bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impacts of Cigarette Smoking Status on Metabolomic and Gut Microbiota Profile in Male Patients With Coronary Artery Disease: A Multi-Omics Study
Authors: Hu Xiaomin , Fan Yue , Li Hanyu , Zhou Ruilin , Zhao Xinyue , Sun Yueshen , Zhang Shuyang 
Published: October 2021

Background: Cigarette smoking has been considered a modifiable risk factor for coronary artery disease (CAD). Changes in gut microbiota and microbe-derived metabolites have been shown to influence atherosclerotic pathogenesis. However, the effect of cigarette smoking on the gut microbiome and serum metabolites in CAD remains unclear.Method: We profiled the gut microbiota and serum metabolites of 113 male participants with diagnosed CAD including 46 current smokers, 34 former smokers, and 33 never smokers by 16S ribosomal RNA (rRNA) gene sequencing and untargeted metabolomics study. A follow-up study was conducted. PICRUSt2 was used for metagenomic functional prediction of important bacterial taxa.Results: In the analysis of the microbial composition, the current smokers were characterized with depleted Bifidobacterium catenulatum, Akkermansia muciniphila, and enriched Enterococcus faecium, Haemophilus parainfluenzae compared with the former and never smokers. In the untargeted serum metabolomic study, we observed and annotated 304 discriminant metabolites, uniquely including ceramides, acyl carnitines, and glycerophospholipids. Pathway analysis revealed a significantly changed sphingolipids metabolism related to cigarette smoking. However, the change of the majority of the discriminant metabolites is possibly reversible after smoking cessation. While performing PICRUSt2 metagenomic prediction, several key enzymes (wbpA, nadM) were identified to possibly explain the cross talk between gut microbiota and metabolomic changes associated with smoking. Moreover, the multi-omics analysis revealed that specific changes in bacterial taxa were associated with disease severity or outcomes by mediating metabolites such as glycerophospholipids.Conclusions: Our results indicated that both the gut microbiota composition and metabolomic profile of current smokers are different from that of never smokers. The present study may provide new insights into understanding the heterogenic influences of cigarette smoking on atherosclerotic pathogenesis by modulating gut microbiota as well as circulating metabolites.
Circum-Arctic Map of the Yedoma Permafrost Domain
Authors: Strauss Jens , Laboor Sebastian , Schirrmeister Lutz , Fedorov Alexander N. , Fortier Daniel , Froese Duane , Fuchs Matthias , Günther Frank , Grigoriev Mikhail , Harden Jennifer , Hugelius Gustaf , Jongejans Loeka L. , Kanevskiy Mikhail , Kholodov Alexander , Kunitsky Viktor , Kraev Gleb , Lozhkin Anatoly , Rivkina Elizaveta , Shur Yuri , Siegert Christine , Spektor Valentin , Streletskaya Irina , Ulrich Mathias , Vartanyan Sergey , Veremeeva Alexandra , Anthony Katey Walter , Wetterich Sebastian , Zimov Nikita , Grosse Guido 
Published: October 2021

Ice-rich permafrost in the circum-Arctic and sub-Arctic (hereafter pan-Arctic), such as late Pleistocene Yedoma, are especially prone to degradation due to climate change or human activity. When Yedoma deposits thaw, large amounts of frozen organic matter and biogeochemically relevant elements return into current biogeochemical cycles. This mobilization of elements has local and global implications: increased thaw in thermokarst or thermal erosion settings enhances greenhouse gas fluxes from permafrost regions. In addition, this ice-rich ground is of special concern for infrastructure stability as the terrain surface settles along with thawing. Finally, understanding the distribution of the Yedoma domain area provides a window into the Pleistocene past and allows reconstruction of Ice Age environmental conditions and past mammoth-steppe landscapes. Therefore, a detailed assessment of the current pan-Arctic Yedoma coverage is of importance to estimate its potential contribution to permafrost-climate feedbacks, assess infrastructure vulnerabilities, and understand past environmental and permafrost dynamics. Building on previous mapping efforts, the objective of this paper is to compile the first digital pan-Arctic Yedoma map and spatial database of Yedoma coverage. Therefore, we 1) synthesized, analyzed, and digitized geological and stratigraphical maps allowing identification of Yedoma occurrence at all available scales, and 2) compiled field data and expert knowledge for creating Yedoma map confidence classes. We used GIS-techniques to vectorize maps and harmonize site information based on expert knowledge. We included a range of attributes for Yedoma areas based on lithological and stratigraphic information from the source maps and assigned three different confidence levels of the presence of Yedoma (confirmed, likely, or uncertain). Using a spatial buffer of 20 km around mapped Yedoma occurrences, we derived an extent of the Yedoma domain. Our result is a vector-based map of the current pan-Arctic Yedoma domain that covers approximately 2,587,000 km2, whereas Yedoma deposits are found within 480,000 km2of this region. We estimate that 35% of the total Yedoma area today is located in the tundra zone, and 65% in the taiga zone. With this Yedoma mapping, we outlined the substantial spatial extent of late Pleistocene Yedoma deposits and created a unique pan-Arctic dataset including confidence estimates.
Hydrological Modeling for Multifunctional Landscape Planning in the Orinoquia Region of Colombia
Authors: Pimentel Jonathan Nogales , Rogéliz Prada Carlos Andres , Walschburger Thomas 
Published: October 2021

