crossing96/oncoscreening huggingface dataset:
MRF-based deformable registration and ventilation estimation of lung CT.	Deformable image registration is an important tool in medical image analysis. In the case of lung computed tomography (CT) registration there are three major challenges: large motion of small features, sliding motions between organs, and changing image contrast due to compression. Recently, Markov random field (MRF)-based discrete optimization strategies have been proposed to overcome problems involved with continuous optimization for registration, in particular its susceptibility to local minima. However, to date the simplifications made to obtain tractable computational complexity reduced the registration accuracy. We address these challenges and preserve the potentially higher quality of discrete approaches with three novel contributions. First, we use an image-derived minimum spanning tree as a simplified graph structure, which copes well with the complex sliding motion and allows us to find the global optimum very efficiently. Second, a stochastic sampling approach for the similarity cost between images is introduced within a symmetric, diffeomorphic B-spline transformation model with diffusion regularization. The complexity is reduced by orders of magnitude and enables the minimization of much larger label spaces. In addition to the geometric transform labels, hyper-labels are introduced, which represent local intensity variations in this task, and allow for the direct estimation of lung ventilation. We validate the improvements in accuracy and performance on exhale-inhale CT volume pairs using a large number of expert landmarks.	esophagus
Low expression of cyclinH and cyclin-dependent kinase 7 can decrease the proliferation of human esophageal squamous cell carcinoma.	BACKGROUND: Increased expression of cyclinH (CCNH) and cyclin-dependent kinase 7 (CDK7) has a relationship with poor prognosis in most human cancers. AIM: Investigate the expression of CCNH and CDK7 in human esophageal squamous cell carcinoma (ESCC) and the effect of chemotherapy on their expression. METHODS: Western blotting and immunohistochemistry were used to measure the expression of CCNH and CDK7 proteins in ESCC and adjacent normal tissue in 98 patients. We use Cell Counting Kit-8 and cell flow to analyze the effects of cisplatin and interference of CCNH and CDK7 in cell cycle process. RESULTS: Immunohistochemical analysis showed that CCNH and CDK7 expression were significantly associated with unfavorable clinicopathologic variables. CCNH and CDK7 protein levels were elevated in ESCC tissues in comparison with adjacent normal tissues. Survival analysis revealed that CCNH and CDK7 overexpression were significantly associated with overall survival (P < 0.001). Cisplatin or interference of CCNH or CDK7 led cells to grow slowly. Overexpression of CCNH and CDK7 in TE1 cells can lead to resistance to cisplatin. CONCLUSIONS: We can conclude that CCNH and CDK7 may play an important role in the tumorigenesis and development of ESCC. CCNH and CDK7 expression affected the chemotherapy of tumor.	esophagus
Treatment strategies for esophageal cancer.	The treatment of esophageal cancer has evolved considerably in the past decade and depends largely on the extent of disease at the time of presentation. For disease confined to the esophageal mucosa, endoscopic therapy is replacing esophagectomy as the standard of care. For locoregional disease, neoadjuvant chemoradiation followed by esophagectomy is the best strategy for optimizing long-term survival. In the minority of patents who present with metastatic disease, the prognosis is poor. Palliative therapies available for these patients include chemotherapy, radiation, endoscopic therapies to ameliorate obstruction or bleeding, and surgical intervention to optimize nutritional status or to relieve obstruction.	esophagus
Endoscopic therapy for Barrett's esophagus and early esophageal adenocarcinoma.	Endoscopic therapy for Barrett's esophagus is feasible and likely to decrease the future risk of development of esophageal adenocarcinoma. The most commonly used therapy is radiofrequency ablation, which has been shown to produce reproducible superficial injury in the esophagus. Other thermal therapies include multipolar coagulation, argon plasma coagulation, and thermal laser therapy. The other end of the ablative spectrum includes cryotherapy, which involves freezing tissue to produce mucosal necrosis. Photodynamic therapy has been used to photochemically eliminate abnormal mucosa. Endoscopic therapy has been demonstrated to be effective in high-risk situations such as Barrett's esophagus with high-grade dysplasia.	esophagus
