bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic rearrangements and evolutionary changes in 3D chromatin topologies in the cotton tribe (Gossypieae)
Authors: Li Xiaochong , Wang Jinbin , Yu Yanan , Li Guo , Wang Jinpeng , Li Changping , Zeng Zixian , Li Ning , Zhang Zhibin , Dong Qianli , Yu Yiyang , Wang Xiaofei , Wang Tianya , Grover Corrinne E. , Wang Bin , Liu Bao , Wendel Jonathan F. , Gong Lei 
Published: March 2023

AbstractBackgroundAnalysis of the relationship between chromosomal structural variation (synteny breaks) and 3D-chromatin architectural changes among closely related species has the potential to reveal causes and correlates between chromosomal change and chromatin remodeling. Of note, contrary to extensive studies in animal species, the pace and pattern of chromatin architectural changes following the speciation of plants remain unexplored; moreover, there is little exploration of the occurrence of synteny breaks in the context of multiple genome topological hierarchies within the same model species.ResultsHere we used Hi-C and epigenomic analyses to characterize and compare the profiles of hierarchical chromatin architectural features in representative species of the cotton tribe (Gossypieae), includingGossypium arboreum,Gossypium raimondii, andGossypioides kirkii, which differ with respect to chromosome rearrangements. We found that (i) overall chromatin architectural territories were preserved inGossypioidesandGossypium, which was reflected in their similar intra-chromosomal contact patterns and spatial chromosomal distributions; (ii) the non-random preferential occurrence of synteny breaks in A compartment significantly associate with the B-to-A compartment switch in syntenic blocks flanking synteny breaks; (iii) synteny changes co-localize with open-chromatin boundaries of topologically associating domains, while TAD stabilization has a greater influence on regulating orthologous expression divergence than do rearrangements; and (iv) rearranged chromosome segments largely maintain ancestralin-cisinteractions.ConclusionsOur findings provide insights into the non-random occurrence of epigenomic remodeling relative to the genomic landscape and its evolutionary and functional connections to alterations of hierarchical chromatin architecture, on a known evolutionary timescale.
Exploring preconception signatures of metabolites in mothers with gestational diabetes mellitus using a non-targeted approach
Authors: Li Ling-Jun , Wang Ximeng , Chong Yap Seng , Chan Jerry Kok Yen , Tan Kok Hian , Eriksson Johan G. , Huang Zhongwei , Rahman Mohammad L. , Cui Liang , Zhang Cuilin 
Published: March 2023

Abstract
Background
Metabolomic changes during pregnancy have been suggested to underlie the etiology of gestational diabetes mellitus (GDM). However, research on metabolites during preconception is lacking. Therefore, this study aimed to investigate distinctive metabolites during the preconception phase between GDM and non-GDM controls in a nested case–control study in Singapore.

Methods
Within a Singapore preconception cohort, we included 33 Chinese pregnant women diagnosed with GDM according to the IADPSG criteria between 24 and 28 weeks of gestation. We then matched them with 33 non-GDM Chinese women by age and pre-pregnancy body mass index (ppBMI) within the same cohort. We performed a non-targeted metabolomics approach using fasting serum samples collected within 12 months prior to conception. We used generalized linear mixed model to identify metabolites associated with GDM at preconception after adjusting for maternal age and ppBMI. After annotation and multiple testing, we explored the additional predictive value of novel signatures of preconception metabolites in terms of GDM diagnosis.

Results
A total of 57 metabolites were significantly associated with GDM, and eight phosphatidylethanolamines were annotated using HMDB. After multiple testing corrections and sensitivity analysis, phosphatidylethanolamines 36:4 (mean difference β: 0.07; 95% CI: 0.02, 0.11) and 38:6 (β: 0.06; 0.004, 0.11) remained significantly higher in GDM subjects, compared with non-GDM controls. With all preconception signals of phosphatidylethanolamines in addition to traditional risk factors (e.g., maternal age and ppBMI), the predictive value measured by area under the curve (AUC) increased from 0.620 to 0.843.

