bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative characterization of breast lesions and normal fibroglandular tissue using compartmentalized diffusion-weighted model: comparison of intravoxel incoherent motion and restriction spectrum imaging
Authors: He Litong , Qin Yanjin , Hu Qilan , Liu Zhiqiang , Zhang Yunfei , Ai Tao 
Published: April 2024

Abstract
Background
To compare the compartmentalized diffusion-weighted models, intravoxel incoherent motion (IVIM) and restriction spectrum imaging (RSI), in characterizing breast lesions and normal fibroglandular tissue.

Methods
This prospective study enrolled 152 patients with 157 histopathologically verified breast lesions (41 benign and 116 malignant). All patients underwent a full-protocol preoperative breast MRI, including a multi-b-value DWI sequence. The diffusion parameters derived from the mono-exponential model (ADC), IVIM model (Dt, Dp, f), and RSI model (C1, C2, C3, C1C2, F1, F2, F3, F1F2) were quantitatively measured and then compared among malignant lesions, benign lesions and normal fibroglandular tissues using Kruskal-Wallis test. The Mann-Whitney U-test was used for the pairwise comparisons. Diagnostic models were built by logistic regression analysis. The ROC analysis was performed using five-fold cross-validation and the mean AUC values were calculated and compared to evaluate the discriminative ability of each parameter or model.

Results
Almost all quantitative diffusion parameters showed significant differences in distinguishing malignant breast lesions from both benign lesions (other than C2) and normal fibroglandular tissue (all parameters) (all P < 0.0167). In terms of the comparisons of benign lesions and normal fibroglandular tissues, the parameters derived from IVIM (Dp, f) and RSI (C1, C2, C1C2, F1, F2, F3) showed significant differences (all P < 0.005). When using individual parameters, RSI-derived parameters-F1, C1C2, and C2 values yielded the highest AUCs for the comparisons of malignant vs. benign, malignant vs. normal tissue and benign vs. normal tissue (AUCs = 0.871, 0.982, and 0.863, respectively). Furthermore, the combined diagnostic model (IVIM + RSI) exhibited the highest diagnostic efficacy for the pairwise discriminations (AUCs = 0.893, 0.991, and 0.928, respectively).

Conclusions
Quantitative parameters derived from the three-compartment RSI model have great promise as imaging indicators for the differential diagnosis of breast lesions compared with the bi-exponential IVIM model. Additionally, the combined model of IVIM and RSI achieves superior diagnostic performance in characterizing breast lesions.
OTUD5 promotes the growth of hepatocellular carcinoma by deubiquitinating and stabilizing SLC38A1
Authors: Yang Yingnan , Jia Siying , Zhu Ning , Xiao Xuelian , Ma Ying , Tu Kangsheng , Guo Yong , Xu Qiuran 
Published: April 2024

Abstract
Background
Deubiquitinating enzymes (DUBs) cleave ubiquitin on substrate molecules to maintain protein stability. DUBs reportedly participate in the tumorigenesis and tumour progression of hepatocellular carcinoma (HCC). OTU deubiquitinase 5 (OTUD5), a DUB family member, has been recognized as a critical regulator in bladder cancer, breast cancer and HCC. However, the expression and biological function of OTUD5 in HCC are still controversial.

Results
We determined that the expression of OTUD5 was significantly upregulated in HCC tissues. High levels of OTUD5 were also detected in most HCC cell lines. TCGA data analysis demonstrated that high OTUD5 expression indicated poorer overall survival in HCC patients. OTUD5 silencing prominently suppressed HCC cell proliferation, while its overexpression markedly enhanced the proliferation of HCC cells. Mass spectrometry analysis revealed solute carrier family 38 member 1 (SLC38A1) as a candidate downstream target protein of OTUD5. Coimmunoprecipitation analysis confirmed the interaction between OTUD5 and SLC38A1. OTUD5 knockdown reduced and OTUD5 overexpression increased SLC38A1 protein levels in HCC cells. However, OTUD5 alteration had no effect on SLC38A1 mRNA expression. OTUD5 maintained SLC38A1 stability by preventing its ubiquitin-mediated proteasomal degradation. SLC38A1 silencing prominently attenuated the OTUD5-induced increase in HCC cell proliferation. Finally, OTUD5 knockdown markedly suppressed the growth of HCC cells in vivo.

