crossing96/oncoscreening huggingface dataset:
Optimal aggregation of binary classifiers for multiclass cancer diagnosis using gene expression profiles.	"Multiclass classification is one of the fundamental tasks in bioinformatics and typically arises in cancer diagnosis studies by gene expression profiling. There have been many studies of aggregating binary classifiers to construct a multiclass classifier based on one-versus-the-rest (1R), one-versus-one (11), or other coding strategies, as well as some comparison studies between them. However, the studies found that the best coding depends on each situation. Therefore, a new problem, which we call the ""optimal coding problem,"" has arisen: how can we determine which coding is the optimal one in each situation? To approach this optimal coding problem, we propose a novel framework for constructing a multiclass classifier, in which each binary classifier to be aggregated has a weight value to be optimally tuned based on the observed data. Although there is no a priori answer to the optimal coding problem, our weight tuning method can be a consistent answer to the problem. We apply this method to various classification problems including a synthesized data set and some cancer diagnosis data sets from gene expression profiling. The results demonstrate that, in most situations, our method can improve classification accuracy over simple voting heuristics and is better than or comparable to state-of-the-art multiclass predictors."	esophagus
Tolfenamic acid inhibits esophageal cancer through repression of specificity proteins and c-Met.	The non-steroidal anti-inflammatory drug tolfenamic acid (TA) inhibits proliferation of SEG-1 and BIC-1 esophageal cancer cells with half-maximal growth inhibitory concentration values of 36 and 48 muM, respectively. TA also increased Annexin V staining in both cell lines, indicative of proapoptotic activity. Treatment of SEG-1 and BIC-1 cells with TA for up to 72 h decreased expression of specificity protein (Sp) transcription factors Sp1, Sp3 and Sp4 and this was accompanied by decreased expression of the well-characterized Sp-regulated genes cyclin D1, vascular endothelial growth factor and survivin. TA also decreased hepatocyte growth factor receptor, (c-Met), a receptor tyrosine kinase that is overexpressed in esophageal cancer cells and tumors and is an important drug target. Knockdown of Sp1, Sp3 and Sp4 by RNA interference in SEG-1 and BIC-1 cells also decreased c-Met expression, demonstrating that c-Met is an Sp-regulated gene in esophageal cancer cells. Sp1 was overexpressed in esophageal cancer cells and tumors and increased Sp1 staining was observed in esophageal tumors from patients. TA (20 mg/kg/day) also decreased tumor growth and weight in athymic nude mice bearing SEG-1 cells as xenografts and this was accompanied by increased apoptosis and decreased Sp1 and c-Met staining in tumors from treated mice. Thus, TA-dependent downregulation of Sp transcription factors and c-Met defines a novel chemotherapeutic approach for treatment of esophageal cancer.	esophagus
Constitutive short telomere length of chromosome 17p and 12q but not 11q and 2p is associated with an increased risk for esophageal cancer.	Shortened telomere length may cause chromosomal instability in Barrett's esophagus and thus promote tumorigenesis. However, whether short telomere length in all chromosomes or just some of them is associated with increased esophageal cancer (EC) risk is largely unknown. To address this question, we examined the overall and chromosome-specific telomere lengths of 17p, 12q, 2p, and 11q and assessed their associations with EC risk. In a case-control study with 94 EC cases and 94 matched controls, the overall telomere length and the chromosome-specific telomere lengths of 17p, 12q, 2p, and 11q in peripheral blood lymphocytes were determined by a real-time PCR and a modified single telomere length analysis assay, respectively. Multivariate logistic regression analysis was used to assess the association between telomere length and EC risk. Compared with controls, EC patients had significantly shorter overall telomere lengths (P = 0.004) and chromosome-specific telomere lengths of 17p (P = 0.003) and 12q (P = 0.006) but not of 11q (P = 0.632) and 2p (P = 0.972). Furthermore, the multivariate logistic regression analysis showed that the short overall telomere length and chromosome-specific telomere lengths of 17p and 12q were associated with a dose-dependent increase in EC risk. Our study provides the first epidemiologic evidence that short telomere length of 17p and 12q plays an important role in esophageal carcinogenesis, suggesting that short telomere length of specific chromosomes is associated with the etiology of different cancer types.	esophagus
