bluuebunny/crossref_metadata_2025_split huggingface dataset:
Research on HIV Spreading by Macroscopic Based on Molecular Phylogeny in Anhui Province, China
Authors: Wang Zhen , Zhang Zhiyuan , Jin Xin , Wu Hui , Ruan Yuhua , Xing Hui , Lou Jie 
Published: November 2020

Abstract
BackgroundAcquired Immune Deficiency Syndrome (AIDS) is a global pandemic. The disease remains the most challenging public health issue of common concern in all countries because of its high fatality rate, the widespread susceptibility of the entire population to HIV, and the lack of an effective vaccine or cure. Therefore, it is of great significance to study and analyze the spread of HIV/AIDS.MethodsWe applied Bayesian phylogenetic methods to the gene sequence of the two main subtypes (CRF 01AE and CRF 07BC, 340 in total) of the HIV virus in Anhui Province to infer the nearest ancestor and its effective reproduction number (Re) to trace the history of HIV transmission in Anhui Province. Based on the characteristics of HIV transmission between heterosexuals and homosexuals, we established a dynamic model to predict the future trend of HIV drug resistance transmission. Through fitting the two effective reproduction numbers (Re) from the two different methods above, we got some important parameter values. By analyzing the sensitive factors affecting the transmission situation, we proposed relevant measures to reduce the transmission of HIV-resistant strains and effectively prevent and control the HIV epidemic.ResultsThrough the study of gene sequences, it was inferred that the nearest ancestor of the 150 CRF 01AE subtypes was in 1982, while the nearest ancestor of the 190 CRF 07BC subtypes was later (1992). Moreover, the effective reproduction number Re of HIV transmission in Anhui Province has been stable at first, then increased, and then remained stable, from 1.33 in 1992 to 2.20 in 2018. The study of macro-transmission dynamics model found that simply increasing the treatment rate had little effect on reducing the infection rate of the entire population, but would lead to the increase of drug resistance rate instead. This may be due to the inverse ratio between the prevalence of HIV and the lifespan of infected patients after treatment. According to the Sensitivity analysis, a more effective way to control transmission is reducing the number of sexual partners of the MSM population. In addition, we also have unexpected new findings regarding the traditional belief that "bisexual men play a bridge role in the transmission of HIV virus": if simply cutting o the sexual relationship between women and bisexual men, the HIV epidemic will be significantly enhanced instead.ConclusionStudy on gene sequences told us the history of HIV/AIDS spreading in Anhui province and the dynamic model told us its future. The link between them is the the effective reproduction number Re.
Urban Population Exposure to Air Pollution in Europe Over the Last Decades
Authors: Sicard Pierre , Agathokleous Evgenios , De Marco Alessandra , Paoletti Elena , Calatayud Vicent 
Published: November 2020

Abstract
Background - The paper presents an overview of air quality in the 27 member countries of the European Union (EU) and the United Kingdom (previous EU-28), from 2000 to 2017. We reviewed the progress made towards meeting the air quality standards established by the EU Ambient Air Quality Directives (Directive 2008/50/EC) and the World Health Organization (WHO) Air Quality Guidelines by estimating the trends (Mann-Kendal test) in national emissions of main air pollutants, urban population exposure to air pollution, and in mortality related to exposure to ambient fine particles (PM2.5) and tropospheric ozone (O3). Results - Despite significant reductions of emissions (e.g. sulfur oxides: ~80%, nitrogen oxides: ~46%, non-methane volatile organic compounds: ~44%, particulate matters with a diameter lower than 2.5µm and 10µm: ~30%), the EU-28 urban population was exposed to PM2.5 and O3 levels widely exceeding the WHO limit values for the protection of human health. Between 2000 and 2017, the annual PM2.5-related number of deaths decreased (- 4.85 per 106 inhabitants) in line with a reduction of PM2.5 levels observed at urban air quality monitoring stations. The rising O3 levels became a major public health issue in the EU-28 cities where the annual O3-related number of premature deaths increased (+ 0.55 deaths per 106 inhabitants). Conclusions - To achieve the objectives of the Ambient Air Quality Directives and mitigate air pollution impacts, actions need to be urgently taken at all governance levels. In this context, greening and re‐naturing cities can help meet air quality standards, but also answer to social needs, as recently highlighted by the COVID-19 lockdowns.
mRNA Profiling of a Well-differentiated G1 Pancreatic NET Correlates with Immunohistochemistry Profile
Authors: Venugopal Abhirami , Gillick-Walker Jessie , Michalczyk Agnes A , Khasraw Mustafa , Ackland M Leigh 
Published: November 2020

