bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alendronate partially rescues the periodontal defects in OIM mouse model of osteogenesis imperfecta
Authors: Chen Po-Jung , Wang Ke , Lin Meng-Hsuan , Sharma Radhika , Kalajzic Zana , O’Brien Mara , Yadav Sumit 
Published: January 2025

AbstractOsteogenesis imperfecta (OI) is a fairly common generalized connective disorder characterized by low bone mass, bone deformities and impaired bone quality that predisposes affected individuals to musculoskeletal fragility. Periodontal ligament (PDL)-alveolar bone and PDL-cementum entheses’ roles under OI conditions during physiological loading and orthodontic forces remain largely unknown. In addition, bisphosphonates (e.g., alendronate) are commonly used therapeutics for the treatment of OI. Our knowledge, in terms of the affects of alendronate treatment on the PDL entheses in OI is also far from complete. In this study, we identified craniofacial skeletal defects in an osteogenesis imperfecta (oim) murine model of OI. Relative to wild-type littermates, oim mice were found to have decreased skull length, cranial height/width/length, nose length, nasal length, and frontal length. Next, we discovered that oim mice exhibited defects in several dental structures, including short roots and decreased volumes of the alveolar bone, dentin, and cellular cementum. Further, we specifically investigated periodontal defects in the oim mice. Alveolar bone loss in oim mice was primarily associated with elevated bone resorption due to an increased osteoclast number, along with reduced bone formation related to increased sclerostin (SOST) expression. PDL fibers in oim mice were disrupted and discontinuous, while Sharpey’s fibers at the PDL-bone entheses were reduced. Mechanism-based studies showed that catabolism of the PDL was elevated in oim mice, as revealed by an increase in MMP13 and CTSK expression. Meanwhile, the quality of the collagen fibers were impaired in oim mice due to a large accumulation of uncleaved collagen I fibers. With alendronate treatment, however, we could partially rescue these phenotypes. This study, for the first time, characterized periodontal defects in oim mice, detailed craniofacial defects and demonstrated the effectiveness of alendronate in partially restoring these defects.
Point spread function estimation with computed wavefronts for deconvolution of hyperspectral imaging data
Authors: Zabic Miroslav , Reifenrath Michel , Wegner Charlie , Bethge Hans , Landes Timm , Rudorf Sophia , Heinemann Dag 
Published: January 2025

AbstractHyperspectral imaging (HSI) systems acquire images with spectral information over a wide range of wavelengths but are often affected by chromatic and other optical aberrations that degrade image quality. Deconvolution algorithms can improve the spatial resolution of HSI systems, yet retrieving the point spread function (PSF) is a crucial and challenging step. To address this challenge, we have developed a method for PSF estimation in HSI systems based on computed wavefronts. The proposed technique optimizes an image quality metric by modifying the shape of a computed wavefront using Zernike polynomials and subsequently calculating the corresponding PSFs for input into a deconvolution algorithm. This enables noise-free PSF estimation for the deconvolution of HSI data, leading to significantly improved spatial resolution and spatial co-registration of spectral channels over the entire wavelength range.
Common biomarkers of idiopathic pulmonary fibrosis and systemic sclerosis based on WGCNA and machine learning
Authors: Shan Ning , Shang Yu , He Yaowu , Wen Zhe , Ning Shangwei , Chen Hong 
Published: January 2025

AbstractInterstitial lung disease (ILD) is known to be a major complication of systemic sclerosis (SSc) and a leading cause of death in SSc patients. As the most common type of ILD, the pathogenesis of idiopathic pulmonary fibrosis (IPF) has not been fully elucidated. In this study, weighted correlation network analysis (WGCNA), protein‒protein interaction, Kaplan–Meier curve, univariate Cox analysis and machine learning methods were used on datasets from the Gene Expression Omnibus database. CCL2 was identified as a common characteristic gene of IPF and SSc. The genes associated with CCL2 expression in both diseases were enriched mainly in chemokine-related pathways and lipid metabolism-related pathways according to Gene Set Enrichment Analysis. Single-cell RNA sequencing (sc-RNAseq) revealed a significant difference in CCL2 expression in alveolar epithelial type 1/2 cells, mast cells, ciliated cells, club cells, fibroblasts, M1/M2 macrophages, monocytes and plasma cells between IPF patients and healthy donors. Statistical analyses revealed that CCL2 was negatively correlated with lung function in IPF patients and decreased after mycophenolate mofetil (MMF) treatment in SSc patients. Finally, we identified CCL2 as a common biomarker from IPF and SSc, revealing the common mechanism of these two diseases and providing clues for the study of the treatment and mechanism of these two diseases.
Association between psoas muscle mass index and bone mineral density in patients undergoing hemodialysis
Authors: Ito Kiyonori , Ookawara Susumu , Sanayama Hidenori , Kakuda Hideo , Kanai Chieko , Iguchi Katsuo , Shindo Mitsutoshi , Tanno Keisuke , Ishibashi Shun , Kakei Masafumi , Tabei Kaoru , Morishita Yoshiyuki 
Published: January 2025

