bluuebunny/crossref_metadata_2025_split huggingface dataset:
The exceptions that prove the rule—a historical view of bedaquiline susceptibility
Authors: Miotto Paolo , Cirillo Daniela M. , Schön Thomas , Köser Claudio U. 
Published: March 2024

AbstractIn the accompanying study, Nimmo and colleagues estimated the dates of emergence of mutations in mmpR5 (Rv0678), the most important resistance gene to the anti-tuberculosis drug bedaquiline, in over 3500 geographically diverse Mycobacterium tuberculosis genomes. This provided important insights to improve the design and analysis of clinical trials, as well as the World Health Organization catalogue of resistance mutations, the global reference for interpreting genotypic antimicrobial susceptibility testing results.
Epigenetic age acceleration and risk of aortic valve stenosis: a bidirectional Mendelian randomization study
Authors: Pan Wanqian , Huang Qi , Zhou Le , Lin Jia , Du Xiaojiao , Qian Xiaodong , Jiang Tingbo , Chen Weixiang 
Published: March 2024

Abstract
Background
Aortic valve stenosis (AVS) is the most prevalent cardiac valve lesion in developed countries, and pathogenesis is closely related to aging. DNA methylation-based epigenetic clock is now recognized as highly accurate predictor of the aging process and associated health outcomes. This study aimed to explore the causal relationship between epigenetic clock and AVS by conducting a bidirectional Mendelian randomization (MR) analysis.

Methods
Summary genome-wide association study statistics of epigenetic clocks (HannumAge, HorvathAge, PhenoAge, and GrimAge) and AVS were obtained and assessed for significant instrumental variables from Edinburgh DataShare (n = 34,710) and FinnGen biobank (cases = 9870 and controls = 402,311). The causal association between epigenetic clock and AVS was evaluated using inverse variance weighted (IVW), weighted median (WM), and MR-Egger methods. Multiple analyses (heterogeneity analysis, pleiotropy analysis, and sensitivity analysis) were performed for quality control assessment.

Results
The MR analysis showed that the epigenetic age acceleration of HorvathAge and PhenoAge was associated with an increased risk of AVS (HorvathAge: OR = 1.043, P = 0.016 by IVW, OR = 1.058, P = 0.018 by WM; PhenoAge: OR = 1.058, P = 0.005 by IVW, OR = 1.053, P = 0.039 by WM). Quality control assessment proved our findings were reliable and robust. However, there was a lack of evidence supporting a causal link from AVS to epigenetic aging.

Conclusion
The present MR analysis unveiled a causal association between epigenetic clocks, especially HorvathAge and PhenoAge, with AVS. Further research is required to elucidate the underlying mechanisms and develop strategies for potential interventions.

Graphical abstract
CT-based pancreatic radiomics predicts secondary loss of response to infliximab in biologically naïve patients with Crohn’s disease
Authors: Yang Tian , Feng Jing , Yao Ruchen , Feng Qi , Shen Jun 
Published: March 2024

Abstract
Objectives
Predicting secondary loss of response (SLR) to infliximab (IFX) is paramount for tailoring personalized management regimens. Concurrent pancreatic manifestations in patients with Crohn’s disease (CD) may correlate with SLR to anti-tumor necrosis factor treatment. This work aimed to evaluate the potential of pancreatic radiomics to predict SLR to IFX in biologic-naive individuals with CD.

Methods
Three models were developed by logistic regression analyses to identify high-risk subgroup prone to SLR. The area under the curve (AUC), calibration curve, decision curve analysis (DCA), and integrated discrimination improvement (IDI) were applied for the verification of model performance. A quantitative nomogram was proposed based on the optimal prediction model, and its reliability was substantiated by 10-fold cross-validation.