Conclusions
OTUD5 is an oncogene in HCC. OTUD5 contributes to HCC cell proliferation by deubiquitinating and stabilizing SLC38A1. These results may provide a theoretical basis for the development of new anti-HCC drugs.
INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance
Authors: Santos João Dourado , Sobral Daniel , Pinheiro Miguel , Isidro Joana , Bogaardt Carlijn , Pinto Miguel , Eusébio Rodrigo , Santos André , Mamede Rafael , Horton Daniel L. , Gomes João Paulo ,   TELEVIR Consortium, Bigarré Laurent , Fernández-Pinero Jovita , Pais Ricardo J. , Marcacci Maurilia , Moreno Ana , Lilja Tobias , Øines Øivind , Rzeżutka Artur , Mathijs Elisabeth , Van Borm Steven , Rasmussen Morten , Spiess Katja , Borges Vítor 
Published: April 2024

AbstractBackgroundImplementation of clinical metagenomics and pathogen genomic surveillance can be particularly challenging due to the lack of bioinformatics tools and/or expertise. In order to face this challenge, we have previously developed INSaFLU, a free web-based bioinformatics platform for virus next-generation sequencing data analysis. Here, we considerably expanded its genomic surveillance component and developed a new module (TELEVIR) for metagenomic virus identification.ResultsThe routine genomic surveillance component was strengthened with new workflows and functionalities, including (i) a reference-based genome assembly pipeline for Oxford Nanopore technologies (ONT) data; (ii) automated SARS-CoV-2 lineage classification; (iii) Nextclade analysis; (iv) Nextstrain phylogeographic and temporal analysis (SARS-CoV-2, human and avian influenza, monkeypox, respiratory syncytial virus (RSV A/B), as well as a “generic” build for other viruses); and (v)algn2phenofor screening mutations of interest. Both INSaFLU pipelines for reference-based consensus generation (Illumina and ONT) were benchmarked against commonly used command line bioinformatics workflows for SARS-CoV-2, and an INSaFLU snakemake version was released. In parallel, a new module (TELEVIR) for virus detection was developed, after extensive benchmarking of state-of-the-art metagenomics software and following up-to-date recommendations and practices in the field. TELEVIR allows running complex workflows, covering several combinations of steps (e.g., with/without viral enrichment or host depletion), classification software (e.g., Kaiju, Kraken2, Centrifuge, FastViromeExplorer), and databases (RefSeq viral genome, Virosaurus, etc.), while culminating in user- and diagnosis-oriented reports. Finally, to potentiate real-time virus detection during ONT runs, we developedfindONTime, a tool aimed at reducing costs and the time between sample reception and diagnosis.ConclusionsThe accessibility, versatility, and functionality of INSaFLU-TELEVIR are expected to supply public and animal health laboratories and researchers with a user-oriented and pan-viral bioinformatics framework that promotes a strengthened and timely viral metagenomic detection and routine genomics surveillance. INSaFLU-TELEVIR is compatible with Illumina, Ion Torrent, and ONT data and is freely available athttps://insaflu.insa.pt/(online tool) andhttps://github.com/INSaFLU(code).
The effect of extracorporeal shock-wave therapy on pain in patients with various tendinopathies: a systematic review and meta-analysis of randomized control trials
Authors: Majidi Lobat , Khateri Sorour , Nikbakht Nikta , Moradi Yousef , Nikoo Mohammad Reza 
Published: April 2024

Abstract
Objectives
Tendinopathy is a common condition that affects the body’s tendon structures, causing discomfort, restricted movement, and reduced functionality. In this study, we looked at how extracorporeal shock wave therapy (ESWT) affected pain levels in individuals with various forms of tendinopathy around the world.

Design
This study is a comprehensive review and meta-analysis of previously published randomized controlled trials. To gather relevant data, the researchers performed keyword searches in international databases, including PubMed (Medline), Scopus, Web of Sciences, Cochrane Central Register of Controlled Trials (CENTRAL), Research Registers of ongoing trials (ClinicalTrials.gov), as well as Embase. The search was conducted up until March 2023. The quality of the selected articles was assessed using the Cochrane risk-of-bias method for randomized trials (RoB2).

