bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combined fine-needle aspiration and selective intraoperative frozen section to optimize prediction of malignant thyroid nodules: A retrospective cohort study of more than 3000 patients
Authors: Mao Zhuochao , Ding Yongfeng , Wen Liping , Zhang Yu , Wu Guofa , You Qihan , Wu Jie , Luo Dingcun , Teng Lisong , Wang Weibin 
Published: February 2023

BackgroundPreoperative fine-needle aspiration (FNA) is widely used to differentiate malignant from benign thyroid nodules, while intraoperative frozen sections (FS) are suggested as a systematic supplement for intraoperative decision-making, but limitations still remain for both procedures.MethodsMedical records of 3807 patients with thyroid nodules who underwent both pathological diagnoses (FS and FNA) at our hospital were reviewed. The diagnostic accuracy, sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of FNA and FS were also evaluated. We further designed an optimal integration scheme (FNA+selective FS) to predict thyroid nodule malignancy. Finally, the efficiency of the proposed integrated diagnostic model was validated using an independent external cohort.ResultsFor distinguishing malignant nodules, FNA had an accuracy of 90.3%, sensitivity of 90.7%, specificity of 85.2%, PPV of 98.8% and NPV of 40.4%. In contrast, the FS represented higher discriminative power (Accuracy, 94.5%; Sensitivity, 94.1%; Specificity, 100%; PPV, 100%; and NPV, 55.6%). we proposed the selective usage of FS (removed nodules with Bethesda category VI from routine FS, ~1/3 of total). The integrated new diagnostic model of FNA plus selective FS (FNA+sFS) achieved accuracy of 96.9%, sensitivity of 97.3%, specificity of 92%, PPV of 99.4%, and NPV of 71.6% (NRI=0.135, 95% CI 0.103-0.167, P &lt;0.001) and was successfully applied to an external cohort (N=554).ConclusionCompared with the FNA diagnostic system, FS has an increased ability to distinguish benign and malignant thyroid nodules. The newly proposed integrated diagnostic model of FNA + selective FS can optimize the accuracy of diagnosis.
Effects of Yulin Tong Bu formula on modulating gut microbiota and fecal metabolite interactions in mice with polycystic ovary syndrome
Authors: Su Ya-Nan , Wang Mei-Jiao , Yang Jun-Pu , Wu Xiang-Lu , Xia Min , Bao Mei-Hua , Ding Yu-Bin , Feng Qian , Fu Li-Juan 
Published: February 2023

BackgroundPolycystic ovarian syndrome (PCOS) is a common endocrine disorder characterized by hyperandrogenism, ovarian dysfunction and polycystic ovarian morphology. Gut microbiota dysbiosis and metabolite are associated with PCOS clinical parameters. Yulin Tong Bu formula (YLTB), a traditional Chinese medicine formula, has been recently indicated to be capable of ameliorating polycystic ovary symptoms and correcting abnormal glucose metabolism. However, the therapeutic mechanism of YLTB on PCOS has not been fully elucidated.MethodsA pseudo sterile mouse model was established during this four-day acclimatization phase by giving the animals an antibiotic cocktail to remove the gut microbiota. Here, the therapeutic effects of YLTB on PCOS were investigated using dehydroepiandrosterone plus high-fat diet-induced PCOS mice model. Female prepuberal mice were randomly divided into three groups; namely, the control group, PCOS group and YLTB (38.68 g·kg-1·day-1) group. To test whether this effect is associated with the gut microbiota, we performed 16S rRNA sequencing studies to analyze the fecal microbiota of mice. The relationships among metabolites, gut microbiota, and PCOS phenotypes were further explored by using Spearman correlation analysis. Then, the effect of metabolite ferulic acid was then validated in PCOS mice.ResultsOur results showed that YLTB treatment ameliorated PCOS features (ovarian dysfunction, delayed glucose clearance, decreased insulin sensitivity, deregulation of glucolipid metabolism and hormones, etc.) and significantly attenuated PCOS gut microbiota dysbiosis. Spearman correlation analysis showed that metabolites such as ferulic acid and folic acid are negatively correlated with PCOS clinical parameters. The effect of ferulic acid was similar to that of YLTB. In addition, the bacterial species such as Bacteroides dorei and Bacteroides fragilis were found to be positively related to PCOS clinical parameters, using the association study analysis.ConclusionThese results suggest that YLTB treatment systematically regulates the interaction between the gut microbiota and the associated metabolites to ameliorate PCOS, providing a solid theoretical basis for further validation of YLTB effect on human PCOS trials.
Pore-scale study of microbial hydrogen consumption and wettability alteration during underground hydrogen storage
Authors: Liu Na , Kovscek Anthony R. , Fernø Martin A. , Dopffel Nicole 
Published: February 2023

