bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of metagenomic next-generation sequencing in the diagnosis of pulmonary invasive fungal disease
Authors: Wang Chengtan , You Zhiqing , Fu Juanjuan , Chen Shuai , Bai Di , Zhao Hui , Song Pingping , Jia Xiuqin , Yuan Xiaoju , Xu Wenbin , Zhao Qigang , Pang Feng 
Published: September 2022

BackgroundMetagenomic next-generation sequencing (mNGS) is increasingly being used to detect pathogens directly from clinical specimens. However, the optimal application of mNGS and subsequent result interpretation can be challenging. In addition, studies reporting the use of mNGS for the diagnosis of invasive fungal infections (IFIs) are rare.ObjectiveWe critically evaluated the performance of mNGS in the diagnosis of pulmonary IFIs, by conducting a multicenter retrospective analysis. The methodological strengths of mNGS were recognized, and diagnostic cutoffs were determined.MethodsA total of 310 patients with suspected pulmonary IFIs were included in this study. Conventional microbiological tests (CMTs) and mNGS were performed in parallel on the same set of samples. Receiver operating characteristic (ROC) curves were used to evaluate the performance of the logarithm of reads per kilobase per million mapped reads [lg(RPKM)], and read counts were used to predict true-positive pathogens.ResultThe majority of the selected patients (86.5%) were immunocompromised. Twenty species of fungi were detected by mNGS, which was more than was achieved with standard culture methods. Peripheral blood lymphocyte and monocyte counts, as well as serum albumin levels, were significantly negatively correlated with fungal infection. In contrast, C-reactive protein and procalcitonin levels showed a significant positive correlation with fungal infection. ROC curves showed that mNGS [and especially lg(RPKM)] was superior to CMTs in its diagnostic performance. The area under the ROC curve value obtained for lg(RPKM) in the bronchoalveolar lavage fluid of patients with suspected pulmonary IFIs, used to predict true-positive pathogens, was 0.967, and the cutoff value calculated from the Youden index was −5.44.ConclusionsIn this study, we have evaluated the performance of mNGS-specific indicators that can identify pathogens in patients with IFIs more accurately and rapidly than CMTs, which will have important clinical implications.
Different response of the oxygen pathway in patients with chronic thromboembolic pulmonary hypertension treated with pulmonary endarterectomy versus balloon pulmonary angioplasty
Authors: Fu Zhihui , Tao Xincao , Xie Wanmu , Yang Peiran , Gao Qian , Wang Jinzhi , Zhai Zhenguo 
Published: September 2022

BackgroundOxygen pathway limitation exists in chronic thromboembolic pulmonary hypertension (CTEPH). Pulmonary endarterectomy (PEA) and balloon pulmonary angioplasty (BPA) are two effective interventions for CTEPH, but their effects and comparison of these two interventions on the oxygen pathway are not well demonstrated.MethodsCTEPH patients with available pulmonary function test, hemodynamics, and blood gas analysis before and after the interventions were included for comparison of oxygen pathway in terms of lung ventilation, lung gas exchange, oxygen delivery, and oxygen extraction between these two interventions.ResultsThe change in the percentage of the predicted forced expiratory volume in the 1 s (−3.4 ± 12.7 vs. 3.8 ± 8.7%, P = 0.006) and forced vital capacity (−5.5 ± 13.0 vs. 4.2 ± 9.9%, P = 0.001) among the PEA group (n = 24) and BPA group (n = 46) were significantly different. Patients in the PEA group had a significant increase in their arterial oxygen saturation (from 92.5 ± 3.6 to 94.6 ± 2.4%, P = 0.022), while those in the BPA group had no change, which could be explained by a significant improvement in ventilation/perfusion (−0.48 ± 0.53 vs. −0.17 ± 0.41, P = 0.016). Compared with patients post-BPA, patients post-PEA were characterized by higher oxygen delivery (756.3 ± 229.1 vs. 628.8 ± 188.5 ml/min, P = 0.016) and higher oxygen extraction (203.3 ± 64.8 vs. 151.2 ± 31.9 ml/min, P = 0.001).ConclusionPartial amelioration of the oxygen pathway limitations could be achieved in CTEPH patients treated with PEA and BPA. CTEPH patients post-PEA had better performance in lung gas exchange, oxygen delivery, and extraction, while those post-BPA had better lung ventilation. Cardiopulmonary rehabilitation may assist in improving the impairment of the oxygen pathway.
Associations of muscle size and fatty infiltration with bone mineral density of the proximal femur bone
Authors: Li Junfei , Wang Yijing , Zhang Xuesong , Zhang Ping , Su Yunshan , Bai Lin , Wang Yali , Wang Ming , Zhao Jian 
Published: September 2022

