bluuebunny/crossref_metadata_2025_split huggingface dataset:
Profiling Cancer-Associated Fibroblasts (CAFs) in Gastric Cancer and Development of a CAF-Based Prognostic Signature Using Integrated Single-Cell RNA Sequencing and TCGA Analysis
Authors: Sun Xiaofei , Gao Song , Hu Lili , Liu Yanli 
Published: March 2024

Abstract
Background: Cancer-associated fibroblasts (CAFs) play critical roles in tumor growth, angiogenesis, metastasis, and therapy resistance. This study aimed to investigate the characteristics of CAFs in gastric cancer (GC) and develop a CAF-based risk signature for predicting the prognosis of GC patients.
Methods: Single-cell RNA sequencing (scRNA-seq) data were obtained from the GEO database. The data related to the survival prognosis of gastric cancer patients is derived from TCGA. The scRNA-seq data were analyzed using the Seurat R package, resulting in the identification of CAF clusters based on characteristic markers. Subsequent differential expression analysis was performed on the TCGA dataset to identify genes exhibiting differential expression (DEGs) between normal and tumor samples. Pearson correlation analysis was then utilized to uncover DEGs correlated with CAF clusters, followed by univariate Cox regression analysis to identify prognostic genes associated with CAFs. Lasso regression was applied to construct a risk signature based on these prognostic CAF-related genes. Lastly, a comprehensive scoring model, integrating the risk signature and clinicopathological characteristics, was meticulously developed.
Results: From the scRNA-seq data of gastric cancer (GC), six distinct clusters of cancer-associated fibroblasts (CAFs) were delineated, among which five clusters exhibited significant associations with GC prognosis. A total of 557 differentially expressed genes (DEGs) were identified that showed strong correlations with these CAF clusters. From this set, a refined risk signature comprising six key genes was derived. These pivotal genes were predominantly implicated in 39 biological pathways, encompassing crucial processes such as angiogenesis, apoptosis, and hypoxia. Notably, the risk signature demonstrated notable correlations with stromal and immune scores, as well as specific immune cell types. Furthermore, multivariate analysis underscored the independent prognostic role of the risk signature in GC, showcasing its potential for predicting outcomes of immunotherapy. The integration of the stage with the CAF-based risk signature yielded a novel scoring model with robust predictive performance and reliability in prognosticating GC outcomes.
Conclusion: The CAF-derived risk signature emerges as a potent prognostic tool for GC, offering valuable insights into the intricate landscape of CAFs within the tumor microenvironment. Such comprehensive profiling may hold promise in guiding personalized immunotherapeutic strategies and refining treatment modalities for GC.
A comprehensive functional investigation of the human translocator protein 18 kDa (TSPO) in a novel human neuronal cell knockout model: from molecule to depression
Authors: Wetzel Christian , Bader Stefanie , Jahner Tatjana , Dörfelt Anett , Melchner Doris , Cardon Iseline , Siegmund Heiko , Brochhausen Christoph , Rupprecht Rainer , Milenkovic Vladimir 
Published: March 2024

Abstract

The translocator protein 18 kDa (TSPO) is a multifunctional outer mitochondrial membrane protein associated with various aspects of mitochondrial physiology and multiple roles in health and disease. Here, we aimed to analyze the impact of TSPO on the regulation of mitochondrial and cellular function in a human neuronal cell model. We used the CRISPR/Cas9 technology and generated TSPO knockout (KO) and control (CTRL) variants of human induced pluripotent stem cells (hiPSCs). In a multimodal phenotyping approach, we investigated cellular and mitochondrial function in neural progenitor cells (NPCs), astrocytes, and neurons differentiated from hiPSC CTRL and TSPO KO cell lines. Our analysis revealed reduced mitochondrial respiration and glycolysis, altered Ca2+ levels in the cytosol and mitochondrial matrix, a depolarized MMP, and increased levels of reactive oxygen species, as well as a reduced cell size. Notably, TSPO deficiency was accompanied by reduced expression of the voltage-dependent anion channel (VDAC). We also observed a reduced TSPO and VDAC expression in cells derived from patients suffering from major depression (MDD). Considering the modulatory function of TSPO and the similar functional phenotype of cells derived from patients with depression, we discuss a role of TSPO in the aetiology or pathology of MDD. Taken together, these findings indicate the impairment of mitochondrial function in TSPO KO cells, contributing to the understanding of the multifaceted role of TSPO and setting the stage for further investigations to unravel the underlying mechanisms and its involvement in various physiological and pathological processes.
Towards a better understanding of the characteristics of electrolytic plasma discharge and spark discharge in ECDM
Authors: Zhan Shunda , Shi Wentao , Liu Mingjun , Tang Wenming , Jiang Kai 
Published: March 2024