Prognostic factors and outcome for patients with esophageal squamous cell carcinoma underwent surgical resection alone: evaluation of the seventh edition of the American Joint Committee on Cancer staging system for esophageal squamous cell carcinoma.	INTRODUCTION: More data are essential to test the efficacy of the seventh edition of the American Joint Committee on Cancer (AJCC) staging system for esophageal squamous cell carcinoma (ESCC). This retrospective study was designed to identify the prognostic factors for survival of patients with ESCC who underwent surgical resection alone and to evaluate the new AJCC staging system for ESCC. METHODS: Data of a single-center cohort of 2011 patients with ESCC who underwent surgical resection alone according to the new staging system were reviewed. Univariate and multivariate analyses were performed to identify prognostic factors. RESULTS: The 1-, 3-, and 5-year overall survival rates were 83.5, 57.4, and 47.4%, respectively, with a median survival time of 51.0 months. Age, histologic grade, R-category, pT category, pN category, pM category, pTNM stage, and the extent of lymph node metastasis were independent prognostic factors (p < 0.05). In separate subgroup analyses, the survival differences were not significant for pN2 versus pN3 category (p = 0.159) and stages IA versus IB (p = 0.922). Subdivisions by depth of infiltration rather than tumor grade for pT1N0M0 cancers and modified nodal categories (0, 1, 2-3, and ≥4 positive lymph nodes) better represented a survival advantage. CONCLUSIONS: The seventh edition of the AJCC staging system for ESCC is acceptable in predicting survival. However, tumor location does not influence survival in our study. Subdivisions of pT1N0M0 cancers and the N-classification may need to be modified.	esophagus
NADPH oxidase NOX5-S and nuclear factor κB1 mediate acid-induced microsomal prostaglandin E synthase-1 expression in Barrett's esophageal adenocarcinoma cells.	The mechanisms of progression from Barrett's esophagus (BE) to esophageal adenocarcinoma (EA) are not known. Cycloxygenase-2 (COX-2)-derived prostaglandin E₂ (PGE₂) has been shown to be important in esophageal tumorigenesis. We have shown that COX-2 mediates acid-induced PGE₂ production. The prostaglandin E synthase (PGES) responsible for acid-induced PGE2 production in BE, however, is not known. We found that microsomal PGES1 (mPGES1), mPGES2, and cytosolic PGES (cPGES) were present in FLO EA cells. Pulsed acid treatment significantly increased mPGES1 mRNA and protein levels but had little or no effect on mPGES2 or cPGES mRNA. Knockdown of mPGES1 by mPGES1 small interfering RNA (siRNA) blocked acid-induced increase in PGE2 production and thymidine incorporation. Knockdown of NADPH oxidase, NOX5-S, a variant lacking calcium-binding domains, by NOX5 siRNA significantly inhibited acid-induced increase in mPGES1 expression, thymidine incorporation, and PGE2 production. Overexpression of NOX5-S significantly increased the luciferase activity in FLO cells transfected with a nuclear factor κB (NF-κB) in vivo activation reporter plasmid pNF-κB-Luc. Knockdown of NF-κB1 p50 by p50 siRNA significantly decreased acid-induced increase in mPGES1 expression, thymidine incorporation, and PGE₂ production. Two novel NF-κB binding elements, GGAGTCTCCC and CGGGACACCC, were identified in the mPGES1 gene promoter. We conclude that mPGES1 mediates acid-induced increase in PGE₂ production and cell proliferation. Acid-induced mPGES1 expression depends on activation of NOX5-S and NF-κB1 p50. Microsomal PGES1 may be a potential target to prevent or treat EA.	esophagus
Esophageal gel-shifting technique facilitating eradicative boost or reirradiation to upper mediastinal targets of recurrent nerve lymph node without damaging esophagus.	We developed a new technique using hyaluronic gel injection as a spacer to safely move the esophagus away from the high-dose area during interstitial brachytherapy of a mediastinal target close to the esophagus. We percutaneously injected a high-molecular-weight hyaluronic gel mixed with contrast medium to create a space between the esophagus and the target during interstitial brachytherapy. We applied this technique to two cases of relapsed recurrent nerve lymph node metastasis from esophageal cancer: one refractory tumor after 50 Gy of radiotherapy, and one recurrence after mediastinal radiotherapy of total 64 Gy. We prescribed 20 Gy and 18 Gy in one fraction to each target, with calculated esophageal D2cc (the minimum dose to the most irradiated volume of 2 cc) of 4.0 Gy and 6.8 Gy, respectively. Calculated enhancement factor by gel shifting in equivalent dose was 2.69 and 