bluuebunny/crossref_metadata_2025_split huggingface dataset:
Achieved low-density lipoprotein cholesterol to high-density lipoprotein cholesterol ratio predicts the pathophysiological evolution of lipid-rich plaques in acute coronary syndromes: an optical coherence tomography study
Authors: He Luping , Yi Boling , Zhang Dirui , Hu Sining , Zhao Chen , Sun Rui , Ma Jianlin , Hou Jingbo , Jia Haibo , Ma Lijia , Yu Bo 
Published: July 2023

BackgroundAs a novel lipoprotein ratio, baseline low-density lipoprotein cholesterol to high-density lipoprotein cholesterol ratio (LHR) is closely related to the clinical outcomes of acute coronary syndromes (ACS) after percutaneous coronary intervention. However, the pathophysiological impact of achieved LHR (aLHR) on the evolution of non-culprit lipid-rich plaques has not been systematically explored.MethodsBetween September 2013 and December 2018, ACS patients with both baseline and 1-year follow-up optical coherence tomography (OCT) examinations were included in current study. They were divided into two groups according to the median value of aLHR at 1 year.ResultsOverall, 132 patients with 215 lipid-rich plaques were enrolled, with a median aLHR: 1.62. There were thinner fibrous cap thickness (FCT) (133.3 [70.0–180.0] µm vs. 160.0 [100.0–208.3] µm, p = 0.025) and higher prevalence of thin-cap fibroatheroma (TCFA) (24 [22.4%] vs. 13 [12.0%], p = 0.044) and CLIMA-defined high-risk plaques (12 [11.2%] vs. 3[2.8%], p = 0.015) in the high aLHR group at 1 year. Compared with other serum lipid indexes, aLHR showed the best robust correlation with the evolution of plaque vulnerability in both unadjusted and adjusted analyses. Cut-off value of aLHR to predict the progression of maximal lipid arc and FCT was 1.51. In the adjusted model, aLHR ≥1.51 was an independent predictor of TCFA [odds ratio (OR): 3.008, 95% CI: 1.370 to 6.605, p = 0.006] at 1 year.ConclusionsaLHR correlates well with the evolution of lipid-rich plaques and vulnerable phenotypes at 1-year follow-up, which might be an important and convenient serum indicator in the secondary prevention of ACS.
Extrusion tectonism of Indochina reassessed: constraints from 40Ar/39Ar geochronology from the Day Nui Con Voi metamorphic massif, Vietnam
Authors: Dinh Thi-Hue , Yeh Meng-Wan , Lee Tung-Yi , Kunk Michael J. , Wintsch Robert P. , McAleer Ryan 
Published: July 2023