Abstract

Electrochemical discharge machining (ECDM) is an essential process for microstructures fabrication of difficult-to-machine materials. Currently, there are various kinds of ECDM, and plasma-assisted electrochemical machining (PA-ECM) is a new and promising ECDM proposed in recent years. However, the differences between electrolytic plasma discharge and conventional spark discharge are unclear. Therefore, this study aims to systematically explain the evolvement mechanism and characteristics of these two kinds of discharge. From the phenomenology, the electrolytic plasma discharge is saffron color determined by electrolyte and wrapped at the entire immersion surface of the tool electrode, while the spark discharge is white color and only excited at the end of the tool electrode. Electrolytic plasma discharge is generated preferentially to spark discharge, and easily transforms to spark discharge in high electric field strength such as large applied voltage or small inter-electrode gap. The discharge energy and emission spectrum of spark discharge is more significant than that of electrolytic plasma discharge. Especially, the electrolytic plasma discharge does not cause any tool electrode wear due to the low discharge energy (discharge current about 0.5 A), and the resulted surface of the workpiece is smooth. On the contrary, the spark discharge energy is high (discharge current about 9 A), which causes noticeable tool electrode wear and leaves discharge craters and thermal damage on the workpiece surface. Considering the obvious flushing effect of bubble flow during plasma ignition, PA-ECM is an ideal method for functional surface micro-dimple array fabrication without using tube central spray and workpiece mask.
The Acute Effect of Two Physical Exercise Programs on Cognitive Performance in Schoolchildren
Authors: Moraes Marcos , Brand Caroline , Silveira João Francisco Castro , Barbian Cheila Daiana , Sisnande Fernando Zaluar , Henriquez-Maquehue Fernanda , Milagres Gabriele Zawacki , Cristi-Montero Carlos , Corbellini Valeriano Antonio , Campos Deivis 
Published: March 2024

Abstract
Aim: To verify the acute effect of two physical exercise programs on cognitive performance (inhibitory control and cognitive flexibility) in schoolchildren. Methods:This is a randomized controlled clinical study with three groups: Experimental Group 1 (EG1) received problem-solving, balance, and movement coordination exercises; Experimental Group 2 (EG2) received exercises involving playful and recreational activities; and Control Group (CG) did not receive any type of intervention. Both interventions were applied at moderate intensity. The study included 94 schoolchildren of nine and 10 years old (48 boys) from public schools. To evaluate cognitive performance, two tests were used: The Trail Test to assess cognitive flexibility and the computerized Stroop Test (Testinpacs) to determine inhibitory control. Generalized Estimating Equations (GEE) were used to construct models with Trail or Stroop tests as dependent variables. Results: in the Trail Test (cognitive flexibility), there was a statistically significant interaction effect in EG1 regarding both execution time (p < 0.01) and the number of errors (p < 0.01), while in EG2, it was only on the number of errors (p < 0.01). Concerning the Stroop test (inhibitory control), both EG1 and EG2 showed a significant reduction in the number of errors (p < 0.01), indicating an acute effect after the intervention in both groups. Conclusion: the exercise programs in EG1 and EG2 positively affected cognitive performance, including inhibitory control and cognitive flexibility in schoolchildren. Moreover, considering all the variables of cognitive performance tests, EG1 was a promising alternative to be developed in schools, positively impacting cognitive performance and, consequently, learning.
The prevalence and factors associated with rheumatoid arthritis-associated interstitial lung disease
Authors: Suppa-udom Benyapa , Disayabutr Supparerk , Wonglaksanapimon Suwimon , Butnian Krittachat , Katchamart Wanruchada 
Published: March 2024

