bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distribution and functional analysis of two types of quorum sensing gene pairs, glaI1/glaR1 and glaI2/glaR2, in Burkholderia gladioli
Authors: Takita Kazumi , Someya Nobutaka , Morohoshi Tomohiro 
Published: January 2025

Abstract
Burkholderia gladioli produces a yellow-pigmented toxin called toxoflavin, and causes disease on a variety of plants. Previous studies have suggested that the pathogenicity of B. gladioli is regulated by an N-acyl-l-homoserine lactone (AHL)-mediated quorum sensing (QS) system. In this study, complete genome sequencing revealed that B. gladioli pv. gladioli MAFF 302385 possesses two types of AHL synthase and AHL receptor gene pairs: glaI1/glaR1 and glaI2/glaR2. Disruption of QS genes revealed that the glaI1/glaR1 QS system regulated swarming motility, biofilm formation, and colony formation via N-octanoyl-l-homoserine lactone. Although Escherichia coli harboring glaI2 produced N-(3-hydroxyoctanoyl)-l-homoserine lactone and N-(3-hydroxydecanoyl)-l-homoserine lactone, the expression of glaI2 was not confirmed in MAFF 302385 cells. We also found that toxoflavin production was regulated by the glaI1/glaR1 QS system in liquid medium, but not on agar medium. When pathogenicity tests were performed on gladiolus leaves, the wild-type and QS mutants showed a similar level of disease. Our results demonstrated that only the glaI1/glaR1-mediated QS system is active in MAFF 302385, but major virulence factors, especially toxoflavin, are not completely dependent on the QS system.
Aryl Hydrocarbon Receptor Activation Promotes Effector CD4+ T Cell Homeostasis and Restrains Salt-sensitive Hypertension
Authors: Molina Patrick A , Edell Claudia J , Dunaway Luke S , Kellum Cailin E , Muir Rachel Q , Jennings Melissa S , Colson Jackson C , De Miguel Carmen , Rhoads Megan K , Buzzelli Ashlyn A , Harrington Laurie E , Meza-Perez Selene , Randall Troy D , Botta Davide , Müller Dominik N , Pollock David M , Maynard Craig L , Pollock Jennifer S 
Published: January 2025

Abstract
Excess dietary salt and salt-sensitivity contribute to cardiovascular disease. Distinct T cell phenotypic responses to high salt and hypertension as well as influences from environmental cues are not well understood. The aryl hydrocarbon receptor (AhR) is activated by dietary ligands, promoting T cell and systemic homeostasis. We hypothesized that activating AhR supports CD4+ homeostatic functions, such as cytokine production and mobilization, in response to high salt intake while mitigating salt-sensitive hypertension. In the intestinal mucosa, we demonstrate that a high salt diet (HSD) is a key driving factor, independent of hypertension, in diminishing interleukin 17A (IL-17A) production by CD4+ T (Th17) cells without disrupting circulating cytokines associated with Th17 function. Previous studies suggest that hypertensive patients and individuals on a high salt diet are deficient in AhR ligands or agonistic metabolites. We found that activating AhR augments Th17 cells during experimental salt-sensitive hypertension. Further, we demonstrate that activating AhR in vitro contributes to sustaining Th17 cells in the setting of excess salt. Using photoconvertible Kikume GreenRed mice, we also revealed that HSD drives CD4+ T cell mobilization. Next, we found that excess salt augments T cell mobilization markers, validating HSD-driven T cell migration. Also, we found that activating AhR mitigates HSD-induced T cell migration markers. Using telemetry in a model of experimental salt-sensitivity, we found that activating AhR prevents the development of salt-sensitive hypertension. Collectively, stimulating AhR through dietary ligands facilitates immunologic and systemic functions amid excess salt intake and restrains the development of salt-sensitive hypertension.
Assessment of the environmental impacts of soybean production within fields in Madhya Pradesh: a life cycle analysis approach
Authors: Khangar Nihal Singh , Thangavel Mohanasundari 
Published: January 2025