Induction of gamma delta T cells using zoledronate plus interleukin-2 in patients with metastatic cancer.	A loss of human leukocyte antigen (HLA) expression in clinical tumors is one of their escape mechanisms from immune attack by HLA-restricted effector cells. In this study, the induction of HLA-unrestricted effector cells, gamma delta T cells, using zoledronate (ZOL) and interleukin (IL)-2 in vitro was investigated in patients with metastatic cancer. Peripheral blood mononuclear cells (PBMCs) from 10 cancer patients (8 colorectal and 2 esophageal) with multiple metastases and ascites lymphocytes from 3 cancer patients (1 gastric and 2 colorectal) were stimulated with varied concentrations of ZOL plus 100 U/ml IL-2 for 48 hr followed by culturing with IL-2 alone for 12 days. Lymphocyte proliferative responses were determined using 3H-TdR uptakes and interferon (IFN)-gamma production was evaluated using enzyme-linked immunosorbent assay. Surface phenotyping was performed using flow cytometry. Cytotoxic activity of effector cells was determined using 51Cr-releasing assay. It was found that proliferative responses of PBMCs were significantly stimulated with ZOL plus IL-2 when compared with IL-2 alone, showing 200 to 500-fold expansions for 2 weeks, although ZOL alone induced no response. The optimal concentration of ZOL was 1-5 microM. Ascites lymphocytes could also be stimulated with ZOL plus IL-2. The proliferative responses were remarkable in patients whose PBMCs could produce high levels of IFN-gamma during an initial 48-hr stimulation using ZOL plus IL-2. Removal of an adherent cell fraction before the induction augmented the proliferative responses in patients who otherwise had low-grade proliferative responses. Generated cells comprising approximately 90 or 20% in PBMCs from healthy donors or cancer patients, respectively, expressed gamma delta-type T-cell receptor. Gamma delta T cells showed high cytotoxic activity against CD166-positive TE12 and TE13 cancer cells but not against CD166-negative MKN45 cells. The cytotoxic activity against TE13 cells was augmented when target cells were pre-treated overnight with ZOL. These results suggest that ZOL in the presence of IL-2 can efficiently stimulate the proliferation of gamma delta T cells, which have cytotoxic properties against cancer cells. The use of zoledronate-activated killer (ZAK) cells should be encouraged in possible adoptive immunotherapy trials for patients with incurable cancer.	esophagus
Food intake and the occurrence of squamous cell carcinoma in different sections of the esophagus in Taiwanese men.	OBJECTIVE: The main objective of this study was to further elucidate the effect of consuming various foods on the development of squamous cell carcinoma (SCC) in three different sections of the esophagus. METHODS: A total of 343 patients with SCC of the esophagus and 755 cancer-free control subjects were recruited for this study from 1996 to 2005. RESULTS: We found that intake of vegetables, raw onions/garlic, and fruits are significantly protective against esophageal SSC risk, whereas intake of hot foods can significantly increase its risk. There was a significant inverse relation between the frequency of tea consumption and esophageal SCC risk (P for trend = 0.005), with a 0.5-fold lower risk associated with the intake of unfermented tea (green tea, oolong tea, or jasmine tea). The effects of dietary factors on esophageal SCC were similar in all subsites, with the exception of consumption of coffee. Coffee consumption was more pronounced in having a protective effect in the middle third section compared with the lower third section of the esophagus (adjusted odds ratio 0.4, 95% confidence interval 0.2-0.9), although this protective effect was marginally significant (adjusted odds ratio 0.6, 95% confidence interval 0.4-1.0) against esophageal SCC in all subsites. Our data also suggest that discomfort when eating hot foods may exert a carcinogenic effect by direct contact with the esophageal mucosa and tend to have more harmful effects in the upper than in the lower esophagus. In contrast, vegetables, fruits, and tea with components that are thought to inhibit carcinogenesis by absorbed components affected all subsites similarly. CONCLUSION: Our results add additional information that certain dietary components may affect carcinogenesis locally and systemically.	esophagus
