bluuebunny/crossref_metadata_2025_split huggingface dataset:
Establishment of Lymph Node Metastasis Prediction Model For T1a Gastric Cancer
Authors: Zeng Zhi , SHI ZHAN , LIU YANG , ZHAO JUNJUN , LU QILIANG , HU LINJUN , GAO YULING , XIAO ZUNQIANG , HUANG DONGSHENG , XU QIURAN 
Published: January 2021

Abstract
Background and Aims: Endoscopic resection has been widely used in the treatment of early gastric cancer recent tears. For patients undergoing endoscopic resection, lymph node metastasis is an important prognostic factor. Thus, we built a model to predict the likelihood of lymph node metastasis in early gastric cancer.Methods: Data of 789 gastric cancer patients were obtained from the Surveillance, Epidemiology, and End Results (SEER) database. We picked several variables and chi-square analysis was used to come up with statistically significant factors. Then, we used these factors to build a nomogram predicting the lymph node metastasis risk in T1a gastric cancer. Finally, we evaluated this nomogram using C-index, ROC curve and DCA.Results: We built a nomogram based on four factors. The C-index of this nomogram was 0.750. The AUC value of ROC curve for this nomogram was 0.750. DCA showed that it would be beneficial to use this nomogram if the threshold probability was between 0.01 and 0.41.Conclusion: This study built a nomogram to predicted the lymph node metastasis risk in T1a gastric cancer based on four factors. Upon evaluation, this nomogram has a good ability of predicting the risk of lymph node metastasis.
Prediction of COVID-19 Prognosis By Heterogeneity Analysis Based on Chest CT Scans
Authors: Yang Bo , Zhang Bei , Gao Lichen , Zhang Jian , Qiu Huaiming , Huang Wencai 
Published: January 2021

Abstract
BackgroundGround-glass opacity (GGO) and consolidation opacity (CLO) are the common CT lung opacities, and their heterogeneity may have potential for prognosis in COVID-19 patients. This study aimed to estimate clinical outcome in individual COVID-19 patient by using histogram heterogeneity analysis based on CT opacities. Methods71 COVID-19 cases’ medical records were retrospectively reviewed from a designated hospital in Wuhan, China, from January 24th to February 28th at the early stage of pandemic. Two characteristic lung abnormity opacities, GGO and CLO were drawn on CT images to identify the heterogeneity by using quantitative histogram analysis. The parameters (mean, mode, kurtosis, skewness) were derived from histograms to evaluate the accuracy of clinical classification and outcome prediction. Nomograms were built to predict the risk of death and median length of hospital stays (LOS), respectively. Results A total of 57 cases were eligible for the study cohort after exclusion 14 cases. The most highly frequency of lung abnormalities was GGO mixed with CLO in both survival population (26 in 42, 61.9%) and died population (10 in 15, 66.7%). The best performance heterogeneity parameters to discriminate severe type from mild/moderate counterparts were as following: GGO_skewness: specificity=66.67%, sensitivity=78.12%, AUC=0.706; CLO_mean: specificity=70.00%, sensitivity=76.92%, AUC=0.746. Nomogram based on histogram parameters has the ability to predict the individual risk of death and the prolonged median LOS of COVID-19 patients. C-indexes were 0.763 and 0.888 for risk of death and prolonged median LOS, respectively.ConclusionsThe histogram analysis method based on GGO and CLO has the ability for individual risk prediction in COVID-19 patients.
miR-3113-5p, miR-223-3p, miR-133a-3p, and miR-499a-5p are Sensitive Biomarkers to Diagnose Sudden Cardiac Death
Authors: Yan Fengping , Chen Yuanyuan , Ye Xing , Zhang Fu , Wang Shiquan , Zhang Le , Luo Xiaoting 
Published: January 2021