Results
Based on the results of the meta-analysis, which included 45 clinical studies, the use of ESWT was found to have a significant impact on reducing pain in various conditions. The standardized mean difference (SMD) in patients with plantar fasciitis (PF) was reduced by 1.63 (SMD: -1.63, 95% CI: -3.04, -0.21; I2: 77.36%; P heterogeneity: 0.0001). For lateral epicondylitis (LE), the SMD was 0.63 (SMD: -0.63, 95% CI: -1.11, -0.16; I2: 67.50%; P heterogeneity: 0.003). In the case of chronic Achilles tendinopathy, the SMD was 1.38 (SMD: -1.38, 95% CI: -1.66, -1.10; I2: 96.44%; P heterogeneity: 0.0001). Additionally, in individuals with rotator cuff tendinopathy, the SMD for pain reduction was 2.37 units (SMD: -2.37, 95% CI: -3.58, -1.15; I2: 98.46%; P heterogeneity: 0.0001).

Conclusion
This study suggests that ESWT can be a highly effective therapy option for relieving pain in people with tendinopathy. Nonetheless, it is encouraged to make additional recommendations based on high-quality clinical research and more accurate information in order to define the optimal therapeutic options for each type of tendinopathy.
Microblading reaction as a manifestation of systemic sarcoidosis: two case reports and a review of the literature
Authors: Merzel Šabović Eva Klara , Starbek Zorko Mateja , Hosta Violeta , Žgavec Borut , Bajuk Vid 
Published: April 2024

Abstract
Background
Sarcoidosis is a multisystemic disease characterized by granulomatous inflammation. Sarcoidosis often poses a diagnostic challenge owing to its nonspecific or mild clinical features. In 20–35% of cases, sarcoidosis initially presents on skin. However, skin lesions commonly mimic dermatological conditions. Therefore, it is important to not underestimate the skin manifestations and perform histopathological examinations to make a timely diagnosis.

Case presentation
We present two cases of 33-year-old Caucasian female patients with orange–red macules and plaques that developed in the eyebrow area 1 and 6 years after microblading, respectively. Histopathological examination confirmed a diagnosis of sarcoidosis. The lymph nodes and lungs were also affected in both patients.

Conclusion
Our two reports suggest that an esthetic procedure involving dermal or subcutaneous injection of foreign materials can trigger the development of cutaneous and systemic sarcoidosis. However, this relationship has not been described yet. Physicians should, therefore, be aware of this complication to properly evaluate and treat such patients in a timely manner.
Human umbilical cord-derived mesenchymal stromal cells improve myocardial fibrosis and restore miRNA-133a expression in diabetic cardiomyopathy
Authors: Liu Boxin , Wei Yan , He Jingjing , Feng Baofeng , Chen Yimeng , Guo Ruiyun , Griffin Matthew D. , Hynes Seán O. , Shen Sanbing , Liu Yan , Cui Huixian , Ma Jun , O’Brien Timothy 
Published: April 2024

Abstract
Background
Diabetic cardiomyopathy (DCM) is a serious health-threatening complication of diabetes mellitus characterized by myocardial fibrosis and abnormal cardiac function. Human umbilical cord mesenchymal stromal cells (hUC-MSCs) are a potential therapeutic tool for DCM and myocardial fibrosis via mechanisms such as the regulation of microRNA (miRNA) expression and inflammation. It remains unclear, however, whether hUC-MSC therapy has beneficial effects on cardiac function following different durations of diabetes and which mechanistic aspects of DCM are modulated by hUC-MSC administration at different stages of its development. This study aimed to investigate the therapeutic effects of intravenous administration of hUC-MSCs on DCM following different durations of hyperglycemia in an experimental male model of diabetes and to determine the effects on expression of candidate miRNAs, target mRNA and inflammatory mediators.

Methods
A male mouse model of diabetes was induced by multiple low-dose streptozotocin injections. The effects on severity of DCM of intravenous injections of hUC-MSCs and saline two weeks previously were compared at 10 and 18 weeks after diabetes induction. At both time-points, biochemical assays, echocardiography, histopathology, polymerase chain reaction (PCR), immunohistochemistry and enzyme-linked immunosorbent assays (ELISA) were used to analyze blood glucose, body weight, cardiac structure and function, degree of myocardial fibrosis and expression of fibrosis-related mRNA, miRNA and inflammatory mediators.

