bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk of gallstones based on ABCG8 rs11887534 single nucleotide polymorphism among Taiwanese men and women
Authors: Liang Keng-Wei , Huang Hsin-Hui , Wang Lee , Lu Wen-Yu , Chou Ying-Hsiang , Tantoh Disline Manli , Nfor Oswald Ndi , Chiu Neng-Yu , Tyan Yeu-Sheng , Liaw Yung-Po 
Published: December 2021

AbstractBackgroundGallstones are abnormal masses caused by impaired metabolism of cholesterol, bilirubin, or bile salts in the gallbladder or biliary tract. ATP-binding cassette subfamily G member 8 (ABCG8) is a protein that regulates cholesterol efflux from the liver. Genome-wide association studies (GWAS) and meta-analyses of GWAS revealed the ABCG8 rs11887534 variant as the most common genetic determinant of gallstones in humans. These findings have not been extensively replicated in Taiwanese. Therefore, we appraised the relationship between gallstones and rs11887534 in a relatively large Taiwanese sample.MethodsWe retrieved data collected through questionnaires, physical and biochemical tests from the Taiwan Biobank Bank (TWB). The study participants comprised 7388 men and 13,880 women who voluntarily enrolled in the Taiwan Biobank project between 2008 and 2019. Gallstones were self-reported.ResultsThe overall sample size was 21,268 comprising 938 gallstone patients and 20,330 non-gallstone individuals. Among the participants, 20,640 had the GG and 628 had the GC + CC genotype. Atp-value < 0.05, the baseline genotypes and gallstone status between men and women were not significantly different. The risk of gallstones was higher in participants having the GC + CC compared to the GG genotype: odds ratio (OR); 95% confidence interval (CI) = 1.698; 1.240–2.325), but was lower in men compared to women (OR = 0.763; 95% CI = 0.638–0.913). Compared to men with the rs11887534 GG genotype, women with the GG and GC + CC genotypes had a higher risk of gallstone (OR; 95% CI = 1.304; 1.087–1.565 for GG and 2.291; 1.514–3.467 for GC + CC). The positive association between GC + CC and gallstones was retained after we restricted the analysis to the female participants (OR; 95% CI = 1.789 = 1.208–2.648). Hormone use was associated with an elevated risk of gallstones (OR; 95% CI = 1.359; 1.107–1.668). Relative to GG and no hormone use, we found a significantly high risk among hormone users with the GC + CC genotype (OR; 95% CI = 3.596; 1.495–8.650).ConclusionsThe rs11887534 GC + CC genotype was independently associated with a higher risk of gallstones. This risk was much higher among women, especially those who used hormones for various gynecological purposes.
Embedding audiological screening within memory clinic care pathway for individuals at risk of cognitive decline—patient perspectives
Authors: McDonough Anna , Dookhy Joshi , McHale Cathy , Sharkey Jennifer , Fox Siobhan , Kennelly Sean P. 
Published: December 2021

Abstract
Background
With the evolving knowledge on hearing as a potentially modifiable mid-life risk factor for dementia, identification of people at risk becomes increasingly important. People with mild cognitive impairment (MCI) presenting to specialist memory services represent a key “at-risk” target population for audiological evaluation, but few services have established this pathway. This study sought to examine the patient experience and understanding of this process.

Methods
All patients with MCI attending a tertiary referral memory service referred for audiology review were contacted. A patient survey was delivered over the phone. Outpatient letters and the memory clinic database were reviewed.

Results
Twenty patients with MCI were included in the survey. Eight (8/20, 40%) had self-reported hearing loss. Upon formal audiological assessment seventeen (17/20, 85%) had objective evidence of hearing loss; nine (9/17, 52.9%) with mild-moderate and eight (8/17, 47%) with moderate-severe hearing loss. Only six patients (6/20, 30%) recalled having the rationale behind having a hearing test as part of their memory work-up explained to them. However, the majority (15/20, 75%) felt a hearing test was an important part of their memory assessment. Just seven patients overall (7/20, 35%) identified a link between hearing-loss and cognition. All patients who provided feedback on the service itself made positive comments, although (4/20, 20%) felt they did not get adequate information about the results.

