bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation of reliability, repeatability and consistency of three-dimensional choroidal vascular index
Authors: Ma Feiyan , Bai Yifan , Duan Jialiang , Liang Yuchen , Shang Qingli 
Published: January 2024

AbstractThis study aimed to investigate the reliability, repeatability and consistency of choroidal vascularity index (CVI) measurements provided by an artificial intelligence-based software in swept-source optical coherence tomography (SS-OCT) in normal subject, and to evaluate the influencing factors for 3D-CVI. Repeatability of 3D-CVI by SS-OCT was evaluated based on different scanning modes including Macular Cubes (3 mm × 3 mm, 6 mm × 6 mm, 9 mm × 9 mm) and Optic Nerve Head 6 mm × 6 mm. Intraclass Correlation Coefficient (ICC) was used to estimate the repeatability and reproducibility of five repeated measurement by SS-OCT. Consistency of CVI between SS-OCT and spectral-domain optical coherence tomography (SD-OCT) was measured and compared in a pilot study of ten eyes and agreement between SS-OCT and SD-OCT was evaluated by Bland–Altman analysis and Deming regression. The influencing factors for 3D-CVI including age, gender, axial length and spherical equivalent on CVI was further investigated in a prospective study of 125 eyes of 125 healthy subjects. ICC between different measurements by SS-OCT was 0.934 (95% CI 0.812–0.956) indicating good repeatability. Intraclass correlation coefficient between CVI measure by SS-OCT and SD-OCT was 0.887 (95% CI 0.796–0.938, P value < 0.001). The mean difference between 3D-CVI measured by SS-OCT and SD-OCT 0.133. CVI measured with SS-OCTA showed stronger correlations with axial length and age but not correlated with gender. There is good agreement between CVIs obtained from the built-in software that requires less timing in manual quantification. Studies investigating choroidal vascularity can be standardized by the AI-based CVI analyze software.
Conversational AI and equity through assessing GPT-3’s communication with diverse social groups on contentious topics
Authors: Chen Kaiping , Shao Anqi , Burapacheep Jirayu , Li Yixuan 
Published: January 2024

AbstractAutoregressive language models, which use deep learning to produce human-like texts, have surged in prevalence. Despite advances in these models, concerns arise about their equity across diverse populations. While AI fairness is discussed widely, metrics to measure equity in dialogue systems are lacking. This paper presents a framework, rooted in deliberative democracy and science communication studies, to evaluate equity in human–AI communication. Using it, we conducted an algorithm auditing study to examine how GPT-3 responded to different populations who vary in sociodemographic backgrounds and viewpoints on crucial science and social issues: climate change and the Black Lives Matter (BLM) movement. We analyzed 20,000 dialogues with 3290 participants differing in gender, race, education, and opinions. We found a substantively worse user experience among the opinion minority groups (e.g., climate deniers, racists) and the education minority groups; however, these groups changed attitudes toward supporting BLM and climate change efforts much more compared to other social groups after the chat. GPT-3 used more negative expressions when responding to the education and opinion minority groups. We discuss the social-technological implications of our findings for a conversational AI system that centralizes diversity, equity, and inclusion.
SpasticSim: a synthetic data generation method for upper limb spasticity modelling in neurorehabilitation
Authors: de-la-Torre Rubén , Oña Edwin Daniel , Victores Juan G. , Jardón Alberto 
Published: January 2024

AbstractIn neurorehabilitation, assessment of functional problems is essential to define optimal rehabilitation treatments. Usually, this assessment process requires distinguishing between impaired and non-impaired behavior of limbs. One of the common muscle motor disorders affecting limbs is spasticity, which is complicated to quantify objectively due to the complex nature of motor control. Thus, the lack of heterogeneous samples of patients constituting an acceptable amount of data is an obstacle which is relevant to understanding the behavior of spasticity and, consequently, quantifying it. In this article, we use the 3D creation suite Blender combined with the MBLab add-on to generate synthetic samples of human body models, aiming to be as sufficiently representative as possible to real human samples. Exporting these samples to OpenSim and performing four specific upper limb movements, we analyze the muscle behavior by simulating the six degrees of spasticity contemplated by the Modified Ashworth Scale (MAS). The complete dataset of patients and movements is open-source and available for future research. This approach advocates the potential to generate synthetic data for testing and validating musculoskeletal models.
Simulation analysis of EGFR mutation detection: Oncomine Dx target test and AmoyDx panel impact on lung cancer treatment decisions
Authors: Hirotsu Yosuke , Nakagomi Takahiro , Nagakubo Yuki , Goto Taichiro , Omata Masao 
Published: January 2024