Abstract
BackgroundSudden cardiac death (SCD) remains a great health threat and diagnostic challenge, especially those cases without positive autopsy findings. Molecular biomarkers have been urgently needed for the diagnosis of SCD displaying negative autopsy results. Due to their nature of stability, microRNAs (miRNAs) have emerged as promising diagnostic biomarkers for cardiovascular diseases. MethodsThis study investigated whether specific cardio-miRNAs (miR-3113-5p, miR-223-3p, miR-499a-5p, and miR-133a-3p) could serve as potential biomarkers for the diagnosis of SCD. Thirty-four SCD cases were selected, 18 categorized as acute myocardial infarction (AMI) without positive autopsy findings and 16 as atherosclerotic cardiovascular diseases (ASCVD) with gross myocardial scar. Carbon monoxide (CO) intoxication (n=14) and fatal injury death (n=14) that displayed no pathological changes of myocardium were selected as control group, respectively. Histological analyses were performed to reveal the pathological changes and real-time quantitative polymerase chain reaction (RT-qPCR) was used to determine the expression of those miRNAs. Resultsit showed that heart samples from the AMI group displayed no remarkable difference with regard to the expression of cleaved-caspase3, CD31, and CD68 and the extent of fibrotic tissue accumulation when compared with control samples. The four cardio-miRNAs were significantly up-regulated in the SCD samples as compared with control. When discriminating SCD from controls, ROC curve analysis revealed that the areas under the curve (AUC) of these 4 miRNAs were from 0.7839 to 0.9043 with sensitivity of 64.71-97.06% and specificity of 70-100%. Moreover, when discriminating the specific causes of SCD, the four miRNA expressions increased in the AMI heart as relative to ASCVD, and a combination of two miRNAs presented higher diagnostic value (AUC=0.7407-0.8667). ConclusionmiR-3113-5p, miR-223-3p, miR-499a-5p, and miR-133a-3p may serve as independent diagnostic biomarkers for SCD, and a combination of two of these miRNAs could further discriminate detailed causes of SCD.
The Efficacy of Genetic Testing for Early Detection of Psoriatic Arthritis in Patients with Psoriasis
Authors: Eder Lihi , Li Quan , Jerome Dana , Farrer Chandra , Yeung Jensen , Rahman Proton 
Published: January 2021

Abstract
Background: Improved understanding of the genetic architecture of psoriatic disease (PsD) and reduction in genotyping costs provide an opportunity to assess the application of genetic testing for psoriatic arthritis (PsA) diagnosis. The study aimed to assess the performance of a multi-marker genetic kit in classifying patients as PsD and PsA and to assess whether the performance has improved by combining genetic and clinical data.Methods: 328 patients with psoriasis and musculoskeletal symptoms (78 PsA and 250 psoriasis alone) who were referred to rheumatology for suspected PsA and 341 non-psoriatic controls were analyzed. A custom multi-SNP genetic assay, including 41 variants based on large scale association genome-wide association studies in PsA, was genotyped. Machine-learning methods were used to identify the optimal classification model by area under the receiver operating curve (AUC). Results: The performance of all three classifiers to distinguish PsD from non-psoriatic controls was moderate with similar AUC (range 0.64 to 0.69). Logistic regression had the highest AUC and showed moderate specificity (61.9%) and specificity (67.9%). The ability of the models to correctly classify PsA among all psoriasis patients was suboptimal with AUC ranging from 0.55 to 0.60 with low sensitivity (1.3% to 34.6%) and moderate to high specificity (69.2% to 99.6%). The combination of genetic and clinical data resulted in an improvement in the performance of the models (AUC 0.65 to 0.69), however, the information contributed by the genetic markers was only marginal. Conclusions: Genetic testing has marginal effect on correctly classifying PsA among psoriasis patients in clinical setting.
LncRNA NCK1-AS1 is overexpressed in esophageal squamous cell carcinoma and predicts survival
Authors: Fu Xin , Chen Xi , Si Yuanyuan , Yao Youjie , Jiang Zhengming , Chen Kui 
Published: January 2021

Abstract
BackgroundsNCK1-AS1 promotes cervical cancer, while its involvement in esophageal cancer is hardly known. We therefore explored the involvement of NCK1-AS1 in esophageal squamous cell carcinoma (ESCC) and analyzed the possible interaction between NCK1-AS1 and TGF-β signaling.MethodsOur study selected 52 cases (30 males and 22 females, 46 to 70 years, 56.4 ± 6.6 years) to be used as the research subjects in this study. RT-qPCR and western blot were used for gene expression analysis. Transient transfections were used to analyze gene interaction. Transwell assays were performed to analyze cell invasion and invasion.ResultsOur data showed that NCK1-AS1 was overexpressed in ESCC patients. NCK1-AS1 in plasma was positively correlated with the NCK1-AS1 in tumor but not in non-tumor tissues. High plasma levels of NCK1-AS1 were accompanied by poor survival. TGF-β1 expression level was also increased in tumor tissues compared to tumor adjacent normal tissues. TGF-β1 was positively correlated with NCK1-AS1 in tumor tissues. TGF-β1 overexpression did not affect NCK1-AS1 expression, while NCK1-AS1 upregulated TGF-β1 in ESCC cells. TGF-β1 and NCK1-AS1 increased ESCC cell migration and invasion, TGF-β inhibitor reduced the effects of NCK1-AS1 overexpression.ConclusionTherefore, NCK1-AS1 may promote ESCC by upregulating TGF-β1.
In-silico trial of intracranial flow diverters confirms and expands insights from conventional clinical trials
Authors: Sarrami-Foroushani Ali , Lassila Toni , Macraild Michael , Asquith Joshua , Roes Kit C. B. , Byrne James V. , Frangi Alejandro F 
Published: January 2021