Conclusions
Our data identified distinctive signatures of GDM-associated preconception phosphatidylethanolamines, which is of potential value to understand the etiology of GDM as early as in the preconception phase. Future studies with larger sample sizes among alternative populations are warranted to validate the associations of these signatures of metabolites and their predictive value in GDM.
Strategies to inTerrupt RAbies Transmission for the Elimination Goal by 2030 In China (STRATEGIC): a modelling study
Authors: Chen Qiulan , Liu Qiuping , Gong Chao , Yin Wenwu , Mu Di , Li Yu , Ding Shujun , Liu Yifang , Yang Hao , Zhou Shuwu , Chen Sa , Tao Zhongfa , Zhang Yanping , Tang Xun 
Published: March 2023

Abstract
Background
A global plan has been set to end human deaths from dog-mediated rabies by 2030 ("Zero-by-30"), but whether it could be achieved in some countries, such as China, remains unclear. Although elimination strategies through post-exposure prophylaxis (PEP) use, dog vaccination, and patient risk assessments with integrated bite case management (IBCM) were proposed to be cost-effective, evidence is still lacking in China. We aim to evaluate the future burdens of dog-mediated human rabies deaths in the next decade and provide quantitative evidence on the cost-effectiveness of different rabies-control strategies in China.

Methods
Based on data from China's national human rabies surveillance system, we used decision-analytic modelling to estimate dog-mediated human rabies death trends in China till 2035. We simulated and compared the expected consequences and costs of different combination strategies of the status quo, improved access to PEP, mass dog vaccination, and use of IBCM.

Results
The predicted human rabies deaths in 2030 in China will be 308 (95%UI: 214–411) and remain stable in the next decade under the status quo. The strategy of improved PEP access alone could only decrease deaths to 212 (95%UI: 147–284) in 2028, remaining unchanged till 2035. In contrast, scaling up dog vaccination to coverage of 70% could eliminate rabies deaths by 2033 and prevent approximately 3,265 (95%UI: 2,477–3,687) extra deaths compared to the status quo during 2024–2035. Moreover, with the addition of IBCM, the "One Health" approach through mass dog vaccination could avoid unnecessary PEP use and substantially reduce total cost from 12.53 (95%UI: 11.71–13.34) to 8.73 (95%UI: 8.09–9.85) billion US dollars. Even if increasing the total costs of IBCM from 100 thousand to 652.10 million US dollars during 2024–2035, the combined strategy of mass dog vaccination and use of IBCM will still dominate, suggesting the robustness of our results.

Conclusions
The combined strategy of mass dog vaccination and IBCM requires collaboration between health and livestock/veterinary sectors, and it could eliminate Chinese rabies deaths as early as 2033, with more deaths averted and less cost, indicating that adding IBCM could reduce unnecessary use of PEP and make the "One Health" rabies-control strategy most cost-effective.
Dose-dependent effect of canine lyophilized platelet on an in vitro hemodilution model
Authors: Kim Mu-Young , Han Hyun-Jung 
Published: March 2023

AbstractThe transfusion of stored platelets has emerged as an efficient method for treating dogs with thrombocytopenia. However, the availability of fresh platelets is limited in veterinary medicine due to demanding storage conditions. Lyophilized platelets have long shelf lives and can be easily stored, increasing their accessibility for thrombocytopenic dogs. Due to the lack of research and information on the dose effect, canine lyophilized platelets are used at a clinical dosage without research-based evidence. This study was to evaluate the dose effect of lyophilized canine platelets on blood coagulability. Three different concentrations of lyophilized canine platelets were added to in vitro hemodilution blood model, increasing the platelet count by 25, 50, and 100 × 106/ml and coagulation profiles were analyzed. The coagulability was evaluated via the plasma fibrinogen concentration, coagulation time, thromboelastography (TEG), and platelet function analyzer (PFA). Higher concentrations of lyophilized platelets showed dose-dependent association with decreased aPTT and R-time of TEG and increased alpha angle and MA of TEG. These results showed the potential that the higher dose of canine lyophilized platelets better improve blood coagulability than the standard dose and provided the basis for further safety and clinical studies.
GAS6-AS1, a long noncoding RNA, functions as a key candidate gene in atrial fibrillation related stroke determined by ceRNA network analysis and WGCNA
Authors: Li Rui-bin , Yang Xiao-hong , Zhang Ji-dong , Cui Wei 
Published: March 2023

Abstract
Background
Stroke attributable to atrial fibrillation (AF related stroke, AFST) accounts for 13 ~ 26% of ischemic stroke. It has been found that AFST patients have a higher risk of disability and mortality than those without AF. Additionally, it’s still a great challenge to treat AFST patients because its exact mechanism at the molecular level remains unclear. Thus, it’s vital to investigate the mechanism of AFST and search for molecular targets of treatment. Long non-coding RNAs (lncRNAs) are related to the pathogenesis of various diseases. However, the role of lncRNAs in AFST remains unclear. In this study, AFST-related lncRNAs are explored using competing endogenous RNA (ceRNA) network analysis and weighted gene co-expression network analysis (WGCNA).

