Prognostic factors in patients with hepatitis B virus-related hepatocellular carcinoma undergoing nucleoside analog antiviral therapy

PubMed Central

NISHIKAWA, HIROKI; NISHIJIMA, NORIHIRO; ARIMOTO, AKIRA; INUZUKA, TADASHI; KITA, RYUICHI; KIMURA, TORU; OSAKI, YUKIO

2013-01-01

In the present era of entecavir (ETV) use for chronic hepatitis B (CHB), the prognostic factors in hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) remain unclear. The aims of the present study were to investigate the prognostic factors in patients with HBV-related HCC treated with ETV who underwent curative therapy. A total of 74 HBV-related HCC patients treated with ETV who underwent curative therapy were analyzed. Predictive factors associated with overall survival (OS) and recurrence-free survival (RFS) were examined using univariate and multivariate analysis. Our study population included 49 males and 25 females with a median age of 62 years. The median observation period was 3.4 years (range, 0.2–11.5 years). The 1-, 3- and 5-year cumulative OS rates were 100, 89.8 and 89.8%, respectively. The corresponding RFS rates were 82.8, 52.1 and 25.6%, respectively. In this study, 73 patients (98.6%) achieved an HBV DNA level of <400 copies/ml during the follow-up period. No viral breakthrough hepatitis, as defined by 1 log increase from nadir, was observed during ETV therapy. According to multivariate analysis, only hepatitis B e antigen (HBeAg) positivity was significantly associated with OS [hazard ratio (HR), 0.058; 95% confidence interval (CI), 0.005–0.645; P=0.020)], whereas HCC stage (HR, 0.359; 95% CI, 0.150–0.859; P=0.021), HBeAg positivity (HR, 0.202; 95% CI, 0.088–0.463; P<0.001) and γ-glutamyl transpeptidase ≥50 IU/l (HR, 0.340; 95% CI, 0.152–0.760; P=0.009) were significant predictive factors linked to RFS. In conclusion, HBeAg positivity was significantly associated with OS and RFS in HBV-related HCC patients treated with ETV who underwent curative therapy. In such patients, close observation is required, even after curative therapy for HCC. PMID:24179497

Failure-to-rescue in patients undergoing surgery for esophageal or gastric cancer.

PubMed

Busweiler, L A; Henneman, D; Dikken, J L; Fiocco, M; van Berge Henegouwen, M I; Wijnhoven, B P; van Hillegersberg, R; Rosman, C; Wouters, M W; van Sandick, J W

2017-10-01

Complex surgical procedures such as esophagectomy and gastrectomy for cancer are associated with substantial morbidity and mortality. The purpose of this study was to evaluate trends in postoperative morbidity, mortality, and associated failure-to-rescue (FTR), in patients who underwent a potentially curative resection for esophageal or gastric cancer in the Netherlands, and to investigate differences between the two groups. All patients with esophageal or gastric cancer who underwent a potentially curative resection, registered in the Dutch Upper GI Cancer Audit (DUCA) between 2011 and 2014, were included. Primary outcomes were (major) postoperative complications, postoperative mortality and FTR. To investigate groups' effect on the outcomes of interest a mixed model was used. Overall, 2644 patients with esophageal cancer and 1584 patients with gastric cancer were included in this study. In patients with gastric cancer, postoperative mortality (7.7% in 2011 vs. 3.8% in 2014) and FTR (38% in 2011 and 19% in 2014) decreased significantly over the years. The adjusted risk of developing a major postoperative complication was lower (OR 0.54; 95% CI 0.42-0.70), but the risk of FTR was higher (OR 1.85; 95% CI 1.05-3.27) in patients with gastric cancer compared to patients with esophageal cancer. Once a postoperative complication occurred, patients with gastric cancer were more likely to die compared to patients with esophageal cancer. Underlying mechanisms like patient selection, and differences in structure and organization of care should be investigated. Next to morbidity and mortality, failure-to-rescue should be considered as an important outcome measure after esophagogastric cancer resections. Copyright © 2017 Elsevier Ltd, BASO ~ The Association for Cancer Surgery, and the European Society of Surgical Oncology. All rights reserved.

Total Pelvic Supralevator Exenteration with Ileo-Colic Orthotopic Neobladder for Locoregional Recurrence after Cervical Cancer - A Case Report.

PubMed

Bacalbaşa, Nicolae; Bălescu, Irina; Braşoveanu, Vladislav

2016-01-01

Pelvic exenteration is one of the most aggressive surgical interventions in gynaecologic surgical oncology, but, in the same time, is the only potentially curative treatment of locoregional recurrence after cervical cancer. Due to improvements in surgical technique and postoperative management, the overall survival increased signifficantly in the last decades. Trying to improve the quality of life, multiple models of reconstruction of urinary and digestive tract have been developed. In this report we present the case of a 51 years old female who underwent a total supralevator exenteration with ileo colic neobladder reconstruction with good oncologic and functional outcomes. Celsius.

Pre-S deletions of hepatitis B virus predict recurrence of hepatocellular carcinoma after curative resection

PubMed Central

Li-Shuai, Qu; Yu-Yan, Chen; Hai-Feng, Zhang; Jin-Xia, Liu; Cui-Hua, Lu

2017-01-01

Abstract The relationship between hepatitis B virus (HBV) and the prognosis of hepatocellular carcinoma (HCC) after surgery remains uncertain. A retrospective cohort study was performed to evaluate the impact of pre-S deletions, T1762/A1764, and A1896 mutations on prognosis of HCC after curative resection. A total of 113 patients with positive serum HBV DNA (>200 IU/mL) who had underwent curative resection of pathologically proven HCC were recruited to determine the risk factors affecting the prognosis. The median follow-up time was 36.5 months and recurrence was detected in 67 patients (59.3%). The cumulative recurrence rates and overall survival rates at 1-, 3-, and 5-year after curative resection were 18.0%, 49.7%, 70.3%, and 93.7%, 61.0%, 42.5%, respectively. Patients with pre-S deletions showed significantly higher recurrence rates compared with those with wild type infection (HR: 1.822, P = .018), but not related with a significantly poor survival (HR: 1.388, P = .235). Subgroup analysis indicated that the patients with type III deletion had significant higher tumor recurrence rates than other deletion types (HR: 2.211, 95% confidence intervals [CI]: 1.008–4.846, P = .048). Multivariate analysis revealed that pre-S deletion, tumor size >3 cm in diameter, and the presence of microvascular invasion were independent risk factors for tumor recurrence. HBV pre-S deletions were found to be clustered primarily in the 5′ end of pre-S2 region and were more often found between amino acids 120 and 142 of the pre-S2 domain. The domains most frequently potentially involved were the transactivator domain in pre-S2 and polymerized human serum albumin binding site. Our cohort showed that pre-S deletions at the time of resection could predict tumor recurrence in HCC patients after curative resection. PMID:29069001

Favourable prognosis of cystadeno- over adenocarcinoma of the pancreas after curative resection.

PubMed

Ridder, G J; Maschek, H; Klempnauer, J

1996-06-01

This report details nine patients after curative surgical resection of histologically proven mucinous cystadenocarcinoma of the pancreas and compares the prognosis with ductal adenocarcinomas. Cystadenocarcinomas represented 2.1% (10/ 466) of a total of 466 patients who underwent surgical exploration and 5.5%, of all curatively resected carcinomas of the exocrine pancreas at Hanover Medical School from 1971 to 1994. Forty percent of adenocarcinomas and 90% of cystadenocarcinomas were resectable. A curative R0 resection was possible in all patients with cystadenocarcinoma and 85 % with adenocarcinoma. Six of the patients with cystadenocarcinoma were female and three were male. Their median age was 54 +/- 12 years (range: 44 to 81 years). Four cystic neoplasms were located in the head, one in the head and body, three in the tail, and one in the body and tail of the pancreas. There was no hospital mortality in this group. The prognosis after resection of cystadenocarcinomas was significantly better compared to ductal adenocarcinomas of the pancreas. The Kaplan-Meier survival was 89% vs 52% after 1 year, and 56% vs 13% at 5 years. Our results indicate the favourable prognosis of cystadeno- over ductal adenocarcinomas of the pancreas in a cohort of patients with curative tumour resection.

Controlling Nutritional Status (CONUT) score is a prognostic marker for gastric cancer patients after curative resection.

PubMed

Kuroda, Daisuke; Sawayama, Hiroshi; Kurashige, Junji; Iwatsuki, Masaaki; Eto, Tsugio; Tokunaga, Ryuma; Kitano, Yuki; Yamamura, Kensuke; Ouchi, Mayuko; Nakamura, Kenichi; Baba, Yoshifumi; Sakamoto, Yasuo; Yamashita, Yoichi; Yoshida, Naoya; Chikamoto, Akira; Baba, Hideo

2018-03-01

Controlling Nutritional Status (CONUT), as calculated from serum albumin, total cholesterol concentration, and total lymphocyte count, was previously shown to be useful for nutritional assessment. The current study investigated the potential use of CONUT as a prognostic marker in gastric cancer patients after curative resection. Preoperative CONUT was retrospectively calculated in 416 gastric cancer patients who underwent curative resection at Kumamoto University Hospital from 2005 to 2014. The patients were divided into two groups: CONUT-high (≥4) and CONUT-low (≤3), according to time-dependent receiver operating characteristic (ROC) analysis. The associations of CONUT with clinicopathological factors and survival were evaluated. CONUT-high patients were significantly older (p < 0.001) and had a lower body mass index (p = 0.019), deeper invasion (p < 0.001), higher serum carcinoembryonic antigen (p = 0.037), and higher serum carbohydrate antigen 19-9 (p = 0.007) compared with CONUT-low patients. CONUT-high patients had significantly poorer overall survival (OS) compared with CONUT-low patients according to univariate and multivariate analyses (hazard ratio: 5.09, 95% confidence interval 3.12-8.30, p < 0.001). In time-dependent ROC analysis, CONUT had a higher area under the ROC curve (AUC) for the prediction of 5-year OS than the neutrophil lymphocyte ratio, the Modified Glasgow Prognostic Score, or pStage. When the time-dependent AUC curve was used to predict OS, CONUT tended to maintain its predictive accuracy for long-term survival at a significantly higher level for an extended period after surgery when compared with the other markers tested. CONUT is useful for not only estimating nutritional status but also for predicting long-term OS in gastric cancer patients after curative resection.

Morbidity of curative cancer surgery and suicide risk.

PubMed

Jayakrishnan, Thejus T; Sekigami, Yurie; Rajeev, Rahul; Gamblin, T Clark; Turaga, Kiran K

2017-11-01

Curative cancer operations lead to debility and loss of autonomy in a population vulnerable to suicide death. The extent to which operative intervention impacts suicide risk is not well studied. To examine the effects of morbidity of curative cancer surgeries and prognosis of disease on the risk of suicide in patients with solid tumors. Retrospective cohort study using Surveillance, Epidemiology, and End Results data from 2004 to 2011; multilevel systematic review. General US population. Participants were 482 781 patients diagnosed with malignant neoplasm between 2004 and 2011 who underwent curative cancer surgeries. Death by suicide or self-inflicted injury. Among 482 781 patients that underwent curative cancer surgery, 231 committed suicide (16.58/100 000 person-years [95% confidence interval, CI, 14.54-18.82]). Factors significantly associated with suicide risk included male sex (incidence rate [IR], 27.62; 95% CI, 23.82-31.86) and age >65 years (IR, 22.54; 95% CI, 18.84-26.76). When stratified by 30-day overall postoperative morbidity, a significantly higher incidence of suicide was found for high-morbidity surgeries (IR, 33.30; 95% CI, 26.50-41.33) vs moderate morbidity (IR, 24.27; 95% CI, 18.92-30.69) and low morbidity (IR, 9.81; 95% CI, 7.90-12.04). Unit increase in morbidity was significantly associated with death by suicide (odds ratio, 1.01; 95% CI, 1.00-1.03; P = .02) and decreased suicide-specific survival (hazards ratio, 1.02; 95% CI, 1.00-1.03, P = .01) in prognosis-adjusted models. In this sample of cancer patients in the Surveillance, Epidemiology, and End Results database, patients that undergo high-morbidity surgeries appear most vulnerable to death by suicide. The identification of this high-risk cohort should motivate health care providers and particularly surgeons to adopt screening measures during the postoperative follow-up period for these patients. Copyright © 2016 John Wiley & Sons, Ltd.

[Results of surgical treatment in ampullary and pancreatic carcinoma and its prognostic parameters after R0-resection].

PubMed

Ridwelski, K; Meyer, F; Schmidt, U; Lippert, H

2005-08-01

Resection is currently the only established reasonable therapeutic option with curative potential in pancreatic and ampullary carcinoma. The aim of the study was i) to analyze value and results of surgical therapy and ii) to detect the prognostic parameters, which determine significantly higher survival rates. Two-hundred-twenty patients with pancreatic and ampullary carcinoma (mean age, 61.4 years; 104 females/116 males) underwent surgery. Histologic investigation revealed 19 carcinomas of the papilla of Vater and 201 ductal pancreatic carcinomas. In 126 patients, stage IV a or b tumors were found, in addition, stage I (n =26), II (n = 17) and III (n = 51). Survival-rate was determined according to the method by Kaplan/Meier. Survival was compared using log-rank test. Association of several or multiple parameters with survival was tested using Cox model. Hundred-ten patients underwent tumor resection with primary curative intention (50 %): 96 resections of the pancreatic head, 2 total pancreatectomies and 12 left resections of the pancreas. R0-resection was achieved in 94 patients (42.7 %), whereas intervention was classified R1 in 10 and R2 in 6 cases. In addition, 60 palliative interventions (28 gastroenterostomies, 17 biliodigestive anastomoses, 15 anastomoses at both sites) and 50 explorative laparotomies were performed. In 42.3 % of patients, postoperative complications were found, but only 12/220 individuals died (overall letality, 5.4 %). Postoperative letality of curative pancreatic resections was 3.6 % (palliative intervention, 6.7 %; explorative laparotomy, 8.8 %). Five-year survival-rate of carcinoma of the papilla of Vater and pancreatic carcinoma was 73.3 % and 16.2 %, respectively (median survival time was 66.0 and 14.0 months, respectively). Taken together all other interventions, median survival time ranged between 4.0 (palliative intervention) to 10.0 months (R1-resection). No patient survived 5 years. Therefore, the most relevant prognostic factor was R0-resection. In addition, prognosis after successful R0-resection is determined significantly by tumor site, stage of the tumor (according to UICC), T- and N-category. Resection of pancreatic and ampullary carcinoma according to oncological criteria with tumor-free margins can be considered a treatment option with curative intention and potential. Despite relative high postoperative morbidity, only a low mortality rate was observed. The 5-year survival-rate of 16.2 % in ductal pancreatic carcinoma underlines the demand for the development of effective multimodal therapeutic concepts. Interventions with primary palliative intention or resections with microscopically or macroscopically detectable tumor residual in situ lead to no significant or only marginal prolongation of survival time. Such interventions in patients with pancreatic carcinoma are no reasonable treatment alternative. They are of value only for treatment of tumor-associated complications and problems.

Lymph nodes ratio based nomogram predicts survival of resectable gastric cancer regardless of the number of examined lymph nodes.

PubMed

Chen, Shangxiang; Rao, Huamin; Liu, Jianjun; Geng, Qirong; Guo, Jing; Kong, Pengfei; Li, Shun; Liu, Xuechao; Sun, Xiaowei; Zhan, Youqing; Xu, Dazhi

2017-07-11

To develop a nomogram to predict the prognosis of gastric cancer patients on the basis of metastatic lymph nodes ratio (mLNR), especially in the patients with total number of examined lymph nodes (TLN) less than 15. The nomogram was constructed based on a retrospective database that included 2,205 patients underwent curative resection in Cancer Center, Sun Yat-sen University (SYSUCC). Resectable gastric cancer (RGC) patients underwent curative resection before December 31, 2008 were assigned as the training set (n=1,470) and those between January 1, 2009 and December 31, 2012 were selected as the internal validation set (n=735). Additional external validations were also performed separately by an independent data set (n=602) from Jiangxi Provincial Cancer Hospital (JXCH) in Jiangxi, China and a data set (n=3,317) from the Surveillance, Epidemiology, and End Results (SEER) database. The Independent risk factors were identified by Multivariate Cox Regression. In the SYSUCC set, TNM (Tumor-node-metastasis) and TRM-based (Tumor-Positive Nodes Ratio-Metastasis) nomograms were constructed respectively. The TNM-based nomogram showed better discrimination than the AJCC-TNM staging system (C-index: 0.73 versus 0.69, p<0.01). When the mLNR was included in the nomogram, the C-index increased to 0.76. Furthermore, the C-index in the TRM-based nomogram was similar between TLN ≥16 (C-index: 0.77) and TLN ≤15 (C-index: 0.75). The discrimination was further ascertained by internal and external validations. We developed and validated a novel TRM-based nomogram that provided more accurate prediction of survival for gastric cancer patients who underwent curative resection, regardless of the number of examined lymph nodes.

FIB-4 Index is a Predictor of Background Liver Fibrosis and Long-Term Outcomes After Curative Resection of Hepatocellular Carcinoma.

PubMed

Okamura, Yukiyasu; Ashida, Ryo; Yamamoto, Yusuke; Ito, Takaaki; Sugiura, Teiichi; Uesaka, Katsuhiko

2016-08-01

The FIB-4 index is a simple formula for predicting the degree of liver fibrosis. This study aimed to examine the relationship between the preoperative FIB-4 index and liver fibrosis in non-tumor regions of surgical specimens and to investigate whether the FIB-4 index is a useful predictor for long-term outcomes experienced by hepatocellular carcinoma (HCC) patients after curative resection. This study retrospectively analyzed 493 HCC patients treated with curative resection. The utility of the FIB-4 index as a predictor of advanced liver fibrosis (F3 or F4) was assessed. The cutoff value for the FIB-4 index was determined using a receiver operating characteristic curve analysis, and the impact of the FIB-4 index on overall and recurrence-free survival after surgery was evaluated. Advanced liver fibrosis was found in 236 patients (47.9 %). The FIB-4 index was significantly higher for the patients with advanced liver fibrosis than for those without this condition (P < 0.001). An FIB-4 index of 2.87 was the optimal cutoff point for predicting advanced liver fibrosis. The multivariate analysis showed the FIB-4 index to be an independent prognostic factor for recurrence-free and overall survival after curative resection only for patients who underwent hepatectomy as initial treatment (hazard ratio, 1.47 and 1.59; 95 % confidence interval, 1.12-1.93 and 1.09-2.32; P = 0.006 and 0.016, respectively). The study showed the FIB4-index to be a predictor of background liver fibrosis and long-term outcomes for HCC patients who underwent hepatectomy as their initial treatment.

Use of an autologous liver round ligament flap zeros postoperative bile leak after curative resection of hilar cholangiocarcinoma.

PubMed

Sun, Da-Xin; Tan, Xiao-Dong; Gao, Feng; Xu, Jin; Cui, Dong-Xu; Dai, Xian-Wei

2015-01-01

Postoperative bile leak is a major surgical morbidity after curative resection with hepaticojejunostomy for hilar cholangiocarcinoma, especially in Bismuth-Corlette types III and IV. This retrospective study assessed the effectiveness and safety of an autologous hepatic round ligament flap (AHRLF) for reducing bile leak after hilar hepaticojejunostomy. Nine type III and IV hilar cholangiocarcinoma patients were consecutively hospitalized for elective perihilar partial hepatectomy with hilar hepaticojejunostomy using an AHRLF between October 2009 and September 2013. The AHRLF was harvested to reinforce the perihilar hepaticojejunostomy. Main outcome measures included operative time, blood loss, postoperative recovery times, morbidity, bile leak, R0 resection rate, and overall survival. All patients underwent uneventful R0 resection with hilar hepaticojejunostomy. No patient experienced postoperative bile leak. The AHRLF was associated with lack of bile leak after curative perihilar hepatectomy with hepaticojejunostomy for hilar cholangiocarcinoma, without compromising oncologic safety, and is recommended in selected patients.