The extrusion tectonic model for the southeastern margin of the Himalayan orogeny links the crustal shear activity along the Red River Shear Zone (RRSZ) to the opening of the South China Sea (SCS). The Day Nui Con Voi (DNCV) metamorphic massif in northern Vietnam strikes NW-SE, is bounded by the RRSZ to the south and continues along the strike where it meets the SCS. The DNCV is thus a critical area to document thermotectonic history in order to advance our understanding of the tectonic evolution of Indochina extrusion and its relationship to the opening of the SCS. Our new 40Ar/39Ar data combined with microstructural and petrological analyses constrained the timing of the left-lateral shearing of the RRSZ and revealed the thermal evolution of the DNCV metamorphic massif. Three ductile deformation events were observed. D1 formed NNW-SSE striking upright folds under granulite to upper amphibolite facies conditions. D2 was a horizontal to sub-horizontal folding event that occurred at amphibolite facies conditions. D3 was a doming event that formed NW-SE striking up-right folds bounded by left-lateral shearing mylonite belts along the two limbs. The S/C fabrics were defined by muscovite fish, quartz + albite + K-feldspar aggregates, and muscovite folia. The D3 doming event exhumed the DNCV metamorphic massif from amphibolite facies conditions to the lower greenschist facies conditions. The 40Ar/39Ar ages obtained from amphibole (∼26 Ma), phlogopite (∼25 Ma), muscovites (∼24-23 Ma), biotite (∼25-23 Ma), and K-feldspars (∼25-22 Ma) from different structural domains of the DNCV metamorphic massif indicated a rapid exhumation ∼26–22 Ma. We interpreted this as the time period for the D3 event, with the onset of left-lateral shearing occurring around 24 Ma based on ages obtained from syn-kinematic muscovites. This age was much younger than the initiation of sea-floor spreading of the SCS (since 32 Ma) but coincided with the age for the ridge jump event in the SCS. Based on these new data, we proposed that extrusion tectonism cannot be the cause for the initial opening of the SCS. Rather, the extrusion of the Indochina block was temporally correlative with the southward ridge jump event of the already opened SCS.
Thermoneutral housing promotes hepatic steatosis in standard diet-fed C57BL/6N mice, with a less pronounced effect on NAFLD progression upon high-fat feeding
Authors: Horakova Olga , Sistilli Gabriella , Kalendova Veronika , Bardova Kristina , Mitrovic Marko , Cajka Tomas , Irodenko Ilaria , Janovska Petra , Lackner Karoline , Kopecky Jan , Rossmeisl Martin 
Published: July 2023

IntroductionNon-alcoholic fatty liver disease (NAFLD) can progress to more severe stages, such as steatohepatitis and fibrosis. Thermoneutral housing together with high-fat diet promoted NAFLD progression in C57BL/6J mice. Due to possible differences in steatohepatitis development between different C57BL/6 substrains, we examined how thermoneutrality affects NAFLD progression in C57BL/6N mice.MethodsMale mice were fed standard or high-fat diet for 24 weeks and housed under standard (22°C) or thermoneutral (30°C) conditions.ResultsHigh-fat feeding promoted weight gain and hepatic steatosis, but the effect of thermoneutral environment was not evident. Liver expression of inflammatory markers was increased, with a modest and inconsistent effect of thermoneutral housing; however, histological scores of inflammation and fibrosis were generally low (&lt;1.0), regardless of ambient temperature. In standard diet-fed mice, thermoneutrality increased weight gain, adiposity, and hepatic steatosis, accompanied by elevated de novo lipogenesis and changes in liver metabolome characterized by complex decreases in phospholipids and metabolites involved in urea cycle and oxidative stress defense.ConclusionThermoneutrality appears to promote NAFLD-associated phenotypes depending on the C57BL/6 substrain and/or the amount of dietary fat.
Genomic comparison between two Inonotus hispidus strains isolated from growing in different tree species
Authors: Wang Qingchun , Bao Haiying , Li Zhijun 
Published: July 2023

Inonotus hispidus mainly growing in broad-leaved trees, including Morus alba, Fraxinus mandshurica, and Ulmus macrocarpa etc. The fruiting body of I. hispidus growing in M. alba (hereafter as MA) is used as a traditional Chinese medicine “Sanghuang”. However, differences between the genetic material basis of I. hispidus growing in other tree species have not been reported. Therefore, in this paper, the genomic comparison between MA and I. hispidus growing in F. mandshurica (hereafter as FM) were studied. The whole genome of MA monokaryon was sequenced by Illumina combined with Pac Bio platform. Next, genome assembly, genome component prediction and genome functional annotation were performed. Comparative genomics analysis was performed between FM monokaryon and MA monokaryon, using MA as the reference. The results showed that, MA had 24 contigs with a N50 length of 2.6 Mb. Specifically, 5,342, 6,564, 1,595, 383 and 123 genes were annotated from GO, KEGG, KOG, CAZymes and CYP450, respectively. Moreover, comparative genomics showed that, the coding genes and total number of genes annotated in different databases of FM were higher than that of MA. This study provides a foundation for the medicinal application of FM as MA from the perspective of genetic composition.
Natural killer cell-related prognostic risk model predicts prognosis and treatment outcomes in triple-negative breast cancer
Authors: Liu Zundong , Ding Mingji , Qiu Pengjun , Pan Kelun , Guo Qiaonan 
Published: July 2023