With over 200,000 km2of natural savannas, the Orinoquia region of Colombia is a key and strategic conservation area. Because of Colombia’s fast economic growth, there are significant plans for agro-industrial expansion in the Orinoquia. This expansion may seriously affect water availability. To evaluate the cumulative impacts on freshwater ecosystems derived by different expansion scenarios, the use of a comprehensive framework for mathematical modeling, able to represent the hydrological processes at a macro-basin scale, is crucial for analysis and as a tool to bridge the gap between science and practice. In this work, we developed a general methodological framework for hydrological analysis at macro-basin scale consisting of four main stages: 1) collection and processing of hydro-climatological data, 2) characterization of hydro dependent water use sectors, 3) mathematical modeling and 4) scenario simulation. As a result of applying the proposed framework, we obtained a coupled hydrological model, which allows us to represent the rain-runoff process, the river-floodplain interaction and anthropic processes such as surface water extraction and groundwater extraction, enabling us to represent the complexity of the Orinoquia region. The model was successfully implemented in Matlab showing a Nash-Sutcliffe efficiency coefficient between 0.62 and 0.92 in calibration and between 0.49 and 0.92 in validation. With this model we analyzed five different agro-industrial expansion scenarios, finding that the Colombian Orinoquia may have future high pressure on water resource areas with critical changes in the water availability regime. The scenarios show reductions of up to 85% in low water flows in more than 50% of the area of the Colombian Orinoco basin. In the most extreme scenarios, the Meta, Vichada and Guaviare rivers show reductions of 95, 98 and 50% in low water flows. The results show an urgent need to consider hydrology in planning processes to ensure the sustainability of this important area in Colombia.
Whole-Genome SNP Characterisation Provides Insight for Sustainable Use of Local South African Livestock Populations
Authors: van Marle-Köster Esté , Lashmar Simon Frederick , Retief Anel , Visser Carina 
Published: October 2021

Local cattle and sheep populations are important for animal production and food security in South Africa. These genetic resources are well adapted to the diverse climatic conditions and hold potential to be utilized in production systems subjected to climate change. The local beef breeds are well integrated into commercial livestock production systems with access to performance recording and genetic evaluations, while local sheep breeds are mainly utilised in smallholder and communal systems. The GeneSeek® Genomic Profiler™ Bovine 150 K SNP genotyping array was used to evaluate the diversity and inbreeding status of four indigenous (Boran, Drakensberger, Nguni, Tuli), two composite (Bonsmara and Beefmaster) and two exotic (SA Hereford and Charolais) beef breeds. The Illumina® Ovine 50 K SNP BeadChip was used to investigate five indigenous (Black Head Persian, Damara, Fat tail, Namaqua Afrikaner, Pedi) and three commercial (Dorper, Dohne Merino and SA Merino) populations. Although ascertainment bias was indicated by the low MAF (the autosome-wide proportion of SNPs with MAF&lt; 0.05 ranged from 6.18 to 9.97% for cattle, and 7.59–13.81% for sheep), moderate genomic diversity was observed (mean Ho ranged from 0.296 to 0.403 for cattle, and 0.327 to 0.367 for sheep). Slightly higher levels of ROH-based inbreeding were calculated for cattle (FROH range: 0.018–0.104), than for sheep populations (FROH range: 0.002–0.031). The abundance of short ROH fragments (mean proportion of &lt;4 Mb fragments: 0.405 for cattle, and 0.794 for sheep) indicated ancient inbreeding in both species. The eight cattle populations were categorized into indicine, taurine or Sanga subspecies based on principal component, model-based clustering and phylogenetic analyses, with high levels of admixture observed within the Drakensberger, Nguni and Tuli breeds. Within the sheep populations, a clear distinction could be seen between the dual-purpose breeds, the meat breed and the indigenous breeds. Despite directional selection practiced in the cattle breeds, genomic diversity was moderate with low inbreeding. The non-commercialized, indigenous sheep populations are more vulnerable with small effective populations. These results emphasise the value of genomic information for effective management to exploit the potential contribution of local genetic cattle and sheep resources in a changing environment.
Identifying miRNA-mRNA Networks Associated With COPD Phenotypes
Authors: Zhuang Yonghua , Hobbs Brian D , Hersh Craig P , Kechris Katerina 
Published: October 2021

