bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploitation of tumor antigens and construction of immune subtype classifier for mRNA vaccine development in bladder cancer
Authors: Zhang Xin , Zhang Yanlong , Zhao Li , Wang Jiayu , Li Jiaxing , Wang Xi , Zhang Min , Hu Xiaopeng 
Published: November 2022

BackgroundBladder cancer (BLCA) is one of the most prevalent urinary system malignancies, with high mortality and recurrence. The present study aimed to identify potential tumor antigens for mRNA vaccines in BLCA and patient subtypes suitable for different immunotherapy.MethodsGene expression profiles, mutation data, methylation data, and corresponding clinical information were obtained from the Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and ArrayExpress databases. Immunohistochemical staining of microarrays was performed to assess protein expression levels of IGF2BP2 and MMP9. Differential gene analysis, survival analysis, correlation analysis, consensus clustering analysis, and immune cell infiltration analysis were conducted using R software. Finally, the R package “immcluster” was used based on Combat and eXtreme Gradient Boosting algorithms to predict immune clusters of BLCA samples.ResultsTwo mutated, amplified, and over-expressed tumor antigens, IGF2BP2 and MMP9, were found to be associated with clinical outcomes and the abundance of antigen-presenting cells (APCs). Subsequently, three immune subtypes (BIS1, BIS2, and BIS3) were defined in the BLCA cohort. BIS3 subtype exhibited an “active” immune phenotype, while BIS1 and BIS2 subtypes have a “suppressive” immune phenotype. Patients in BIS1 and BIS2 had a poor prognosis compared to BIS3. BIS3 had a higher score in checkpoints or immunomodulators (CP) and immunophenoscore (IPS), while BIS1 and BIS2 scored higher in major histocompatibility complex-related molecules (MHC molecules). Meanwhile, BIS2 and BIS3 had a significantly higher tumor mutational burden (TMB) compared to patients with BIS1. Finally, the “immcluster” package was applied to the dataset, which has been shown to accurately predict the immune subtypes of BLCA samples in many cohorts.ConclusionsIGF2BP2 and MMP9 were potential antigens for developing mRNA vaccines against BLCA. The results in the present study suggested that immunotherapy targeting these two antigens would be suitable for patients falling under the BIS2 subtype. R package “immcluster” could assist in screening suitable BLCA patients for antitumor therapy.
Indirubin combined with umbilical cord mesenchymal stem cells to relieve psoriasis-like skin lesions in BALB/c mice
Authors: Lu XiaoJuan , Wang Hao , Wang Hongwei , Xie Fan , Jiang Cuibao , Shen Danpeng , Zhang Hongpeng , Yang Jie , Lin Youshu 
Published: November 2022

ObjectiveTo investigate the efficacy of indirubin combined with human umbilical cord mesenchymal stem cells (hUC-MSCs) in the treatment of psoriatic lesions in BALB/c mice and to explore the related mechanism of indirubin in the treatment of psoriasis.MethodsA BALB/c mouse psoriasis model induced by imiquimod was established and randomly divided into the control group, model group, indirubin group, hUC-MSCs group, and indirubin combined with hUC-MSCs group. Psoriasis area and severity index (PASI) score was used to observe skin lesion changes in the psoriasis-like mouse model. The epidermal scale, the degree of keratinization, and the infiltration of inflammatory cells were observed by hematoxylin eosin (HE) staining. The concentrations of TNF-α, IFN-γ, IL-17A, and IL-23 in serum of mice were measured using enzyme-linked immunosorbent assay (ELISA).ResultsThe PASI integral trend chart indicates that hUC-MSCs and indirubin and the combination of drugs could relieve the appearance of skin lesions and accelerate the recovery of skin lesions. The indirubin group had the best effect in improving the scale of skin lesions. HE staining showed that the number of parakeratosis cells in the three treatment groups was significantly reduced, the degree of erythrocyte extravasation dermis hyperplasia and inflammatory cell infiltration was significantly lower than that in the model group, and the skin thickness and spleen index of the combined treatment group exhibited the most noticeable improvement. ELISA showed that the concentrations of TNF-α, IFN-γ, IL-17A, and IL-23 in serum of mice in the hUC-MSCs treatment group, indirubin group, and combined administration group were all decreased compared with those in the model group, and the concentrations of IFN-γ, IL-17A, and IL-23 could be decreased significantly in the indirubin group.ConclusionsBoth hUC-MSCs and indirubin can effectively reduce psoriasis-like lesions in BALB/c mice, and the combined administration of these drugs has the best effect.
Circulating mitochondrial cell-free DNA dynamics in patients with mycobacterial pulmonary infections: Potential for a novel biomarker of disease
Authors: Pan Sheng-Wei , Syed Rehan R. , Catanzaro Donald G. , Ho Mei-Lin , Shu Chin-Chung , Tsai Tsung-Yeh , Tseng Yen-Han , Feng Jia-Yih , Chen Yuh-Min , Su Wei-Juin , Catanzaro Antonino , Rodwell Timothy C. 
Published: November 2022

