bluuebunny/crossref_metadata_2025_split huggingface dataset:
Retrospective testing for the presence of monkeypox virus in a high-risk population from February–June 2022 in Alberta, Canada
Authors: Kanji Jamil N , Dieu Paul , Wong Anita , Pabbaraju Kanti , Shokoples Sandra , Smyczek Petra , Gratrix Jennifer , Singh Ameeta E , Charlton Carmen L , Zhou Hong Yuan , Zelyas Nathan , Hinshaw Deena , Tipples Graham 
Published: March 2023

Background: A multi-country outbreak of monkeypox virus (MPXV) infections was identified by the World Health Organization in May 2022. The western Canadian province of Alberta identified its first case of MPXV in a returning traveller on June 2, 2022. We undertook a retrospective testing exercise to evaluate whether MPXV may have been circulating in the province earlier. Methods: Skin (genital and non-genital) and mucosal lesion swabs submitted for herpes simplex virus (HSV)/varicella zoster virus (VZV)/syphilis testing from male patients attending sexually-transmitted infection clinics across the province of Alberta from January 28 to May 30, 2022 were retrieved from storage. The population tested was selected based on the epidemiology of the current 2022 multi-country MPXV outbreak. Samples underwent viral nucleic acid extraction and testing for the presence of Orthopoxvirus DNA using a commercial real-time polymerase chain reaction (PCR) kit. Results: A total of 392 samples (representing 341 unique individuals of median age 31 years) were retrieved. Of them, 349 (89.0%) samples were submitted for HSV/VZV/syphilis testing, 13 (3.3%) for HSV/VZV only, and 30 (7.7%) for syphilis PCR only. None of the 392 samples tested were found to be positive for Orthopoxvirus DNA. Conclusions: The results of this study indicate that circulation of MPXV in a higher-risk population in Alberta, prior to the first case, was less likely. We recommend that other provinces/territories review their local epidemiology, context and resources prior to conducting similar studies.
Evaluating the performance of the RANS turbulence models for simulating wave propagation over a submerged breakwater using openfoam
Authors: Linh Luong Cao , Tri Mai Cao 
Published: March 2023

The present work is to evaluate the performance of the RANS turbulence models for simulating regular wavepropagation over a submerged breakwater using the open-source Computational Fluid Dynamics (CFD) software OpenFOAM. The present numerical results of four turbulence models (k-ε model, k-ω SST model, buoyancy-modified k-ω SST model, and stabilized k-ω SST model) are compared with published experimental data for free surface elevations and velocities at gauges. Moreover, the results of the turbulent kinetic energy (TKE) are compared and assessed between the turbulence models. Results show that the buoyancy-modified k-ω SST model and the stabilized k-ω SST model predictions agree very well with the experimental data, although the turbulence kinetic energy is still significant differences between the two models. Therefore, these two models should be used in the future for simulating the interaction between waves and submerged breakwaters.
Temporal Muscle Thickness Correlates with Sarcopenia in Parkinson’s Disease
Authors: Peball Marina , Valent Dora , Grossauer Anna , Marini Kathrin , Ellmerer Philipp , Wallnöfer Jonas , Krismer Florian , Djamshidian Atbin , Seppi Klaus , Heim Beatrice 
Published: March 2023

Background: Sarcopenia is characterized by a progressive loss of muscle mass, strength, and function resulting in adverse health outcomes. Current assessment strategies are bothersome and means to simplify the diagnosis are an unmet medical need in Parkinson’s disease (PD). Objective: To evaluate temporal muscle thickness (TMT) obtained on routine cranial MRI as a surrogate marker of sarcopenia in PD patients. Methods: We correlated TMT from axial non-contrast-enhanced T1-weighted sequences of MRI close (±12 months) to an outpatient visit including sarcopenia (EWGSOP1, EWGSOP2, SARC-F), frailty (Fried’s criteria, clinical frailty scale), and disease characteristics of Parkinson’s patients (Hoehn and Yahr-scale, Movement Disorder Society-Unified Parkinson’s Disease Rating Scale, quality of life with the Parkinson’s Disease Questionnaire-8) assessments. Results: Cranial MRI was available in 32 patients with a mean age of 73.56±5.14 years, mean disease duration of 11.46±5.66 years, and median Hoehn and Yahr stage of 2.5. The mean TMT was 7.49±2.76 (7.15) mm. Mean TMT was significantly associated with sarcopenia (EWGSOP2, p = 0.018; EWGSOP1, p = 0.023) and frailty status (physical phenotype; p = 0.045). Moreover, there were significant moderate to strong correlations between TMT measurement and appendicular skeletal muscle mass index ( r: 0.437, p = 0.012), as well as handgrip strength ( r: 0.561, p < 0.001). Conclusion: Reduced TMT seems to be a promising surrogate marker for sarcopenia (EWGSOP2) and muscle strength in this pilot study in PD patients.
A retrospective analysis of phosphatase catalytic subunit gene variants in patients with rare disorders identifies novel candidate neurodevelopmental disease genes
Authors: Lyulcheva-Bennett Ekaterina , Genomics England Research Consortium  , Bennett Daimark 
Published: March 2023