AbstractLung cancer is a leading cause of cancer-related deaths worldwide. Epidermal growth factor receptor (EGFR) driver mutations are crucial for treatment decisions for patients with non-small cell lung cancer (NSCLC). This study aimed to assess the differences in EGFR mutation detection between two companion diagnostic (CDx) tests—the Oncomine Dx Target Test (ODxTT) and the AmoyDx Pan Lung Cancer PCR Panel—and their impact on treatment applicability. To this end, we used an in-house targeted sequencing dataset of 282 samples from 127 EGFR-mutated NSCLC patients to simulate the concordance between the EGFR variants targeted by the ODxTT and AmoyDx panel, the oncogenicity of the variants, and their therapeutic potential. Of the 216 EGFR mutations identified by the in-house panel, 51% were detectable by both CDx tests, 3% were specific to ODxTT, and 46% were not targeted by either test. Most non-targeted mutations did not have oncogenicity and were located outside exons 18–21. Notably, 95% of the mutations detectable by both tests had potential oncogenicity. Furthermore, among the 96 patients harboring actionable EGFR mutations, 97% had mutations detectable by both CDx tests and 1% by ODxTT, while 2% had mutations not covered by either test. These findings suggest that while both CDx tests are effective in detecting almost all actionable EGFR mutations, ODxTT provides slightly broader coverage. These results emphasize the importance of selecting appropriate CDx tests to inform treatment decisions for EGFR-positive NSCLC patients.
Therapeutic effect of sodium alginate on bleomycin, etoposide and cisplatin (BEP)-induced reproductive toxicity by inhibiting nitro-oxidative stress, inflammation and apoptosis
Authors: Moradi Mojtaba , Hashemian Mohammad Arshia , Faramarzi Azita , Goodarzi Nader , Hashemian Amir Hossein , Cheraghi Hadi , Jalili Cyrus 
Published: January 2024

AbstractImpaired spermatogenesis and male infertility are common consequences of chemotherapy drugs used in patients with testicular cancer. The present study investigated the effects of sodium alginate (NaAL) on testicular toxicity caused by bleomycin, etoposide, and cisplatin (BEP). Rats in group 1 received normal saline, while groups 2 and 3 were treated with 25 and 50 mg/kg of NaAL, respectively. Group 4 was treated with a 21-day cycle of BEP (0.5 mg/kg bleomycin, 5 mg/kg etoposide, and 1 mg/kg cisplatin), and groups 5 and 6 received BEP regimen plus 25 and 50 mg/kg of NaAL, respectively. Then, sperm parameters, testosterone levels, testicular histopathology and stereological parameters, testicular levels of malondialdehyde (MDA), nitric oxide (NO), and total antioxidant capacity (TAC), and the expression of apoptosis-associated genes including Bcl2, Bax, Caspase3, p53, and TNF-α were evaluated. Our findings revealed that NaAL improved sperm parameters, testosterone levels, histopathology, and stereology parameters in BEP-administrated rats. NaAL also improved testis antioxidant status by enhancing TAC and ameliorating MDA and NO. Further, modifications to the expression of Bcl2, Bax, Caspase3, p53, and TNF-α suggested that NaAL alleviated BEP-induced apoptosis and inflammation. Collectively, NaAL protects rats’ testes against BEP-evoked toxicity damage through the modulation of nitro-oxidative stress, apoptosis, and inflammation.
Enhanced antifungal activity of posaconazole against Candida auris by HIV protease inhibitors, atazanavir and saquinavir
Authors: Elgammal Yehia , Salama Ehab A. , Seleem Mohamed N. 
Published: January 2024