Chronic obstructive pulmonary disease (COPD) is characterized by expiratory airflow limitation and symptoms such as shortness of breath. Although many studies have demonstrated dysregulated microRNA (miRNA) and gene (mRNA) expression in the pathogenesis of COPD, how miRNAs and mRNAs systematically interact and contribute to COPD development is still not clear. To gain a deeper understanding of the gene regulatory network underlying COPD pathogenesis, we used Sparse Multiple Canonical Correlation Network (SmCCNet) to integrate whole blood miRNA and RNA-sequencing data from 404 participants in the COPDGene study to identify novel miRNA–mRNA networks associated with COPD-related phenotypes including lung function and emphysema. We hypothesized that phenotype-directed interpretable miRNA–mRNA networks from SmCCNet would assist in the discovery of novel biomarkers that traditional single biomarker discovery methods (such as differential expression) might fail to discover. Additionally, we investigated whether adjusting -omics and clinical phenotypes data for covariates prior to integration would increase the statistical power for network identification. Our study demonstrated that partial covariate adjustment for age, sex, race, and CT scanner model (in the quantitative emphysema networks) improved network identification when compared with no covariate adjustment. However, further adjustment for current smoking status and relative white blood cell (WBC) proportions sometimes weakened the power for identifying lung function and emphysema networks, a phenomenon which may be due to the correlation of smoking status and WBC counts with the COPD-related phenotypes. With partial covariate adjustment, we found six miRNA–mRNA networks associated with COPD-related phenotypes. One network consists of 2 miRNAs and 28 mRNAs which had a 0.33 correlation (p = 5.40E-12) to forced expiratory volume in 1 s (FEV1) percent predicted. We also found a network of 5 miRNAs and 81 mRNAs that had a 0.45 correlation (p = 8.80E-22) to percent emphysema. The miRNA–mRNA networks associated with COPD traits provide a systems view of COPD pathogenesis and complements biomarker identification with individual miRNA or mRNA expression data.
Immune-Related Molecular Profiling of Thymoma With Myasthenia Gravis
Authors: Zhuang Jinman , Guan Maohao , Liu Maolin , Liu Yuhang , Yang Shuyan , Hu Zhijian , Lai Fancai , He Fei 
Published: October 2021

Background: Approximately 50% of thymoma patients also show myasthenia gravis (MG), which is an autoimmune disease; however, the pathogenesis of MG-associated thymoma remains elusive. Our aim was to investigate immune-related lncRNA profiles of a set of candidate genes for better understanding of the molecular mechanism underlying the pathogenesis of thymoma with or without MG.Methods: Molecular profiles of thymoma with or without MG were downloaded from The Cancer Genome Atlas, and Pearson’s correlation analysis was performed to identify immune-related lncRNAs. T test was used to examine the differential expression and differential methylation between thymoma patients with or without MG. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed to predict the function of target genes of immune-related lncRNAs.Results: Analyses of the 87 thymoma samples with complete MG information revealed that 205 mRNAs and 56 lncRNAs showed up-regulated expression in thymoma with MG patients, while 458 mRNAs and 84 lncRNAs showed down-regulated expression. The methylation level of three immune-related lncRNAs (AP000787.1, AC004943.1, WT1-AS, FOXG1-AS1) was significantly decreased in thymoma tissues, and the methylation level of these immune-related lncRNAs (WT1-AS: Cor = 0.368, p &lt; 0.001; FOXG1-AS1: Cor = 0.288, p &lt; 0.01; AC004943.1: Cor = -0.236, p &lt; 0.05) correlated with their expression. GO and KEGG pathway analysis revealed that targets of the immune-related lncRNA FOXG1-AS1 were enriched in small GTPase binding and herpes simplex virus 1 infection. Transcription coregulator activity and cell cycle were the most enriched pathways for targets of lncRNA AC004943.1. LncRNA WT1-AS targets were most enriched in actin binding and axon guidance.Conclusion: Our results revealed the immune-related molecular profiling of thymoma with MG and without MG and identified key pathways involved in the underlying molecular mechanism of thymoma-related MG. These findings provide insights for further research of potential markers for thymoma-related MG.
Associations of ADL Disability With Trunk Muscle Mass and Muscle Quality Indicators Measured by Opportunistic Chest Computed Tomography Imaging Among Older Inpatients
Authors: Jing Xiaofan , Tan Lingling , Fu Hongbo , Yang Ling , Yang Ming 
Published: October 2021