Abstract
Background
Interstitial lung disease (ILD) is a significant extra-articular manifestation of rheumatoid arthritis (RA). The prevalence and risk factors for ILD in RA exhibit considerable variation. This study aimed to determine the prevalence and factors associated with ILD in Thai patients with RA.
Methods
This cross-sectional study enrolled 290 RA patients from the Siriraj Rheumatoid Arthritis Registry between March and December 2022. Patient characteristics, disease activity, and functional status were documented. Chest X-ray (CXR) was employed for ILD screening, and suspected cases were further evaluated using high-resolution computed tomography (HRCT) and pulmonary function tests.
Results
Among the 290 patients, the majority were female (89.7%) with mean age (SD) of 59±12 years, and the median disease duration was 10 years. Patients exhibited low disease activity (with a mean Disease Activity Score 28-erythrocyte sedimentation rate score of 2.69±0.90) and mild functional impairment (with a median Health Assessment Questionnaire score of 0.25). Thirteen patients (4.5%) were diagnosed with ILD via HRCT (RA-ILD), with nonspecific interstitial pneumonia being the predominant ILD pattern (76.9%). Pulmonary function tests showed normal results in most patients, with only 15.4% presenting restrictive ventilatory defects. Age (P = 0.04), breathlessness (P < 0.001), bibasilar crackles (P < 0.001), and functional impairment (P = 0.02) exhibited significant associations with RA-ILD.
Conclusions
ILD is relatively infrequent in Thai patients with RA. Older age, breathlessness, crackles, and functional impairment should prompt investigations for ILD in RA patients.
State-of-the-Art and Future Directions
Authors: Khan Mohammad Salman , Imran Ayesha 
Published: March 2024

Abstract
In our daily lives, smart AI-powered devices including computers are becoming more common. But the problem is that sometimes these AI systems make decisions that seem like magic, making it hard for us to know how they work and also, we are not able to predict the future (like after making a decision, we are not able to predict whether the result will be positive or negative). This research paper is all about fixing this issue and making the AI strong enough to make a decision and learn each positive and negative thing from the surroundings. We dive into the world of Explainable Artificial Intelligence (XAI), finding new and simple ways to make complex AI systems easy for people to understand. In this Research paper, we are also going to make the AI that much more powerful so that it can learn itself and gather information from its surroundings. This would be a fantastic step for AI to learn Patterns, Structures, and Unlabeled data allowing it to identify hidden relationships and features without explicit guidance. This would be Self-Supervised Learning in which the AI would be able to create its labels or predictions based on input data, generating a form of supervision. This system would be able to do facial detection and compare the Raw info with the DataSet. The system would also be able to make the most suitable and accurate decisions. With time this machine would be able to upgrade its memory (taking a human baby as an example/consideration).
In a nutshell, our research aims to make AI systems not just powerful, but also easy to understand and trustworthy for everyone and make them Self-Supervised.
Clinical features and prognosis of prosthetic valve endocarditis due to Staphylococcus aureus
Authors: Calderón-Parra Jorge , Ramos-Martínez Antonio , Muñoz Patricia , Martínez-Sellés Manuel , Machado-Vilchez Marina , Alarcón Arístides , Miró José M , Rodríguez-García Raquel , Gutiñerrez-Díez Jose Francisco , Hidalgo-Tenorio Carmen , Loeches-Yagüe Belén , López-Azor Juan Carlos 
Published: March 2024