2.34, respectively. In each patient, accumulated esophageal D1cc (minimum dose to the most irradiated volume of p cc. minimum dose to the most irradiated volume of 1 cc) was 74.4 Gy and 85.6 Gy without shifting, and 59.1 Gy and 37.6 Gy with shifting, respectively. There were no procedure-related complications. Four months after the brachytherapy, each tumor was remarkably diminished. No evidence of recurrences or late complications were observed 8 months and 9 months after the procedure, respectively. The esophageal gel-shifting technique may facilitate eradicative brachytherapy to upper mediastinal targets without damaging the esophagus, and can be used in conjunction with boost irradiation or reirradiation to overcome the problem of salvage failure.	esophagus
Comparison of advanced adenocarcinomas of esophagogastric junction and distal stomach in Japanese patients.	BACKGROUND: There have been no reports on the incidence, characteristics, treatment outcomes, and prognosis of inoperably advanced or recurrent adenocarcinoma of the esophagogastric junction (AEGJ) in Japan. METHODS: We investigated the clinicopathological characteristics, treatment outcomes, and prognosis for 816 patients with esophagogastric junctional and gastric adenocarcinoma who received first-line chemotherapy between 2004 and 2009. RESULTS: Of 816 patients, 82 (10 %) had AEGJ. The patients with AEGJ had significantly more lung and lymph node metastasis, but less peritoneal metastasis, than those with gastric adenocarcinoma (GAC). The objective response rate to first-line chemotherapy was 23.3 % for patients with AEGJ and 22.6 % in patients with GAC (p = 0.90). The median survival was 13.0 months in AEGJ and 11.8 months in GAC (p = 0.445). In no patient was tumor site a significant prognostic factor (p = 0.472). In patients with AEGJ, ECOG PS ≥ 2, presence of liver metastasis, and absence of lung metastasis were significantly associated with poor prognosis. CONCLUSIONS: No significant differences were observed in treatment outcomes between advanced AEGJ and GAC. Therefore, the same chemotherapy regimen can be given as a treatment arm in future Japanese clinical trials to both patients with inoperably advanced or recurrent AEGJ and those with GAC.	esophagus
Esophagogastric metaplasia relates to nodal metastases in adenocarcinoma of esophagus and cardia.	BACKGROUND: Immunohistochemical profiles of esophageal and cardia adenocarcinoma differ according to the presence or absence of Barrett's epithelium (BIM) and gastric intestinal metaplasia (GIM) in the fundus and antrum. Different lymphatic spreading has been demonstrated in esophageal adenocarcinoma. We investigated the correlation among the presence or absence of intestinal metaplasia in the esophagus and stomach and lymphatic metastases in patients who underwent radical surgery for esophageal and cardia adenocarcinoma. METHODS: The mucosa surrounding the adenocarcinoma and the gastric mucosa were analyzed. The BIM+ patients underwent subtotal esophagectomy and gastric pull up, and the BIM- patients underwent esophagectomy at the azygos vein, total gastrectomy, and esophagojejunostomy. The radical thoracic (station numbers 2, 3, 4R, 7, 8, and 9) and abdominal (station numbers 15 through 20) lymphadenectomy was identical in both procedures except for the greater curvature. RESULTS: One hundred ninety-four consecutive patients were collected in three major groups: BIM+/GIM-, 52 patients (26.8%); BIM-/GIM-, 90 patients (46.4%); BIM-/GIM+, 50 patients (25.8%). Two patients (1%) were BIM+/GIM+. A total of 6,010 lymph nodes were resected: 1,515 were recovered in BIM+, 1,587 in BIM-/GIM+, and 2,908 in BIM-/GIM- patients. The percentage of patients with pN+ stations 8 and 9 was higher in BIM+ (p=0.001), and the percentage of patients with pN+ perigastric stations was higher in BIM- (p=0.001). The BIM-/GIM- patients had a number of abdominal metastatic lymph nodes higher than did the BIM-/GIM+ patients (p=0.0001). CONCLUSIONS: According to the presence or absence of BIM and GIM in the esophagus and cardia, adenocarcinoma correspond to three different patterns of lymphatic metastasization, which may reflect different biologic and carcinogenetic pathways.	esophagus