Abstract
Soybean is a versatile crop that can be used as an oilseed or food crop. Increasing soybean production is beneficial to agricultural economies, but significant concerns have been raised about its environmental impacts. This study evaluates the environmental footprint of soybean production using life cycle assessment (LCA) within the “cradle-to-gate” system in Madhya Pradesh (central India) for the first time. The analysis demonstrated that untreated residue on the ground increases the global warming potential by 19.78 kg CO2 eq ha−1 and land use emissions by 3.61 m2a crop eq ha−1. Additionally, burning residue significantly increases global warming potential by 210.80 kg CO2 eq. ha−1. Furthermore, the potential for aquatic eutrophication ranges between 0.38 and 0.80 kg N eq. and between 0.16 and 0.21 kg P eq ha−1 for marine and freshwater systems, respectively. This assessment reinforces that global warming potential, fossil resource scarcity, acidification, and land use emissions are the primary environmental concerns linked to soybean cultivation. These issues predominantly arise from fuel combustion in agricultural machinery and the application of soil nutrients throughout the production process. This investigation provides a basis for informed decision-making and the development of sustainable practices to balance the agricultural significance of soybean with environmental considerations.
Research on pavement maintenance planning using reinforcement learning
Authors: Li Hui , Wang Shuo , Pan Jie , Shan Fei , Jiang Yuzhe , Zhang Haopeng , Dai Zhenhua , Shi Qingjiang 
Published: January 2025

Abstract
A mature theoretical model is an integral component of pavement management systems. Typically, such models encompass pavement performance prediction, cost–benefit analysis of maintenance measures, and decision-making frameworks for maintenance strategies. This paper primarily investigates the economic analysis and decision planning aspects of pavement maintenance measures. Initially, considering greenhouse gas emissions, a comprehensive cost evaluation is conducted for three typical maintenance measures (microsurfacing, slurry sealing, and milling with overlay), encompassing carbon emission costs, delay costs, and construction costs, to establish comprehensive cost indicators for subsequent decision optimization models. Subsequently, an optimization algorithm with Clip pruning is introduced for near-end strategy optimization, along with the development of suitable evaluation functions for maintenance measure effectiveness, thereby establishing a reinforcement learning-based optimization model for pavement maintenance decisions. Regarding the model results, the costs of microsurfacing, 4 cm AC slurry seal, 4 cm SMA slurry seal, and 4 cm milling with overlay are 10 ¥(m2), 50 ¥(m2), 66 ¥(m2), and 60 ¥(m2), respectively. Furthermore, by comparing the reinforcement learning decision model developed in this study with the Q-learning algorithm, the model demonstrates a 60% improvement in convergence speed and a 20% increase in average reward.
Educate, Advocate, Act Now: a sustainable approach to combating antimicrobial resistance TODAY
Authors: Ohemu Godwin Pius , Read Carrie , Onwukwe Chimaobi David , Olorunleke Solomon Olabiyi , Mugo Noel Kambi , Charles Richard , Afegbua Seniyat Larai 
Published: January 2025

Abstract
Antimicrobial resistance (AMR) poses a great challenge to health systems all over the world. It is exacerbated by the abuse, misuse and overuse of antimicrobials in humans, animals, plants and the environment. This viewpoint emphasizes the critical need to address the challenges of AMR through an integrated, long-term approach that focuses on education, advocacy and collective action. This article stresses that the fight against AMR is not a battle for governments and scientists alone but requires engagement at every level. The article concludes that we can reduce the spread of AMR by exploring the potential of education, advocacy and collective action.
Impact of osteosarcopenia on short- and long-term outcomes in patients with gastric cancer
Authors: Kai Wataru , Takano Yasuhiro , Kobayashi Yasunobu , Kanno Hironori , Hanyu Nobuyoshi , Eto Ken 
Published: January 2025

Abstract

Backgrounds
Osteopenia and sarcopenia are associated with adverse clinical outcomes. This study investigated the impact of osteosarcopenia on short- and long-term outcomes after gastrectomy for gastric cancer.

Methods
The present study included patients who underwent gastrectomy for gastric cancer. Osteopenia was evaluated by bone mineral density measurement in the midvertebral core of the 11th thoracic vertebra on preoperative computed tomography images. Sarcopenia was evaluated by measuring the skeletal muscle cross-sectional area at the third lumbar vertebra level. Osteosarcopenia was defined as the coexistence of osteopenia and sarcopenia. We investigated the relationship of preoperative osteosarcopenia with short- and long-term outcomes after gastrectomy for gastric cancer.

Results
Of all 122 patients, 38 (31%) patients were diagnosed with osteosarcopenia. Multivariate logistic regression analysis revealed that osteosarcopenia (P = .008) was an independent risk factor for postoperative complications. Furthermore, multivariate Cox regression analysis revealed that male sex (P = .007), and osteosarcopenia (P = .038) were independent predictors of disease-free survival, while osteosarcopenia (P = .045) and pathological T stage ≥3 (P = .033) were independent predictors of overall survival.

