bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three-dimensional microstructure reconstruction for two-phase materials from three orthogonal surface maps
Authors: Eshlaghi G. Tolooei , Egels G. , Benito S. , Stricker M. , Weber S. , Hartmaier A. 
Published: June 2023

Introduction: A full three-dimensional (3D) microstructure characterization that captures the essential features of a given material is oftentimes desirable for determining critical mechanisms of deformation and failure and for conducting computational modeling to predict the material’s behavior under complex thermo-mechanical loading conditions. However, acquiring 3D microstructure representations is costly and time-consuming, whereas 2D surface maps taken from orthogonal perspectives can be readily produced by standard microscopic procedures. We present a robust and comprehensive approach for such 3D microstructure reconstructions based on three electron backscatter diffraction (EBSD) maps from orthogonal surfaces of two-phase materials.Methods: It is demonstrated that processing surface maps by spatial correlation functions combined with principal component analysis (PCA) results in a small set of unique descriptors that serve as a representative fingerprint of the 2D maps. In this way, the differences between surface maps of the real microstructure and virtual surface maps of a reconstructed 3D microstructure can be quantified and iteratively minimized by optimizing the 3D reconstruction.Results: To demonstrate the applicability of the method, the microstructure of a metastable austenitic steel in the two-phase region, where austenite and deformation-induced martensite coexist at room temperature, was characterized and reconstructed. After convergence, the synthetic 3D microstructure accurately describes the experimental system in terms of physical parameters such as volume fractions and phase shapes.Discussion: The resulting 3D microstructures represent the real microstructure in terms of their characteristic features such that multiple realizations of statistically equivalent microstructures can be generated easily. Thus, the presented approach ensures that the 3D reconstructed sample and the associated 2D surface maps are statistically equivalent.
Assessment of the prognostic value of preoperative high-sensitive troponin T for myocardial injury and long-term mortality for groups at high risk for cardiovascular events following noncardiac surgery: a retrospective cohort study
Authors: Zhu Yingchao , Bi Yaodan , Yu Qian , Liu Bin 
Published: June 2023

BackgroundFew studies explored the association between high-sensitive cardiac troponin T (hs-cTnT) and long-term mortality for patients after surgery. This study was conducted to assess the association of hs-cTnT with long-term mortality and to investigate the extent to which this association is mediated via myocardial injury after noncardiac surgery (MINS).MethodsThis retrospective cohort study included all patients with hs-cTnT measurements who underwent non-cardiac surgery at Sichuan University West China Hospital. Data were collected from February 2018 and November 2020, with follow-up through February 2022. The primary outcome was all-cause mortality within 1 year. As secondary outcomes, MINS, length of hospital stay (LOS), and ICU admission were analyzed.ResultsThe cohort included 7,156 patients (4,299 [60.1%] men; 61.0 [49.0–71.0] years). Among 7,156 patients, there were 2,151 (30.05%) with elevated hs-cTnT(&gt;14 ng/L). After more than 1 year of follow-up, more than 91.8% of mortality information was available. During one-year follow-up after surgery, there were 308 deaths (14.8%) with a preoperative hs-cTnT &gt;14 ng/L, compared with 192 deaths (3.9%) with a preoperative hs-cTnT &lt;=14 ng/L(adjusted hazard ratio [aHR] 1.93, 95% CI 1.58–2.36; p &lt; 0.001). Elevated preoperative hs-cTnT was also associated with several other adverse outcomes (MINS: adjusted odds ratio [aOR] 3.01; 95% CI, 2.46–3.69; p &lt; 0.001; LOS: aOR 1.48, 95%CI 1.34–1.641; p &lt; 0.001; ICU admission: aOR 1.52, 95%CI 1.31–1.76; p &lt; 0.001). MINS explained approximately 33.6% of the variance in mortality due to preoperative hs-cTnT levels.ConclusionPreoperative elevated hs-cTnT concentrations have a significant association with long-term mortality after noncardiac surgery, one-third of which may by accounted for by MINS.
Ischemia/reperfusion-activated ferroptosis in the early stage triggers excessive inflammation to aggregate lung injury in rats
Authors: Liu Xiujie , Pan Binhui , Wang Xiaoting , Xu Junpeng , Wang Xinyu , Song Zhengyang , Zhang Eryao , Wang Fangyan , Wang Wantie 
Published: June 2023

