crossing96/oncoscreening huggingface dataset:
Esophageal Cancer Surgery: Spontaneous Centralization in the US Contributed to Reduce Mortality Without Causing Health Disparities.	BACKGROUND: Improvement in mortality has been shown for esophagectomies performed at high-volume centers. OBJECTIVE: This study aimed to determine if centralization of esophageal cancer surgery occurred in the US, and to establish its impact on postoperative mortality. In addition, we aimed to analyze the relationship between regionalization of cancer care and health disparities. METHODS: A retrospective population-based analysis was performed using the National Inpatient Sample for the period 2000-2014. Adult patients (≥ 18 years of age) diagnosed with esophageal cancer and who underwent esophagectomy were included. Yearly hospital volume was categorized as low (< 5 procedures), intermediate (5-20 procedures), and high (> 20 procedures). Multivariable analyses on the potential effect of hospital volume on patient outcomes were performed, and the yearly rate of esophagectomies was estimated using Poisson regression. RESULTS: A total of 5235 patients were included. Esophagectomy at low- [odds ratio (OR) 2.17] and intermediate-volume (OR 1.62) hospitals, compared with high-volume hospitals, was associated with a significant increase in mortality. The percentage of esophagectomies performed at high-volume centers significantly increased during the study period (29.2-68.5%; p < 0.0001). The trend towards high-volume hospitals was different among the different US regions: South (7.7-54.3%), West (15.0-67.6%), Midwest (37.3-67.7%), and Northeast (55.8-86.8%) [p < 0.0001]. Overall, the mortality rate of esophagectomy dropped from 10.0 to 3.5% (p = 0.006), with non-White race, public insurance, and low household income patients also showing a significant reduction in mortality. CONCLUSIONS: A spontaneous centralization for esophageal cancer surgery occurred in the US. This process was associated with a decrease in the mortality rate, without contributing to health disparities.	esophagus
Esophageal leiomyoma in a dog causing esophageal distension and treated by transcardial placement of a self-expanding, covered, nitinol esophageal stent.	CASE DESCRIPTION A 10-year-old spayed female Rottweiler was referred for evaluation because of a 2-month history of regurgitation and weight loss, despite no apparent change in appetite. The dog had received antiemetic and antacid treatment, without improvement. CLINICAL FINDINGS Physical examination revealed a low body condition score (2/5), but other findings were unremarkable. Diffuse, global esophageal dilatation was noted on plain thoracic radiographs, and normal motility was confirmed through videofluoroscopic evaluation of swallowing. Transhepatic ultrasonographic and CT examination revealed a circumferential, intraparietal lesion in the distal portion of the esophagus causing distal esophageal or cardial subobstruction and no metastases. Incisional biopsy of the lesion was performed, and findings of histologic examination supported a diagnosis of esophageal leiomyoma. TREATMENT AND OUTCOME In view of numerous possible complications associated with esophageal surgery, the decision was made to palliatively treat the dog by transcardial placement of a self-expanding, covered, nitinol esophageal stent under endoscopic guidance. Two weeks after stent placement, radiography revealed complete migration of the stent into the gastric lumen. Gastrotomy was performed, and the stent was replaced and fixed in place. Twenty-four months after initial stent placement, the dog had a healthy body condition and remained free of previous clinical signs. CLINICAL RELEVANCE Diffuse benign muscular neoplasia should be considered as a differential diagnosis for acquired esophageal dilatation in adult and elderly dogs. In the dog of this report, transcardial stent placement resulted in resolution of the clinical signs, with no apparent adverse effect on digestive function. The described procedure could be beneficial for nonsurgical treatment of benign esophageal tumors in dogs.	esophagus