Abstract
Background: Neuroendocrine neoplasms (NENs) are a complex group of tumours that occur in many organs. The routinely used IHC markers for NEN diagnosis include CgA, synaptophysin, Ki67 and CD56. These have limitations, including lack of correlation to clinical outcomes and their presence in non-tumour tissue. Identification of additional markers and more quantitative analyses of tumour tissue has the potential to contribute to improved clinical outcomes. We used qRT-PCR to profile the expression levels of a panel of markers in tumour and matched non-tumour tissue from a G1 pancreatic neuroendocrine tumour. Differences in mRNA levels between tumour and non-tumour tissue were compared with IHC analyses of the same sample.Methods: Twenty-seven markers associated with tumour characteristics including neuroendocrine status, proliferation, stem cell phenotype, angiogenesis, epithelial to mesenchymal transition, cell adhesion, differentiation and tumour suppression were selected from previous studies. mRNA levels of these markers were measured in tumour and non-tumour in a G1 pancreatic tissue sample using qRT-PCR. IHC was carried out on the same tissue to detect the corresponding marker proteins. Results: Of the twenty seven markers analysed, seven showed higher mRNA levels in tumour relative to non-tumour while thirteen markers had lower expression in tumour relative to non-tumour tissue. The most substantial difference in mRNA levels were a gain of CgA, CD56, b-catenin, CK20, PDX1 and p53 and loss of Ki67, PCAD, CK7, CD31, MENA, ECAD, EPCAM, CDX2 and CK6. Comparison of qRT-PCR data with IHC showed correlation between fifteen markers.Conclusions: qRT-PCR is a relatively quantitative diagnostic tool with the advantage of being reproducible, fast, cheap and accurate. Differential marker profiling using qRT-PCR has the potential to improve the defining of tumour phenotypes and, in combination with IHC may have clinical utility towards improving stratification or distinguishing tumour grades. The inclusion of matched controls enables a more comparative analysis in comparison to many previous studies that report tumour data only. The results need to be validated in a cohort of different grades of NENs and related to clinical outcomes.
Identification of Robust Immune‐Associated lncRNAs Signature for Immune Checkpoint Blockade and Prognosis in Breast Cancer
Authors: Xu Qianhui , Wang Yuxin , Huang Wen 
Published: November 2020

Abstract
Background: There have numerous evidences to support that long non-coding RNAs (lncRNAs) may be crucial parts in cancer immunity. We aimed to establish a novel and robust immune-associated lncRNAs signature to improve prognostic precision in patients with breast cancer(BRCA).Methods: BRCA cases were obtained from the The Cancer Genome Atlas (TCGA) database. Immune‐related lncRNAs presenting significant association with prognosis were screened through stepwise univariate Cox regression and LASSO algorithm, and multivariate Cox regression. Kaplan-Meier analysis, ROC analyses, and proportional hazards model further conducted. The prediction reliability was further estimated in the internal validation set and combination set. Gene set enrichment analysis (GSEA) was applied for functional annotation. The correlation between immune checkpoint inhibitors and this signature was employed. Results: 13 immune-related lncRNAs were systematically identified to establish immune-related lncRNAs predictive prognosis signature. The risk model we built showed significant correlation with BRCA patients’ prognosis. The value of ROC for this lncRNAs model was up to 0.821. This immune‐related lncRNAs signature can serve as an independent prognostic biomolecular factor. Our lncRNAs signature involved in chondrocyte development, endoderm development and so forth. This lncRNAs risk model was associated with tumor immune infiltration (i.e., B cells, Dendritic, Neutrophils, CD8 T cells and CD4 T cells, etc.,) and immune checkpoint blockade (ICB) therapy key molecules (i.e., PDCD1).Conclusion: The immune‐related lncRNA signature we established possesses latent prognostic value for patients with BRCA and may have the capability to predict the clinical outcome of ICB treatment, which could provide guidance for immunological decision in patients with BRCA.
SEC23A Regulated by Splicing Factor EIF3A may be Involved in the Development of Cervical Squamous Cell Cancer via Adherens Junction Pathway
Authors: Li Chen , Yan Fang , Wan Ting , Gu Haifeng , Chen Gang , Li Qiang , Xian Hua , Xie Jingdun 
Published: November 2020

