bluuebunny/crossref_metadata_2025_split huggingface dataset:
The novel transcriptomic signature of angiogenesis predicts clinical outcome, tumor microenvironment and treatment response for prostate adenocarcinoma
Authors: Gu Cheng-Yuan , Dai Bo , Zhu Yao , Lin Guo-Wen , Wang Hong-Kai , Ye Ding-Wei , Qin Xiao-Jian 
Published: July 2022

AbstractAngiogenesis plays the critical roles in promoting tumor progression, aggressiveness, and metastasis. Although few studies have revealed some angiogenesis-related genes (ARGs) could serve as prognosis-related biomarkers for the prostate cancer (PCa), the integrated role of ARGs has not been systematically studied. The RNA-sequencing data and clinical information of prostate adenocarcinoma (PRAD) were downloaded from The Cancer Genome Atlas (TCGA) as discovery dataset. Twenty-three ARGs in total were identified to be correlated with prognosis of PRAD by the univariate Cox regression analysis, and a 19-ARG signature was further developed with significant correlation with the disease-free survival (DFS) of PRAD by the least absolute shrinkage and selection operator (LASSO) Cox regression with tenfold cross-validation. The signature stratified PRAD patients into high- and low-ARGs signature score groups, and those with high ARGs signature score were associated with significantly poorer outcomes (median DFS: 62.71 months vs unreached, p < 0.0001). The predicting ability of ARGs signature was subsequently validated in two independent cohorts of GSE40272 & PRAD_MSKCC. Notably, the 19-ARG signature outperformed the typical clinical features or each involved ARG in predicting the DFS of PRAD. Furthermore, a prognostic nomogram was constructed with three independent prognostic factors, including the ARGs signature, T stage and Gleason score. The predicted results from the nomogram (C-index = 0.799, 95%CI = 0.744–0.854) matched well with the observed outcomes, which was verified by the calibration curves. The values of area under receiver operating characteristic curve (AUC) for DFS at 1-, 3-, 5-year for the nomogram were 0.82, 0.83, and 0.83, respectively, indicating the performance of nomogram model is of reasonably high accuracy and robustness. Moreover, functional enrichment analysis demonstrated the potential targets of E2F targets, G2M checkpoint pathways, and cell cycle pathways to suppress the PRAD progression. Of note, the high-risk PRAD patients were more sensitive to immune therapies, but Treg might hinder benefits from immunotherapies. Additionally, this established tool also could predict response to neoadjuvant androgen deprivation therapy (ADT) and some chemotherapy drugs, such as cisplatin, paclitaxel, and docetaxel, etc. The novel ARGs signature, with prognostic significance, can further promote the application of targeted therapies in different stratifications of PCa patients.
m6A-modified circRNAs: detections, mechanisms, and prospects in cancers
Authors: Qin Shiyi , Zhang Qi , Xu Yanhua , Ma Shuo , Wang Tianyi , Huang Yuejiao , Ju Shaoqing 
Published: July 2022

AbstractCircular RNAs (circRNAs) have become a research hotspot in recent years with their universality, diversity, stability, conservativeness, and spatiotemporal specificity. N6-methyladenosine (m6A), the most abundant modification in the eukaryotic cells, is engaged in the pathophysiological processes of various diseases. An increasing amount of evidence has suggested that m6A modification is common in circRNAs and is associated with their biological functions. This review summarizes the effects of m6A modification on circRNAs and their regulation mechanisms in cancers, providing some suggestions of m6A-modified circRNAs in cancer therapy.
Uncertainty Analysis and Optimization of Quasi-Zero Stiffness Air Suspension Based on Polynomial Chaos Method
Authors: Xu Xing , Liu Huan , Jiang Xinwei , Atindana Akolbire Vincent 
Published: July 2022

