bluuebunny/crossref_metadata_2025_split huggingface dataset:
An automated tool to classify and transform unstructured MRI data into BIDS datasets
Authors: Bartnik Alexander , Singh Sujal , Sum Conan , Smith Mackenzie , Bergsland Niels , Zivadinov Robert , Dwyer Michael 
Published: September 2023

Abstract
The increasing use of neuroimaging in clinical research has driven the creation of many large imaging datasets. However, these datasets often rely on inconsistent naming conventions in image file headers to describe acquisition, and time-consuming manual curation is necessary. Therefore, we sought to automate the process of classifying and organizing magnetic resonance imaging (MRI) data according to acquisition types common to the clinical routine, as well as automate the transformation of raw, unstructured images into Brain Imaging Data Structure (BIDS) datasets. To do this, we trained an XGBoost model to classify MRI acquisition types using relatively few acquisition parameters that are automatically stored by the MRI scanner in image file metadata, which are then mapped to the naming conventions prescribed by BIDS to transform the input images to the BIDS structure. The model recognizes MRI types with 99.475% accuracy, as well as a micro/macro-averaged precision of 0.9995/0.994, a micro/macro-averaged recall of 0.9995/0.989, and a micro/macro-averaged F1 of 0.9995/0.991. Our approach accurately and quickly classifies MRI types and transforms unstructured data into standardized structures with little-to-no user intervention, reducing the barrier of entry for clinical scientists and increasing the accessibility of existing neuroimaging data.
LoGD-ai: An Efficient Network Intrusion Detection System Using a Soft Voting-Based Ensemble Learner
Authors: Agyapong Isaac , Boateng Samuel , Prempeh Isaac , Acheampong Rebecca 
Published: September 2023

Abstract
Network attacks detection is still a difficult task because of the large data volumes needed for training a cutting-edge machine learning algorithms to unearth network invasions. Recently, a number of data mining methods have been put out for network intrusion detection. Meanwhile, each of them encounters certain difficulties resulting from the sophisticated nature of threats the existing models cannot detect. The NSL-KDD dataset containing four different form of attacks was employed in this paper. In this paper, we demonstrate the efficiency of LoGD-ai, a soft voting-based ensemble learner as network intrusion detection system to classify network data to normal and malicious. This soft-voting based ensemble classifier employs logistic regression, gradient boosting and decision tree algorithms for intrusion detection. Finally, the performance of the LoGD-ai classifier is compared to the popular gradient boosting machine (GBM), random forests (RF), and AdaBoost. Scoring 98.05% on accuracy, the LoGD-ai classifier performs better than GBM, RF and AdaBoost classifiers, efficiently detecting and classifying network traffic as normal or malicious. Compared to gradient boosting, our proposed methodology increases accuracy by 0.52%, which is critical for network intrusion detection.
Safety and health economic evaluation of different materials of peripheral intravenous catheters
Authors: Liang Shanshan , Zhou Zhaoju , Jiang Liping , Ding Huirong 
Published: September 2023

Abstract
Background
To explore the safety and economics of two materials of peripheral intravenous catheters based on propensity score matching.
Methods
A multi-center prospective survey on inpatients in 5 hospitals in Shanghai, Sichuan, and Shandong. Propensity score matching (PSM) was used to analyze the complications, indwelling time, comfort, and economic comparison.
Results
The data of 3,245 patients were matched by PSM. There were 1812 patients with two different materials, 906 cases in each group. The complication rate in the Vialon group (22.4% vs 29.5%) was lower than that in the Teflon group, and its average indwelling time was significantly longer than that of the Teflon material group (0.13 days) (p < 0.05). The comfort evaluation of patients in the Vialon group was 5.5% higher than that in the Teflon group. The additional cost of unplanned extubation of Vialon material was lower than that of Teflon material.
Conclusions
The peripheral intravenous catheters made of Vialon material can reduce complications and the total cost.
Unleashing Nature's Defense: Potent Antimicrobial Power of Mediterranean Ethyl Acetate Extracts against Oral Pathogens and Streptococcus mutans Biofilms
Authors: Hickl Joachim , Argyropoulou Aikaterini , Al-Ahmad Ali , Hellwig Elmar , Skaltsounis Alexios Leandros , Wittmer Annette , Vach Kirstin , Karygianni Lamprini 
Published: September 2023

