), the most prevalent modification found in eukaryotic mRNAs, is recognized and interpreted by m6A‐binding proteins called m6A readers.The EVOLUTIONARILY CONSERVED C‐TERMINAL REGION (ECT) proteins have increasingly been identified as m6A readers in plants. A recent study has demonstrated that the loss‐of‐function ect8 mutant is sensitive to salt stress by enhancing the stability of negative salt stress regulators in Arabidopsis (Arabidopsis thaliana). In this study, we generated and analyzed the ECT8‐overexpressing transgenic Arabidopsis plants to further explore the function of ECT8 in salt stress response. The electrophoretic mobility shift assay in vitro showed that ECT8 binds to the m6A‐modified synthetic RNAs, preferring UGUm6AA and UACm6AGA motifs over the GGm6ACU motif. Contrary to the ect8 mutant exhibiting salt hypersensitivity by enhancing the stability of salt stress negative regulators, the ECT8‐overexpressing transgenic Arabidopsis plants displayed salt tolerance by increasing the stability and expression levels of salt stress positive regulators. Moreover, RNA‐immunoprecipitation assay demonstrated that ECT8 binds to the m6A‐modified salt stress‐responsive mRNAs in planta. Collectively, our current and previous findings highlight that ECT8‐mediated stabilization and destabilization of the genes encoding salt stress positive or negative regulators, respectively, contribute to the salt stress tolerance of Arabidopsis.
Simulation model to estimate the burden of disease due to hepatitis E virus in Dutch pig meat and cost‐effectiveness of control measures
Authors: Focker M. , van Wagenberg C. P. A. , van Asseldonk M. A. P. M. , Boxman I. L. A. , Hakze ‐ van der Honing R. W. , van Asselt E. D. 
Published: February 2025

AbstractHepatitis E virus (HEV) can lead to liver disease in humans. In the Netherlands, the consumption of pig meat is thought to be the main contributor to the total burden of disease caused by HEV. In this study, the number of cases and lost disability‐adjusted‐life‐years (DALYs) due to HEV in pig meat were estimated by simulating HEV through the pig supply chain, including the farm, transport, lairage, slaughtering, processing, and consumption stages. The first four stages were modeled using a susceptible‐exposed‐infected‐recovered (SEIR) model. For the last two stages, pig meat and liver products were divided into six product categories commonly consumed by Dutch consumers. Depending on the product category, different ways of heating and storing, leading to the reduction of infectious HEV genome copies, were assumed. Furthermore, the model was challenged by four selected control options at the pig farm: the cleaning of driving boards, the use of predatory flies, the use of rubber mats, and the vaccination of finishing pigs. Finally, the cost‐effectiveness of these control measures was estimated by estimating the costs per avoided DALY. For the baseline situation, it was estimated that HEV in pig meat would lead to 70 cases and 21 DALYs per year. All control measures led to a decreased number of DALYs, with vaccination leading to the largest decrease: five DALYs per year. However, the costs per avoided DALY ranged from €0.5 to €7.5 million, making none of the control measures cost‐effective unless the control measures are also effective against other pathogens.
Evaluation of T‐cell repertoire by flow cytometric analysis in primary immunodeficiencies with DNA repair defects
Authors: Karaaslan Betul Gemici , Demirkale Zeynep Hizli , Turan Isilay , Aydemir Sezin , Meric Zeynep , Taskin Zuleyha , Kilinc Ozgur Can , Burtecene Nihan , Topcu Birol , Yucel Esra , Aydogmus Cigdem , Cokugras Haluk , Kiykim Ayca 
Published: February 2025