AbstractThe increasing incidence and dissemination of multidrug-resistant Candida auris represents a serious global threat. The emergence of pan-resistant C. auris exhibiting resistance to all three classes of antifungals magnifies the need for novel therapeutic interventions. We identified that two HIV protease inhibitors, atazanavir and saquinavir, in combination with posaconazole exhibited potent activity against C. auris in vitro and in vivo. Both atazanavir and saquinavir exhibited a remarkable synergistic activity with posaconazole against all tested C. auris isolates and other medically important Candida species. In a time-kill assay, both drugs restored the fungistatic activity of posaconazole, resulting in reduction of 5 and 5.6 log10, respectively. Furthermore, in contrast to the individual drugs, the two combinations effectively inhibited the biofilm formation of C. auris by 66.2 and 81.2%, respectively. Finally, the efficacy of the two combinations were tested in a mouse model of C. auris infection. The atazanavir/posaconazole and saquinavir/posaconazole combinations significantly reduced the C. auris burden in mice kidneys by 2.04- (99.1%) and 1.44-log10 (96.4%) colony forming unit, respectively. Altogether, these results suggest that the combination of posaconazole with the HIV protease inhibitors warrants further investigation as a new therapeutic regimen for the treatment of C. auris infections.
CPT1A as a potential therapeutic target for lipopolysaccharide-induced acute lung injury in mice
Authors: Wang Gui-Yun , Xu Xia , Xiong Da-Yan , Deng Lang , Liu Wei , Huang Xiao-Ting 
Published: January 2024

AbstractAcute lung injury (ALI) remains a high mortality rate with dramatic lung inflammation and alveolar epithelial cell death. Although fatty acid β-oxidation (FAO) impairment has been implicated in the pathogenesis of ALI, whether Carnitine palmitoyltransferase 1A (CPT1A), the rate-limiting enzyme for FAO, plays roles in lipopolysaccharide (LPS)-induced ALI remains unclear. Accordingly, we focused on exploring the effect of CPT1A in the context of ALI and the underlying mechanisms. We found that overexpression of CPT1A (AAV-CPT1A) effectively alleviated lung injury by reduction of lung wet-to-dry ratio, inflammatory cell infiltration, and protein levels in the BALF of ALI mice. Meanwhile, AAV-CPT1A significantly lessened histopathological changes and several cytokines’ secretions. In contrast, blocking CPT1A with etomoxir augmented inflammatory responses and lung injury in ALI mice. Furthermore, we found that overexpression of CPT1A with lentivirus reduced the apoptosis rates of alveolar epithelial cells and the expression of apoptosis-related proteins induced by LPS in MLE12 cells, while etomoxir increased the apoptosis of MLE12 cells. Overexpression of CPT1A prevented the drop in bioenergetics, palmitate oxidation, and ATP levels. In conclusion, the results rendered CPT1A worthy of further development into a pharmaceutical drug for the treatment of ALI.
Intense pulsed light annealing of solution-based indium–gallium–zinc–oxide semiconductors with printed Ag source and drain electrodes for bottom gate thin film transistors
Authors: Moon Chang-Jin , Park Jong-Whi , Jang Yong-Rae , Kim Hak-Sung 
Published: January 2024

AbstractIn this study, an intense pulsed light (IPL) annealing process for a printed multi-layered indium–gallium–zinc–oxide (IGZO) and silver (Ag) electrode structure was developed for a high performance all-printed inorganic thin film transistor (TFT). Through a solution process using IGZO precursor and Ag ink, the bottom gate structure TFT was fabricated. The spin coating method was used to form the IGZO semiconductor layer on a heavily-doped silicon wafer covered with thermally grown silicon dioxide. The annealing process of the IGZO layer utilized an optimized IPL irradiation process. The Ag inks were printed on the IGZO layer by screen printing to form the source and drain (S/D) pattern. This S/D pattern was dried by near infrared radiation (NIR) and the dried S/D pattern was sintered with intense pulsed light by varying the irradiation energy. The performances of the all-printed TFT such as the field effect mobility and on–off ratio electrical transfer properties were measured by a parameter analyzer. The interfacial analysis including the contact resistance and cross-sectional microstructure analysis is essential because diffusion phenomenon can occur during the annealing and sintering process. Consequently, this TFT device showed noteworthy performance (field effect mobility: 7.96 cm2/V s, on/off ratio: 107). This is similar performance compared to a conventional TFT, which is expected to open a new path in the printed metal oxide-based TFT field.
Multi-omic analyses of m5C readers reveal their characteristics and immunotherapeutic proficiency
Authors: Xu Rui , Wang Yue , Kuang Ye 
Published: January 2024

