bluuebunny/crossref_metadata_2025_split huggingface dataset:
MRI-Based Nomogram Analysis: Recognization of Anterior Peritoneal Reflection and Its Relationship to Rectal Cancers
Authors: Zhang Shaoting , Chen Fangying , Ma Xiaolu , Wang Minjie , Yu Guanyu , Shen Fu , Gao Xianhua , Lu Jianping 
Published: January 2021

Abstract
Background: This study is aimed to explore the factors influencing the visualization of the APR and evaluated the feasibility of measuring the distance from the anal verge to APR (AV-APR), the tumor height on MRI and the accuracy of determining the tumor location with regard to APR. Methods: We retrospectively analyzed 110 patients with rectal cancer. A univariate and multivariate logistic regression was performed to identify the independent factors (age, gender, T stage, the degree of bladder filling, pelvic effusion, intraoperative tumor location, BMI, uterine orientation, the distance from seminal vesicle/uterus to rectum) associated with the visualization of the APR on MRI. The nomogram diagram and receiver operating characteristic curve (ROC curve) were established. Intraclass correlation coefficient (ICC) was used to evaluate the consistency of the distance of AV-APR. The Pearson correlation coefficient was used to characterize the agreement between measurements of the tumor height by colonoscopy and MRI. The Kappa statistics was used to evaluate the value of MRI in the diagnosis of the tumor location with regard to the APR. Results: Multivariate logistic regression showed that BMI (P=0.031, odds ratio, OR=0.835), pelvic effusion (P=0.020, OR=7.107) and the distance from seminal vesicle/uterus to the rectum (P=0.001, OR=0.276) were correlated with the visualization of APR. The cut-off point of BMI and the distance from seminal vesicle/uterus to the rectum is 25.845kg/m2 and 1.15cm. The area under curve (AUC) （95% Confidence Interval, 95%CI）of the combined model is 0.840 (0.750-0.930). The favorable calibration of the nomogram showed a non-significant Hosmer-Lemeshow test statistic (P=0.195). The ICC value (95%CI) of the distance of AV-APR measured by two radiologists was 0.981 (0.969-0.989). The height measured by MRI and colonoscopy were correlated with each other (r=0.699, P＜0.001). The Kappa value was 0.854. Conclusions: BMI, pelvic effusion, and the distance from seminal vesicle/uterus to rectum could affect the visualization of APR on MRI. Also, it’s feasible to measure the distance of AV-APR, the tumor height, and to evaluate the tumor location with regard to APR using MRI.
ggtreeExtra: Compact visualization of richly annotated phylogenetic data
Authors: Yu Guangchuang , xu shuangbin , Dai Zehan , Guo Pingfan , Fu Xiaocong , Liu Shanshan , Zhou Lang , Tang Wenli , Feng Tingze , Chen Meijun , Zhan Li , Wu Tianzhi , Hu Erqiang 
Published: January 2021

Abstract
We present the ggtreeExtra package for visualizing heterogeneous data with a phylogenetic tree (https://www.bioocnductor.org/packages/ggtreeExtra). It supports more data types and visualization methods than other tools and has many features that are not available elsewhere. The ggtreeExtra package is a universal tool for tree data visualization. It extends the applications of phylogenetic tree in different disciplines by making more domain specific data to be available to visualize and interpret on the evolutionary context.
Quality of Life and Health Status among those receiving Renal Replacement Therapy in Trinidad and Tobago. West Indies.
Authors: Sanchez Sharlene Maria , Teelucksingh Surujpal , Ali Ronan , Bailey Henry , Legall George 
Published: January 2021

