bluuebunny/crossref_metadata_2025_split huggingface dataset:
MAGCNSE: predicting lncRNA-disease associations using multi-view attention graph convolutional network and stacking ensemble model
Authors: Liang Ying , Zhang Ze-Qun , Liu Nian-Nian , Wu Ya-Nan , Gu Chang-Long , Wang Ying-Long 
Published: May 2022

AbstractBackgroundMany long non-coding RNAs (lncRNAs) have key roles in different human biologic processes and are closely linked to numerous human diseases, according to cumulative evidence. Predicting potential lncRNA-disease associations can help to detect disease biomarkers and perform disease analysis and prevention. Establishing effective computational methods for lncRNA-disease association prediction is critical.ResultsIn this paper, we propose a novel model named MAGCNSE to predict underlying lncRNA-disease associations. We first obtain multiple feature matrices from the multi-view similarity graphs of lncRNAs and diseases utilizing graph convolutional network. Then, the weights are adaptively assigned to different feature matrices of lncRNAs and diseases using the attention mechanism. Next, the final representations of lncRNAs and diseases is acquired by further extracting features from the multi-channel feature matrices of lncRNAs and diseases using convolutional neural network. Finally, we employ a stacking ensemble classifier, consisting of multiple traditional machine learning classifiers, to make the final prediction. The results of ablation studies in both representation learning methods and classification methods demonstrate the validity of each module. Furthermore, we compare the overall performance of MAGCNSE with that of six other state-of-the-art models, the results show that it outperforms the other methods. Moreover, we verify the effectiveness of using multi-view data of lncRNAs and diseases. Case studies further reveal the outstanding ability of MAGCNSE in the identification of potential lncRNA-disease associations.ConclusionsThe experimental results indicate that MAGCNSE is a useful approach for predicting potential lncRNA-disease associations.
Genomic analysis of qnr-harbouring IncX plasmids and their transferability within different hosts under induced stress
Authors: Nohejl Tomas , Valcek Adam , Papousek Ivo , Palkovicova Jana , Wailan Alexander M. , Pratova Hana , Minoia Marco , Dolejska Monika 
Published: May 2022

Abstract
Background
Conjugative plasmids play a major role in the dissemination of antibiotic resistance genes. Knowledge of the plasmid characteristics and behaviour can allow development of control strategies. Here we focus on the IncX group of plasmids carrying genes conferring quinolone resistance (PMQR), reporting their transfer and persistence within host bacteria of various genotypes under distinct conditions and levels of induced stress in form of temperature change and various concentrations of ciprofloxacin supplementation.

Methods
Complete nucleotide sequences were determined for eight qnr-carrying IncX-type plasmids, of IncX1 (3), IncX2 (3) and a hybrid IncX1-2 (2) types, recovered from Escherichia coli of various origins. This data was compared with further complete sequences of IncX1 and IncX2 plasmids carrying qnr genes (n = 41) retrieved from GenBank and phylogenetic tree was constructed. Representatives of IncX1 (pHP2) and IncX2 (p194) and their qnrS knockout mutants, were studied for influence of induced stress and genetic background on conjugative transfer and maintenance.

Results
A high level of IncX core-genome similarity was found in plasmids of animal, environmental and clinical origin. Significant differences were found between the individual IncX plasmids, with IncX1 subgroup plasmids showing higher conjugative transfer rates than IncX2 plasmids. Knockout of qnr modified transfer frequency of both plasmids. Two stresses applied simultaneously were needed to affect transfer rate of wildtype plasmids, whereas a single stress was sufficient to affect the IncX ΔqnrS plasmids. The conjugative transfer was shown to be biased towards the host phylogenetic proximity. A long-term cultivation experiment pointed out the persistence of IncX plasmids in the antibiotic-free environment.

Conclusions
The study indicated the stimulating effect of ciprofloxacin supplementation on the plasmid transfer that can be nullified by the carriage of a single PMQR gene. The findings present the significant properties and behaviour of IncX plasmids carrying antibiotic resistance genes that are likely to play a role in their dissemination and stability in bacterial populations.
Complete genome sequence of Pseudomonas stutzeri S116 owning bifunctional catalysis provides insights into affecting performance of microbial fuel cells
Authors: Li Peng , Yuan Wenfeng , Huang Yitie , Zhang Caiyu , Ni Chide , Lin Qi , Zhu Zhihuang , Wang Jianxin 
Published: May 2022

Abstract
Background
Pseudomonas stutzeri S116 is a sulfur-oxidizing bacteria isolated from marine sludge. It exhibited excellent electricity generation as bioanode and biocathode applied in microbial fuel cells (MFCs). Complete genome sequencing of P. stutzeri and cyclic voltammetry method were performed to reveal its mechanism in microbial fuel cells system.