Abstract

Objectives
The increasing demand for alternatives to antibiotics against resistant bacteria has led to research on natural products. The aim of this study was to analyze the antimicrobial and antibiofilm activity of 16 Mediterranean herb extracts.
Materials and Methods
The extracts were analyzed using High Performance Thin Layer Chromatography. The minimum inhibitory concentration and minimum bactericidal concentration of the extracts from Achillea taygetea, Cistus creticus ssp. creticus, Cistus monspeliensis, Lavandula stoechas, Mentha aquatica, Mentha longifolia, Origanum vulgare, Phlomis cretica, Rosmarinus officinalis, Salvia sclarea, Satureja parnassica, Satureja thymbra, Sideritis euboea, Sideritis syriaca, Stachys spinosa, and Thymus longicaulis were determined against eight oral bacteria and fungus Candida albicans. Microtiter plate test was conducted to evaluate the antibiofilm activity against Streptococcus mutans.
Results
Overall, all tested extracts efficiently suppressed the growth of obligate anaerobic bacteria. When applied at concentrations ≥ 0.15 mg / ml, the extracts exhibited moderate to high antibiofilm activity comparable to that of chlorhexidine (CHX) against S. mutans. Interestingly, R. officinalis (MIC: 0.01–0.06 mg / ml) and O. vulgare (MIC: 0.04–1.25 mg / ml) demonstrated the highest antibacterial activity against oral bacteria. Additionally, R. officinalis and L. stoechas significantly inhibited S. mutans biofilm formation at 0.15 mg / ml.
Conclusions
The tested plant extracts can be considered as alternative natural antimicrobial and antibiofilm agents.
Clinical Relevance:
Mediterranean herb extracts show promise as natural alternatives to combat oral bacteria and biofilm formation, offering potential new therapies for infectious oral diseases in the context of antibiotic resistance.
Multi-silicone Bilateral Soft Physical Twin as an Alternative to Traditional User Interfaces for Remote Palpation: a Comparative Study
Authors: Costi Leone , Iida Fumiya 
Published: September 2023

Abstract
Teleoperated medical technologies are a fundamental part of the healthcare system. From telemedicine to remote surgery, they allow remote diagnosis and treatment. However, the absence of any interface able to effectively reproduce the sense of touch and interaction with the patient prevents the implementation of teleoperated systems for primary care examinations, such as palpation. In this paper, we propose the first reported case of a soft robotic bilateral physical twin for remote palpation. By creating an entirely soft interface that can be used both to control the robot and receive feedback, the proposed device allows the user to achieve remote palpation by simply palpating the soft physical twin. This is achieved through a compact design showcasing 9 pneumatic chambers and exploiting multi-silicone casting to minimize cross-noise and allow teleoperation. A comparative study has been run against a traditional setup, and both the control and feedback of the physical twin are carefully analyzed. Despite distributed tactile feedback not achieving the same performance as the visual map, the soft control and visual feedback combination showcases a 5.1% higher accuracy. Moreover, the bilateral soft physical twin results always in a less invasive procedure, with 41% lower mechanical work exchanged with the remote phantom.
TRIM58 downregulation maintains stemness via MYH9-GRK3-Hippo/YAP axis activation in triple-negative breast cancer stem cells
Authors: Li Xujun , Cai Ting , Wu Qian , Jiang Jing , You Tianzi , Guo Linyan , Liu Huina , Yang Fan 
Published: September 2023