Hydrogen can be a renewable energy carrier and is suggested to store renewable energy and mitigate carbon dioxide emissions. Subsurface storage of hydrogen in salt caverns, deep saline formations, and depleted oil/gas reservoirs would help to overcome imbalances between supply and demand of renewable energy. Hydrogen, however, is one of the most important electron donors for many subsurface microbial processes, including methanogenesis, sulfate reduction, and acetogenesis. These processes cause hydrogen loss and changes of reservoir properties during geological hydrogen storage operations. Here, we report the results of a typical halophilic sulfate-reducing bacterium growing in a microfluidic pore network saturated with hydrogen gas at 35 bar and 37°C. Test duration is 9 days. We observed a significant loss of H2 from microbial consumption after 2 days following injection into a microfluidic device. The consumption rate decreased over time as the microbial activity declined in the pore network. The consumption rate is influenced profoundly by the surface area of H2 bubbles and microbial activity. Microbial growth in the silicon pore network was observed to change the surface wettability from a water-wet to a neutral-wet state. Due to the coupling effect of H2 consumption by microbes and wettability alteration, the number of disconnected H2 bubbles in the pore network increased sharply over time. These results may have significant implications for hydrogen recovery and gas injectivity. First, pore-scale experimental results reveal the impacts of subsurface microbial growth on H2 in storage, which are useful to estimate rapidly the risk of microbial growth during subsurface H2 storage. Second, microvisual experiments provide critical observations of bubble-liquid interfacial area and reaction rate that are essential to the modeling that is needed to make long-term predictions. Third, results help us to improve the selection criteria for future storage sites.
Blood transcriptome reveals immune and metabolic-related genes involved in growth of pasteurized colostrum-fed calves
Authors: Li Chenglong , Li Shuzhen , Yang Chaoyun , Ding Yanling , Zhang Yanfeng , Wang Xiaowei , Zhou Xiaonan , Su Zonghua , Ming Wenxuan , Zeng Ling , Ma Yun , Shi Yuangang , Kang Xiaolong 
Published: February 2023

The quality of colostrum is a key factor contributing to healthy calf growth, and pasteurization of colostrum can effectively reduce the counts of pathogenic microorganisms present in the colostrum. Physiological changes in calves fed with pasteurized colostrum have been well characterized, but little is known about the underlying molecular mechanisms. In this study, key genes and functional pathways through which pasteurized colostrum affects calf growth were identified through whole blood RNA sequencing. Our results showed that calves in the pasteurized group (n= 16) had higher body height and daily weight gain than those in the unpasteurized group (n= 16) in all months tested. Importantly, significant differences in body height were observed at 3 and 4 months of age (p&lt; 0.05), and in daily weight gain at 2, 3, and 6 months of age (p&lt; 0.05) between the two groups. Based on whole blood transcriptome data from 6-months old calves, 630 differentially expressed genes (DEGs), of which 235 were upregulated and 395 downregulated, were identified in the pasteurized compared to the unpasteurized colostrum groups. Most of the DEGs have functions in the immune response (e.g.,CCL3,CXCL3, andIL1A) and metabolism (e.g.,PTX3andEXTL1). Protein-protein interaction analyses of DEGs revealed three key subnetworks and fifteen core genes, including UBA52 and RPS28, that have roles in protein synthesis, oxidative phosphorylation, and inflammatory responses. Twelve co-expression modules were identified through weighted gene co-expression network analysis. Among them, 17 genes in the two modules that significantly associated with pasteurization were mainly involved in the tricarboxylic acid cycle, NF-kappa B signaling, and NOD-like receptor signaling pathways. Finally, DEGs that underwent alternative splicing in calves fed pasteurized colostrum have roles in the immune response (SLCO4A1,AKR1C4, andMED13L), indicative of potential roles in immune regulation. Results from multiple analytical methods used suggest that differences in calf growth between the pasteurized and unpasteurized groups may be due to differential immune activity. Our data provide new insights into the impact of pasteurization on calf immune and metabolic-related pathways through its effects on gene expression.
Identification of immune-related molecular clusters and diagnostic markers in chronic kidney disease based on cluster analysis
Authors: Yan Peng , Ke Ben , Song Jianling , Fang Xiangdong 
Published: February 2023