[Diagnostic and curative bronchoscopy for purulent-destructive pulmonary diseases].

PubMed

Pinchuk, T P; Yasnogorodsky, O O; Guryanova, Yu V; Taldykin, M V; Kachikin, A S; Catane, Yu A

To assess an efficacy of diagnostic and curative bronchoscopy in patients with purulent-destructive pulmonary diseases. Diagnosis and treatment of 34 patients with purulent-destructive pulmonary diseases including small-focal destruction (14) and lung abscesses (19) were analyzed. 33 patients underwent diagnostic fibrobronchoscopy (FBS) with brush and transbronchial biopsy. Curative endoscopy included bronchial tree sanation, peribronchial administration of antibiotics (5) and transbronchial drainage of abscess (14). Atrophic bronchitis and cicatricial deformity of the 2-3rd segmental bronchi were revealed in 81.8% and 15.2% respectively. Transbronchial biopsy confirmed malignant neoplasms (15.2%) and pulmonary tuberculosis (6.1%). Peribronchial administration of amikacin in patients with small-focal pulmonary destruction and transbronchial drainage of abscesses accelerated pulmonary tissue repair and complete recovery. Transbronchial biopsy in patients with destructive pulmonary diseases verifies pathological process and excludes malignant and specific pulmonary damage. Complex use of endoscopic methods is associated with positive clinical result in all patients with pulmonary destruction.

Preoperative serum C-reactive protein levels and post-operative lymph node ratio are important predictors of survival after pancreaticoduodenectomy for pancreatic ductal adenocarcinoma.

PubMed

Sanjay, Pandanaboyana; de Figueiredo, Rodrigo S; Leaver, Heather; Ogston, Simon; Kulli, Christoph; Polignano, Francesco M; Tait, Iain S

2012-03-10

There is paucity of data on the prognostic value of pre-operative inflammatory response and post-operative lymph node ratio on patient survival after pancreatic-head resection for pancreatic ductal adenocarcinoma. To evaluate the role of the preoperative inflammatory response and postoperative pathology criteria to identify predictive and/or prognostic variables for pancreatic ductal adenocarcinoma. All patients who underwent pancreaticoduodenectomy for pancreatic ductal adenocarcinoma between 2002 and 2008 were reviewed retrospectively. The following impacts on patient survival were assessed: i) preoperative serum CRP levels, white cell count, neutrophil count, neutrophil/lymphocyte ratio, lymphocyte count, platelet/lymphocyte ratio; and ii) post-operative pathology criteria including lymph node status and lymph node ratio. Fifty-one patients underwent potentially curative resection for pancreatic ductal adenocarcinoma during the study period. An elevated preoperative CRP level (greater than 3 mg/L) was found to be a significant adverse prognostic factor (P=0.015) predicting a poor survival, whereas white cell count (P=0.278), neutrophil count (P=0.850), neutrophil/lymphocyte ratio (P=0.272), platelet/lymphocyte ratio (P=0.532) and lymphocyte count (P=0.721) were not significant prognosticators at univariate analysis. Presence of metastatic lymph nodes did not adversely affect survival (P=0.050), however a raised lymph node ratio predicted poor survival at univariate analysis (P<0.001). The preoperative serum CRP level retained significance at multivariate analysis (P=0.011), together with lymph node ratio (P<0.001) and tumour size (greater than 2 cm; P=0.008). A pre-operative elevated serum CRP level and raised post-operative lymph node ratio represent significant independent prognostic factors that predict poor prognosis in patients undergoing curative resection for pancreatic ductal adenocarcinoma. There is potential for future neo-adjuvant and adjuvant treatment strategies in pancreatic cancer to be tailored based on preoperative and postoperative factors that predict a poor survival.

Proton Beam Reirradiation for Recurrent Head and Neck Cancer: Multi-institutional Report on Feasibility and Early Outcomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Romesser, Paul B.; Cahlon, Oren; ProCure Proton Therapy Center, Somerset, New Jersey

Purpose: Reirradiation therapy (re-RT) is the only potentially curative treatment option for patients with locally recurrent head and neck cancer (HNC). Given the significant morbidity with head and neck re-RT, interest in proton beam radiation therapy (PBRT) has increased. We report the first multi-institutional clinical experience using curative-intent PBRT for re-RT in recurrent HNC. Methods and Materials: A retrospective analysis of ongoing prospective data registries from 2 hybrid community practice and academic proton centers was conducted. Patients with recurrent HNC who underwent at least 1 prior course of definitive-intent external beam radiation therapy (RT) were included. Acute and late toxicitiesmore » were assessed with the National Cancer Institute Common Terminology Criteria for Adverse Events version 4.0 and the Radiation Therapy Oncology Group late radiation morbidity scoring system, respectively. The cumulative incidence of locoregional failure was calculated with death as a competing risk. The actuarial 12-month freedom–from–distant metastasis and overall survival rates were calculated with the Kaplan-Meier method. Results: Ninety-two consecutive patients were treated with curative-intent re-RT with PBRT between 2011 and 2014. Median follow-up among surviving patients was 13.3 months and among all patients was 10.4 months. The median time between last RT and PBRT was 34.4 months. There were 76 patients with 1 prior RT course and 16 with 2 or more courses. The median PBRT dose was 60.6 Gy (relative biological effectiveness, [RBE]). Eighty-five percent of patients underwent prior HNC RT for an oropharynx primary, and 39% underwent salvage surgery before re-RT. The cumulative incidence of locoregional failure at 12 months, with death as a competing risk, was 25.1%. The actuarial 12-month freedom–from–distant metastasis and overall survival rates were 84.0% and 65.2%, respectively. Acute toxicities of grade 3 or greater included mucositis (9.9%), dysphagia (9.1%), esophagitis (9.1%), and dermatitis (3.3%). There was 1 death during PBRT due to disease progression. Grade 3 or greater late skin and dysphagia toxicities were noted in 6 patients (8.7%) and 4 patients (7.1%), respectively. Two patients had grade 5 toxicity due to treatment-related bleeding. Conclusions: Proton beam re-RT of the head and neck can provide effective tumor control with acceptable acute and late toxicity profiles likely because of the decreased dose to the surrounding normal, albeit previously irradiated, tissue, although longer follow-up is needed to confirm these findings.« less

Antioxidant Effect of Sepia Ink Extract on Extrahepatic Cholestasis Induced by Bile Duct Ligation in Rats.

PubMed

Saleh, Hanan; Soliman, Amel M; Mohamed, Ayman S; Marie, Mohamed-Assem S

2015-08-01

The aim of our study was to assess the complications of hepatic fibrosis associated with bile duct ligation and the potential curative role of sepia ink extract in hepatic damage induced by bile duct ligation. Rattus norvegicus rats were divided into 3 groups: Sham-operated group, model rats that underwent common bile duct ligation (BDL), and BDL rats treated orally with sepia ink extract (200 mg/kg body weight) for 7, 14, and 28 d after BDL. There was a significant reduction in hepatic enzymes, ALP, GGT, bilirubin levels, and oxidative stress in the BDL group after treatment with sepia ink extract. Collagen deposition reduced after sepia ink extract treatment as compared to BDL groups, suggesting that the liver was repaired. Histopathological examination of liver treated with sepia ink extract showed moderate degeneration in the hepatic architecture and mild degeneration in hepatocytes as compared to BDL groups. Sepia ink extract provides a curative effect and an antioxidant capacity on BDL rats and could ameliorate the complications of liver cholestasis. Copyright © 2015 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

Survival Outcomes and Patterns of Recurrence in Patients with Stage III or IV Oropharyngeal Cancer Treated with Primary Surgery or Radiotherapy.

PubMed

Debenham, Brock J; Banerjee, Robyn; Warkentin, Heather; Ghosh, Sunita; Scrimger, Rufus; Jha, Naresh; Parliament, Matthew

2016-07-26

To compare and contrast the patterns of failure in patients with locally advanced squamous cell oropharyngeal cancers undergoing curative-intent treatment with primary surgery or radiotherapy +/- chemotherapy. Two hundred and thirty-three patients with stage III or IV oropharyngeal squamous cell carcinoma who underwent curative-intent treatment from 2006-2012, were reviewed. The median length of follow-up for patients still alive at the time of analysis was 4.4 years. Data was collected retrospectively from a chart review. One hundred and thirty-nine patients underwent primary surgery +/- adjuvant therapy, and 94 patients underwent primary radiotherapy +/- chemotherapy (CRT). Demographics were similar between the two groups, except primary radiotherapy patients had a higher age-adjusted Charleston co-morbidity score (CCI). Twenty-nine patients from the surgery group recurred; 15 failed distantly only, seven failed locoregionally, and seven failed both distantly and locoregionally. Twelve patients recurred who underwent chemoradiotherapy; ten distantly alone, and two locoregionally. One patient who underwent radiotherapy (RT) alone failed distantly. Two and five-year recurrence-free survival rates for patients undergoing primary RT were 86.6% and 84.9% respectively. Two and five-year recurrence-free survival rates for primary surgery was 80.9% and 76.3% respectively (p=0.21). There was no significant difference in either treatment when they were stratified by p16 status or smoking status. Our analysis does not show any difference in outcomes for patients treated with primary surgery or radiotherapy. Although the primary pattern of failure in both groups was distant metastatic disease, some local failures may be preventable with careful delineation of target volumes, especially near the base of skull region.

The Importance of Contamination Knowledge in Curation - Insights into Mars Sample Return

NASA Technical Reports Server (NTRS)

Harrington, A. D.; Calaway, M. J.; Regberg, A. B.; Mitchell, J. L.; Fries, M. D.; Zeigler, R. A.; McCubbin, F. M.

2018-01-01

The Astromaterials Acquisition and Curation Office at NASA Johnson Space Center (JSC), in Houston, TX (henceforth Curation Office) manages the curation of extraterrestrial samples returned by NASA missions and shared collections from international partners, preserving their integrity for future scientific study while providing the samples to the international community in a fair and unbiased way. The Curation Office also curates flight and non-flight reference materials and other materials from spacecraft assembly (e.g., lubricants, paints and gases) of sample return missions that would have the potential to cross-contaminate a present or future NASA astromaterials collection.

Prognostic impacts of postoperative complications in patients with intrahepatic cholangiocarcinoma after curative operations.

PubMed

Miyata, Tatsunori; Yamashita, Yo-Ichi; Yamao, Takanobu; Umezaki, Naoki; Tsukamoto, Masayo; Kitano, Yuki; Yamamura, Kensuke; Arima, Kota; Kaida, Takayoshi; Nakagawa, Shigeki; Imai, Katsunori; Hashimoto, Daisuke; Chikamoto, Akira; Ishiko, Takatoshi; Baba, Hideo

2017-06-01

The postoperative complication is one of an indicator of poor prognosis in patients with several gastroenterological cancers after curative operations. We, herein, examined prognostic impacts of postoperative complications in patients with intrahepatic cholangiocarcinoma after curative operations. We retrospectively analyzed 60 patients with intrahepatic cholangiocarcinoma who underwent primary curative operations from June 2002 to February 2016. Prognostic impacts of postoperative complications were analyzed using log-rank test and Cox proportional hazard model. Postoperative complications (Clavien-Dindo classification grade 3 or more) occurred in 13 patients (21.7%). Overall survival of patients without postoperative complications was significantly better than that of patients with postoperative complications (p = 0.025). Postoperative complications are independent prognostic factor of overall survival (hazard ratio 3.02; p = 0.030). In addition, bile duct resection and reconstruction (Odds ratio 59.1; p = 0.002) and hepatitis C virus antibody positive (Odds ratio 7.14; p= 0.022), and lymph node dissection (Odds ratio 6.28; p = 0.040) were independent predictors of postoperative complications. Postoperative complications may be an independent predictor of poorer survival in patients with intrahepatic cholangiocarcinoma after curative operations. Lymph node dissection and bile duct resection and reconstruction were risk factors for postoperative complications, therefore we should pay attentions to perform lymph node dissections, bile duct resection and reconstruction in patients with intrahepatic cholangiocarcinoma.

Metavir and FIB-4 scores are associated with patient prognosis after curative hepatectomy in hepatitis B virus-related hepatocellular carcinoma: a retrospective cohort study at two centers in China.

PubMed

Liao, Rui; Fu, Yi-Peng; Wang, Ting; Deng, Zhi-Gang; Li, De-Wei; Fan, Jia; Zhou, Jian; Feng, Gen-Sheng; Qiu, Shuang-Jian; Du, Cheng-You

2017-01-03

Although Metavir and Fibrosis-4 (FIB-4) scores are typically used to assess the severity of liver fibrosis, the relationship between these scores and patient outcome in hepatocellular carcinoma (HCC) is unclear. The aim of this study was to evaluate the prognostic value of the severity of hepatic fibrosis in HBV-related HCC patients after curative resection. We examined the prognostic roles of the Metavir and preoperative FIB-4 scores in 432 HBV-HCC patients who underwent curative resection at two different medical centers located in western (Chongqing) and eastern (Shanghai) China. In the testing set (n = 108), the Metavir, FIB-4, and combined Metavir/FIB-4 scores were predictive of overall survival (OS) and recurrence-free survival (RFS). Additionally, they were associated with several clinicopathologic variables. In the validation set (n = 324), the Metavir, FIB-4, and combined Metavir/FIB-4 scores were associated with poor prognosis in HCC patients after curative resection. Importantly, in the negative alpha-fetoprotein subgroup (≤ 20 ng/mL), the FIB-4 index (I vs. II) could discriminate between patient outcomes (high or low OS and RFS). Thus Metavir, preoperative FIB-4, and combined Metavir/FIB-4 scores are prognostic markers in HBV-HCC patients after curative hepatectomy.

Metavir and FIB-4 scores are associated with patient prognosis after curative hepatectomy in hepatitis B virus-related hepatocellular carcinoma: a retrospective cohort study at two centers in China

PubMed Central

Li, De-Wei; Fan, Jia; Zhou, Jian; Feng, Gen-Sheng; Qiu, Shuang-Jian; Du, Cheng-You

2017-01-01

Although Metavir and Fibrosis-4 (FIB-4) scores are typically used to assess the severity of liver fibrosis, the relationship between these scores and patient outcome in hepatocellular carcinoma (HCC) is unclear. The aim of this study was to evaluate the prognostic value of the severity of hepatic fibrosis in HBV-related HCC patients after curative resection. We examined the prognostic roles of the Metavir and preoperative FIB-4 scores in 432 HBV-HCC patients who underwent curative resection at two different medical centers located in western (Chongqing) and eastern (Shanghai) China. In the testing set (n = 108), the Metavir, FIB-4, and combined Metavir/FIB-4 scores were predictive of overall survival (OS) and recurrence-free survival (RFS). Additionally, they were associated with several clinicopathologic variables. In the validation set (n = 324), the Metavir, FIB-4, and combined Metavir/FIB-4 scores were associated with poor prognosis in HCC patients after curative resection. Importantly, in the negative alpha-fetoprotein subgroup (≤ 20 ng/mL), the FIB-4 index (I vs. II) could discriminate between patient outcomes (high or low OS and RFS). Thus Metavir, preoperative FIB-4, and combined Metavir/FIB-4 scores are prognostic markers in HBV-HCC patients after curative hepatectomy. PMID:27662665

Sympathicotomy for Palmar Hyperhidrosis: The Association between Intraoperative Palm Temperature Change and the Curative Effect

PubMed Central

Liu, Yanguo; Li, Hao; Zheng, Xia; Li, Xiao; Li, Jianfeng; Jiang, Guanchao

2015-01-01

Purpose: To investigate the association between intraoperative palm temperature change and the curative effect of sympathicotomy. Methods: 49 patients with palmar hyperhidrosis were treated with bilateral endoscopic sympathicotomy. Ipsilateral palm temperature was monitored before and at 3–5 min increments after the sympathetic trunk was transected. The maximum temperature elevation (Tmax) was calculated and used to evaluate the effect on postoperative cure rates. Results: Forty-nine patients underwent 98 sympathicotomies. There were 77 T4 sympathicotomies, 15 T4 + T5 sympathicotomies, and six T3 sympathicotomies due to pleural adhesions or neurovascular proximity. The Tmax was ≤1°C in 49 (50.0%), 1–1.5°C in 17 (17.3%), and >1.5°C in 32 (32.7%) palms. Ninety-two palms of 46 patients were followed with complete efficacy, and three patients were lost to follow up. Cure was achieved in 86 palms (93.4%). Of the 71 palms which underwent T4 sympathicotomy, cure was achieved in 67 palms (94.3%). In those palms which did not achieve cure, the Tmax was less than 1°C in each case, while in palms with a Tmax ≤1°C, 32 of 36 (88.9%) were cured. Conclusion: There is an association between intraoperative palmar temperature change and curative effect. However, palmar temperature change cannot be used to predict cure or guide surgical approach. PMID:26041256

A laboratory marker, FIB-4 index, as a predictor for long-term outcomes of hepatocellular carcinoma patients after curative hepatic resection.

PubMed

Toyoda, Hidenori; Kumada, Takashi; Tada, Toshifumi; Kaneoka, Yuji; Maeda, Atsuyuki

2015-04-01

Liver fibrosis is associated with the prognosis of patients with hepatocellular carcinoma (HCC) after treatment. The laboratory marker for liver fibrosis, the FIB-4 index, is reportedly correlated with the degree of liver fibrosis. We evaluated the predictive value of FIB-4 index on the recurrence and survival of HCC patients who underwent curative hepatectomy. A total of 431 consecutive patients who underwent hepatectomy for primary, nonrecurrent HCC were analyzed. The FIB-4 index was calculated from the patient's age, serum alanine aminotransferase and aspartate aminotransferase levels, and platelet count at the time of HCC diagnosis. Postoperative recurrence and survival rates were compared according to tumor characteristics, tumor markers, Child-Pugh class, and the FIB-4 index. The pretreatment FIB-4 index was associated with recurrence and survival rates, independent of HCC progression or tumor marker levels in a multivariate analysis. Recurrence rates after hepatectomy were higher in patients with a FIB-4 index >3.25 versus ≤3.25 (5-year recurrence rates 69.6% vs 54.8%; P = .0049). Survival was also worse in patients with a FIB-4 index >3.25 than those with a FIB-4 index ≤3.25 (5-year survival rates 67.1% vs 72.2%; P = .0030). The FIB-4 index is a predictive marker for long-term outcomes in patients with HCC treated with curative hepatic resection. Copyright © 2015 Elsevier Inc. All rights reserved.

[Chonic diarrhea and malabsorption due to common variable immunodeficiency, gastrectomy and giardiasis infection: a difficult nutritional management].

PubMed

Domínguez-López, M E; González-molero, I; Ramírez-Plaza, C P; Soriguer, F; Olveira, G

2011-01-01

Gastric cancer is a frequent cause of cancer-related mortality in the world. Surgery is the only potentially curative therapy, although the adverse effects of surgery are common and considerable. Common variable immunodeficiency is in many cases cause of gastrointestinal system problems such as chronic diarrhea caused by infestation with giardia lamblia, nodular lymphoid hiperplasia ad loss of villi leading frequently to malapsortion and malnutrition. Nutritional deficiencies due to malapsorption (postgastrectomy and secondary to loss of villi, giardiasis and common variable inmunodeficiency) are common. We present the case of a patient with gastric cancer who underwent a gastrectomy with common variable hipogammaglobulinemia and chronic infestation by giardia lamblia, with serious diarrhea resistant to treatment and malabsorption.

[Conversion Therapy of Initially Unresectable Rectal Cancer with Perforation via FOLFOX4 Chemotherapy].

PubMed

Yamada, Chizu; Ishikawa, Fumihiko; Nitta, Hiroshi; Fujita, Yoshihisa; Omoto, Hideyuki; Kamata, Shigeyuki; Ito, Hiroshi

2015-11-01

We describe a case of perforated rectal cancer that became curatively resectable after FOLFOX4 chemotherapy. An 81- year-old woman was transferred to our hospital with a diagnosis of bowel perforation. She underwent emergency transverse colostomy, peritoneal lavage, and the insertion of indwelling drainage tubes, because the perforated rectal cancer was considered unresectable. After recuperation, she received chemotherapy consisting of FOLFOX4 and bevacizumab. Owing to a good response to the treatment after 4 months, rectal resection was achieved curatively. Wound dehiscence occurred as a postoperative complication. The patient chose not to receive adjuvant chemotherapy. Currently, she has been alive for more than 1 year 3 months after resection without recurrence.