Abstract

Background
TRIM58 is, a member of the TRIM protein family, which possess with E3 ubiquitin ligase activities. Studies have revealed that weak expression of TRIM58 plays key roles, has been implicated in the tumor progression of tumor formation due to its reduced expression. However, its role in regulating the stemness of breast cancer stem cells (CSCs) remains unexplored.
Methods
The expression of TRIM58 was examined in breast cancer cells and triple-negative breast cancer (TNBC) patient specimens. Human TNBC CSCs were enriched from TNBC patient cancer tissues using serum-free medium. Stemness functions of TRIM58 in CSCs were assessed using western blot, cell viability analysis, tumorsphere formation assay, and subcutaneous tumorigenesis assays. Mechanistic investigations of TRIM58 on stemness and differentiation were conducted using co-immunoprecipitation, mass spectrometry, q-PCR, ubiquitination detection, label-free quantitative proteomics, and dual luciferase reporter assays.
Results
TRIM58 was underexpressed in TNBC tissues and cells compared to adjacent mucosa tissue, and its downregulation was significantly associated with shorter survival. Overexpression of TRIM58 reduced the proportion of CD44+/CD24- cells, upregulated differentiation genes, and inhibited stemness-related gene expression in TNBC CSCs. In vitro and in vivo experiments revealed that TRIM58 overexpression in CSCs suppressed tumor sphere formation and tumorigenic capacity. Co-IP results indicated direct interaction between TRIM58 and MYH9, with TRIM58 inducing MYH9 degradation via ubiquitination in differentiated cells. Label-free quantitative proteomics identified GRK3 and Hippo-YAP as downstream targets and signaling pathways of MYH9. TIMER database analysis, immunohistochemistry, western blotting, DNA-protein pulldown experiments, and dual luciferase reporter assays demonstrated that MYH9 regulated GRK3 transcriptional activation in CSCs.
Conclusions
This study highlights the negative impact of TRIM58 on the stemness of triple-negative breast CSCs. Elevated TRIM58 expression in CSCs downregulates MYH9 protein levels by promoting ubiquitin-mediated degradation, thereby inhibiting downstream GRK3 transcription, inactivating the Hippo-YAP stemness pathway, and ultimately promoting CSC differentiation.
The Diagnostic Degree and Diagnostic Algorithmfor t/s in Hierarchical Star Graphs
Authors: Gao Yangyang 
Published: September 2023

Abstract
This article establishes the kn −k(k+1)2 + 1/kn −k(k+1)2 + k − 1-diagnosability of n-dimensional hierarchical star graphs HSn (n ≥ 4) underthe PMC model and the MM* model, where 2 ≤ k ≤ n − 2. Moreover, novelt/s diagnostic algorithms are proposed for the rapid localization of faulty processors within both the PMC model and the MM* model. These algorithms exhibita time complexity of O(N log2 N), where N represents the total number ofprocessors in the system.
Influence of ultrasound transmit frequency on measurement of global longitudinal strain on 2D speckle tracking echocardiography
Authors: Iwakura Katsuomi , Onishi Toshinari , Koyama Yasushi , Iwamoto Mutsumi , Watanabe Satoshi , Tanaka Koji , Sumiyoshi Akinori , Okada Masato , Tanaka Kota , Harada Shinichi , Watanabe Heitaro , Okamura Atsunori 
Published: September 2023