Conclusions
Osteosarcopenia was a strong predictor of short- and long-term outcomes after gastrectomy for gastric cancer. Preoperative screening of osteosarcopenia may be helpful for better management of patients with gastric cancer.
Metastatic multicentric epithelioid angiosarcoma of bone. A case report with pitfalls. Tumor seeding after percutaneous biopsy and hypercalcemia
Authors: Fuentes-Sánchez Jorge , Pena-Burgos Eva Manuela , Tapia-Viñe Mar , Pozo-Kreilinger Jose Juan , Ortiz-Cruz Eduardo Jose 
Published: January 2025

Abstract
Angiosarcomas are a type of malignant tumor of vascular origin. They represent &lt;1% of all primary bone tumors. The multicentric or metastatic does not differ in its high aggressiveness and poor prognosis. A 72-year-old male with bone angiosarcoma initially located in proximal femur. After biopsy in a non-expert sarcoma center, he presented tumor involvement in the needle trajectory and multicentric/metastatic involvement at the sacro-coccygeal level. He associated tumoral-hypercalcemia and was referred to our sarcoma center. He was treated by tumoral resection and tumor prosthesis. In the follow-up he presented pulmonary metastasis and new implants, dying 2 months later. Multicentric or metastatic bone involvement in angiosarcomas has only theoretical relevance for their management. Biopsy should be performed in sarcoma centers due to the risk of dissemination. Although hypercalcemia in sarcomas is uncommon, we highlight its investigation.
The XMM Cluster Survey: automating the estimation of hydrostatic mass for large samples of galaxy clusters – I. Methodology, validation, and application to the SDSSRM-XCS sample
Authors: Turner D J , Giles P A , Romer A K , Pilling J , Lingard T K , Wilkinson R , Hilton M , Upsdell E W , Al-Serkal R , Cheng T , Eappen R , Rooney P J , Bhargava S , Collins C A , Mayers J , Miller C , Nichol R C , Sahlén M , Viana P T P 
Published: January 2025

ABSTRACT
We describe features of the X-ray: Generate and Analyse (xga) open-source software package that have been developed to facilitate automated hydrostatic mass ($M_{\rm hydro}$) measurements from XMM X-ray observations of clusters of galaxies. This includes describing how xga measures global, and radial, X-ray properties of galaxy clusters. We then demonstrate the reliability of xga by comparing simple X-ray properties, namely the X-ray temperature and gas mass, with published values presented by the XMM Cluster Survey (XCS), the Ultimate XMM eXtragaLactic survey project (XXL), and the Local Cluster Substructure Survey (LoCuSS). xga measured values for temperature are, on average, within 1 per cent of the values reported in the literature for each sample. xga gas masses for XXL clusters are shown to be ${\sim }$10 per cent lower than previous measurements (though the difference is only significant at the $\sim 1.8\sigma$ level), LoCuSS $R_{2500}$ and $R_{500}$ gas mass re-measurements are 3 per cent and 7 per cent lower, respectively (representing 1.5$\sigma$ and 3.5$\sigma$ differences). Like-for-like comparisons of hydrostatic mass are made to LoCuSS results, which show that our measurements are $10{\pm }3~{{\rm per\ cent}}$ ($19{\pm }7~{{\rm per\ cent}}$) higher for $R_{2500}$ ($R_{500}$). The comparison between $R_{500}$ masses shows significant scatter. Finally, we present new $M_{\rm hydro}$ measurements for 104 clusters from the Sloan Digital Sky Survey (SDSS) DR8 redMaPPer XCS sample (SDSSRM-XCS). Our SDSSRM-XCS hydrostatic mass measurements are in good agreement with multiple literature estimates, and represent one of the largest samples of consistently measured hydrostatic masses. We have demonstrated that xga is a powerful tool for X-ray analysis of clusters; it will render complex-to-measure X-ray properties accessible to non-specialists.
The JCMT Gould Belt Survey: first results from the Corona Australis molecular cloud and evidence of variable dust emissivity indices in the Coronet region
Authors: Pattle K , Bresnahan D , Ward-Thompson D , Kirk H , Kirk J M , Berry D S , Broekhoven-Fiene H , Hatchell J , Jenness T , Johnstone D , Mottram J C , Duarte-Cabral A , Francesco J Di , Hogerheijde M R , Bastien P , Butner H M , Chen M , Chrysostomou A , Coudé S , Currie M J , Davis C J , Drabek-Maunder E , Fich M , Fiege J , Friberg P , Friesen R , Fuller G A , Graves S , Greaves J , Holland W , Joncas G , Knee L B G , Mairs S , Marsh K , Matthews B C , Moriarty-Schieven G , Mowat C , Rawlings J , Retter B , Richer J , Robertson D , Rosolowsky E , Sadavoy S , Thomas H , Tothill N , Viti S , White G J , Wouterloot J , Yates J , Zhu M 
Published: January 2025