ObjectiveLung ischemia/reperfusion injury (LIRI) is a clinical syndrome of acute lung injury that occurs after lung transplantation or remote organ ischemia. Ferroptosis and inflammation are involved in the pathogenesis of LIRI according to the results of several studies on animal models. However, the interactive mechanisms between ferroptosis and inflammation contributing to LIRI remain unclear.MethodsHE staining and indicators of oxidative stress were used to evaluated the lung injury. The reactive oxygen species (ROS) level was examined by DHE staining. The quantitative Real-time PCR (qRT-PCR) and western blot analysis were employed to detect the level of inflammation and ferroptosis, and deferoxamine (DFO) was used to assess the importance of ferroptosis in LIRI and its effect on inflammation.ResultsIn the present study, the link of ferroptosis with inflammation was evaluated at reperfusion 30-, 60- and 180-minute time points, respectively. As the results at reperfusion 30-minute point shown, the pro-ferroptotic indicators, especially cyclooxygenase (COX)-2 and acyl-CoA synthetase long-chain family member 4 (ACSL4), were upregulated while the anti-ferroptotic factors glutathione peroxidase 4 (GPX4), cystine-glumate antiporter (XCT) and ferritin heavy chain (FTH1) were downregulated. Meanwhile, the increased level of interleukin (IL)-6, tumor necrosis factor alpha (TNF-α) and IL-1β were observed beginning at reperfusion 60-minute point but mostly activated at reperfusion 180-minute point. Furthermore, deferoxamine (DFO) was employed to block ferroptosis, which can alleviate lung injury. Expectedly, the survival rate of rats was increased and the lung injury was mitigated containing the improvement of type II alveolar cells ultrastructure and ROS production. In addition, at the reperfusion 180-minute point, the inflammation was observed to be dramatically inhibited after DFO administration as verified by IL-6, TNF-α and IL-1β detection.ConclusionThese findings suggest that ischemia/reperfusion-activated ferroptosis plays an important role as the trigger for inflammation to further deteriorate lung damages. Inhibiting ferroptosis may have therapeutic potential for LIRI in clinical practice.
Quantification of Torque Teno Virus (TTV) in plasma and saliva of individuals with liver cirrhosis: a cross sectional study
Authors: Falabello de Luca Ana Clara , Marinho Gabriella Bueno , Franco Juliana Bertoldi , Tenório Jefferson da Rocha , Andrade Natália Silva , Batista Alexandre Mendes , Mamana Ana Carolina , Tozetto-Mendoza Tânia Regina , Pérez Sayáns Mário , Braz-Silva Paulo Henrique , Ortega Karem L. 
Published: June 2023

IntroductionTorque teno virus (TTV) has been pointed as an endogenous marker of immune function, the objective of this study was to investigate the TTV viral load in plasma and saliva of cirrhotic individuals and correlate it with clinical characteristics.MethodsBlood, saliva, clinical data from records and laboratory tests were collected from 72 cirrhotic patients. Plasma and saliva were submitted to real-time polymerase chain reaction for quantification of TTV viral load.ResultsThe majority of the patients presented decompensated cirrhosis (59.7%) and 47.2% had alterations in the white blood series. TTV was identified in 28 specimens of plasma (38.8%) and in 67 specimens of saliva (93.0%), with median values of TTV copies/mL of 90.6 in plasma and 245.14 in saliva. All the patients who were positive for TTV in plasma were also positive in saliva, with both fluids having a moderately positive correlation for the presence of TTV. There was no correlation between TTV viral load, either in plasma or in saliva, and any of the variables studied.ConclusionTTV is more frequently found and in greater amount in the saliva than in the plasma of cirrhotic patients. There was no correlation between TTV viral load and clinical parameters.
Association of x-ray velocimetry (XV) ventilation analysis compared to spirometry
Authors: Kirkness Jason P. , Dusting Jonathan , Eikelis Nina , Pirakalathanan Piraveen , DeMarco John , Shiao Stephen L. , Fouras Andreas 
Published: June 2023

