bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimized screening of DNA methylation sites combined with gene expression analysis to identify diagnostic markers of colorectal cancer
Authors: Ye Zhen , Song Guangle , Liang Jianwei , Yi Shuying , Gao Yuqi , Jiang Hanming 
Published: March 2023

Abstract
Background
The prognosis of patients with colorectal cancer is related to early detection. However, commonly used screening markers lack sensitivity and specificity. In this study, we identified diagnostic methylation sites for colorectal cancer.
Methods
After screening the colorectal cancer methylation dataset, diagnostic sites were identified via survival analysis, difference analysis, and ridge regression dimensionality reduction. The correlation between the selected methylation sites and the estimation of immune cell infiltration was analyzed. The accuracy of the diagnosis was verified using different datasets and the 10-fold crossover method.
Results
According to Gene Ontology, the main enrichment pathways of genes with hypermethylation sites are axon development, axonogenesis, and pattern specification processes. However, the Kyoto Encyclopedia of Genes and Genomes (KEGG) suggests the following main enrichment pathways: neuroactive ligand–receptor interaction, calcium signaling, and cAMP signaling. In The Cancer Genome Atlas (TCGA) and GSE131013 datasets, the area under the curve of cg07628404 was >0.95. For the NaiveBayes machine model of cg02604524, cg07628404, and cg27364741, the accuracies of 10-fold cross-validation in the GSE131013 and TCGA datasets were 95% and 99.4%, respectively. The survival prognosis of the hypomethylated group (cg02604524, cg07628404, and cg27364741) was better than that of the hypermethylated group. The mutation risk did not differ between the hypermethylated and hypomethylated groups. A weak negative correlation was observed between cg27364741 and hematopoietic stem cell infiltration estimation (r = -0.33, p <0.05).
Conclusion
In cases of colorectal cancer, the main enrichment pathway of genes with hypermethylated sites was axon and nerve development. In the biopsy tissues, the hypermethylation sites were diagnostic for colorectal cancer, and the NaiveBayes machine model of the three loci showed good diagnostic performance. Site (cg02604524, cg07628404, and cg27364741) hypermethylation predicts poor survival for colorectal cancer. Three methylation sites were weakly correlated with individual immune cell infiltration. Hypermethylation sites may be a useful repository for diagnosing colorectal cancer.
P53 expression, Genome-wide transcriptome profiling and LGS test (a blood test to detect cancer): comparison of UVA exposed lymphocytes from malignant melanoma patients and healthy controls.
Authors: Najafzadeh Mojgan , Naeem Parisa , Ghaderi Nader , Jafarinejad Shohreh , Karimi Zahra , Ghaderi Mehran , Akhbari Pouria , Ghaderi Rojan , Farsi Pedram , Wright Andrew , Anderson Diana 
Published: March 2023

Abstract
This study aimed to evaluate the expression of the P53 gene following exposure to varying doses of UVA radiation, using lymphocytes as surrogates. Lymphocytes from malignant melanoma (MM) patients (n = 20) with positive sentinel nodes were compared to healthy controls (HC)(volunteers) (n = 20). These samples were processed by Comet assay following the Lymphocyte Genome Sensitivity (LGS) test, quantitative real-time Polymerase Chain Reaction (qPCR), western blotting and whole genome transcriptome profiling. LGS test evaluates the level of alterations in lymphocytes resulting from continuous exposure to various physical and chemical insults in the blood, promoting DNA damage, ultimately leading to oxidative stress. It is believed that in cancer, the circulatory tumour cells, exosomes and cytokines impact peripheral lymphocytes. The Comet assay performed within the LGS test indicated a significant difference between the lymphocytes from two groups of HC and MM patients. The qPCR data demonstrated an overall 43.8-fold increase in TP53 gene expression in lymphocytes from MM patients after treatment with 0.2mW/cm2 UVA intensity radiation, compared to healthy and untreated controls. Western blotting was used to confirm gene expression. The p53 protein expression was significantly increased in MM lymphocytes after UVA exposure compared to healthy individuals (p-value < 0.05). The genome transcriptome profiling data also displayed differences in gene expression between the UV-treated lymphocytes from healthy groups as compared to melanoma samples. Nine out of the 23 (~ 40%) genes displaying differences in gene expression were mitochondrial genes, which were increased in lymphocytes from MM compared to HCs. The genes that play an important role in oxidative phosphorylation, such as MT-CYB, MT-CO2, MT-ND2, MT-ND6 and MTRNR2L12, were upregulated in lymphocytes from MM patients compared to HCs. The down-regulated genes in lymphocytes from MM, such as MYH9, RN7SL2, ACTB, AHNAK and FLNA, are related to cell structure, migration and tumour metastasis. Peripheral lymphocytes from MM patients are more sensitive and susceptible to the genotoxic effects of UVA compared to healthy individuals. Our previous studies showed that UVA exposure in various intensities distinguishes differences in the level of DNA damage between lymphocytes from cancer patients compared to HCs through the LGS test. The current results provide further credibility to the LGS assay as a screening test for detecting cancer. This feature could be a promising blood biopsy biomarker for staging and preventing carcinomas at early stages.
Prevalence of hepatitis B and C viral co-infection and associated factors with HIV infection in children in South Kivu, Democratic Republic of the Congo
Authors: Miyanga Serge Ahuka , Shindano Tony Akilimali , Shindano Etienne Mwamba , Kyambikwa Célestin Bisangamo , Kabinda Jeff Maotela 
Published: March 2023