Endoscopic submucosal dissection for early esophageal neoplasms using the stag beetle knife

PubMed Central

Kuwai, Toshio; Yamaguchi, Toshiki; Imagawa, Hiroki; Miura, Ryoichi; Sumida, Yuki; Takasago, Takeshi; Miyasako, Yuki; Nishimura, Tomoyuki; Iio, Sumio; Yamaguchi, Atsushi; Kouno, Hirotaka; Kohno, Hiroshi; Ishaq, Sauid

2018-01-01

AIM To determine short- and long-term outcomes of endoscopic submucosal dissection (ESD) using the stag beetle (SB) knife, a scissor-shaped device. METHODS Seventy consecutive patients with 96 early esophageal neoplasms, who underwent ESD using a SB knife at Kure Medical Center and Chugoku Cancer Center, Japan, between April 2010 and August 2016, were retrospectively evaluated. Clinicopathological characteristics of lesions and procedural adverse events were assessed. Therapeutic success was evaluated on the basis of en bloc, histologically complete, and curative or non-curative resection rates. Overall and tumor-specific survival, local or distant recurrence, and 3- and 5-year cumulative overall metachronous cancer rates were also assessed. RESULTS Eligible patients had dysplasia/intraepithelial neoplasia (22%) or early cancers (squamous cell carcinoma, 78%). The median procedural time was 60 min and on average, the lesions measured 24 mm in diameter, yielding 33-mm tissue defects. The en bloc resection rate was 100%, with 95% and 81% of dissections deemed histologically complete and curative, respectively. All procedures were completed without accidental incisions/perforations or delayed bleeding. During follow-up (mean, 35 ± 23 mo), no local recurrences or metastases were observed. The 3- and 5-year survival rates were 83% and 70%, respectively, with corresponding rates of 85% and 75% for curative resections and 74% and 49% for non-curative resections. The 3- and 5-year cumulative rates of metachronous cancer in the patients with curative resections were 14% and 26%, respectively. CONCLUSION ESD procedures using the SB knife are feasible, safe, and effective for treating early esophageal neoplasms, yielding favorable short- and long-term outcomes. PMID:29686470

Endoscopic submucosal dissection for early esophageal neoplasms using the stag beetle knife.

PubMed

Kuwai, Toshio; Yamaguchi, Toshiki; Imagawa, Hiroki; Miura, Ryoichi; Sumida, Yuki; Takasago, Takeshi; Miyasako, Yuki; Nishimura, Tomoyuki; Iio, Sumio; Yamaguchi, Atsushi; Kouno, Hirotaka; Kohno, Hiroshi; Ishaq, Sauid

2018-04-21

To determine short- and long-term outcomes of endoscopic submucosal dissection (ESD) using the stag beetle (SB) knife, a scissor-shaped device. Seventy consecutive patients with 96 early esophageal neoplasms, who underwent ESD using a SB knife at Kure Medical Center and Chugoku Cancer Center, Japan, between April 2010 and August 2016, were retrospectively evaluated. Clinicopathological characteristics of lesions and procedural adverse events were assessed. Therapeutic success was evaluated on the basis of en bloc , histologically complete, and curative or non-curative resection rates. Overall and tumor-specific survival, local or distant recurrence, and 3- and 5-year cumulative overall metachronous cancer rates were also assessed. Eligible patients had dysplasia/intraepithelial neoplasia (22%) or early cancers (squamous cell carcinoma, 78%). The median procedural time was 60 min and on average, the lesions measured 24 mm in diameter, yielding 33-mm tissue defects. The en bloc resection rate was 100%, with 95% and 81% of dissections deemed histologically complete and curative, respectively. All procedures were completed without accidental incisions/perforations or delayed bleeding. During follow-up (mean, 35 ± 23 mo), no local recurrences or metastases were observed. The 3- and 5-year survival rates were 83% and 70%, respectively, with corresponding rates of 85% and 75% for curative resections and 74% and 49% for non-curative resections. The 3- and 5-year cumulative rates of metachronous cancer in the patients with curative resections were 14% and 26%, respectively. ESD procedures using the SB knife are feasible, safe, and effective for treating early esophageal neoplasms, yielding favorable short- and long-term outcomes.

Use of an Autologous Liver Round Ligament Flap Zeros Postoperative Bile Leak after Curative Resection of Hilar Cholangiocarcinoma

PubMed Central

Sun, Da-Xin; Tan, Xiao-Dong; Gao, Feng; Xu, Jin; Cui, Dong-Xu; Dai, Xian-Wei

2015-01-01

Background Postoperative bile leak is a major surgical morbidity after curative resection with hepaticojejunostomy for hilar cholangiocarcinoma, especially in Bismuth-Corlette types III and IV. This retrospective study assessed the effectiveness and safety of an autologous hepatic round ligament flap (AHRLF) for reducing bile leak after hilar hepaticojejunostomy. Methods Nine type III and IV hilar cholangiocarcinoma patients were consecutively hospitalized for elective perihilar partial hepatectomy with hilar hepaticojejunostomy using an AHRLF between October 2009 and September 2013. The AHRLF was harvested to reinforce the perihilar hepaticojejunostomy. Main outcome measures included operative time, blood loss, postoperative recovery times, morbidity, bile leak, R0 resection rate, and overall survival. Results All patients underwent uneventful R0 resection with hilar hepaticojejunostomy. No patient experienced postoperative bile leak. Conclusions The AHRLF was associated with lack of bile leak after curative perihilar hepatectomy with hepaticojejunostomy for hilar cholangiocarcinoma, without compromising oncologic safety, and is recommended in selected patients. PMID:25938440

Abdominal Emergencies in Patients with Stage IV Melanoma: The Role of Surgery: A Single-centre Experience.

PubMed

Mantas, Dimitrios; Damaskos, Christos; Garmpis, Nikolaos; Dimitroulis, Dimitrios; Garmpi, Anna; Gogas, Helen

2018-06-01

Metastatic melanoma is an aggressive disease with poor prognosis. Melanoma can potentially involve any organ. In this article, we report on a single-centre experience in emergency surgery for M1c melanoma. Twenty-eight consecutive patients with M1c melanoma underwent surgical exploration due to abdominal emergencies. Pre-operative computed tomography confirmed the diagnosis and the location of the affected site. Pre-operative lactate dehydrogenase serum levels and post-operative histopathology findings were recorded. Intestinal obstruction was the most frequent intraoperative finding (75%). The ileum was most frequently affected (28.6%). Multifocal disease and extra-gastrointestinal tract metastases were present in 25% of cases each. Lactate dehydrogenase serum level was increased in 75% of the patients. Most patients underwent an enterectomy. Curative surgery for stage IV melanoma remains debatable, but surgery for patients presenting with abdominal emergencies appears to improve both survival rate and prognosis. Combined novel therapies and surgical resection is currently being studied with promising results. Copyright© 2018, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

Hospital of Diagnosis Influences the Probability of Receiving Curative Treatment for Esophageal Cancer.

PubMed

van Putten, Margreet; Koëter, Marijn; van Laarhoven, Hanneke W M; Lemmens, Valery E P P; Siersema, Peter D; Hulshof, Maarten C C M; Verhoeven, Rob H A; Nieuwenhuijzen, Grard A P

2018-02-01

The aim of this article was to study the influence of hospital of diagnosis on the probability of receiving curative treatment and its impact on survival among patients with esophageal cancer (EC). Although EC surgery is centralized in the Netherlands, the disease is often diagnosed in hospitals that do not perform this procedure. Patients with potentially curable esophageal or gastroesophageal junction tumors diagnosed between 2005 and 2013 who were potentially curable (cT1-3,X, any N, M0,X) were selected from the Netherlands Cancer Registry. Multilevel logistic regression was performed to examine the probability to undergo curative treatment (resection with or without neoadjuvant treatment, definitive chemoradiotherapy, or local tumor excision) according to hospital of diagnosis. Effects of variation in probability of undergoing curative treatment among these hospitals on survival were investigated by Cox regression. All 13,017 patients with potentially curable EC, diagnosed in 91 hospitals, were included. The proportion of patients receiving curative treatment ranged from 37% to 83% and from 45% to 86% in the periods 2005-2009 and 2010-2013, respectively, depending on hospital of diagnosis. After adjustment for patient- and hospital-related characteristics these proportions ranged from 41% to 77% and from 50% to 82%, respectively (both P < 0.001). Multivariable survival analyses showed that patients diagnosed in hospitals with a low probability of undergoing curative treatment had a worse overall survival (hazard ratio = 1.13, 95% confidence interval 1.06-1.20; hazard ratio = 1.15, 95% confidence interval 1.07-1.24). The variation in probability of undergoing potentially curative treatment for EC between hospitals of diagnosis and its impact on survival indicates that treatment decision making in EC may be improved.

Risk factors of early recurrence after curative hepatectomy in hepatocellular carcinoma.

PubMed

Hong, Young Mi; Cho, Mong; Yoon, Ki Tae; Chu, Chong Woo; Yang, Kwang Ho; Park, Yong Mok; Rhu, Je Ho

2017-10-01

Early recurrence is common after curative hepatectomy for hepatocellular carcinoma and is associated with poor prognosis. This study aimed to identify risk factors of early recurrence after curative hepatectomy in hepatocellular carcinoma. Overall, 63 patients who underwent curative hepatectomy for hepatocellular carcinoma were enrolled. Patients were divided into the early recurrence group, who developed recurrence within 12 months after hepatectomy (n = 10), and the non-early recurrence group (n = 53). Clinicopathological factors of early recurrence were retrospectively analyzed. Among the 63 patients, 10 (15.9%) patients experienced early recurrence. Univariate analysis showed tumor necrosis (p = 0.012), level of PIVKA-II (prothrombin induced by vitamin K absence or antagonist-II; p = 0.002), and microvascular invasion (p = 0.029) to be associated with early recurrence. By multivariate analysis, there were significant differences in high PIVKA-II (p < 0.001) and tumor necrosis (p = 0.012) in patients with early recurrence. The optimal cutoff values of PIVKA-II and tumor necrosis were 46 mAU/mL and 3% of total tumor volume, respectively. Patients with a high preoperative PIVKA-II level and extent of tumor necrosis, which are independent risk factors for early recurrence, should be actively treated and monitored closely after hepatectomy.

Curative Intent Treatment of Hepatocellular Carcinoma - 844 Cases Treated in a General Surgery and Liver Transplantation Center.

PubMed

Grigorie, Răzvan; Alexandrescu, Sorin; Smira, Gabriela; Ionescu, Mihnea; Hrehoreţ, Doina; Braşoveanu, Vladislav; Dima, Simona; Ciurea, Silviu; Boeţi, Patricia; Dudus, Ionut; Picu, Nausica; Zamfir, Radu; David, Leonard; Botea, Florin; Gheorghe, Liana; Tomescu, Dana; Lupescu, Ioana; Boroş, Mirela; Grasu, Mugur; Dumitru, Radu; Toma, Mihai; Croitoru, Adina; Herlea, Vlad; Pechianu, Cătălin; Năstase, Anca; Popescu, Irinel

2017-01-01

Background: The objective of this study is to assess the outcome of the patients treated for hepatocellular carcinoma (HCC) in a General Surgery and Liver Transplantation Center. Methods: This retrospective study includes 844 patients diagnosed with HCC and surgically treated with curative intent methods. Curative intent treatment is mainly based on surgery, consisting of liver resection (LR), liver transplantation (LT). Tumor ablation could become the choice of treatment in HCC cases not manageable for surgery (LT or LR). 518 patients underwent LR, 162 patients benefited from LT and in 164 patients radiofrequency ablation (RFA) was performed. 615 patients (73%) presented liver cirrhosis. Results: Mordidity rates of patient treated for HCC was 30% and mortality was 4,3% for the entire study population. Five year overall survival rate was 39 % with statistically significant differences between transplanted, resected, or ablated patients (p 0.05) with better results in case of LT followed by LR and RFA. Conclusions: In HCC patients without liver cirrhosis, liver resection is the treatment of choice. For early HCC occurred on cirrhosis, LT offers the best outcome in terms of overall and disease free survival. RFA colud be a curative method for HCC patients not amenable for LT of LR. Celsius.

Limitations and pitfalls of 99mTc-EDDA/HYNIC-TOC (Tektrotyd) scintigraphy.

PubMed

Garai, Ildikó; Barna, Sandor; Nagy, Gabor; Forgacs, Attila

2016-01-01

Tektrotyd kit was developed by Polatom company for 99mTc labeling to make an alternative tracer of somatostatin receptor scintigraphy available. Since 2005, 99mTc-EDDA/HYNIC-Tyr3-Octreotide has been used in clinical imaging and achieved high impact in management of patients with neuroendocrine tumors. Knowing the limitations and pitfalls is essential to provide ac-curate diagnosis. Therefore, the potential pitfalls associated with the use of 99mTc-EDDA/HYNIC-TOC are reviewed on the basis of own experience. Data were analyzed of 310 patients who underwent somatostatin receptor scintigraphy with 99mTc-Tektrotyd. Pitfalls during radiolabeling process or acquisition can worsen the sensitivity of SRS (somatostatin receptor scintigraphy). Recognizing physi-ological and clinical pitfalls, the diagnostic accuracy will improve.

Priority Science Targets for Future Sample Return Missions within the Solar System Out to the Year 2050

NASA Technical Reports Server (NTRS)

McCubbin, F. M.; Allton, J. H.; Barnes, J. J.; Boyce, J. W.; Burton, A. S.; Draper, D. S.; Evans, C. A.; Fries, M. D.; Jones, J. H.; Keller, L. P.;

Late presentation of esophageal cancer: observations in a multiracial South-East Asian population.

PubMed

Abdullah, Muhammad; Karim, Adil Abdel; Goh, Khean-Lee

2010-02-01

Esophageal cancer (ECA) is an important cancer in Malaysia. The aim of the study is to review the demographic data and clinical presentation of patients with ECA seen at the University of Malaya Medical Centre, Kuala Lumpur. Patients with histologically proven ECA were recruited for the study. Patients' case notes, endoscopy and operating theater records were reviewed. All cases were histologically confirmed. A total of 143 patients with ECA was diagnosed between 1998 and 2003. The mean age of the patients was 63.1 +/- 12.1 years with a male : female ratio of 1.8:1. Of these 50.3 percent were Indians, 32.9 percent, Chinese and 16.8 percent Malays. The overall hospital-based prevalence rates per 100 000 admissions according to races were: Malay; 23.5, Chinese; 57.4 and Indian; 134.1. The location of the tumors was: upper; 16 (11.2%) middle; 52 (36.4%) and lower; 75 (52.4%). The histological type of ECA were: squamous cell carcinomas; 113 (79.0%) and adenocarcinomas; 30 (21.0%). The ECA stage at diagnosis, was: II; 18 (12.6%), III; 23 (16.1%) and IV; 102 (71.3%). Only 24 (16.8%) patients underwent surgery and13 (9.1%) were considered curative. Overall 114 (79.7%) patients underwent palliative endoscopic stenting and six (4.2%) were given other palliative therapy including radiotherapy. Squamous cell cancer was the predominant type. ECA presents late in our patients and only a minority of patients underwent curative surgery.

Investigating Astromaterials Curation Applications for Dexterous Robotic Arms

NASA Technical Reports Server (NTRS)

Snead, C. J.; Jang, J. H.; Cowden, T. R.; McCubbin, F. M.

2018-01-01

The Astromaterials Acquisition and Curation office at NASA Johnson Space Center is currently investigating tools and methods that will enable the curation of future astromaterials collections. Size and temperature constraints for astromaterials to be collected by current and future proposed missions will require the development of new robotic sample and tool handling capabilities. NASA Curation has investigated the application of robot arms in the past, and robotic 3-axis micromanipulators are currently in use for small particle curation in the Stardust and Cosmic Dust laboratories. While 3-axis micromanipulators have been extremely successful for activities involving the transfer of isolated particles in the 5-20 micron range (e.g. from microscope slide to epoxy bullet tip, beryllium SEM disk), their limited ranges of motion and lack of yaw, pitch, and roll degrees of freedom restrict their utility in other applications. For instance, curators removing particles from cosmic dust collectors by hand often employ scooping and rotating motions to successfully free trapped particles from the silicone oil coatings. Similar scooping and rotating motions are also employed when isolating a specific particle of interest from an aliquot of crushed meteorite. While cosmic dust curators have been remarkably successful with these kinds of particle manipulations using handheld tools, operator fatigue limits the number of particles that can be removed during a given extraction session. The challenges for curation of small particles will be exacerbated by mission requirements that samples be processed in N2 sample cabinets (i.e. gloveboxes). We have been investigating the use of compact robot arms to facilitate sample handling within gloveboxes. Six-axis robot arms potentially have applications beyond small particle manipulation. For instance, future sample return missions may involve biologically sensitive astromaterials that can be easily compromised by physical interaction with a curator; other potential future returned samples may require cryogenic curation. Robot arms may be combined with high resolution cameras within a sample cabinet and controlled remotely by curator. Sophisticated robot arm and hand combination systems can be programmed to mimic the movements of a curator wearing a data glove; successful implementation of such a system may ultimately allow a curator to virtually operate in a nitrogen, cryogenic, or biologically sensitive environment with dexterity comparable to that of a curator physically handling samples in a glove box.

Prostate Cancer Radiation Therapy and Risk of Thromboembolic Events

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bosco, Cecilia, E-mail: Cecilia.t.bosco@kcl.ac.uk; Garmo, Hans; Regional Cancer Centre, Uppsala, Akademiska Sjukhuset, Uppsala

Purpose: To investigate the risk of thromboembolic disease (TED) after radiation therapy (RT) with curative intent for prostate cancer (PCa). Patients and Methods: We identified all men who received RT as curative treatment (n=9410) and grouped according to external beam RT (EBRT) or brachytherapy (BT). By comparing with an age- and county-matched comparison cohort of PCa-free men (n=46,826), we investigated risk of TED after RT using Cox proportional hazard regression models. The model was adjusted for tumor characteristics, demographics, comorbidities, PCa treatments, and known risk factors of TED, such as recent surgery and disease progression. Results: Between 2006 and 2013, 6232more » men with PCa received EBRT, and 3178 underwent BT. A statistically significant association was found between EBRT and BT and risk of pulmonary embolism in the crude analysis. However, upon adjusting for known TED risk factors these associations disappeared. No significant associations were found between BT or EBRT and deep venous thrombosis. Conclusion: Curative RT for prostate cancer using contemporary methodologies was not associated with an increased risk of TED.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ben-David, Merav A.; Griffith, Kent A.; Abu-Isa, Eyad

Purpose: The role of radiation therapy (RT) in extrahepatic cholangiocarcinoma (EHCC) is not clear and only limited reports exist on the use of this modality. We have reviewed our institutional experience to determine the pattern of failure in patients after potentially curative resection and the expected outcomes after adjuvant RT and in unresectable patients. Methods and Materials: After institutional review board approval, 81 patients diagnosed with EHCC (gallbladder 28, distal bile duct 24, hilar 29) between June 1986 and December 2004 were identified and their records reviewed. Twenty-eight patients (35%) underwent potentially curative resection with R0/R1 margins. Fifty-two patients (64%)more » were unresectable or underwent resection with macroscopic residual disease (R2). All patients received three-dimensional planned megavoltage RT. The dose for each patient was converted to the equivalent total dose in a 2 Gy/fraction, using the linear-quadratic formalism and {alpha}/{beta} ratio of 10. The median dose delivered was 58.4 Gy (range, 23-88.2 Gy). 54% received concomitant chemotherapy. Results: With a median follow-up time of 1.2 years (range, 0.1-9.8 years) 75 patients (93%) have died. Median overall survival (OS) and progression-free survival (PFS) were 14.7 (95% CI, 13.1-16.3) and 11 (95% CI, 7.6-13.2) months, respectively. There was no difference among the three disease sites in OS (p = 0.70) or PFS (p = 0.80). Complete resection (R0) was the only predictive factor significantly associated with increase in both OS and PFS (p = 0.002), and there was no difference in outcomes between R1 and R2 resections. The first site of failure was predominantly locoregional (68.8% of all failures). Conclusion: Local failure is a major problem in EHCC, suggesting the need for more intense radiation schedules and better radiosensitizing strategies. Because R1 resection appears to convey no benefit, it appears that surgery should be contemplated only when an R0 resection is likely. Borderline-resectable patients might be better served by neoadjuvant therapy.« less

Utility of Brainstem Trigeminal Evoked Potentials in Patients With Primary Trigeminal Neuralgia Treated by Microvascular Decompression.