Results
Saline-treated diabetic male mice had impaired cardiac function and increased cardiac fibrosis after 10 and 18 weeks of diabetes. At both time-points, cardiac dysfunction and fibrosis were improved in hUC-MSC-treated mice. Pro-fibrotic indicators (α-SMA, collagen I, collagen III, Smad3, Smad4) were reduced and anti-fibrotic mediators (FGF-1, miRNA-133a) were increased in hearts of diabetic animals receiving hUC-MSCs compared to saline. Increased blood levels of pro-inflammatory cytokines (IL-6, TNF, IL-1β) and increased cardiac expression of IL-6 were also observed in saline-treated mice and were reduced by hUC-MSCs at both time-points, but to a lesser degree at 18 weeks.

Conclusion
Intravenous injection of hUC-MSCs ameliorated key functional and structural features of DCM in male mice with diabetes of shorter and longer duration. Mechanistically, these effects were associated with restoration of intra-myocardial expression of miRNA-133a and its target mRNA COL1AI as well as suppression of systemic and localized inflammatory mediators.
GC–IMS facilitates identification of carbapenem-resistant Klebsiella pneumoniae in simulated blood cultures
Authors: Li Fuxing , Zheng Yunwei , Zhao Chuwen , Zhu Junqi , Hang Yaping , Fang Youling , Hu Longhua 
Published: April 2024

AbstractThis study aimed to identify carbapenem-resistant Klebsiella pneumoniae (CRKP) based on changes in levels of its volatile organic compounds (VOCs) in simulated blood cultures (BCs) using the gas chromatography–ion mobility spectrometry (GC–IMS) technique. A comprehensive analysis of volatile metabolites produced by Klebsiella pneumoniae (K. pneumoniae) in BC bottles was conducted using GC–IMS. Subsequently, the released VOCs were analyzed to examine differences in VOC release between CRKP and carbapenem-susceptible Klebsiella pneumoniae (CSKP). A total of 54 VOCs were detected, of which 18 (6 VOCs found in both monomer and dimer forms) were successfully identified. The VOCs produced by K. pneumoniae in BC bottles (BacT/ALERT® SA) were primarily composed of organic acids, alcohols, esters, and ketones. The content of certain VOCs was significantly different between CRKP and CSKP after the addition of imipenem (IPM). Moreover, the inclusion of carbapenemase inhibitors facilitated the identification of carbapenemase-producing K. pneumoniae based on the variations in VOCs. This study demonstrates the utility of GC–IMS technology in identifying CRKP, and reveals that changes in VOCs are closely related to the growth and metabolism of K. pneumoniae, indicating that they can be leveraged to promote early identification of CRKP bacteremia. However, further in-depth studies and experiments are needed to validate our findings.
The impact of resource limitation on the pest-natural enemy ecosystem with anti-predator behavior and fear effect
Authors: Qin Wenjie , Dong Zhengjun 
Published: April 2024

AbstractResearch on agricultural pest control data indicates that the actual effectiveness of insecticides may exhibit slight variations, influenced by factors such as the type and quantity of pests. Additionally, the development of resistance by pests, as a result of adaptation to the environment, can impact the precision of pest control strategies. Hence we suggest implementing a nonlinear pulse state-dependent feedback control system, considering resource limitations, to investigate the influence of varying pesticide fatality rates on pest outbreaks. This paper takes into account the fear effect and anti-predator behavior to accurately portray the farmland ecosystem. We assessed the phase set and Poincaré map under the conditions for the existence of order-k (where $k=1,2,3$
k
=
1
,
2
,
3
) periodic solutions and examined their stability behavior. Remarkably, the system exhibited diverse bifurcation phenomena associated with pesticide-related parameters. Furthermore, the system demonstrated a multistability phenomenon involving the coexistence of the order-1 periodic solution and the limit cycle. This suggests that altering control strategies can disturb the initial coexistence status of pests and natural enemies. It also underscores that resource limitations can indeed impact the outbreak patterns and frequencies of pests. In addition to the variability in pesticide fatality rates, the inclusion of natural enemy releases in the nonlinear pulse strategy contributes to the model exhibiting complex dynamic characteristics. All these findings are substantiated by numerical simulations.
Quantum mechanical analysis of yttrium-stabilized zirconia and alumina: implications for mechanical performance of esthetic crowns
Authors: Saini Ravinder S. , Alshadidi Abdulkhaliq Ali F. , Gurumurthy Vishwanath , Okshah Abdulmajeed , Vaddamanu Sunil Kumar , Binduhayyim Rayan Ibrahim H. , Chaturvedi Saurabh , Bavabeedu Shashit Shetty , Heboyan Artak 
Published: April 2024