IntroductionX-ray Velocimetry (XV) ventilation analysis is a 4-dimensional imaging-based method for quantifying regional ventilation, aiding in the assessment of lung function. We examined the performance characteristics of XV ventilation analysis by examining correlation to spirometry and measurement repeatability.MethodsXV analysis was assessed in 27 patients receiving thoracic radiotherapy for non-lung cancer malignancies. Measurements were obtained pre-treatment and at 4 and 12-months post-treatment. XV metrics such as ventilation defect percent (VDP) and regional ventilation heterogeneity (VH) were compared to spirometry at each time point, using correlation analysis. Repeatability was assessed between multiple runs of the analysis algorithm, as well as between multiple breaths in the same patient. Change in VH and VDP in a case series over 12 months was used to determine effect size and estimate sample sizes for future studies.ResultsVDP and VH were found to significantly correlate with FEV1 and FEV1/FVC (range: −0.36 to −0.57; p &lt; 0.05). Repeatability tests demonstrated that VDP and VH had less than 2% variability within runs and less than 8% change in metrics between breaths. Three cases were used to illustrate the advantage of XV over spirometry, where XV indicated a change in lung function that was either undetectable or delayed in detection by spirometry. Case A demonstrated an improvement in XV metrics over time despite stable spirometric values. Case B demonstrated a decline in XV metrics as early as 4-months, although spirometric values did not change until 12-months. Case C demonstrated a decline in XV metrics at 12 months post-treatment while spirometric values remained normal throughout the study. Based on the effect sizes in each case, sample sizes ranging from 10 to 38 patients would provide 90% power for future studies aiming to detect similar changes.ConclusionsThe performance and safety of XV analysis make it ideal for both clinical and research applications across most lung indications. Our results support continued research and provide a basis for powering future studies using XV as an endpoint to examine lung health and determine therapeutic efficacy.
Surface proteins of Shiga toxin-producing Escherichia coli mediate association with milk fat globules in raw milk
Authors: Bagel Arthur , Bouvier-Crozier Marion , Canizares Mélissa , Hamadou Badis , Courcol Louise , Lopez Christelle , Michel Valérie , Douellou Thomas , Sergentet Delphine 
Published: June 2023

IntroductionBy adhering to host cells and colonizing tissues, bacterial pathogens can successfully establish infection. Adhesion is considered the first step of the infection process and bacterial adhesion to anti-adhesive compounds is now seen as a promising strategy to prevent infectious diseases. Among the natural sources of anti-adhesive molecules, the membrane of milk fat globules (MFGs) is of interest because of its compositional diversity of proteins and glycoconjugates. However, few studies have focused on the bacterial molecules involved in MFG- mediated inhibition of bacterial adhesion to enterocytes.MethodsWe used three pathogenic Shiga toxin-producing Escherichia coli (STEC) strains (O26:H11 str. 21765, O157:H7 str. EDL933, and O103:H3 str. PMK5) as models to evaluate whether STEC surface proteins are involved in the affinity of STEC for MFG membrane proteins (MFGMPs). The affinity of STEC for MFGMPs was assessed both indirectly by a natural raw milk creaming test and directly by an adhesion test. Mass spectrometry was used to identify enriched STEC proteins within the protein fraction of MFGMs. Bacterial mutants were constructed and their affinity to MFGs were measured to confirm the role of the identified proteins.ResultsWe found that free STEC surface proteins inhibit the concentration of the pathogen in the MFG-enriched cream in a strain-dependent manner. Moreover, the OmpA and FliC proteins were identified within the protein fraction of MFGMs. Our results suggest that FliC protein participates in STEC adhesion to MFGMPs but other STEC molecules may also participate.DiscussionFor the first time, this study highlighted, the involvement of STEC surface proteins in the affinity for MFGs. The mechanism of STEC-MFG association is still not fully understood but our results confirm the existence of receptor/ligand type interactions between the bacteria and MFGs. Further studies are needed to identify and specify the molecules involved in this interaction. These studies should consider the likely involvement of several factors, including adhesion molecules, and the diversity of each STEC strain.
Genomic changes underpinning the emergence of a successful Mycobacterium tuberculosis Latin American and Mediterranean clonal complex
Authors: Dekhil Naira , Mardassi Helmi 
Published: June 2023