Abstract5-methylcytosine (m5C) is a post-transcriptional RNA modification identified, m5C readers can specifically identify and bind to m5C. ALYREF and YBX1 as members of m5C readers that have garnered increasing attention in cancer research. However, comprehensive analysis of their molecular functions across pancancer are lacking. Using the TCGA and GTEx databases, we investigated the expression levels and prognostic values of ALYREF and YBX1. Additionally, we assessed the tumor microenvironment, immune checkpoint-related genes, immunomodulators, Tumor Immune Dysfunction and Exclusion (TIDE) score and drug resistance of ALYREF and YBX1. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) analyses were performed to investigate the potential functions associated with m5C readers and coexpressed genes. Aberrant expression of ALYREF and YBX1 was observed and positively associated with prognosis in KIRP, LGG and LIHC. Furthermore, the expression levels of ALYREF and YBX1 were significantly correlated with immune infiltration of the tumor microenvironment and immune-related modulators. Last, our analysis revealed significant correlations between ALYREF, YBX1 and eIFs. Our study provides a substantial understanding of m5C readers and the intricate relationship between ALYREF, YBX1, eIFs, and mRNA dynamics. Through multidimensional analysis of immune infiltration and drug sensitivity/resistance in ALYREF and YBX1, we propose a possibility for combined modality therapy utilizing m5C readers.
Anoikis related genes may be novel markers associated with prognosis for ovarian cancer
Authors: Yang Chen , Zhu LuChao , Lin Qin 
Published: January 2024

AbstractThe aim of this study was to determine the prognostic significance of anoikis related genes (ARGs) in ovarian cancer (OC) and to develop a prognostic signature based on ARG expression. We analyzed cohorts of OC patients and used nonnegative matrix factorization (NMF) for clustering. Single-sample gene-set enrichment analysis (ssGSEA) was employed to quantify immune infiltration. Survival analyses were performed using the Kaplan–Meier method, and differences in survival were determined using the log-rank test. The extent of anoikis modification was quantified using a risk score generated from ARG expression. The analysis of single-cell sequencing data was performed by the Tumor Immune Single Cell Hub (TISCH). Our analyses revealed two distinct patterns of anoikis modification. The risk score was used to evaluate the anoikis modification patterns in individual tumors. Three hub-genes were screened using the LASSO (Least Absolute Shrinkage and Selection Operator) method and patients were classified into different risk groups based on their individual score and the median score. The low-risk subtype was characterized by decreased expression of hub-genes and better overall survival. The risk score, along with patient age and gender, were considered to identify the prognostic signature, which was visualized using a nomogram. Our findings suggest that ARGs may play a novel role in the prognosis of OC. Based on ARG expression, we have developed a prognostic signature for OC that can aid in patient stratification and treatment decision-making. Further studies are needed to validate these results and to explore the underlying mechanisms.
Research on the influence of different sampling resolution and spatial resolution in sampling strategy on landslide susceptibility mapping results
Authors: Yu Xianyu , Chen Huihui 
Published: January 2024

AbstractLandslides, recognized as a significant global natural disaster, necessitate an exploration of the impact of various resolution types in sampling strategies on Landslide Susceptibility Mapping (LSM) results. This study focuses on the segment from Zigui to Badong within the Three Gorges Reservoir Area, utilizing two resolution types: sampling resolution and spatial resolution, The Support Vector Machine (SVM) is employed to obtain LSM results, which are then analyzed using Receiver Operating Characteristic (ROC) curve, specific category accuracy and statistical methods. Artificial Neural Network (ANN) and Convolutional Neural Network (CNN) were used to verify the reliability of the results. Additionally, five common machine learning models, including Logistic Regression (LR), are used to conduct experiments on four sampling resolutions (10 m,30 m,50 m and 70 m) to further investigate the effect of sampling resolution on LSM results. These are evaluated using a comprehensive quantitative method. The results reveal that increasing spatial resolution improves the prediction accuracy, while increasing sampling resolution produces a contrary effect. Furthermore, the impact of spatial resolution on LSM results is more pronounced than that of sampling resolution. Finally, Fanjiaping landslide and Huangtupo landslide are selected as references for comparative analysis, with the results aligning with engineering reality.
2-Dimensional Ti3C2Tx/NaF nano-composites as electrode materials for hybrid battery-supercapacitor applications
Authors: Riaz M. Bilal , Hussain Danish , Awan Saif Ullah , Rizwan Syed , Zainab Sana , Shah Saqlain A. 
Published: January 2024