Application of a modified McKeown procedure (thoracoscopic esophageal mobilization three-incision esophagectomy) in esophageal cancer surgery: initial experience with 30 cases.	Early efforts with minimally invasive esophagectomy (MIE) were hybrid approaches. No conclusive benefit was seen with this approach compared with the standard open procedure. Total MIE has demonstrated its advantages in single institution series. The drawbacks of total MIE include the steep learning curve and the high cost of the disposable instrumentation. We sought to determine the feasibility of modifying the surgical technique involved in the hybrid approach in an effort to decrease the cost of the surgery without compromising the outcome. From December 2007 to September 2008, the modified McKeown procedure (thoracoscopic esophageal mobilization three-incision esophagectomy) was performed in 30 cases. The median operative time was 225 minutes (range, 195 -290 minutes) and the median average time of VATS was 70 minutes (range, 50 -130 minutes). Median lymph node retrieval was 25.6 +/- 4.8 nodes (15.1 +/- 3.4 intrathoracic) per patient. The median postoperative hospital stay was 17.1 +/- 6.3 days. There was no in-hospital (30 days) mortality. Postoperative complications occurred in 9 patients (30%), including 2 (6.7%) pneumonia, 1 (3.3%) chylothorax, 1 (3.3%) delayed gastric emptying, 1 (3.3%) vocal cord palsy, 2 (6.7%) neck anastomotic leaks, and 2 (6.7%) arrhythmias. This procedure is technically feasible and safe with lower mortality and mobility. The short-term surgical outcomes are comparable with most of the total MIE reports. Performing the gastric mobilization and spontaneous neck anastomosis first greatly facilitate and simplifies the VATS maneuver.	esophagus
Polymorphisms of HLA-A and HLA-B genes in genetic susceptibility to esophageal carcinoma in Chaoshan Han Chinese.	Esophageal carcinoma (EC) occurs at high rate in Chaoshan region of southern China. Human leukocyte antigen (HLA) polymorphism has been implicated in risk for various cancers. To investigate the impact of HLA-A and HLA-B polymorphisms on susceptibility to EC, a case-control study was conducted among 206 patients with esophageal squamous cell carcinoma and 524 controls from Chaoshan Han population. HLA-A and HLA-B polymorphisms were genotyped by polymerase chain reaction-sequence-specific primers. Genotypic association tests for dominant, recessive, and additive models, and haplotypic association were calculated using unconditional logistic regression. A*11 was identified in a recessive model as an only allele strongly associated with EC risk (odds ratios [OR]=2.10, 95% confidence interval [CI]=1.33-3.31) even after correction for multiple test. The haplotypes A*02-B*46 (OR=1.53, 95% CI=1.04-2.24) and A*11-B*51 (OR=2.29, 95% CI=1.20-4.40) showed association with increased risk for EC, whereas A*11-B*58 (OR=0.00, 95% CI=0.00-0.82) was associated with decreased risk, though the significance of these haplotypes was lost after correction. This is a first association study at genetic level identifying HLA-A and HLA-B-related variations in genetic susceptibility to EC among Chaoshan population. The variation pattern is likely to be EC-specific because it is different from that observed for nasopharyngeal carcinoma in the same study population and might, at least in part, explain the high rate of EC in this ethnic group.	esophagus
Systematic approach of postoperative gastric conduit complications after esophageal resection.	Complications after esophagectomy related to ischemia of the graft are dreaded. Prompt assessment of the situation is essential. The series presented describes our experience regarding the evaluation of gastric tube complications. A score is presented classifying flexible endoscopy and CT-scan findings. A retrospective analysis from the charts of 47 consecutive patients who underwent esophagectomy for cancer was conducted. Patients who underwent upper endoscopy during admittance were entered in this study. Findings on flexible endoscopy and CT scan were systematic scored. According to the findings, different attitudes were taken. Between January 2006 and December 2007, 47 patients underwent esophagectomy for cancer. Eleven (23%) out of 47 patients were suspected to have complications related to the viability of the anastomosis. Median period to deterioration was 5 days. In 3 (27%) patients, stent placement was the only intervention necessary. In 2 (18%) patients, stent placement was combined with drainage of abscesses in the upper mediastinum. Five (46%) patients required a new right thoracotomy, with drainage of mediastinal abscesses and empyema. In 2 patients a limited resection and a new cervical anastomosis with a stent was created. Mean intensive care admission and hospital admittance was 30.2 days and 67.9 days, respectively. Two patients (18%) died during hospital admittance. All cervical anastomosis required postoperative dilatation. No complications related to the use of flexible endoscopy were seen. An aggressive policy is adopted in patients deteriorating following esophagectomy. CT-scanning of the thorax and a flexible endoscopy of the gastric conduit should always be performed. Direct therapy should be adopted without delay.	esophagus