Abstract
Purpose:The determinants of quality of life for patients on renal replacement therapy vary across the world. In this cross sectional study, the factors accounting for a good quality of life in the resource-constrained twin-island of Trinidad and Tobago will be explored.Patients and methods:Five hundred and fifty three patients met inclusion criteria for the study. From the 103 patients receiving renal transplants, 100 participated and among the 84 on peritoneal dialysis, 80 took part in the study. Among the 1000-odd patients who were receiving hemodialysis, 350 were studied using convenience sampling. To be included, one had to be on renal replacement therapy for 3 months or more and at least 18 years of age. The Kidney Disease Quality of Life (KDQOL-36) and the EuroQol (EQ-5D-3L) instruments were administered after demographic data was collected. Transplant recipients were further evaluated with the Kidney Transplant Questionnaire (KTQ). Inferential analysis of data included 95% confidence intervals, ordinary least squares regression, analysis of variance, pairwise correlation and Pearson’s bivariate analysis. SPSS24, STATA14 and MINITAB18 were used.Results:Of the 530 patients, 52.5% were male, 37.5% were in the 56-65 years age group and 51.3% were of Indo-Trinbagonian descent. Hypertension (25.5%) and type 2 diabetes mellitus (62.0%) were reported as the main causes of kidney disease in the dialysis group. In the transplant category, chronic glomerulonephritis (45%) was the main aetiology of kidney disease. The KDQOL-36 domain scores and significantly associated variables included modality of renal replacement, Charlson’s Comorbidity Index, ethnicity, income and employment status. Transplant patients performed the best in the KDQOL-36 and EQ-5D-3L. Patients on peritoneal dialysis had a better quality of life than hemodialysis patients. Increasing patients’ access to renal transplantation or peritoneal dialysis will markedly improve health status for the number of years on renal replacement therapy. Among patients on hemodialysis, an arteriovenous fistula or graft significantly impacted on quality of life.Conclusion:Renal transplant recipients enjoy the best quality of life and health state among patients on renal replacement therapy in Trinidad and Tobago. Given the limitations in resources, patients on peritoneal dialysis also enjoy a good quality of life while the presence of an arteriovenous fistula or graft improved quality of life scores for those receiving hemodialysis. Policies should be implemented to achieve an acceptable quality of life for all patients receiving renal replacement therapy.
Site-specific metastases of gallbladder adenocarcinoma and their prognostic value for survival: a SEER-based study
Authors: Yang Yingnan , Tu Zhuolong , Ye Chentao , Cai Huajie , Yang Shouzhang , Chen Xuehai , Tu Jinfu 
Published: January 2021

Abstract
Background: Gallbladder cancer is a rare but highly malignant cancer, which often progresses to a metastatic stage when diagnosed because of its asymptomatic manifestation. In this study, we intended to analyze the prognostic value of metastatic gallbladder adenocarcinoma (GBA) with site-specific metastases.Methods: Using the Surveillance, Epidemiology, and End Results (SEER) database, GBA patients diagnosed with metastases between 2010 and 2016 were selected to identify the prognosis according to the isolated metastatic sites, including liver, lung, bone, brain and distant lymph nodes (DL). Kaplan-Meier methods were used for survival comparisons and multivariable Cox regression models were constructed to find out independent factors that associated with survival.Results: Data from 1526 eligible patients were extracted from the SEER database. Among the patients, 788 (51.6%) had isolated liver metastases, 80 (5.2%) had isolated distant nodal involvement, 45 (2.9%) had isolated lung metastases, 21 (1.4%) had isolated bone metastases, 2 (0.1%) had isolated brain metastases and 590 (38.7%) had multiple metastases. No significant survival difference was shown between patients with single or multisite metastases (P>0.05). Patients with isolated lung or DL metastases had significant better survival outcomes than those with isolated bone metastases (P<0.05). Multivariate analysis showed that performing surgery at primary site, receiving chemotherapy were associated with better OS and CSS for patients with isolated liver or DL metastases.Conclusions: The study showed that different metastatic sites affect survival outcomes in metastatic GBA patients. Highly selected subset of patients with liver or DL metastases might benefit from surgery at primary site.
TGF-β-induced α-SMA expression is mediated by C/EBPβ acetylation in human alveolar epithelial cells
Authors: Ding Hui , Chen Jinjun , Qin Jingping , Chen Ruhua , Yi Zili 
Published: January 2021

Abstract
Background: The morbidity and mortality rates associated with IPF are high, while powerful and precise therapeutic options with IPF are lacking. Object: Through in vitro model, this study sought to determine whether binding of acetylated CCAAT/enhancer binding protein β (C/EBPβ) to alpha-smooth muscle actin (α-SMA) promoter could affect the activity of the latter as well as assess if it is essential for epithelial-to-mesenchymal transition (EMT) and extracellular matrix deposition in idiopathic pulmonary fibrosis (IPF). Methods: The expression of EMT and C/EBPβ in A549 cells with transforming growth factor-beta (TGF-β) as pulmonary fibrotic model were detected by western blotting and qPCR. Collagen-I expression using ELISA was performed. The luciferase activity was used to examine the activity of C/EBPβ. Knockdown of C/EBPβ was performed by siRNA. We also investigated the effect of deacetylation of C/EBPβ on EMT using sirtuin 1 (SIRT1). The binding ability of C/EBPβ with α-SMA promoter was affirmed via chromatin immunoprecipitation (ChIP) and electrophoresis mobility shift assay (EMSA). The relationship of α-SMA and acetylated C/EBPβ was investigated by co-immunoprecipitation (Co-IP). SiRNA-mediated knockdown of C/EBPβ in A549 cells attenuated TGF-β1-induced myofibroblast differentiation and ECM deposition. The extent of association between acetylated C/EBPβ and α-SMA promoter was dynamically monitored. Results: It was confirmed that deacetylation of C/EBPβ in A549 cells successfully ameliorated TGF-β1-induced EMT, as shown by reduction in α-SMA expression and excessive collagen-I accumulation. Conclusion: The EMT and fibrotic effect of TGF-β1 is dependent on acetylated C/EBPβ-mediated regulation of α-SMA gene activity. C/EBPβ acetylation may play a central role in pulmonary fibrosis.
Implementation and effectiveness of continuous kangaroo mother care: a participatory action research protocol
Authors: Mohammadi Marzieh , Bergh Anne Marie , Heidarzadeh Mohammad , Hosseini Mohammad Baghr , Sattarzadeh Niloufar , Valizadeh Leila , Sarvaran Behzad , Hakimi Sevil 
Published: January 2021