Results
This study indicated that the MFCs generated a maximum output voltage of 254.2 mV and 226.0 mV, and maximum power density of 765 mW/m2 and 656.6 mW/m2 respectively. Complete genome sequencing of P. stutzeri S116 was performed to indicate that most function genes showed high similarities with P. stutzeri, and its primary annotations were associated with energy production and conversion (6.84%), amino acid transport and metabolism (6.82%) and inorganic ion transport and metabolism (6.77%). Homology of 36 genes involved in oxidative phosphorylation was detected, which suggests the strain S116 possesses an integrated electron transport chain. Additionally, many genes encoding pilus-assembly proteins and redox mediators (riboflavin and phenazine) were detected in the databases. Thiosulfate oxidization and dissimilatory nitrate reduction were annotated in the sulfur metabolism pathway and nitrogen metabolism pathway, respectively. Gene function analysis and cyclic voltammetry indicated that P. stutzeri probably possesses cellular machinery such as cytochrome c and redox mediators and can perform extracellular electron transfer and produce electricity in MFCs.

Conclusion
The redox mediators secreted by P. stutzeri S116 were probably responsible for performance of MFCs. The critical genes and metabolic pathways involved in thiosulfate oxide and nitrate reduction were detected, which indicated that the strain can treat wastewater containing sulfide and nitrite efficiently.
Overexpression of AHL9 accelerates leaf senescence in Arabidopsis thaliana
Authors: Zhou Yusen , Zhang Xiaomin , Chen Jing , Guo Xiaopeng , Wang Hongyan , Zhen Weibo , Zhang Junli , Hu Zhubing , Zhang Xuebing , Botella José Ramón , Ito Toshiro , Guo Siyi 
Published: May 2022

Abstract
Background
Leaf senescence, the final stage of leaf growth and development, is regulated by numerous internal factors and environmental cues. Ethylene is one of the key senescence related hormones, but the underlying molecular mechanism of ethylene-induced leaf senescence remains poorly understood.

Results
In this study, we identified one AT-hook like (AHL) protein, AHL9, as a positive regulator of leaf senescence in Arabidopsis thaliana. Overexpression of AHL9 significantly accelerates age-related leaf senescence and promotes dark-induced leaf chlorosis. The early senescence phenotype observed in AHL9 overexpressing lines is inhibited by the ethylene biosynthesis inhibitor aminooxyacetic acid suggesting the involvement of ethylene in the AHL9-associated senescence. RNA-seq and quantitative reverse transcription PCR (qRT-PCR) data identified numerous senescence-associated genes differentially expressed in leaves of AHL9 overexpressing transgenic plants.

Conclusions
Our investigation demonstrates that AHL9 functions in accelerating the leaf senescence process via ethylene synthesis or signalling.
Association between arthritis and cardiovascular risk factors in community-based adults: an opportunity to target cardiovascular risk
Authors: Sewell Julia , Hussain Sultana Monira , Wang Yuanyuan , Wluka Anita E. , Lim Yuan Z. , Carrington Melinda J. , Samaras Katherine , Cicuttini Flavia M. 
Published: May 2022

Abstract
Background
Undertreated risk factors are major contributors to the burden of cardiovascular disease (CVD). Those with arthritis have an increased prevalence of CVD risk factors. CVD risk factors are often asymptomatic, which may be a barrier their treatment. Arthritis causes pain and immobility, and is a common reason for individuals to seek healthcare. Our aims were to (1) examine the relationship between arthritis and CVD risk factors in Australian adults, and (2) calculate the proportion of CVD risk factors that could be reduced if individuals with arthritis were targeted.

Methods
This cross-sectional study uses data from the 2017–18 Australian National Health Survey which included 13,776 participants, categorised into young (18–39 years), middle aged (40–64 years) and older (≥ 65 years) adults. Hypertension, height and weight were measured. Arthritis, dyslipidemia and diabetes were self-reported. The associations between arthritis and CVD risk factors were examined using logistic regression, and the population attributable fraction (PAF) of arthritis for each CVD risk factor was calculated.