ObjectivesHuman mitochondrial cell-free DNA (Mt-cfDNA) may serve as a useful biomarker for infectious processes. We investigated Mt-cfDNA dynamics in patients with pulmonary mycobacterial infections to determine if this novel biomarker could be used to differentiate disease states and severity.MethodsPatients with pulmonary tuberculosis (PTB), latent tuberculosis infection (LTBI), and nontuberculous mycobacterial-lung disease (NTM-LD) were enrolled at a tertiary care hospital in Taiwan between June 2018 and August 2021. Human Mt-cfDNA and nuclear-cfDNA (Nu-cfDNA) copy numbers were estimated by quantitative polymerase chain reaction. Variables associated with PTB and 2-month sputum culture-positivity, indicating poor treatment response, were assessed using logistic regression.ResultsAmong 97 patients with PTB, 64 with LTBI, and 51 with NTM-LD, Mt-cfDNA levels were higher in patients with PTB than in LTBI (p=0.001) or NTM-LD (p=0.006). In the Mycobacterium tuberculosis-infected population, Mt-cfDNA levels were highest in smear-positive PTB patients, followed by smear-negative PTB (p&lt;0.001), and were lowest in LTBI persons (p=0.009). A Mt-cfDNA, but not Nu-cfDNA, level higher than the median helped differentiate culture-positive PTB from culture-negative PTB and LTBI (adjusted OR 2.430 [95% CI 1.139–5.186], p=0.022) and differentiate PTB from NTM-LD (adjusted OR 4.007 [1.382–12.031], p=0.011). Mt-cfDNA levels decreased after 2 months of treatment in PTB patients (p=0.010). A cutoff Mt-cfDNA level greater than 62.62 x 106 copies/μL-plasma was associated with a 10-fold risk of 2-month culture-positivity (adjusted OR 9.691 [1.046–89.813], p=0.046).ConclusionElevated Mt-cfDNA levels were associated with PTB disease and failed sputum conversion at 2 months in PTB patients, and decreased after treatment.
Label-free quantitative proteomics and immunoblotting identifies immunoreactive and other excretory-secretory (E/S) proteins of Anoplocephala perfoliata
Authors: Hautala Katja , Pursiainen Jami , Näreaho Anu , Nyman Tuula , Varmanen Pekka , Sukura Antti , Nielsen Martin K. , Savijoki Kirsi 
Published: November 2022

Anoplocephala perfoliata is a common tapeworm in horses causing colic and even mortalities. Current diagnostic tests to detect A. perfoliata infections have their limitations and an improved method is needed. Immunoreactive excretory/secretory proteins (E/S proteome) of this parasite can provide promising candidates for diagnostic tests. We compared E/S proteins produced by small (length &lt; 20 mm, width &lt; 5 mm) and large (length 20 to 40 mm, width 5 to 10 mm) A. perfoliata worms in vitro by label-free quantitative proteomics using a database composed of related Hymenolepis diminuta, Echinococcus multilocularis/granulosus and Taenia aseatica proteins for protein identifications. Altogether, 509 E/S proteins were identified after incubating the worms in vitro for three and eight hours. The greatest E/S proteome changes suggested both worm size- and time-dependent changes in cytoskeleton remodeling, apoptosis, and production of antigens/immunogens. The E/S proteins collected at the three-hour time point represented the natural conditions better than those collected at the eight-hour time point, and thereby contained the most relevant diagnostic targets. Immunoblotting using antibodies from horses tested positive/negative for A. perfoliata indicated strongest antigenicity/immunogenicity with 13-, 30- and 100-kDa proteins, involving a thioredoxin, heat-shock chaperone 90 (Hsp90), dynein light chain component (DYNLL), tubulin-specific chaperone A (TBCA) and signaling pathway modulators (14-3-3 and Sj-Ts4). This is among the first studies identifying new diagnostic targets and A. perfoliata antigens eliciting a IgG-response in horses.
Brain-gut axis and psychiatric disorders: A perspective from bibliometric and visual analysis
Authors: Chen Pan , Zhang Ling , Feng Yuan , Liu Yu-Fei , Si Tong Leong , Su Zhaohui , Cheung Teris , Ungvari Gabor S. , Ng Chee H. , Xiang Yu-Tao 
Published: November 2022