Abstract
Background
Yttrium-stabilized zirconia (YSZ) and alumina are the most commonly used dental esthetic crown materials. This study aimed to provide detailed information on the comparison between yttrium-stabilized zirconia (YSZ) and alumina, the two materials most often used for esthetic crowns in dentistry.

Methodology
The ground-state energy of the materials was calculated using the Cambridge Serial Total Energy Package (CASTEP) code, which employs a first-principles method based on density functional theory (DFT). The electronic exchange–correlation energy was evaluated using the generalized gradient approximation (GGA) within the Perdew (Burke) Ernzerhof scheme.

Results
Optimization of the geometries and investigation of the optical properties, dynamic stability, band structures, refractive indices, and mechanical properties of these materials contribute to a holistic understanding of these materials. Geometric optimization of YSZ provides important insights into its dynamic stability based on observations of its crystal structure and polyhedral geometry, which show stable configurations. Alumina exhibits a distinctive charge, kinetic, and potential (CKP) geometry, which contributes to its interesting structural framework and molecular-level stability. The optical properties of alumina were evaluated using pseudo-atomic computations, demonstrating its responsiveness to external stimuli. The refractive indices, reflectance, and dielectric functions indicate that the transmission of light by alumina depends on numerous factors that are essential for the optical performance of alumina as a material for esthetic crowns. The band structures of both the materials were explored, and the band gap of alumina was determined to be 5.853 eV. In addition, the band structure describes electronic transitions that influence the conductivity and optical properties of a material. The stability of alumina can be deduced from its bandgap, an essential property that determines its use as a dental material. Refractive indices are vital optical properties of esthetic crown materials. Therefore, the ability to understand their refractive-index graphs explains their transparency and color distortion through how the material responds to light..The regulated absorption characteristics exhibited by YSZ render it a highly attractive option for the development of esthetic crowns, as it guarantees minimal color distortion.

Conclusion
The acceptability of materials for esthetic crowns is strongly determined by mechanical properties such as elastic stiffness constants, Young's modulus, and shear modulus. YSZ is a highly durable material for dental applications, owing to its superior mechanical strength.
Prioritization of therapeutic targets for cancers using integrative multi-omics analysis
Authors: Jin Xin , Mei Yunyun , Yang Puyu , Huang Runze , Zhang Haifeng , Wu Yibin , Wang Miao , He Xigan , Jiang Ziting , Zhu Weiping , Wang Lu 
Published: April 2024

Abstract
Background
The integration of transcriptomic, proteomic, druggable genetic and metabolomic association studies facilitated a comprehensive investigation of molecular features and shared pathways for cancers’ development and progression.

Methods
Comprehensive approaches consisting of transcriptome-wide association studies (TWAS), proteome-wide association studies (PWAS), summary-data-based Mendelian randomization (SMR) and MR were performed to identify genes significantly associated with cancers. The results identified in above analyzes were subsequently involved in phenotype scanning and enrichment analyzes to explore the possible health effects and shared pathways. Additionally, we also conducted MR analysis to investigate metabolic pathways related to cancers.

Results
Totally 24 genes (18 transcriptomic, 1 proteomic and 5 druggable genetic) showed significant associations with cancers risk. All genes identified in multiple methods were mainly enriched in nuclear factor erythroid 2-related factor 2 (NRF2) pathway. Additionally, biosynthesis of ubiquinol and urate were found to play an important role in gastrointestinal tumors.

Conclusions
A set of putatively causal genes and pathways relevant to cancers were identified in this study, shedding light on the shared biological processes for tumorigenesis and providing compelling genetic evidence to prioritize anti-cancer drugs development.