Methods
GSE66724 and GSE58294 datasets were downloaded from GEO database. After data preprocessing and probe reannotation, differentially expressed lncRNAs (DELs) and differentially expressed mRNAs (DEMs) between AFST and AF samples were explored. Then, functional enrichment analysis and protein-protein interaction (PPI) network analysis of the DEMs were performed. At the meantime, ceRNA network analysis and WGCNA were performed to identify hub lncRNAs. The hub lncRNAs identified both by ceRNA network analysis and WGCNA were further validated by Comparative Toxicogenomics Database (CTD).

Results
In all, 19 DELs and 317 DEMs were identified between the AFST and AF samples. Functional enrichment analysis suggested that the DEMs associated with AFST were mainly enriched in the activation of the immune response. Two lncRNAs which overlapped between the three lncRNAs identified by the ceRNA network analysis and the 28 lncRNAs identified by the WGCNA were screened as hub lncRNAs for further validation. Finally, lncRNA GAS6-AS1 turned out to be associated with AFST by CTD validation.

Conclusion
These findings suggested that low expression of GAS6-AS1 might exert an essential role in AFST through downregulating its downstream target mRNAs GOLGA8A and BACH2, and GAS6-AS1 might be a potential target for AFST therapy.
Development and validation of cuproptosis-related lncRNA signatures for prognosis prediction in colorectal cancer
Authors: Pang Lin , Wang Qingqing , Wang Lingxiao , Hu Zhen , Yang Chong , Li Yiqun , Wang Zhenqi , Li Yaoping 
Published: March 2023

Abstract
Background
Cuproptosis, a novel form of programmed cell death, plays an essential role in various cancers. However, studies of the function of cuproptosis lncRNAs (CRLs) in colorectal cancer (CRC) remain limited. Thus, this study aims to identify the cuprotosis-related lncRNAs (CRLs) in CRC and to construct the potential prognostic CRLs signature model in CRC.

Methods
First, we downloaded RNA-Seq data and clinical information of CRC patients from TCGA database and obtained the prognostic CRLs based on typical expression analysis of cuproptosis-related genes (CRGs) and univariate Cox regression. Then, we constructed a prognostic model using the Least Absolute Shrinkage and Selection Operator algorithm combined with multiple Cox regression methods (Lasso-Cox). Next, we generated Kaplan–Meier survival and receiver operating characteristic curves to estimate the performance of the prognostic model. In addition, we also analysed the relationships between risk signatures and immune infiltration, mutation, and drug sensitivity. Finally, we performed quantitative reverse transcription polymerase chain reaction (qRT -PCR) to verify the prognostic model.

Result
Lasso-Cox analysis revealed that four CRLs, SNHG16, LENG8-AS1, LINC0225, and RPARP-AS1, were related to CRC prognosis. Receiver operating characteristic (ROC) and Kaplan–Meier analysis curves indicated that this model performs well in prognostic predictions of CRC patients. The DCA results also showed that the model included four gene signatures was better than the traditional model. In addition, GO and KEGG analyses revealed that DE-CRLs are enriched in critical signalling pathway, such as chemical carcinogenesis-DNA adducts and basal cell carcinoma. Immune infiltration analysis revealed significant differences in immune infiltration cells between the high-risk and low-risk groups. Furthermore, significant differences in somatic mutations were noted between the high-risk and low-risk groups. Finally, we also validated the expression of four CRLs in FHCs cell lines and CRC cell lines using qRT-PCR.

Conclusion
The signature composed of SNHG16, LENG8-AS1, LINC0225, and RPARP-AS1, which has better performance in predicting colorectal cancer prognosis and are promising biomarkers for prognosis prediction of CRC.
Effects of gastroesophageal reflux disease treatment with proton pump inhibitors on the risk of acute exacerbation and pneumonia in patients with COPD
Authors: Kang Jieun , Lee Rugyeom , Lee Sei Won 
Published: March 2023