Abstract
Although the cost of clinical trials is ever-increasing, in-silico trials, which rely on virtual populations and interventions simulated using patient-specificc models, may offer a solution to contain these costs. However, in-silico trial endpoints need to be compared to those available from conventional clinical trials to ensure that the predictions of safety or effcacy from the in-silico approach are valid. Here, we present the flow diverter performance assessment (FDPASS) in-silico trial, which modelled the treatment of intracranial aneurysms in 82 virtual patients with a flow-diverting stent, using computational fluid dynamics (CFD) to quantify post-treatment flow reduction in the aneurysm sac. The predicted FD-PASS flow-diversion success rate replicated the values previously reported in three reference clinical trials. The in-silico approach allowed broader investigation of factors associated with insuficient flow reduction and increased stroke risk after flow diversion than would be feasible in a conventional trial. These ndings demonstrate for the rst time that in-silico trials of medical devices can (i) replicate ndings of conventional clinical trials and (ii) incorporate virtual experiments that are impossible in conventional trials.
The extent of resection and adjuvant treatment are beneficial to the outcome of secondary glioblastoma
Authors: Hu Yan , Tu Ze-wei , Ji Pei-gang , Xu Meng , Chao Min , Cao Hai-yan , Ge Shunnan , Guo Hua , Gao Guo-dong , Qu Yan , Zhu Xin-gen , Wang Liang 
Published: January 2021

Abstract
Backgroud: to investigate secondary glioblastoma (sGBM) patients undergoing resection and evaluate the impact of treatment on survival of malignant progression (PMS) and the prognostic factors of secondary glioblastoma. Method: the prognostic factors of secondary glioblastoma were analyzed retrospectively including gender, age, the interval between first diagnosis and second, the extent of resection, adjuvant treatment, postoperative Karnofsky score (KPS), 06-methylguanine-DNA methytransferase (MGMT) status, IDH1 mutation status, and PMS in patients with sGBM. Result: Thirty-four patients with sGBM were included in this study. Sixteen patients were female and eighteen were male. Median PMS in females was longer than male patients with sGBM (17.38 (95%CI 10.63–24.12) vs 10.06(95%CI 5.32–14.79), p = 0.032). 22(64.7%) patients achieved gross total resection (GTR),12(35.3%) patients achieved subtotal resection (STR). Kaplan-Meier analysis showed that GTR significantly improved survival after malignant progression (PMS) compared with STR (17.18(95%CI 10.97–23.40) vs 7.17(95%CI 4.97–9.36), p = 0.004). Adjuvant treatment after resection was executed in 17 (50.0%) patients, radiotherapy in one (2.9%) patient, chemotherapy in seven (20.6%) patients, and radio-chemotherapy in nine (26.5%) patients. Median preoperative KPS was 80(range 30–100), and 85(range 30–100) after surgery. The difference in PMS probability was significant between patients having a good postoperative clinical status (KPS༞70)versus poor (KPS ≤ 70). Long term survival could be achieved in patients with a good clinical status (16.57(95%CI 10.54–22.60) vs 9.00(95%CI 3.66–14.34), p = 0.02). Patients with a greater interval after initial diagnosis had longer survival than those with intervals less than 26.5 months (18.62(95%CI 10.81–26.43) vs 9.22(95%CI 5.61–12.83), p = 0.025). Conclusion: GTR and any adjuvant treatment significantly improved PMS in patients with secondary glioblastoma. Gender, postoperative KPS, time interval since the first diagnosis are associated with prognosis.
HOXB7 overexpression leads triple-negative breast cancer cells to a less aggressive phenotype
Authors: Garcia Simone Aparecida de Bessa , Araújo Mafalda , Pereira Tiago , Freitas Renata 
Published: January 2021

Abstract
Background

Breast cancer is a serious public health issue worldwide and, despite the advances in the understanding of this disease, its great complexity and heterogeneity still represent a major hurdle for accurate diagnosis and therapy decision-making. In addition to the biomarkers found to be useful in the prognosis a treatment of breast cancer, HOX genes have been proposed to be involved in the progression of this disease. For example, HOXB7 alterations in the expression and methylation patterns have been reported to promote breast cancer progression, most likely in a molecular subtype dependent way.
Methods