IntroductionThe Latin American and Mediterranean sublineage (L4.3/LAM) is the most common generalist sublineage of Mycobacterium tuberculosis lineage 4 (L4), yet certain L4.3/LAM genotypes appear to be confined to particular geographic regions. This is typically the case of a L4.3/LAM clonal complex (CC), TUN4.3_CC1, which is the most preponderant in Tunisia (61.5% of L4.3/LAM).MethodsHere, we used whole-genome sequencing data of 346 globally distributed L4 clinical strains, including 278 L4.3/LAM isolates, to reconstruct the evolutionary history of TUN4.3_CC1 and delineate critical genomic changes underpinning its success.Results and DiscussionPhylogenomic coupled to phylogeographic analyses indicated that TUN4.3_CC1 has evolved locally, being confined mainly to North Africa. Maximum likelihood analyses using the site and branch-site models of the PAML package disclosed strong evidence of positive selection in the gene category “cell wall and cell processes” of TUN4.3_CC1. Collectively, the data indicate that TUN4.3_CC1 has inherited several mutations, which could have potentially contributed to its evolutionary success. Of particular interest are amino acid replacements at the esxK and eccC2 genes of the ESX/Type VII secretion system, which were found to be specific to TUN4.3_CC1, being common to almost all isolates. Because of its homoplastic nature, the esxK mutation could potentially have endowed TUN4.3_CC1 with a selective advantage. Moreover, we noticed the occurrence of additional, previously described homoplasic nonsense mutations in ponA1 and Rv0197. The mutation in the latter gene, a putative oxido-reductase, has previously been shown to be correlated with enhanced transmissibility in vivo. In sum, our findings unveiled several features underpinning the success of a locally evolved L4.3/LAM clonal complex, lending further support to the critical role of genes encoded by the ESX/type VII secretion system.
Molecular epidemiological characteristics of Brucella in Guizhou Province, China, from 2009 to 2021
Authors: Tan Qinqin , Wang Yue , Liu Ying , Tao Zhongfa , Yu Chun , Huang Yan , Yang Xinggui , Ying Xia , Hu Yong , Li Shijun 
Published: June 2023

IntroductionBrucellosis was made statutorily notifiable in 1955, in China, while in Guizhou Province, the pathogen of human brucellosis was isolated for the first time in 2011. However, currently, the brucellosis epidemic is becoming more and more severe in Guizhou Province. The type distribution and genetic characteristics of Brucella in Guizhou Province, as well as its evolutionary relationship with domestic and foreign strains, are still unclear.MethodsMLST, MLVA, and rpoB typing techniques were used for the molecular epidemiological study of the 83 Brucella isolates in Guizhou province.ResultsAmong the 83 Brucella strains, MLST identified three ST genotypes, of which ST39 is a newly reported type in China. MLVA-16 generated 49 genotypes, and MLVA-11 generated 5 known genotypes and 2 unreported genotypes. Six genotypes were identified by rpoB technology.DiscussionMLVA has a high resolution, but differences at the Bruce 04 and 16 loci cannot exclude associations between epidemics, and combining MLST and rpoB typing methods for epidemiologic tracing can avoid erroneous judgments. Moreover, through the combined analysis of the three typing techniques, the possible origin of the new Brucella can be reasonably inferred, which is also conducive to promoting the subsequent research of the novel Brucella.
Causal relationship between gut microbiota and urticaria: a bidirectional two-sample mendelian randomization study
Authors: Shi Yun-Zhou , Tao Qing-Feng , Qin Hai-Yan , Li Ying , Zheng Hui 
Published: June 2023

BackgroundCumulative evidence showed an association between gut microbiota and urticaria, but the causal relationship between them is unclear. We aimed to verify whether there is a causal relationship between the composition of gut microbiota and urticaria and explore whether the causal effect was bidirectional.MethodsWe obtained genome-wide association studies (GWAS) summary data of 211 gut microbiota and urticaria from the most extensive available GWAS database. A bidirectional two-sample mendelian randomization (MR) study was used to test the causal relationship between the gut microbiota and urticaria. The MR analysis was primarily performed with the inverse variance weighted (IVW) method, and MR-Egger, weighted median (WM), and MR-PRESSO were performed as sensitivity analyses.ResultsThe Phylum Verrucomicrobia (OR 1.27, 95%CI 1.01 to 1.61; p = 0.04), Genus Defluviitaleaceae UCG011 (OR 1.29, 95%CI 1.04 to 1.59; p = 0.02), and Genus Coprococcus 3 (OR 1.44, 95%CI 1.02 to 2.05; p = 0.04) was a risk effect against urticaria. And Order Burkholderiales (OR 0.68, 95%CI 0.49 to 0.99; p = 0.04) and Genus Eubacterium xylanophilum group (OR 0.78, 95%CI 0.62 to 0.99; p = 0.04) were negatively associated with urticaria, suggesting a protective effect. At the same time, urticaria had a positively causal effect on gut microbiota (Genus Eubacterium coprostanoligenes group) (OR 1.08, 95%CI 1.01 to 1.16; p = 0.02). These findings showed no influence by heterogeneity or horizontal pleiotropy. Moreover, most sensitivity analyses showed results consistent with those of IVW analysis.ConclusionOur MR study confirmed the potential causal relationship between gut microbiota and urticaria, and the causal effect was bidirectional. Nevertheless, these findings warrant further examination owing to the unclear mechanisms.
Comprehensive analysis of the microbiome and metabolome in pus from pyogenic liver abscess patients with and without diabetes mellitus
Authors: Guo Yawen , Wang Hairui , Liu Zhaoyu , Chang Zhihui 
Published: June 2023