AbstractBackgroundGastroesophageal reflux disease (GERD) has been suggested as a risk factor for acute exacerbation of chronic obstructive pulmonary disease (COPD). However, it remains undetermined whether proton pump inhibitor (PPI) treatment reduces the risk of exacerbation or affects the risk of pneumonia. This study aimed to evaluate the risks of both exacerbation and pneumonia following PPI treatment for GERD in patients with COPD.MethodsThis study used a reimbursement database of the Republic of Korea. Patients aged ≥ 40 years with COPD as a main diagnosis and who received PPI treatment for GERD at least for 14 consecutive days between January 2013 and December 2018 were included in the study. A self-controlled case series analysis was conducted to calculate the risk of moderate and severe exacerbation and pneumonia.ResultsA total of 104,439 patients with prevalent COPD received PPI treatment for GERD. The risk of moderate exacerbation was significantly lower during the PPI treatment than at baseline. The risk of severe exacerbation increased during the PPI treatment but significantly decreased in the post-treatment period. Pneumonia risk was not significantly increased during the PPI treatment. The results were similar in patients with incident COPD.ConclusionsThe risk of exacerbation was significantly reduced after PPI treatment compared with the non-treated period. Severe exacerbation may increase due to uncontrolled GERD but subsequently decrease following PPI treatment. There was no evidence of an increased risk of pneumonia.
National, subnational and risk attributed burden of chronic respiratory diseases in Iran from 1990 to 2019
Authors: Heidari-Foroozan Mahsa , Aryan Alisam , Esfahani Zahra , Shahrbaf Mohammad Amin , Moghaddam Sahar Saeedi , Keykhaei Mohammad , Ghasemi Erfan , Rashidi Mohammad-Mahdi , Rezaei Nazila , Ghamari Seyyed-Hadi , Abbasi-Kangevari Mohsen , Fateh Sahar Mohammadi , Farzi Yousef , Rezaei Negar , Larijani Bagher 
Published: March 2023

Abstract
Introduction
Data on the distribution of the burden of diseases is vital for policymakers for the appropriate allocation of resources. In this study, we report the geographical and time trends of chronic respiratory diseases (CRDs) in Iran from 1990 to 2019 based on the Global burden of the Disease (GBD) study 2019.

Methods
Data were extracted from the GBD 2019 study to report the burden of CRDs through disability-adjusted life years (DALYs), mortality, incidence, prevalence, Years of Life lost (YLL), and Years Lost to Disability (YLD). Moreover, we reported the burden attributed to the risk factors with evidence of causation at national and subnational levels. We also performed a decomposition analysis to determine the roots of incidence changes. All data were measured as counts and age-standardized rates (ASR) divided by sex and age group.

Results
In 2019, the ASR of deaths, incidence, prevalence, and DALYs attributed to CRDs in Iran were 26.9 (23.2 to 29.1), 932.1 (799.7 to 1091.5), 5155.4 (4567.2 to 5859.6) and 587,911 (521,418 to 661,392) respectively. All burden measures were higher in males than females, but in older age groups, CRDs were more incident in females than males. While all crude numbers increased, all ASRs except for YLDs decreased over the studied period. Population growth was the main contributor to the changes in incidence at a national and subnational levels. The ASR of mortality in the province (Kerman) with the highest death rate (58.54 (29.42 to 68.73) was four times more than the province (Tehran) with the lowest death rate (14.52 (11.94 to 17.64)). The risk factors which imposed the most DALYs were smoking (216 (189.9 to 240.8)), ambient particulate matter pollution (117.9 (88.1 to 149.4)), and high body mass index (BMI) (57 (36.3 to 81.8)). Smoking was also the main risk factor in all provinces.

Conclusion
Despite the overall decrease in ASR of burden measures, the crude counts are rising. Moreover, the ASIR of all CRDs except asthma is increasing. This suggests that the overall incidence of CRDs will continue to grow in the future, which calls for immediate action to reduce exposure to the known risk factors. Therefore, expanded national plans by policymakers are essential to prevent the economic and human burden of CRDs.
Dietary patterns, lung function and asthma in childhood: a longitudinal study
Authors: Talaei Mohammad , Emmett Pauline M. , Granell Raquel , Tabatabaeian Hossein , Northstone Kate , Bergström Anna , Shaheen Seif O. 
Published: March 2023

Abstract
Background
Longitudinal epidemiological data are scarce examining the relationship between dietary patterns and respiratory outcomes in childhood. We investigated whether three distinct dietary patterns in mid-childhood were associated with lung function and incident asthma in adolescence.

Methods
In the Avon Longitudinal Study of Parents and Children, ‘processed’, ‘traditional’, and ‘health-conscious’ dietary patterns were identified using principal components analysis from food frequency questionnaires at 7 years of age. Post-bronchodilator forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC), and forced expiratory flow at 25–75% of FVC (FEF25–75) were measured at 15.5 years and were transformed to z-scores based on the Global Lung Function Initiative curves. Incident asthma was defined by new cases of doctor-diagnosed asthma at age 11 or 14 years.