PubMed

Zhu, Jin; Zhang, Xin; Zhao, Hua; Tang, Yin-Da; Ying, Ting-Ting; Li, Shi-Ting

2017-09-01

To investigate the characteristics of brainstem trigeminal evoked potentials (BTEP) waveform in patients with and without trigeminal neuralgia (TN), and to discuss the utility of BTEP in patients with primary TN treated by microvascular decompression (MVD). A retrospective review of 43 patients who underwent BTEP between January 2016 and June 2016, including 33 patients with TN who underwent MVD and 10 patients without TN. Brainstem trigeminal evoked potentials characteristics of TN and non-TN were summarized, in particular to compare the BTEP changes between pre- and post-MVD, and to discover the relationship between BTEP changes and surgical outcome. Brainstem trigeminal evoked potentials can be recorded in patients without trigeminal neuralgia. Abnormal BTEP could be recorded when different branches were stimulated. After decompression, the original W2, W3 disappeared and then replaced by a large wave in most patients, or original wave poorly differentiated improved in some patients, showed as shorter latency and (or) amplitude increased. Brainstem trigeminal evoked potentials waveform of healthy side in patients with trigeminal neuralgia was similar to the waveform of patients without TN. In 3 patients, after decompression the W2, W3 peaks increased, and the latency, duration, IPLD did not change significantly. Until discharge, 87.9% (29/33) of the patients presented complete absence of pain without medication (BNI I) and 93.9% (31/33) had good pain control without medication (BNI I-II). Brainstem trigeminal evoked potentials can reflect the conduction function of the trigeminal nerve to evaluate the functional level of the trigeminal nerve conduction pathway. The improvement and restoration of BTEP waveforms are closely related to the postoperative curative effect.

Is Duodenal Invasion a Relevant Prognosticator in Patients Undergoing Adjuvant Chemoradiotherapy for Distal Common Bile Duct Cancer?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Kyubo; Chie, Eui Kyu, E-mail: ekchie93@snu.ac.k; Jang, Jin-Young

2010-07-15

Purpose: To analyze the outcome of adjuvant chemoradiotherapy for patients with distal common bile duct (CBD) cancer who underwent curative surgery, and to identify the prognostic factors for these patients. Methods and Materials: Between January 1991 and December 2002, 38 patients with adenocarcinoma of the distal CBD underwent curative resection followed by adjuvant chemoradiotherapy. There were 27 men and 11 women, and the median age was 60 years (range, 34-73). Adjuvant radiotherapy was delivered to the tumor bed and regional lymph nodes up to 40 Gy at 2 Gy/fraction with a 2-week planned rest. Intravenous 5-fluorouracil (500mg/m{sup 2}/day) was givenmore » on day 1 to day 3 of each split course. The median follow-up period was 39 months. Results: The 5-year overall survival rate of all patients was 49.1%. On univariate analysis, only histologic differentiation (p = 0.0005) was associated with overall survival. Tumor size ({<=}2cm vs. >2cm) had a marginally significant impact on the treatment outcome (p = 0.0624). However, there was no difference in overall survival rates between T3 and T4 tumors (p = 0.6189), for which the main determinants were pancreatic and duodenal invasion, respectively. On multivariate analysis, histologic differentiation (p = 0.0092) and tumor size (p = 0.0046) were independent risk factors for overall survival. Conclusions: Long-term survival can be expected in patients with distal CBD cancer undergoing curative surgery and adjuvant chemoradiotherapy. Histologic differentiation and tumor size were significant prognostic factors predicting overall survival, whereas duodenal invasion was not. This finding suggests the need for further refinement in tumor staging.« less

18F-FDG PET-CT after Neoadjuvant Chemoradiotherapy in Esophageal Cancer Patients to Optimize Surgical Decision Making

PubMed Central

Anderegg, Maarten C. J.; de Groof, Elisabeth J.; Gisbertz, Suzanne S.; Bennink, Roel J.; Lagarde, Sjoerd M.; Klinkenbijl, Jean H. G.; Dijkgraaf, Marcel G. W.; Bergman, Jacques J. G. H. M.; Hulshof, Maarten C. C. M.; van Laarhoven, Hanneke W. M.; van Berge Henegouwen, Mark I.

2015-01-01

Background Prognosis of esophageal cancer patients can be significantly improved by neoadjuvant chemoradiotherapy (nCRT). Given the aggressive nature of esophageal tumors, it is conceivable that in a significant portion of patients treated with nCRT, dissemination already becomes manifest during the period of nCRT. The aim of this retrospective study was to determine the value and diagnostic accuracy of PET-CT after neoadjuvant chemoradiotherapy to identify patients with metastases preoperatively in order to prevent non-curative surgery. Methods From January 2011 until February 2013 esophageal cancer patients deemed eligible for a curative approach with nCRT and surgical resection underwent a PET-CT after completion of nCRT. If abnormalities on PET-CT were suspected metastases, histological proof was acquired. A clinical decision model was designed to assess the cost-effectiveness of this diagnostic strategy. Results 156 patients underwent a PET-CT after nCRT. In 31 patients (19.9%) PET-CT showed abnormalities suspicious for dissemination, resulting in 17 cases of proven metastases (10.9%). Of the patients without proven metastases 133 patients were operated. In 6 of these 133 cases distant metastases were detected intraoperatively, corresponding to 4.5% false-negative results. The standard introduction of a post-neoadjuvant therapy PET-CT led to a reduction of overall health care costs per patient compared to a scenario without restaging with PET-CT ($34,088 vs. $36,490). Conclusion In 10.9% of esophageal cancer patients distant metastases were detected by standard PET-CT after neoadjuvant chemoradiotherapy. To avoid non-curative resections we advocate post-neoadjuvant therapy PET-CT as a cost-effective step in the standard work-up of candidates for surgery. PMID:26529313

Agile Data Curation Case Studies Leading to the Identification and Development of Data Curation Design Patterns

NASA Astrophysics Data System (ADS)

Benedict, K. K.; Lenhardt, W. C.; Young, J. W.; Gordon, L. C.; Hughes, S.; Santhana Vannan, S. K.

2017-12-01

The planning for and development of efficient workflows for the creation, reuse, sharing, documentation, publication and preservation of research data is a general challenge that research teams of all sizes face. In response to: requirements from funding agencies for full-lifecycle data management plans that will result in well documented, preserved, and shared research data products increasing requirements from publishers for shared data in conjunction with submitted papers interdisciplinary research team's needs for efficient data sharing within projects, and increasing reuse of research data for replication and new, unanticipated research, policy development, and public use alternative strategies to traditional data life cycle approaches must be developed and shared that enable research teams to meet these requirements while meeting the core science objectives of their projects within the available resources. In support of achieving these goals, the concept of Agile Data Curation has been developed in which there have been parallel activities in support of 1) identifying a set of shared values and principles that underlie the objectives of agile data curation, 2) soliciting case studies from the Earth science and other research communities that illustrate aspects of what the contributors consider agile data curation methods and practices, and 3) identifying or developing design patterns that are high-level abstractions from successful data curation practice that are related to common data curation problems for which common solution strategies may be employed. This paper provides a collection of case studies that have been contributed by the Earth science community, and an initial analysis of those case studies to map them to emerging shared data curation problems and their potential solutions. Following the initial analysis of these problems and potential solutions, existing design patterns from software engineering and related disciplines are identified as a starting point for the development of a catalog of data curation design patterns that may be reused in the design and execution of new data curation processes.

Proximal migration of transanastomotic pancreatic stent following pancreaticoduodenectomy and pancreaticojejunostomy.

PubMed

Ammori, B J; White, C M

1999-06-01

The use of catheters to stent the pancreaticojejunal anastomosis following pancreaticoduodenectomy is practiced by some surgeons. Their long-term effects in this setting, however, remain unknown. A 60-yr-old woman underwent a potentially curative pylorus preserving pancreaticoduodenectomy for Stage I ampullary carcinoma. Roux-en-Y pancreaticojejunostomy was constructed over a short stent. She presented 4 yr later with abdominal pain, steatorrhea, and weight loss. Computed tomography revealed a stent within the proximal pancreatic duct, with gross upstream ductal dilatation and parenchymal features of chronic pancreatitis. Laparotomy revealed no disease recurrence. The stent, removed through a jejunotomy, was occluded. On-table pancreatogram demonstrated a 3-cm proximal duct stricture. Drainage was achieved with a lateral pancreaticojejunostomy (modified Puestow procedure). Recovery was uneventful, with clinical recovery of pancreatic exocrine function at 6 mo follow-up. Proximal migration of transanastomotic pancreatic stent with subsequent development of chronic pancreatitis is a potential complication following pancreaticoduodenectomy. It can be managed effectively with stent removal and a lateral pancreaticojejunostomy.

Can we replace curation with information extraction software?

PubMed

Karp, Peter D

2016-01-01

Can we use programs for automated or semi-automated information extraction from scientific texts as practical alternatives to professional curation? I show that error rates of current information extraction programs are too high to replace professional curation today. Furthermore, current IEP programs extract single narrow slivers of information, such as individual protein interactions; they cannot extract the large breadth of information extracted by professional curators for databases such as EcoCyc. They also cannot arbitrate among conflicting statements in the literature as curators can. Therefore, funding agencies should not hobble the curation efforts of existing databases on the assumption that a problem that has stymied Artificial Intelligence researchers for more than 60 years will be solved tomorrow. Semi-automated extraction techniques appear to have significantly more potential based on a review of recent tools that enhance curator productivity. But a full cost-benefit analysis for these tools is lacking. Without such analysis it is possible to expend significant effort developing information-extraction tools that automate small parts of the overall curation workflow without achieving a significant decrease in curation costs.Database URL. © The Author(s) 2016. Published by Oxford University Press.

Palliative photodynamic therapy for biliary tract carcinoma may improve survival and has a similar outcome to attempted curative surgery with positive resection margins

NASA Astrophysics Data System (ADS)

Pereira, Stephen P.; Matull, W. Rudiger; Dhar, Dipok K.; Ayaru, Laskshmana; Sandanayake, Neomal S.; Chapman, Michael H.

2009-06-01

There is a need for better management strategies to improve survival and quality of life in patients with biliary tract cancer (BTC). We compared treatment outcomes in 321 patients (median age 65 years, range 29-102; F:M; 1:1) with a final diagnosis of BTC (cholangiocarcinoma n=237, gallbladder cancer n=84) seen in a tertiary referral cancer centre between 1998-2007. Of 89 (28%) patients who underwent surgical intervention with curative intent, 38% had R0 resections and had the most favourable outcome, with a 3 year survival of 57%. Even though PDT patients had more advanced clinical T-stages, their survival was similar to those treated with attempted curative surgery which resulted in R1/2 resections (median survival 12 vs. 13 months, ns). In a subgroup of 36 patients with locally advanced BTC treated with PDT as part of a prospective phase II study, the median survival was 12 (range 2-51) months, compared with 5 months in matched historical controls treated with stenting alone (p < 0.0001). In this large UK series, long-term survival with BTC was only achieved in surgical patients with R0 resection margins. Palliative PDT resulted in similar survival to those with curatively intended R1/R2 resections.

CMR Metadata Curation

NASA Technical Reports Server (NTRS)

Shum, Dana; Bugbee, Kaylin

2017-01-01

This talk explains the ongoing metadata curation activities in the Common Metadata Repository. It explores tools that exist today which are useful for building quality metadata and also opens up the floor for discussions on other potentially useful tools.

Acute aortic dissection involving the root: operative and long-term outcome after curative proximal repair†

PubMed Central

Urbanski, Paul P.; Lenos, Aristidis; Irimie, Vadim; Bougioukakis, Petros; Zacher, Michael; Diegeler, Anno

2016-01-01

OBJECTIVES The aim of the study was to evaluate operative and long-term results after surgery of acute aortic dissection involving the root, in which the proximal repair consisted of curative resection of all dissected aortic sinuses and was performed using either valve-sparing root repair or complete root replacement with a valve conduit. METHODS Between August 2002 and March 2013, 162 consecutive patients (mean age 63 ± 14 years) underwent surgery for acute type A aortic dissection. Eighty-six patients with an involvement of the aortic root underwent curative surgery of the proximal aorta consisting of valve-sparing root repair (n = 54, 62.8%) or complete valve and root replacement using composite valve grafts (n = 32, 37.2%). In patients with root repair, all dissected aortic walls were resected and root remodelling using the single patch technique (n = 53) or root repair with valve reimplantation (n = 1) was performed without the use of any glue. All perioperative data were collected prospectively and retrospective statistical examination was performed using univariate and multivariate analyses. RESULTS The mean follow-up was 5.2 ± 3.5 years for all patients (range 0–12 years) and 6.1 ± 3.3 years for survivors. The 30-day mortality rate was 5.8% (5 patients), being considerably lower in the repair sub-cohort (1.9 vs 12.5%). The estimated survival rate at 5 and 10 years was 80.0 ± 4.5 and 69.1 ± 6.7%, respectively. No patient required reoperation on the proximal aorta and/or aortic valve during the follow-up time and there were only two valve-related events (both embolic, one in each group). Among those patients with repaired valves, the last echocardiography available showed no insufficiency in 40 and an irrelevant insufficiency (1+) in 14. CONCLUSIONS Curative repair of the proximal aorta in acute dissection involving the root provides favourable operative and long-term outcome with very low risk of aortic complications and/or reoperations, regardless if a valve-sparing procedure or replacement with a valve conduit is used. Valve-sparing surgery is frequently suitable, providing excellent outcome and very high durability. PMID:26848190

Survival significance of coexisting chronic obstructive pulmonary disease in patients with early lung cancer after curative surgery

PubMed Central

Miyazawa, Tomoyuki; Sakai, Hiroki; Kimura, Yusuke; Tsuda, Masataka; Wakiyama, Yoichi; Marushima, Hideki; Kojima, Koji; Nakamura, Haruhiko

2017-01-01

Background The impact of chronic obstructive pulmonary disease (COPD) severity on survival after curative resection of early‐stage lung cancer (NSCLC) has not been sufficiently elucidated. Methods We retrospectively reviewed 250 consecutive patients who underwent lobectomy with lymph nodal dissection for pathological stage I–II NSCLC. Results Among the COPD patients, 28 were classified as Global Initiative for Chronic Obstructive Lung Disease (GOLD) 1, 21 as GOLD 2, and one as GOLD 3. The cumulative overall survival (OS) of the non‐COPD, GOLD 1, and GOLD 2–3 groups at five years was 90.7%, 85.7%, and 55.3%, respectively, (P < 0.0001), while recurrence‐free survival (RFS) between the groups at five years was 84.7%, 80.7%, and 72.9%, respectively. Although RFS in the GOLD 2–3 group tended to indicate a poor prognosis, there was no statistical difference between the groups (P = 0.385). In multivariate analysis, age ≥75 years, pN1, and GOLD 2–3 COPD were independent factors for a poor prognosis (P = 0.034, P = 0.010, and P = 0.030, respectively). Conclusions Our results indicate that early stage NSCLC patients with COPD had a significantly increased risk of poorer OS and potentially an increased risk of poor RFS. PMID:28976075

Elevated C-reactive protein and hypoalbuminemia measured before resection of colorectal liver metastases predict postoperative survival.

PubMed

Kobayashi, Takashi; Teruya, Masanori; Kishiki, Tomokazu; Endo, Daisuke; Takenaka, Yoshiharu; Miki, Kenji; Kobayashi, Kaoru; Morita, Koji

2010-01-01

Few studies have investigated whether the Glasgow Prognostic Score (GPS), an inflammation-based prognostic score measured before resection of colorectal liver metastasis (CRLM), can predict postoperative survival. Sixty-three consecutive patients who underwent curative resection for CRLM were investigated. GPS was calculated on the basis of admission data as follows: patients with both an elevated C-reactive protein (>10 mg/l) and hypoalbuminemia (<35 g/l) were allocated a GPS score of 2. Patients in whom only one of these biochemical abnormalities was present were allocated a GPS score of 1, and patients with a normal C-reactive protein and albumin were allocated a score of 0. Significant factors concerning survival were the number of liver metastases (p = 0.0044), carcinoembryonic antigen level (p = 0.0191), GPS (p = 0.0029), grade of liver metastasis (p = 0.0033), and the number of lymph node metastases around the primary cancer (p = 0.0087). Multivariate analysis showed the two independent prognostic variables: liver metastases > or =3 (relative risk 2.83) and GPS1/2 (relative risk 3.07). GPS measured before operation and the number of liver metastases may be used as novel predictors of postoperative outcomes in patients who underwent curative resection for CRLM. Copyright 2010 S. Karger AG, Basel.

Survival from colorectal cancer in Victoria: 10-year follow up of the 1987 management survey.

PubMed

McLeish, John A; Thursfield, Vicky J; Giles, Graham G

2002-05-01

In 1987, the Victorian Cancer Registry identified a population-based sample of patients who underwent surgery for colorectal cancer for an audit of management following resection. Over 10 years have passed since this survey, and data on the survival of these patients (incorporating various prognostic indicators collected at the time of the survey) are now discussed in the present report. Relative survival analysis was conducted for each prognostic indicator separately and then combined in a multivariate model. Relative survival at 5 years for patients undergoing curative resections was 76% compared with 7% for those whose treatment was considered palliative. Survival at 10 years was little changed (73% and 7% respectively). Survival did not differ significantly by sex or age irrespective of treatment intention. In the curative group, only stage was a significant predictor of survival. Multivariate analysis was performed only for the curative group. Adjusting for all variables simultaneously,stage was the only -significant predictor of survival. Patients with Dukes' stage C disease were at a significantly greater risk (OR 5.5 (1.7-17.6)) than those with Dukes' A. Neither tumour site, sex, age, surgeon activity level nor adjuvant therapies made a significant contribution to the model.

Hydronephrosis does not preclude curative resection of pelvic recurrences after colorectal surgery.

PubMed

Henry, Leonard R; Sigurdson, Elin; Ross, Eric; Hoffman, John P

2005-10-01

In one third of patients who die of rectal cancer, a pelvic recurrence after resection represents isolated disease for which re-resection may provide cure. These extensive resections can carry high morbidity. Proper patient selection is desirable but difficult. Hydronephrosis has been documented previously to portend a poor prognosis, and some consider it a contraindication to attempted resection. It was our goal to review our experience and either confirm or refute these conclusions. We performed a retrospective analysis of 90 patients resected with curative intent for pelvic recurrence at our center from 1988 through 2003. Seventy-one records documented the preoperative presence or absence of hydronephrosis. Clinical and pathologic data were recorded. The groups with and without hydronephrosis were compared. There were 15 patients with hydronephrosis in this study and 56 without. Although patients with hydronephrosis had shorter overall survival, disease-free survival, and rate of local control, none of these differences was statistically significant. Patients in the hydronephrosis group were younger and had higher-stage primary tumors and larger recurrent tumors. Subsequently, they underwent more extensive resections and were more likely to be treated with adjuvant therapies. There was no difference in the rate of margin-negative resections between the groups. Hydronephrosis correlates with younger patients with larger recurrent tumors undergoing more extensive operations and multimodality therapy but does not preclude curative (R0) resection or independently affect overall survival, disease-free survival, or local control. We believe that it should not be considered a contraindication to attempting curative resection.