BackgroundNatural killer (NK) cells are crucial to the emergence, identification, and prognosis of cancers. The roles of NK cell-related genes in the tumor immune microenvironment (TIME) and immunotherapy treatment are unclear. Triple-negative breast cancer (TNBC) is a highly aggressive malignant tumor. Hence, this study was conducted to develop a reliable risk model related to NK cells and provide a novel system for predicting the prognosis of TNBC.MethodsNK cell-related genes were collected from previous studies. Based on TCGA and GEO database, univariate and LASSO cox regression analysis were used to establish the NK cell-related gene signature. The patients with TNBC were separated to high-risk and low-risk groups. After that, survival analysis was conducted and the responses to immunotherapies were evaluated on the basis of the signature. Moreover, the drug sensitivity of some traditional chemotherapeutic drugs was assessed by using the “oncoPredict” R package. In addition, the expression levels of the genes involved in the signature were validated by using qRT-PCR in TNBC cell lines.ResultsThe patients with TNBC were divided into high- and low-risk groups according to the median risk score of the 5-NK cell-related gene signature. The low-risk group was associated with a better clinical outcome. Besides, the differentially expressed genes between the different risk groups were enriched in the biological activities associated with immunity. The tumor immune cells were found to be highly infiltrated in the low-risk groups. In accordance with the TIDE score and immune checkpoint-related gene expression analysis, TNBC patients in the low-risk groups were suggested to have better responses to immunotherapies. Eventually, some classical anti-tumor drugs were shown to be less effective in high-risk groups than in low-risk groups.ConclusionThe 5-NK cell-related gene signature exhibit outstanding predictive performance and provide fresh viewpoints for evaluating the success of immunotherapy. It will provide new insights to achieve precision and integrated treatment for TNBC in the future.
Immunogenicity of Bacillus Calmette-Guérin in pigs: potential as a translational model of non-specific effects of BCG
Authors: Jensen Kristoffer Jarlov , Hansen Mette Sif , Skovgaard Kerstin , Svensson Erik , Larsen Lars Erik , Heegaard Peter M. H. , Benn Christine Stabell , Jungersen Gregers 
Published: July 2023

BackgroundClinical and immunological studies in humans show that the live attenuated Bacillus Calmette-Guérin (BCG) vaccine has beneficial non-specific effects, increasing resistance against diseases other than tuberculosis. The underlying mechanisms are currently being explored. The pig exhibits considerable physiological similarity to humans in anatomy and physiology, suggesting that similar responses to BCG could be expected. Studies of the non-specific effects of BCG in pigs are scarce. We investigated the feasibility of using pigs as a large animal model to investigate the non-specific immunological effects of BCG.MethodsIn a series of experiments, we randomized newborn or young piglets from conventional farms to receiving BCG or placebo and investigated the persistence of live BCG bacteria in various tissues, the immunogenicity of BCG in ex vivo blood and in vitro stimulation assays, and the acute phase protein and clinical responses to heterologous infectious challenge with influenza A virus or Actinobacillus pleuropneumoniae.ResultsThe BCG vaccine was generally well tolerated. In contrast to humans, no skin reaction in the form of abscesses, ulcers, or scars was observed. Live BCG was recovered from draining lymph nodes in 2/13 animals 20 weeks after vaccination. Specific in vitro responses of IFN-γ to antigen-specific re-stimulation with mycobacterial antigen were increased but not TNF-responses to TLR2 or TLR4 agonists. A few genes were differentially expressed in blood after vaccination, including the antiviral genes RIG-I and CSF1, although the effect disappeared after correction for multiple testing. Clinical symptoms after heterologous bacterial or viral respiratory infections did not differ, nor did virus copies in nasopharyngeal samples after the challenge. However, the acute phase protein response was significantly reduced in BCG-vaccinated animals after influenza challenge but not after A. pleuropneumoniae challenge.DiscussionBCG was safe in pigs, inducing specific immunological responses, but our model did not corroborate the innate immunological responsiveness to BCG seen in humans. The dose of BCG or the bacterial and viral challenges may have been sub-optimal. Even so, the acute phase protein response to influenza infection was significantly reduced in BCG-vaccinated animals.
Genomic analysis of circulating HIV and hepatitis C virus infections and coinfections in Cameroon: 2005–2006 and 2015–2016
Authors: Tamim Sana , Nwobegahay Julius , Fepa Kwesseu Armelle Gaelle , Guiateu Tamo Ida Marlene , Djuidje Ngounoue Marceline 
Published: July 2023