AbstractTo improve the vibration isolation performance of suspensions, various new structural forms of suspensions have been proposed. However, there is uncertainty in these new structure suspensions, so the deterministic research cannot reflect the performance of the suspension under actual operating conditions. In this paper, a quasi-zero stiffness isolator is used in automotive suspensions to form a new suspension−quasi-zero stiffness air suspension (QZSAS). Due to the strong nonlinearity and structural complexity of quasi-zero stiffness suspensions, changes in structural parameters may cause dramatic changes in suspension performance, so it is of practical importance to study the effect of structural parameter uncertainty on the suspension performance. In order to solve this problem, three suspension structural parameters d0, L0 and Pc0 are selected as random variables, and the polynomial chaos expansion (PCE) theory is used to solve the suspension performance parameters. The sensitivity of the performance parameters to different structural parameters was discussed and analyzed in the frequency domain. Furthermore, a multi-objective optimization of the structural parameters d0, L0 and Pc0 of QZSAS was performed with the mean and variance of the root-mean-square (RMS) acceleration values as the optimization objectives. The optimization results show that there is an improvement of about 8%−10% in the mean value and about 40%−55% in the standard deviation of acceleration (RMS) values. This paper verifies the feasibility of the PCE method for solving the uncertainty problem of complex nonlinear systems, which provide a reference for the future structural design and optimization of such suspension systems.
METTL3 mediates Ang-II-induced cardiac hypertrophy through accelerating pri-miR-221/222 maturation in an m6A-dependent manner
Authors: Zhang Rui , Qu Yangyang , Ji Zhenjun , Hao Chunshu , Su Yamin , Yao Yuyu , Zuo Wenjie , Chen Xi , Yang Mingming , Ma Genshan 
Published: July 2022

Abstract
Background
METTL3 is the core catalytic enzyme in m6A and is involved in a variety of cardiovascular diseases. However, whether and how METTL3 plays a role during angiotensin II (Ang-II)-induced myocardial hypertrophy is still unknown.

Methods
Neonatal rat cardiomyocytes (NRCMs) and C57BL/6J mice were treated with Ang-II to induce myocardial hypertrophy. qRT-PCR and western blots were used to detect the expression of RNAs and proteins. Gene function was verified by knockdown and/or overexpression, respectively. Luciferase and RNA immunoprecipitation (RIP) assays were used to verify interactions among multiple genes. Wheat germ agglutinin (WGA), hematoxylin and eosin (H&E), and immunofluorescence were used to examine myocardial size. m6A methylation was detected by a colorimetric kit.

Results
METTL3 and miR-221/222 expression and m6A levels were significantly increased in response to Ang-II stimulation. Knockdown of METTL3 or miR-221/222 could completely abolish the ability of NRCMs to undergo hypertrophy. The expression of miR-221/222 was positively regulated by METTL3, and the levels of pri-miR-221/222 that bind to DGCR8 or form m6A methylation were promoted by METTL3 in NRCMs. The effect of METTL3 knockdown on hypertrophy was antagonized by miR-221/222 overexpression. Mechanically, Wnt/β-catenin signaling was activated during hypertrophy and restrained by METTL3 or miR-221/222 inhibition. The Wnt/β-catenin antagonist DKK2 was directly targeted by miR-221/222, and the effect of miR-221/222 inhibitor on Wnt/β-catenin was abolished after inhibition of DKK2. Finally, AAV9-mediated cardiac METTL3 knockdown was able to attenuate Ang-II-induced cardiac hypertrophy in mouse model.

Conclusions
Our findings suggest that METTL3 positively modulates the pri-miR221/222 maturation process in an m6A-dependent manner and subsequently activates Wnt/β-catenin signaling by inhibiting DKK2, thus promoting Ang-II-induced cardiac hypertrophy. AAV9-mediated cardiac METTL3 knockdown could be a therapeutic for pathological myocardial hypertrophy.
Toward a standard formal semantic representation of the model card report
Authors: Amith Muhammad Tuan , Cui Licong , Zhi Degui , Roberts Kirk , Jiang Xiaoqian , Li Fang , Yu Evan , Tao Cui 
Published: July 2022

Abstract
Background
Model card reports aim to provide informative and transparent description of machine learning models to stakeholders. This report document is of interest to the National Institutes of Health’s Bridge2AI initiative to address the FAIR challenges with artificial intelligence-based machine learning models for biomedical research. We present our early undertaking in developing an ontology for capturing the conceptual-level information embedded in model card reports.

Results
Sourcing from existing ontologies and developing the core framework, we generated the Model Card Report Ontology. Our development efforts yielded an OWL2-based artifact that represents and formalizes model card report information. The current release of this ontology utilizes standard concepts and properties from OBO Foundry ontologies. Also, the software reasoner indicated no logical inconsistencies with the ontology. With sample model cards of machine learning models for bioinformatics research (HIV social networks and adverse outcome prediction for stent implantation), we showed the coverage and usefulness of our model in transforming static model card reports to a computable format for machine-based processing.