AbstractThe increasing global demand for energy storage solutions has spurred interest in advanced materials for electrochemical energy storage devices. Transition-metal carbides and nitrides, known as MXenes, are characterized by remarkable conductivity and tunable properties, They have gained significant attention for their potential in energy storage applications. The properties of two-dimensional (2-D) MXenes can be tuned by doping or composite formation. We report a novel Ti3C2Tx/NaF composite prepared via a straightforward hydrothermal process for supercapacitor electrode applications. Three composites with varying NaF concentrations (1%, 3%, and 5%) were synthesized under similar conditions. Structural characterization using X-ray diffraction (XRD) and scanning electron microscopy confirmed the successful formation of the composites, whereas distinct shifts in XRD peaks and new peaks revealed the presence of NaF. Electrochemical performance was evaluated by cyclic voltammetry, galvanostatic charging-discharging, and electrochemical impedance spectroscopy. The composites exhibited pseudo-capacitive behavior with reversible redox reactions during charge and discharge cycles. Specific capacitance of 191 F/g at scan rates of 2 mV/s was measured in 1 M KOH. Electrochemical impedance spectroscopy revealed an escalating impedance factor as NaF content increases within Ti3C2Tx. This study underscores the versatile energy storage potential of Ti3C2Tx/NaF composites, offering insights into their tailored properties and behavior.
Histopathology images-based deep learning prediction of prognosis and therapeutic response in small cell lung cancer
Authors: Zhang Yibo , Yang Zijian , Chen Ruanqi , Zhu Yanli , Liu Li , Dong Jiyan , Zhang Zicheng , Sun Xujie , Ying Jianming , Lin Dongmei , Yang Lin , Zhou Meng 
Published: January 2024

AbstractSmall cell lung cancer (SCLC) is a highly aggressive subtype of lung cancer characterized by rapid tumor growth and early metastasis. Accurate prediction of prognosis and therapeutic response is crucial for optimizing treatment strategies and improving patient outcomes. In this study, we conducted a deep-learning analysis of Hematoxylin and Eosin (H&E) stained histopathological images using contrastive clustering and identified 50 intricate histomorphological phenotype clusters (HPCs) as pathomic features. We identified two of 50 HPCs with significant prognostic value and then integrated them into a pathomics signature (PathoSig) using the Cox regression model. PathoSig showed significant risk stratification for overall survival and disease-free survival and successfully identified patients who may benefit from postoperative or preoperative chemoradiotherapy. The predictive power of PathoSig was validated in independent multicenter cohorts. Furthermore, PathoSig can provide comprehensive prognostic information beyond the current TNM staging system and molecular subtyping. Overall, our study highlights the significant potential of utilizing histopathology images-based deep learning in improving prognostic predictions and evaluating therapeutic response in SCLC. PathoSig represents an effective tool that aids clinicians in making informed decisions and selecting personalized treatment strategies for SCLC patients.
Peptidyl nitroalkene inhibitors of main protease rationalized by computational and crystallographic investigations as antivirals against SARS-CoV-2
Authors: Medrano Francisco J. , de la Hoz-Rodríguez Sergio , Martí Sergio , Arafet Kemel , Schirmeister Tanja , Hammerschmidt Stefan J. , Müller Christin , González-Martínez Águeda , Santillana Elena , Ziebuhr John , Romero Antonio , Zimmer Collin , Weldert Annabelle , Zimmermann Robert , Lodola Alessio , Świderek Katarzyna , Moliner Vicent , González Florenci V. 
Published: January 2024

AbstractThe coronavirus disease 2019 (COVID-19) pandemic continues to represent a global public health issue. The viral main protease (Mpro) represents one of the most attractive targets for the development of antiviral drugs. Herein we report peptidyl nitroalkenes exhibiting enzyme inhibitory activity against Mpro (Ki: 1–10 μM) good anti-SARS-CoV-2 infection activity in the low micromolar range (EC50: 1–12 μM) without significant toxicity. Additional kinetic studies of compounds FGA145, FGA146 and FGA147 show that all three compounds inhibit cathepsin L, denoting a possible multitarget effect of these compounds in the antiviral activity. Structural analysis shows the binding mode of FGA146 and FGA147 to the active site of the protein. Furthermore, our results illustrate that peptidyl nitroalkenes are effective covalent reversible inhibitors of the Mpro and cathepsin L, and that inhibitors FGA145, FGA146 and FGA147 prevent infection against SARS-CoV-2.