Results
Arthritis was reported by 4.0% of young adults, 28.8% of middle-aged adults and 54.5% of older adults. Those with arthritis were at increased odds of obesity (2.07 fold in young, 1.75 fold in middle-aged and 1.89 fold in older adults), increased odds of diabetes (5.70 fold in young, 1.64 fold in middle-aged and 1.37 fold in older adults), increased odds of hypertension (2.72 fold in young, 1.78 fold in middle-aged and 1.48 fold in older adults) and an increased odds of dyslipidaemia (4.64 fold in young, 2.14 fold in middle-aged and 1.22 fold in older adults) compared to those without arthritis. This elevated chance remained significant even after adjusting for obesity, with the exception of diabetes in the older population. This elevated chance remained significant even after adjusting for obesity, with the exception of diabetes in the older population. The PAF of the presence of arthritis for having at least one CVD risk factor was 30.7% in middle-aged adults and 70.4% in older adults.

Conclusion
Australian adults of all ages with arthritis are at increased odds of having CVD risk factors. For young and middle-aged adults, this increased odds remains significant even when adjusted for obesity. Presentation to healthcare practitioners with arthritis is an opportunity to screen for asymptomatic CVD risk factors with the potential of improving outcomes for both diseases. By adopting an approach of managing arthritis and CVD risk factors in parallel, rather than in silos, we could reduce the burden of CVD risk factors by 20–30%.
Scoping review and characteristics of publicly available checklists for assessing clinical trial feasibility
Authors: Gloy Viktoria , Speich Benjamin , Griessbach Alexandra , Taji Heravi Ala , Schulz Alexandra , Fabbro Thomas , Magnus Christiane Pauli , McLennan Stuart , Bertram Wendy , Briel Matthias 
Published: May 2022

AbstractBackgroundWhether there is sufficient capacity and capability for the successful conduct and delivery of a clinical trial should be assessed by several stakeholders according to transparent and evidence-based criteria during trial planning. For this openly shared, user-tested, and validated tools are necessary. Therefore, we systematically examined the public availability and content of checklists which assess the study-level feasibility in the planning phase of clinical trials.MethodsIn our scoping review we systematically searched Medline, EMBASE, and Google (last search, June 2021). We included all publicly available checklists or tools that assessed study level feasibility of clinical trials, examined their content, and checked whether they were user-tested or validated in any form. Data was analysed and synthesised using conventional content analysis.ResultsA total of 10 publicly available checklists from five countries were identified. The checklists included 48 distinct items that were classified according to the following seven different domains of clinical trial feasibility: regulation, review and oversight; participant recruitment; space, material and equipment; financial resources; trial team resources; trial management; and pilot or feasibility studies. None of the available checklists appeared to be user-tested or validated.ConclusionsAlthough a number of publicly available checklists to assess the feasibility of clinical trials exist, their reliability and usefulness remain unclear. Openly shared, user-tested, and validated feasibility assessment tools for a better planning of clinical trials are lacking.
Association of socioeconomic status measures with physical activity and subsequent frailty in older adults
Authors: Kheifets Mark , Goshen Abigail , Goldbourt Uri , Witberg Guy , Eisen Alon , Kornowski Ran , Gerber Yariv 
Published: May 2022

Abstract
Background
Despite increased recognition, frailty remains a significant public health challenge.

Objective
we aimed to assess the role of education and income, as well as neighborhood socioeconomic status, on physical activity and subsequent frailty in older adults.

Methods
Using a population-based cohort of older adults, this study examined the relationship between socioeconomic status (SES) factors, physical activity and frailty. The study included 1,799 participants (mean [SD], 74.6 (6.2), 53.3% female) from the "National Health and Nutrition Survey of Older Adults Aged 65 and Over in Israel", conducted in 2005–2006. A follow-up interview was performed 12–14 years later in a subgroup of 601 subjects (mean [SD], age 84[4]; 56% women). Self-reported leisure-time physical activity (LTPA) was measured at both baseline and follow-up. SES measures were assessed at baseline. Frailty was measured at follow-up, using the Fried's Phenotype Model.