Rare genetic disorders represent some of the most severe and life-limiting conditions that constitute a considerable burden on global healthcare systems and societies. Most individuals affected by rare disorders remain undiagnosed, highlighting the unmet need for improved disease gene discovery and novel variant interpretation. Aberrant (de) phosphorylation can have profound pathological consequences underpinning many disease processes. Numerous phosphatases and associated proteins have been identified as disease genes, with many more likely to have gone undiscovered thus far. To begin to address these issues, we have performed a systematic survey of de novo variants amongst 189 genes encoding phosphatase catalytic subunits found in rare disease patients recruited to the 100,000 Genomes Project (100 kGP), the largest national sequencing project of its kind in the United Kingdom. We found that 49% of phosphatases were found to carry de novo mutation(s) in this cohort. Only 25% of these phosphatases have been previously linked to genetic disorders. A gene-to-patient approach matching variants to phenotypic data identified 9 novel candidate rare-disease genes: PTPRD, PTPRG, PTPRT, PTPRU, PTPRZ1, MTMR3, GAK, TPTE2, PTPN18. As the number of patients undergoing whole genome sequencing increases and information sharing improves, we anticipate that reiterative analysis of genomic and phenotypic data will continue to identify candidate phosphatase disease genes for functional validation. This is the first step towards delineating the aetiology of rare genetic disorders associated with altered phosphatase function, leading to new biological insights and improved clinical outcomes for the affected individuals and their families.
Body roundness index is related to the low estimated glomerular filtration rate in Chinese population: A cross-sectional study
Authors: Zhang Yue , Gao Wenxing , Ren Rui , Liu Yang , Li Binqi , Wang Anping , Tang Xulei , Yan Li , Luo Zuojie , Qin Guijun , Chen Lulu , Wan Qin , Gao Zhengnan , Wang Weiqing , Ning Guang , Mu Yiming 
Published: March 2023

BackgroundKidney disease is related to visceral obesity. As a new indicator of obesity, body roundness index (BRI) has not been fully revealed with kidney disease. This study’s objective is to assess the relationship between estimated glomerular filtration rate (eGFR) and BRI among the Chinese population.MethodsThis study enrolled 36,784 members over the age of 40, they were from 7 centers in China by using a random sampling method. BRI was computed using height and waist circumference, eGFR ≤ 90 mL/min/1.73 m2 was considered to indicate low eGFR. To lessen bias, propensity score matching was employed, multiple logistic regression models were utilized to examine the connection between low eGFR and BRI.ResultsThe age, diabetes and coronary heart disease rates, fasting blood glucose, and triglycerides were all greater in participants with low eGFR. The BRI quartile was still positively connected with low eGFR after controlling for confounding variables, according to multivariate logistic regression analysis. (OR [95%CI] Q2:1.052 [1.021-1.091], OR [95%CI] Q3:1.189 [1.062-1.284], OR [95%CI] Q4:1.283 [1.181-1.394], P trend &lt; 0.001). Stratified research revealed that the elders, women, habitual smokers, and those with a history of diabetes or hypertension experienced the connection between BRI level and low eGFR. According to ROC, BRI was able to detect low eGFR more accurately.ConclusionLow eGFR in the Chinese community is positively connected with BRI, which has the potential to be used as an effective indicator for screening kidney disease to identify high-risk groups and take appropriate measures to prevent subsequent complications.
Can artificial intelligence achieve carbon neutrality? Evidence from a quasi-natural experiment
Authors: Chen Siqi , Zhang Shuyunfan , Zeng Qihua , Ao Jiaxuan , Chen Xiaohua , Zhang Shizhao 
Published: March 2023