Conclusions
A significant proportion of people with MCI had de-novo evidence of hearing impairment upon assessment. Patients are satisfied with incorporating audiological evaluation into a memory clinic assessment, however clear communication around indication, recommendations, and follow-up ensuring compliance is required.
The value of multimodal ultrasonography in differential diagnosis of tuberculous and non-tuberculous superficial lymphadenitis
Authors: Chu Jie , Zhang Ying , Zhang Wenzhi , Zhao Dan , Xu Jianping , Yu Tianzhuo , Yang Gaoyi 
Published: December 2021

Abstract
Background
To investigate the value of multimodal ultrasonography in differentiating tuberculosis from other lymphadenopathy.

Methods
Sixty consecutive patients with superficial lymphadenopathy treated at our hospital from January 2017 to December 2018 were categorized into four types based on the color Doppler ultrasound, five types based on contrast-enhanced ultrasound, and five types based on elastography. Sensitivity and specificity were calculated of all the three imaging, including color Doppler examination, contrast-enhanced ultrasound and one individual multimodal method, for detecting lymph nodes.

Results
A total of 60 patients were included in the final analysis. Of those, Mycobacterium tuberculosis was positive in 38 patients and negative in 22 patients. Among the 38 patients who were positive for Mycobacterium tuberculosis, of which 23 had a history of pulmonary tuberculosis, accounting for 60.53% of the positive cases, and the remaining patients did not combine lesions of other organs. Among the 60 superficial lymph nodes, 63.3% presented with tuberculous lymphadenitis. The sensitivity, specificity, and accuracy of the color Doppler examination were 73.68%, 68.18%, and 71.67%, respectively. The sensitivity, specificity and accuracy of contrast-enhanced ultrasound were 89.47%, 63.64% and 80.00%, respectively. The sensitivity, specificity and accuracy of the elastography were 63.16%, 63.64% and 63.33%, respectively. The sensitivity, specificity and accuracy of one individual multimodal method were 42.11%, 95.45% and 61.67%, respectively. The sensitivity, specificity and accuracy of all modes combined were 100.00%, 27.27% and 73.33%, respectively.

Conclusion
Multimodal ultrasonography has high predictive value for the differential diagnosis of superficial tuberculous lymphadenitis.
Implementation of a structured practical activity to analyse student healthcare worker perceptions and compliance with prescribed infection control procedures
Authors: Pelzer Elise S. , Stewart Zachary , Peters Holly , O’Callaghan Jessica , Bryan Emily , Wager Lucas , Chiruta Juliana 
Published: December 2021

Abstract
Background
Non-compliance with infection control guidelines has been reported within healthcare settings. Infection control education in undergraduate healthcare education programs forms a critical component in preparing student healthcare workers for vocational roles.

Methods
Clinical sciences students (nutrition science, paramedicine, pharmacy, podiatry, optometry studying for qualifications recognised by the Australian Health Practitioner Regulation Agency) self-reported hygiene perceptions and practices and collected microbiological swabs from personal or medical equipment items before and after recommended disinfection procedures.

Results
Cultivable microorganisms were isolated from 95% of student medical equipment items. Disinfection significantly reduced microbial growth on student medical equipment items (P < 0.05).

Conclusions
Student perceptions of infection control procedures do not always correlate with infection control practice. Infection control education of undergraduate healthcare students requires ongoing assessment to ensure successful translation into clinical practice.
Effectiveness of virtual simulation and jaw model for undergraduate periodontal teaching
Authors: Zhang Jie , Xing Jiawei , Zheng Min , Sheng Jie , Zhang Kailiang , Zhang Baoping 
Published: December 2021

Abstract
Background
The current study explored the effect of virtual simulation and jaw model on development of preclinical periodontal skills in undergraduate students. The study also sought to explore effectiveness of VR in periodontal preclinical training and determine adequate performance mode in basic periodontal education to improve future preclinical training strategies.

Methods
Sixty volunteer sophomores and juniors from the stomatology department in Lanzhou university were enrolled to the current study. Participants were randomly assigned into four groups (each group, n = 15) including the traditional jaw model group (Group J) which was the control group, virtual reality group (Group V), virtual-jaw group (Group V-J), and jaw-virtual group (Group J-V). Participants received training on uniform basic periodontal knowledge before completing the first theoretical assessment. Participants further underwent a total 8 h of operation training and completed a second theoretical assessment. Performance of participants was evaluated using the supragingival scaling processes, and clinical operation scores were graded by a blinded professional using an established standard scoring system.