Results
All SES measures were strongly and positively associated with LTPA (all p < 0.001). Eighty-two participants (14%) were classified as frail at follow-up. After age and sex adjustment and accounting for attrition bias using inverse probability weighting, baseline LTPA (OR = 2.77, 95% CI: 1.57–4.90, for inactivity; OR = 1.41, 95% CI: 0.75–2.68, for insufficient activity, compared with sufficient activity, Ptrend < 0.001) was inversely associated with incident frailty. The association persisted after further adjustment for SES and comorbidity.

Conclusion
Among older individuals, multiple SES measures were positively associated with LTPA, which was a strong predictor of lower subsequent frailty risk.
Trends and associated factors in the uptake of HIV testing among female sex workers in Sino-Vietnam border areas in Guangxi, China: a cross-sectional study
Authors: Liang Bingyu , Huang Qianni , Ou Yanyun , Zhang Fei , Zhang Peidong , Nong Aidan , Mo Shide , Wu Zhenxian , Xie Hai , Liang Huayue , Liu Jie , Jiang Junjun , Liang Hao , Liu Deping , Ye Li 
Published: May 2022

Abstract
Background
HIV testing is a primary prevention strategy against the HIV epidemic and an entry point for HIV/AIDS-related care, prevention and treatment. This study aimed to estimate the uptake of HIV testing among Sino-Vietnam female sex workers (FSWs) in Guangxi, China, from 2016 to 2018, and to identify the factors influencing HIV testing uptake.

Methods
A cross-sectional survey was conducted among FSWs in two Sino-Vietnam border cities of Guangxi, China. The survey was conducted through face-to-face interview, the data were collected by a structured questionnaire, and HIV-1 infection was detected simultaneously. Logistic regression analysis was used to determine the factors associated with uptake of HIV testing.

Results
In total, 4565 Chinese local FSWs (CL-FSWs) and 636 cross-border migrant Vietnamese FSWs (CMV-FSWs) were recruited into this study. HIV-1 prevalence in CL-FSWs and CMV-FSWs was 0.70% and 3.14%, respectively. The rate of self-reported uptake of HIV testing in CL-FSWs and CMV-FSWs was 54.56% and 45.44%, respectively. The rates of self-reported uptake of HIV testing declined in both groups from 2016 to 2018. Logistic regression analysis indicated that a number of factors, including socio-demographic characteristics (age < 35 years, higher education, location in Chongzuo City), behaviour factors (having received free AIDS education, condom distribution services and peer education services, high risk sexual behaviours such as inconsistent condom use, having regular commercial sexual partners, etc.), psychological factors (perception of vulnerability to HIV/STIs, perception of risk for HIV infection) were the factors significantly related to uptake of HIV testing.

Conclusion
In recent years, the rate of HIV testing uptake among Sino-Vietnam border FSWs in Guangxi, China was low, which may be an important reason for the high HIV-1 prevalence among FSWs in the region. A number of factors were identified to be associated with HIV-1 testing uptake, suggesting that HIV testing prevention strategies in this region could include accelerating AIDS education training, raising personal awareness of HIV testing, and improving accessibility of HIV testing.
KDM3A-mediated SP1 activates PFKFB4 transcription to promote aerobic glycolysis in osteosarcoma and augment tumor development
Authors: Wang Wei , Wang Bin 
Published: May 2022

Abstract
Background
Lysine-specific histone demethylase 3A (KDM3A) is a potent histone modifier that is frequently implicated in the progression of several malignancies. However, its role in aerobic glycolysis of osteosarcoma (OS) remains unclear.

Methods
KDM3A expression in OS tissues was determined by immunohistochemistry, and that in acquired OS cells was determined by RT-qPCR and western blot assays. KDM3A was silenced in OS cells to examine cellular behaviors and the aerobic glycolysis. Stably transfected cells were injected into nude mice for in vivo experiments. The downstream targets of KDM3A were predicted by bioinformatics systems and validated by ChIP-qPCR. Rescue experiments of SP1 and PFKFB4 were performed to examine their roles in the KDM3A-mediated events.