IntroductionAs the global climate crisis worsens, carbon neutrality has attracted the attention of various nations.MethodsBased on panel data from 282 Chinese prefecture-level cities from 2008 to 2019, this research considers the execution of the artificial intelligence strategy as a quasi-natural experiment. It uses the difference-in-differences (DID) model to evaluate the effect of artificial intelligence construction on carbon emission reduction.ResultsThe findings indicate that implementing the artificial intelligence strategy into practice can lower carbon emissions and advance carbon neutrality, and this conclusion still passes after various robustness tests. The mediating effects reveal that developing green technologies and upgrading the industrial structure are crucial mechanisms for achieving carbon neutrality. The implementation effect varies with time, geographical location, natural resource endowment, and city level.DiscussionThis article examines the influence of artificial intelligence on urban carbon neutrality at the city level, adding to the notion of urban carbon neutrality and providing research support for urban development transformation.
Assessing the causal relationships between human blood metabolites and the risk of NAFLD: A comprehensive mendelian randomization study
Authors: Guo Ziwei , Zhang Tingyu , Yun Zhangjun , Jin Qian , Cao Xu , Kong Deming , Yao Yuhao , Li Xiaoke , Zhang Jiaxin , Ye Yong’An 
Published: March 2023

Background: Non-alcoholic fatty liver disease (NAFLD) is a liver disease associated with obesity, insulin resistance, type 2 diabetes mellitus (T2DM), and metabolic syndrome. The risk factors for NAFLD have not been identified. Metabolic dysfunction has been found to be an important factor in the pathogenesis and progression of NAFLD. However, the causal impact of blood metabolites on NAFLD is unclear.Methods: We performed a two-sample Mendelian randomization (MR) study. A genome-wide association study (GWAS) with 7824 participants provided data on 486 human blood metabolites. Outcome information was obtained from a large-scale GWAS meta-analysis of NAFLD, which contained 8,434 cases and 770,180 controls of Europeans. The inverse variance weighted (IVW) model was chosen as the primary two-sample MR analysis approach, followed by sensitivity analyses such as the heterogeneity test, horizontal pleiotropy test, and leave-one-out analysis. In addition, we performed replication, meta-analysis, and metabolic pathway analysis. We further conducted colocalization analysis to deeply reflect the causality.Results: After rigorous genetic variant selection, IVW, sensitivity analysis, replication, and meta-analysis, two known metabolites were identified as being associated with the development of NAFLD [biliverdin: OR = 1.45; 95% CI 1.20-1.75; p = 0.0001; myristoleate: OR = 0.57; 95% CI 0.39-0.83; p = 0.0030].Conclusion: By combining genomics with metabolomics, our findings provide a new perspective on the underlying mechanisms of NAFLD and have important implications for the screening and prevention of NAFLD.
Immunotherapy efficacy predictive tool for lung adenocarcinoma based on neural network
Authors: Li Wei , Fu Siyun , Gao Xiang , Lu Zhendong , Jin Renjing , Qin Na , Zhang Xinyong , Wu Yuhua , Li Weiying , Wang Jinghui 
Published: March 2023

BackgroundRemarkably, the anti-cancer efficacy of immunotherapy in lung adenocarcinoma (LUAD) has been demonstrated. However, predicting the beneficiaries of this expensive treatment is still a challenge.Materials and methodsA group of patients (N = 250) diagnosed with LUAD and receiving immunotherapy were retrospectively studied. They were randomly divided into a training dataset (80%) and a test dataset (20%). The training dataset was utilized to train neural network models to predict patients’ objective response rate (ORR), disease control rate (DCR), responders (progression-free survival time &gt; 6 months), and overall survival (OS) possibility, which were validated by both the training and test datasets and packaged into a tool later.ResultsIn the training dataset, the tool scored 0.9016 area under the receiver operating characteristic (AUC) curve on ORR judgment, 0.8570 on DCR, and 0.8395 on responder prediction. In the test dataset, the tool scored 0.8173 AUC on ORR, 0.8244 on DCR, and 0.8214 on responder determination. As for OS prediction, the tool scored 0.6627 AUC in the training dataset and 0.6357 in the test dataset.ConclusionsThis immunotherapy efficacy predictive tool for LUAD patients based on neural networks could predict their ORR, DCR, and responder well.
Combined analysis of bulk and single-cell RNA sequencing reveals novel natural killer cell-related prognostic biomarkers for predicting immunotherapeutic response in hepatocellular carcinoma
Authors: Zhang Kai , Yuan Enwu 
Published: March 2023