Abstract
The reproducibility of longitudinal strain measured by 2D speckle tracking echocardiography (2DSTE) may be affected by ultrasound settings. This study investigated the effect of transmit ultrasound frequency on global longitudinal strain (GLS) by 2DSTE. Apical, 2- and 4-chamber, and long-axis views were obtained in a consecutive group of 162 patients using Philips ultrasound devices. Three different frequency presets were used sequentially: high resolution (HRES, 1.9 to 2.1 MHz), general (HGEN, 1.6 to 1.8 MHz), and penetration mode (HPEN, 1.3 to 1.6 MHz). GLS values were determined for each preset using the Philips Q-station software, resulting in GLS-HRES, GLS-HGEN, and GLS-HPEN. Among the 151 patients with successfully measured GLS, a significant difference in GLS was observed among the three presets (p < 0.0001). GLS-HRES (-17.9 ± 4.4%) showed a slightly smaller magnitude compared to GLS-HGEN (-18.8 ± 4.5%, p < 0.0001) and GLS-HPEN (-18.8 ± 4.5%, p < 0.0001), with absolute differences of 1.1 ± 1.0% and 1.1 ± 1.2%, respectively. This variation in GLS with frequency was evident in patients with both optimal (n = 104) and suboptimal (n = 47) image quality and remained consistent regardless of ischemic etiology or ejection fraction. In conclusion, ultrasound frequency had only a modest effect on GLS measurements. GLS may be reliably assessed in most cases regardless of the ultrasound frequency used.
Polymer free Nanocomposite from Zeolite and Carbon Black as Glassy Carbon modifier platform for Simultaneous Electrochemical Quantification of Acetaminophen and Caffeine
Authors: Tchoumi Firmin Parfait , Tamo Arnaud Kamdem , Doungmo Giscard , Fotsop Cyrille Ghislain , Kemmegne-Mbouguen Justin Claude , Ngameni Emmanuel 
Published: September 2023

Abstract

Nanocomposite nanozeolite/acetylene black carbon was prepared by combining a type A zeolite with acetylene carbon black (AcB) and used to modify glassy carbon electrode (GCE) without polymer. The zeolite was prepared by hydrothermal method using natural kaolin. The physicochemical characterization of the composite showed a well-integrated composite in which the cubic crystal of the zeolite A and the graphitic aggregate of the carbon black were maintained. The electrochemical impedance spectroscopy study revealed that the composite film GCE (ZA-AcB/GCE) prepared by drop coating displayed a higher kinetic charge transfer compared to pristine zeolite modified GCE (ZA/GCE) and bare GCE. ZA-AcB/GCE, ZA/GCE and GCE were subsequently used to investigate the electrochemical behaviour of acetaminophen (AC) in acidic, neutral and alkaline pHs. The results demonstrate a good electrocatalytic property toward AC at composite film GCE in all these electrolytes compared to bare GCE and confirm the dependence of the electrochemical reaction mechanism of AC on the electrolyte’s pHs. Under optimal conditions, ZA-AcB/GCE exhibited higher sensitivity and selectivity toward both analytes taken individually or simultaneously within large concentration range: 0.5–89 µM for AC and 5–99 µM for CAF with the respective limit of detection of 0.38 and 0.82 µM. The developed sensors were applied successfully in the quantification of the both analytes in pharmaceutical tablets.
Dual-region-based computed tomography radiomics analysis for the non-invasive prediction of telomerase reverse transcriptase status and clinical prognosis in liver cancer
Authors: Zhou Yong , Sun Fengguo , Zhang Changlei , Li Zhaohua 
Published: September 2023

Abstract
Background: Telomerase reverse transcriptase (TERT) can directly regulate various hallmarks of cancer. We aimed to estimate the prognostic value of TERT expression levels in patients with liver cancer and build a radiomics model that can predict the TERT expression levels using The Cancer Imaging Archive (TCIA) and The Cancer Genome Atlas (TCGA) databases.
Methods: Preoperative CT images stored in TCIA with genomic data from TCGA were used for radiomics feature extraction and model construction. The radiomics features were extracted using least absolute shrinkage and selection operator regression analysis. A logistic regression algorithm was used to construct the model and to extract features based on whole tumor and whole tumor-peritumoral regions; a prognostic scoring system incorporating a radiomics signature based on the TERT expression levels was accepted for survival prediction.
Results: TCGA data on 295 liver cancer cases (203 men; age <60 years, 142 and ≥60 years, 153 participants) were used for gene-based survival analysis. High TERT expression was an independent risk factor for overall survival (OS) deterioration, involved in immune cell infiltration and ferroptosis, and closely related to several signaling pathways. The 34 cases included in the radiomics model for predicting TERT expression levels achieved areas under the curve of 0.827 and 0.803 in the training and validation sets, respectively. The inclusion of clinical features and important imaging biomarkers can improve the model’s accuracy of OS estimation.
Conclusion: Radiomics can predict the prognosis of patients with hepatocellular carcinoma by predicting TERT expression. CT-based radiomics can serve as a novel and effective tool for predicting prognosis in clinical settings.
Expression profile of tsRNAs in white adipose tissue of vitamin D deficiency young male mice with or without obesity
Authors: Jia Qiaowei , Zhao Yan 
Published: September 2023