Background: Chronic kidney disease (CKD) is a heterogeneous disease with multiple etiologies, risk factors, clinical manifestations, and prognosis. The aim of this study was to identify different immune-related molecular clusters in CKD, their functional immunological properties, and to screen for promising diagnostic markers.Methods: Datasets of 440 CKD patients were obtained from the comprehensive gene expression database. The core immune-related genes (IRGs) were identified by weighted gene co-expression network analysis. We used unsupervised clustering to divide CKD samples into two immune-related subclusters. Then, functional enrichment analysis was performed for differentially expressed genes (DEGs) between clusters. Three machine learning methods (LASSO, RF, and SVM-RFE) and Venn diagrams were applied to filter out 5 significant IRGs with distinguished subtypes. A nomogram diagnostic model was developed, and the prediction effect was verified using calibration curve, decision curve analysis. CIBERSORT was applied to assess the variation in immune cell infiltration among clusters. The expression levels, immune characteristics and immune cell correlation of core diagnostic markers were investigated. Finally, the Nephroseq V5 was used to assess the correlation among core diagnostic markers and renal function.Results: The 15 core IRGs screened were differentially expressed in normal and CKD samples. CKD was classified into two immune-related molecular clusters. Cluster 2 is significantly enriched in biological functions such as leukocyte adhesion and regulation as well as immune activation, and has a severe immune prognosis compared to cluster 1. A nomogram diagnostic model with reliable prediction of immune-related clusters was developed based on five signature genes. The core diagnostic markers LYZ, CTSS, and ISG20 were identified as playing an important role in the immune microenvironment and were shown to correlate meaningfully with immune cell infiltration and renal function.Conclusion: Our study identifies two subtypes of CKD with distinct immune gene expression patterns and provides promising predictive models. Along with the exploration of the role of three promising diagnostic markers in the immune microenvironment of CKD, it is anticipated to provide novel breakthroughs in potential targets for disease treatment.
Single-cell RNA sequencing reveals the immune microenvironment and signaling networks in cystitis glandularis
Authors: Zhou Tai Lai , Chen Heng Xin , Wang Yin Zhao , Wen Si Jie , Dao Ping Hong , Wang Yu Hang , Chen Min Feng 
Published: February 2023

IntroductionCystitis glandularis (CG) is a rare chronic bladder hyperplastic disease that mainly manifests by recurrent frequent urination, dysuria and gross hematuria. The current lack of unified diagnosis and treatment criteria makes it essential to comprehensively describe the inflammatory immune environment in CG research.MethodsHere, we performed scRNA-sequencing in CG patients for the first time, in which four inflamed tissues as well as three surrounding normal bladder mucosa tissues were included. Specifically, we isolated 18,869 cells to conduct bioinformatic analysis and performed immunofluorescence experiments.ResultsOur genetic results demonstrate that CG does not have the classic chromosomal variation observed in bladder tumors, reveal the specific effects of TNF in KRT15 epithelial cells, and identify a new population of PIGR epithelial cells with high immunogenicity. In addition, we confirmed the activation difference of various kinds of T cells during chronic bladder inflammation and discovered a new group of CD27-Switch memory B cells expressing a variety of immunoglobulins.DiscussionCG was regarded as a rare disease and its basic study is still weak.Our study reveals, for the first time, the different kinds of cell subgroups in CG and provides the necessary basis for the clinical treatment of cystitis glandularis. Besides, our study significantly advances the research on cystitis glandularis at the cellular level and provides a theoretical basis for the future treatment of cystitis glandularis.
A semi high-throughput whole blood-based flow cytometry assay to detect and monitor Bordetella pertussis-specific Th1, Th2 and Th17 responses
Authors: Corbière Véronique , Lambert Eleonora E. , Rodesch Marine , van Gaans-van den Brink Jacqueline A. M. , Misiak Alicja , Simonetti Elles , Van Praet Anne , Godefroid Audrey , Diavatopoulos Dimitri A. , van Els Cécile A. C. M. , Mascart Françoise ,   PERISCOPE WP5 Task 7 working group
Published: February 2023