Injury of the thoracic aorta during laparoscopic esophagectomy.	We report an unusual complication of laparoscopic esophagectomy for carcinoma. During posterior transhiatal dissection, massive bleeding occurred from the left side of the supradiaphragmatic thoracic aorta. A small tear was clearly visible and temporary bleeding control by packing and pressure with a grasper through one of the trocars was effective. A median laparotomy was performed and the aorta was sutured using a standard laparoscopic needle holder. The esophagectomy was successfully completed through a right thoracic approach. Injury to the intrathoracic aorta may occur during transhiatal dissection of the lower mediastinum. Use of a laparoscopic needle holder allowed to repair the supradiaphragmatic aorta through a laparotomy without the need of patient repositioning for a transthoracic approach.	esophagus
[Self-expanding metal stents for palliation of malignant oesophageal obstruction].	BACKGROUND: Malignant oesophageal stenosis can be caused by cancer of the oesophagus, gastric cardia, lungs, mediastinum or, rarely, breast. Most of these cases are inoperable due to advanced stage of the disease, comorbidities or age of the patients; and palliative treatment can be applied only. The quality of life is mostly determined by the extent of dysphagia. Several methods are available to palliate dysphagia. Hereby, the authors review their results with palliation of malignant oesophageal obstruction applying self-expanding metal stents. PATIENTS AND METHODS: 68 endoscopic stent implantations were performed in 64 patients (15 female and 49 male) with malignant dysphagia between 2003 and 2008. After radiological investigations, distally deployed covered stents with or without an antireflux valve were placed, depending on the localization of the tumour. In one patient with a stenosis localized in the upper third of the oesophagus a proximally deployed covered stent was used. The aim was to re-establish oral nutrition and cover possible fistulas. RESULTS: Significant improvement of swallowing was detected in every patient. Average dysphagia score has improved from 3.2 to 1.7. Technical difficulties during stenting occurred in a relatively low percentage of patients only (2 in 68; i.e. 2.94%). Fistulas were covered in every case. Early stent migration (<7 days) happened in one case. One patient suffered non-fatal myocardial infarction two days after stent placement. In 5 cases tumour in- and overgrowth, in 4 cases bleeding was seen as late complications. Oesophago-tracheal fistula was noted in three patients after stent implantation. Late stent migration (>7 days) occurred in two patients. Re-stenting was necessary in four cases, while three patients needed an upper GI endoscopy for cleansing the stent caused by food obstruction. CONCLUSIONS: According to our data self-expanding metal stents are highly effective and safe for improving dysphagia. Stent-related complications are relatively rare. This method is highly recommended for palliation of malignant dysphagia.	esophagus
p53 Arg72Pro and MDM2 T309G polymorphisms, histology, and esophageal cancer prognosis.	PURPOSE: This study aimed to evaluate the prognostic significance of two functional single nucleotide polymorphisms (SNP) in the p53 pathway (p53 Arg72Pro and MDM2 T309G) in patients with esophageal cancer, and to determine the importance of histologic subtype in the SNP-outcome relationships. EXPERIMENTAL DESIGN: A cohort of 371 patients with esophageal carcinoma enrolled in Boston, USA from 1999 to 2004 were genotyped for the p53 and MDM2 SNPs. Associations between genotypes and overall survival (OS; the primary outcome) and progression-free survival (PFS) were assessed using the Kaplan-Meier method. Cox proportional hazard models, adjusted for age, stage, performance status, and smoking were developed. Interaction analyses were done for histology (adenocarcinoma versus squamous cell carcinoma). RESULTS: At the median follow-up of 33 months, median survival (MS) and PFS were 29.1 and 15.7 months, respectively. p53 Pro/Pro was strongly associated with shorter survival in the entire cohort (MS of 11.8 versus 29.1 months, P < 0.0001; adjusted hazard ratio for death, 2.05; 95% confidence interval, 1.30-3.24; P = 0.002 for Pro/Pro versus Arg/Arg). MDM2 G/G was associated with markedly reduced survival in squamous cell carcinoma (MS of 10.3 versus 49.4 months; adjusted hazard ratio for death, 7.9; 95% confidence interval, 2.4-26.0; P = 0.0007 for G/G versus T/T) but not in adenocarcinoma (SNP-histology interaction P = 0.004). CONCLUSIONS: In a large prospective cohort, p53 Arg72Pro Pro/Pro was associated with a 2-fold increased risk of death in all esophageal cancers, whereas MDM2 T309G G/G was associated with a 7-fold increased risk of death in squamous cell carcinoma.	esophagus
