bluuebunny/crossref_metadata_2025_split huggingface dataset:
THRIL mediates endothelial progenitor cells autophagy via AKT pathway and FUS
Authors: Xiao Jiandong , Lu Yuli , Yang Xinchun 
Published: September 2020

Abstract
Background
This study focused on the roles of lncRNA THRIL in coronary atherosclerotic heart disease (CAD) through regulating AKT signaling pathway and directly interacting with FUS.

Methods
QRT-PCR was conducted to detect the expression of THRIL in CAD blood samples and endothelial progenitor cells (EPCs). Cell autophagy of EPCs was examined through Cyto-ID Autophagy Detection Kit. CCK-8 assay and flow cytometry were carried out to assess cell viability and apoptosis under various interference conditions. Western blotting was conducted to detect the expression of interest proteins. The expression levels of vascular cell adhesion molecule-1 (VCAM-1) and intercellular adhesion molecule-1 (ICAM-1) were measured by qRT-PCR. The direct interactions between HCG18 and FUS was confirmed through RNA electrophoretic mobility shift assay (RNA EMSA) and RNA immunoprecipitation (RIP) assay.

Results
THRIL was upregulated in CAD blood samples and EPCs. Knockdown of THRIL in EPCs promoted cell viability, inhibited cell autophagy and further suppressed the development of CAD. Over-expression of THRIL induced inactivation of AKT pathway, while knockdown of THRIL played reversed effects. THRIL directly interacted with FUS protein and knockdown of FUS reversed the over-expressing effect of THRIL on cell proliferation, autophagy and the status of AKT pathway.

Conclusion
THRIL inhibits the proliferation and mediates autophagy of endothelial progenitor cells via AKT pathway and FUS.
Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation
Authors: Brackmann Lara Kim , Poplawski Alicia , Grandt Caine Lucas , Schwarz Heike , Hankeln Thomas , Rapp Steffen , Zahnreich Sebastian , Galetzka Danuta , Schmitt Iris , Grad Christian , Eckhard Lukas , Mirsch Johanna , Blettner Maria , Scholz-Kreisel Peter , Hess Moritz , Binder Harald , Schmidberger Heinz , Marron Manuela 
Published: September 2020

Abstract
Background
Exposure to ionizing radiation induces complex stress responses in cells, which can lead to adverse health effects such as cancer. Although a variety of studies investigated gene expression and affected pathways in human fibroblasts after exposure to ionizing radiation, the understanding of underlying mechanisms and biological effects is still incomplete due to different experimental settings and small sample sizes. Therefore, this study aims to identify the time point with the highest number of differentially expressed genes and corresponding pathways in primary human fibroblasts after irradiation at two preselected time points.

Methods
Fibroblasts from skin biopsies of 15 cell donors were exposed to a high (2Gy) and a low (0.05Gy) dose of X-rays. RNA was extracted and sequenced 2 h and 4 h after exposure. Differentially expressed genes with an adjusted p-value < 0.05 were flagged and used for pathway analyses including prediction of upstream and downstream effects. Principal component analyses were used to examine the effect of two different sequencing runs on quality metrics and variation in expression and alignment and for explorative analysis of the radiation dose and time point of analysis.

Results
More genes were differentially expressed 4 h after exposure to low and high doses of radiation than after 2 h. In experiments with high dose irradiation and RNA sequencing after 4 h, inactivation of the FAT10 cancer signaling pathway and activation of gluconeogenesis I, glycolysis I, and prostanoid biosynthesis was observed taking p-value (< 0.05) and (in) activating z-score (≥2.00 or ≤ − 2.00) into account. Two hours after high dose irradiation, inactivation of small cell lung cancer signaling was observed. For low dose irradiation experiments, we did not detect any significant (p < 0.05 and z-score ≥ 2.00 or ≤ − 2.00) activated or inactivated pathways for both time points.