IntroductionPyogenic liver abscess (PLA) patients combined with diabetes mellitus (DM) tend to have more severe clinical manifestations than without DM. The mechanism responsible for this phenomenon is not entirely clear. The current study therefore aimed to comprehensively analyze the microbiome composition and metabolome in pus from PLA patients with and without DM, to determine the potential reasons for these differences.MethodsClinical data from 290 PLA patients were collected retrospectively. We analyzed the pus microbiota using 16S rDNA sequencing in 62 PLA patients. In addition, the pus metabolomes of 38 pus samples were characterized by untargeted metabolomics analysis. Correlation analyses of microbiota, metabolites and laboratory findings were performed to identify significant associations.ResultsPLA patients with DM had more severe clinical manifestations than PLA patients without DM. There were 17 discriminating genera between the two groups at the genus level, among which Klebsiella was the most discriminating taxa. The ABC transporters was the most significant differential metabolic pathway predicted by PICRUSt2. Untargeted metabolomics analysis showed that concentrations of various metabolites were significantly different between the two groups and seven metabolites were enriched in the ABC transporters pathway. Phosphoric acid, taurine, and orthophosphate in the ABC transporters pathway were negatively correlated with the relative abundance of Klebsiella and the blood glucose level.DiscussionThe results showed that the relative abundance of Klebsiella in the pus cavity of PLA patients with DM was higher than those without DM, accompanied by changes of various metabolites and metabolic pathways, which may be associated with more severe clinical manifestations.
Pyridylnidulin exerts anti-diabetic properties and improves non-alcoholic fatty liver disease in diet-induced obesity mice
Authors: Likitnukul Sutharinee , Tepaarmorndech Surapun , Kaewamatawong Theerayuth , Yangchum Arunrat , Duangtha Chanathip , Jongjang Pimrapat , Mangmool Supachoke , Pinthong Darawan , Isaka Masahiko 
Published: June 2023

Introduction: Non-alcoholic fatty liver disease (NAFLD) is one of the metabolic disorders related to the pathophysiology of type 2 diabetes mellitus (T2DM). Therapeutic strategies are focused on the improvement of energy balance and lifestyle modification. Additionally, the derivative of the bioactive fungal metabolite is of interest to provide health benefits, especially in obese and pre-diabetic conditions. In our screening of anti-diabetic compounds from fungal metabolites and semisynthetic derivatives, a depsidone derivative, namely pyridylnidulin (PN), showed potent glucose uptake-inducing activity. The present study aimed to investigate the liver lipid metabolism and anti-diabetic properties of PN in diet-induced obesity mice.Methods: Male C57BL/6 mice were induced obesity and pre-diabetic conditions by dietary intervention with a high-fat diet (HFD) for 6 weeks. These obese mice were orally administered with PN (40 or 120 mg/kg), metformin (150 mg/kg), or vehicle for 4 weeks. Glucose tolerance, plasma adipocytokines, hepatic gene and protein expressions were assessed after treatment.Results: Improved glucose tolerance and reduced fasting blood glucose levels were found in the PN and metformin-treated mice. Additionally, hepatic triglyceride levels were consistent with the histopathological steatosis score regarding hepatocellular hypertrophy in the PN and metformin groups. The levels of plasma adipocytokines such as tumor necrosis factor-α (TNF-α) and monocyte chemoattractant protein-1 (MCP-1) were reduced in the PN (120 mg/kg) and metformin-treated mice. In addition, hepatic gene expression involved in lipid metabolism, including lipogenic enzymes was significantly reduced in the PN (120 mg/kg) and metformin-treated mice. The increased protein expression levels of phosphorylated AMP-activated protein kinase (p-AMPK) was also found in PN and metformin-treated mice.Discussion: Considering the increased p-AMPK protein expression levels in PN and metformin-treated mice were revealed as the underlying mechanisms to improve metabolic parameters. These results suggested that PN provided the health benefit to slow the progression of NAFLD and T2DM in obese and pre-diabetic conditions.