BackgroundThe Brain-Gut Axis, a bidirectional signaling pathway that connects the intestinal and central nervous systems, plays an important role in the development of psychiatric disorders. However, the overall research trends in this field are unclear. This study explored the patterns of research on the brain-gut axis and psychiatric disorders from a bibliometric perspective.MethodsRelevant data were retrieved from the Web of Science Core Collection, with search terms on psychiatric disorders and the brain-gut axis. R (version 4.2.0), VOSviewer (version 1.6.17), CiteSpace software, and the online bibliometric platform were used in the data analysis.ResultsA total of 2,298 articles published between 1993 and 2022 were identified, showing an increasing trend over time. China (1,859; 20.70%) was the country that contributed the most publications. The journal Nutrients (95; 4.13%) published the most publications. Cryan JF (153; H-index=73) and University College Cork (559; 22.54%) were the most influential author and the most productive institution, respectively. The high-frequency keywords were clustered into six themes, including neurodegenerative diseases, stress-related diseases, immune, brain behavior, depression, and probiotic-related topics; of which, depression (880; 2019), anxiety (207; 2018) and autism (191; 2019) were the most studied psychiatric disorders in the past 5 years. “Depressive symptom” (2019-2020) and “probiotic treatment” (2019-2020) were the main areas addressed in recent years.ConclusionResearch on the brain-gut axis and psychiatric disorders has attracted increasing attention in the past decade, with most publications originating from high-income level countries. This study provides a useful perspective on understanding the research trends, key hot topics, and research gaps in this expanding field.
Neutrophils inhibit γδ T cell functions in the imiquimod-induced mouse model of psoriasis
Authors: Costa Sara , Bevilacqua Dalila , Caveggion Elena , Gasperini Sara , Zenaro Elena , Pettinella Francesca , Donini Marta , Dusi Stefano , Constantin Gabriela , Lonardi Silvia , Vermi William , De Sanctis Francesco , Ugel Stefano , Cestari Tiziana , Abram Clare L. , Lowell Clifford A. , Rodegher Pamela , Tagliaro Franco , Girolomoni Giampiero , Cassatella Marco A. , Scapini Patrizia 
Published: November 2022

BackgroundPsoriasis is a chronic skin disease associated with deregulated interplays between immune cells and keratinocytes. Neutrophil accumulation in the skin is a histological feature that characterizes psoriasis. However, the role of neutrophils in psoriasis onset and development remains poorly understood.MethodsIn this study, we utilized the model of psoriasiform dermatitis, caused by the repeated topical application of an imiquimod containing cream, in neutrophil-depleted mice or in mice carrying impairment in neutrophil functions, including p47phox -/- mice (lacking a cytosolic subunit of the phagocyte nicotinamide adenine dinucleotide phosphate - NADPH - oxidase) and Sykfl/fl MRP8-cre+ mice (carrying the specific deletion of the Syk kinase in neutrophils only), to elucidate the specific contribution of neutrophils to psoriasis development.ResultsBy analyzing disease development/progression in neutrophil-depleted mice, we now report that neutrophils act as negative modulators of disease propagation and exacerbation by inhibiting gammadelta T cell effector functions via nicotinamide adenine dinucleotide phosphate (NADPH) oxidase-mediated reactive oxygen species (ROS) production. We also report that Syk functions as a crucial molecule in determining the outcome of neutrophil and γδ T cell interactions. Accordingly, we uncover that a selective impairment of Syk-dependent signaling in neutrophils is sufficient to reproduce the enhancement of skin inflammation and γδ T cell infiltration observed in neutrophil-depleted mice.ConclusionsOverall, our findings add new insights into the specific contribution of neutrophils to disease progression in the IMQ-induced mouse model of psoriasis, namely as negative regulatory cells.
Clinical analysis of 96 patients with intraorbital foreign bodies: A 10-year retrospective study
Authors: You Yayan , Wang Xinghua , Cheng Shengnan , Zhu Ru , Wang Bowen , Li Shuang , Jiang Fagang 
Published: November 2022