IntroductionThe characterization of B. pertussis (Bp) antigen-specific CD4+ T cell cytokine responses should be included in the evaluation of immunogenicity of pertussis vaccines but is often hindered by the lack of standardized robust assays.MethodsTo overcome this limitation, we developed a two-step assay comprising a short-term stimulation of fresh whole blood with Bp antigens and cryopreservation of the stimulated cells, followed later on by batch-wise intracellular cytokine analysis by flow cytometry. Blood samples collected from recently acellular (aP) vaccine boosted subjects with a whole-cell- or aP-primed background was incubated for 24 hrs with Pertussis toxin, Filamentous hemagglutinin or a Bp lysate (400µl per stimulation). Antigen-specific IFN-γ-, IL-4/IL-5/IL-13-, IL-17A/IL-17F- and/or IL-22-producing CD4+ T cells were quantified by flow cytometry to reveal Th1, Th2, and Th17-type responses, respectively. The frequencies of IFN-γ-producing CD8+ T cells were also analyzed.ResultsWe demonstrate high reproducibility of the Bp-specific whole blood intracellular staining assay. The results obtained after cryopreservation of the stimulated and fixed cells were very well correlated to those obtained without cryopreservation, an approach used in our previously published assay. Optimization resulted in high sensitivity thanks to very low non-specific backgrounds, with reliable detection of Bp antigen-specific Th1, Th2 and Th17-type CD4+ T cells, in the lowest range frequency of 0.01-0.03%. Bp antigen-specific IFN-γ+ CD8+ T lymphocytes were also detected. This test is easy to perform, analyse and interpret with the establishment of strict criteria defining Bp antigen responses.DiscussionThus, this assay appears as a promising test for evaluation of Bp antigen-specific CD4+ T cells induced by current and next generation pertussis vaccines.
Biomass-derived fiber materials for biomedical applications
Authors: Li Daixiu , Wang Yilin , Huang Wenhua , Gong Haihuan 
Published: February 2023

Graphical AbstractSchema of biomass-derived fiber materials (cellulose, chitin, alginate, silk fibroin, collagen, hyaluronic acid, etc.,) for biomedical applications, such as antibacterial skin-wound dressings, tissue engineering, and drug delivery.
Effects of laser energy density on morphology features and microstructures of the single molten track in selective laser melting
Authors: Wang Sen , Wang Linzhi , Liu Jiquan , Yang Runqi , Li Jing , Wang Guoyu 
Published: February 2023

Single molten track (SMT) is the basic unit of the selective laser melting (SLM) process, of which the morphology features and microstructures have great significance on the molding quality. In this study, the effects of laser energy density (LED) on characteristics of SMT were studied with 316 L stainless steel processing by SLM. The results indicate that an optimized range of LED was between 200 and 500 J/mm3, which was the best for SLM process of 316 L leading to beautiful SMT appearance such as continuous uniform water-ridge-like surface, good contour straightness, smooth edges, little adhesive powder, and high densification. The microstructures of the SMT molten pool are mainly composed of equiaxed cellular and columnar dendrites. As the LED decreased, the cellular became smaller and disappeared, while the length and width of columnar crystals even gradually increased. The size of the cellular varies between 0.43 and 1.70 μm with the LEDs increase. The relationship between SMT characteristics and LED found in this work can be readily used to optimize SMT and control the microstructures in situ, and the laser energy density range that the work has identified will simplify most of the guess work in additive manufacturing.
Numerical and experimental investigation of gas flow field variations in three-dimensional printed gas-dynamic virtual nozzles
Authors: Nazari Reza , Ansari Adil , Herrmann Marcus , Adrian Ronald J. , Kirian Richard A. 
Published: February 2023