ABSTRACT
We present 450  and 850 $\mu$m James Clerk Maxwell Telescope (JCMT) observations of the Corona Australis (CrA) molecular cloud taken as part of the JCMT Gould Belt Legacy Survey (GBLS). We present a catalogue of 39 starless and protostellar sources, for which we determine source temperatures and masses using SCUBA-2 450 $\mu$m/850 $\mu$m flux density ratios for sources with reliable 450 $\mu$m detections, and compare these to values determined using temperatures measured by the Herschel Gould Belt Survey (HGBS). In keeping with previous studies, we find that SCUBA-2 preferentially detects high-volume-density starless cores, which are most likely to be prestellar (gravitationally bound). We do not observe any anticorrelation between temperature and volume density in the starless cores in our sample. Finally, we combine our SCUBA-2 and Herschel data to perform SED fitting from 160–850 $\mu$m across the central Coronet region, thereby measuring dust temperature T, dust emissivity index $\beta$, and column density $N({\rm H}_2)$ across the Coronet. We find that $\beta$ varies across the Coronet, particularly measuring $\beta = 1.55 \pm 0.35$ in the colder starless SMM-6 clump to the north of the B star R CrA. This relatively low value of $\beta$ is suggestive of the presence of large dust grains in SMM-6, even when considering the effects of $T\!-\!\beta$ fitting degeneracy and $^{12}$CO contamination of SCUBA-2 850 $\mu$m data on the measured $\beta$ values.
Defining serine tRNA knockout as a strategy for effective repression of gene expression in organisms with a recoded genome
Authors: Voorhees Peter J , Chang Xinyou , Lai Samuel K 
Published: January 2025

Abstract
Whole genome codon compression—the reassignment of all instances of a specific codon to synonymous codons—can generate organisms capable of tolerating knockout of otherwise essential transfer RNAs (tRNAs). As a result, such knockout strains enable numerous unique applications, such as high-efficiency production of DNA encoding extremely toxic genes or non-canonical proteins. However, achieving stringent control over protein expression in these organisms remains challenging, particularly with proteins where incomplete repression results in deleterious phenotypes. One platform enjoying increasing popularity utilizes serine TCA codon compression, relying on the prevailing understanding that deletion of tRNASer(UGA) (serT) would render the serine codon compressed organism incapable of translating any genes containing TCA codons. Here, we report evidence that tRNASer(CGA) (serU) can, surprisingly, also decode TCA, thereby precluding complete control over expression of TCA-containing genes in organisms with serT deletion. We then demonstrate the conditions necessary, including the precise modifications to the GRO and codon usage within the transgene, to overcome this interaction and achieve exceptionally stringent control over protein expression. Our findings provide critical insights and corresponding methods for guiding future use of serine codon compression for absolute control over protein expression, as well as a general strategy for optimizing repression via compression of other codons.
Single-molecule analysis reveals that IPMK enhances the DNA-binding activity of the transcription factor SRF
Authors: Ahn Hyoungjoon , Yu Jeongmin , Ryu Kwangmin , Ryu Jaeseung , Kim Sera , Park Jae Yeong , Kim Ji Kwang , Jung Inhong , An Haejin , Hong Sehoon , Kim Eunha , Park Kihyun , Ahn Myunghwan , Min Sunwoo , Jung Inkyung , Lee Daeyoup , Lee Thomas , Byun Youngjoo , Song Ji-Joon , Kim Jaehoon , Cho Won-Ki , Lee Gwangrog , Kim Seyun 
Published: January 2025