The Role of Surgery in Treating Resectable Limited Disease of Esophageal Neuroendocrine Carcinoma.	BACKGROUND: Esophageal neuroendocrine carcinoma (NEC) is a rare malignant tumor. The role of surgery in resectable limited disease of esophageal NEC remains unclear. How to select a specific group of limited disease of esophageal NEC who might benefit from surgery remains to be answered. METHODS: Patients undergoing esophagectomy for resectable limited disease of esophageal NEC in our department from January 2007 to June 2015 were analyzed. TNM staging system was applied to describe those patients, and according to their different long-term prognosis after surgery, those patients were subgrouped into surgery response limited disease (SRLD) group and surgery non-response limited disease (SNRLD) group. Both univariate and multivariate analyses were applied to identify potential prognostic factors. RESULTS: A total of 72 patients with resectable limited disease of esophageal NEC were identified for analysis. The median survival time of those patients was 21.5 months. There was no significant survival differences among stage I, stage IIA, and stage IIB patients, but all these patients had significantly longer survival than stage III patients. Therefore, stage I, stage IIA, and stage IIB patients were aggregated together as SRLD group, and stage III patients were aggregated as SNRLD group. SRLD patients obtained significantly longer survival than SNRLD patients in both univariate analysis and multivariate analysis. Moreover, adjuvant therapy could significantly benefit SRLD patients (P = 0.004) but could not benefit SNRLD patients (P = 0.136). CONCLUSIONS: Different responses to surgery existed in resectable limited disease of esophageal NEC indicating the need of further subgrouping for those patients. The resectable limited disease of esophageal NEC could be further subgrouped into SRLD group and SNRLD group according to the TNM staging system.	esophagus
Multi-institutional Analysis of Recurrence and Survival After Neoadjuvant Chemoradiotherapy of Esophageal Cancer: Impact of Histology on Recurrence Patterns and Outcomes.	OBJECTIVE: To determine the impact of histology on pathologic response, survival outcomes, and recurrence patterns in patients with esophageal cancer (EC) who received neoadjuvant chemoradiotherapy (CRT). SUMMARY OF BACKGROUND DATA: There is a paucity of data regarding comparative outcomes after neoadjuvant CRT between esophageal squamous cell carcinoma (SCC) and adenocarcinoma. METHODS: Between 2002 and 2015, 895 EC patients who underwent neoadjuvant CRT followed by esophagectomy at 3 academic institutions were retrospectively reviewed, including 207 patients with SCC (23.1%) and 688 patients with adenocarcinoma (76.9%). Pathologic response, survival, recurrence pattern, and potential prognostic factors were compared. RESULTS: Pathologic complete response (pCR) rate was significantly higher for SCC compared with adenocarcinoma (44.9% vs 25.9%, P < 0.001). After a median follow-up of 52.9 months, 71 patients (34.3%) with SCC versus 297 patients (43.2%) with adenocarcinoma had recurrent disease (P = 0.023). For patients who achieved a pCR, no significant differences were found in recurrence pattern, sites, or survival end-points between the 2 histology groups. For non-pCR patients, the SCC group demonstrated significantly higher regional and supraclavicular recurrence rates but a lower hematogenous metastasis rate than adenocarcinoma patients, whereas the adenocarcinoma patients had a more favorable locoregional failure-free survival (P = 0.005) and worse distant metastasis-free survival (P = 0.024). No differences were found in overall survival (P = 0.772) or recurrence-free survival (P = 0.696) between groups. CONCLUSIONS: SCC was associated with a significantly higher pCR rate than adenocarcinoma. Recurrence pattern and survival outcomes were significantly different between the 2 histology subtypes in non-pCR patients.	esophagus
Short- and long-term outcomes of minimally invasive esophagectomy in elderly patients with esophageal squamous cell carcinoma.	PURPOSE: In recent years, there has been an increase in the number of elderly patients undergoing surgery for esophageal squamous cell carcinoma (ESCC). However, there are few studies on short- and long-term outcomes of minimally invasive esophagectomy (MIE) in such patients. The purpose of this study was to report both short- and long-term outcomes of MIE in elderly patients with ESCC. METHODS: A total of 273 patients with ESCC underwent MIE at our hospital from January 2010 to December 2016. Patients were divided into elderly (≥70 years) and nonelderly (<70 years) groups based on age at the time of surgery. Groups were compared with regard to general preoperative data, intraoperative data, postoperative 30-day complications and their severity, pathological result, recurrence, overall survival (OS), and disease-free survival (DFS) rates. RESULTS: The elderly group was characterized by higher Charlson Comorbidity Index >2 and American Society of Anesthesiologists (ASA) grade. Comparisons of other general preoperative data showed no significant differences. In addition, there were no significant differences in short-term outcomes except for postoperative 30-day complication rate. Although 30-day postoperative complication rate was higher in the elderly group compared with the nonelderly group, the incidence of major complications was similar between groups. Cancer recurrence, 5-year OS, and 5-year DFS rates also were similar between groups. CONCLUSION: Although elderly patients with ESCC had higher Charlson Comorbidity Index and ASA grade, they could achieve short- and long-term outcomes of MIE similar to those of nonelderly patients.	esophagus