Abstract
BACKGROUND
Achieving the World Health Organization's (WHO) 2030 goal of eradicating Hepatitis B and C viruses must also include HIV co-infected children. However, data on the prevalence of this condition are lacking in the Democratic Republic of Congo (DRC), which is considered as one of the high-prevalence countries for these viruses. The need to assess the extent of this co-infection in these children is hence important in order to capitalize on efforts to improve prevention and management.
METHODOLOGY
This was a comparative cross-sectional study conducted from February 04, 2015 to September 03, 2019 in a group of Reference General Hospitals with a pediatric HIV management program in South Kivu province. The study compared the frequency of hepatitis B (HBV) and C (HCV) markers and associated factors for these two viruses in two equal groups : HIV-positive and HIV-negative children. The data were analyzed using SPSS version 20.0 software and the significance level was set at p-value less than 0.05.
RESULTS
The study enrolled a total of 594 children, of whom 297 were HIV-positive and 297 negative. HBsAg was found in 8.7% of HIV-positive patients and 0.7% for HCV antibodies. On the other hand, among HIV-negative patients, the proportion of HBsAg was 0.7% but no cases with anti-HCV antibodies were detected. HIV status increases by 14 times the risk of co-occurring of HBV [OR 14.1 (95% CI: 3.33–60.2); p < 0.001] and this risk is not apparent for HCV (p = 0.297). The fact that the presence of jaundice in the family environment of the patient appears to be associated with HIV status (p = 0.028) strongly suggests that the family context could play an important role in this double contamination.
CONCLUSION
This study documents the importance of co-infection with HBV and HCV in HIV-positive children in South Kivu. Particular attention should be paid to prevention and early detection of these co-infections in this population.
Perspectives on Research Priorities for Linked Prescription Drug Monitoring Program Data: A Survey
Authors: Cummins Mollie , Turcotte Catherine , Pan Huaizhong , Staes Catherine 
Published: March 2023

Abstract
Background: In addition to its clinical value in supporting prescribing decisions, Prescription Drug Monitoring Program (PDMP) data is important for surveillance and research. PDMP data has been used to conduct varied research related to prescribed controlled substances, including topics in epidemiology, addiction, and health services research. There is rich potential to gain further insight by linking PDMP data to additional data resources that include biological, social, environmental, and other variables.The focus of this study was to identify priority research topics, along with examples of research questions, that could be addressed using linked prescription drug monitoring program (PDMP) data which we defined as PDMP data linked to other large clinical, public health or administrative data sets.
Methods: We surveyed researchers affiliated with any of three research-engaged Utah universities, using a web-based survey distributed by e-mail. The survey included demographic questions and questions pertaining to research use of linked PDMP data, generating both structured and free text responses.
Results: The response rate was 11.9% (47/395), and the completion rate was 85.1% (40/ 47). Respondents identified research value corresponding to ten themes reflecting specific domains of discovery and cross-cutting value for research. Respondents support routine linkage of multiple data sources, including new, currently unlinked data sources. They identified multiple high-priority research questions corresponding to eight thematic categories.
Conclusions: Respondents readily identified multiple points of research value, including specific research topics across the translational spectrum, and overall value in establishing a complete record of prescription drug use for populations and individuals. High-priority research questions related to varied dimensions of prescription drug misuse, including its relationship to health outcomes, and advancement of prevention and intervention strategies.
A comparative study of hot and cold executive function between children with growth retardation and normal children
Authors: Liang Yi-qun 
Published: March 2023