Results
In multivariable-adjusted models, the ‘health-conscious’ pattern was positively associated with FEV1 (regression coefficient comparing top versus bottom quartile of pattern score 0.16, 95% CI 0.01 to 0.31, P for trend 0.04) and FVC (0.18, 95% CI 0.04 to 0.33, P for trend 0.02), while the ‘processed’ pattern was negatively associated with FVC (− 0.17, 95% CI − 0.33 to − 0.01, P for trend 0.03). Associations between the ‘health-conscious’ and ‘processed’ patterns and lung function were modified by SCGB1A1 and GPX4 gene polymorphisms. We found no evidence of an association between the ‘traditional’ pattern and lung function, nor between any pattern and FEF25–75 or incident asthma.

Conclusions
A ‘health-conscious’ diet in mid-childhood was associated with higher subsequent lung function, while a diet high in processed food was associated with lower lung function.
Pseudomonas aeruginosa isolation is an important predictor for recurrent hemoptysis after bronchial artery embolization in patients with idiopathic bronchiectasis: a multicenter cohort study
Authors: Wang Le-Le , Lu Hai-Wen , Li Ling-Ling , Gao Yong-Hua , Xu Yu-Hua , Li Hong-Xiao , Xi Yun-Zhu , Jiang Fu-Sheng , Ling Xue-Feng , Wei Wei , Li Fa-Jiu , Mao Bei , Jiang Sen , Xu Jin-Fu 
Published: March 2023

Abstract
Background
Nearly half of bronchiectasis patients receiving bronchial artery embolization (BAE) still have recurrent hemoptysis, which may be life-threatening. Worse still, the underlying risk factors of recurrence remain unknown.

Methods
A retrospective cohort was conducted of patients with idiopathic bronchiectasis who received BAE from 2015 to 2019 at eight centers. Patients were followed up for at least 24 months post BAE. Based on the outcomes of recurrent hemoptysis and recurrent severe hemoptysis, a Cox regression model was used to identify risk factors for recurrence.

Results
A total of 588 individuals were included. The median follow-up period was 34.0 months (interquartile range: 24.3–53.3 months). The 1-month, 1-year, 2-year, and 5-year cumulative recurrent hemoptysis-free rates were 87.2%, 67.5%, 57.6%, and 49.4%, respectively. The following factors were relative to recurrent hemoptysis: 24-h sputum volume (hazard ratio [HR] = 1.99 [95% confidence interval [95% CI]: 1.25–3.15, p = 0.015]), isolation of Pseudomonas aeruginosa (HR = 1.50 [95% CI: 1.13–2.00, p = 0.003]), extensive bronchiectasis (HR = 2.00 [95% CI: 1.29–3.09, p = 0.002]), and aberrant bronchial arteries (AbBAs) (HR = 1.45 [95% CI: 1.09–1.93, p = 0.014]). The area under the receiver operating characteristic curve of the nomogram was 0.728 [95% CI: 0.688–0.769].

Conclusions
Isolation of Pseudomonas aeruginosa is an important independent predictor of recurrent hemoptysis. The clearance of Pseudomonas aeruginosa might effectively reduce the hemoptysis recurrence rate.
No increased prevalence of autoantibodies neutralizing type I IFNs in idiopathic pulmonary fibrosis patients
Authors: Philippot Quentin , Bastard Paul , Puel Anne , Casanova Jean-Laurent , Cobat Aurélie , Laouénan Cédric , Tardivon Coralie , Crestani Bruno , Borie Raphael 
Published: March 2023

AbstractSARS-CoV2 infection has a poor prognosis in patients affected of idiopathic pulmonary fibrosis (IPF). Autoantibodies (auto-Abs) neutralizing type I interferons (IFNs) are found in the blood of at least 15% of patients with life-threatening COVID-19 pneumonia. Because of the elevated prevalence of some auto-Abs in IPF patients, we hypothesize that the prevalence of auto-Abs neutralizing type I IFNs might be increased in the IPF population and then explained specific poor outcome after COVID-19. We screened the plasma of 247 consecutive IPF patients for the presence of auto-Abs neutralizing type I IFNs. Three patients displayed auto-Abs neutralizing type I IFNs. Among them, the only patient with documented SARS-CoV-2 infection experienced life threatening COVID-19 pneumonia. The prevalence of auto-Abs neutralizing type I IFNs in this cohort of IPF patients was not significantly different from the one of the general population. Overall, this study did not suggest any association between auto-Abs neutralizing type I IFNs and IPF.