IntroductionNatural killer (NK) cells play an irreplaceable and important role as a subtype of innate immune cells in the contemporary setting of antitumor immunity.MethodsWe chose a total of 1,196 samples for this analysis from the public dataset’s six separate cohorts. To identify 42 NK cell marker genes, we first carried out a thorough study of single-cell RNA sequencing data from the GSE149614 cohort of hepatocellular carcinoma (HCC).ResultsUsing the NK cell marker genes in the TCGA cohort, we next created a seven-gene prognostic signature, separating the patients into two categories with distinct survival patterns. This signature’s prognostic prediction ability was well verified across several validation cohorts. Patients with high scores had higher TIDE scores but lower immune cell infiltration percentages. Importantly, low-scoring patients had superior immunotherapy response and prognosis than high-scoring patients in an independent immunotherapy cohort (IMvigor210). Finally, we used CD56 and TUBA1B antibodies for immunohistochemical labeling of HCC tissue sections, and we discovered a lower number of CD56+ cells in the HCC tissue sections with high TUBA1B expression.DiscussionIn summary, our research created a unique prognostic profile based on NK cell marker genes that may accurately predict how well immunotherapy would work for HCC patients.
Global, regional, and national burden of chronic respiratory diseases and associated risk factors, 1990–2019: Results from the Global Burden of Disease Study 2019
Authors: Chen Xiang , Zhou Cheng-Wei , Fu Yang-Yang , Li Yao-Zhe , Chen Lei , Zhang Qing-Wei , Chen Yan-Fan 
Published: March 2023

BackgroundThe burden of chronic respiratory diseases has changed over the three decades. This study aims to describe the spatiotemporal trends of prevalence, mortality, and disability-adjusted life years (DALY) due to chronic respiratory diseases (CRDs) worldwide during 1990–2019 using data from the Global Burden of Disease Study 2019 (GBD 2019).MethodsThe prevalence, mortality, and DALY attributable to CRDs and risk factors from 1990 to 2019 were estimated. We also assessed the driving factors and potentiality for improvement with decomposition and frontier analyses, respectively.ResultsIn 2019, 454.56 [95% uncertainty interval (UI): 417.35–499.14] million individuals worldwide had a CRD, showing a 39·8% increase compared with 1990. Deaths due to CRDs were 3.97 (95%UI: 3.58–4.30) million, and DALY in 2019 was 103.53 (95%UI: 94.79–112.27) million. Declines by average annual percent change (AAPC) were observed in age-standardized prevalence rates (ASPR) (0.64% decrease), age-standardized mortality rates (ASMR) (1.92%), and age-standardized DALY rates (ASDR) (1.72%) globally and in 5 socio-demographic index (SDI) regions. Decomposition analyses represented that the increase in overall CRDs DALY was driven by aging and population growth. However, chronic obstructive pulmonary disease (COPD) was the leading driver of increased DALY worldwide. Frontier analyses witnessed significant improvement opportunities at all levels of the development spectrum. Smoking remained a leading risk factor (RF) for mortality and DALY, although it showed a downward trend. Air pollution, a growing factor especially in relatively low SDI regions, deserves our attention.ConclusionOur study clarified that CRDs remain the leading causes of prevalence, mortality, and DALY worldwide, with growth in absolute numbers but declines in several age-standardized estimators since 1990. The estimated contribution of risk factors to mortality and DALY demands the need for urgent measures to improve them.Systematic review registrationhttp://ghdx.healthdata.org/gbd-results-tool.
The alterations in multiple neurophysiological procedures are associated with frailty phenotype in older adults
Authors: Jiang Xin , Zhou Junhong , Yu Chengyuan , Chen Wenbo , Huang Baofeng , Chen Yurong , Zhong Lilian , Guo Yi , Geng Qingshan , Cai Yurun 
Published: March 2023