Results
The findings showed no significant difference in the first theoretical outcomes between the four groups (P > 0.05). The scores of the second theoretical assessment were significantly improved for the V-J and J-V groups (60.00 ± 4.47, 58.33 ± 4.35) compared with the scores of the first theoretical exam (49.67 ± 4.81, 48.00 ± 4.93, P < 0.05). The operation process scores of students in Group V-J and J-V (72.00 ± 5.92; 70.00 ± 3.05) were significantly higher compared with the scores in the other two groups (V: 61.67 ± 7.85; J: 60.67 ± 2.58). The scaling process performance of students in Group V-J and J-V (53.00 ± 3.05; 63.40 ± 4.39) was improved compared with that of students in the other two groups (V: 41.90 ± 5.23; J: 47.40 ± 4.31).

Conclusion
The findings show that combination of virtual reality and jaw model during periodontal preclinical training increases students’ grades and improves acquiring of professional skills. Findings from the current study indicate that the jaw model should be applied prior to virtual reality to ensure high efficacy.
Underlying factors and challenges of implementing the urban family physician program in Iran
Authors: Mehrolhassani Mohammad Hossein , Jahromi Vahid Kohpeima , Dehnavieh Reza , Iranmanesh Mahla 
Published: December 2021

AbstractBackgroundThe family physician program was launched in 2005 in rural areas of Iran and then piloted in 2012 in the cities of Fars and Mazandaran provinces due to insufficient health coverage in these cities. However, despite its pivotal role in the health system, this program has not progressed according to the policies. This study aimed to explain the underlying factors and challenges of implementing the urban family physician program in Iran.MethodsThis qualitative study was conducted on 44 policy-makers and managers at national and provincial levels selected via snowball and purposive sampling with maximum variation. The data were managed in MAXQDA 2020 and analyzed by directed content analysis. A triangulation method was adopted for this purpose.ResultsA total of 10 categories, 18 sub-categories, and 29 codes were formed. Most challenges related to underlying factors included precipitancy, economic sanctions, belief in traditional medicine, belief in the expertise of previous physicians, and global ranking of countries. For program implementation, most challenges included a diversity of insurance organizations, budget allocation, referral system, electronic file, educational system, and culture building.ConclusionsThe major challenges pertaining to underlying factors included international pressure for reforms and precipitancy in program implementation due to management changes. The challenges associated with program implementation included budget provision and interaction with insurance organizations. Therefore, to expand this program to other provinces in Iran, the identified factors should be carefully considered so that sufficient confidence and commitment can be guaranteed for all stakeholders.
Rapid screening and identification of viral pathogens in metagenomic data
Authors: Song Shiyang , Ma Liangxiao , Xu Xintian , Shi Han , Li Xuan , Liu Yuanhua , Hao Pei 
Published: December 2021

Abstract
Background
Virus screening and viral genome reconstruction are urgent and crucial for the rapid identification of viral pathogens, i.e., tracing the source and understanding the pathogenesis when a viral outbreak occurs. Next-generation sequencing (NGS) provides an efficient and unbiased way to identify viral pathogens in host-associated and environmental samples without prior knowledge. Despite the availability of software, data analysis still requires human operations. A mature pipeline is urgently needed when thousands of viral pathogen and viral genome reconstruction samples need to be rapidly identified.

Results
In this paper, we present a rapid and accurate workflow to screen metagenomics sequencing data for viral pathogens and other compositions, as well as enable a reference-based assembler to reconstruct viral genomes. Moreover, we tested our workflow on several metagenomics datasets, including a SARS-CoV-2 patient sample with NGS data, pangolins tissues with NGS data, Middle East Respiratory Syndrome (MERS)-infected cells with NGS data, etc. Our workflow demonstrated high accuracy and efficiency when identifying target viruses from large scale NGS metagenomics data. Our workflow was flexible when working with a broad range of NGS datasets from small (kb) to large (100 Gb). This took from a few minutes to a few hours to complete each task. At the same time, our workflow automatically generates reports that incorporate visualized feedback (e.g., metagenomics data quality statistics, host and viral sequence compositions, details about each of the identified viral pathogens and their coverages, and reassembled viral pathogen sequences based on their closest references).