PurposeTo investigate the relationship of muscle atrophy and fat infiltration around the hip joint with areal bone mineral density (aBMD) in each subregion of the proximal femur.Materials and methodsIn total, 144 participants (66 women and 78 men) were examined by quantitative computed tomography (QCT), and areal bone mineral density (aBMD) of the femoral neck (FN), trochanter (TR), and intertrochanter (IT) of the proximal femur were obtained. The cross-sectional area (CSA) and proton density fat fraction (PDFF) of the gluteus maximus (G.MaxM), gluteus medius (G.MedM), gluteus minimus (G.MinM), and iliopsoas (IliopM) were obtained via magnetic resonance imaging (MRI) using the mDIXON-Quant sequence. A multivariate generalized linear model was used to evaluate the correlation of the CSA and PDFF of muscles with aBMD in all subregions of the proximal femur.ResultsThe FN integral (Int) aBMD was significantly associated with the G.MaxM CSA (men: P = 0.002; women: P = 0.008) and PDFF (men: P &lt; 0.001; women: P = 0.047). Some muscle indexes were related to the FN aBMD in males or females, including the CSA of G.MedM, G.MinM, and IliopM as well as the PDFF of IliopM and G.MinM. Associations of hip muscle parameters with the TR Int aBMD in both males and females were observed, including G.MaxM CSA (men: P &lt; 0.001; women: P = 0.028) and G.MaxM PDFF (men: P = 0.031; women: P = 0.038). Other muscle indexes, including G.MedM and IliopM, were related to the TR aBMD, mainly affecting the aBMD of TR cortical (Cort) and TR Int. The IT Int aBMD and IT Cort aBMD showed significant correlation with the muscle indexes of G. MaxM, IliopM, and G.MedM, including the PDFF and CSA in males and females. Further, more indicators of the G.MedM and IliopM correlated with the TR and IT aBMD compared to the FN aBMD.ConclusionsThe CSA of gluteus muscles and iliopsoas had a positive association with the aBMD in the proximal femur, and the PDFF of gluteus muscles and iliopsoas had a negative correlation with the aBMD in the proximal femur. In addition, there was an interaction of the proximal femur aBMD with the muscle size and fatty infiltration of hip muscles.
Machine learning reveals two heterogeneous subtypes to assist immune therapy based on lipid metabolism in lung adenocarcinoma
Authors: Gu Xuyu , Wei Shiyou , Li Zhixin , Xu Huan 
Published: September 2022

BackgroundLipid metabolism pivotally contributes to the incidence and development of lung adenocarcinoma (LUAD). The interaction of lipid metabolism and tumor microenvironment (TME) has become a new research direction.MethodsUsing the 1107 LUAD records from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, a comprehensive exploration was performed on the heterogeneous lipid metabolism subtypes based on lipid metabolism genes (LMGs) and immune-related genes (LRGs). The clinical significance, functional status, TME interaction and genomic changes of different subtypes were further studied. A new scoring system, lipid-immune score (LIS), was developed and validated.ResultsTwo heterogeneous subtypes, which express more LMGs and show the characteristics of tumor metabolism and proliferation, are defined as lipid metabolism phenotypes. The prognosis of lipid metabolism phenotype is poor, and it is more common in patients with tumor progression. Expressing more IRGs, enrichment of immunoactive pathways and infiltration of effector immune cells are defined as immunoactive phenotypes. The immunoactive phenotype has a better prognosis and stronger anti-tumor immunity and is more sensitive to immunotherapy. In addition, KEAP1 is a driving mutant gene in the lipid metabolism subtype. Finally, LIS was developed and confirmed to be a robust predictor of overall survival (OS) and immunotherapy in LUAD patients.ConclusionTwo heterogeneous subtypes of LUAD (lipid metabolism subtype and immune activity subtype) were identified to evaluate prognosis and immunotherapy sensitivity. Our research promotes the understanding of the interaction between lipid metabolism and TME and offers a novel direction for clinical management and precision therapy aimed to LUAD patients.
Identification of stage-associated exosome miRNAs in colorectal cancer by improved robust and corroborative approach embedded miRNA-target network
Authors: Long Fei , Tian Luyao , Chai Zixuan , Li Jing , Tang Ying , Liu Mingwei 
Published: September 2022