BackgroundOlder adults oftentimes suffer from the conditions in multiple physiologic systems, interfering with their daily function and thus contributing to physical frailty. The contributions of such multisystem conditions to physical frailty have not been well characterized.MethodsIn this study, 442 (mean age = 71.4 ± 8.1 years, 235 women) participants completed the assessment of frailty syndromes, including unintentional weight loss, exhaustion, slowness, low activity, and weakness, and were categorized into frail (≥3 conditions), pre-frail (1 or 2 conditions), and robust (no condition) status. Multisystem conditions including cardiovascular diseases, vascular function, hypertension, diabetes, sleep disorders, sarcopenia, cognitive impairment, and chronic pain were assessed. Structural equation modeling examined the interrelationships between these conditions and their associations with frailty syndromes.ResultsFifty (11.3%) participants were frail, 212 (48.0%) were pre-frail, and 180 (40.7%) were robust. We observed that worse vascular function was directly associated with higher risk of slowness [standardized coefficient (SC) = −0.419, p &lt; 0.001], weakness (SC = −0.367, p &lt; 0.001), and exhaustion (SC = −0.347, p &lt; 0.001). Sarcopenia was associated with both slowness (SC = 0.132, p = 0.011) and weakness (SC = 0.217, p = 0.001). Chronic pain, poor sleep quality, and cognitive impairment were associated with exhaustion (SC = 0.263, p &lt; 0.001; SC = 0.143, p = 0.016; SC = 0.178, p = 0.004, respectively). The multinomial logistic regression showed that greater number of these conditions were associated with increased probability of being frail (odds ratio&gt;1.23, p &lt; 0.032).ConclusionThese findings in this pilot study provide novel insights into how multisystem conditions are associated with each other and with frailty in older adults. Future longitudinal studies are warranted to explore how the changes in these health conditions alter frailty status.
Porphyromonas gingivalis-induced periodontitis could contribute to cognitive impairment in Sprague–Dawley rats via the P38 MAPK signaling pathway
Authors: Jin Ru , Ning Xiaoqiao , Liu Xiang , Zhao Yueyang , Ye Guo 
Published: March 2023

BackgroundPeriodontitis is one of the most common oral diseases and has been shown to be a risk factor for systemic diseases. Our aim was to investigate the relationship between periodontitis and cognitive impairment and to explore the role of the P38 MAPK signaling pathway in this process.MethodsWe established a periodontitis model by ligating the first molars of SD rats with silk thread and injecting Porphyromonas gingivalis (P. gingivalis) or P. gingivalis plus the P38 MAPK inhibitor SB203580 at the same time for ten weeks. We assessed alveolar bone resorption and spatial learning and memory using microcomputed tomography and the Morris water maze test, respectively. We used transcriptome sequencing to explore the genetic differences between the groups. The gingival tissue, peripheral blood and hippocampal tissue were assessed for the cytokines TNF-α, IL-1β, IL-6, IL-8 and C reactive protein (CRP) with enzyme-linked immunosorbent assay (ELISA) and reverse transcription polymerase chain reaction (RT–PCR). We observed the presence of P. gingivalis in the hippocampus of rats by paraffin-fluorescence in situ hybridization (FISH). We determined the activation of microglia by immunofluorescence. Finally, Western blot analysis was employed to determine the expression of amyloid precursor protein (APP), β-site APP-cleaving enzyme 1 (BACE1) and P38MAPK pathway activation.ResultsWe demonstrated that silk ligature-induced periodontitis plus injection of P. gingivalis into subgingival tissue could lead to memory and cognitive impairment. Transcriptome sequencing results suggested that there were neurodegenerative diseases in the P. gingivalis group, and the MWM test showed that periodontitis reduced the spatial learning and memory ability of mild cognitive impairment (MCI) model rats. We found high levels of inflammatory factors (TNF-α, IL-1β, IL-6, and IL-8) and CRP in the gingiva, peripheral blood and hippocampus, and the expression of APP and BACE1 was upregulated, as was the P38 MAPK pathway activation. Activated microglia and the presence of P. gingivalis were also found in the hippocampus. P38 MAPK inhibitors mitigated all of these changes.ConclusionOur findings strongly suggest that topical application of P. gingivalis increases the inflammatory burden in the peripheral and central nervous systems (CNS) and that neuroinflammation induced by activation of P38 MAPK leads to impaired learning and memory in SD rats. It can also modulate APP processing. Therefore, P38 MAPK may serve as a linking pathway between periodontitis and cognitive impairment.