Results
KDM3A was highly expressed in OS tissues and cells. Knockdown of KDM3A weakened OS cell growth and metastasis in vivo and in vitro, and it suppressed the aerobic glycolysis in OS cells. KDM3A enhanced the transcription of SP1 by demethylating H3K9me2 on its promoter. Restoration of SP1 rescued growth and metastasis of OS cells and recovered the glycolytic flux in cells suppressed by knockdown of KDM3A. SP1 bound to the PFKFB4 promoter to activate its transcription and expression. PFKFB4 expression in OS cells was suppressed by KDM3A silencing but increased after SP1 restoration. Overexpression of PFKFB4 significantly promoted OS cell growth and metastasis as well as the glycolytic flux in cells.

Conclusion
This paper elucidates that upregulation of PFKFB4 mediated by the KDM3A-SP1 axis promotes aerobic glycolysis in OS and augments tumor development.
Surgical outcome of epicanthus and telecanthus correction by C-U medial canthoplasty with lateral canthoplasty in treatment of Blepharophimosis syndrome
Authors: Amer Ahmed Ali , Abdellah Marwa Mahmoud , Hassan Nader Hussein Fouad , Mounir Amr 
Published: May 2022

Abstract
Purpose
To evaluate the surgical outcome of epicanthus and telecanthus correction by C-U medial canthoplasty with lateral canthoplasty in Blepharophimosis Syndrome.

Patients and methods
This was a retrospective single arm interventional study including 18 eyes of 9 patients with Blepharophimosis-ptosis-epicanthus inversus syndrome who presented to oculoplastic clinic, ophthalmology department, Qena university hospital in the period of between July 2020 to April 2021. All the patients had BPES with epicanthus and telecanthus. All cases were subjected to by C plasty with medial and lateral canthoplasty for correction of epicanthus and telecanthus correction followed by frontalis suspension surgery to correct the co-existing blepharoptosis.

Results
The study included 9 cases of BPES, 6 boys and 3 girls, the mean age was 5.4 ± 1.5 in the study group, all patients had a positive family history for BPES. After surgery, the mean IICD decreased from 38.44 mm preoperatively to 32.8 mm postoperatively, with a mean difference of 6.2 mm (P <  0.001). Likewise, the mean PFL increased from 20.78 mm preoperatively to 26.63 mm postoperatively, with a mean difference of 5.8 mm (P <  0.001). Epicanthus skin fold disappeared in all cases and medical canthus could be seen with well healed difficulty seen scars.

Conclusion
C-U medial canthoplasty with lateral canthoplasty in Blepharophimosis Syndrome was found to be an effective procedure in the correction of epicanthus and telecanthus.
The Active Recovery Triad monitor: evaluation of a model fidelity scale for recovery-oriented care in long-term mental health care settings
Authors: Zomer Lieke Johanna Cornelia , van der Meer Lisette , van Weeghel Jaap , van Melle Anne Laura , de Vet Henrica Cornelia Wilhelmina , Kemper Martijn , Antoine Marie Widdershoven Guy , Voskes Yolande 
Published: May 2022

Abstract
Objective
The Active Recovery Triad (ART) model is a recently developed care model for people who are admitted to an institutional setting for several years and receive 24-h mental health care and support. This study focuses on the ART monitor, a model fidelity scale that measures the degree of compliance with the ART model. Our aim is to evaluate the psychometric properties of the ART monitor and to further improve the instrument.

Methods
Fifteen teams at the start (n = 7, group 1) or in the process (6 months to three years) of implementing care according to the ART model (n = 8, group 2) were audited using the ART monitor. Auditors were trained care workers, peer workers, and family peer workers. Auditors and team members provided feedback on the instrument. The content validity, construct validity and inter-rater reliability of the ART monitor were investigated. Based on the outcomes of these psychometric properties, the ART monitor was finalized.

Results
Regarding content validity, auditors and teams indicated that they perceived the ART monitor to be a useful instrument. In terms of construct validity, a significant difference (t(13) = 2.53, p < 0.05) was found between teams at the start of the implementation process (group 1, average score of 2.42 (SD = 0.44)) and teams with a longer duration of implementation (group 2, average score of 2.95 (SD = 0.37)). When allowing for a one-point difference in scores, 88% of the items had an inter-rater agreement over 65%. Items with a relatively low inter-rater reliability, in combination with feedback from auditors and teams regarding content validity, provided direction for further improvement and revision of the instrument.

Conclusions
We concluded that the revised ART monitor is feasible and useful in mental health care practice. However, further evaluation of its psychometric properties will be needed.