Conclusions
Overall, our system enabled the rapid screening and identification of viral pathogens from metagenomics data, providing an important piece to support viral pathogen research during a pandemic. The visualized report contains information from raw sequence quality to a reconstructed viral sequence, which allows non-professional people to screen their samples for viruses by themselves (Additional file 1).
Ferroptosis-related gene signature predicts the prognosis of papillary thyroid carcinoma
Authors: Shi Jinyuan , Wu Pu , Sheng Lei , Sun Wei , Zhang Hao 
Published: December 2021

Abstract
Background
Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer (TC), accounting for more than 80% of all cases. Ferroptosis is a novel iron-dependent and Reactive oxygen species (ROS) reliant type of cell death which is distinct from the apoptosis, necroptosis and pyroptosis. Considerable studies have demonstrated that ferroptosis is involved in the biological process of various cancers. However, the role of ferroptosis in PTC remains unclear. This study aims at exploring the expression of ferroptosis-related genes (FRG) and their prognostic values in PTC.

Methods
A ferroptosis-related gene signature was constructed using lasso regression analysis through the PTC datasets of the Cancer Genome Atlas (TCGA). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to investigate the bioinformatics functions of significantly different genes (SDG) of ferroptosis. Additionally, the correlations of ferroptosis and immune cells were assessed through the single-sample gene set enrichment analysis (ssGSEA) and CIBERSORT database. Finally, SDG were test in clinical PTC specimens and normal thyroid tissues.

Results
LASSO regression model was utilized to establish a novel FRG signature with 10 genes (ANGPTL7, CDKN2A, DPP4, DRD4, ISCU, PGD, SRXN1, TF, TFRC, TXNRD1) to predicts the prognosis of PTC, and the patients were separated into high-risk and low-risk groups by the risk score. The high-risk group had poorer survival than the low-risk group (p < 0.001). Receiver operating characteristic (ROC) curve analysis confirmed the signature's predictive capacity. Multivariate regression analysis identified the prognostic signature-based risk score was an independent prognostic indicator for PTC. The functional roles of the DEGs in the TGCA PTC cohort were explored using GO enrichment and KEGG pathway analyses. Immune related analysis demonstrated that the most types of immune cells and immunological function in the high-risk group were significant different with those in the low-risk group. Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) verified the SDG have differences in expression between tumor tissue and normal thyroid tissue. In addition, cell experiments were conducted to observe the changes in cell morphology and expression of signature’s genes with the influence of ferroptosis induced by sorafenib.

Conclusions
We identified differently expressed FRG that may involve in PTC. A ferroptosis-related gene signature has significant values in predicting the patients’ prognoses and targeting ferroptosis may be an alternative for PTC’s therapy.
Targeted intervention of eIF4A1 inhibits EMT and metastasis of pancreatic cancer cells via c-MYC/miR-9 signaling
Authors: Zhao Yuchong , Wang Yun , Chen Wei , Bai Shuya , Peng Wang , Zheng Mengli , Yang Yilei , Cheng Bin , Luan Zhou 
Published: December 2021

Abstract
Background
Owing to the lack of effective treatment options, early metastasis remains the major cause of pancreatic ductal adenocarcinoma (PDAC) recurrence and mortality. However, the molecular mechanism of early metastasis is largely unknown. We characterized the function of eukaryotic translation initiation factors (eIFs) in epithelial-mesenchymal-transition (EMT) and metastasis in pancreatic cancer cells to investigate whether eIFs and downstream c-MYC affect EMT and metastasis by joint interference.

Methods
We used The Cancer Genome Atlas (TCGA) and Genome Tissue Expression (GTEx) databases to analyze eIF4A1 expression in PDAC tissues and further validated the findings with a microarray containing 53 PDAC samples. Expression regulation and pharmacological inhibition of eIF4A1 and c-MYC were performed to determine their role in migration, invasion, and metastasis in pancreatic cancer cells in vitro and in vivo.