Here we induced HOXB7 overexpression in MDA-MB-231 cells, cellular model of Triple-Negative Breast Cancer, and evaluated the phenotypic changes in cell viability, morphogenesis, migration, invasion and formation of colonies. We also evaluated the expression of putative downstream targets and their direct binding to HOXB7 by Chip-qPCR in HOXB7-overexpressing cells and controls, namely CTNNB1, EGFR, FGF2, CDH1, DNMT3B and COMMD7.
Result

During the phenotypic characterization of the HOXB7-overexpressing cells, we found consistently a less aggressive behavior represented by lower cell viability, inhibition of cell migration, invasion and attachment-independent colony formation capacities added to the more compact and organized spheroids growth in 3D culture. In addition, we detected that these phenotypic changes may relate to the direct or indirect interaction of the HOXB7 protein with CTNNB1, EGFR, FGF2, CDH1, DNMT3B and COMMD7 genes.
Conclusion

Taken together, these results highlight the plasticity of the HOXB7 function in breast cancer, according to the cellular genetic background and expression levels and provide evidence that in triple-negative breast cancer cells, HOXB7 overexpression has the potential to promote less aggressive phenotypes.
HnRNP-L regulated circCSPP1/miR-520h/EGR1 axis modulates autophagy and promotes progression in prostate cancer
Authors: Lu Jianming , Zhong Chuanfan , Shu Fangpeng , Lv Daojun , Liu Zezhen , Tan Xiao , Wang Shuo , Wu Kaihui , Yang Taowei , Zhong Weibo , Wang Bin , Chen Yanfei , Li Yuehan , Jia Zhenyu , Zou Yaguan , Zhong Weide , Mao Xiangming 
Published: January 2021

Abstract
Background
The circRNAs, a new subclass of non-coding RNAs that are catalyzed by RNA-binding proteins (RBPs), have been reported to be associated with the progression of multiple types of cancers. We previously discovered that heterogeneous nuclear ribonucleoprotein L (HnRNP-L), a multi-functional RNA RBP, is associated with pro-proliferation and anti-apoptosis activities in prostate tumor cells. In this study, we aim to establish the biological relevance of circCSPP1 (a newly discovered signature circRNA in prostate cancer) and HnRNP-L to prostate cancer (PCa) progression.
Methods
The specific expression level of circCSPP1 (not confounded by the linear-CSPP1) in PCa was investigated and analyzed based on the publicly available datasets, and was quantified in vitro or in vivo using FISH and RT-qPCR in the current study. The RT-qPCR, RNA immunoprecipitation (RIP) and mini-gene system were utilized to confirm that the expression of circCSPP1 was determined by HnRNP-L. We verified the autophagy-induced tumor-promoting effect of circCSPP1 in PCa through a series of gain-of-function and loss-of-function experiments in vitro or in vivo. The western blot, confocal microscope and transmission electron microscope (TEM) were employed in autophagy assays. Advanced bioinformatics analyses, dual-luciferase reporter assay, FISH and AGO2 RIP were applied to identify the endogenous RNA network involving circCSPP1/miR-520 h/EGR1 axis in PCa, which promote PCa progression through regulating autophagy activities.
Results
First, we demonstrated that circCSPP1 expression was higher in PCa tissues than in benign tissues, and higher in PCa cells than in the benign cells. Then, the in vitro gain- and loss-of-function experiments showed that the circCSPP1 expression in PCa cells was regulated by HnRNP-L, and the increased circCSPP1 significantly induced autophagy which led to an enhanced potential in proliferation, migration and invasion of PCa cells. These results were consistent with the in vivo experiment where increased circCSPP1 was associated with higher growth rate in grafted tumors. Finally, we demonstrated the potential competing endogenous RNA network, involving circCSPP1, miR-520 h, and EGR1, in PCa cells, which may play an important role in PCa progression.
Conclusions
Our study indicated that the increase in circCSPP1 in PCa, which may be catalyzed by HnRNP-L, can induce cellular autophagy through the CircCSPP1-miR-520 h-EGR1 axis, leading to the progression of prostate tumor. This newly discovered circRNA biomarker may be used for clinical prognosis of PCa as well as for development of novel therapy plans.
Landscape Characteristics Influence Ranging Behavior of Asian Elephants at the Human-wildlands Interface in Myanmar
Authors: Chan Aung Nyein , Wittemyer G. , McEvoy J. , Williams Amirtharaj Christy , Cox N. , Soe P. , Grindley M. , Shwe Nay Myo , Chit Aung Myo , Oo Zaw Min , Leimgruber P. 
Published: January 2021