IntroductionIn humans, RNA viruses are responsible for a wide range of acute, chronic, emerging and re-emerging infections. Human Immunodeficiency virus (HIV) and hepatitis C virus (HCV) rank as some of the most important public health challenges affecting Africa.MethodsWe performed enzyme-linked immune-sorbent assays to confirm positive specimens, and the genomic characterization on two cohorts of people living with HIV in Douala and Yaoundé for the periods 2005-2006 and 2015-2016. These groups were tested for co-infection with HCV using the enzyme-linked immunosorbent assays. Viral RNA was extracted from positive patients’ plasma samples by QIAGEN method, and specific primers were used to amplify the genes of interest on HIV and HCV genomes. The amplification products were subsequently cloned and sequenced. The nucleotide sequences were aligned, genotyped and phylogenetically analyzed.ResultsThe HIV isolate identified in this study belongs to HIV-1 group M Subtype A1. The HCV subtypes characterized in this study are 1h and 4t corresponding to the dominant strains that circulate in Cameroon. Phylogenetic analysis of the HCV NS5B gene showed that the study viruses cluster with Gabonese, Canadian, and previously sequenced viruses from Cameroon.Conclusion and perspectivesThese results shed light on the genetic diversity of HIV and HCV in Cameroon. Virulent HCV infections are common in Cameroon, and therefore there is a great need for further analysis of the viral evolutionary and spatio-temporal patterns.
A comparative study of Sr-loaded nano-textured Ti and TiO2 nanotube implants on osseointegration immediately after tooth extraction in Beagle dogs
Authors: Li Yongfeng , Tang Li , Shen Mingming , Wang Zhen , Huang Xiaofeng 
Published: July 2023

Dental implantation, when performed immediately after tooth extraction, simplifies the treatment procedure, resulting in satisfaction for dentists and patients. Dental implants with nanotopography surface modification have been used to promote osseointegration immediately after implantation. We compared two different nanotopography surface implants on the effects of osseointegration immediately after tooth extraction: TiO2 nanotubes (NT-TiO2) fabricated by anodization and Sr-loaded nanotopography Ti (NT-Sr) formed via magnetron sputtering technology. Sr-loaded nanotextured Ti nanotubes (NT-Sr) were fabricated via magnetron sputtering using 99.99% SrTiO3 as the sputtering target. TiO2 nanotubes (NT-TiO2) were fabricated by anodization in 0.5 wt% hydrofluoric acid (HF). After the surface topography, hydrophilicity, chemical components, and interface bonding strength were analyzed, two different nano-topographies were applied for in vivo cellular activity evaluation. Subsequently, the implants with NT-Sr and NT-TiO2 surfaces were inserted into the fresh socket immediately after tooth extraction. Radiological scanning, histological analysis, and biomechanical tests were carried out to investigate implant osseointegration. The results showed that nanotubes with diameters of 15–80 nm were distributed on the NT-TiO2 surface, while the NT-Sr group showed 20–40 nm nanoparticles deposited on the surface. Compared to NT-Sr, the NT-TiO2 surface possessed better hydrophilicity and favorable cellular adhesion and proliferation. The NT-Sr surface possessed greater interfacial bonding strength than the NT-TiO2 group, and greater bone formation, higher bone-to-implant contact (BIC%), and maximum pull-out force were observed in the NT-Sr group. The above results indicated that although the NT-TiO2 surface showed favorable in vitro bioactivity, the NT-Sr surface, with higher interface bonding strength, showed better in vitro osteogenesis, and would be more favorable for immediate implantation.
A comparative study on the application of different endoscopic diagnostic methods in the differential diagnosis of benign and malignant bile duct strictures
Authors: Zhu Liang , Huang Zhi-Quan , Wang Zhen-Wen , Yang Xue-Ping , Hong Jun-Bo , Yang Zhen-Zhen , Yu Zheng-Ping , Cao Rong-Lai , He Jin-Li , Chen You-Xiang 
Published: July 2023