Results
In total, 184 CD patients were enrolled in the period January 2016 to February 2022. The clinical model incorporated age of onset, disease duration, disease location, and disease behavior, whereas the radiomics model consisted of five texture features. These clinical parameters and the radiomics score calculated by selected texture features were applied to build the combined model. Compared to other two models, combined model achieved favorable, significantly improved discrimination power (AUCcombined vs clinical 0.851 vs 0.694, p = 0.02; AUCcombined vs radiomics 0.851 vs 0.740, p = 0.04) and superior clinical usefulness, which was further converted into reliable nomogram with an accuracy of 0.860 and AUC of 0.872.

Conclusions
The first proposed pancreatic-related nomogram represents a credible, noninvasive predictive instrument to assist clinicians in accurately identifying SLR and non-SLR in CD patients.

Critical relevance statement
This study first built a visual nomogram incorporating pancreatic texture features and clinical factors, which could facilitate clinicians to make personalized treatment decisions and optimize cost-effectiveness ratio for patients with CD.

Key points
• The first proposed pancreatic-related model predicts secondary loss of response for infliximab in Crohn’s disease.
• The model achieved satisfactory predictive accuracy, calibration ability, and clinical value.
• The model-based nomogram has the potential to identify long-term failure in advance and tailor personalized management regimens.

Graphical Abstract
Short cell cycle duration is a phenotype of human epidermal stem cells
Authors: Xiao Tong , Eze Ugomma C , Charruyer-Reinwald Alex , Weisenberger Tracy , Khalifa Ayman , Abegaze Brook , Schwab Gabrielle K , Elsabagh Rasha H , Parenteau T. Richard , Kochanowski Karl , Piper Merisa , Xia Yumin , Cheng Jeffrey B , Cho Raymond J , Ghadially Ruby 
Published: March 2024

Abstract
Background
A traditional view is that stem cells (SCs) divide slowly. Meanwhile, both embryonic and pluripotent SCs display a shorter cell cycle duration (CCD) in comparison to more committed progenitors (CPs).

Methods
We examined the in vitro proliferation and cycling behavior of somatic adult human cells using live cell imaging of passage zero keratinocytes and single-cell RNA sequencing.

Results
We found two populations of keratinocytes: those with short CCD and protracted near exponential growth, and those with long CCD and terminal differentiation. Applying the ergodic principle, the comparative numbers of cycling cells in S phase in an enriched population of SCs confirmed a shorter CCD than CPs. Further, analysis of single-cell RNA sequencing of cycling adult human keratinocyte SCs and CPs indicated a shortening of both G1 and G2M phases in the SC.

Conclusions
Contrary to the pervasive paradigm, SCs progress through cell cycle more quickly than more differentiated dividing CPs. Thus, somatic human adult keratinocyte SCs may divide infrequently, but divide rapidly when they divide. Additionally, it was found that SC-like proliferation persisted in vitro.
Menstrual blood-derived mesenchymal stem cells combined with collagen I gel as a regenerative therapeutic strategy for degenerated disc after discectomy in rats
Authors: Yu Li , Wu Honghao , Zeng Shumei , Hu Xiaojian , Wu Yuxu , Zhou Jinhong , Yuan Li , Zhang Qingqing , Xiang Charlie , Feng Zhiyun 
Published: March 2024

Abstract
Background
Annulus fibrosis (AF) defects have been identified as the primary cause of disc herniation relapse and subsequent disc degeneration following discectomy. Stem cell-based tissue engineering offers a promising approach for structural repair. Menstrual blood-derived mesenchymal stem cells (MenSCs), a type of adult stem cell, have gained attention as an appealing source for clinical applications due to their potential for structure regeneration, with ease of acquisition and regardless of ethical issues.

Methods
The differential potential of MenSCs cocultured with AF cells was examined by the expression of collagen I, SCX, and CD146 using immunofluorescence. Western blot and ELISA were used to examine the expression of TGF-β and IGF-I in coculture system. An AF defect animal model was established in tail disc of Sprague-Dawley rats (males, 8 weeks old). An injectable gel containing MenSCs (about 1*106/ml) was fabricated and transplanted into the AF defects immediately after the animal model establishment, to evaluate its repairment properties. Disc degeneration was assessed via magnetic resonance (MR) imaging and histological staining. Immunohistochemical analysis was performed to assess the expression of aggrecan, MMP13, TGF-β and IGF-I in discs with different treatments. Apoptosis in the discs was evaluated using TUNEL, caspase3, and caspase 8 immunofluorescence staining.