Abstract
Background: Cervical squamous cell cancer is a common malignancy in women globally. Increasing studies have indicated that there was an indivisible association between alternative splicing and cancer. However, comprehensive analysis of alternative splicing is scarce in cervical squamous cell cancer. Methods: Alternative mRNA splicing events data and clinical information of 216 cervical squamous cell cancer patients were downloaded from TCGA SpliceSeq database and TCGA website. We used identified survival-associated splicing events to construct prognostic signatures. Kaplan-Meier survival analysis and receiver operating characteristic curve were performed to evaluate the clinical value of prognostic signatures. A nomogram was carried out to quantitatively predict individuals’ survival probability. Regulatory network between splicing factors and survival-associated splicing events was analyzed. Additionally, we performed Pearson’s correlation analysis between survival-associated splicing events and pathways to explore potential downstream pathways. In order to verify the relationships between EIF3A and cell proliferation and migration, CCK8 and wound healing assays were conducted.Results: After sorting out survival-associated splicing events, multivariable regression analysis was used to acquire 70 survival-associated splicing events that could be independent prognostic factors for overall survival in cervical squamous cell cancer. A nomogram was constructed with a concordance index of 0.82. EIF3A positively regulated SEC23A-27346-AP with highest correlation coefficient (P＜0.001, R=0.69). The most significant KEGG pathways was adherens junction pathway (P=0.02, R=0.65). Cell proliferation and wound healing assays showed that EIF3A knockdown decreases cell proliferation and cell migration. Conclusion: Prognostic signatures of survival-associated splicing events were independent prognostic factors for overall survival among cervical squamous cell cancer patients. A nomogram could quantitatively predict individuals’ survival probability by integrating multiple risk factors. Moreover, SEC23A positively regulated by EIF3A may contribute to cervical squamous cell cancer via adherens junction pathway. This study may offer new direction for subsequent experimental research in cervical squamous cell cancer.
The Future of Mesenchymal Stromal Cells in cancer – A Bibliometric Analysis
Authors: O'Connor Dómhnall J , Barkley Laura R , Kerin Michael J 
Published: November 2020

Abstract
BackgroundMesenchymal stromal/stem cells have garnered much interest in the field of cancer biology. Bibliometric analysis of a scientific field has the potential to reveal insights pertaining to the maturity of the field, the hotspot sources of publication and temporal shifts in research subcategories within the field. Despite the benefits of such an analysis, one has not been conducted to date.MethodsThe Web of Science™database and VOSviewer software were used to analyse publication and citation data for all publications relating to Mesenchymal Stromal/Stem Cells in oncology. Contributions to the literature were also identified by country, journal and cancer type. Keyword analysis identified trends in developing research categories.Results9927 published articles were analysed. The current publication rate fits an exponential trend(r2 = 0.97). The U.S. and the People’s Republic of China have the highest overall publications but when corrected for population and citations per article, the most successful countries are Singapore, Luxembourg and Switzerland. In the past 15 years 74% of articles have been in cancer specific journals. Breast cancer publications account for 42% of common cancer articles. Most articles were published in journals that had a basic science focus (44%). Keyword analysis resulted in 3 distinct clusters aligned with 1. Characterisation and nomenclature, 2.Clinical and 3.Molecular function. The most recent publications favour topics on Molecular function. ConclusionsResearch on Mesenchymal Stromal/Stem Cells in oncology is experiencing exponential growth. There is widespread acceptance of basic science research on MSCs in cancer specific journals and a niche for more translational and clinically focused studies.
A Prospective, Randomized Comparison of Functional Bracing Versus Rigid Immobilization after Modified Percutaneous Achilles Tendon Repair Under Local Anesthesia
Authors: CRETNIK ANDREJ , Košir Roman 
Published: November 2020