Results of a pancreatectomy with a limited venous resection for pancreatic cancer.

PubMed

Illuminati, Giulio; Carboni, Fabio; Lorusso, Riccardo; D'Urso, Antonio; Ceccanei, Gianluca; Papaspyropoulos, Vassilios; Pacile, Maria Antonietta; Santoro, Eugenio

2008-01-01

The indications for a pancreatectomy with a partial resection of the portal or superior mesenteric vein for pancreatic cancer, when the vein is involved by the tumor, remain controversial. It can be assumed that when such involvement is not extensive, resection of the tumor and the involved venous segment, followed by venous reconstruction will extend the potential benefits of this resection to a larger number of patients. The further hypothesis of this study is that whenever involvement of the vein by the tumor does not exceed 2 cm in length, this involvement is more likely due to the location of the tumor being close to the vein rather than because of its aggressive biological behavior. Consequently, in these instances a pancreatectomy with a resection of the involved segment of portal or superior mesenteric vein for pancreatic cancer is indicated, as it will yield results that are superposable to those of a pancreatectomy for cancer without vascular involvement. Twenty-nine patients with carcinoma of the pancreas involving the portal or superior mesenteric vein over a length of 2 cm or less underwent a macroscopically curative resection of the pancreas en bloc with the involved segment of the vein. The venous reconstruction procedures included a tangential resection/lateral suture in 15 cases, a resection/end-to-end anastomosis in 11, and a resection/patch closure in 3. Postoperative mortality was 3.4%; morbidity was 21%. Local recurrence was 14%. Cumulative (standard error) survival rate was 17% (9%) at 3 years. A pancreatectomy combined with a resection of the portal or superior mesenteric vein for cancer with venous involvement not exceeding 2 cm is indicated in order to extend the potential benefits of a curative resection.

Diversion procto-colitis: response to treatment with short-chain fatty acids.

PubMed

Kiely, E M; Ajayi, N A; Wheeler, R A; Malone, M

2001-10-01

Diversion procto-colitis (DPC) results from a deficiency of luminal short-chain fatty acids (SCFAs). Endoscopic and histopathologic features of the disorder are almost universally present in defunctioned bowel, but symptomatic DPC is less common. Five children with symptomatic DPC underwent endoscopy and rectosigmoid biopsies. An endoscopic index (EI) was used to quantify disease severity. An SCFA mixture was administered into the defunctioned bowel. A good clinical response and improvement in the endoscopic index occurred in all children. Undiversion or rectal excision was carried out in 4 and was curative in each case. One child is awaiting a redo pull through. DPC should be considered in children with a defunctioned colon presenting with evidence of colitis. Histopathology provides supportive evidence and SCFAs may provide effective relief of symptoms. Stoma reversal or rectal excision is curative. Copyright 2001 by W.B. Saunders Company.

Perioperative FOLFOX4 plus bevacizumab for initially unresectable advanced colorectal cancer (NAVIGATE-CRC-01).

PubMed

Suenaga, Mitsukuni; Fujimoto, Yoshiya; Matsusaka, Satoshi; Shinozaki, Eiji; Akiyoshi, Takashi; Nagayama, Satoshi; Fukunaga, Yosuke; Oya, Masatoshi; Ueno, Masashi; Mizunuma, Nobuyuki; Yamaguchi, Toshiharu

2015-01-01

Perioperative chemotherapy combined with surgery for liver metastases is considered an active strategy in metastatic colorectal cancer (CRC). However, its impact on initially unresectable, previously untreated advanced CRC, regardless of concurrent metastases, remains to be clarified. A Phase II study was conducted to evaluate the safety and efficacy of perioperative FOLFOX4 plus bevacizumab for initially unresectable advanced CRC. Patients with previously untreated advanced colon or rectal cancer initially diagnosed as unresectable advanced CRC (TNM stage IIIb, IIIc, or IV) but potentially resectable after neoadjuvant chemotherapy (NAC) were studied. Preoperatively, patients received six cycles of NAC (five cycles of neoadjuvant FOLFOX4 plus bevacizumab followed by one cycle of FOLFOX4 alone). The interval between the last dose of bevacizumab and surgery was at least 5 weeks. Six cycles of adjuvant FOLFOX4 plus bevacizumab were given after surgery. The completion rate of NAC and feasibility of curative surgery were the primary endpoints. An interim analysis was performed at the end of NAC in the 12th patient to assess the completion rate of NAC. The median follow-up time was 56 months. The characteristics of the patients were as follows: sex, eight males and four females; tumor location, sigmoid colon in three, ascending colon in one, and rectum (above the peritoneal reflection) in eight; stage, III in eight and IV in four (liver or lymph nodes). All patients completed six cycles of NAC. There were no treatment-related severe adverse events or deaths. An objective response to NAC was achieved in nine patients (75%), and no disease progression was observed. Eleven patients underwent curative tumor resection, including metastatic lesions. In December 2012, this Phase II study was terminated because of slow registration. Perioperative FOLFOX4 plus bevacizumab is well tolerated and has a promising response rate leading to curative surgery, which offers a survival benefit in initially unresectable advanced CRC with concurrent metastatic lesions.

Treatment of gastric epithelial tumours by endoscopic submucosal dissection using an insulated-tip diathermic knife

PubMed Central

Hua, Xu Li; Bo, Qian Jun; Gen, Gu Liu; Fei, Lu; Min, Wang Ya; Ming, Li Yu; Sheng, Lu Hua

2011-01-01

BACKGROUND: Endoscopic submucosal dissection (ESD) is a promising technique for the treatment of large, pre- and early malignant gastrointestinal lesions. OBJECTIVE: To assess the rates of en bloc resection, incidence of complications, procedure times and therapeutic outcomes of ESD using an insulated-tip diathermic knife; and to investigate predictors of these outcomes based on the final pathological features of biopsy specimens. METHODS: One hundred twenty patients with endoscopically suspected gastric epithelial tumours who were treated with ESD from January 2006 to December 2009 were evaluated. RESULTS: The mean diameter of the gastric epithelial tumours in the present cohort was 1.88 cm. The mean diameter of the resected specimens was 3.33 cm. The en bloc resection rate was 90% (108 of 120). The median length of the operation was 64.6 min. The bleeding and perforation complication rates were 5.0% (six of 120) and 2.5% (three of 120), respectively. Of 10 gastric tumours initially diagnosed as adenocarcinoma on biopsy, four were found to be low-grade dysplasia and six were found to be high-grade dysplasia after resection and final pathological examination. A total of 112 (93.33%) patients underwent curative treatment, eight patients (6.67%) underwent noncurative treatment with ESD, and two patients (1.67%) experienced local recurrence and subsequently underwent surgery. CONCLUSIONS: ESD is a promising local curative treatment option for gastric epithelial tumours, but still carries the risks of bleeding and/or perforation. Differences in the interpretation of histological results among different pathologists and/or between biopsy specimens before ESD and the en bloc tissue specimens after ESD will result in discrepancies. PMID:21321682

Text Mining to Support Gene Ontology Curation and Vice Versa.

PubMed

Ruch, Patrick

2017-01-01

In this chapter, we explain how text mining can support the curation of molecular biology databases dealing with protein functions. We also show how curated data can play a disruptive role in the developments of text mining methods. We review a decade of efforts to improve the automatic assignment of Gene Ontology (GO) descriptors, the reference ontology for the characterization of genes and gene products. To illustrate the high potential of this approach, we compare the performances of an automatic text categorizer and show a large improvement of +225 % in both precision and recall on benchmarked data. We argue that automatic text categorization functions can ultimately be embedded into a Question-Answering (QA) system to answer questions related to protein functions. Because GO descriptors can be relatively long and specific, traditional QA systems cannot answer such questions. A new type of QA system, so-called Deep QA which uses machine learning methods trained with curated contents, is thus emerging. Finally, future advances of text mining instruments are directly dependent on the availability of high-quality annotated contents at every curation step. Databases workflows must start recording explicitly all the data they curate and ideally also some of the data they do not curate.

Five-year follow-up of a patient with bilateral carotid body tumors after unilateral surgical resection.

PubMed

Demir, Tolga; Uyar, Ibrahim; Demir, Hale Bolgi; Sahin, Mazlum; Gundogdu, Gokcen

2014-10-03

Carotid body tumors are rare, highly vascularized neoplasms that arise from the paraganglia located at the carotid bifurcation. Surgery is the only curative treatment. However, treatment of bilateral carotid body tumors represents a special challenge due to potential neurovascular complications. We present the therapeutic management of a 34-year-old woman with bilateral carotid body tumors. The patient underwent surgical resection of the largest tumor. It was not possible to resect the tumor without sacrificing the ipsilateral vagal nerve. Due to unilateral vagal palsy, we decide to withhold all invasive therapy and to observe contralateral tumor growth with serial imaging studies. The patient is free of disease progression 5 years later. Treatment of bilateral CBTs should focus on preservation of the quality of life rather than on cure of the disease. In patients with previous contralateral vagal palsies, the choice between surgery and watchful waiting is a balance between the natural potential morbidity and the predictable surgical morbidity. Therefore, to avoid bilateral cranial nerve deficits, these patients may be observed until tumor growth is determined, and, if needed, treated by radiation therapy.

Hiatal Hernia as a Total Gastrectomy Complication

PubMed Central

Santos, Bruna do Nascimento; de Oliveira, Marcos Belotto; Peixoto, Renata D'Alpino

2016-01-01

Introduction According to the Brazilian National Institute of Cancer, gastric cancer is the third leading cause of death among men and the fifth among women in Brazil. Surgical resection is the only potentially curative treatment. The most serious complications associated with surgery are fistulas and dehiscence of the jejunal-esophageal anastomosis. Hiatal hernia refers to herniation of elements of the abdominal cavity through the esophageal hiatus of the diaphragm, though this occurrence is rarely reported as a complication in gastrectomy. Case Report A 76-year-old man was diagnosed with intestinal-type gastric adenocarcinoma. He underwent a total laparoscopic-assisted gastrectomy and D2 lymphadenectomy on May 19, 2015. The pathology revealed a pT4pN3 gastric adenocarcinoma. The patient became clinically stable and was discharged 10 days after surgery. He was subsequently started on adjuvant FOLFOX chemotherapy; however, 9 days after the second cycle, he was brought to the emergency room with nausea and severe epigastric pain. A CT scan revealed a hiatal hernia with signs of strangulation. The patient underwent emergent repair of the hernia and suffered no postoperative complications. He was discharged from the hospital 9 days after surgery. Conclusion Hiatal hernia is not well documented, and its occurrence in the context of gastrectomy is an infrequent complication. PMID:27293395

A case of a resectable single hepatic epithelioid hemangioendothelioma with characteristic imaging by ADC map.

PubMed

Okano, Hiroshi; Nakajima, Hideki; Tochio, Tomomasa; Suga, Daisuke; Kumazawa, Hiroaki; Isono, Yoshiaki; Tanaka, Hiroki; Matsusaki, Shimpei; Sase, Tomohiro; Saito, Tomonori; Mukai, Katsumi; Nishimura, Akira; Matsushima, Nobuyoshi; Baba, Youichirou; Murata, Tetsuya; Hamada, Takashi; Taoka, Hiroki

2015-12-01

A 47-year-old woman with a single-nodule hepatic tumor was referred to our hospital. She had no symptoms. The tumor was located at the surface of the right lobe of the liver; it showed peripheral low signal intensity on a magnetic resonance imaging apparent diffusion coefficient (ADC) map, and an influx of blood flow into the peripheral area of the tumor at the early vascular phase on perflubutane microbubble (Sonazoid(®)) contrast-enhanced (CE) ultrasonography. Since we suspected a malignant tumor, the patient underwent surgical resection. The hepatic tumor was resected curatively. Pathological examination revealed that the tumor was composed of epithelioid cells with an epithelioid structure and/or cord-like structure. Immunohistochemical staining was positive for cluster of differentiation 34 and factor VIII-related antigen. Based on the above, a final diagnosis of hepatic epithelioid hemangioendothelioma (EHE) was made. Hepatic EHE is a rare hepatic tumor: only a few cases of hepatic EHE with curative resection have been reported. We were unable to reach a diagnosis of hepatic EHE by imaging studies; however, an ADC map was useful in showing the malignant potential of the tumor, and CE ultrasonography was useful in revealing the peripheral blood flow of the tumor. When an unusual hepatic mass is encountered, hepatic EHE should be kept in mind, and the mass should be inspected with more than one imaging modality, including an ADC map, in the process of differential diagnosis.

Curative procedures of oral health and structural characteristics of primary dental care.

PubMed

Baumgarten, Alexandre; Hugo, Fernando Neves; Bulgarelli, Alexandre Fávero; Hilgert, Juliana Balbinot

2018-04-09

To evaluate if the provision of clinical dental care, by means of the main curative procedures recommended in Primary Health Care, is associated with team structural characteristics, considering the presence of a minimum set of equipment, instrument, and supplies in Brazil's primary health care services. A cross-sectional exploratory study based on data collected from 18,114 primary healthcare services with dental health teams in Brazil, in 2014. The outcome was created from the confirmation of five clinical procedures performed by the dentist, accounting for the presence of minimum equipment, instrument, and supplies to carry them out. Covariables were related to structural characteristics. Poisson regression with robust variance was used to obtain crude and adjusted prevalence ratios, with 95% confidence intervals. A total of 1,190 (6.5%) dental health teams did not present the minimum equipment to provide clinical dental care and only 2,498 (14.8%) had all the instrument and supplies needed and provided the five curative procedures assessed. There was a positive association between the outcome and the composition of dental health teams, higher workload, performing analysis of health condition, and monitoring of oral health indicators. Additionally, the dental health teams that planned and programmed oral health actions with the primary care team monthly provided the procedures more frequently. Dentists with better employment status, career plans, graduation in public health or those who underwent permanent education activities provided the procedures more frequently. A relevant number of Primary Health Care services did not have the infrastructure to provide clinical dental care. However, better results were found in dental health teams with oral health technicians, with higher workload and that plan their activities, as well as in those that employed dentists with better working relationships, who had dentists with degrees in public health and who underwent permanent education activities.

Long-Term Results of Radiochemotherapy for Solitary Lymph Node Metastasis After Curative Resection of Esophageal Cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jingu, Keiichi, E-mail: kjingu-jr@rad.med.tohoku.ac.jp; Ariga, Hisanori; Nemoto, Kenji

2012-05-01

Purpose: To evaluate the long-term efficacy and toxicity of definitive radiochemotherapy for solitary lymph node metastasis after curative surgery of esophageal cancer. Methods and Materials: We performed a retrospective review of 35 patients who underwent definitive radiochemotherapy at Tohoku University Hospital between 2000 and 2009 for solitary lymph node metastasis after curative esophagectomy with lymph node dissection for esophageal cancer. Radiotherapy doses ranged from 60 to 66 Gy (median, 60 Gy). Concurrent chemotherapy was platinum based in all patients. The endpoints of the present study were overall survival, cause-specific survival, progression-free survival, irradiated-field control, overall tumor response, and prognostic factors.more » Results: The median observation period for survivors was 70.0 months. The 5-year overall survival was 39.2% (median survival, 39.0 months). The 5-year cause-specific survival, progression-free survival, and irradiated-field control were 43.3%, 31.0% and 59.9%, respectively. Metastatic lesion, size of the metastatic lymph node, and performance status before radiochemotherapy were significantly correlated with prognosis. Complete response and partial response were observed in 22.9% and 57.1% of the patients, respectively. There was no Grade 3 or higher adverse effect based on theCommon Terminology Criteria for Adverse Events (CTCAE v3.0) in the late phase. Conclusions: Based on our study findings, approximately 40% of patients with solitary lymph node metastasis after curative resection for esophageal cancer have a chance of long-term survival with definitive radiochemotherapy.« less

Analysis of factors in successful nasal endoscopic resection of nasopharyngeal angiofibroma.

PubMed

Ye, Dong; Shen, Zhisen; Wang, Guoli; Deng, Hongxia; Qiu, Shijie; Zhang, Yuna

2016-01-01

Endoscopic resection of nasopharyngeal angiofibroma is less traumatic, causes less bleeding, and provides a good curative effect. Using pre-operative embolization and controlled hypotension, reasonable surgical strategies and techniques lead to successful resection tumors of a maximum Andrews-Fisch classification stage of III. To investigate surgical indications, methods, surgical technique, and curative effects of transnasal endoscopic resection of nasopharyngeal angiofibroma, this study evaluated factors that improve diagnosis and treatment, prevent large intra-operative blood loss and residual tumor, and increase the cure rate. A retrospective analysis was performed of the clinical data and treatment programs of 23 patients with nasopharyngeal angiofibroma who underwent endoscopic resection with pre-operative embolization and controlled hypotension. The surgical method applied was based on the size of tumor and extent of invasion. Curative effects were observed. No intra-operative or perioperative complications were observed in 22 patients. Upon removal of nasal packing material 3-7 days post-operatively, one patient experienced heavy bleeding of the nasopharyngeal wound, which was treated compression hemostasis using post-nasal packing. Twenty-three patients were followed up for 6-60 months. Twenty-two patients experienced cure; one patient experienced recurrence 10 months post-operatively, and repeat nasal endoscopic surgery was performed and resulted in cure.

Curating Media Learning: Towards a Porous Expertise

ERIC Educational Resources Information Center

McDougall, Julian; Potter, John

2015-01-01

This article combines research results from a range of projects with two consistent themes. Firstly, we explore the potential for curation to offer a productive metaphor for the convergence of digital media learning across and between home/lifeworld and formal educational/system-world spaces--or between the public and private spheres. Secondly, we…

Is an aggressive surgical approach to the patient with gastric lymphoma warranted?

PubMed Central

Rosen, C B; van Heerden, J A; Martin, J K; Wold, L E; Ilstrup, D M

1987-01-01

At the Mayo Clinic, from 1970 through 1979, 84 patients (52 males and 32 females) had abdominal exploration for primary gastric lymphoma. All patients were observed a minimum of 5 years or until death. The histologic findings for all 84 patients were reviewed. Forty-four patients had "curative resection," and 40 patients had either biopsy alone or a palliative procedure. The probability of surviving 5 years was 75% for patients after potentially curative resection and 32% for patients after biopsy and palliation (p less than 0.001). The operative mortality rate was 5% overall and 2% after potentially curative resection. Increased tumor size (p less than 0.02), increased tumor penetration (p less than 0.01), and lymph node involvement (p less than 0.02) decreased the probability of survival, whereas histologic classification did not affect survival. Radiation therapy after surgery did not significantly affect the survival rate for the entire group or the survival rate for patients who had potentially curative resection. Resectability was associated with increased patient survival--independent of other prognostic factors--when our experience was analyzed by the Cox proportional-hazards model (p less than 0.005). It was concluded that an aggressive surgical attitude in the treatment of primary gastric lymphoma is warranted. The role of radiotherapy remains in question. PMID:3592805

Recent advances in multidisciplinary management of hepatocellular carcinoma

PubMed Central

Gomaa, Asmaa I; Waked, Imam

2015-01-01

The incidence of hepatocellular carcinoma (HCC) is increasing, and it is currently the second leading cause of cancer-related death worldwide. Potentially curative treatment options for HCC include resection, transplantation, and percutaneous ablation, whereas palliative treatments include trans-arterial chemoembolization (TACE), radioembolization, and systemic treatments. Due to the diversity of available treatment options and patients’ presentations, a multidisciplinary team should decide clinical management of HCC, according to tumor characteristics and stage of liver disease. Potentially curative treatments are suitable for very-early- and early-stage HCC. However, the vast majority of HCC patients are diagnosed in later stages, where the tumor characteristics or progress of liver disease prevent curative interventions. For patients with intermediate-stage HCC, TACE and radioembolization improve survival and are being evaluated in addition to potentially curative therapies or with systemic targeted therapy. There is currently no effective systemic chemotherapy, immunologic, or hormonal therapy for HCC, and sorafenib is the only approved molecular-targeted treatment for advanced HCC. Other targeted agents are under investigation; trials comparing new agents in combination with sorafenib are ongoing. Combinations of systemic targeted therapies with local treatments are being evaluated for further improvements in HCC patient outcomes. This article provides an updated and comprehensive overview of the current standards and trends in the treatment of HCC. PMID:25866604

Delayed diagnosis of endobronchial mucoepidermoid carcinoma in a 29-year-old male

PubMed Central

Jain, Akanksha; Madan, Neha Kawatra; Arava, Sudheer; Pandey, Durgatosh; Madan, Karan

2016-01-01

Mucoepidermoid carcinoma (MEC) is an uncommon primary lung tumor. It usually involves large airways and presents clinically and radiologically with nonspecific features. Because of nonspecific presentation diagnosis is frequently delayed. We report the case of a 29-year-old male patient wherein a clinico-radiological consideration of tuberculosis (TB) led to a prolonged treatment with anti-TB medications without response. Flexible bronchoscopic biopsy confirmed the diagnosis of MEC following that the patient underwent curative surgical resection. PMID:27186000

Do patients requiring a multivisceral resection for rectal cancer have worse oncologic outcomes than patients undergoing only abdominoperineal resection?