IntroductionTo investigate the clinical manifestations, diagnosis, and surgical treatment of intraorbital foreign bodies (IOFBs).MethodsPatients with IOFBs were enrolled from Wuhan Union Hospital between January 2011 and January 2021. Demographic and clinical information was extracted, including gender, age, cause and entrance of the trauma, material, size and quantity of foreign body, visual function, ocular complications, imaging findings, and surgical intervention. The patients were divided into two groups according to the timeline, group A (from January 2011 to December 2015, n = 39) and group B (from January 2016 to January 2021, n = 57).ResultsThe 96 patients (81 men and 15 women) were enrolled in this series, with a median age of 39.5 (1.6–76.0) years. Work-related injuries were the cause of IOFBs in 45 individuals (46.9%). Three patients (3.3%) presented severe visual impairment, and 39 patients (42.4%) presented blindness. The majority of foreign bodies were metal (44.8%), followed by wood (26.0%). Computed tomography (CT) and magnetic resonance imaging (MRI) were performed, respectively, on 89 (92.7%) and 21 (21.9%) patients with IOFBs, in which the detection rate was 80.9% for CT and 81.0% for MRI. Among the 25 patients with intraorbital wooden foreign bodies (IOWFBs), the utilization and detection rates of MRI were 50.0% and 40.0% in group A, and 93.3% and 92.9% in group B, with significant differences in both rates between the two groups (both P &lt; 0.05). The IOWFBs detection rate in MRI was significantly higher than that in CT (78.9% vs. 45.8% overall and 92.9% vs. 53.5% in group B). The detection rates of IOFBs and IOWFBs in initial surgery were statistically different between the two groups, of which the rates were 84.6% and 40.0% in group A and 98.2% and 93.3% in group B. The reoperation rate of IOWFBs in group B (20.0%) was significantly lower than that in group A (70.0%).ConclusionIOFBs were mainly caused by work-related injuries and might lead to serious visual impairment. The application and detectability of MRI in IOWFBs improved in recent years, and MRI presented better detectability than CT in diagnosing IOWFBs. Thus, MRI should be recommended despite negative CT findings.
Closed–loop oxygen control improves oxygenation in pediatric patients under high–flow nasal oxygen—A randomized crossover study
Authors: Sandal Ozlem , Ceylan Gokhan , Topal Sevgi , Hepduman Pinar , Colak Mustafa , Novotni Dominik , Soydan Ekin , Karaarslan Utku , Atakul Gulhan , Schultz Marcus J. , Ağın Hasan 
Published: November 2022

BackgroundWe assessed the effect of a closed–loop oxygen control system in pediatric patients receiving high–flow nasal oxygen therapy (HFNO).MethodsA multicentre, single–blinded, randomized, and cross–over study. Patients aged between 1 month and 18 years of age receiving HFNO for acute hypoxemic respiratory failure (AHRF) were randomly assigned to start with a 2–h period of closed–loop oxygen control or a 2–h period of manual oxygen titrations, after which the patient switched to the alternative therapy. The endpoints were the percentage of time spent in predefined SpO2ranges (primary), FiO2, SpO2/FiO2, and the number of manual adjustments.FindingsWe included 23 patients, aged a median of 18 (3–26) months. Patients spent more time in a predefined optimal SpO2range when the closed–loop oxygen controller was activated compared to manual oxygen titrations [91⋅3% (IQR 78⋅4–95⋅1%) vs. 63⋅0% (IQR 44⋅4–70⋅7%)], mean difference [28⋅2% (95%–CI 20⋅6–37⋅8%);P&lt; 0.001]. Median FiO2was lower [33⋅3% (IQR 26⋅6–44⋅6%) vs. 42⋅6% (IQR 33⋅6–49⋅9%);P= 0.07], but median SpO2/FiO2was higher [289 (IQR 207–348) vs. 194 (IQR 98–317);P= 0.023] with closed–loop oxygen control. The median number of manual adjustments was lower with closed–loop oxygen control [0⋅0 (IQR 0⋅0–0⋅0) vs. 0⋅5 (IQR 0⋅0–1⋅0);P&lt; 0.001].ConclusionClosed-loop oxygen control improves oxygenation therapy in pediatric patients receiving HFNO for AHRF and potentially leads to more efficient oxygen use. It reduces the number of manual adjustments, which may translate into decreased workloads of healthcare providers.Clinical trial registration[www.ClinicalTrials.gov], identifier [NCT 05032365].
Multi-view SoftPool attention convolutional networks for 3D model classification
Authors: Wang Wenju , Wang Xiaolin , Chen Gang , Zhou Haoran 
Published: November 2022