Objectives: Sarcopenia is an important predictor of dependence in activities of daily living (ADL disability); however, the association between muscle quality and ADL disability has not been established. We aimed (1) to assess the feasibility of measuring trunk muscle mass and muscle quality by chest CT images; and (2) to explore the possible associations of ADL disability with these muscle mass and muscle quality indicators among older inpatients.Methods: We included older patients in an acute care ward. ADL disability was defined as the Barthel Index (BI) score ≤ 60 points. Unenhanced chest CT images at the 12th thorax (T12) vertebral level were used to segment skeletal muscle area (SMA) and intermuscular adipose tissue (IMAT) and to measure the mean skeletal muscle radiodensity (SMD). Skeletal muscle index (SMI), the muscle mass indicator, was calculated by SMA (cm2)/body height squared (m2). The percentage of IMAT (IMAT%) was calculated using the equation: IMAT% = IMAT/(SMA+ IMAT) ×100%. Skeletal muscle radiodensity, IMAT, and IMAT% were the muscle quality indicators. Kendall's tau rank correlation coefficients (τ) were calculated to explore the correlations. Univariate and multivariate logistic regression models were performed to calculate odds ratios (OR) and 95% confidence interval (CI).Results: We included 212 participants. Skeletal muscle index and SMD were positively and significantly associated with the BI score (τ = 0.14 and 0.31, respectively, both P &lt; 0.001); whereas IMAT and IMAT% were negatively and significantly associated with the BI score (τ = −0.21, P &lt; 0.001; τ = −0.21, P &lt; 0.012). After adjusting for confounders, SMI (adjusted OR 1.03, 95% CI 0.97–1.09) was not independently associated with ADL disability; however, SMD (adjusted OR 0.94, 95% CI 0.88–0.99), IMAT (adjusted OR 1.11, 95% CI 1.03–1.20), and IMAT% (adjusted OR 1.09, 95% CI 1.02–1.16) were independently associated with ADL disability. Subgroup analysis found similar results in men; however, none of these indicators were independently associated with ADL disability in women.Conclusion: Trunk muscle quality indicators (SMD, IMAT, and IMAT%) measured by chest CT images, but not SMI, are independently associated with ADL disability in a single-center study population of older inpatients, especially in men. Further research is necessary to validate our findings.
Trends in Corneal Transplantation and Characteristics of Donors in the Chongqing Eye Bank, China: A Retrospective Study, 1999–2018
Authors: Tan Handan , Lin Meng , Gou Qingqing , Li Aijia , Gu Fengjuan , Liu Quan , Zhang Qi , Xu Mei , Kijlstra Aize , Yang Peizeng , Li Hong 
Published: October 2021