AbstractPatients undergoing dialysis are at risk of osteoporosis and sarcopenia because of mineral and bone disorders or malnutrition. Additionally, maintaining muscle mass is important to prevent osteoporosis. The psoas muscle mass index (PMI) was recently used to evaluate muscle mass. However, few studies have evaluated the association between the PMI and bone mineral density (BMD); therefore, we examined the association between PMI and BMD in the femoral neck (FN) of 80 patients (45 males, age, 71 (60–76) years; dialysis duration, 74 (36–140) months) undergoing hemodialysis. FN-BMD was measured using dual-energy X-ray absorptiometry, and PMI was evaluated using psoas muscle areas on computed tomography. FN-BMD and PMI were significantly higher in males than in females. In a correlation analysis, sex, BMI, serum creatinine levels, HbA1c levels, and PMI were positively correlated with FN-BMD, whereas age, history of bone fracture, difficulty in walking and bone-specific alkaline phosphatase level were negatively correlated. In the multivariate regression analysis using clinical factors significantly correlated to FN-BMD, including PMI, both sex (standardized coefficient: 0.249, p = 0.028) and PMI (standardized coefficient: 0.249, p = 0.038) were extracted. Multivariable linear regression analysis using PMI and traditional osteoporosis factors revealed that PMI was significantly and independently associated with FN-BMD (standardized coefficient: 0.308, p = 0.010). In conclusion, PMI was positively associated with FN-BMD. Attention should be paid to the possibility of decreased BMD with decreased muscle mass.
Enzymatic synthesis of reactive RNA probes containing squaramate-linked cytidine or adenosine for bioconjugations and cross-linking with lysine-containing peptides and proteins
Authors: Ivancová Ivana , Quirante Tania Sánchez , Ondruš Marek , Pohl Radek , Vlková Marta , Žilecká Eva , Bouřa Evžen , Hocek Michal 
Published: January 2025

AbstractProtein-RNA interactions play important biological roles and hence reactive RNA probes for cross-linking with proteins are important tools in their identification and study. To this end, we designed and synthesized 5′-O-triphosphates bearing a reactive squaramate group attached to position 5 of cytidine or position 7 of 7-deazaadenosine and used them as substrates for polymerase synthesis of modified RNA. In vitro transcription with T7 RNA polymerase or primer extension using TGK polymerase was used for synthesis of squaramate-modified RNA probes which underwent covalent bioconjugations with amine-linked fluorophore and lysine-containing peptides and proteins including several viral RNA polymerases or HIV reverse transcriptase. Inhibition of RNA-depending RNA polymerases from Japanese Encephalitis virus was observed through formation of covalent cross-link which was partially identified by MS/MS analysis. Thus, the squaramate-linked NTP analogs are useful building blocks for the synthesis of reactive RNA probes for bioconjugations with primary amines and cross-linking with lysine residues.
Circulating tumor cell plasticity determines breast cancer therapy resistance via neuregulin 1–HER3 signaling
Authors: Würth Roberto , Donato Elisa , Michel Laura L. , Saini Massimo , Becker Lisa , Cheytan Tasneem , Doncevic Daria , Messmer Tobias , Gutjahr Ewgenija , Weber Rebecca , Klein Corinna , Alborzinia Hamed , Yildiz Umut , Vogel Vanessa , Hlevnjak Mario , Kozyulina Polina , Neuberth Sarah-Jane , Schwerd-Kleine Paul , Jakab Sevinç , Pfarr Nicole , Angeles Arlou Kristina , Laut Astrid K. , Karpova Darja , Falcone Mattia , Hardt Olaf , Theek Benjamin , Wagner Celina V. , Becker Mirjam , Wagner Sabine , Haselmayr Martina , Schmitt Anita , Müller-Tidow Carsten , Riethdorf Sabine , Pantel Klaus , Zapatka Marc , Sültmann Holger , Herrmann Carl , Thewes Verena , Lichter Peter , Schneeweiss Andreas , Sprick Martin R. , Trumpp Andreas 
Published: January 2025