Conclusions
Compared to 2 h after irradiation, a higher number of differentially expressed genes were found 4 h after exposure to low and high dose ionizing radiation. Differences in gene expression were related to signal transduction pathways of the DNA damage response after 2 h and to metabolic pathways, that might implicate cellular senescence, after 4 h. The time point 4 h will be used to conduct further irradiation experiments in a larger sample.
A comparison of BeadChip and WGS genotyping outputs using partial validation by sanger sequencing
Authors: Danilov Kirill A. , Nikogosov Dimitri A. , Musienko Sergey V. , Baranova Ancha V. 
Published: September 2020

Abstract
Background
Head-to-head comparison of BeadChip and WGS/WES genotyping techniques for their precision is far from straightforward. A tool for validation of high-throughput genotyping calls such as Sanger sequencing is neither scalable nor practical for large-scale DNA processing. Here we report a cross-validation analysis of genotyping calls obtained via Illumina GSA BeadChip and WGS (Illumina HiSeq X Ten) techniques.

Results
When compared to each other, the average precision and accuracy of BeadChip and WGS genotyping techniques exceeded 0.991 and 0.997, respectively. The average fraction of discordant variants for both platforms was found to be 0.639%. A sliding window approach was utilized to explore genomic regions not exceeding 500 bp encompassing a maximal amount of discordant variants for further validation by Sanger sequencing. Notably, 12 variants out of 26 located within eight identified regions were consistently discordant in related calls made by WGS and BeadChip. When Sanger sequenced, a total of 16 of these genotypes were successfully resolved, indicating that a precision of WGS and BeadChip genotyping for this genotype subset was at 0.81 and 0.5, respectively, with accuracy values of 0.87 and 0.61.

Conclusions
We conclude that WGS genotype calling exhibits higher overall precision within the selected variety of discordantly genotyped variants, though the amount of validated variants remained insufficient.
De novo sequencing, assembly and functional annotation of Armillaria borealis genome
Authors: Akulova Vasilina S. , Sharov Vadim V. , Aksyonova Anastasiya I. , Putintseva Yuliya A. , Oreshkova Natalya V. , Feranchuk Sergey I. , Kuzmin Dmitry A. , Pavlov Igor N. , Litovka Yulia A. , Krutovsky Konstantin V. 
Published: September 2020

Abstract
Background
Massive forest decline has been observed almost everywhere as a result of negative anthropogenic and climatic effects, which can interact with pests, fungi and other phytopathogens and aggravate their effects. Climatic changes can weaken trees and make fungi, such as Armillaria more destructive. Armillaria borealis (Marxm. & Korhonen) is a fungus from the Physalacriaceae family (Basidiomycota) widely distributed in Eurasia, including Siberia and the Far East. Species from this genus cause the root white rot disease that weakens and often kills woody plants. However, little is known about ecological behavior and genetics of A. borealis. According to field research data, A. borealis is less pathogenic than A. ostoyae, and its aggressive behavior is quite rare. Mainly A. borealis behaves as a secondary pathogen killing trees already weakened by other factors. However, changing environment might cause unpredictable effects in fungus behavior.

Results
The de novo genome assembly and annotation were performed for the A. borealis species for the first time and presented in this study. The A. borealis genome assembly contained ~ 68 Mbp and was comparable with ~ 60 and ~ 79.5 Mbp for the A. ostoyae and A. mellea genomes, respectively. The N50 for contigs equaled 50,544 bp. Functional annotation analysis revealed 21,969 protein coding genes and provided data for further comparative analysis. Repetitive sequences were also identified. The main focus for further study and comparative analysis will be on the enzymes and regulatory factors associated with pathogenicity.

Conclusions
Pathogenic fungi such as Armillaria are currently one of the main problems in forest conservation. A comprehensive study of these species and their pathogenicity is of great importance and needs good genomic resources. The assembled genome of A. borealis presented in this study is of sufficiently good quality for further detailed comparative study on the composition of enzymes in other Armillaria species. There is also a fundamental problem with the identification and classification of species of the Armillaria genus, where the study of repetitive sequences in the genomes of basidiomycetes and their comparative analysis will help us identify more accurately taxonomy of these species and reveal their evolutionary relationships.
Parallel analysis of miRNAs and mRNAs suggests distinct regulatory networks in Crassostrea gigas infected by Ostreid herpesvirus 1
Authors: Rosani Umberto , Abbadi Miriam , Green Timothy , Bai Chang-Ming , Turolla Edoardo , Arcangeli Giuseppe , Wegner K. Mathias , Venier Paola 
Published: September 2020