ObjectiveTo compare the diagnostic value of cytobrush, ERCP-guided biopsy, SpyGlass direct visual impression and SpyGlass-guided biospy (SpyBite) in the differential diagnosis of benign and malignant bile duct strictures.MethodsThe data of 1,008 patients who were clinically diagnosed with indeterminate biliary strictures and underwent ERCP-guided biopsy, cytobrush, SpyGlass direct visual impression or SpyBite at the First Affiliated Hospital of Nanchang University between January 2010 and December 2019 were collected and analyzed retrospectively. The final diagnose was determined by surgical pathological specimen or follow-up (Malignant stricture can be identified if the stricture showed malignant progression during one year of follow-up). The differential diagnostic value of the above endoscopic diagnostic methods was evaluated by means of sensitivity, specificity, accuracy, positive predictive value, negative predictive value, etc. and safety was evaluated by the incidence rate of adverse events.ResultsIn terms of sensitivity, standard biopsy group (48.6%) and SpyBite group (61.5%) were significantly higher than cytobrush group (32.0%), and visual impression group (100%) was significantly higher than any other group. As far as specificity was concerned, cytobrush group (99.0%), standard biopsy group (99.3%) and the SpyBite group (100%) were significantly higher than visual impression (55.6%), but there was no statistical difference among the three groups above. As far as accuracy was concerned, standard biopsy group (65.3%), and SpyBite group (80.0%) were significantly higher than cytobrush group (44.4%), and SpyBite group (80.0%) was significantly higher than visual impression group (54.8%). In terms of safety, visual impression group and SpyBite group were significantly higher than cytobrush group and standard biopsy group in post-ERCP cholangitis.ConclusionSpyBite combined with SpyGlass-guided visual impression was better for differential diagnosis of benign and malignant bile duct strictures in terms of sensitivity and accuracy compared with conventional endoscopic diagnostic methods such as cytobrush and standard biopsy. Furthmore, the incidence rates of adverse events after SpyGlass examination was similar to those after conventional endoscopic diagnostic methods except for higher cholangitis, which could be controlled by antibiotics and might be avoided by adequate biliary drainage.
Intact glycopeptides identified by LC-MS/MS as biomarkers for response to chemotherapy of locally advanced cervical cancer
Authors: Li Jing , Feng Xiaoxiao , Zhu Chongying , Jiang Yahui , Liu Hua , Feng Weiwei , Lu Haojie 
Published: July 2023