Abstract
Context Asian elephant numbers are declining across much of their range, driven largely by serious threats from land use change resulting in habitat loss and fragmentation. Myanmar, holding critical range for the species, is undergoing major developments due to recent sociopolitical changes. To effectively manage and conserve the remaining populations of endangered elephants in the country, it is crucial to understand their ranging behavior.Objectives Our objectives were to (1) quantify dry season range sizes of elephants in Myanmar and assess how they vary with different configurations of agriculture and natural vegetation; and (2) evaluate how percentage of agriculture within dry core range of elephants relates to their daily distance travelled.Methods We estimated dry season, wet season, and annual range sizes with autocorrelated kernel density estimator (AKDE) using a continuous-time movement modeling (ctmm) framework and reported the 95% and 50% AKDE and 95% Minimum Convex Polygon (MCP) range sizes. In a multiple regression framework, we developed candidate model sets to explain the variation in AKDE range sizes during the better sampled dry season when human-elephant interactions are the most likely to occur.Results Elephant dry season ranges were highly variable averaging 792 km2 and 184.2 km2 for the 95% and 50% AKDE home ranges, respectively. We found both the shape and spatial configuration of agriculture and natural vegetation patches within an individual elephant’s home range play a significant role in determining the size of its range. We also found that elephants are moving more (larger energy expenditure) in ranges with higher percentages of agricultural area.Conclusion Our results provide baseline information for advancing future land use planning that takes into account space-use requirements for elephants. Failing to do so may seriously further endangered declining elephant populations in Myanmar and across the species’ range.
Variants in PRKCE and KLC1, Potential Negative Regulators of Type I Psoriasis
Authors: Xing Jianxiao , Wang Ying , Zhao Xincheng , Li Junqin , Hou Ruixia , Niu Xuping , Yin Guohua , Li Xinhua , zhang kaiming 
Published: January 2021

Abstract
Background: Psoriasis is a multifactorial disease with a complex genetic predisposition. The pathophysiology of psoriasis is associated with genetic variants, especially in negative regulatory genes. To better characterize gene variants in psoriasis and identify the relationship between clinical characteristics and variant genes in its pathogenesis. DNA was extracted from 282 type Ⅰ psoriasis patients and purified, and 13 variable genes were amplified and sequenced using the Sanger method. Results: Among the 13 investigated genes, the variants frequencies of protein kinase C epsilon (PRKCE) (c.240T>C, 35.9% vs 47.7%, P< .05) and kinesin light chain 1 (KLC1) (c.216A>G, 2.9% vs 98.1%, P< .01) were significantly lower in patients than in normal Asian individuals. Additionally, we found considerable differences in the relationship between variants in genes CADM2, JPH2, SPTLC3 and clinical characteristics stratified by medical history and family history. Moreover, MEGF6 gene variants (39.52% vs. 22.50%, χ2=3.83, p < .05) showed a stronger association with the group as mild (PASI≤10) than with the group as heavy. Conclusions: Our results provide a comprehensive correlation analysis of negative regulatory genes that are regulated in psoriasis. This integrated analysis offers novel insight into the pathogenic mechanisms involved in psoriasis.
Genome Wide SSR Development and Their Application in Genetic Diversity Analysis in Wax Gourd
Authors: Hu Qianmei , Wang Haiping , Jiang Biao , Zhu Huayu , He Xiaoming , Song Pengyao , Song Jiangping , Yang Sen , Shen Junjun , Li Zheng , Jianbin Hu , Sun Shouru , Yang Luming 
Published: January 2021

Abstract
Background: Wax gourd (Benincasa hispida Cong., 2n=2x=24) is one of the most important winter vegetables of the Cucurbitaceae family. There are only limited markers available for this crop and the draft genome of wax gourd provides a powerful tool for SSR marker development.Results: In this study, we developed genome-wide SSR markers from wax gourd genome and characterized their distribution and frequency of different motifs and repeats. A total of 52,431 microsatellites from wax gourd genome were identified, of which 39,319 SSR markers were developed. 1,152 non-wax gourd SSR markers were selected from cucumber, melon, watermelon and pumpkin to test their transferability in wax gourd. 580 SSR markers could be transferable in wax gourd, and 42 of them were detected with polymorphic in 11 tested accessions of wax gourd. In addition, 11 good polymorphic transferrable SSR markers and 21 SSR markers of wax gourd were selected to investigate the genetic diversity and population structure of 129 wax gourd accessions. 112 alleles were detected by these 32 SSR markers. The result of population structure showed that the 129 wax gourd accessions were divided into two main populations, and the genetic diversity analysis separated them into two clusters. Conclusions: The large number of wax gourd SSR markers developed in this study provides a valuable resource for genetic linkage map construction, molecular mapping, and marker-assisted selection (MAS) in wax gourd.