Does morbid obesity worsen outcomes after esophagectomy?	BACKGROUND: With worldwide increases in esophageal cancer and obesity, esophagectomies in the morbidly obese (MO) will only increase. Risk stratification and patient counseling require more information on the morbidity associated with esophagectomy in the obese. METHODS: We studied nonemergent subtotal or total esophagectomies with reconstruction in the National Surgical Quality Improvement Project (NSQIP) database from 2005 to 2010. After excluding patients with disseminated disease and body mass index (BMI) less than 18.5, we compared outcomes of patients with normal BMI (18.5-25) to those of MO patients (BMI ≥ 35). Outcomes were mortality and morbidity. Multivariable regression controlled for age and comorbidities differing between groups. RESULTS: Of 794 patients, 578 (73%) had a normal BMI and 216 (27%) patients were morbidly obese (MO). The population was 75% men, with a mean age of 62 years. Patients with a normal BMI were older and more likely to smoke (p < 0.001). MO patients had a higher incidence of hypertension (65% versus 41%) and diabetes (20% versus 10%), and fewer had preoperative weight loss greater than 10% (9% versus 31%) (p < 0.001). Overall, morbidity was 48.5% and mortality was 3%; there was no difference between the groups. On multivariable analysis, all outcomes were the same between groups except deep space infections and pulmonary embolism (PE), for which the obese were at 52% and 48% higher risk, respectively (p = 0.02). CONCLUSIONS: In our study, postoperative mortality and pulmonary, cardiac, and thromboembolic morbidity were similar between MO patients and patients with a normal BMI. MO increased the odds of deep wound infections. Overall, BMI greater than 35 does not confer significant morbidity after esophagectomy. Patients with esophageal pathologic conditions should not be denied resection based on MO alone.	esophagus
Endoluminal high-dose-rate brachytherapy for early stage and recurrent esophageal cancer in medically inoperable patients.	PURPOSE: The management of superficial primary and recurrent esophageal cancer (EC) in medically inoperable patients is complex. Endoluminal high-dose-rate (HDR) brachytherapy has shown mixed results in terms of toxicity and local control. In this study, we examined the outcomes and toxicities in a set of patients with superficial primary and recurrent EC treated with a consistent HDR technique. METHODS AND MATERIALS: Between 8/2008 and 7/2011, 14 patients were treated with HDR intraluminal brachytherapy, 10 (71.4%) with recurrent disease, and 4 (28.6%) with previously unirradiated lesions. Patients received three weekly fractions to a median dose of 12 Gy (range, 10-15 Gy); dose was prescribed to 7-mm median depth with mucosal dose limited to 8-10 Gy using a 12-14-mm applicator. RESULTS: Median followup was 15.4 months. Overall freedom from failure (OFFF) and overall survival (OS) at 18 months were 30.8% (95% confidence interval [CI]: 5.2, 56.4) and 72.7% (95% CI: 45.3, 100), respectively. For patients with recurrent disease, OFFF and OS at 18 months were 11.1% (95% CI: 0, 32.1) and 55.6% (95% CI: 15.4, 95.8), respectively. For patients with previously unirradiated disease, OFFF and OS at 18 months were 75.0% (95% CI: 31.6, 100) and 100.0%, respectively. Eight (57.1%) patients had Grade 1 acute adverse effects; 6 (42.9%) patients had chronic Grade 1 adverse effects; 1 (7.1%) patient developed Grade 2 stricture. Grade 3 tracheoesophageal fistula occurred in 1 (7.1%) patient. One patient died before completion of treatment of unrelated causes. CONCLUSIONS: HDR endoluminal brachytherapy is a well-tolerated treatment for superficial primary and recurrent EC in medically inoperable patients.	esophagus
Clinical utility and interobserver agreement of autofluorescence imaging and magnification narrow-band imaging for the evaluation of Barrett's esophagus: a prospective tandem study.	BACKGROUND: New endoscopic imaging techniques, such as autofluorescence imaging (AFI) and narrow-band imaging (NBI), have been developed to improve the detection of neoplastic lesions in Barrett's esophagus (BE). OBJECTIVE: To evaluate the clinical utility of AFI and magnification NBI to detect high-grade dysplasia (HGD) and early esophageal adenocarcinoma (EAC) and the interobserver agreement. DESIGN: Prospective tandem study of eligible patients. SETTING: Single, academic tertiary care center. PATIENTS: Forty-two patients with a history of confirmed BE were prospectively enrolled. INTERVENTIONS: The BE segment was examined under high-definition white-light endoscopy, and the presence of visible lesions was recorded. Subsequently, AFI and magnification NBI were performed in tandem on areas of the BE segment away from visible lesions; images obtained by these 2 systems were graded according to the color of reflected light and surface patterns, respectively. Biopsy specimens were obtained at the end of the procedure. MAIN OUTCOME MEASUREMENTS: The sensitivity, specificity, positive predictive value, and negative predictive value (NPV) of the AFI and NBI patterns for the detection of HGD/EAC and interobserver