Abstract
Background
The expression of tsRNA in white adipose tissue (WAT) of VD deficiency male mice with obesity has not been reported.
Methods
The healthy male C57BL/6J mice aged 4–6 weeks were divided into 4 groups according to the VD3 and fat energy supplement in daily diets.
Results
The qPCR verification further demonstrated that 1 tsRNAs (tRF5-20-HisGTG-3, all P < 0.05) were significantly up-regulated and 1 tsRNA (mt-tRF3a-ProTGG, all P < 0.05) was significantly down-regulated not only in HFVDD vs HFVDS, but aslo in HFVDD vs ConVDS. 1 tsRNAs (tRF5-22-CysGCA-27, P < 0.05) were significantly up-regulated and 3 tsRNA (mt-5'tiRNA-32-SerTGA, mt-5'tiRNA-33-SerTGA and mt-5'tiRNA-33-AlaTGC, all P < 0.05) was significantly down-regulated only in HFVDD vs ConVDS. Enrichment analysis of the qPCR verified DE tsRNAs showed that the 3 up-regulated tsRNAs seemed to be associated with FoxO signaling pathway, GnRH secretion, 2 − Oxocarboxylic acid metabolism, Autophagy – animal, Glucagon signaling pathway, AGE − RAGE signaling pathway in diabetic complications, Insulin signaling pathway, Apelin signaling pathway, Alzheimer disease, Pathways of neurodegeneration − multiple diseases, while 4 down-regulated tsRNA seemed to be associated with cell communication, primary metabolic process, metabolic process, response to stimulus, multicellular organismal process, cellular metabolic process, regulation of cellular process, regulation of biological process, and biological regulation.
Conclusions
The tsRNAs were differentially expressed in VD deficiency with obesity, especially tRF5-20-HisGTG-3, tRF5-22-CysGCA-27, tRF3a-GlyGCC-1, mt-5'tiRNA-33-AlaTGC, mt-5'tiRNA-33-SerTGA, mt-5'tiRNA-32-SerTGA and mt-tRF3a-ProTGG. These tsRNAs seemed to be associated with FoxO signaling pathway, GnRH secretion, 2 − oxocarboxylic acid metabolism, autophagy, glucagon and insulin signaling pathway, pathways of neurodegeneration − multiple diseases, metabolic process and biological regulation.
Amplifying Antitumor Efficacy: The Role of UDCA in Modulating Autophagy and Enhancing DOX Response in NSCLC
Authors: Li Ying , Zhao Helian , Shen Zhoumin , Chen Hongjiao , Zheng Yao , Jiang Yuanyuan , song Ying , Cai Yimin 
Published: September 2023