Results
Elevated eIF4A1 expression was positively correlated with lymph node infiltration, tumor size, and indicated a poor prognosis. eIF4A1 decreased E-cadherin expression through the c-MYC/miR-9 axis. Loss of eIF4A1 and c-MYC decreased the EMT and metastasis capabilities of pancreatic cancer cells, whereas upregulation of eIF4A1 attenuated the inhibition of EMT and metastasis induced by c-MYC downregulation. Treatment with the eIF4A1 inhibitor rocaglamide (RocA) or the c-MYC inhibitor Mycro3 either alone or in combination significantly decreased the expression level of EMT markers in pancreatic cancer cells in vitro. However, the efficiency and safety of RocA alone were not inferior to those of the combination treatment in vivo.

Conclusion
Overexpression of eIF4A1 downregulated E-cadherin expression through the c-MYC/miR-9 axis, which promoted EMT and metastasis of pancreatic cancer cells. Despite the potential feedback loop between eIF4A1 and c-MYC, RocA monotherapy is a promising treatment inhibiting eIF4A1-induced PDAC metastasis.
Assessment of Plasmodium falciparum anti-malarial drug resistance markers in pfcrt and pfmdr1 genes in isolates from Honduras and Nicaragua, 2018–2021
Authors: Fontecha Gustavo , Pinto Alejandra , Archaga Osman , Betancourth Sergio , Escober Lenin , Henríquez Jessica , Valdivia Hugo O. , Montoya Alberto , Mejía Rosa Elena 
Published: December 2021

Abstract
Background
Central America and the island of Hispaniola have set out to eliminate malaria by 2030. However, since 2014 a notable upturn in the number of cases has been reported in the Mosquitia region shared by Nicaragua and Honduras. In addition, the proportion of Plasmodium falciparum malaria cases has increased significantly relative to vivax malaria. Chloroquine continues to be the first-line drug to treat uncomplicated malaria in the region. The objective of this study was to evaluate the emergence of chloroquine resistant strains of P. falciparum using a genetic approach. Plasmodium vivax populations are not analysed in this study.

Methods
205 blood samples from patients infected with P. falciparum between 2018 and 2021 were analysed. The pfcrt gene fragment encompassing codons 72–76 was analysed. Likewise, three fragments of the pfmdr1 gene were analysed in 51 samples by nested PCR and sequencing.

Results
All samples revealed the CVMNK wild phenotype for the pfcrt gene and the N86, Y184F, S1034C, N1042D, D1246 phenotype for the pfmdr1 gene.

Conclusions
The increase in falciparum malaria cases in Nicaragua and Honduras cannot be attributed to the emergence of chloroquine-resistant mutants. Other possibilities should be investigated further. This is the first study to report the genotype of pfmdr1 for five loci of interest in Central America.
The association between acute fatty liver disease and nitric oxide during malaria in pregnancy
Authors: Niikura Mamoru , Fukutomi Toshiyuki , Mineo Shoichiro , Mitobe Jiro , Kobayashi Fumie 
Published: December 2021

Abstract
Background
Liver disease is a common feature of malaria in pregnancy, but its pathogenesis remains unclear.

Methods
To understand the pathogenesis of liver disease during malaria in pregnancy, comparative proteomic analysis of the liver in a mouse model of malaria in pregnancy was performed.

Results
Decreased levels of mitochondrial and peroxisomal proteins were observed in the livers of pregnant mice infected with the lethal rodent malaria parasite Plasmodium berghei strain NK65. By contrast, increased levels of perilipin-2, amyloid A-1, and interferon (IFN)-γ signalling pathway-related proteins were observed in the livers of infected pregnant mice, suggesting that IFN-γ signalling may contribute to the development of liver disease during malaria in pregnancy. IFN-γ signalling is a potential trigger of inducible nitric oxide synthase (iNOS) expression. Liver disease associated with microvesicular fatty infiltration and elevated liver enzymes in pregnant wild-type mice infected with malaria parasites was improved by iNOS deficiency.

Conclusions
In this study, a causative role of iNOS in liver disease associated with microvesicular fatty infiltration during malaria in pregnancy was demonstrated. These findings provide important insight for understanding the role of iNOS-mediated metabolic responses and the pathogenesis of high-risk liver diseases in pregnancy, such as acute fatty liver.