Abstract
Circulating tumor cells (CTCs) drive metastasis, the leading cause of death in individuals with breast cancer. Due to their low abundance in the circulation, robust CTC expansion protocols are urgently needed to effectively study disease progression and therapy responses. Here we present the establishment of long-term CTC-derived organoids from female individuals with metastatic breast cancer. Multiomics analysis of CTC-derived organoids along with preclinical modeling with xenografts identified neuregulin 1 (NRG1)–ERBB2 receptor tyrosine kinase 3 (ERBB3/HER3) signaling as a key pathway required for CTC survival, growth and dissemination. Genome-wide CRISPR activation screens revealed that fibroblast growth factor receptor 1 (FGFR1) signaling serves a compensatory function to the NRG1–HER3 axis and rescues NRG1 deficiency in CTCs. Conversely, NRG1–HER3 activation induced resistance to FGFR1 inhibition, whereas combinatorial blockade impaired CTC growth. The dynamic interplay between NRG1–HER3 and FGFR1 signaling reveals the molecular basis of cancer cell plasticity and clinically relevant strategies to target it. Our CTC organoid platform enables the identification and validation of patient-specific vulnerabilities and represents an innovative tool for precision medicine.
Projected changes in African easterly wave activity due to climate change
Authors: Akinsanola Akintomide A. , Adebiyi Adeyemi A. , Bobde Vishal , Adeyeri Oluwafemi E. , Tamoffo Alain T. , Danso Derrick K. 
Published: January 2025

AbstractAfrican easterly waves significantly influence regional hydroclimate, making it crucial to understand how global warming will impact their activity. Here, we investigate future changes in wave activity and assess the underlying mechanisms using an ensemble of Earth system models. We find a robust increase in wave activity over the Sahel–Sahara region by the end of the 21st century under two emission scenarios. This intensification is linked to increased baroclinicity associated with a strengthening of the meridional temperature gradient between the Guinea Coast and the Sahara. Our results also indicate that low-level warming enhances the waves by reinforcing monsoon flow, leading to increased convergence and vertical motion along the intertropical discontinuity. These energetic alterations significantly modify the conditions that currently produce these waves. Overall, our findings suggest that changes in wave activity could impact the transport of Saharan dust and mesoscale convective activity over the Sahel.
Cardiac conduction system regeneration prevents arrhythmias after myocardial infarction
Authors: Sayers Judy R. , Martinez-Navarro Hector , Sun Xin , de Villiers Carla , Sigal Sarah , Weinberger Michael , Rodriguez Claudio Cortes , Riebel Leto Luana , Berg Lucas Arantes , Camps Julia , Herring Neil , Rodriguez Blanca , Sauka-Spengler Tatjana , Riley Paul R. 
Published: January 2025

Abstract
Arrhythmias are a hallmark of myocardial infarction (MI) and increase patient mortality. How insult to the cardiac conduction system causes arrhythmias following MI is poorly understood. Here, we demonstrate conduction system restoration during neonatal mouse heart regeneration versus pathological remodeling at non-regenerative stages. Tissue-cleared whole-organ imaging identified disorganized bundling of conduction fibers after MI and global His–Purkinje disruption. Single-cell RNA sequencing (scRNA-seq) revealed specific molecular changes to regenerate the conduction network versus aberrant electrical alterations during fibrotic repair. This manifested functionally as a transition from normal rhythm to pathological conduction delay beyond the regenerative window. Modeling in the infarcted human heart implicated the non-regenerative phenotype as causative for heart block, as observed in patients. These findings elucidate the mechanisms underpinning conduction system regeneration and reveal how MI-induced damage elicits clinical arrhythmogenesis.
MTCH2 controls energy demand and expenditure to fuel anabolism during adipogenesis
Authors: Chourasia Sabita , Petucci Christopher , Shoffler Clarissa , Abbasian Dina , Wang Hu , Han Xianlin , Sivan Ehud , Brandis Alexander , Mehlman Tevie , Malitsky Sergey , Itkin Maxim , Sharp Ayala , Rotkopf Ron , Dassa Bareket , Regev Limor , Zaltsman Yehudit , Gross Atan 
Published: January 2025