Abstract
Background
Since 2008, the aquaculture production of Crassostrea gigas was heavily affected by mass mortalities associated to Ostreid herpesvirus 1 (OsHV-1) microvariants worldwide. Transcriptomic studies revealed the major antiviral pathways of the oyster immune response while other findings suggested that also small non-coding RNAs (sncRNA) such as microRNAs might act as key regulators of the oyster response against OsHV-1. To explore the explicit connection between small non-coding and protein-coding transcripts, we performed paired whole transcriptome analysis of sncRNA and messenger RNA (mRNA) in six oysters selected for different intensities of OsHV-1 infection.

Results
The mRNA profiles of the naturally infected oysters were mostly governed by the transcriptional activity of OsHV-1, with several differentially expressed genes mapping to the interferon, toll, apoptosis, and pro-PO pathways. In contrast, miRNA profiles suggested more complex regulatory mechanisms, with 15 differentially expressed miRNAs (DE-miRNA) pointing to a possible modulation of the host response during OsHV-1 infection. We predicted 68 interactions between DE-miRNAs and oyster 3′-UTRs, but only few of them involved antiviral genes. The sncRNA reads assigned to OsHV-1 rather resembled mRNA degradation products, suggesting the absence of genuine viral miRNAs.

Conclusions
We provided data describing the miRNAome during OsHV-1 infection in C. gigas. This information can be used to understand the role of miRNAs in healthy and diseased oysters, to identify new targets for functional studies and, eventually to disentangle cause and effect relationships during viral infections in marine mollusks.
Natural killer cell levels in adults living with type 2 diabetes: a systematic review and meta-analysis of clinical studies
Authors: Mxinwa Vuyolwethu , Dludla Phiwayinkosi V. , Nyambuya Tawanda M. , Mokgalaboni Kabelo , Mazibuko-Mbeje Sithandiwe E. , Nkambule Bongani B. 
Published: September 2020

AbstractBackgroundChronic immune activation and hyperglycaemia are a hallmark of type 2 diabetes mellitus (T2D) while natural killer (NK) cells are involved in the pathogenesis of T2D. Dysregulated NK cell responses are associated with an increased risk of cardiovascular disease in patients living with T2D.ObjectiveTo provide a comprehensive and systematic evidence-based estimate on the levels of NK cells in patients living with T2D.ResultsThis systematic review and meta-analysis included 13 studies reporting on 491 adult patients with T2D and 1064 nondiabetic controls. The pooled effect estimates showed increased levels of NK cells in adult patients with T2D compared to controls (MD: 0.03 [− 3.20, 3.26], I2 = 97%,p < 0.00001).ConclusionOverall, the evidence presented in this systematic review shows that the changes in NK cells in patients living with T2D are still unclear and further studies are needed.
Phosphodiesterase 5 inhibitor sildenafil in patients with heart failure with preserved ejection fraction and combined pre- and postcapillary pulmonary hypertension: a randomized open-label pilot study
Authors: Belyavskiy Evgeny , Ovchinnikov Artem , Potekhina Alexandra , Ageev Fail , Edelmann Frank 
Published: September 2020

Abstract
Background
Heart failure with preserved ejection fraction (HFpEF) is frequently complicated by pulmonary hypertension (PH). A pulmonary vascular contribution could be considered as a substantial therapeutic target in HFpEF and PH and combined pre- and postcapillary PH (Cpc-PH).

Methods
We enrolled 50 patients with HFpEF and Cpc-PH who were determined by echocardiography to have pulmonary artery systolic pressure (PASP) > 40 mmHg, pulmonary vascular resistance > 3 Wood units, and/or transpulmonary gradient > 15 mmHg.

Results
The patients were assigned to the phosphodiesterase 5 (PDE5) inhibitor sildenafil group (25 mg TID for 3 months followed by 50 mg TID for 3 months; n = 30) or the control group (n = 20). In the sildenafil group after 6 months, the 6-min walk distance increased by 50 m (95% CI, 36 to 64 m); substantial improvement in NYHA functional class and exercise capacity during diastolic stress test were revealed; decreases in early mitral inflow to mitral annulus relaxation velocities ratio by 2.4 (95% CI, − 3.3 to − 1.4) and PASP by 17.0 mmHg (95% CI, 20.4 to 13.5) were observed; right ventricular systolic function (M-mode tricuspid annular plane systolic excursion) increased by 0.42 cm (95% CI, 0.32 to 0.52 cm; P < 0.01 for all). No changes occurred in the control group.