Abstract
Objective: to explore the characteristics of executive function in children with growth retardation.
Methods: 46 children with growth retardation were evaluated for cold executive function (dimension change card classification task) and hot executive function (delayed gratification task).
Results: the score of dimension change card classification task (6.83±0.05) was lower than that of the control group, P <0.05; the waiting time of delayed gratification task (80.32±0.03) was lower than that of the control group, P<0.05.
Conclusion: the cold executive function and hot executive function of the children with growth retardation were lower than those of the control group, which had statistical significance.
Progressive multifocal leukoencephalopathy in a patient with B-cell chronic lymphocytic leukemia after Covid 19 vaccination, complicated with Covid-19 and mucormycosis: a case report
Authors: Amirifard Hamed , Shahbazi Mojtaba , Ranjbar Zahra , Kaeedi Maryam , Havadaragh Sanaz Heydari , Farahmand Ghasem 
Published: March 2023

Abstract

Background: Progressive multifocal leukoencephalopathy (PML) is an opportunistic viral demyelinating infectious disease of the central nervous system (CNS) which is rare & fetal. There is various clinical presenting symptoms for the disease.
Case presentation: This paper presents a clinical case of PML in a patient with B-CLL in remission, previously treated with Chlorambucil that complicated later in disease course with Covid-19 and mucormycosis.
Conclusion: like many other viruses, the more relevant immune-competent cells in host defense against JCV, appear to be T cells. This issue is recently also suggested in Covid 19 patients which a dissociation between severity and seroconversion has been reported. The case reported due to its rarity and multiple challenges in its diagnosis and treatment.
Impacts of age on the gut microbiota in captive giant pandas
Authors: Li Huixin , Lu Kangning , Li Guo , Li Ti , Zhang Le , Li Chao , Xie Qingyang , Liu Huaiting , Zhang Xinxing , Gong Minghao , Liu Gang , Zhang Guiquan 
Published: March 2023

Abstract
The gut microbiota is the most complex and most abundant symbiotic microbial ecosystem in animals. Aging is one of the main factors that cause gut microbiota structure changes, and the relationship between age and the gut microbiota in the giant panda has been a key focus of attention. The giant panda has a specialized diet of bamboo, and it relies on the microbiota that colonizes its gut to complete digestion. However, there is no in-depth understanding of the changes in the gut microbiota across the lifespan of giant pandas. Here, we identified the differences in the gut microbiota between four age groups (cubs, juveniles, adults, and geriatrics) using 16S rRNA gene high-throughput sequencing on an Illumina MiSeq platform. The results revealed that Firmicutes (mean ± SD: 65.45 ± 30.21%; range: 0.91–99.62%) and Proteobacteria (mean ± SD: 31.49 ± 27.99%; range: 0.26–85.35%) were the dominant phyla. The relative abundance of Escherichia-Shigella was high in both the cubs and juveniles. It is interesting to note that the adults had the highest richness and lowest diversity, while the cubs had the opposite. In summary, our study indicates that the gut microbial community composition, abundance, and functional pathways differ across four age groups of giant pandas. Exploring the influence of age, an endogenous influencing factor, on gut microbes provides basic scientific data for monitoring gut microbial dynamics and formulating gut microbial health management approaches, thereby improving the protection of giant pandas.
Workplace barriers and facilitators to nurses’ healthy eating behaviour: Qualitative Systematic Review
Authors: Sajwani Arsheen , Alomari Albara , Hashi Fatima , Fawzy Eman , alananzeh Ibrahim 
Published: March 2023