Abstract
Serum response factor (SRF) is a master transcription factor that regulates immediate early genes and cytoskeletal remodeling genes. Despite its importance, the mechanisms through which SRF stably associates with its cognate promoter remain unknown. Our biochemical and protein-induced fluorescence enhancement analyses showed that the binding of SRF to serum response element was significantly increased by inositol polyphosphate multikinase (IPMK), an SRF cofactor. Moreover, real-time tracking of SRF loci in live cell nuclei demonstrated that the chromatin residence time of SRF was reduced by IPMK depletion in fibroblasts. Conversely, elevated IPMK levels extended the SRF–chromatin association. We identified that IPMK binds to the intrinsically disordered region of SRF, which is required for the IPMK-induced stable interaction of SRF with DNA. IPMK-mediated conformational changes in SRF were observed by single-molecule fluorescence resonance energy transfer assays. Therefore, our findings demonstrate that IPMK is a critical factor for promoting high-affinity SRF–chromatin association and provide insights into the mechanisms of SRF-dependent transcription control via chaperone-like activity.
CRISPR/Cas13X-assisted programmable and multiplexed translation regulation for controlled biosynthesis
Authors: Xu Xianhao , Lv Xueqin , Liu Yanfeng , Li Jianghua , Du Guocheng , Chen Jian , Ledesma-Amaro Rodrigo , Liu Long 
Published: January 2025

Abstract
Developing efficient gene regulation tools is essential for optimizing microbial cell factories, but most existing tools only modulate gene expression at the transcriptional level. Regulation at the translational level provides a faster dynamic response, whereas developing a programmable, efficient and multiplexed translational regulation tool remains a challenge. Here, we have developed CRISPRi and CRISPRa systems based on hfCas13X that can regulate gene translation in Bacillus subtilis. First, we constructed a CRISPRi system to regulate gene translation based on catalytically deactivated hfCas13X (dhfCas13X). Second, we designed unique mRNA–crRNA pairs to construct DiCRISPRa (degradation-inhibited CRISPRa) and TsCRISPRa (translation-started CRISPRa) systems, which can activate downstream gene translation by enhancing mRNA stability or initiating mRNA translation. In addition, we found that fusing dhfCas13X with the RNA-binding chaperone BHfq significantly improved the activation efficiency of the DiCRISPRa and TsCRISPRa systems (43.2-fold). Finally, we demonstrated that the constructed CRISPR systems could be used to optimize the metabolic networks of two biotechnologically relevant compounds, riboflavin and 2′-fucosyllactose, increasing their titers by 3- and 1.2-fold, respectively. The CRISPRa and CRISPRi systems developed here provide new tools for the regulation of gene expression at the translation level and offer new ideas for the construction of CRISPRa systems.
The Effect of Gluon Condensate on the Entanglement Entropy in a Holographic Model
Authors: Chen Xun , Yu Bo , Chu Peng-Cheng , Li Xiao-Hua , Fujita Mitsutoshi 
Published: January 2025

Abstract
In this study, we examine the impact of the gluon condensate on holographic entanglement entropy within an Einstein-Dilaton model at both zero and finite temperatures. A critical length exists for the difference in entanglement entropy between connected and disconnected surfaces in this model, which is typically interpreted as an indicator of phase transition. As the gluon condensate increases, the critical length decreases, suggesting that confinement strengthens at zero temperature. Additionally, the entropic C-function abruptly drops to zero at the critical length, indicating the absence of entangled states. At finite temperatures, the results show that the effect of the gluon condensate on the critical length is qualitatively similar to that at zero temperature. We observe that the entropic C-function increases as a function of L at finite temperature, though it exhibits competitive behaviors when the gluon condensate is large.
New moderationism: medical discourses on alcohol and the decline of drunkenness in interwar Britain
Authors: Yokoe Ryosuke 
Published: January 2025

Abstract
This article explores the significant yet underappreciated role of medical experts in consolidating the promotion of moderate drinking as a viable solution to Britain’s alcohol problem during the interwar period. The country’s experience with alcohol regulation in the First World War showed that widespread drunkenness could be effectively managed through policies that restricted the availability of alcohol and encouraged moderation. This realization weakened the political standing of the temperance movement, as support for alcohol prohibition and abstinence waned, leading to the liberalization of social attitudes towards drinking. Such circumstances facilitated the emergence of New Moderationism, a renewed policy approach that regarded moderate drinking as relatively benign while cautioning against the dangers of heavy consumption. Medical professionals provided the conceptual foundation for New Moderationism by reassessing several assumptions on alcohol’s conflicting reputation as either a ‘poison’ or a ‘food’, its benefits to drinkers, and its potential to cause disease. These considerations led to the conclusion that alcohol policy should focus not on whether people should drink, but on how much. This study thus underscores the pivotal contribution of medical professionals in the evolution of the alcohol debate between the two world wars, revealing the transformative impact of expertise on policymaking and social change in modern Britain.