Conclusions
The benefit of our work is that it utilizes expansive and standard terminologies and scientific rigor promoted by biomedical ontologists, as well as, generating an avenue to make model cards machine-readable using semantic web technology. Our future goal is to assess the veracity of our model and later expand the model to include additional concepts to address terminological gaps. We discuss tools and software that will utilize our ontology for potential application services.
MicroRNA-145-5p modulates Krüppel-like factor 5 and inhibits cell proliferation, migration, and invasion in nasopharyngeal carcinoma
Authors: Yuan Chien-Han , Hsu Wei-Chi , Huang A.-Mei , Yuan Ben-Chih , Chen I.-Hung , Hsu Chia-An , Chen Rong-Feng , Chu Yih-Min , Lin Hui-Hui , Ke Hung-Lung 
Published: July 2022

Abstract
Background
In several human cancers, Krüppel-like factor 5 (KLF5), a zinc finger transcription factor, can contribute to both tumor progression or suppression; however, the precise role of KLF5 in nasopharyngeal carcinoma (NPC) remains poorly understood. In this study, the association between KLF5 and microRNA-145-5p (miR-145-5p) in NPC cells was elucidated.

Results
Our results showed that KLF5 expression was up-regulated in NPC group compared to normal group. We found that KLF5 exhibited an oncogenic role in NPC cells. The upregulation of miR-145-5p inhibited the proliferation, migration, and invasion of NPC cells. It was observed that miR-145-5p could down-regulate the mRNA and protein expression of KLF5 in NPC cell lines. Additionally, the activity of focal adhesion kinase (FAK), a migration marker, was regulated by miR-145-5p and KLF5 in NPC cells.

Conclusions
The results of this study indicated that miR-145-5p could repress the proliferation, migration, and invasion of NPC cells via KLF5/FAK regulation, and could be a potential therapeutic target for patients with NPC.
Does group-based trajectory modeling estimate spurious trajectories?
Authors: Mésidor Miceline , Rousseau Marie-Claude , O’Loughlin Jennifer , Sylvestre Marie-Pierre 
Published: July 2022

Abstract
Background
Group-based trajectory modelling (GBTM) is increasingly used to identify subgroups of individuals with similar patterns. In this paper, we use simulated and real-life data to illustrate that GBTM is susceptible to generating spurious findings in some circumstances.

Methods
Six plausible scenarios, two of which mimicked published analyses, were simulated. Models with 1 to 10 trajectory subgroups were estimated and the model that minimized the Bayes criterion was selected. For each scenario, we assessed whether the method identified the correct number of trajectories, the correct shapes of the trajectories, and the mean number of participants of each trajectory subgroup. The performance of the average posterior probabilities, relative entropy and mismatch criteria to assess classification adequacy were compared.

Results
Among the six scenarios, the correct number of trajectories was identified in two, the correct shapes in four and the mean number of participants of each trajectory subgroup in only one. Relative entropy and mismatch outperformed the average posterior probability in detecting spurious trajectories.

Conclusion
Researchers should be aware that GBTM can generate spurious findings, especially when the average posterior probability is used as the sole criterion to evaluate model fit. Several model adequacy criteria should be used to assess classification adequacy.
Patient perspectives on the management of COPD and Type 2 Diabetes in general practice: an interview study
Authors: Lee Kim , Titlestad Signe Beck , Nørgaard Birgitte , Bentzen Niels , Søndergaard Jens , Marcussen Michael 
Published: July 2022

Abstract
Background
The Danish healthcare system has undergone fundamental organisational changes. In recent years, treatment of most patients with chronic obstructive pulmonary disease (COPD) and type 2 diabetes (T2D) in Denmark has been transferred from specialised hospitals to general practices, and only the most complicated cases are treated at hospital outpatients clinics or are admitted. This transfer aimed to reduce costs without compromising quality of care and ensure that the treatment was managed by general practitioners (GPs) who had personal knowledge of the patient. In this paper, we explore patients’ perceptions of the quality of care provided by their GPs.

Methods
A qualitative research study was conducted with semi-structured interviews of 24 informants; nine were diagnosed with COPD and 15 were diagnosed with T2D. Snowball sampling was used for recruitment. Data were analysed using systematic text condensation.

Results
The interviews revealed four main themes:
1) The informants perceived the quality of their treatment in general practice to be high due to their personal relationship with their GPs.
2) The informants valued their GP’s knowledge about them, their lives, and their illnesses.
3) The informants expressed a high degree of satisfaction with the quality of care received in general practice.
4) The informants expressed that geographical distance to the general practice was of minor importance to them.