Results
Coculturing MenSCs with AF cells demonstrated ability to express collagen I and biomarkers of AF cells. Moreover, the coculture system presented upregulation of the growth factors TGF-β and IGF-I. After 12 weeks, discs treated with MenSCs gel exhibited significantly lower Pffirrmann scores (2.29 ± 0.18), compared to discs treated with MenSCs (3.43 ± 0.37, p < 0.05) or gel (3.71 ± 0.29, p < 0.01) alone. There is significant higher MR index in disc treated with MenSCs gel than that treated with MenSCs (0.51 ± 0.05 vs. 0.24 ± 0.04, p < 0.01) or gel (0.51 ± 0.05 vs. 0.26 ± 0.06, p < 0.01) alone. Additionally, MenSCs gel demonstrated preservation of the structure of degenerated discs, as indicated by histological scoring (5.43 ± 0.43 vs. 9.71 ± 1.04 in MenSCs group and 10.86 ± 0.63 in gel group, both p < 0.01), increased aggrecan expression, and decreased MMP13 expression in vivo. Furthermore, the percentage of TUNEL and caspase 3-positive cells in the disc treated with MenSCs Gel was significantly lower than those treated with gel alone and MenSCs alone. The expression of TGF-β and IGF-I was higher in discs treated with MenSCs gel or MenSCs alone than in those treated with gel alone.

Conclusion
MenSCs embedded in collagen I gel has the potential to preserve the disc structure and prevent disc degeneration after discectomy, which was probably attributed to the paracrine of growth factors of MenSCs.
Automated molecular structure segmentation from documents using ChemSAM
Authors: Tang Bowen , Niu Zhangming , Wang Xiaofeng , Huang Junjie , Ma Chao , Peng Jing , Jiang Yinghui , Ge Ruiquan , Hu Hongyu , Lin Luhao , Yang Guang 
Published: March 2024

AbstractChemical structure segmentation constitutes a pivotal task in cheminformatics, involving the extraction and abstraction of structural information of chemical compounds from text-based sources, including patents and scientific articles. This study introduces a deep learning approach to chemical structure segmentation, employing a Vision Transformer (ViT) to discern the structural patterns of chemical compounds from their graphical representations. The Chemistry-Segment Anything Model (ChemSAM) achieves state-of-the-art results on publicly available benchmark datasets and real-world tasks, underscoring its effectiveness in accurately segmenting chemical structures from text-based sources. Moreover, this deep learning-based approach obviates the need for handcrafted features and demonstrates robustness against variations in image quality and style. During the detection phase, a ViT-based encoder-decoder model is used to identify and locate chemical structure depictions on the input page. This model generates masks to ascertain whether each pixel belongs to a chemical structure, thereby offering a pixel-level classification and indicating the presence or absence of chemical structures at each position. Subsequently, the generated masks are clustered based on their connectivity, and each mask cluster is updated to encapsulate a single structure in the post-processing workflow. This two-step process facilitates the effective automatic extraction of chemical structure depictions from documents. By utilizing the deep learning approach described herein, it is demonstrated that effective performance on low-resolution and densely arranged molecular structural layouts in journal articles and patents is achievable.
Time-varying graph learning from smooth and stationary graph signals with hidden nodes
Authors: Ye Rong , Jiang Xue-Qin , Feng Hui , Wang Jian , Qiu Runhe , Hou Xinxin 
Published: March 2024