BackgroundColorectal cancer (CRC) is a common gastrointestinal tumor with high morbidity and mortality. At the molecular level, patients at different stages present considerable heterogeneity. Although the miRNA in exosome is an effective biomarker to reveal tumor progression, studies based on stage-associated exosome miRNA regulatory network analysis still lacking. This study aims to identify CRC stage-associated exosome miRNAs and reveal their potential function in tumor progression.MethodsIn this study, serum and cellular exosome miRNA expression microarrays associated with CRC were downloaded from GEO database. Stage-common (SC) and stage-specific (SS) differentially expressed miRNAs were extracted and their targets were identified based on 11 databases. Furthermore, miRNA SC and SS regulatory function networks were built based on the CRC phenotypic relevance of miRNA targets, and the corresponding transcription factors were identified. Concurrently, the potential stage-associated miRNAs were identified by receiver-operating characteristic (ROC) curve analysis, survival analysis, drug response analysis, ceRNA analysis, pathway analysis and a comprehensive investigation of 159 publications.ResultsTen candidate stage-associated miRNAs were identified, with three SC (miR-146a-5p, miR-22-3p, miR-23b-3p) and seven SS (I: miR-301a-3p, miR-548i; IIIA: miR-23a-3p; IV: miR-194-3p, miR-33a-3p, miR-485-3p, miR-194-5p) miRNAs. Additionally, their targets were enriched in several vital cancer-associated pathways such as TGF-beta, p53, and hippo signaling pathways. Moreover, five key hotspot target genes (CCNA2, MAPK1, PTPRD, MET, and CDKN1A) were demonstrated to associated with better overall survival in CRC patients. Finally, miR-23b-3p, miR-301a-3p and miR-194-3p were validated being the most stably expressed stage-associated miRNAs in CRC serum exosomes, cell exosomes and tissues.ConclusionsThese CRC stage-associated exosome miRNAs aid to further mechanism research of tumor progression and provide support for better clinical management in patients with different stages.
Triglyceride affects the association between estimated glomerular filtration rate and the onset of non-alcoholic fatty liver disease: A second analysis of a Chinese cohort study
Authors: Hu Haofei , Cao Changchun , Han Yong , He Yongcheng 
Published: September 2022

ObjectiveThe role of triglyceride (TG) and estimated glomerular filtration rate (eGFR) effect modifiers on the risk of non-alcoholic fatty liver disease (NAFLD) is unknown. This study examined whether TG modifies the relationship between eGFR and incident NAFLD.MethodsIn a Chinese hospital from January 2010 to December 2014, 15,555 non-obese subjects were collected systematically for this retrospective cohort study. The target-independent and dependent variables were eGFR measured at baseline and NAFLD appearing during follow-up. The modified variable was TG measured at baseline. The multivariate Cox proportional hazards model was used to explore eGFR and TG’s association with NAFLD risk. We explored a priori interaction between eGFR and TG, and performed subgroup analyses to further assess whether the relationship between eGFR and incident NAFLD was modified by TG. We also explored the effect of TG and eGFR interaction on the risk of NAFLD.ResultsThe mean age was 43.09 ± 14.92 years, and 8,131 (52.27%) were males. During a median follow-up time of 35.8 months, 2,077 (13.35%) individuals developed NAFLD. In the adjusted model, eGFR was negatively associated with incident NAFLD (HR = 0.984, 95% CI: 0.982, 0.987), while TG was positively related to NAFLD (HR = 1.582, 95% CI: 1.490, 1.681). TG could modify the relationship between eGFR and incident NAFLD. A stronger association between eGFR and NAFLD could be found in the participants without hypertriglyceridemia (HTG) (HR = 0.981, 95% CI: 0.978–0.984, P for interaction = 0.0139). In contrast, the weaker association was probed in the population with HTG (HR = 0.986, 95% CI: 0.983–0.989). At the same time, we also found an interaction between eGFR and TG in influencing NAFLD risk. In participants with decreased eGFR and HTG, the risk of NAFLD was significantly increased. Further, compared to non-HTG subjects with eGFR ≥ 116.56 ml/min/1.73 m2, participants with HTG and eGFR &lt; 82.88 ml/min/1.73 m2 had about a fourfold increase in the risk (HR = 4.852 95% CI: 3.943–5.970) of NAFLD.ConclusioneGFR and TG is independently associated with NAFLD risk. The association of eGFR with incident NAFLD is likely to be modified by TG in the Chinese non-obese population. There was an interactive effect between eGFR and TG in affecting NAFLD risk. In participants with decreased eGFR and hypertriglyceridemia, the risk of NAFLD is significantly increased.
General anesthesia in children and long-term neurodevelopmental deficits: A systematic review
Authors: Xiao Aoyi , Feng Yingying , Yu Shan , Xu Chunli , Chen Jianghai , Wang Tingting , Xiao Weimin 
Published: September 2022