Gas-dynamic virtual nozzles (GDVNs) play a vital role in delivering biomolecular samples during diffraction measurements at X-ray free-electron laser facilities. Recently, submicrometer resolution capabilities of two-photon polymerization 3D printing techniques opened the possibility to quickly fabricate gas-dynamic virtual nozzles with practically any geometry. In our previous work, we exploited this capability to print asymmetric gas-dynamic virtual nozzles that outperformed conventional symmetric designs, which naturally leads to the question of how to identify the optimal gas-dynamic virtual nozzle geometry. In this work, we develop a 3D computational fluid dynamics pipeline to investigate how the characteristics of microjets are affected by gas-dynamic virtual nozzle geometry, which will allow for further geometry optimizations and explorations. We used open-source software (OpenFOAM) and an efficient geometric volume-of-fluid method (isoAdvector) to affordably and accurately predict jet properties for different nozzle geometries. Computational resources were minimized by utilizing adaptive mesh refinement. The numerical simulation results showed acceptable agreement with the experimental data, with a relative error of about 10% for our test cases that compared bell- and cone-shaped sheath-gas cavities. In these test cases, we used a relatively low sheath gas flow rate (6 mg/min), but future work including the implementation of compressible flows will enable the investigation of higher flow rates and the study of asymmetric drip-to-jet transitions.
Minimally invasive 1,444-nm Nd:YAG laser treatment for axillary bromhidrosis
Authors: Piccolo Domenico , Mutlag Mohammed Hussein , Pieri Laura , Fusco Irene , Conforti Claudio , Crisman Giuliana , Bonan Paolo 
Published: February 2023

BackgroundAxillary bromhidrosis is an apocrine glands hyperactivity disease.MethodsA total of 24 patients (15 men and 9 women) with axillary bromhidrosis underwent a laser procedure with a 1,444-nm Nd:YAG laser. Parameters evaluated in this study were as follows: the degree of malodor (T0, baseline; T30, after 1 month; and T180, after 6 months), postoperative pain, short-term decreased mobility (T1, after 1 day; T7, after 7 days; and T30, after 1 month), and overall satisfaction (T30, after 1 month and T180, after 6 months). A visual analog scale (VAS), from 0 to 10, was used to assess pain and decreased mobility, with lower values denoting less severity.ResultsA total of 24 patients were followed up for 6 months after laser treatment. At baseline, all patients (100%) complained of a strong axillary malodor (mean degree of malodor at T0 = 2.0 ± 0.00). It decreased to 0.50 ± 0.64 at T30. At T180, the degree of malodor was 0.54 ± 0.57. Both T30 and T180 degrees of malodor significantly decreased from the baseline value (p &lt; 0.01). The mean degree of patient satisfaction at T30 was 1.75 ± 0.52, and at T180, it was 1.67 ± 0.21. Among the 24 patients, eight complained of moderated pain 1 day after treatment. The pain subsided on day 7, except for two patients, with VAS = 1. Pain and mobility restrictions were in any case resolved within T30.ConclusionTreatment with a 1,444-nm Nd:YAG laser for subdermal interstitial coagulation could be a less invasive and more effective option treatment for axillary bromhidrosis.
Mobility and associations with levels of cerebrospinal fluid amyloid β and tau in a memory clinic cohort
Authors: Tangen Gro Gujord , Sverdrup Karen , Taraldsen Kristin , Persson Karin , Engedal Knut , Bekkhus-Wetterberg Peter , Knapskog Anne-Brita 
Published: February 2023

BackgroundMobility impairments, in terms of gait and balance, are common in persons with dementia. To explore this relationship further, we examined the associations between mobility and cerebrospinal fluid (CSF) core biomarkers for Alzheimer’s disease (AD).MethodsIn this cross-sectional study, we included 64 participants [two with subjective cognitive decline (SCD), 13 with mild cognitive impairment (MCI) and 49 with dementia] from a memory clinic. Mobility was examined using gait speed, Mini-Balance Evaluation Systems test (Mini-BESTest), Timed Up and Go (TUG), and TUG dual-task cost (TUG DTC). The CSF biomarkers included were amyloid-β 42 (Aβ42), total-tau (t-tau), and phospho tau (p-tau181). Associations between mobility and biomarkers were analyzed through correlations and multiple linear regression analyses adjusted for (1) age, sex, and comorbidity, and (2) SCD/MCI vs. dementia.ResultsAβ42 was significantly correlated with each of the mobility outcomes. In the adjusted multiple regression analyses, Aβ42 was significantly associated with Mini-BESTest and TUG in the fully adjusted model and with TUG DTC in step 1 of the adjusted model (adjusting for age, sex, and comorbidity). T-tau was only associated with TUG DTC in step 1 of the adjusted model. P-tau181 was not associated with any of the mobility outcomes in any of the analyses.ConclusionBetter performance on mobility outcomes were associated with higher levels of CSF Aβ42. The association was strongest between Aβ42 and Mini-BESTest, suggesting that dynamic balance might be closely related with AD-specific pathology.