Aim: This study aimed to analyze corneal transplantation trends and voluntary donor characteristics at the Chongqing Eye Bank in China.Methods: We retrospectively reviewed and analyzed data from January 1, 1999, to December 31, 2018, covering 5,397 preregistered voluntary donors, 1,955 actual donors, 3,910 donated tissues, and 2,374 corneal transplantations.Results: The 5,397 preregistered donors included 13 ethnic groups, with an overall mean age of 39.6 years (SD 21.5) and 3,010 were women (55.8%). The most prevalent education level was college and above (2,546, 47.2%), and the most common ethnic group was Han (5,335, 98.85%). Of the 1,955 actual donors, the male-to-female ratio was 3.3, and the mean age was 57.1 (SD 23.0 years). Based on population size in 2018, Jiangbei county was the most active in donation willingness, with ~60 × 10−6 per capita, and the Yuzhong county was the most active in cornea donations, with ~451 × 0−6 per capita. Of the 3,910 donated corneas, 2,540 (65.0%) were clinically used. Of those not used, 978 (71.4%) were rejected for poor corneal quality. The 2,374 (93.5%) corneal transplantation procedures were done at the Department of Ophthalmology of the First Affiliated Hospital of Chongqing Medical University and the rest (n = 166, 6.5%) were performed in other centers. Of those 2,374 corneal transplantations, there were 1,671 penetrating keratoplasty (70.39%), 700 anterior lamellar keratoplasty (29.49%), and three corneal endothelial transplantations in our center (0.13%). The number of annual corneal transplantations increased by nearly 10 times, from 35 cases in 1999 to 327 cases in 2018. Among them, cases of penetrating keratoplasty and anterior lamellar keratoplasty increased from 27, and eight cases in 1999 to 230 and 94 cases in 2018, respectively. Infectious keratitis (37.0%) was the leading indication for keratoplasty, followed by corneal scar (19.8%). Over the study period, corneal scars dropped from the first (41.1% in 1999–2003) to the second indication (20.5% in 2014–2018), while infectious keratitis advanced to take the lead, ranging from 12.2% in 1999–2003 to 26.3% in 2014–2018.Conclusion: Our study reports corneal donation and transplantation trends in Chongqing over 20 years, showing that infectious keratitis is a leading indication for keratoplasty and that penetrating keratoplasty and anterior lamellar keratoplasty show upward trends. The analysis further suggests that a potential preregistered cornea donor is a female Han, with a higher education level.
Improving Access to Refractive Services in Adults: A Health Examination Center-Based Model
Authors: Lin Haishuang , Sun Jing , Congdon Nathan , Xu Meiping , Liu Shanshan , Liang Yuanbo , Wang Hailin , Zhang Shaodan 
Published: October 2021

Purpose: To assess the potential of a health examination center-based screening model in improving service for uncorrected refractive error.Methods: Individuals aged ≥18 years undergoing the routine physical examinations at a tertiary hospital in the northeast China were invited. Presenting visual acuity, noncycloplegic autorefraction, noncontact tonometry, fundus photography, and slit-lamp examination were performed. Refractive error was defined as having spherical equivalent ≤ -0.75 D or ≥ +1 D and uncorrected refractive error was considered as refractive error combined with presenting visual acuity &lt; 6/12 in the better eye. Costs for the screening were assessed.Results: A total of 5,284 participants (61 ± 14 years) were included. The overall prevalence of myopia and hyperopia was 38.7% (95% CI, 37.4–40.0%) and 23.5% (95% CI, 22.3–24.6%), respectively. The prevalence of uncorrected refractive error was 7.85% (95% CI, 7.13–8.58%). Women (p &lt; 0.001 and p = 0.003), those with age ≥ 70 years (p &lt; 0.001 and p = 0.003), and myopia (p &lt; 0.001 and p &lt; 0.001) were at higher risk of uncorrected refractive error and uncorrected refractive error-related visual impairment. Spectacle coverage rate was 70.6% (95% CI, 68.2–73.0%). The cost to identify a single case of refractive error and uncorrected refractive error was US$3.2 and US$25.2, respectively.Conclusion: The prevalence of uncorrected refractive error is high in the urban Chinese adults. Health examination center-based refractive error screening is able to provide an efficient and low-cost model to improve the refractive services in China.
Middle Meningeal Artery Embolization for the Treatment of Bilateral Chronic Subdural Hematoma
Authors: Wei Qi , Fan Gangxian , Li Zhenzhu , Wang Qingbo , Li Ke , Wang Chao , Li Zefu 
Published: October 2021

Background: Bilateral chronic subdural hematoma (bCSDH) is a frequent condition commonly linked to the need for retreatment; however, the reason for this high retreatment rate remains unclear. The middle meningeal artery (MMA) was found to have a relationship with the occurrence and development of chronic subdural hematomas. This study examines a possible method to reduce bCSDH recurrence using bilateral MMA embolization combined with bilateral burr-hole drainage.Materials and Methods: Ten patients with bCSDH who underwent bilateral MMA embolization combined with bilateral burr-hole drainage at our hospital between June 2018 and May 2020, were retrospectively analyzed. Patients' clinical information, prognoses, imaging results, as well as surgical results were documented and analyzed.Results: Ten patients were diagnosed with bCSDH with no comorbid brain diseases. They underwent bilateral MMA embolization combined with bilateral burr-hole drainage. We embolized the MMA immediately before burr hole drainage successfully and employed angiography to validate these results. All the patients attained relief of symptoms without adverse events, and no re-expansion or relapse was reported in the follow-up computed tomography.Conclusion: Bilateral MMA embolization combined with bilateral burr-hole drainage is an available treatment for patients with bCSDH and may have the potential for preventing recurrence.