Abstract
Background
Non-small cell lung cancer (NSCLC) has long been challenged by the complexities of chemotherapeutic resistance, with autophagy playing a pivotal role in this resistance matrix. The multifaceted interplay between autophagy and tumor behavior, particularly in the context of NSCLC, demands nuanced understanding, given its contradictory roles in tumorigenesis and tumor survival.
Methods
We embarked on an intricate exploration of UDCA's potential in modulating the MAPK pathway, which is instigated by DOX. A systematic evaluation was undertaken of its influence on key autophagy-associated proteins and the cascading effects on pivotal signaling pathways, accentuating the role of TGFβ in this network.
Results
Our data illuminated that UDCA exerts a discernible inhibitory effect on tumor cell proliferation and alters the MAPK dynamics intricately associated with key proteins. Notably, the combined might of UDCA and DOX demonstrated a significant downregulation of TGFβ expression, thereby achieving a pronounced retardation in tumor progression without amplifying associated toxicities. Yet, exogenously introduced TGF-β presented a mitigating counter-effect.
Conclusions
Our findings advocate for UDCA's prospective utility as a potent chemosensitizer, amplifying the therapeutic efficacy of DOX against NSCLC by tactically inhibiting autophagy. This underscores the imperative for further exploration, moving us closer to tailoring precision-based therapeutic regimens centered on UDCA’s unique autophagy modulation capabilities.
Modulatory effect of blood LDL cholesterol on the association between cerebral Aβ and tau deposition in older adults
Authors: Han Seung Min , Byun Min Soo , Yi Dahyun , Jung Joon Hyung , Kong Nayeong , Chang Yoonyoung , Keum Musung , Jung Gi Jung , Lee Jun-Young , Lee Yun-Sang , Kim Yu Kyeong , Kang Koung Mi , Sohn Chul-Ho , Lee Dong Young 
Published: September 2023

Abstract
Background: We aimed to examine whether higher blood low-density lipoprotein cholesterol (LDL-C) synergistically moderates the association of cerebral beta-amyloid (Aβ) with tau deposition in older adults with diverse cognitive spectrum. The associations of various blood lipids, including total cholesterol (TC), LDL-C, high-density lipoprotein cholesterol (HDL-C), and triglyceride (TG) with cerebral Aβ and tau, and white matter hyperintensities (WMHs) were also explored.
Methods: A comprehensive clinical evaluation, serum lipid measurements, [11C] Pittsburgh Compound B-positron emission tomography (PET), [18F] AV-1451 PET, and magnetic resonance imaging were performed on all participants.
Results: A total of 136 older adults with normal cognition, mild cognitive impairment or Alzheimer’s disease (AD) dementia were included. There was a significant Aβ x LDL-C interaction effect on tau deposition indicating a synergistic moderation effect of LDL-C on the relationship between Aβ and tau deposition. Subsequent subgroup analysis showed that the positive association between Aβ and tau deposition was stronger in higher LDL-C group than in lower LDL-C group. In contrast, other lipids (i.e., TC, HDL-C and TG) did not show a similar moderation effect on the relationship between Aβ deposition and tau deposition. Exploratory analysis showed a positive relationship between serum LDL-C and WMH volume, while there were no significant association between any lipids and AD pathologies.
Conclusion: Our findings suggest that blood LDL-C synergistically increases tau pathology with Aβ deposition. In terms of AD pathophysiology, more attention needs to be paid to the role of LDL-C.
Inhaled amphotericin B to prevent invasive fungal disease in patients with severe aplastic anemia after intensive immunotherapy
Authors: CHEN XI , Chai Xingxing , Gong Yuemin , Chen Xiaoyu , Xu Dan , He Guangsheng , Li Jianyong 
Published: September 2023

Abstract
Objective
To evaluate the efficacy and safety of aerosol inhalation of amphotericin B (AmB) in preventing invasive fungal disease (IFD) in patients with severe aplastic anemia (SAA) after intensive immunosuppressive therapy (IST).
Methods
The efficacy and safety of aerosol inhalation of amphotericin B or gargling with sodium bicarbonate/nystatin to prevent IFD in SAA patients within 28 days were compared. Thirty-three cases were assigned to the Am AmB nebulization group and 65 cases to the mouthwash group. Breakthrough fungal infection and related mortality were evaluated.
Results
Five cases of breakthrough fungal infection occurred in the AmB nebulization group, compared to 34 cases in the mouthwash group (15.2% vs 52.3%, p = 0.00083). In the 3 months after IST, no patient died of fungal infection in the AmB nebulization group, as compared to two cases in the mouthwash group (0% vs 28.5%, p = 0.021). No grade III or above AmB-related toxicity events occurred in the aerosol inhalation group.
Conclusion
Aerosol inhalation of AmBB could effectively prevent IFD and related mortality in SAA patients during IST, and the treatment was well-tolerated.