Abstract
Background: There is ongoing controversy over the optimal treatment and rehabilitation strategy of an acute Achilles tendon rupture (ATR). Percutaneous suturing seems to bridge the gap between open surgical and conservative treatment, but still raises scepticism due to concerns like strength of the repair, approximation of torn ends, re-rupture rate, sural nerve injuries, early functional rehabilitation and thus final outcome. The purpose of the study was to analyze the results of two ways of postoperative regimen after treatment with the modified and biomechanically significantly stronger percutaneous repair under local anesthesia.Methods: In a prospective, randomized study from the year 2001 to 2004, with a 3-year follow-up, there were 31 patients (32 ruptures) in the functional bracing group (FG) and 30 patients, who wore rigid immobilization for the period of 6 weeks (IG).Results: Both groups were comparable for gender (3 vs 2 women) and average age (41.93 years, SD ± 12.29 vs 42.20 years, SD ± 10.53). Most ATRs were sports related (62.5% in FG vs 60.0% in IG). There was 1 (3.3%) re-rupture in IG and no re-rupture in FG (1.6% altogether), 2 (6.2%) transient sural nerve disturbances in FG and 1 (3.3%) in IG (4.8% altogether), one suture extrusion problem in IG (3.3%) with no other major or minor complications (6.2% of altogether complications in FG vs 10.0% in IG)(p > 0.05)(overall 8.1%). Patients in FG were (subjectively) more satisfied with the treatment, reached sooner final range of motion (ROM) and muscular strength without limping and had higher average AOFAS score (96.87 vs 95.96)(p > 0.05). There were no statistically significant differences observed between groups according to final ROM, strength and return to pre-injury activities or sports.Conclusions: The results of the study support the choice of presented modified percutaneous suturing under local anesthesia with functional treatment and early mobilization as a reasonable treatment option for an acute ATR.Trial registration: KME, 54/03/00, 21. 03. 2000
Analysis of Three Primary mtDNA Mutations in 155 Patients with Leber’s Hereditary Optic Neuropathy
Authors: Yao Yan-Jiao , Zhuang Xue-Mei , Zheng Fan 
Published: November 2020

Abstract
Background: Leber’s Hereditary Optic Neuropathy (LHON) is a maternal inherited disease caused by mitochondrial DNA (mtDNA) mutations. The aim of the current study is to analysis the frequencies of mitochondrial ND1 G3460A, ND4 G11778A and ND6 T14484C mutations in patients with LHON.Methods: Our study enrolled 155 patients with LHON and 83 controls, PCR-Sanger sequencing was performed to screen the presence of these primary mutations. Moreover, we performed clinical, genetic and molecular characterizations of five Chinese families carrying LHON-related three primary mutations.Results: 28 patients with G3460A (18.1%), 86 patients with G11778A (55.5%) and 32 patients carrying T14484C mutation (20.6%) were identified. However, none of these primary mutations were identified in controls. Among them, one patient carrying G3460A, two patients with G11778A and two patients with T14484C mutation had an obvious family history of LHON. Clinical evaluation of these pedigrees showed the variable clinical phenotypes with different age at onset of LHON. Sequence analysis of the complete mtDNA genes from the matrilineal relatives suggested the presence of these primary mutations. However, the lack of any functional variants in mtDNA genes revealed that mitochondrial haplogroups or haplotypes may not play important roles in the clinical phenotypic manifestation of LHON-associated primary mutations.Conclusions: Our data indicated that screening for the mtDNA primary mutations was necessary for early detection, prevention and diagnosis of LHON.
Design of a Novel Cross Beam Six-Dimensional Force Sensor
Authors: Zhang Chun , Wang Yong , Li Chunfeng , Hu Shanshan , Zhong Jinhong 
Published: November 2020

Abstract
To measure dynamic forces more accurately, a novel elastomer of a six-dimensional force sensor was proposed. The sensor adopted a new inner ring to replace the center platform of the traditional cross beam sensor. Determined the connection mode of the Wheatstone full-bridge circuit, which could realize theoretical decoupling. Then, the key size parameters of the sensor were analyzed by response surface analysis ,and the regression equations between the response value and the key sizes of the elastomer were established, which provided a theoretical basis for the sensor design. The analysis results of the examples in this paper show the sensor has good dynamic performance, with the first-order natural frequency as high as 3196.30Hz. Designed the size parameters by response surface analysis to improve the sensitivity of each force component, which increased the sensitivity of Fx direction by 26.09%.
Global Survey of miRNAs&nbsp;and tRNA-derived Small RNAs&nbsp;From Human Parasitic Protist Trichomonas Vaginalis
Authors: Wang Zhensheng , Zhou Hongchang , Wei Chunyan , Wang Zhihua , Hao Xiao , Zhang Lianhui , Li Jingzhong , Wang Zenglei , Wang Heng 
Published: November 2020