AbstractLearning graph structure from observed signals over graph is a crucial task in many graph signal processing (GSP) applications. Existing approaches focus on inferring static graph, typically assuming that all nodes are available. However, these approaches ignore the situation where only a subset of nodes are available from spatiotemporal measurements, and the remaining nodes are never observed due to application-specific constraints, resulting in time-varying graph estimation accuracy declines dramatically. To handle this problem, we propose a framework that consider the presence of hidden nodes to identify time-varying graph. Specifically, we assume that the graph signals are smooth and stationary on the graphs and only a small number of edges are allowed to change between two consecutive graphs. With these assumptions, we present a challenging time-varying graph inference problem, which models the influence of hidden nodes in terms of estimating the graph-shift operator matrices that have a form of graph Laplacian. Moreover, we emphasize similar edge pattern (column-sparsity) between different graphs. Finally, our method is evaluated on both synthetic and real-world data. The experimental results demonstrate the advantage of our method when compared to existing benchmarking methods.
Routing networking technology based on improved ant colony algorithm in space-air-ground integrated network
Authors: Nie Wuzhou , Chen Yong , Wang Yuhao , Wang Peizheng , Li Meng , Ning Lei 
Published: March 2024

AbstractSpace-air-ground integrated networks comprise a multi-level heterogeneous integrated network that combines satellite-based, aerial, and terrestrial networks. With the increasing human exploration of space and growing demands for internet applications, space-air-ground integrated networks have gradually emerged as the direction for communication network development. These networks face various challenges such as extensive coverage, diverse communication node types, low-quality communication links, and simultaneous operation of multiple network protocols. However, the rapid development and widespread application of artificial intelligence and machine learning technologies in recent years have offered new perspectives and solutions for the communication architecture and routing algorithm research within space-air-ground integrated networks. In these networks, not all nodes can typically communicate directly with satellites; instead, a specific set of specialized communication nodes facilitates data communication between aerial and satellite networks due to their superior communication capabilities. Consequently, in contrast to traditional communication architectures, space-air-ground integrated networks, particularly in the terrestrial layer, often need to address challenges related to the diversity of communication node types and low-quality communication links. A well-designed routing approach becomes crucial in addressing these issues. Therefore, this paper proposes an AODV routing network protocol based on an improved ant colony algorithm (AC-AODV), specifically designed for the terrestrial layer within the space-air-ground integrated networks. By integrating information such as the type, energy, and location of communication nodes, this protocol aims to facilitate network communication. The objective is to guide information flow through nodes that are more suitable for communication, either by relaying communication or by connecting with satellites through specialized nodes. This approach alleviates the burden on ordinary nodes within the terrestrial communication network, thereby enhancing the overall network performance. In this protocol, specialized nodes hold a higher forwarding priority than regular nodes. When a source node needs to transmit data, it enters the route discovery phase, utilizing its own type, location, and energy information as heuristic data to calculate forwarding probabilities. Subsequently, it broadcasts route request (RREQ) messages to find the path. Upon receiving the RREQ message, the destination node sends an RREP message for updating information elements and selects the optimal path based on these information elements. Compared to AODV, AC-AODV shows significant improvements in performance metrics such as transmission latency, throughput, energy conversion rate, and packet loss rate.
The impact of school-based creative bibliotherapy interventions on child and adolescent mental health: a systematic review and realist synthesis protocol
Authors: Redman Hayley , Melendez-Torres G. J. , Bethel Alison , Green Judith 
Published: March 2024

Abstract
Background
There is a need to identify evidence-based interventions to be delivered in schools that can be used to improve child and adolescent mental health and wellbeing. Creative bibliotherapy is one proposed intervention. However, there has been, to date, no comprehensive assessment of the evidence for its impact on mental health and wellbeing. To fill this gap, we will conduct a systematic review and realist synthesis.