Abstract
Mitochondrial carrier homolog 2 (MTCH2) is a regulator of apoptosis, mitochondrial dynamics, and metabolism. Loss of MTCH2 results in mitochondrial fragmentation, an increase in whole-body energy utilization, and protection against diet-induced obesity. In this study, we used temporal metabolomics on HeLa cells to show that MTCH2 deletion results in a high ATP demand, an oxidized cellular environment, and elevated utilization of lipids, amino acids, and carbohydrates, accompanied by a decrease in several metabolites. Lipidomics analysis revealed a strategic adaptive reduction in membrane lipids and an increase in storage lipids in MTCH2 knockout cells. Importantly, MTCH2 knockout cells showed an increase in mitochondrial oxidative function, which may explain the higher energy demand. Interestingly, this imbalance in energy metabolism and reductive potential triggered by MTCH2-deletion prevents NIH3T3L1 preadipocytes from differentiating into mature adipocytes, an energy consuming reductive biosynthetic process. In summary, the loss of MTCH2 leads to increased mitochondrial oxidative activity and energy demand, creating a catabolic and oxidative environment that fails to fuel the anabolic processes required for lipid accumulation and adipocyte differentiation.
HDAC6 deacetylates TRIM56 to negatively regulate cGAS-STING-mediated type I interferon responses
Authors: Zeng Qiongzhen , Chen Zixin , Li Shan , Huang Ziwei , Ren Zhe , Ye Cuifang , Wang Xiao , Zhou Jun , Liu Kaisheng , Zheng Kai , Wang Yifei 
Published: January 2025

Abstract
Histone deacetylase HDAC6 has been implicated in regulating antiviral innate immunity. However, its precise function in response to DNA virus infection remains elusive. Herein, we find that HDAC6 deficiency promotes the activation of cGAS-STING signaling and type I interferon (IFN) production, both in vitro and in vivo, resulting in a decrease in HSV-1 infection. Mechanistically, HDAC6 deacetylates tripartite motif protein 56 (TRIM56) at K110 in mice, thereby impairing the monoubiquitination cGAS and its DNA binding ability. Overexpression of TRIM56 K110Q protects mice against HSV-1 infection. Notably, different amino acids at position 110 of TRIM56 in human and mouse cause species-specific IFN responses. Further, we show that during early stages of HSV-1 infection, the viral protein US3 phosphorylates HDAC6 to inhibit the cGAS-mediated antiviral response. Our results suggest that HDAC6 inhibits cGAS activation through TRIM56 deacetylation in a species-specific manner.
Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks
Authors: Lubrano Paul , Smollich Fabian , Schramm Thorben , Lorenz Elisabeth , Alvarado Alejandra , Eigenmann Seraina Carmen , Stadelmann Amelie , Thavapalan Sevvalli , Waffenschmidt Nils , Glatter Timo , Hoffmann Nadine , Müller Jennifer , Peter Silke , Drescher Knut , Link Hannes 
Published: January 2025

Abstract
Metabolic variation across pathogenic bacterial strains can impact their susceptibility to antibiotics and promote the evolution of antimicrobial resistance (AMR). However, little is known about how metabolic mutations influence metabolism and which pathways contribute to antibiotic susceptibility. Here, we measured the antibiotic susceptibility of 15,120 Escherichia coli mutants, each with a single amino acid change in one of 346 essential proteins. Across all mutants, we observed modest increases of the minimal inhibitory concentration (twofold to tenfold) without any cases of major resistance. Most mutants that showed reduced susceptibility to either of the two tested antibiotics carried mutations in metabolic genes. The effect of metabolic mutations on antibiotic susceptibility was antibiotic- and pathway-specific: mutations that reduced susceptibility against the β-lactam antibiotic carbenicillin converged on purine nucleotide biosynthesis, those against the aminoglycoside gentamicin converged on the respiratory chain. In addition, metabolic mutations conferred tolerance to carbenicillin by reducing growth rates. These results, along with evidence that metabolic bottlenecks are common among clinical E. coli isolates, highlight the contribution of metabolic mutations for AMR.
PlexinD1 is a driver and a therapeutic target in advanced prostate cancer
Authors: Wei Jing , Wang Jing , Guan Wen , Li Jingjing , Pu Tianjie , Corey Eva , Lin Tzu-Ping , Gao Allen C , Wu Boyang Jason 
Published: January 2025