Abstract
Background The efficacy of continuous kangaroo mother care (C-KMC) in reducing neonatal mortality and morbidity among low birth weight and premature infants has been confirmed. Despite the recommendations of the World Health Organization, UNICEF, and the Ministry of Health of Iran to use C-KMC for eligible hospitalized neonates, this type of care is not performed due to implementation problems. This protocol aims to describe the design, implementation, and assessment of C-KMC in one tertiary hospital by means of participatory action research.Methods The objective of this study is to design and implement a C-KMC program for neonates that will be performed in two phases using a stages-of-change model. The first phase will be conducted in three consecutive activities of designing, implementing, and assessing the introduction of C-KMC. The second phase of the study has a before-and-after design to assess the effectiveness of C-KMC by comparing the length of preterm neonates’ stay in hospital and exclusive breastfeeding at discharge before and after implementing C-KMC.Discussion KMC is an important component of neonatal developmental care as part of family-centered care. Applying this type of care requires creating appropriate strategies, budget allocation, and clear and coordinated planning at different levels of the health system. The stages-of-change model is one of the appropriate approaches to the implementation of C-KMC.
Pulmonary fibrosis and its related factors in discharged patients with new coronavirus pneumonia: A cohort study
Authors: Li Xiaohe , Shen Chenguang , Wang Lifei , Majumder Sumit , Zhang Die , Deen M. Jamal , Li Yanjie , Qing Ling , Zhang Ying , Chen Chuming , Zou Rongrong , Lan Jianfeng , Huang Ling , Peng Cheng , Zeng Lijiao , Liang Yanhua , Cao Mengli , Yang Yang , Yang Minghui , Tan Guoyu , Tang Shenghong , Liu Lei , Yuan Jing , Liu Yingxia 
Published: January 2021

Abstract
Background: Thousands of the Coronavirus Disease 2019 (COVID-19) patients have been discharged from hospitals, persistent follow-up studies are required to evaluate the prevalence of post-COVID-19 fibrosis.Methods: This study involves 462 laboratory confirmed patients with COVID-19 who were admitted to Shenzhen Third People’s Hospital from January 11, 2020 to April 26, 2020. A total of 457 patients underwent thin-section chest CT scans during the hospitalization or after discharge to identify the pulmonary lesion. A total of 287 patients were followed up from 90 days to 150 days after the onset of the disease, and lung function tests were conducted in about three months after the onset. The risk factors affecting the persistence of pulmonary fibrosis were identified through regression analysis and the prediction model of the persistence of pulmonary fibrosis was established.Results: Parenchymal bands, irregular interfaces, reticulation and traction bronchiectasis were the most common CT features in all COVID-19 patients. During the 0-30, 31-60, 61-90, 91-120 and >120 days after onset, 86.87%, 74.40%, 79.56%, 68.12% and 62.03% patients developed with pulmonary fibrosis and 4.53%, 19.61%, 18.02%, 38.30% and 48.98% patients reversed pulmonary fibrosis, respectively. It was observed that Age, BMI, Fever, and Highest PCT were predictive factors for sustaining fibrosis even after 90 days from onset. A predictive model of the persistence with pulmonary fibrosis was developed based-on the Logistic Regression method with an accuracy, PPV, NPV, Sensitivity and Specificity of the model of 76%, 71%, 79%, 67%, and 82%, respectively. More than half of COVID-19 patients revealed abnormal condition in lung function after 90 days from onset, and the ratio of abnormal lung function did not differ on a statistically significant level between the fibrotic and non-fibrotic groups.Conclusions: Persistent pulmonary fibrosis was more likely to develop in patients with older age, high BMI, severe/critical condition, fever, long time to turn the viral RNA negative, pre-existing disease and delay to admission. Fibrosis developed in COVID-19 patients could be reversed in about a third of the patients after 120 days from onset. The pulmonary function of less than half of COVID-19 patients could turn to normal condition after three months from onset. An effective prediction model with an average Area Under the Curve (AUC) of 0.84 was established to predict the persistence of pulmonary fibrosis in COVID-19 patients for early diagnosis.
Circulating Tight-junction Proteins are Potential Biomarkers for Blood-Brain Barrier Function in a Model of Neonatal Hypoxic/Ischemic Brain Injury
Authors: Andersson Axel Erik , Mallard Carina , Ek Carl Joakim 
Published: January 2021