Abstract

Purpose. Staphylococcus aureus prosthetic valve endocarditis (SAPVE) is a serious infection with high mortality. The main objective of this study was to identify factors associated with in-hospital mortality.
Methods. From January 2008 to December 2021, consecutive patients from a Spanish cohort of infective endocarditis with a definitive diagnosis of SAPVE were analyzed.
Results. During the study period, 219 cases of definitive SAPVE were diagnosed, which accounted for 16.7% of a total of 1309 cases of definitive prosthetic valve endocarditis (PVE). Patients presented advanced age and marked comorbidity. There was a higher incidence of persistent bacteremia, septic shock, stroke, and acute kidney injury than in cases of PVE caused by other microorganisms. Methicillin resistance was not associated with differences in clinical presentation, echocardiographic findings, or mortality. Only 50.6% of the patients with surgical indications (88 patients) underwent surgery. Overall, in-hospital mortality was 47.9%. The variables associated with in-hospital mortality were age (OR:1.03, 95% CI: 1.00-1.05; p = 0.016), heart failure (OR:2.86, 95% CI: 1.53–5.32; p = 0.001), acute kidney injury (OR:2.42, 95%CI:1.28–4.58; p = 0.006), stroke (OR:3.53, 95%CI:1.79–6.96; p < 0.001) and surgery indicated but not performed (OR:2.01, 95%CI:1.06–3.8; p = 0.030). On the other hand, the performance of surgery per se in patients with SAPVE, regardless of whether there was a surgical indication according to the guidelines, was not associated with a reduction in in-hospital mortality.
Conclusions. SAPVE is characterized by high mortality, which is more marked in patients who present a surgical indication but do not undergo surgery.
Dynamic evolution of nitrogen cycle and pH homeostasis genes enabled the diversification of Pampinifervens gen. nov. (Aquificaceae)
Authors: Palmer Marike , Nou Nancy O. , Turello Lara A. , Power Carolyn E. , Ong John C. , Lai Dengxun , Reysenbach Anna-Louise , Qi Yan-Ling , Dodsworth Jeremy A. , Jiao Jian-Yu , Liu Lan , Lian Zheng-Han , Li Meng-Meng , Liu Yitai , Briggs Brandon R. , Zuo Hongyan , Quake Stephen R. , Eloe-Fadrosh Emiley A. , Woyke Tanja , Dong Hailiang , Li Wen-Jun , Hua Zhengshuang , Hedlund Brian P. 
Published: March 2024

Abstract
Background: Members of the phylum Aquificota were initially documented more than a century ago and play important roles in hydrogen, sulfur, and carbon cycles in geothermal systems as ubiquitous and abundant chemolithoautotrophs; however, their roles in the nitrogen cycle are not well defined.
Results: Here, we show that a novel Aquificaceae isolate from Tengchong, China, fixes nitrogen in pure culture and that nitrogen fixation (nif) genes are transcribed in situ. We propose the name Pampinifervens diazotrophicum gen. et sp. nov. to accommodate this organism, with strain T-2T as the nomenclatural type. Analysis of metagenomes from physicochemically diverse springs in Tengchong showed that Pampinifervens dominates the Aquificota populations in most springs, consistent with a wide pH growth range for strain T-2T (pH 6.0-9.5) and another isolate, strain T-8T (pH 5.5-10.0). Despite the role of P. diazotrophicum in nitrogen fixation, strain T-8T does not fix nitrogen, but respires nitrate. Analysis of 104 metagenome-assembled genomes from 84 metagenomes globally, including at least 16 sympatric Pampinifervens species and other species from Canada, Japan, Malaysia, and Russia, revealed the variable presence of nif and denitrification genes. In contrast, genes for hydrogen chemolithotrophy, sulfur chemolithotrophy, and autotrophy were more conserved. Genes required for homeostasis were also present in the genus, with a proliferation of these genes in species recovered from Tengchong, China, that likely allowed them to diversify from neutral and alkaline bicarbonate-buffered springs into acidic sulfuric acid-buffered springs.
Conclusions: Together, this work presents a widespread but overlooked genus of Aquificaceae and evolutionary patterns that suggest an important role for nitrogen metabolism and pH homeostasis in the local speciation of Pampinifervens in Southwest China. We suggest that Pampinifervens and possibly other Aquificaceae have underappreciated but diverse roles in nitrogen cycling.
Based on ecological risk assessment of landscape from the perspective of Saihanba landscape pattern changes
Authors: Kang Jiemin , Yang Jinyu , Qing Yunxian , Lu Wei 
Published: March 2024

Abstract
Examining the Saihanba Mechanical Forest Farm, this study utilized landsat remote sensing data from 1987, 1997, 2001, 2013, and 2020 to interpret land use from the vector machine method, and to decipher evolving land use patterns over the last four decades. Grounded in landscape ecology theory, an innovative evaluation index for landscape ecological risk was introduced, leading to the delineation of 382 ecological risk evaluation units based on the degree of global landscape risk. Employing landscape pattern indices and a method around spatial autocorrelation, we analyzed the spatial and temporal distribution characteristics and spatial correlation patterns of landscape ecological risk across five distinct periods. Geostatistical approaches were used to explore the driving factors of landscape risk. Results indicate significant shifts in land use types since 1987, notably with a evident increase in forest landscape predominantly at the expense of grassland and sandy land. Over the 1987 to 2020 period, landscape risk demonstrated a gradual decline, with mid-high and high-risk areas clustering in specific locales, while the broader region predominantly featured low landscape risk. The landscape ecological risks in each period of the study area showed a positive spatial correlation and tended to gather in space. Since its establishment in 1962, the landscape changes caused by human factors such as afforestation projects and scientific forest management methods have reduced the ecological risk of the landscape. A comprehensive exploration using geographic detectors identified nine ecological driving factors, with soil type emerging as the principal risk determinant, and its synergistic interaction with precipitation and other factors surpassing the individual factor effects.
Natural Non-Hermitian Control of High-Dimensional Rabi Oscillating of Tri-photon Using Multi-dressing Quantization
Authors: Wei Jiaxuan , Yang Qinyue , Wei Jiajia , Zhuang Rui , Tang Haitian , Chen Qingyu , Li Feng , Liu Fu , Zhang Lei , Cai Yin , Zhang Yanpeng 
Published: March 2024