PubMed

Dosokey, Eslam M G; Brady, Justin T; Neupane, Ruel; Jabir, Murad A; Stein, Sharon L; Reynolds, Harry L; Delaney, Conor P; Steele, Scott R

2017-09-01

Abdominoperineal Resection (APR) remains an important option for patients with advanced rectal cancer though some may require multivisceral resection (MVR) in addition to APR. We hypothesized that oncological outcomes would be worse with MVR. A retrospective review from 2006 to 2015 of 161 patients undergoing APR or MVR for rectal cancer, of whom 118 underwent curative APR or APR with MVR. Perioperative, oncologic and survival metrics were evaluated. There were 82 patients who underwent APR and 36 who underwent MVR. Surgical approach and incidence of complications were similar (All P > 0.05). There was 1 local recurrence in each of the APR and MVR groups at a mean follow-up of 34 and 32 months, respectively. Distant recurrences occurred in 3 APR patients and 4 MVR patients. APR and APR with MVR can be performed with comparable morbidity and oncologic outcomes. Copyright © 2017 Elsevier Inc. All rights reserved.

Discovering New Global Climate Patterns: Curating a 21-Year High Temporal (Hourly) and Spatial (40km) Resolution Reanalysis Dataset

NASA Astrophysics Data System (ADS)

Hou, C. Y.; Dattore, R.; Peng, G. S.

2014-12-01

The National Center for Atmospheric Research's Global Climate Four-Dimensional Data Assimilation (CFDDA) Hourly 40km Reanalysis dataset is a dynamically downscaled dataset with high temporal and spatial resolution. The dataset contains three-dimensional hourly analyses in netCDF format for the global atmospheric state from 1985 to 2005 on a 40km horizontal grid (0.4°grid increment) with 28 vertical levels, providing good representation of local forcing and diurnal variation of processes in the planetary boundary layer. This project aimed to make the dataset publicly available, accessible, and usable in order to provide a unique resource to allow and promote studies of new climate characteristics. When the curation project started, it had been five years since the data files were generated. Also, although the Principal Investigator (PI) had generated a user document at the end of the project in 2009, the document had not been maintained. Furthermore, the PI had moved to a new institution, and the remaining team members were reassigned to other projects. These factors made data curation in the areas of verifying data quality, harvest metadata descriptions, documenting provenance information especially challenging. As a result, the project's curation process found that: Data curator's skill and knowledge helped make decisions, such as file format and structure and workflow documentation, that had significant, positive impact on the ease of the dataset's management and long term preservation. Use of data curation tools, such as the Data Curation Profiles Toolkit's guidelines, revealed important information for promoting the data's usability and enhancing preservation planning. Involving data curators during each stage of the data curation life cycle instead of at the end could improve the curation process' efficiency. Overall, the project showed that proper resources invested in the curation process would give datasets the best chance to fulfill their potential to help with new climate pattern discovery.

Potential of a cure in patients with colorectal liver metastases and concomitant extrahepatic disease.

PubMed

Imai, Katsunori; Castro Benitez, Carlos; Allard, Marc-Antoine; Vibert, Eric; Sa Cunha, Antonio; Cherqui, Daniel; Castaing, Denis; Bismuth, Henri; Baba, Hideo; Adam, René

2017-03-01

We aimed to define the cure rate in patients with colorectal liver metastases (CRLM) and concomitant extrahepatic disease (EHD) on the 5-year disease-free survival (DFS) after surgery, and identify the factors for predicting a cure. Patients who underwent hepatectomy for CRLM with concomitant EHD were identified. Those followed for >5 years after surgery were enrolled. A cure was defined as DFS of >5 years after the last curative surgery. A cure was achieved in 24/175 (13%) patients (intention-to-treat [ITT] cohort), and 22/109 (19%) patients who underwent complete resection for both hepatic and extrahepatic metastases (EHD resection cohort). A multivariate analysis identified primary T1-2 (relative risk [RR] 47.4, P = 0.0001), metachronous metastasis (RR 4.9, P = 0.026), carbohydrate antigen 19-9 (CA19-9) ≤37 U/mL (RR 8.37, P = 0.015), number of liver and EHD tumors (RR 11.2, P = 0.0058), and non-incidental EHD diagnosis (RR 8.41, P = 0.018) as independent factors that predicted a cure in the ITT cohort; and primary T1-2 (RR 22.2, P = 0.013), primary N0 (RR 4.42, P = 0.031), metachronous metastasis (RR 6.48, P = 0.013), and CA19-9 ≤37 U/mL (RR 27.4, P = 0.012) in the EHD resection cohort. Even when concomitant EHD is present, a potential of cure could be achieved with aggressive oncosurgical approach. © 2017 Wiley Periodicals, Inc.

[A Curatively Resected Case of Lateral Lymph Node Metastasis Five-Years after Initial Surgery for Rectal Cancer].

PubMed

Miura, Takayuki; Tsunenari, Takazumi; Sasaki, Tsuyoshi; Yokoyama, Tadaaki; Fukuhara, Kenji

2017-11-01

A 74-year-old male had undergone laparoscopic abdominoperineal resection for lower rectal cancer in July 2009. The pathological diagnosis was T2, N0, M0, pStage I (TNM 7th). Because of pathological venous invasion, adjuvant chemotherapy with Tegafur-uracil(UFT)plus Leucovorin for a year was performed. A CT examination revealed slowly growing peripheral right internal iliaclymph node. PET-CT demonstrated a 20mm right lateral lymph node(LLN)metastasis without other distant metastases. On diagnosis of solitary LLN metastasis of rectal cancer, the patient underwent surgical lymph node resection in September 2014. The pathological diagnosis was lymph node metastasis from rectal cancer. Subsequently, the patient received mFOLFOX6 adjuvant chemotherapy for 6 months. The patient remains alive without any recurrence 31 months after the second surgical treatment. lt is important to consider that LLN metastasis of Stage I rectal cancer might still occur a long time after the curative operation.

Prognostic significance of cancer family history for patients with gastric cancer: a single center experience from China.

PubMed

Liu, Xiaowen; Cai, Hong; Yu, Lin; Huang, Hua; Long, Ziwen; Wang, Yanong

2016-06-14

Family history of cancer is a risk factor for gastric cancer. In this study, we investigated the prognoses of gastric cancer patients with family history of cancer. A total of 1805 gastric cancer patients who underwent curative gastrectomy from 2000 to 2008 were evaluated. The clinicopathologic parameters and prognoses of gastric cancer patients with a positive family history (PFH) of cancer were compared with those with a negative family history (NFH). Of 1805 patients, 382 (21.2%) patients had a positive family history of cancer. Positive family history of cancer correlated with younger age, more frequent alcohol and tobacco use, worse differentiation, smaller tumor size, and more frequent tumor location in the lower 1/3 of the stomach. The prognoses of patients with a positive family history of cancer were better than that of patients with a negative family history. Family history of cancer independently correlated with better prognosis after curative gastrectomy in gastric cancer patients.

[Surgical treatment of pulmonary metastases from colon and rectal cancer].

PubMed

Togashi, Ken-ichi; Aoki, K; Hirahara, H; Sugawara, M; Oguma, F

2004-09-01

We retrospectively studied the surgical treatment for pulmonary metastases from colon and rectal cancer. A total of 24 patients (9 males and 15 females; mean age 61 years) underwent 29 thoracotomies for metastatic colon carcinoma, while 22 patients (16 males and 6 females; mean age 63 years) underwent 29 thoracotomies for metastatic rectal cancer. The median interval between the primary procedure and lung resection for metastases was 26 months in the patients with colon carcinoma and 32 months in the patients with rectal cancer. In the patients with colon carcinoma, 16 underwent wedge resection or segmentectomy (including 4 video-assisted procedures) and 13 (54%) underwent lobectomy or pneumonectomy. In the patients with rectal cancer, 15 underwent wedge or segmentectomy (including 1 video-assisted procedure), 13 (59%) underwent lobectomy or pneumonectomy, and 1 underwent exploratory thoracotomy. All procedures except exploratory thoracotomy were curative operations. There was no mortality. Overall 5-year survival was 56% (n=46). Five-year survival was 65% for patients with colon metastases (n=24) and 45% for patients with rectal metastases (n=22), and there was no significant difference. Recurrent sites were 4 lungs (36%), 4 livers (36%), 1 bone, 1 uterus, and 1 peritoneum in patients with colon carcimoma, and 10 lungs (43%), 5 brains (22%), 3 livers (13%), 1 bone, and 1 vagina in patients with rectal cancer. Pulmonary resection for metastases from colon carcinoma may have better prognosis than that from rectal cancer. However, further investigation may be required to obtain convincing conclusions.

Impact of MLH1 expression on tumor evolution after curative surgical tumor resection in a murine orthotopic xenograft model for human MSI colon cancer.

PubMed

Meunier, Katy; Ferron, Marianne; Calmel, Claire; Fléjou, Jean-François; Pocard, Marc; Praz, Françoise

2017-09-01

Colorectal cancers (CRCs) displaying microsatellite instability (MSI) most often result from MLH1 deficiency. The aim of this study was to assess the impact of MLH1 expression per se on tumor evolution after curative surgical resection using a xenograft tumor model. Transplantable tumors established with the human MLH1-deficient HCT116 cell line and its MLH1-complemented isogenic clone, mlh1-3, were implanted onto the caecum of NOD/SCID mice. Curative surgical resection was performed at day 10 in half of the animals. The HCT116-derived tumors were more voluminous compared to the mlh1-3 ones (P = .001). Lymph node metastases and peritoneal carcinomatosis occurred significantly more often in the group of mice grafted with HCT116 (P = .007 and P = .035, respectively). Mlh1-3-grafted mice did not develop peritoneal carcinomatosis or liver metastasis. After surgical resection, lymph node metastases only arose in the group of mice implanted with HCT116 and the rate of cure was significantly lower than in the mlh1-3 group (P = .047). The murine orthotopic xenograft model based on isogenic human CRC cell lines allowed us to reveal the impact of MLH1 expression on tumor evolution in mice who underwent curative surgical resection and in mice whose tumor was left in situ. Our data indicate that the behavior of MLH1-deficient CRC is not only governed by mutations arising in genes harboring microsatellite repeated sequences but also from their defect in MLH1 as such. © 2017 Wiley Periodicals, Inc.

Curated eutherian third party data gene data sets.

PubMed

Premzl, Marko

2016-03-01

The free available eutherian genomic sequence data sets advanced scientific field of genomics. Of note, future revisions of gene data sets were expected, due to incompleteness of public eutherian genomic sequence assemblies and potential genomic sequence errors. The eutherian comparative genomic analysis protocol was proposed as guidance in protection against potential genomic sequence errors in public eutherian genomic sequences. The protocol was applicable in updates of 7 major eutherian gene data sets, including 812 complete coding sequences deposited in European Nucleotide Archive as curated third party data gene data sets.

Effect of Cushing's syndrome - Endogenous hypercortisolemia on cardiovascular autonomic functions.

PubMed

Jyotsna, V P; Naseer, Ali; Sreenivas, V; Gupta, Nandita; Deepak, K K

2011-02-24

Cushing's syndrome is associated with increased cardiovascular morbidity and mortality. It's also associated with other cardiac risk factors like hypertension, diabetes mellitus and obesity. Cardiovascular autonomic function impairment could predict cardiovascular morbidity and mortality. Twenty five patients with Cushing's syndrome without diabetes and twenty five age matched healthy controls underwent a battery of cardiovascular autonomic function tests including deep breath test, Valsalva test, hand grip test, cold pressor test and response to standing from lying position. The rise in diastolic blood pressure on hand grip test and diastolic BP response to cold pressor test in Cushing's patients were significantly less compared to healthy controls (9.83 ± 3.90 vs 20.64 ± 9.55, p<0.001 and 10.09 ± 4.07 vs 15.33 ± 6.26, p<0.01 respectively). The E:I ratio on deep breathing test was also less in the patients in comparison to controls (1.36 ± 0.21 vs 1.53 ± 0.19, p<0.01). Seven patients underwent the same battery of tests 6 months after a curative surgery showing a trend towards normalization with significant improvement in expiratory to inspiratory ratio and sinus arrhythmia delta heart rate. To conclude, this study showed that chronic endogenous hypercortisolism in Cushing's is associated with an impaired sympathetic cardiovascular autonomic functioning. After a curative surgery, some of the parameters tend to improve. Copyright © 2010 Elsevier B.V. All rights reserved.

[D2 lymph node dissection in gastric cancer surgery: long term results--analysis of an experience with 227 patients].

PubMed

Vasilescu, C; Herlea, V; Tidor, S; Ivanov, B; Stănciulea, Oana; Mănuc, M; Gheorghe, C; Ionescu, M; Diculescu, M; Popescu, I

2006-01-01

The main objective of the study was to evaluate the postoperative mortality and 5 year survival in gastric cancer patients undergoing a minimum of D2 lymphadenectomy. A retrospective study was conducted on 1170 patients operated for gastric adenocarcinoma in the Department of General Surgery and Liver Transplantation of Fundeni Clinical Institute, between 1997 and April 2005. Only 443 patients underwent a curative resection, from which 216 patients had D1 resection and in 227 cases a D2 or D3/D4 lymphadenectomy was performed. Information about survival was available for 189 patients of those who had a D1 resection and for 210 of those who underwent a D2 or D3/D4 lymphadenectomy. Postoperative mortality was 6.5% in the group of curative resection, with 9.2% for D1 and 3.9% for D2/D3 D4. Five year survival according to Kaplan Meier curves was 32 % in the D1 group vs. 51,8% in D2/D3-D4 (p <0.0001). Significant differences were noted in the median survival-- D2/D3-D4 group 63 months vs. 28 months in D1 group. Our data support the gastric resection with a minimum of D2 lymphadenectomy in the radical surgery of gastric cancer. However, an accurate interpretation of the statistical interpretation between the different groups of patients is difficult, mainly because of the retrospective character of the study.

Should elderly patients with higher-risk myelodysplastic syndromes undergo allogeneic hematopoietic stem cell transplantation?

PubMed

Zeidan, Amer M; Gore, Steven D

2013-10-01

Myelodysplastic syndromes (MDS) include a group of hematopoietic malignancies characterized by dysplastic changes, ineffective hematopoiesis and variable risk of leukemic progression. At diagnosis, 86% of MDS patients are ≥60 years. Azacitidine, the only drug that prolongs life in high-risk (HR)-MDS patients, adds a median of only 9.5 months to life. Allogeneic stem cell transplantation (alloSCT) remains the only potentially curative approach. Despite recent improvements including use of reduced intensity conditioning (RIC) that decrease transplant-related mortality, alloSCT continues to be used rarely in elderly MDS. There is paucity of data regarding outcomes of RIC alloSCT in elderly MDS patients, especially in direct comparison with azanucleosides. In this paper, the authors discuss the recent Markov decision analysis by Koreth et al. in which investigators demonstrated superior survival of patients with HR-MDS aged 60-70 years who underwent RIC alloSCT in comparison with those who were treated with azanucleosides.

Pilot study of postoperative adjuvant chemoradiation for advanced gastric cancer: Adjuvant 5-FU/cisplatin and chemoradiation with capecitabine

PubMed Central

Lee, Hyung-Sik; Choi, Youngmin; Hur, Won-Joo; Kim, Hyo-Jin; Kwon, Hyuk-Chan; Kim, Sung-Hyun; Kim, Jae-Seok; Lee, Jong-Hoon; Jung, Ghap-Joong; Kim, Min-Chan

2006-01-01

AIM: To evaluate the efficacy and toxicity of postoperative chemoradiation using FP chemotherapy and oral capecitabine during radiation for advanced gastric cancer following curative resection. METHODS: Thirty-one patients who had underwent a potentially curative resection for Stage III and IV (M0) gastric cancer were enrolled. Therapy consists of one cycle of FP (continuous infusion of 5-FU 1000 mg/m2 on d 1 to 5 and cisplatin 60 mg/m2 on d 1) followed by 4500 cGy (180 cGy/d) with capecitabine (1650 mg/m2 daily throughout radiotherapy). Four wk after completion of the radiotherapy, patients received three additional cycles of FP every three wk. The median follow-up duration was 22.2 mo. RESULTS: The 3-year disease free and overall survival in this study were 82.7% and 83.4%, respectively. Four patients (12.9%) showed relapse during follow-up. Eight patients did not complete all planned adjuvant therapy. Grade 3/4 toxicities included neutropenia in 50.2%, anemia in 12.9%, thrombocytopenia in 3.2% and nausea/vomiting in 3.2%. Neither grade 3/4 hand foot syndrome nor treatment related febrile neutropenia or death were observed. CONCLUSION: These preliminary results suggest that this postoperative adjuvant chemoradiation regimen of FP before and after capecitabine and concurrent radiotherapy appears well tolerated and offers a comparable toxicity profile to the chemoradiation regimen utilized in INT-0116. This treatment modality allowed successful loco-regional control rate and 3-year overall survival. PMID:16489675

Discrepancy between recurrence-free survival and overall survival in patients with resectable colorectal liver metastases: a potential surrogate endpoint for time to surgical failure.

PubMed

Oba, Masaru; Hasegawa, Kiyoshi; Matsuyama, Yutaka; Shindoh, Junichi; Mise, Yoshihiro; Aoki, Taku; Sakamoto, Yoshihiro; Sugawara, Yasuhiko; Makuuchi, Masatoshi; Kokudo, Norihiro

2014-06-01

Recurrence-free survival (RFS) may not be a surrogate for overall survival (OS) in patients with resectable colorectal liver metastases (CLM). We investigated whether a new composite tool-time to surgical failure (TSF)-is a suitable endpoint. The medical records of consecutive patients who underwent curative resection for CLM at our center over a 17-year period were reviewed. Patients with liver-limited tumors (n = 371) who had not received previous treatment for metastasis were eligible for analysis. TSF was defined as the time until unresectable relapse or death. The correlations between TSF and OS, and between RFS and OS, were assessed for all the eligible patients. The median OS, TSF, and RFS were 5.7, 2.7, and 0.7 years, respectively, and the 5-year OS, TSF, and RFS rates were 52.6, 39.8, and 23.7 %, respectively, for all patients. The rates of first, second, and third relapse were 75.5, 77.6, and 70.8 %, respectively, and repeat resections were performed in 54.3 % (first relapses), 40.7 % (second relapses), and 47.1 % (third relapses) of patients. The concordance proportions of TSF and RFS for OS events were 0.83 and 0.65, respectively. The correlation between TSF and OS was stronger than that between RFS and OS in terms of the predicted probabilities. The correlation between TSF and OS was stronger than that between RFS and OS after curative hepatic resection. TSF could be a suitable endpoint for CLM overall management.

Emerging role of multimodality treatment in gall bladder cancer: Outcomes following 510 consecutive resections in a tertiary referral center.