BackgroundMillions of children experienced surgery procedures requiring general anesthesia (GA). Any potential neurodevelopmental risks of pediatric anesthesia can be a serious public health issue. Various animal studies have provided evidence that commonly used GA induced a variety of morphofunctional alterations in the developing brain of juvenile animals.MethodsWe conducted a systematic review to provide a brief overview of preclinical studies and summarize the existing clinical studies. Comprehensive literature searches of PubMed, EMBASE, CINAHL, OVID Medline, Web of Science, and the Cochrane Library were conducted using the relevant search terms “general anesthesia,” “neurocognitive outcome,” and “children.” We included studies investigating children who were exposed to single or multiple GA before 18, with long-term neurodevelopment outcomes evaluated after the exposure(s).ResultsSeventy-two clinical studies originating from 18 different countries published from 2000 to 2022 are included in this review, most of which are retrospective studies (n = 58). Two-thirds of studies (n = 48) provide evidence of negative neurocognitive effects after GA exposure in children. Neurodevelopmental outcomes are categorized into six domains: academics/achievement, cognition, development/behavior, diagnosis, brain studies, and others. Most studies focusing on children &lt;7 years detected adverse neurocognitive effects following GA exposure, but not all studies consistently supported the prevailing view that younger children were at greater risk than senior ones. More times and longer duration of exposures to GA, and major surgeries may indicate a higher risk of negative outcomes.ConclusionBased on current studies, it is necessary to endeavor to limit the duration and numbers of anesthesia and the dose of anesthetic agents. For future studies, we require cohort studies with rich sources of data and appropriate outcome measures, and carefully designed and adequately powered clinical trials testing plausible interventions in relevant patient populations.
Distal extrahepatic cholangiocarcinoma mimicking groove pancreatitis: A case report and literature review
Authors: Han Chaoqun , Ling Xin , Sheng Liping , Yang Ming , Lin Rong , Ding Zhen 
Published: September 2022

BackgroundThe differential diagnosis between cholangiocarcinoma and groove pancreatitis is quite challenging. Groove pancreatitis is commonly misdiagnosed as periampullary tumors. We reported a case of distal extrahepatic cholangiocarcinoma mimicking groove pancreatitis.Case reportA 57-year-old male patient was transferred to our hospital after endoscopic retrograde cholangiopancreatography (ERCP) with stent placement in the common bile duct due to obstructive jaundice at a local hospital. Groove pancreatitis was considered based on the clinical manifestations and multiple examinations [including computed tomography (CT), magnetic resonance cholangiopancreatography (MRCP), and endoscopic ultrasonography (EUS)]. The patient’s symptoms and laboratory results almost returned to normal after conservative treatments. Interestingly, his symptoms and laboratory results worsened after the stent was removed. We performed a second EUS process and found a lesion in the lower common bile duct. Finally, the patient underwent pancreatoduodenectomy, and the diagnosis was confirmed as moderately differentiated adenocarcinoma of the common bile duct.ConclusionOur case highlights the fact that distal extrahepatic cholangiocarcinoma, which is a malignant disease, can mimic a benign condition like groove pancreatitis. Our case also raises the concern that performing stent placement through ERCP to relieve jaundice without a clear diagnosis could interfere with further evaluation of the disease.
Development and validation of a prognostic nomogram for predicting cancer-specific survival in patients with metastatic clear cell renal carcinoma: A study based on SEER database
Authors: Huang Guangyi , Liao Jie , Cai Songwang , Chen Zheng , Qin Xiaoping , Ba Longhong , Rao Jingmin , Zhong Weimin , Lin Ying , Liang Yuying , Wei Liwei , Li Jinhua , Deng Kaifeng , Li Xiangyue , Guo Zexiong , Wang Liang , Zhuo Yumin 
Published: September 2022