ObjectiveFor locally advanced cervical cancer (LACC), patients who respond to chemotherapy have a potential survival advantage compared to nonresponsive patients. Thus, it is necessary to explore specific biological markers for the efficacy of chemotherapy, which is beneficial to personalized treatment.MethodsIn the present study, we performed a comprehensive screening of site-specific N-glycopeptides in serum glycoproteins to identify glycopeptide markers for predicting the efficacy of chemotherapy, which is beneficial to personalized treatment. In total, 20 serum samples before and after neoadjuvant chemotherapy (NACT) from 10 LACC patients (NACT response, n=6) and NACT nonresponse, n=4) cases) were analyzed using LC-MS/MS, and 20 sets of mass spectrometry (MS) data were collected using liquid chromatography coupled with high-energy collisional dissociation tandem MS (LC-HCD-MS/MS) for quantitative analysis on the novel software platform, Byos. We also identified differential glycopeptides before and after chemotherapy in chemo-sensitive and chemo-resistant patients.ResultsIn the present study, a total of 148 glycoproteins, 496 glycosylation sites and 2279 complete glycopeptides were identified in serum samples of LACC patients. Before and after chemotherapy, there were 13 differentially expressed glycoproteins, 654 differentially expressed glycopeptides and 93 differentially expressed glycosites in the NACT responsive group, whereas there were 18 differentially expressed glycoproteins, 569 differentially expressed glycopeptides and 99 differentially expressed glycosites in the NACT nonresponsive group. After quantitative analysis, 6 of 570 glycopeptides were identified as biomarkers for predicting the sensitivity of neoadjuvant chemotherapy in LACC. The corresponding glycopeptides included MASP1, LUM, ATRN, CO8A, CO8B and CO6. The relative abundances of the six glycopeptides, including MASP1, LUM, ATRN, CO8A, CO8B and CO6, were significantly higher in the NACT-responsive group and were significantly decreased after chemotherapy. High levels of these six glycopeptides may indicate that chemotherapy is effective. Thus, these glycopeptides are expected to serve as biomarkers for predicting the efficacy of neoadjuvant chemotherapy in locally advanced cervical cancer.ConclusionThe present study revealed that the N-glycopeptide of MASP1, LUM, ATRN, CO8A, CO8B and CO6 may be potential biomarkers for predicting the efficacy of chemotherapy for cervical cancer.
Identify and validate RUNX2 and LAMA2 as novel prognostic signatures and correlate with immune infiltrates in bladder cancer
Authors: Jin Yi , Huang Siwei , Wang Zhanwang 
Published: July 2023

BackgroundMuscle-invasive bladder cancer (MIBC) develops lymph node (LN) metastasis or distant metastasis, leading to recurrence and poor prognosis. The five-year survival rate of MIBC with LN or distant metastasis is only 8.1%; therefore, there is an urgent need to identify reliable biomarkers for prognosis and treatment regimen for patients with bladder cancer (BLCA).MethodsSEER database was used to select important clinical characteristics for MIBC. Then, weighted gene co-expression network analysis (WGCNA) was employed to identify differentially expressed genes (DEGs) to recognize significant co-expression modules by calculating the correlation between the modules and clinical data. Furthermore, Cox regression and lasso analysis were applied to screen prognostic hub genes and establish the risk predictive model. Bladder cancer cell lines (UMUC3 and 5637) were used for experimental validation in vitro.ResultsCox analysis of 122,600 MIBC patients showed that the N stage was the most important clinical factor. A total of 4,597 DEGs were calculated between N0 and N+ patients, and WGCNA with these DEGs in 368 samples revealed that expression of turquoise was positively and strongly correlated with the N stage. Eight genes were identified as important prognostic candidates using lasso regression based on Cox analysis and STRING database. Combining GEO datasets, literature, and clinical factors, we identified LAMA2 and RUNX2 as novel prognostic biomarkers. CCK8 assay showed that depletion of LAMA2 or RUNX2 significantly inhibited the proliferation of BLCA cells, and flow cytometry indicated that knockdown of LAMA2 or RUNX2 induced the apoptosis of BLCA cells. Transwell assay also showed that silencing of LAMA2 or RUNX2 weakened the migration and invasiveness of BLCA cells.ConclusionsWe constructed a new eight-gene risk model to provide novel prognostic biomarkers and therapeutic targets for BLCA.