PubMed

Patkar, Shraddha; Ostwal, Vikas; Ramaswamy, Anant; Engineer, Reena; Chopra, Supriya; Shetty, Nitin; Dusane, Rohit; Shrikhande, Shailesh V; Goel, Mahesh

2018-03-01

Gall bladder cancer (GBC) is a disease with high incidence in India. We analyzed the outcomes of patients with suspected GBC who underwent surgical exploration. Analysis of a prospectively maintained database of patients undergoing surgical exploration for clinic-radiologically suspected GBC from January 2010 to August 2015. Outcomes as well as factors influencing survival were analyzed. Five hundred and ten patients underwent surgery for suspected GBC. Of these 400 had histologically proven malignancy. Eighty patients were deemed inoperable. Radical cholecystectomy was performed in 153 patients, revision surgery for incidental GBC in 160 and port site excision in seven patients. A total of 112 received peri-operative chemotherapy or chemoradiation. Majority were stage III (36%, n = 144) and stage II (31.8% n = 127). At a median follow up of 28.4 months, the median overall survival (OS) was not yet reached. Median disease free survival (DFS) was 33.4 months. Lymph node involvement, stage of the disease and resection status were the main factors influencing outcomes (P = 0.0001). Surgery alone is curative only for early GBC (Stage I). Combination of surgery and peri-operative systemic therapy results in favorable outcomes even in stage II/III disease. Potentially, multimodality treatment may add meaningful survival for this disease with inherently aggressive tumor biology. © 2017 Wiley Periodicals, Inc.

Outcomes After En Bloc Iliac Vessel Excision and Reconstruction During Pelvic Exenteration.

PubMed

Brown, Kilian G M; Koh, Cherry E; Solomon, Michael J; Qasabian, Raffi; Robinson, David; Dubenec, Steven

2015-09-01

Advanced pelvic cancers involving the lateral pelvic compartment, and particularly the iliac vasculature, are difficult to manage. Common or external iliac vessel involvement has traditionally been considered a contraindication for curative surgery. The purpose of this study was to investigate pathological and surgical outcomes, particularly postoperative morbidity of pelvic exenteration with en bloc major iliac vascular excision and reconstruction. This study was a case series. The study was conducted at a quaternary referral center for pelvic exenteration in Sydney. Patients included those undergoing en bloc iliac vessel excision as part of their pelvic exenteration for a locally advanced pelvic malignancy. Over the study period, 336 patients underwent pelvic exenteration. Twenty-one patients (6.3%) underwent en bloc vascular excision of 29 vessels for tumor involvement. Twenty-four vessels required reconstruction. The primary outcomes were postoperative complications and pathologic outcomes. Survival rates were estimated using the Kaplan-Meier technique. Operating time for patients who underwent vascular excision and reconstruction was longer, but this did not reach significance (631 vs 531 minutes; p = 0.052). Mean blood loss was significantly higher in the vascular excision and reconstruction group (6.8 vs 3.4 L; p < 0.001). Patients who required en bloc vascular excision were less likely to have R0 margins compared with patients who did not (38% vs 78%; p < 0.001). There was no intraoperative or 30-day mortality. Overall graft patency and limb loss at 1 year were 96% and 0%. A total of 52% of patients had at least 1 vascular related complication. Median overall and disease-free survival times were 34 and 26 months. This study is limited by a relatively small number of heterogeneous patients. En bloc vascular resection and reconstruction for contiguous tumor involvement is feasible and safe in selected patients. Advanced pelvic tumors involving iliac vessels should not be precluded from curative surgery in specialized institutions.

Diagnosis and treatment of solid pseudopapillary tumor of the pancreas: experience of one single institution from Turkey

PubMed Central

2013-01-01

Background Solid pseudopapillary neoplasia (SPN) of the pancreas is an extremely rare epithelial tumor of low malignant potential. SPN accounts for less than 1% to 2% of exocrine pancreatic tumors. The aim of this study is to report our experience with SPN of the pancreas. It includes a summary of the current literature to provide a reference for the management of this rare clinical entity. Methods A retrospective analysis was performed of all patients diagnosed and treated for SPN in our hospital over the past 15 years (1998 to 2013). A database of the characteristics of these patients was developed, including age, gender, tumor location and size, treatment, and histopathological and immunohistochemical features. Results During this time period, 255 patients with pancreatic malignancy (which does not include ampulla vateri, distal choledocal and duodenal tumor) were admitted to our department, only 10 of whom were diagnosed as having SPN (2.5%). Nine patients were women (90%) and one patient was a man (10%). Their median age was 38.8 years (range 18 to 71). The most common symptoms were abdominal pain and dullness. Seven patients (70%) presented with abdominal pain or abdominal dullness and three patient (30%) were asymptomatic with the diagnosis made by an incidental finding on routine examination. Abdominal computed tomography and/or magnetic resonance imaging showed the typical features of solid pseudopapillary neoplasm in six (60%) of the patients. Four patients underwent distal pancreatectomy with splenectomy, one patient underwent a total mass excision, and one patient underwent total pancreatic resection. Two required extended distal pancreatectomy with splenectomy. Two underwent spleen-preserving distal pancreatectomy. Conclusions SPN is a rare neoplasm that primarily affects young women. The prognosis is favorable even in the presence of distant metastasis. Although surgical resection is generally curative, a close follow-up is advised in order to diagnose a local recurrence or distant metastasis and choose the proper therapeutic option for the patient. PMID:24289652

Deviating colostomy construction versus stent placement as bridge to surgery for malignant left-sided colonic obstruction.

PubMed

Amelung, Femke J; Ter Borg, Frank; Consten, Esther C J; Siersema, Peter D; Draaisma, Werner A

2016-12-01

Acute colonic decompression using a deviating colostomy (DC) or a self-expandable metal stent (SEMS) has been shown to lead to fewer complications and permanent stomas compared to acute resection in elderly patients with malignant left-sided colonic obstruction (LSCO). However, no consensus exists on which decompression method is superior, especially in patients treated with curative intend. This retrospective study therefore aimed to compare both decompression methods in potentially curable LSCO patients. All LSCO patients treated with curative intent between 2004 and 2013 in two teaching hospitals were retrospectively identified. In one institution, a DC was the standard of care, whereas in the other all patients were treated with SEMS. In total, 88 eligible LSCO patients with limited disease and curative treatment options were included; 51 patients had a SEMS placed and 37 patients a DC constructed. All patients eventually underwent a subsequent elective resection. In sum, 235 patients were excluded due to benign or inoperable disease. No significant differences were found for hospital stay, morbidity, disease-free and overall survival and mortality. Major complications were seen in 13/51 (25.5 %) patients in the SEMS group and were mostly due to stent dysfunction (n = 7). Also, one stent-related perforation occurred. Major complications occurred in 4/37 (10.8 %) patients in the DC group, including abdominal sepsis (n = 3) and wound dehiscence (n = 1). Long-term complication rate was significantly higher in the DC group (29.7 vs. 9.8 %, p = 0.01), mainly due to a high incisional hernia rate. Fewer patients had a temporary colostomy following elective resection after SEMS placement (62.2 vs. 17.6 %, p < 0.01). Permanent colostomy rate was not significantly different. SEMS and DC are both effective decompression methods for curable LSCO patients with comparable short- and long-term oncological outcomes; however, more surgical procedures are performed after DC due to an increased number of temporary colostomies and incisional hernia repairs.

Development of Gene Therapy for Thalassemia

PubMed Central

Nienhuis, Arthur W.; Persons, Derek A.

2012-01-01

Retroviral vector–mediated gene transfer into hematopoietic stem cells provides a potentially curative therapy for severe β-thalassemia. Lentiviral vectors based on human immunodeficiency virus have been developed for this purpose and have been shown to be effective in curing thalassemia in mouse models. One participant in an ongoing clinical trial has achieved transfusion independence after gene transfer into bone marrow stem cells owing, in part, to a genetically modified, dominant clone. Ongoing efforts are focused on improving the efficiency of lentiviral vector–mediated gene transfer into stem cells so that the curative potential of gene transfer can be consistently achieved. PMID:23125203

Body mass index and buttock circumference are independent predictors of disintegration failure in extracorporeal shock wave lithotripsy for ureteral calculi.

PubMed

Yang, Teng-Kai; Yang, Hung-Ju; Lee, Liang-Min; Liao, Chun-Hou

2013-07-01

Effective stone disintegration by extracorporeal shockwave lithotripsy (ESWL) may depend on patient- and stone-related factors. We investigated predictors of disintegration failure in ESWL for a solitary ureteral calculus. From July 2008 to May 2010, 203 patients who underwent ESWL for a solitary ureteral calculus were enrolled. Clinical and radiologic data were collected, and factors related to ESWL failure were analyzed. Fifty-two patients (25.6%) showed ESWL failure, with a mean follow-up of 41 days. Forty patients (19.7%) required retreatment, including 12 who underwent repeat ESWL and 28 who underwent curative ureteroscopy. Patients with ESWL failure had significantly higher body weight, body mass index (BMI), and buttock circumference (BC) than patients for whom ESWL was successful. Univariate analysis showed that stone burden (odds ratio [OR], 1.04; 95% confidence interval [CI], 1.03-1.06) and BC (OR, 1.06; 95% CI, 1.01-1.11) were predictors of ESWL failure, while BMI was a potential predictor with borderline significance (OR, 1.09; 95% CI, 0.99-1.20). Multivariate analysis showed that stone burden (OR, 1.04; 95% CI, 1.03-1.06) was a significant predictor for all patients. On stratifying patients according to the level of ureteral calculi, BC was found to be an independent predictor (OR, 1.35; 95% CI, 1.02-1.80) for ESWL failure for middle/lower ureteral calculi and BMI (OR, 1.47; 95% CI, 1.13-1.91) for upper ureteral calculi. Stone burden is the main predictor of ESWL failure for all patients with ureteral calculi. BC and BMI are independent predictors for ESWL failure for middle/lower and upper ureteral calculi, respectively. Copyright © 2012. Published by Elsevier B.V.

Outcomes of the 'Data Curation for Geobiology at Yellowstone National Park' Workshop

NASA Astrophysics Data System (ADS)

Thomer, A.; Palmer, C. L.; Fouke, B. W.; Rodman, A.; Choudhury, G. S.; Baker, K. S.; Asangba, A. E.; Wickett, K.; DiLauro, T.; Varvel, V.

2013-12-01

The continuing proliferation of geological and biological data generated at scientifically significant sites (such as hot springs, coral reefs, volcanic fields and other unique, data-rich locales) has created a clear need for the curation and active management of these data. However, there has been little exploration of what these curation processes and policies would entail. To that end, the Site-Based Data Curation (SBDC) project is developing a framework of guidelines and processes for the curation of research data generated at scientifically significant sites. A workshop was held in April 2013 at Yellowstone National Park (YNP) to gather input from scientists and stakeholders. Workshop participants included nine researchers actively conducting geobiology research at YNP, and seven YNP representatives, including permitting staff and information professionals from the YNP research library and archive. Researchers came from a range of research areas -- geology, molecular and microbial biology, ecology, environmental engineering, and science education. Through group discussions, breakout sessions and hands-on activities, we sought to generate policy recommendations and curation guidelines for the collection, representation, sharing and quality control of geobiological datasets. We report on key themes that emerged from workshop discussions, including: - participants' broad conceptions of the long-term usefulness, reusability and value of data. - the benefits of aggregating site-specific data in general, and geobiological data in particular. - the importance of capturing a dataset's originating context, and the potential usefulness of photographs as a reliable and easy way of documenting context. - researchers' and resource managers' overlapping priorities with regards to 'big picture' data collection and management in the long-term. Overall, we found that workshop participants were enthusiastic and optimistic about future collaboration and development of community approaches to data sharing. We hope to continue discussion of geobiology data curation challenges and potential strategies at AGU. Outcomes from the workshop are guiding next steps in the SBDC project, led by investigators at the Center for Informatics Research in Science and Scholarship and Institute for Genomic Biology at the University of Illinois, in collaboration with partners at Johns Hopkins University and YNP.

MortalityPredictors.org: a manually-curated database of published biomarkers of human all-cause mortality

PubMed Central

Winslow, Ksenia; Ho, Andrew; Fortney, Kristen; Morgen, Eric

2017-01-01

Biomarkers of all-cause mortality are of tremendous clinical and research interest. Because of the long potential duration of prospective human lifespan studies, such biomarkers can play a key role in quantifying human aging and quickly evaluating any potential therapies. Decades of research into mortality biomarkers have resulted in numerous associations documented across hundreds of publications. Here, we present MortalityPredictors.org, a manually-curated, publicly accessible database, housing published, statistically-significant relationships between biomarkers and all-cause mortality in population-based or generally healthy samples. To gather the information for this database, we searched PubMed for appropriate research papers and then manually curated relevant data from each paper. We manually curated 1,576 biomarker associations, involving 471 distinct biomarkers. Biomarkers ranged in type from hematologic (red blood cell distribution width) to molecular (DNA methylation changes) to physical (grip strength). Via the web interface, the resulting data can be easily browsed, searched, and downloaded for further analysis. MortalityPredictors.org provides comprehensive results on published biomarkers of human all-cause mortality that can be used to compare biomarkers, facilitate meta-analysis, assist with the experimental design of aging studies, and serve as a central resource for analysis. We hope that it will facilitate future research into human mortality and aging. PMID:28858850

MortalityPredictors.org: a manually-curated database of published biomarkers of human all-cause mortality.

PubMed

Peto, Maximus V; De la Guardia, Carlos; Winslow, Ksenia; Ho, Andrew; Fortney, Kristen; Morgen, Eric

2017-08-31

Biomarkers of all-cause mortality are of tremendous clinical and research interest. Because of the long potential duration of prospective human lifespan studies, such biomarkers can play a key role in quantifying human aging and quickly evaluating any potential therapies. Decades of research into mortality biomarkers have resulted in numerous associations documented across hundreds of publications. Here, we present MortalityPredictors.org , a manually-curated, publicly accessible database, housing published, statistically-significant relationships between biomarkers and all-cause mortality in population-based or generally healthy samples. To gather the information for this database, we searched PubMed for appropriate research papers and then manually curated relevant data from each paper. We manually curated 1,576 biomarker associations, involving 471 distinct biomarkers. Biomarkers ranged in type from hematologic (red blood cell distribution width) to molecular (DNA methylation changes) to physical (grip strength). Via the web interface, the resulting data can be easily browsed, searched, and downloaded for further analysis. MortalityPredictors.org provides comprehensive results on published biomarkers of human all-cause mortality that can be used to compare biomarkers, facilitate meta-analysis, assist with the experimental design of aging studies, and serve as a central resource for analysis. We hope that it will facilitate future research into human mortality and aging.

Curation and Analysis of Samples from Comet Wild-2 Returned by NASA's Stardust Mission

NASA Technical Reports Server (NTRS)

Nakamura-Messenger, Keiko; Walker, Robert M.

2015-01-01

The NASA Stardust mission returned the first direct samples of a cometary coma from comet 81P/Wild-2 in 2006. Intact capture of samples encountered at 6 km/s was enabled by the use of aerogel, an ultralow dense silica polymer. Approximately 1000 particles were captured, with micron and submicron materials distributed along mm scale length tracks. This sample collection method and the fine scale of the samples posed new challenges to the curation and cosmochemistry communities. Sample curation involved extensive, detailed photo-documentation and delicate micro-surgery to remove particles without loss from the aerogel tracks. This work had to be performed in highly clean facility to minimize the potential of contamination. JSC Curation provided samples ranging from entire tracks to micrometer-sized particles to external investigators. From the analysis perspective, distinguishing cometary materials from aerogel and identifying the potential alteration from the capture process were essential. Here, transmission electron microscopy (TEM) proved to be the key technique that would make this possible. Based on TEM work by ourselves and others, a variety of surprising findings were reported, such as the observation of high temperature phases resembling those found in meteorites, rarely intact presolar grains and scarce organic grains and submicrometer silicates. An important lesson from this experience is that curation and analysis teams must work closely together to understand the requirements and challenges of each task. The Stardust Mission also has laid important foundation to future sample returns including OSIRIS-REx and Hayabusa II and future cometary nucleus sample return missions.

Radical cystectomy at Roswell Park Memorial Institute. Preoperative and post operative observations.

PubMed

Eisenkraft, S; Pontes, J E

1984-01-01

Between January 1979 and March 1983, 63 consecutive patients underwent cystectomy and urinary diversion for primary carcinoma of the bladder at Roswell Park Memorial Institute (RPMI). Fifty-five patients had transitional cell carcinoma, 6 squamous cell carcinoma and 2 adenocarcinoma of the bladder. Twelve patients with bladder cancer were found to have adenocarcinoma of the prostate on the pathological specimen. Preoperative radiation was given to 41 patients. Thirty-six patients received 4000 rads preoperatively followed by radical cystectomy, 5 patients received 2000 rads. Thirteen patients received 6000 rads as curative treatment and underwent salvage cystectomy and colon conduit because of failure. There was no operative mortality. Severe complications in the early postoperative period occurred in 19 instances, some patients having more than one complication. Late complications necessitating surgical correction occurred in 5 patients. Although radical cystectomy is effective in controlling the local disease, most patients still died of metastatic transitional cell carcinoma.

Integrating text mining into the MGI biocuration workflow

PubMed Central

Dowell, K.G.; McAndrews-Hill, M.S.; Hill, D.P.; Drabkin, H.J.; Blake, J.A.

2009-01-01

A major challenge for functional and comparative genomics resource development is the extraction of data from the biomedical literature. Although text mining for biological data is an active research field, few applications have been integrated into production literature curation systems such as those of the model organism databases (MODs). Not only are most available biological natural language (bioNLP) and information retrieval and extraction solutions difficult to adapt to existing MOD curation workflows, but many also have high error rates or are unable to process documents available in those formats preferred by scientific journals. In September 2008, Mouse Genome Informatics (MGI) at The Jackson Laboratory initiated a search for dictionary-based text mining tools that we could integrate into our biocuration workflow. MGI has rigorous document triage and annotation procedures designed to identify appropriate articles about mouse genetics and genome biology. We currently screen ∼1000 journal articles a month for Gene Ontology terms, gene mapping, gene expression, phenotype data and other key biological information. Although we do not foresee that curation tasks will ever be fully automated, we are eager to implement named entity recognition (NER) tools for gene tagging that can help streamline our curation workflow and simplify gene indexing tasks within the MGI system. Gene indexing is an MGI-specific curation function that involves identifying which mouse genes are being studied in an article, then associating the appropriate gene symbols with the article reference number in the MGI database. Here, we discuss our search process, performance metrics and success criteria, and how we identified a short list of potential text mining tools for further evaluation. We provide an overview of our pilot projects with NCBO's Open Biomedical Annotator and Fraunhofer SCAI's ProMiner. In doing so, we prove the potential for the further incorporation of semi-automated processes into the curation of the biomedical literature. PMID:20157492

Integrating text mining into the MGI biocuration workflow.

PubMed

Dowell, K G; McAndrews-Hill, M S; Hill, D P; Drabkin, H J; Blake, J A

2009-01-01

A major challenge for functional and comparative genomics resource development is the extraction of data from the biomedical literature. Although text mining for biological data is an active research field, few applications have been integrated into production literature curation systems such as those of the model organism databases (MODs). Not only are most available biological natural language (bioNLP) and information retrieval and extraction solutions difficult to adapt to existing MOD curation workflows, but many also have high error rates or are unable to process documents available in those formats preferred by scientific journals.In September 2008, Mouse Genome Informatics (MGI) at The Jackson Laboratory initiated a search for dictionary-based text mining tools that we could integrate into our biocuration workflow. MGI has rigorous document triage and annotation procedures designed to identify appropriate articles about mouse genetics and genome biology. We currently screen approximately 1000 journal articles a month for Gene Ontology terms, gene mapping, gene expression, phenotype data and other key biological information. Although we do not foresee that curation tasks will ever be fully automated, we are eager to implement named entity recognition (NER) tools for gene tagging that can help streamline our curation workflow and simplify gene indexing tasks within the MGI system. Gene indexing is an MGI-specific curation function that involves identifying which mouse genes are being studied in an article, then associating the appropriate gene symbols with the article reference number in the MGI database.Here, we discuss our search process, performance metrics and success criteria, and how we identified a short list of potential text mining tools for further evaluation. We provide an overview of our pilot projects with NCBO's Open Biomedical Annotator and Fraunhofer SCAI's ProMiner. In doing so, we prove the potential for the further incorporation of semi-automated processes into the curation of the biomedical literature.