AbstractThe group of patients with DNA‐repair‐defects increases susceptibility to infections due to impaired repertoire diversity. In this context, we aimed to investigate the TCRvβ‐repertoire by flow cytometric analysis and its correlation with clinical entities in a group of IEI patients with DNA repair defects. Peripheral lymphocyte subset and TCRvβ‐repertoire analyses were performed by flow cytometric analysis. The aim was to explore the changing TCR‐Vβ‐repertoire that can predict some clinical entities by investigating the repertoire using flow‐cytometric‐analysis‐based TCR‐Vβ and its interaction with clinical entities in a group of IEI patients with DNA repair defects. TCR‐repertoire of the patients with DNA‐repair‐defects and healthy controls was analysed with flow‐cytometer. The potential of flow‐cytometric analysis of the TCR repertoire as a practical and easily accessible clinical prediction method was investigated. Thirty‐nine‐IEI patients with DNA‐repair‐defects and 15 age‐matched healthy‐controls were included in this study. Peripheral lymphocyte subset and TCR‐Vβ repertoire analyses were performed by flow cytometry. Compared to the control group, 9 out of 24 clones (37.5%) exhibited a statistically significant reduction, while only 3 clones showed a statistically significant increase (p < 0.05). Preferential use of vβ‐genes was associated with some clinical entities. Lower TCR‐vβ‐9 and TCR‐vβ23, higher TCR‐vβ7.2 were found in the patients with pneumonia (n = 13) (p = 0.018, p = 0.044 p = 0.032). AT patients with pneumonia had lower TCR‐vβ‐9 clone than patients without pneumonia (p = 0.008). Skewed proliferation of most TCR‐vβ clones was seen DNA‐repair‐defects, especially AT. In addition, this study showed that preferential use of TCR‐vβ genes could be predictive for some clinical entities.
Between space, relational sociology, and Lefebvre's critique of modernity: An understanding of relational spatiality in trans‐actional perspective
Authors: Fu Yongxuan 
Published: February 2025

AbstractAlthough the ongoing Lefebvre renaissance has recently generated interest in many areas of sociology, contemporary relational sociology has not specifically considered Lefebvre's potential contribution to it. The article introduces a concept of relational spatiality based on the epistemology of relational sociology by reconsidering Lefebvre's inquiry into modernity and space. The article first briefly explains Lefebvre's epistemological critique of modernity, including everyday life and space, and then constructs the relational spatiality by combining Lefebvre with the relational and processual viewpoints of relational sociology. The article accordingly characterizes relational spatiality by combining Lefebvre's critique of “abstract space” as a crucial case with the de‐reification of relational sociology. At last, we further explore the trans‐actional perspective of relational sociology to motivate the deep relationalist understanding of space. From the “inter‐actional” premise to “trans‐actional” processes, relational spatiality reveals and avoids the underlying abstract purification, substantialism, and dualism in the analysis and cognition of space. We hope to lead sociologists to recognize that space involves a relational‐sociological concept constantly produced, functioned, and emerging through iterative trans‐actions rather than an objective entity or geographical premise waiting to be influenced by society, demonstrating the possibility of a spatial epistemology based on relational sociology.
Seizures and Lung Lesions in a Solid Organ Transplant Recipient: Bringing Things Together
Authors: Roberts Matthew B. , Coussement Julien , Lebeaux David , Coates P. Toby , Clemente Wanessa Trindade 
Published: February 2025

ABSTRACTA 28‐year‐old male presented to an Australian hospital with sudden‐onset headache and seizure following a kidney transplant for end‐stage renal disease due to IgA nephropathy. Clinical approach to the cases and management of the diagnosed disease are discussed.
Genome editing, an opportunity to revive soybean cultivation in Europe
Authors: Monfort Manon , Buitink Julia , Roeber Frank , Nogué Fabien 
Published: February 2025

SUMMARYSoybean (Glycine max Merr.) is the world's most important oilseed crop and its ability to fix atmospheric nitrogen makes it a cornerstone of sustainable agriculture. Despite its importance, Europe relies heavily on imports, leading to environmental and economic vulnerabilities. To address these challenges, the European Union has implemented policies to boost local soybean production, emphasizing sustainable practices and reduced dependency on imports. However, conventional breeding methods are time‐consuming and may not keep pace with the rapid environmental and consumer habit changes. Genome‐editing technologies, such as CRISPR‐Cas, offer precise and efficient tools for developing soybean varieties tailored to European conditions. These technologies can enhance traits related to precocity, stress responses, yield and quality that are essential for adapting to climate change and promoting ecological sustainability. This review explores the integration of genome editing (GE) in soybean breeding, highlighting its potential in advancing the agroecological transition in Europe. By having a clear regulation and enhancing breeding efforts, GE can significantly contribute to developing resilient and sustainable soybean varieties, fostering a competitive and environmentally friendly European agriculture.