ObjectivesClear cell renal cell carcinoma (ccRCC) is highly prevalent, prone to metastasis, and has a poor prognosis after metastasis. Therefore, this study aimed to develop a prognostic model to predict the individualized prognosis of patients with metastatic clear cell renal cell carcinoma (mccRCC).Patients and MethodsData of 1790 patients with mccRCC, registered from 2010 to 2015, were extracted from the Surveillance, Epidemiology and End Results (SEER) database. The included patients were randomly divided into a training set (n = 1253) and a validation set (n = 537) based on the ratio of 7:3. The univariate and multivariate Cox regression analyses were used to identify the important independent prognostic factors. A nomogram was then constructed to predict cancer specific survival (CSS). The performance of the nomogram was internally validated by using the concordance index (C-index), calibration plots, receiver operating characteristic curves, net reclassification improvement (NRI), integrated discrimination improvement (IDI), and decision curve analysis (DCA). We compared the nomogram with the TNM staging system. Kaplan–Meier survival analysis was applied to validate the application of the risk stratification system.ResultsDiagnostic age, T-stage, N-stage, bone metastases, brain metastases, liver metastases, lung metastases, chemotherapy, radiotherapy, surgery, and histological grade were identified as independent predictors of CSS. The C-index of training and validation sets are 0.707 and 0.650 respectively. In the training set, the AUC of CSS predicted by nomogram in patients with mccRCC at 1-, 3- and 5-years were 0.770, 0.758, and 0.757, respectively. And that in the validation set were 0.717, 0.700, and 0.700 respectively. Calibration plots also showed great prediction accuracy. Compared with the TNM staging system, NRI and IDI results showed that the predictive ability of the nomogram was greatly improved, and DCA showed that patients obtained clinical benefits. The risk stratification system can significantly distinguish the patients with different survival risks.ConclusionIn this study, we developed and validated a nomogram to predict the CSS rate in patients with mccRCC. It showed consistent reliability and clinical applicability. Nomogram may assist clinicians in evaluating the risk factors of patients and formulating an optimal individualized treatment strategy.
Effect of lymph node resection on prognosis of resectable intrahepatic cholangiocarcinoma: A systematic review and meta-analysis
Authors: Li Feiyu , Jiang Yong , Jiang Liyong , Li Qingbin , Yan Xiangyu , Huang Songhan , Chen Ji , Yuan Shuai , Fu Yingda , Liu Jun 
Published: September 2022

BackgroundThe purpose of this meta-analysis was to evaluate the efficacy of lymph node dissection in patients with intrahepatic cholangiocarcinoma (ICC).MethodsThe literature from January 2009 to December 2021 was searched to determine the comparative study of lymph node dissection and non-lymph node dissection in patients with ICC.ResultsSeventeen studies were included in the analysis. There were no significant differences in 1-, 3-, and 5-year overall survival (OR = 0.80, p = 0.10; OR = 0.93, p = 0.71; OR = 0.80, p = 0.21) and 1-, 3-, and 5-year disease-free survival (OR = 0.89, p = 0.73; OR = 0.92, p = 0.81; OR = 0.85, p = 0.62).ConclusionsLymph node dissection does not seem to have a positive effect on the overall survival and disease-free survival.
Public Perception of Pharmacist's Role during COVID-19 Outbreak in Jordan
Authors: Jarab Anan S. , Al-Qerem Walid , Mukattash Tareq L. , Alqudah Salam G. , Abu-Zaytoun Lina , Al-Azayzih Ahmad , Khdour Maher 
Published: September 2022

Background: The pandemic COVID-19 requires collaborative teamwork by all healthcare professionals including Pharmacists who could help in combating epidemic diseases by providing several pharmaceutical services. Nevertheless, public perception of pharmacist’s role in providing health service is controversial
Methods: A cross-sectional web-based design validated survey of 25 items was used to explore patients’ opinion about pharmacist’s ability to provide different health services during COVID-19 pandemic. Exploratory factor analysis (EFA) was conducted to evaluate the best model for the questionnaire. The association between different demographic variables and awareness about pharmacist’s role was evaluated using Pearson correlation, Mann-Whitney u test and Kruskal–Wallis one-way analysis of variance.
Results: A total of 668 persons participated in the study. The mean (SD) of the respondent questionnaire scores was 97.1 (12.6) and the possible maximum score was 115 (12.9). Higher awareness score was associated with increased age, female gender, lower educational level, living out of Amman the capital, being college or university student or being employed in medical field.
Conclusion: The positive public perception toward pharmacist role shown in the present study enlighten the need to expand pharmacist role to be more engaged in providing different health services during the disaster or normal conditions.