Abstract
Background Neonatal encephalopathy often leads to lifelong disabilities with limited treatments currently available. The brain vasculature is an important factor in many neonatal neurological disorders but there is a lack of diagnostic tools to evaluate the brain vascular dysfunction of neonates in the clinical setting. Measurement of blood-brain barrier tight-junction proteins have shown promise as biomarkers for brain injury in the adult. Here we tested the biomarker potential of tight-junctions in the context of neonatal brain injury.Methods The levels of TJ-proteins (occluding, claudin-5, and zonula occludens protein 1) in both blood plasma and cerebrospinal fluid (CSF) as well as blood-brain barrier function via 14C-sucrose (342 Da) and Evans blue extravasation were measured in a hypoxia/ischemia brain-injury model in neonatal rats.Results Time-dependent changes of occludin and claudin-5 levels could be measured in blood and CSF after hypoxia/ischemia with males generally having higher levels than females. The levels of claudin-5 in CSF correlated with the severity of the brain injury at 24h post- hypoxia/ischemia. Simultaneously, we detected early increase in blood-brain barrier-permeability at 6 and 24h after hypoxia/ischemia.Conclusions Levels of circulating claudin-5 and occludin are increased after hypoxic/ischemic brain injuries and blood-brain barrier-impairment and have promise as early biomarkers for cerebral vascular dysfunction and as a tool for risk assessment of neonatal brain injuries.
Efficacy and Safety of Arbidol in Treatment of Patients with COVID-19 Infection: A Randomized Clinical Trial
Authors: ghaderkhani Sara , khaneshan Arezoo salami , Salami Amir , alavijeh Parvaneh ebrahimi , Kouchak Hamid Emadi , khalili Hossein , SeyedAlinaghi SeyedAhmad , Ahmadinejad Zahra , Rasolinejad Mehrnaz , Hajiabdolbaghi Mahboubeh , Jafari Sirous , Hasannezhad Malihe , Seifi Arash , abasian Ladan , ghiasvand fereshte , Avanaki Foroogh Alborzi , edalatifard Maryam , Rahimi Mojgan 
Published: January 2021

Abstract
Background: The outbreak of COVID-19has led to a high demand for finding effective antiviral agents. Preliminary experiments showed that Umifenovir could inhibit coronavirus replication in vivo. There is limited data on the clinical efficacy of COVID-19-infected pneumonia. Therefore, we aimed to evaluate this medication based on clinical findings.Methods: The present study was designed as a clinical trial to investigate the advantages and disadvantages of this medicine compared to empirical treatment. For this purpose, multi-stage sampling was considered. 56 people who have mild to moderate symptoms without signs of sever pneumonia , were selected by accidental non-random sampling method. This sample size was subsequently divided into two groups (group A threated with hydroxycloroquine and group B who threated with combination hydroxycloroquine and Umifenovir) by randomized block sampling (1:1). During the study, three patients left the case group. Their clinical sighns and symptoms were evaluated on 3 th and 7 th and 14 th days after oncet illness while taking these medicines in the disease course. The SPSS software was used for data analysis and the significance level was considered to be P<0.05.Results: On the seventh days after visit patients , there were statistically significant differences in recuperation dry cough(p = 0.001), weakness(p = 0.004), gastrointestinal symptoms(p = 0.043) and shortness of breath (p = 0.001) between the two groups, so that in patients who under orescription combination HCQ and Umifenovir group had a faster recovery.Generally during illness , there were statistically significantly faster melioratation myalgia(p = 0.03), gastrointestinal symptoms(p = 0.047), and weakness(p = 0.007)in patients who threated with both HCQ and Umifenovir .Conclusion: Evaluation clinical findings in mild to moderate COVID-19 patients symptoms and sighns recuperation faster in group who under orescription combination HCQ and Umifenovir .regimen. In other words, adding Umifenovir to the empirical treatment accelerated the recovery process of patients’ clinical symptoms.
BiVO4/Fe3O4@Polydopamine Superparticles for Tumor Multimodal Imaging and Synergistic Therapy
Authors: Wang Ze , Wang Guan , Kang Tingting , Liu Shuwei , Wang Lu , Zou Haoyang , Chong Yu , Liu Yi 
Published: January 2021