Conclusions
In a subset of patients with HFpEF and Cpc-PH assessed by echocardiography, PDE5 inhibition was associated with an improvement in exercise capacity, pulmonary haemodynamic parameters, and right ventricular function. The role of sildenafil needs to be considered in randomized trials in selected patients with HFpEF with invasively confirmed Cpc-PH.

Trial registration
Russian National Information System of Research, Development and Technology Data of Civilian Usage (NIS, https://rosrid.ru), registration number 01201257849. Registered 20 April 2012.
This manuscript adheres to the CONSORT guidelines.
Analysis of the status quo of the Elderly’s demands of medical and elderly care combination in the underdeveloped regions of Western China and its influencing factors: a case study of Lanzhou
Authors: Wang Jiancheng , Wang Yunhua , Cai Hui , Zhang Juxia , Pan Bei , Bao Guoxian , Guo Tiankang 
Published: September 2020

Abstract
Background
This study aims to analyse the current demand by senior citizens in Lanzhou, China for a combination of medical and elderly care services and to identify the factors influencing their needs.

Methods
7500 participants aged 60 or above living in Lanzhou, China, were recruited, a unified questionnaire concerning elderly people’s demand for a service combining medical and elderly care has been adopted to survey these subjects. The status quo of the demand of the service combining medical and elderly care and its influencing factors were analysed with the single-factor Chi-square test and multi-factor binomial logistic regression method.

Results
3772 of 7320 older people have the demand for the service combining medical and elderly care, accounting for 53.15% of survey respondents. Many factors are in play, including gender, marital status, degree of education, occupation before retirement, number of children, monthly income, health self-assessment status, endowment insurance type, medical insurance type, current nursing arrangements, old-age demands, self-care ability and the knowledge of combining medical and elderly care and the willingness to pay for the combination of medical and elderly care have statistical significance (P < 0.05) with the elderly’s needs, different ages, living styles and the prevalence of chronic diseases, have no statistical significance (P > 0.05) with the elderly’s care needs in Lanzhou. The number of children, type of medical insurance and willingness to pay for the combination of medical treatment and nursing care are major influencing factors among the complex factors influencing the elderly’s demand for the proposed service.

Conclusions
The low knowledge rate and demand rate, the number of children, the type of medical insurance, and the willingness to pay for the medical-nursing combination service for the elderly in Lanzhou have a great impact on the elderly’s demand rate for combining medical and elderly care. Meanwhile, relevant government departments should focus more on the promotion of the endowment model of combining medical and elderly care and provide integrated medical care services by integrating multiple resources, and improving social security.
HIV knowledge and stigma among dietetic students in Indonesia: implications for the nutrition education system
Authors: Kusuma Mutiara Tirta Prabandari Lintang , Kidd Tandalayo , Muturi Nancy , Procter Sandra B. , Yarrow Linda , Hsu Wei-Wen 
Published: September 2020