Conclusion
The patients perceived that the quality of the care and treatment they received were high following the transfer of COPD and T2D treatment to general practice. A strong, trusting relationship between the GP and the patient and the increased availability of the GP both contributed to their satisfaction with the GPs’ services.
Translation and psychometric validation of the Arabic version of Summary of the Diabetes Self-Care Activities (SDSCA) among pregnant women with gestational diabetes
Authors: Al Hashmi I. , Al-Noumani H. , Alaloul F. , Murthi S. , Khalaf A. 
Published: July 2022

Abstract
Background and purpose
There is a lack of validated tools to assess adherence to gestational diabetes (GDM) management plan among women with GDM. This study aimed to translate the Summary of Diabetes Self-Care Activity (SDSCA) into Arabic, culturally adapt it, and test its psychometric properties among women with GDM.

Methods
A multiphase study was used to translate and evaluate the psychometric properties of the Arabic version of SDSCA using the following steps: (1) cultural and linguistic validation; (2) content and face validity testing; (3) construct validity testing; and (4) internal validity testing. Nineghty pregnant women with GDM were recruited to meet the purpose of this study.

Results
The Arabic version of the adapted SDSCA tool revealed adequate content validity, satisfactory internal consistency (Cronbach’s alpha = 0.74), and test-retest reliability (Pearson correlation coefficient = .67). Exploratory factor analysis revealed three factors that fit data satisfactory: diet, exercise, and blood glucose monitoring.

Conclusions
This study showed that the adapted Arabic SDSCA tool is an easy, valid, and reliable tool to assess pregnant women’s adherence to GDM management plan.
Anesthetic propofol enhances cisplatin-sensitivity of non-small cell lung cancer cells through N6-methyladenosine-dependently regulating the miR-486-5p/RAP1-NF-κB axis
Authors: Ling Quan , Wu Shaoyong , Liao Xiaozu , Liu Chiyi , Chen Yong 
Published: July 2022

Abstract
Background
Drug resistance is a considerable challenge for chemotherapy in non-small cell lung cancer (NSCLC). Propofol, a commonly used intravenous anesthetics, has been reported to suppress the malignancy of various cancers. However, the effects of propofol on cisplatin (DDP) sensitivity in NSCLC and its molecular mechanisms have not been clearly clarified yet, and the present study aimed to resolve this problem.

Methods
NSCLC cells were co-treated with propofol and DDP, Cell Counting kit-8 assay, colony formation assay and flow cytometry were conducted to test the role of propofol in regulating DDP-resistance in NSCLC. Next, through conducting quantitative real-time polymerase chain reaction, dual-luciferase gene reporter system and western blot, the responsible molecular axis in propofol regulating the DDP sensitivity in NSCLC was uncovered, and the function verification experiments were performed by transfection with the inhibitors or small interfering RNAs of those molecules.

Results
Propofol suppressed cell viability, colony formation ability, tumorigenesis, and promoted cell apoptosis to enhance DDP-sensitivity in NSCLC in vitro and in vivo. Propofol increased miR-486-5p level in NSCLC cells and xenograft tumors tissues in a N6-methyladenosine (m6A)-dependent manner, thus inactivating the Ras-associated protein1 (RAP1)-NF-kappaB (NF-κB) axis. Propofol regulated the miR-486-5p/RAP1-NF-κB axis to improve DDP-sensitivity in NSCLC.

Conclusions
Taken together, this study firstly investigates the detailed molecular mechanisms by which propofol enhanced DDP-sensitivity in NSCLC cells, and a novel m6A-dependent miR-486-5p/RAP1-NF-κB axis is identified to be closely associated with the process.
Comparative analysis of a presbyopia-correcting intraocular lens that combines extended depth-of-focus and bifocal profiles with a standard monofocal intraocular lens
Authors: Shin Da Eun , Lee Hun , Koh Kyungmin 
Published: July 2022