Abstract
Aggressive prostate cancer (PCa) variants associated with androgen receptor signaling inhibitor (ARSI) resistance and metastasis remain poorly understood. Here, we identify the axon guidance semaphorin receptor PlexinD1 as a crucial driver of cancer aggressiveness in metastatic castration-resistant prostate cancer (CRPC). High PlexinD1 expression in human PCa is correlated with adverse clinical outcomes. PlexinD1 critically maintains CRPC aggressive behaviors in vitro and in vivo, and confers stemness and cellular plasticity to promote multilineage differentiation including a neuroendocrine-like phenotype for ARSI resistance. Mechanistically, PlexinD1 is upregulated upon relief of AR-mediated transcriptional repression of PlexinD1 under ARSI treatment, and subsdquently transactivates ErbB3 and cMet via direct interaction, which triggers the ERK/AKT pathways to induce noncanonical Gli1-dictated Hedgehog signaling, facilitating the growth and plasticity of PCa cells. Blockade of PlexinD1 by the protein inhibitor D1SP restricted CRPC growth in multiple preclinical models. Collectively, these findings characterize PlexinD1’s contribution to PCa progression and offer a potential PlexinD1-targeted therapy for advanced PCa.
Blockchain in the banking industry: Unravelling thematic drivers and proposing a technological framework through systematic review with bibliographic network mapping
Authors: Rahman S. M. Masudur , Saif Abu Naser Mohammad , Kabir Sadman , Bari Md. Fakhrudoza , Alom Md. Mahabub , Rayhan Md. Johir , Zan Fangfang , Chu Mingyue , Talukder Ashis 
Published: January 2025

AbstractIn the new era of adopting and managing new and robust technologies in banking, the use of blockchain technology has significantly transformed overall banking systems. To add new insights to the body of existing knowledge, the authors conducted a systematic review with bibliographic network mapping to identify and analyse the factors contributing to adopting blockchain in the banking industry. Following the latest protocols of the PRISMA flowchart, this study acknowledged 16 relevant publications from 2590 papers in the databases, namely Scopus, ScienceDirect, Web of Science, and IEEE Xplore. The bibliographic data were grouped and analysed using VOSviewer to create network visualization maps that included citation and co‐citation, bibliographic coupling, co‐authorship, and co‐occurrence of terms. Subsequently, significant terms were identified through the analyses and compared with those found in the 16 relevant papers. The aggregate findings suggest that multiple influencing factors have been recognized and later categorized into three thematic drivers: transparency‐driven security, collaborative interoperability, and organizational infrastructure. The current research provides valuable insights for policymakers, technologists, researchers, consultants, and practitioners of information systems by proposing a technological framework, which will aid in developing tailored strategies to facilitate the sustainable practice of blockchain in the banking industry to a wider extent.
K$K$‐user cyclic shift‐aided serial concatenated code for Gaussian multiple access channel
Authors: He Meilin , Zhu Mingjue , Zhang Zhaoyang , Guo Rui , Wang Haiquan 
Published: January 2025

AbstractA ‐user cyclic shift‐aided serial concatenated code (SCC) is proposed over a Gaussian multiple access channel (MAC). In this code, a cyclic shift‐aided SCC, which integrates a regular repeat‐accumulate code with rate‐ and cyclic shift spreading (CSS), is employed for each user. Here, CSS consists of a length‐ bit spreading, a same chip‐level interleaver and a user‐specific cyclic shifter. This change avoids repeated complex interleaver generation operation and the main objective is to replace the random interleaver. At the receiver, iterative decoding is considered. For the design and optimization of the proposed code, a fixed point analysis (FPA) is developed to obtain the optimal and that achieves the maximum sum rate. Then, an analytic expression of collision probability is derived as a function of and . Finally, the advantage is analysed by comparing the generation time of interleaver. Moreover, FPA provides lower computation complexity in optimizing system parameters than the traditional EXIT chart method. Numerical results show that the design and optimization of the proposed code is more accurate, and support distinguishing between the users. The proposed code not only outperforms the traditional IDMA scheme in the bit error rate performance, but also provides much lower generation time of interleaver, especially for multiuser scenarios.
Scaling AI filmmaking with collaborative networking
Authors: Wang Haohong , Smith Daniel , Demir Ugur 
Published: January 2025

AbstractIn this work, MineStudio is introduced, a novel AI filmmaking framework designed to facilitate future creative collaborative networks. MineStudio uses a hybrid digitization approach that involves reconstructing 3D digital environments, capturing 2D live‐action performances, employing AI tools to generate synthetic images and videos, and compositing with AI assistance. This method effectively addresses the main challenges in the current AI video generation, including consistency, directability, and issues with human actions and interactions. MineStudio has been utilized to create pioneering AI films, such as the love story “Next Stop Paris” and the sci‐fi short film “Message in a Bot”, and has been recognized as a trailblazer in the AI filmmaking industry.