Prognostic significance of miR-21 and PDCD4 in patients with stage II esophageal carcinoma after surgical resection.	Many studies have shown that randomized clinical trial with long-term follow-up found no improvement in stage II esophageal carcinoma (EC) patients receiving preoperative neoadjuvant chemoradiotherapy or chemotherapy treatment, this limitation underscored the urgent need for novel and reliable biomarkers for prognosis and prediction in stage II EC. miR-21 is frequently over-expressed while programmed cell death 4 (PDCD4) is often down-regulated in solid tumors. This study aimed to investigate the clinicopathological and prognostic significance of miR-21 and PDCD4 expression and to elucidate any correlation between miR-21 and PDCD4 expression in stage II EC patients. The expression level of miR-21 was up-regulated while the PDCD4 protein was down-regulated in stage II EC tissues compared with the adjacent non-cancerous tissues. Analyses of the clinicopathological parameters indicated that miR-21 expression was associated with differentiation grade, T stage, and N stage. PDCD4 protein expression was associated with T stage, N stage, and tumor size. The univariate linear regression analysis suggested a significant negative correlation between miR-21 and PDCD4 expression. The Kaplan-Meier curve showed that high miR-21 expression or low PDCD4 expression predicted poor progression-free survival (PFS) and overall survival (OS) of patients with stag II EC. In conclusion, both up-regulated miR-21 and down-regulated PDCD4 expression were associated with the aggressive progression and poor prognosis of stage II EC. miR-21 and PDCD4 might be potential biomarkers of tumor progression and indicators of prognosis of stag II EC.	esophagus
Tumor suppressor miR-128-3p inhibits metastasis and epithelial-mesenchymal transition by targeting ZEB1 in esophageal squamous-cell cancer.	MicroRNAs (miRNAs) are some short RNAs that regulate multiple biological functions at post-transcriptional levels, such as tumorigenic processes, inflammatory lesions and cell apoptosis. Zinc finger E-box binding homeobox factor 1 (ZEB1) is a crucial mediator of epithelial-mesenchymal transition (EMT). It induces malignant progression of various cancers including human esophageal squamous-cell carcinoma (ESCC). In this study, we found that miR-128-3p was downregulated in ESCC tissues and cells by using PCR. Moreover, down-regulated expression of miR-128-3p was testified to be associated with poor prognosis of ESCC patients and might be regarded as an independent prognostic factor. Then, we examined the role of miR-128-3p in ESCC cells, and found that miR-128-3p could suppress the cell migration and invasion in vitro. Furthermore, ZEB1 was confirmed to be a direct target of miR-128-3p by luciferase reporter assay. Rescue experiments proved that EMT was regulated by miR-128-3p via suppression of ZEB1. Taken all together, we conclude that miR-128-3p suppresses EMT and metastasis via ZEB1, and miR-128-3p may be a critical mediator in ESCC.	esophagus
Intravoxel incoherent motion diffusion-weighted imaging of resectable oesophageal squamous cell carcinoma: association with tumour stage.	OBJECTIVE: To determine whether intravoxel incoherent motion (IVIM) diffusion-weighted imaging (DWI) derived parameters can be associated with tumour stage of oesophageal squamous cell carcinoma (SCC). METHODS: 60 patients with resectable oesophageal SCC and 20 healthy individuals underwent oesophageal DWI-using multi b-values with a 3.0 T MR system. Pure diffusion coefficient (D), perfusion-related incoherent microcirculation (D*), microvascular volume fraction (f) and apparent diffusion coefficient (ADC) were measured on DWI. Statistical analyses were performed to determine associations of DWI-derived parameters with T-stage. RESULTS: ADC (r = -0.842), D (r = -0.729), D* (r = -0.301) and f (r = -0.817) were negatively correlated with T-stage of oesophageal SCC (all p < 0.01), and the multinominal regression analyses revealed that IVIM-derived parameters including D (p = 0.038; odds ratio <1) and f (p < 0.001; odds ratio <1) were associated with T-stage. The Mann-Whitney U tests with Bonferroni correction showed that D, f and ADC could discriminate oesophageal SCC, especially T(1)-staged tumour, from normal oesophagus (all p < 0.05) while D* could not (p > 0.05). By receiver operating characteristic analyses, f could be the best indicator for detecting oesophageal SCC with an area under receiver operating characteristic (AUC) of 0.964, especially T(1)-staged cancer with an AUC of 0.984, and for discriminating T(1)-stages between T(0-1) and T(2)(-)(3) with an AUC of 0.957, and between T(0)(-)(2) and T(3) with an AUC of 0.945 in comparison with any other DWI-derived parameter. CONCLUSIONS: IVIM derived parameters can be associated with T-stage of oesophageal SCC. Advances in knowledge (1) IVIM-derived parameters are negatively correlated with stage of oesophageal SCC. (2) Among IVIM-derived parameters, microvascular volume fraction helps detect and stage oesophageal SCC.	esophagus
EGBMMDA: Extreme Gradient Boosting Machine for MiRNA-Disease Association prediction.	Associations between microRNAs (miRNAs) and human diseases have been identified by increasing studies and discovering new ones is an ongoing process in medical laboratories. To improve experiment productivity, researchers computationally infer potential associations from biological data, selecting the most promising candidates for experimental verification. Predicting potential miRNA-disease association has become a research area of growing importance. This paper presents a model of Extreme Gradient Boosting Machine for MiRNA-Disease Association (EGBMMDA) prediction by integrating the miRNA functional similarity, the disease semantic similarity, and known miRNA-disease associations. The statistical measures, graph theoretical measures, and matrix factorization results for each miRNA-disease pair were calculated and used to form an informative feature vector. The vector for known associated pairs obtained from the HMDD v2.0 database was used to train a regression tree under the gradient boosting framework. EGBMMDA was the first decision tree learning-based model used for predicting miRNA-disease associations. Respectively, AUCs of 0.9123 and 0.8221 in global and local leave-one-out cross-validation proved the model's reliable performance. Moreover, the 0.9048 ± 0.0012 AUC in fivefold cross-validation confirmed its stability. We carried out three different types of case studies of predicting potential miRNAs related to Colon Neoplasms, Lymphoma, Prostate Neoplasms, Breast Neoplasms, and Esophageal Neoplasms. The results indicated that, respectively, 98%, 90%, 98%, 100%, and 98% of the top 50 predictions for the five diseases were confirmed by experiments. Therefore, EGBMMDA appears to be a useful computational resource for miRNA-disease association prediction.	esophagus
MicroRNA-30c functions as a tumor suppressor via targeting SNAI1 in esophageal squamous cell carcinoma.	BACKGROUND: Aberrant expression of miRNAs was involved in tumor initiation, progression and metastasis in multiple cancers. Many kinds of microRNAs in esophageal squamous cell carcinoma (ESCC) have been researched, whereas miR-30c has not been included. METHODS: Firstly, we explored the expression of miR-30c in ESCC tissue and serum samples and its relations to the survival. To further investigate its effects on ESCC cells, we completed a series of experiments. We detected the effects of ectopic miR-30c expression on the proliferation, migration and invasion of ESCC cells in vitro. We identified the target role of SNAI1 in ESCC using Dual-luciferase reporter assay and western blot assay. RESULTS: The results showed miR-30c was significant down-regulated in ESCC tissues and cell lines. Clinically, we found lower miR-30c expression was significantly correlated with worse ESCC progression and survival. Also we clarified that miR-30c suppressed cell proliferation, invasion and epithelial to mesenchymal transition (EMT) of ESCC cell lines. What's more, we figured out that miR-30c inhibits ESCC biological behaviors and EMT progress by directly binding to the 3'-UTR of SNAI1. CONCLUSION: This study provides new insight into the mechanism responsible for the development of human ESCC. Therefore, miR-30c could be a promising biomarker and a therapeutic target for ESCC in the future.	esophagus