Abstract

Background: Workplace environment has greatly impacted the eating practices of nurses that led to them being overweight and obese. Obesity still exists because of the unhealthy eating habits in the workplace – which eventually effects patients’ care, nurses’ health, and one’s capability to work properly. The aim is to conduct a systematic review to find the healthy eating barriers and facilitators among nurses in the clinical workplace.
Methods:This review was conducted using the Joanna Briggs Institute methodology for systematic reviews. Sources searched through eight electronic databases: PROQUEST CENTRAL, SCIENCEDIRECT, MEDLINE, CINAHL, PsycINFO, WEB SCIENCE, PUB MED and SCOPUS were conducted. All articles were imported into JBI SUMARI for screening purpose. Quality appraisal of the included articles were performed through JBI critical appraisal checklist for qualitative studies. All findings of the included articles were extracted through the JBI data extraction tool.
Results: Nine qualitative studies were included in the review. The experiences of488 nurses generated a total of 37 findings. Two synthesized findings were generated from the categories: (i) Barriers to healthy eating; and (ii) Facilitators to healthy eating. Most studies reported facilitators and barriers to healthy eating. Most of the barriers and the facilitator were related to the organization (night shift and long working hours), personal, physical workplace environment and social.
Conclusions: The review results, illustrate clear direction to promote healthy eating on organizational, personal, environmental, and social levels that are attainable in a workplace.
Registration: PROSPERO International prospective register of systematic reviews, ID: CRD42022309259
The effects of hemodialysis on the functional brain connectivity in patients with end–stage renal disease: A functional near–infrared spectroscopy study
Authors: Park Kang Min , Heo Chang Min , Lee Yoo Jin , Park Sihyung , Kim Yang Wook , Lee Dong Ah , Park Bong Soo 
Published: March 2023

Abstract
Background: This study aimed to investigate functional brain connectivity in patients with end–stage renal disease (ESRD) undergoing hemodialysis using functional near–infrared spectroscopy (fNIRS) and to analyze the effect of hemodialysis on functional brain connectivity.
Methods: We prospectively enrolled patients with ESRD undergoing hemodialysis for >six months without any history of neurological or psychiatric disorders. fNIRS data were acquired using a NIRSIT Lite device. Measurements were performed thrice in the resting state for each patient: before the start of hemodialysis (pre–HD), 1 h after the start of hemodialysis (mid–HD), and after the end of hemodialysis (post–HD). We processed and exported all data and created a weighted connectivity matrix using Pearson correlation analysis. We obtained functional connectivity measures from the connectivity matrix by applying a graph theoretical analysis. Then, we compared differences in functional connectivity measures according to hemodialysis in patients with ESRD.
Results: We included 34 patients with ESRD. There were significant changes in the mean clustering coefficient, transitivity, and assortative coefficient between the pre– and post–HD periods (0.353 vs. 0.399, p=0.047; 0.523 vs. 0.600, p=0.042; and 0.043 vs. –0.012, p=0.044, respectively). However, there were no changes in the mean clustering coefficient, transitivity, and assortative coefficient between the pre– and mid–HD periods and between the mid– and post–HD periods. In addition, there were no significant differences in the average strength, global efficiency, and local efficiency among the pre–, mid–, and post–HD periods.
Conclusions: We demonstrated a significant effect of hemodialysis on functional brain connectivity in patients with ESRD. Functional brain connectivity changes more efficiently during hemodialysis.
Altered hippocampal intra-networks in mild cognitive impairment: a structural MRI study in a general elderly Japanese population
Authors: Kasai Sera , Watanabe Keita , Umemura Yoshihito , Ishimoto Yuka , Sasaki Miho , Nagaya Haruka , Tatsuo Soichiro , Mikami Tatsuya , Tamada Yoshinori , Ide Satoru , Tomiyama Masahiko , Kakeda Shingo 
Published: March 2023

Abstract
Although altered networks inside the hippocampus (hippocampal intra-networks) have been observed in dementia, the evaluation of hippocampal intra-networks using magnetic resonance imaging (MRI) is challenging. We employed conventional structural imaging and incident component analysis (ICA) to investigate the structural covariance of the hippocampal intra-networks. We aimed to assess altered hippocampal intra-networks in patients with mild cognitive impairment (MCI). A cross-sectional study of 2122 participants with 3T MRI (median age 69 years, 60.9% female) were divided into 218 patients with MCI and 1904 cognitively normal older adults (CNOA). By employing 3D T1-weighted imaging and ICA, we extracted the structural covariance intra-networks in the hippocampus. The ICA extracted 16 intra-networks from the hippocampal structural images, which were divided into two bilateral networks and 14 ipsilateral networks. Of the 16 intra-networks, four (one bilateral network and three ipsilateral networks) were significant predictors of MCI from the CNOA after adjusting for age, sex, education, disease history, and hippocampal volume/total intracranial volume ratio. In conclusion, we found that the relationship between hippocampal intra-networks and MCI was independent from the hippocampal volume. Our results suggest that altered hippocampal intra-networks may reflect a different pathology in MCI from that of brain atrophy.
Comparative assessment of the biological activity of the green synthesized silver nanoparticles and aqueous leaf extract of Perilla frutescens (L.)
Authors: Tavan Mansoureh , Hanachi Parichehr , Mirjalili Mohammad Hossein , Dashtbani-Roozbehani Abolfazl 
Published: March 2023