Abstract
BackgroundSmall non-coding RNAs play critical regulatory roles in post-transcription. However, their characteristics in Trichomonas vaginalis (T. vaginalis), the causative agent of human sexually transmitted trichomoniasis, still remain to be unveiled. MethodsSmall RNA transcriptomes from Trichomonas trophozoites were deeply sequenced through Illumina NextSeq 500 system and comprehensively analyzed to identify Trichomonas miRNAs and tRNA-derived small RNAs (tsRNAs). The tsRNAs candidates were confirmed by stem-loop RT-PCR and motifs to guide the cleavage of tsRNAs were predicted by performing GLAM2 algorithm. ResultsThe miRNAs were found at extremely low abundance (0.0046%) in T. vaginalis. Three categories of endogenous Trichomonas tsRNAs were identified as 5'tritsRNAs, mid-tritsRNAs and 3'tritsRNAs, with 5'tritsRNAs dominating (67.63%) in tsRNAs. Interestingly, the cleavage site analysis verified both conventional classes of tRFs and tRNA-halves in tritsRNAs, indicating the expression of tRNA-halves in non-stress condition. A total of 25 tritsRNAs were experimentally confirmed, accounting for 78.1% of all tested candidates. Three motifs were predicted to guide the production of tritsRNAs. This proved the expression of tRFs and tRNA-halves in T. vaginalis transcriptome. ConclusionsThis is the first report of genome-wide investigation of small RNAs, particularly tsRNAs and miRNAs, from Trichomonas parasites. Our findings demonstrate the expression profile of tsRNAs in T. vaginalis, while miRNA was hardly discovered. These results might promote the further research to better understand the evolution of small non-coding RNA in T. vaginalis and their functions in pathogenesis of trichomoniasis.
Cerebral Ischemia is Associated With Corneal Nerve Loss and Brain Atrophy in Mild Cognitive Impairment and Dementia
Authors: Ponirakis Georgios , Elsotouhy Ahmed , Hamad Hanadi Al , Vattoth Surjith , Petropoulos Ioannis N. , Khan Adnan , Gad Hoda , Al-Khayat Fatima , Chandran Mani , Ramadan Marwan , Elorrabi Marwa , Gadelseed Masharig , Tosino Rhia , Gawhale Priya V. , Alobaidi Maryam , Khan Shafi , Manikoth Pravija , Hamdi Yasmin , Thodi Noushad , Almuhannadi Hamad , Al-Mohannadi Salma , AlMarri Fatema , Qazi Murtaza , Own Ahmed , Mahfoud Ziyad R. , Shuaib Ashfaq , Malik Rayaz A 
Published: November 2020

Abstract
BackgroundThe prevalence of cerebral ischemia increases with age and is a risk factor for cognitive impairment and dementia. This study assessed the association of brain ischemic lesions with the severity of neurodegeneration utilizing brain volumetric MRI and corneal confocal microscopy (CCM) in patients with mild cognitive impairment (MCI) and dementia.MethodsSubjects with MCI and dementia without diabetes underwent cognitive screening, CCM, assessment of ischemic lesions and quantitative brain MRI.ResultsOf 63 subjects with MCI (n=44) and dementia (n=19), 11 had no ischemia, 32 had subcortical ischemia and 20 had both cortical and subcortical ischemia. Subjects with MCI and dementia had comparable percentage of cerebral ischemia (P=0.25). Global cognitive function was significantly impaired in subjects with both cortical and subcortical ischemia (P<0.05) but not in those with subcortical ischemia (P=0.10) compared to those without ischemia. Corneal nerve fiber density (CNFD)(P<0.01), branch density (CNBD) (P<0.05) and fiber length (CNFL) (P<0.01) were significantly lower in subjects with both cortical and subcortical ischemia compared to those without ischemia and CNFD (P<0.05), CNBD (P<0.05) and CNFL (P<0.05) were significantly lower in subjects with both cortical and subcortical ischemia compared to those with subcortical ischemia. In subjects with both cortical and subcortical ischemia whole brain (P<0.01) and hippocampal volume (P<0.001) were significantly lower and ventricle volume was higher (P<0.05) compared to those without ischemia and hippocampal volume (P<0.01) was lower and ventricle volume was higher (P<0.01) in subjects with both cortical and subcortical ischemia compared to those with subcortical ischemia.ConclusionsThe presence of cortical and subcortical ischemia is associated with cognitive impairment, corneal nerve loss and brain atrophy in patients with MCI and dementia.