Network-Based Differential Analysis to Identify Molecular Features of Tumorigenesis for Esophageal Squamous Carcinoma.	Esophageal cancer has a poor prognosis and high mortality rate across the world. The diagnosis and treatment of esophageal cancer are hindered by the limited knowledge about the pathogenesis mechanisms of esophageal cancer. Esophageal cancer has two major subtypes, squamous and adenocarcinoma. In this work, we proposed a method to select candidate biomarkers of esophageal squamous carcinoma based on the topological differential analysis between the gene-gene interaction networks for esophageal squamous carcinoma and normal cells. We established the gene-gene interaction networks for esophageal squamous carcinoma and normal based on the correlation of genes. For each gene, we firstly calculated and compared five centrality measures, which could reflect the topological property of a network. According to five centrality measures, the genes with large differences between the two networks were regarded as candidate biomarkers for esophageal squamous carcinoma. A total of 21 candidate biomarkers were identified for esophageal squamous carcinoma, and seven of them have been confirmed to be biomarkers of esophageal-12 squamous carcinoma by previous research. In addition, six genes (RBPMS2, PDK4, IGK, SBSN, IFIT3 and HSPB6) were likely to be the biomarkers of tumorigenesis for esophageal squamous carcinoma due to the fact that the biological processes in which they participate are closely related with the development of esophageal squamous carcinoma. Statistical analysis indicates that effectiveness of the detected biomarkers of esophageal squamous carcinoma. The proposed method could be extended to other complex diseases for detecting the molecular features of pathopoiesis and targets for targeted therapy.	esophagus
A clinical trial protocol paper discussing the BRIGHTER study.	Napabucasin is a novel oral first-in-class cancer stemness inhibitor. Preclinical and early phase clinical trials showed promising antitumor efficacy signals for napabucasin in a variety of malignancies. In this article, we describe the design and rationale for the now completed BRIGHTER trial, a multicenter, randomized, placebo-controlled, Phase III study designed to determine the efficacy and safety of combining napabucasin with paclitaxel in previously treated patients with advanced gastric and gastroesophageal junction adenocarcinoma (NCT02178956). Patients were randomized in a 1:1 fashion to receive weekly paclitaxel with either napabucasin or placebo. The study failed to achieve its primary end point of overall survival in the intention to treat population. Ongoing analysis of the secondary end points includes progression-free survival, objective response rate, disease control rate, the safety of the combination therapy and evaluation of efficacy in the biomarker-positive subpopulation.	esophagus
TFF1 hypermethylation and decreased expression in esophageal squamous cell carcinoma and histologically normal tumor surrounding esophageal cells.	BACKGROUND: Esophageal squamous cell carcinoma (ESCC) is one of the 10 most incident cancer types in the world, and it is mainly associated with tobacco and alcohol consumption. ESCC mortality rates stand very close to its incidence, which is a direct consequence of a late diagnosis and an inefficient treatment. Although this scenery is quite alarming, the major molecular alterations that drive this carcinogenesis process remain unclear. We have previously shown through the first ESCC methylome analysis that TFF1 promoter is frequently hypermethylated in ESCC. Here, to evaluate TFF1 methylation as a potential biomarker of early ESCC diagnosis, we investigated the status of TFF1 promoter methylation and its expression in ESSC and histologically normal tumor surrounding tissue of ESCC patients in comparison to healthy esophagus of non-cancer individuals. RESULTS: Analysis of TFF1 promoter methylation, and gene and protein expression in 65 ESCC patients and 88 controls revealed that TFF1 methylation levels were already increased in histologically normal tumor surrounding tissue of ESCC patients when compared to healthy esophagus of non-cancer individuals. This increase in DNA methylation was followed by the reduction of TFF1 mRNA expression. Interestingly, TFF1 expression was capable of distinguishing tumor surrounding normal tissue from normal mucosa of healthy individuals with 92% accuracy. In addition, TFF1 protein was undetectable both in tumor and surrounding mucosa by immunohistochemistry, while submucosa glands of the healthy esophagus showed positive staining. Furthermore, treatment of TE-1 and TE-13 ESCC cell lines with decitabine led to a reduction of promoter methylation and consequent upregulation of TFF1 gene and protein expression. Finally, using TCGA data we showed that TFF1 loss is observed in ESCC, but not in esophageal adenocarcinoma, highlighting the different molecular mechanisms involved in the development of each histological subtype of esophageal cancer. CONCLUSIONS: This study shows that TFF1 expression is silenced in early phases of ESCC development, which seems to be mediated at least in part by promoter hypermethylation, and provides the basis for the use of TFF1 expression as a potential biomarker for early ESCC detection.	esophagus