Abstract
Non-Hermitian degeneracies, also known as exceptional points, have recently emerged as a new way to engineer the response of open physical systems, we construct non-Hermitian systems through atomic electromagnetically induced transparency structures, based on which we study energy-level high-dimensional quantized photon correlations under dressing field induced parity-time (PT) symmetry and symmetry breaking. We study the symmetry breaking through exceptional point (EP) control in dressing-controlled energy-level process is natural EP, which are born to be non-Hermitian without artificial photonic structures. When the dressing Rabi frequency (de-phase rate) dominates, the real part (imaginary part) splits, and leads to in-phase (out-of-phase) constructive (destructive) dressing quantization. It can also be used to develop atomic-like symmetry-breaking photonic chips and pseudo-spin devices in the future.
Edge information preserving generative adversarial network combining Transformer and multi-scale fusion for MRI modality transfer
Authors: Li Yang , Wang Wendong , Bai Bingyang 
Published: March 2024

Abstract

Magnetic Resonance Imaging (MRI) is a multi-sequence imaging technology that assists clinicians in diagnosis. However, due to factors such as long scanning time, inability of patients to cooperate, and high cost of obtaining the full sequence, clinically only Part of the comparison sequence. However, often missing sequences can help diagnose clinical diseases. Therefore, generating missing MRI sequences is very important for clinical diagnosis. However, most existing methods for MRI generation lack the learning of global context information, thereby losing part of the task-related feature information, or only consider the pixel-level difference between the generated image and the real image, ignoring the details and details of the image. Texture information affects the quality of image generation. In response to the above problems, a edge information preserving generative adversarial network combining Transformer and multi-scale fusion (ETF-GAN) for MRI modality transfer was proposed.. This model combined with Transformer improves the accuracy of To capture global context information, the Iterative Multi-scale Concatenate Fusion (IMCF) module is proposed in the decoder part to enhance the decoder’s ability to utilize features of different scales, while also introducing Sobel Edge Extraction (SEE) module to retain the edge information of the image and improve the quality of image generation. Experiments show that the proposed method is superior to other advanced MRI modality transfer methods in quantitative comparison and visual comparison.
Design and verification of universal virtual shopping mall application
Authors: Lee Danbi , Kim Hyun K. , Park Jaehyun 
Published: March 2024

Abstract

The aim of this study was to design the user experience for a head-mounted display (HMD)-based universal virtual shopping mall by conducting a literature analysis and employing video ethnography techniques. Subsequently, a prototype was developed to validate the outcomes. Despite the growing trend of contactless shopping, with various brands launching virtual mall platforms, these often lack the elements and experiences that users find satisfying. To address this gap, we analysed users' offline shopping experiences using video ethnography. The insights gained informed the development of a prototype that adopts a universal design approach, incorporating key features and interface designs tailored for a virtual mall environment. The prototype includes innovative features include tutorials, avatar-based virtual fitting, user location/orientation control, and voice guidance. It also incorporates design features such as colour customisation, high contrast, central interface placement, and visual cues for differentiating product types. To validate the prototype’s usability, a study was conducted with 30 university students in their 20s (mean age 23.3 years, SD = 1.8), revealing high levels of satisfaction with its functionality and interface design. Further, in-depth interviews revealed that the appropriate design of features and interfaces, aligned with shopping goals and intentions, significantly enhanced interest in and engagement with virtual shopping. The prototype's key features, representative of the main outcomes of this study, provide valuable insights for the future development of related services.