Abstract
Green synthesized‎ nanoparticles (GSNPs) display fascinating properties compared to physical and chemical synthesized ones. GSNPs‎ are currently used in numerous applications such as food packaging, surface ‎coating agents, environmental remediation, antimicrobial, and medicine. In the present ‎study, the aqueous leaf extract of Perilla frutescens L. having suitable capping, reducing, and stabilizing compounds was used for green synthesis of silver nanoparticles (Pf-AgNPs).‎‏ ‏The ‎bioreductant capacity of aqueous leaf extract of P. frutescens for Pf-AgNPs was determined by ‎different confirmatory techniques including‎ UV-Visible spectroscopy, XRD, FESEM, EDX‎, zeta potential, DLS, SERS, and FTIR‎ analysis. The results exhibited that Pf-AgNPs had optimal size (< 61nm), shape (spherical), and ‎stability (-18.1 mV). The antioxidant activity of Pf-AgNPs with both DPPH and FRAP assays ‎was significantly higher compared to P. frutescens ‎extract. Furthermore, Pf-AgNPs had high antimicrobial activity against ‎Escherichia coli and Staphylococcus aureus (MIC=‎ ‎‎0.78 mg/mL), and Candida albicans (MIC=‎ ‎‎8 ‎mg/mL)‎ while the plant ‎extract showed ‎low antimicrobial activity‎ against both bacterial strains and the fungus tested. Pf-AgNPs ‎and P. frutescens ‎extract also ‎exhibited moderate toxicity on MCF-7‎ cancer cells‎ with IC50 values ‎of ‎346.2‎ and ‎467.4 µg/mL‎, respectively. The results provide insights into using the biosynthesized Pf-AgNPs as an eco-friendly material for a wide range of biomedical applications.
Nurse- and self-collected dried blood spots for the assessment of cardiovascular risk factors: A randomised study of the Understanding Society Innovation Panel
Authors: Kumari Meena , Andrayas Alexandria , Baghal Tarek Al , Burton Jonathon , Crossley Thomas F. , Jones Kerry S. , Parkington Damon A. , Koulman Albert , Benzeval Michaela 
Published: March 2023

Abstract
Background
Dried blood spot (DBS) sample collection has been suggested as a less invasive, cheaper and more convenient alternative to venepuncture, which requires trained personnel, making it a potentially viable approach for self-collection of blood on a large scale. We examine whether participants in a longitudinal survey were willing to provide a DBS sample in different interview settings, and how resulting cardiovascular risk biomarkers compared with those from venous blood to calculate clinical risk.
Methods
Participants of the Understanding Society Innovation Panel, a representative sample of UK households, were randomly assigned to three modes of interview. Most participants (84%) were interviewed in their allocated mode. Participants (n = 2162) were interviewed by a nurse who collected both a blood sample by venepuncture and a DBS card (‘nurse collection’) or participants were seen by an interviewer or took part in the survey online to self-collect a DBS card (‘self-collection’). All DBS cards were returned in the post after the sample had dried. Lipids (total cholesterol, HDL-cholesterol, triglycerides), HbA1c and C-reactive protein were measured in venous and DBS samples and equivalence calculated. The resultant values were used to confirm equivalent prevalence of risk of cardiovascular disease in each type of blood sample by mode of participation.
Results
Of participants interviewed by a nurse 69% consented to venous blood sample and 74% to a DBS sample, while in the self-collection modes, 35% consented to DBS collection. Demographic characteristics of participants in self-collection mode was not different to those in nurse collection mode. The percentage of participants with clinically raised biomarkers did not significantly differ between type of blood collection (for example, 62% had high cholesterol (> 5 mmol/l) measured by venepuncture and 67% had high cholesterol within the self-collected DBS sample (p = 0.13)).
Conclusion
While self-collected DBS sampling had a lower response rate to DBS collected by a nurse, participation did not vary by key demographic characteristics. This study demonstrates that DBS collection is a feasible method of sample collection that can provide acceptable measures of clinically relevant biomarkers, enabling the calculation of population levels of cardiovascular disease risk.