AbstractBackgroundStudies have demonstrated that health care students and practitioners are not immune to stigma towards people living with HIV (PLHIV). This attitude could lead to poor quality of care if it remains uncorrected. However, little is known about dietetic students’ acceptance of PLHIV despite their substantial role in treatment. This study aimed to measure the extent of knowledge and stigma towards PLHIV among dietetic students and to determine the associated factors using the attribution theory.MethodsStudents from three dietetics schools in Indonesia (n = 516) were recruited to participate in this cross-sectional study. Survey questions covered demographic information, interaction with PLHIV, access to information sources, cultural values, and beliefs as predictor variables. The outcome variables were comprehensive knowledge of HIV, HIV and nutrition-specific knowledge, and attitudes. Analyses with linear regression and the stepwise selection were performed to determine factors related to the outcome.ResultsThe levels of HIV comprehensive knowledge and HIV-nutrition specific knowledge among dietetic students were low, as indicated by the average score of 19.9 ± 0.19 (maximum score = 35) and 8.0 ± 0.11 (maximum score = 15), respectively. The level of negative attitudes towards PLHIV was high, with 99.6% of participants reported having a high stigma score. Types of university affiliation (public or private), beliefs and values, exposure to HIV discourse, access to printed media, and years of study were significantly related to HIV comprehensive knowledge (p < 0.05). Nutrition-specific knowledge was also correlated with university affiliation, beliefs and values, participation in HIV discussion, and years of study (p < 0.05). HIV comprehensive knowledge, university affiliation, discussion participation, and ethnicities were associated with attitudes (p < 0.05).ConclusionsAwareness and acceptance of PLHIV must be further improved throughout dietetic training to ensure patients’ quality of care since students represent future dietary care providers. Considering the consistent findings that affiliation to education institution correlates with HIV knowledge and attitude, some examinations concerning the curriculum and teaching conduct might be necessary.
The coronavirus diseases 2019 (COVID-19) pneumonia with spontaneous pneumothorax: a case report
Authors: Chen Xiaoxing , Zhang Guqin , Tang Yueting , Peng Zhiyong , Pan Huaqin 
Published: September 2020

Abstract
Background
The outbreak of the novel coronavirus (COVID-19) that was firstly reported in Wuhan, China, with cases now confirmed in more than 100 countries. However, COVID-19 pneumonia with spontaneous pneumothorax is unknown.

Case presentation
We reported a case of 66-year-old man infected with COVID-19, presenting with fever, cough and myalgia; The patient received supportive and empirical treatment including antiviral treatment, anti-inflammatory treatment, oxygen supply and inhalation therapy; The symptoms, CT images, laboratory results got improved after the treatments, and a throat swab was negative for COVID-19 PCR test; However, on the hospital day 30, the patient presented with a sudden chest pain and dyspnea. CT showed a 30–40% left-sided pneumothorax. Immediate thoracic closed drainage was performed and his dyspnea was rapidly improved. With five more times negative PCR tests for SARS-CoV-2 virus, the patient was discharged and home quarantine.

Conclusion
This case highlights the importance for clinicians to pay attention to the appearance of spontaneous pneumothorax, especially patients with severe pulmonary damage for a long course, as well as the need for early image diagnose CT and effective treatment once pneumothorax occurs.
Polymicrobial infections and microbial patterns in infected nonunions – a descriptive analysis of 42 cases
Authors: Rupp Markus , Kern Stefanie , Weber Tobias , Menges Tamina D. , Schnettler Reinhard , Heiß Christian , Alt Volker 
Published: September 2020

Abstract
Background
Frequencies of polymicrobial infection and pathogens evidenced in course of infected nonunion treatment are largely unknown. Therefore, this study aims at investigating microbial patterns in infected nonunions.

Methods
Surgically treated patients with long bone infected nonunion admitted between January 2010 and March 2018 were included in the study. Microbiological culture and polymerase-chain-reaction results of tissue samples of initial and follow-up revision surgeries were assessed and compared with patient and treatment characteristics.

Results
Forty two patients with a mean age of 53.9 ± 17.7 years were included. In six patients (14.3%) polymicrobial infection was evident. A change of pathogens evidenced in course of the treatment occurred in 21 patients (50%). In 16 patients (38.1%) previously detected bacteria could be determined by microbial testing after further revision surgery. Staphylococcus aureus was most often detected (n = 34, 30.6%), followed by Enterococcus spp. (n = 25, 22.5%) and Staphylococcus epidermidis (n = 18, 16.2%). Five Staphylococcus aureus were resistant to methicillin (MRSA). In patients without polymicrobial infection or further germ detection in course of the treatment, 86.4% of the infections were due to Staphylococcus spp.. Infections due to Streptococcus spp. and gram-negative bacteria were only present in patients with polymicrobial infection and germ-change in course of the treatment.

Conclusion
A low rate of polymicrobial infections was evidenced in the present study. Germ-change often occurs in course of revision surgeries. Prospective studies with more sensitive diagnostic tools are necessary to elucidate the therapeutical relevance of microbiological testing results for surgical as well as medical treatment in infected nonunions.