agreement. RESULTS: Of the 42 patients enrolled, 14 (33%) had HGD/EAC. On patient-based analysis, AFI alone had a sensitivity, specificity, and NPV of 50%, 61%, and 71%, respectively, and the overall accuracy for the detection of HGD/EAC patients was 57%. By using magnification NBI in tandem fashion, the sensitivity and NPV improved to 71% and 76%, respectively, with a decrease in specificity to 46% and in overall accuracy to 55%. The 2 techniques had moderate interobserver agreement for both the patterns and prediction of histology. LIMITATIONS: Uncontrolled study performed at an academic center by expert endoscopists in a high-risk population. CONCLUSIONS: By using a multimodality endoscope, both AFI and magnification NBI had limited clinical accuracy and moderate overall interobserver agreement. AFI does not appear to be useful as a broad-based technique for the detection of neoplasia in patients with BE.	esophagus
Preoperative cetuximab, irinotecan, cisplatin, and radiation therapy for patients with locally advanced esophageal cancer.	PURPOSE: To determine the efficacy and toxicity of weekly neoadjuvant cetuximab combined with irinotecan, cisplatin, and radiation therapy in patients with locally advanced esophageal or gastroesophageal junction cancer. METHODS AND MATERIALS: Patients with stage IIA-IVA esophageal or gastroesophageal junction cancer were enrolled in a Simon's two-stage phase II study. Patients received weekly cetuximab on weeks 0-8 and irinotecan and cisplatin on weeks 1, 2, 4, and 5, with concurrent radiotherapy (50.4 Gy on weeks 1-6), followed by surgical resection. RESULTS: In the first stage, 17 patients were enrolled, 16 of whom had adenocarcinoma. Because of a low pathologic complete response (pCR) rate in this cohort, the trial was discontinued for patients with adenocarcinoma but squamous cell carcinoma patients continued to be enrolled; two additional patients were enrolled before the study was closed as a result of poor accrual. Of the 19 patients enrolled, 18 patients proceeded to surgery, and 16 patients underwent an R0 resection. Three patients (16%) had a pCR. The median progression-free survival interval was 10 months, and the median overall survival duration was 31 months. Severe neutropenia occurred in 47% of patients, and severe diarrhea occurred in 47% of patients. One patient died preoperatively from sepsis, and one patient died prior to hospital discharge following surgical resection. CONCLUSIONS: This schedule of cetuximab in combination with irinotecan, cisplatin, and radiation therapy was toxic and did not achieve a sufficient pCR rate in patients with localized esophageal adenocarcinoma to undergo further evaluation.	esophagus
Risk factors for esophageal adenocarcinoma after antireflux surgery.	OBJECTIVES: Gastroesophageal reflux is the main risk factor for esophageal adenocarcinoma, but there is no strong support for any cancer-protective effect after antireflux surgery. We hypothesized that recurrent reflux or high exposure to other established risk factors, that is, obesity and tobacco smoking, are overrepresented among patients who despite antireflux surgery develop esophageal adenocarcinoma. DESIGN: A population-based case-control study was nested within an antireflux surgery cohort from the Swedish Patient Register between 1965 and 2006. Cases were patients who developed esophageal adenocarcinoma more than 5 years after antireflux surgery, whereas randomly selected controls were matched to the cases regarding age, sex, and calendar year of the antireflux surgery. Study exposures among cases and controls were collected through review of medical records. Data on cancer were assessed through the Swedish Cancer Register. Odds ratios (ORs) with 95% confidence intervals (CIs) were calculated using multivariable conditional logistic regression, adjusted for recurrent reflux, body mass index (BMI), tobacco smoking, and type of antireflux surgery. RESULTS: From 14,102 patients in the total antireflux surgery cohort, 55 cases and 240 controls were included. Patients who developed esophageal adenocarcinoma were 3 times more likely to have recurrent reflux after their antireflux surgery, compared with those who had not (OR: 3.1, 95% CI: 1.5-6.3). There were no statistically significant differences in risk when comparing BMI of 30 kg/m or more with BMI of less than 25 kg/m (OR: 1.6, CI: 0.8-3.5), ever smokers with never smokers (OR: 1.4, 95% CI: 0.7-2.8), or total fundoplication with partial fundoplication (OR: 0.6, 95% CI: 0.3-1.3). CONCLUSIONS: Recurrence of reflux might explain the lack of protective effect of antireflux surgery regarding risk of developing esophageal adenocarcinoma.	esophagus