IntroductionExisting multi-view-based 3D model classification methods have the problems of insufficient view refinement feature extraction and poor generalization ability of the network model, which makes it difficult to further improve the classification accuracy. To this end, this paper proposes a multi-view SoftPool attention convolutional network for 3D model classification tasks.MethodsThis method extracts multi-view features through ResNest and adaptive pooling modules, and the extracted features can better represent 3D models. Then, the results of the multi-view feature extraction processed using SoftPool are used as the Query for the self-attentive calculation, which enables the subsequent refinement extraction. We then input the attention scores calculated by Query and Key in the self-attention calculation into the mobile inverted bottleneck convolution, which effectively improves the generalization of the network model. Based on our proposed method, a compact 3D global descriptor is finally generated, achieving a high-accuracy 3D model classification performance.ResultsExperimental results showed that our method achieves 96.96% OA and 95.68% AA on ModelNet40 and 98.57% OA and 98.42% AA on ModelNet10.DiscussionCompared with a multitude of popular methods, our algorithm model achieves the state-of-the-art classification accuracy.
Alteration of gut microbiota in migraine patients with irritable bowel syndrome in a Chinese Han population
Authors: Liu Jieqiong , Tang Wenjing , Hou Lei , Wang Jing , Wang Rongfei , Zhang Yaofen , Dong Zhao , Liu Ruozhuo , Yu Shengyuan 
Published: November 2022

ObjectiveMigraine is frequently reported in patients with irritable bowel syndrome (IBS), and emerging evidence suggests that gut microbiota plays a role in migraine and IBS. However, alterations in the gut microbiome in migraine patients with IBS remain unknown. This study aimed to explore the compositions of gut microbiota in migraine patients with IBS in a Chinese Han population.MethodsSixteen migraine patients with IBS and thirteen age- and gender-matched IBS patients with similar dietary and lifestyle habits were enrolled in this pilot study. Demographic data, clinical data, eating habits, lifestyle habits, comorbidities, and medications were recorded using a unified case registration form. Questionnaires for the Migraine Disability Assessment (MIDAS), Pittsburgh Sleep Quality Index (PSQI), Hamilton Anxiety Scale (HAMA), and Hamilton Depression Scale (HAMD) were completed. Fecal samples were collected, and microbial DNA was extracted. Gut microbiota 16S ribosomal RNA (16S rRNA) gene sequencing targeting the V4 region was performed using the Illumina HiSeq 2500 high-throughput sequencing platform. The relationships between gut microbiota and clinical characteristics of migraine were analyzed.ResultsThe structure of gut microbiota differed between migraine patients with IBS and patients with IBS, while the richness and diversity of gut microbiota in migraine patients with IBS showed no significant difference from that of patients with IBS. We found a higher relative abundance of the genus Parabacteroides and a lower relative abundance of the genera Paraprevotella, Lachnospiraceae_UCG-010, Lactococcus, Collinsella, and Comamonas in migraine patients with IBS than in patients with IBS. According to random forest predictive models, the phylum Bacteroidota shows the most important role in migraine patients with IBS. Furthermore, no statistical correlation was found between significantly different taxa at the genus level and migraine clinical data.ConclusionThis study identified that altered gut microbiota occurred in Chinese Han migraine patients with IBS, but no correlation was found between gut microbiota and the clinical characteristics of migraine. Further study is needed to better understand the role of gut microbiota in the pathogenesis of migraine in IBS.
Food preservation by cold plasma from dielectric barrier discharges in agri-food industries
Authors: Jiang Hao , Lin Qian , Shi Wenqing , Yu Xiuzhu , Wang Shaojin 
Published: November 2022

BackgroundCold plasma (CP) can be defined as partially or wholly ionized gas carrying myriads of highly reactive products, such as electrons, negative ions, positive ions, free radicals, excited or non-excited atoms, and photons at ambient temperature. It is generated at 30–60°C under atmospheric or reduced pressure (vacuum). In contrast to thermal plasma, it requires less power, exhibits electron temperatures much higher than the corresponding gas (macroscopic temperature), and does not present a local thermodynamic equilibrium. Dielectric barrier discharges (DBD) are one of the most convenient and efficient methods to produce CP.Scope and approachCold plasma technology has the potential to replace traditional agri-food processing purification methods because of its low energy requirements and flexible system design. CP technology works by reducing bacteria levels and removing pests and mycotoxins from your produce at harvest. It can also catalyze physiological and biochemical reactions and modify materials. It can meet microbial food safety standards, improve the physical, nutritional, and sensory characteristics of the products, preserve unstable bioactive compounds, and modulate enzyme activities. This manuscript also discusses the quality characteristics of food components before/after CP treatment.Key findings and conclusionIn the past decade, CP treatments of food products have experienced increased popularity due to their potential contributions to non-thermal food processing. There is no doubt that CP treatment is a flexible approach with demonstrated efficacy for controlling many risks across food and agricultural sustainability sectors. In addition, CP technologies also can be applied in food-related areas, including modification of chemical structures and desensitization treatments. There is a need to fully assess the benefits and risks of stand-alone CP unit processes or their integration as a processing chain as soon as the economic, ecological, and consumer benefits and acceptability are considered.