Surgical resection of esophageal gastrointestinal stromal tumors.	BACKGROUND: Due to the rarity of esophageal gastrointestinal stromal tumors (GISTs), their clinical course and treatment are poorly understood. We have assessed our experience in the diagnosis and management of esophageal GISTs. METHODS: We performed a retrospective chart review of patients diagnosed with esophageal GISTs who underwent surgical resection. RESULTS: We identified 7 patients (6 males and 1 female) who underwent surgical procedures due to esophageal GISTs between 2001 and 2003; their median age was 46 years (range, 39 to 68 years). Four patients presented with dysphagia. Two patients were diagnosed with GIST by endoscopic biopsy before surgery. Five patients underwent enucleation, and two underwent esophagectomy. All tumors were resected completely and no patient received perioperative imatinib therapy. Median postoperative follow-up was 4.4 years (range, 2.2 to 7.0 years), during which two patients were diagnosed with recurrences. CONCLUSIONS: Esophageal GIST is a rare disease, and complete surgical resection is the standard treatment. Regular follow-up is needed even if resection is complete and negative margins are achieved.	esophagus
Positron emission tomography-computed tomography in predicting locoregional invasion in esophageal squamous cell carcinoma.	BACKGROUND: In order to clarify the role of positron emission tomography-computed tomography (PET/CT) in thoracic esophageal squamous cell carcinoma we investigated its value in predicting locoregional invasion. METHODS: Forty-five patients receiving curative esophagectomy and lymph node dissection were included. The relationship between PET/CT findings and pathology results were studied. Correlation between nodal uptake and the modified lymph node staging, which is based on number of involved nodes (N0 = no nodes; N1 = 1 to 3 nodes; N2 = more than 3 nodes), was evaluated. RESULTS: The mean maximal standardized uptake value (SUV(max)) was 5.09 +/- 4.00 in T1, 14.17 +/- 2.46 in T2, 13.32 +/- 3.96 in T3, and 10.37 +/- 1.94 in T4 primary tumor. The SUV(max) was significantly lower in stage T1 tumors than in stage T2 and T3 tumors. For regional nodal involvement, PET/CT findings significantly correlated with pathology results. However, the sensitivity, specificity, and accuracy of PET/CT were only 57.1%, 83.3%, and 71.1%, respectively, and even lower for detecting nonregional lymph node metastasis. When stratified by the modified staging system, the mean SUV(max) was 0.64 +/- 1.60 in N0, 1.43 +/- 2.08 in N1, and 4.67 +/- 4.32 in N2 regional lymph node metastases, and was significantly higher in patients with N2 metastasis than in patients with N0 and N1 metastases. CONCLUSIONS: Locoregional invasion in esophageal cancer can be predicted by PET/CT. The SUV(max) of the primary tumor helped identify T1 tumor, and the SUV(max) of the regional lymph nodes correlated with the severity of nodal involvement.	esophagus
Relapse patterns and related prognostic factors in patients with mobile tongue cancer treated with postoperative radiotherapy.	PURPOSE: To retrospectively assess prognostic factors and patterns of relapse in patients with oral tongue cancer treated by adjuvant radiotherapy (RT). PATIENTS AND METHODS: Between 1995 and 2005, 65 patients with stage II-IV oral tongue cancer were treated with postoperative adjuvant RT at our institution. The influence of multiple patient- and treatment-related factors on local and regional control, and overall survival (OS), locoregional failure- free survival (LRFFS) and cause-specific survival (CSS) were evaluated. Median patient follow-up was 74 months. RESULTS: Five-year disease-free survival (DFS), LRFFS and CSS rates were 56, 60 and 58%, respectively. During the study period 27 (41.5%) patients had locoregional failures. Seventeen of the recurrences were in the primary tumor region, 4 in the neck, 6 in both regions. Most of the local failures occurred in the first year (median 13 months, range 5-15). Gender, T stage, stage (AJCC TN stage), surgical margin, localization of tumor, and hemoglobin level had predictive value for improved local-regional control in univariate analysis. In total, 35 deaths occurred: 28 patients died of progressive disease, one patient died due to another primary tumor (esophageal cancer) and 6 patients died of other causes. CONCLUSION: Local failure was the most important problem concerning the final outcome. High local recurrence rates and poor survival rates are important issues in the management of oral tongue cancer. Further strategies should be directed to enhancing cure rates.	esophagus