Methods
A systematic search of the bibliographic databases APA PsycINFO, Medline (via Ovid), CINAHL, ERIC, Education Research Complete (via EBSCOhost) and Web of Science (SCI, SSCI, AHCI, ESCI) for school-based creative bibliotherapy interventions on child and adolescent mental health. Types of study to be included: cohort studies, non-randomised comparative evaluations, randomised controlled trials. The data from all included studies will be summarised descriptively and strength of evidence appraised. This is a potentially large field of practice, with heterogeneous interventions; we will use methods from intervention components analysis to describe and categorise the range of components and approaches used in included interventions. To understand how interventions work and in which contexts, we will use methods from realist synthesis to develop an exploratory account of mechanisms in different settings and for different young people (contexts).

Discussion
Findings will assess the range of evidence for the impact of creative bibliotherapy on child and adolescent mental health and wellbeing, the strength of evidence for the impact identified, and describe potential mechanisms. This review will be useful for a wide range of stakeholders considering implementing or developing interventions using creative bibliotherapy in school-based settings.

Systematic review registration
This protocol was registered at the International Prospective Register of Systematic Reviews (https://www.crd.york.ac.uk/prospero/), registration number CRD42023410333. This review is funded by Wellcome Trust (221457/Z/20/Z).
Existence and multiplicity of solutions for fractional $p_{1}(x,\cdot )\& p_{2}(x,\cdot )$-Laplacian Schrödinger-type equations with Robin boundary conditions
Authors: Zhang Zhenfeng , An Tianqing , Bu Weichun , Li Shuai 
Published: March 2024

AbstractIn this paper, we study fractional$p_{1}(x,\cdot )\& p_{2}(x,\cdot )$p1(x,⋅)&p2(x,⋅)-Laplacian Schrödinger-type equations for Robin boundary conditions. Under some suitable assumptions, we show that two solutions exist using the mountain pass lemma and Ekeland’s variational principle. Then, the existence of infinitely many solutions is derived by applying the fountain theorem and the Krasnoselskii genus theory, respectively. Different from previous results, the topic of this paper is the Robin boundary conditions in$\mathbb{R}^{N}\setminus \overline{\Omega}$RN∖Ω‾for fractional order$p_{1}(x,\cdot )\& p_{2}(x,\cdot )$p1(x,⋅)&p2(x,⋅)-Laplacian Schrödinger-type equations, including concave-convex nonlinearities, which has not been studied before. In addition, two examples are given to illustrate our results.
Network pharmacology and molecular docking analysis on Shenfu Qiangxin indicate mTOR is a potential target to treat heart failure
Authors: Zou Peilin , Li Jiajun , Zhang Yucong , Qian Zonghao , Nie Hao , Yang Ni , Zhang Le , Lin Li , Peng Dewei , Zhang Cuntai 
Published: March 2024

Abstract
Background
Heart failure (HF) is one of the major causes of mortality worldwide with high recurrence rate and poor prognosis. Our study aimed to investigate potential mechanisms and drug targets of Shenfu Qiangxin (SFQX), a cardiotonic-diuretic traditional Chinese medicine, in treating HF.

Methods
An HF-related and SFQX-targeted gene set was established using disease-gene databases and the Traditional Chinese Medicine Systems Pharmacology database. We performed gene function and pathway enrichment analysis and constructed protein–protein interaction (PPI) network to investigate the potential mechanisms. We also performed molecular docking to analyze the interaction patterns between the active compounds and targeted protein.

Results
A gene set with 217 genes was identified. The gene function enrichment indicated that SFQX can regulate apoptotic process, inflammatory response, response to oxidative stress and cellular response to hypoxia. The pathway enrichment indicated that most genes were involved in PI3K–Akt pathway. Eighteen hub target genes were identified in PPI network and subnetworks. mTOR was the key gene among hub genes, which are involved in PI3K–Akt pathway. The molecular docking analysis indicated that 6 active compounds of SFQX can bind to the kinase domain of mTOR, which exerted potential therapeutic mechanisms of SFQX in treating HF.

Conclusions
The results of network pharmacology analysis highlight the intervention on PI3K–Akt pathway of SFQX in the treatment of HF. mTOR is a key drug target to help protect myocardium.