Abstract
Background: Despite tremendous progress has been achieved in tumor theranostic over the past decade, accurate identification and complete eradication of tumor cells remain a great challenge owing to the limitation of single imaging modality and therapeutic strategy. Results: Herein, we successfully design and construct BiVO4/Fe3O4@polydopamine (PDA) superparticles (SPs) for computed tomography (CT)/photoacoustic (PA)/magnetic resonance (MR) multimodal imaging and radiotherapy (RT)/photothermal therapy (PTT) synergistic therapy toward oral epithelial carcinoma. On the one hand, BiVO4 NPs endow BiVO4/Fe3O4@PDA SPs with impressive X-ray absorption capability due to the high X-ray attenuation coefficient of Bi, which is beneficial for their utilization as radiosensitizers for CT imaging and RT. On the other hand, Fe3O4 NPs impart BiVO4/Fe3O4@PDA SPs with the superparamagnetic property as a T2-weighted contrast agent for MR imaging. Importantly, the aggregation of Fe3O4 NPs in SPs and the presence of PDA shell greatly improve the photothermal conversion capability of SPs, making BiVO4/Fe3O4@PDA SPs as an ideal photothermal transducer for PA imaging and PTT. By integrating advantages of various imaging modalities (CT/PA/MR) and therapeutic strategies (RT/PTT), our BiVO4/Fe3O4@PDA SPs exhibit the sensitive multimodal imaging feature and superior synergistic therapeutic efficacy on tumors. Conclusion: Since there are many kinds of building blocks with unique properties appropriating for self-assembly, our work may largely enrich the library of nanomateirals for tumor diagnosis and treatment.
Single-Cell Transcriptomic Profiling and Characterization of Endothelial Progenitor Cells: New Approach for Finding Novel Markers
Authors: Abdelgawad Mohamed Essameldin , Desterke Christophe , Uzan Georges , Naserian Sina 
Published: January 2021

Abstract
Background: Endothelial progenitor cells (EPCs) are promising candidates for the cellular therapy of peripheral arterial & cardiovascular diseases. However, hitherto there is no specific marker(s) defining precisely EPCs. Herein, we are proposing a new in-silico approach for finding novel EPCs markers. Methods: we assembled five groups of chosen EPCs-related genes/factors using Pubmed literature & gene ontology databases. This shortened database of EPCs factors was fed into publically-published transcriptome matrix to compare their expression between endothelial colony-forming cells (ECFCs), HUVECs and two adult endothelial cell types (ECs) from skin and adipose tissue. Further, the database was used for functional enrichment on mouse phenotype database and protein-protein interaction network analyses. Moreover, we built a digital matrix of healthy donors' PBMCs (33 thousand single cell transcriptomes) and analyzed the expression of these EPCs factors Results: Transcriptome analyses showed that BMP2,4 & ephrinB2 were exclusively highly expressed in EPCs; the expression of neuropilin-1 & VEGF-C were significantly higher in EPCs & HUVECs compared with other ECs; Notch 1 was highly expressed in EPCs & skin-ECs; MIR21 was highly expressed in skin-ECs; PECAM-1 were significantly higher in EPCs & adipose ECs. Moreover, functional enrichment of EPCs-related genes on mouse phenotype and STRING protein database has revealed significant relations between chosen EPCs factors and endothelial & vascular functions, development and morphogenesis, where ephrinB2, BMP2 and BMP4 were highly expressed in EPCs and were connected to abnormal vascular functions. Single cell RNA-sequencing analyses has revealed that among the EPCs regulated markers in transcriptome analyses: i-ICAM1 & Endoglin were weekly expressed in the monocyte compartment of peripheral blood; ii-CD163 & CD36 were highly expressed in CD14+ monocyte compartment whereas CSF1R was highly expressed in CD16+ monocyte compartment; iii-L-selectin & IL6R were globally expressed in the lymphoid/myeloid compartments; iv-interestingly, PLAUR/UPAR & NOTCH2 were highly expressed in both CD14+ & CD16+ monocytic compartments. Conclusions: The current study has identified novel EPCs markers that could be used for better characterization of EPCs sub-population in adult peripheral blood and subsequent usage of EPCs for various cell therapy and regenerative medicine applications.