AbstractBackgroundRecently, a new presbyopia-correcting intraocular lens (IOL) that combines extended depth-of-focus and bifocal profiles (ZFR00: Tecnis® Synergy®, Johnson & Johnson Vision, Santa Ana, CA, USA) has been established and several studies have been reported. We attempted to compare the performance with a standard IOL (ZCB00: Tecnis® monofocal, Johnson & Johnson Vision, Santa Ana, CA, USA) manufactured using the same material from the same company, which has been extensively used worldwide.MethodsThe medical records of patients undergoing cataract surgery with ZCB00 or ZFR00 implantation between March 2021 and September 2021 and with available 3-month visit data were reviewed. Uncorrected near, intermediate, and distance visual acuity (VA), corrected distance VA, and optical quality were the main outcome measures.ResultsThis study included forty-six patients (64 eyes), with twenty-one patients (32 eyes) implanted with ZCB00 and twenty-five patients (32 eyes) implanted with ZFR00. The average age of the patients was 66.0 ± 10.1 (range: 40 to 82) and 65.1 ± 4.7 (range: 59 to 77) years in the ZCB00 and ZFR00 groups, respectively. The preoperative characteristics did not differ significantly between the two groups. Compared to the ZCB00 group, the ZFR00 group demonstrated significantly superior intermediate and near VA (p < 0.001) at 3 months postoperatively. The ZFR00 group showed significantly lower objective measured optical quality than that in the ZCB00 group.ConclusionsThe ZFR00 exhibited a continuous range of vision and a smooth defocus curve, while the ZCB00 provided superior objective optical quality.
Precocious puberty or growth hormone deficiency as initial presentation in Mayer-Rokitansky-kuster-Hauser syndrome: a clinical report of 5 cases
Authors: Ai Zhuanzhuan , Zhu Xiaoyun , Chen Hong , Chen Ruimin 
Published: July 2022

Abstract
Background
We report five patients with Mayer-Rokitansky-Küster-Hauser syndrome (MRKHS), four of whom presented with precocious puberty and one with growth hormone deficiency (GHD. Our five children add to the growing endocrine data base of MRKHS.

Case presentation
We retrospectively reviewed clinical data of 5 MRKHS patients from 2017 to 2020. The clinical features, hormonal profiles, radiological imaging and genetic analyses were collated. The age range of the 5 patients at diagnosis was 6.7–9.1 years. Four presented with premature thelarche, and one presented with short stature. External genitalia were normal in all patients. Gonadotropin-releasing hormone stimulation tests for the 5 patients revealed peak luteinizing hormone and follicular stimulating hormone levels of 3.57, 6.24, 11.5, 4.44 and 4.97 IU/L and 9.41, 16.7, 13.8, 14.2 and 10.3 mIU/mL, respectively. Growth hormone stimulation for one patient with short stature was consistent with GHD with a peak level of GH was 7.30 ng/mL. Imaging disclosed advanced bone age in four patients and no skeletal abnormalities in any of the patients. Ultrasonography of the abdomen revealed bilateral polycystic kidneys in one patient. Pelvic magnetic resonance imaging confirmed no uterus in five patients. All of the patients had a normal karyotype (46, XX). In one patient, whole-exome sequencing detected a deletion of 17q12(chr17:36,046,434–36,105,050, hg19) encompassing the HNF1B gene.

Conclusions
We report the unusual co-occurrence of precocious puberty and GHD in patients with MRKHS, highlighting that abnormal puberty and growth development may represent initial unexplained manifestations. Whether the deletion of 17q 22 begat GHD is unclear.
Household access to basic drinking water, sanitation and hygiene facilities: secondary analysis of data from the demographic and health survey V, 2017–2018
Authors: Gaffan Nicolas , Kpozèhouen Alphonse , Dégbey Cyriaque , Glèlè Ahanhanzo Yolaine , Glèlè Kakaï Romain , Salamon Roger 
Published: July 2022

Abstract
Background
In Benin, access to water, sanitation and hygiene (WASH) remains an issue. This study aims to provide an overview of household access to basic WASH services based on nationally representative data.

Method
Secondary analyses were run using the ‘HOUSEHOLD’ dataset of the fifth Demographic and Health Survey 2017–2018. The dependent variables were household access to individual and combined basic WASH services. The characteristics of the household head and those related to the composition, wealth and environment of the household were independent variables. After a descriptive analysis of all study variables, multivariate logistic regression was performed to identify predictors of outcome variables.

Results
The study included 14,156 households. Of these, 63.98% (95% CI = 61.63–66.26), 13.28% (95% CI = 12.10–14.57) and 10.11% (95% CI = 9.19–11.11) had access to individual basic water, sanitation and hygiene facilities, respectively. Also, 3% (95% CI = 2.53–3.56) of households had access to combined basic WASH services. Overall, the richest households and few, and those headed by people aged 30 and over, female and with higher levels of education, were the most likely to have access to individual and combined basic WASH services. In addition, disparities based on the department of residence were observed.

Conclusion
The authors suggest a multifactorial approach that addresses the identified determinants.