Clinical Interpretation and Implications of Whole-Genome Sequencing

PubMed Central

Dewey, Frederick E.; Grove, Megan E.; Pan, Cuiping; Goldstein, Benjamin A.; Bernstein, Jonathan A.; Chaib, Hassan; Merker, Jason D.; Goldfeder, Rachel L.; Enns, Gregory M.; David, Sean P.; Pakdaman, Neda; Ormond, Kelly E.; Caleshu, Colleen; Kingham, Kerry; Klein, Teri E.; Whirl-Carrillo, Michelle; Sakamoto, Kenneth; Wheeler, Matthew T.; Butte, Atul J.; Ford, James M.; Boxer, Linda; Ioannidis, John P. A.; Yeung, Alan C.; Altman, Russ B.; Assimes, Themistocles L.; Snyder, Michael; Ashley, Euan A.; Quertermous, Thomas

2014-01-01

IMPORTANCE Whole-genome sequencing (WGS) is increasingly applied in clinical medicine and is expected to uncover clinically significant findings regardless of sequencing indication. OBJECTIVES To examine coverage and concordance of clinically relevant genetic variation provided by WGS technologies; to quantitate inherited disease risk and pharmacogenomic findings in WGS data and resources required for their discovery and interpretation; and to evaluate clinical action prompted by WGS findings. DESIGN, SETTING, AND PARTICIPANTS An exploratory study of 12 adult participants recruited at Stanford University Medical Center who underwent WGS between November 2011 and March 2012. A multidisciplinary team reviewed all potentially reportable genetic findings. Five physicians proposed initial clinical follow-up based on the genetic findings. MAIN OUTCOMES AND MEASURES Genome coverage and sequencing platform concordance in different categories of genetic disease risk, person-hours spent curating candidate disease-risk variants, interpretation agreement between trained curators and disease genetics databases, burden of inherited disease risk and pharmacogenomic findings, and burden and interrater agreement of proposed clinical follow-up. RESULTS Depending on sequencing platform, 10% to 19% of inherited disease genes were not covered to accepted standards for single nucleotide variant discovery. Genotype concordance was high for previously described single nucleotide genetic variants (99%-100%) but low for small insertion/deletion variants (53%-59%). Curation of 90 to 127 genetic variants in each participant required a median of 54 minutes (range, 5-223 minutes) per genetic variant, resulted in moderate classification agreement between professionals (Gross κ, 0.52; 95%CI, 0.40-0.64), and reclassified 69%of genetic variants cataloged as disease causing in mutation databases to variants of uncertain or lesser significance. Two to 6 personal disease-risk findings were discovered in each participant, including 1 frameshift deletion in the BRCA1 gene implicated in hereditary breast and ovarian cancer. Physician review of sequencing findings prompted consideration of a median of 1 to 3 initial diagnostic tests and referrals per participant, with fair interrater agreement about the suitability of WGS findings for clinical follow-up (Fleiss κ, 0.24; P < 001). CONCLUSIONS AND RELEVANCE In this exploratory study of 12 volunteer adults, the use of WGS was associated with incomplete coverage of inherited disease genes, low reproducibility of detection of genetic variation with the highest potential clinical effects, and uncertainty about clinically reportable findings. In certain cases, WGS will identify clinically actionable genetic variants warranting early medical intervention. These issues should be considered when determining the role of WGS in clinical medicine. PMID:24618965

Management of Laryngoceles by Transoral Robotic Approach.

PubMed

Kayhan, Fatma Tülin; Güneş, Selçuk; Koç, Arzu Karaman; Yiğider, Ayşe Pelin; Kaya, Kamil Hakan

2016-06-01

Laryngoceles are air-filled sacs which communicate with the laryngeal lumen. When filled with mucus or pus, they are called laryngomucoceles and laryngopyoceles, respectively. Transoral robotic surgery (TORS) is a new and remarkable technique that expands its usefullness in otorhinolaryngology. Conventional treatments for laryngoceles were previously performed using external approaches, with aesthetically unfavorable and less function-sparing results. Transoral laser microsurgical approaches for laryngoceles were seldom reported. It is aimed to present authors' clinical experience on laryngocele management with TORS which is a rather new technique. A retrospective patient serial. Patients were evaluated for demographic data, type of lesion, reasons for hospital admittance, complaint duration, and previous surgery. Robotic surgery panel including anesthesia time, duration of surgery, need for tracheotomy, postoperative care, follow-up, and recurrence rates were also summarized. Six men (mean age 51.7 years; range 41-62) with laryngoceles underwent successful TORS. Dyspnea and hoarseness were the main complaints. Two patients had undergone previous laryngeal surgery due to laryngeal cancer, with no recurrence of malignancy at admittance for laryngocele. Three had simple laryngocele, 2 had laryngomucocele, and 1 had laryngopyocele. No laryngoceles recurred and no complication such as dysphonia or prolonged dysphagia occurred. Transoral robotic surgery was found superior in safety, technical feasibility and curative effectiveness, when compared with classical methods, especially due to absence of skin incisions. Surgical modalities for laryngocele excision should be directed toward a curative target including cosmetic and functional success, technical achievability, and surgically curative methods. Transoral robotic surgery provided all these features.

Regulation and Function of Cytokines that Predict Prostate Cancer Metastasis

DTIC Science & Technology

2012-08-01

one given the potential for attempts at local curative therapy (whether it be surgery, radiation or cryotherapy ) to subject the patient to both short...from the prostate cancer [2]. Next, following local curative therapy the issue of requirement and timing for second line adjuvant therapy becomes...with locally advanced disease. W81XWH-09-1-0503 Bhowmick, Neil A. 6 f. References [1] Jemal A, Tiwari RC, Murray T, Ghafoor

Curative effects of microneedle fractional radiofrequency system on skin laxity in Asian patients: A prospective, double-blind, randomized, controlled face-split study.

PubMed

Lu, Wenli; Wu, Pinru; Zhang, Zhen; Chen, Jinan; Chen, Xiangdong; Ewelina, Biskup

2017-04-01

To date, no studies compared curative effects of thermal lesions in deep and superficial dermal layers in the same patient (face-split study). To evaluate skin laxity effects of microneedle fractional radiofrequency induced thermal lesions in different dermal layers. 13 patients underwent three sessions of a randomized face-split microneedle fractional radiofrequency system (MFRS) treatment of deep dermal and superficial dermal layer. Skin laxity changes were evaluated objectively (digital images, 2 independent experts) and subjectively (patients' satisfaction numerical rating). 12 of 13 subjects completed a course of 3 treatments and a 1-year follow-up. Improvement of nasolabial folds in deep dermal approach was significantly better than that in superficial approach at three months (P=.0002) and 12 months (P=.0057) follow-up. Effects on infraorbital rhytides were only slightly better (P=.3531). MFRS is an effective method to improve skin laxity. Thermal lesion approach seems to provide better outcomes when applied to deep dermal layers. It is necessary to consider the skin thickness of different facial regions when choosing the treatment depth.

How do we value a cure?

PubMed

Husereau, Don

2015-01-01

Future perceptions of the value of curative therapies will likely reflect debates happening today about preferences for funding of preventive versus treatment programs, as well as funding orphan drugs. Little is known about how society will value curative therapies versus standard treatments, and the significant role of a host of psychological factors compared to overarching concerns about opportunity costs will likely lead to significant tension between payers and the public. More research to clarify societal preferences and healthcare goals in regards to curative therapies and in light of the potential for significant opportunity costs will be required. Given what we know about preferences for the funding of prevention and treatment measures, we should expect that cures will not be held to a different measure.

Curative effect and safety of vascularized fibula grafting in renal transplant recipients with osteonecrosis of the femoral head: three case reports.

PubMed

Guo, Y J; Jin, D X; Zhang, C Q; Chen, S B; Sheng, J G; Lee, H S; Zhang, K G; Zeng, B F

2009-11-01

Osteonecrosis of the femoral head is a common and severe complication after renal transplantation. It is characterized by deterioration of hip joint function, which impairs quality of life. We present 3 renal transplant case reports of patients with osteonecrosis of the femoral head who underwent free vascularized fibular grafting at our hospital. Follow-up was from 1(1/2) to 2 years. All 3 patients exhibited good recovery with substantial improvement in joint function. Intraoperative and postoperative findings demonstrated the safety of this surgical procedure.

Laryngeal chondroradionecrosis following radiotherapy.

PubMed

Melo, Giulianno Molina; Souza, Paula Demetrio; Bastos, Luiz Castro; Neves, Murilo Catafesta; Espirito Santo, Kleber Simões do; Cervantes, Onivaldo; Abrahão, Márcio

2017-01-01

to study larynx chondroradionecrosis related to radiotherapy and chemotherapy treatment and provide a treatment flowchart. retrospective study with clinical data analysis of all larynx cancer patients admitted in a two tertiary hospital in a five years period. from 131 patients treated for larynx cancer, 28 underwent chemoradiotherapy with curative intent and three of them presented chondroradionecrosis. They were treated with hiperbaric oxigen therapy and surgical debridment following our flowchart, preserving the larynx in all. the incidence of chondroradionecrosis as a complication of chemoradiotherapy in our series was 10,7% and the treatment with hiperbaric oxigen therapy, based in our flowchart, was effective to control this complication.

Endoscopic management of sinonasal hemangiopericytoma.

PubMed

Tessema, Belachew; Eloy, Jean Anderson; Folbe, Adam J; Anstead, Amy S; Mirani, Neena M; Jourdy, Deya N; Joudy, Deya N; Ruiz, Jose W; Casiano, Roy R

2012-03-01

Sinonasal hemangiopericytomas (SNHPCs) are rare perivascular tumors with low-grade malignant potential. Traditionally, these tumors have been treated with open approaches such as lateral rhinotomy, Caldwell-Luc, or transfacial approaches. Increased experience with endoscopic management of benign and malignant sinonasal tumors has led to a shift in management of SNHPC. The authors present their experience in the largest series of patients with SNHPC managed endoscopically. Case series at a tertiary care medical center. A retrospective chart review of all patients undergoing endoscopic management of SNHPC at the University of Miami between 1999 and 2008 was conducted. All endoscopic resections were performed with curative intent. Twelve patients with the diagnosis of SNHPC were treated endoscopically. Mean age was 62.5 years (range, 51-83 years). There were 6 men and 6 women. The mean follow-up was 41 months (range, 15-91 months). Seven (58.3%) presented with nasal obstruction, whereas 4 (41.6%) had epistaxis as their initial presenting symptom. Preoperative angiography or embolization was not performed in any case. Mean estimated blood loss was 630 mL (range, 100-1500 mL). Six patients underwent endonasal endoscopic anterior skull base resection; 4 had complete endoscopic resection all with negative margins. None underwent postoperative adjuvant treatment. No recurrence or metastatic disease was observed in this patient population. Endoscopic management of SNHPC is a feasible approach and did not compromise outcomes in this experience. In this series, familiarity with advance endoscopic sinus surgery was necessary to manage these patients. Postoperative adjuvant therapy was not necessary in this cohort.

Nutritional status and postoperative outcomes in patients with gastrointestinal cancer in Vietnam: a retrospective cohort study.

PubMed

Loan, Bui Thi Hong; Nakahara, Shinji; Tho, Bui An; Dang, Tran Ngoc; Anh, Le Ngoc; Huy, Nguyen Do; Ichikawa, Masao

2018-04-01

Nutritional support for surgical care is crucial because hospital malnutrition is rather common. However, low- and middle-income countries have not adequately addressed nutritional management of surgical patients. To highlight need for nutritional management in surgical patients, the present study aimed to describe preoperative nutritional status in patients who underwent gastrointestinal cancer surgery in Vietnam and to investigate the relationship between preoperative malnutrition and adverse outcomes, such as postoperative complications and prolonged length of hospital stay. We reviewed medical records of patients who underwent a major curative surgery for gastrointestinal cancer at the national hospital in Ho Chi Minh City, Vietnam. We identified preoperative malnutrition based on body mass index and serum albumin level, and postoperative complications in the first 30 d postoperative. We estimated the relative influence of malnutrition on complications and length of hospital stay using multivariate regression models. Of 459 eligible patients, 63% had colorectal cancer, 33% gastric cancer, and 4% esophageal cancer. The prevalence of malnutrition was 19%. No patients died during hospitalization; however, 26% developed complications after surgery. The average length of hospital stay was 14 d. After controlling for potential confounders, preoperative malnutrition was associated with an increased risk of postoperative complications (odds ratio = 1.97) and prolonged hospital stay (2.8 d). Preoperative malnutrition affects surgical outcomes among patients with gastrointestinal cancer in Vietnam. We recommend implementing preoperative nutritional interventions to achieve better outcomes among surgical cancer patients. Copyright © 2017 Elsevier Inc. All rights reserved.

Radiofrequency Catheter Ablation for Atrial Fibrillation Elicited "Jackhammer Esophagus": A New Complication Due to Vagal Nerve Stimulation?

PubMed

Tolone, Salvatore; Savarino, Edoardo; Docimo, Ludovico

2015-10-01

Radiofrequency catheter ablation (RFCA) is a potentially curative method for treatment of highly symptomatic and drug-refractory atrial fibrillation (AF). However, this technique can provoke esophageal and nerve lesion, due to thermal injury. To our knowledge, there have been no reported cases of a newly described motor disorder, the Jackhammer esophagus (JE) after RFCA, independently of GERD. We report a case of JE diagnosed by high-resolution manometry (HRM), in whom esophageal symptoms developed 2 weeks after RFCA, in absence of objective evidence of GERD. A 65-year-old male with highly symptomatic, drug-refractory paroxysmal AF was candidate to complete electrical pulmonary vein isolation with RFCA. Prior the procedure, the patient underwent HRM and impedance-pH to rule out GERD or hiatal hernia presence. All HRM parameters, according to Chicago classification, were within normal limits. No significant gastroesophageal reflux was documented at impedance pH monitoring. Patient underwent RFCA with electrical disconnection of pulmonary vein. After two weeks, patient started to complain of dysphagia for solids, with acute chest-pain. The patient repeated HRM and impedance-pH monitoring 8 weeks after RFCA. HRM showed in all liquid swallows the typical spastic hypercontractile contractions consistent with the diagnosis of JE, whereas impedance-pH monitoring resulted again negative for GERD. Esophageal dysmotility can represent a possible complication of RFCA for AF, probably due to a vagal nerve injury, and dysphagia appearance after this procedure must be timely investigated by HRM.

Patient Perceptions Regarding the Likelihood of Cure After Surgical Resection of Lung and Colorectal Cancer

PubMed Central

Kim, Yuhree; Winner, Megan; Page, Andrew; Tisnado, Diana M.; Martinez, Kathryn A.; Buettner, Stefan; Ejaz, Aslam; Spolverato, Gaya; Morss, Sydney E.; Pawlik, Timothy M.

2016-01-01

BACKGROUND The objective of the current study was to characterize the prevalence of the expectation that surgical resection of lung or colorectal cancer might be curative. The authors sought to assess patient-level, tumor-level, and communication-level factors associated with the perception of cure. METHODS Between 2003 and 2005, a total of 3954 patients who underwent cancer-directed surgery for lung (30.3%) or colorectal (69.7%) cancer were identified from a population-based and health system-based survey of participants from multiple US regions. RESULTS Approximately 80.0% of patients with lung cancer and 89.7% of those with colorectal cancer responded that surgery would cure their cancer. Even 57.4% and 79.8% of patients with stage IV lung and colorectal cancer, respectively, believed surgery was likely to be curative. On multivariable analyses, the odds ratio (OR) of the perception of curative intent was found to be higher among patients with colorectal versus lung cancer (OR, 2.27). Patients who were female, with an advanced tumor stage, unmarried, and having a higher number of comorbidities were less likely to believe that surgery would cure their cancer; educational level, physical function, and insurance status were not found to be associated with perception of cure. Patients who reported optimal physician communication scores (reference score, 0–80; score of 80–100 [OR, 1.40] and score of 100 [OR, 1.89]) and a shared role in decision-making with their physician (OR, 1.16) or family (OR, 1.17) had a higher odds of perceiving surgery would be curative, whereas patients who reported physician-controlled (OR, 0.56) or family-controlled (OR, 0.72) decision-making were less likely to believe surgery would provide a cure. CONCLUSIONS Greater focus on patient-physician engagement, communication, and barriers to discussing goals of care with patients who are diagnosed with cancer is needed. PMID:26094729

Patient perceptions regarding the likelihood of cure after surgical resection of lung and colorectal cancer.

PubMed

Kim, Yuhree; Winner, Megan; Page, Andrew; Tisnado, Diana M; Martinez, Kathryn A; Buettner, Stefan; Ejaz, Aslam; Spolverato, Gaya; Morss Dy, Sydney E; Pawlik, Timothy M

2015-10-15

The objective of the current study was to characterize the prevalence of the expectation that surgical resection of lung or colorectal cancer might be curative. The authors sought to assess patient-level, tumor-level, and communication-level factors associated with the perception of cure. Between 2003 and 2005, a total of 3954 patients who underwent cancer-directed surgery for lung (30.3%) or colorectal (69.7%) cancer were identified from a population-based and health system-based survey of participants from multiple US regions. Approximately 80.0% of patients with lung cancer and 89.7% of those with colorectal cancer responded that surgery would cure their cancer. Even 57.4% and 79.8% of patients with stage IV lung and colorectal cancer, respectively, believed surgery was likely to be curative. On multivariable analyses, the odds ratio (OR) of the perception of curative intent was found to be higher among patients with colorectal versus lung cancer (OR, 2.27). Patients who were female, with an advanced tumor stage, unmarried, and having a higher number of comorbidities were less likely to believe that surgery would cure their cancer; educational level, physical function, and insurance status were not found to be associated with perception of cure. Patients who reported optimal physician communication scores (reference score, 0-80; score of 80-100 [OR, 1.40] and score of 100 [OR, 1.89]) and a shared role in decision-making with their physician (OR, 1.16) or family (OR, 1.17) had a higher odds of perceiving surgery would be curative, whereas patients who reported physician-controlled (OR, 0.56) or family-controlled (OR, 0.72) decision-making were less likely to believe surgery would provide a cure. Greater focus on patient-physician engagement, communication, and barriers to discussing goals of care with patients who are diagnosed with cancer is needed. © 2015 American Cancer Society.

Prostate cancer. Mortality and morbidity after non-curative treatment with aspects on diagnosis and treatment.

PubMed

Aus, G

1994-01-01

To investigate the mortality, need for hospital care and palliative treatments in patients with prostate cancer (PC) treated with non-curative intention (i.e. deferred or hormonal treatment). To evaluate acceptance by patients and complications of a new diagnostic procedure for PC -- transrectal ultrasound (TRUS) and core biopsies. To investigate if knowledge of prostate volume enhances the accuracy of prostate specific antigen (PSA) to indicate non-palpable PC. Finally, to investigate how neo-adjuvant hormonal treatment before radical prostatectomy affected PSA and tumour volume. In a retrospective analysis of all 536 patients with a known diagnosis of PC who died in the city of Göteborg during the years 1988-90, age at diagnosis, survival time, need for hospital care and cause of death were registered (I and II). A questionnaire was sent to 511 patients who underwent TRUS with or without prostatic biopsies (III). In 120 consecutive patients admitted for TURP due to presumed benign prostatic hyperplasia, a comparison was made between PSA and prostate-volume-adjusted (measured via TRUS) PSA (PSADensity) to indicate the presence of non-palpable PC (IV). Of 56 patients who underwent radical prostatectomy, 28 received 3 months' pretreatment with a GnRH-agonist. The effects on tumour volumes (assessed by the planimetric method on whole mount slides) and PSA were studied (V). Overall, 62% of patients with a known diagnosis of PC died of the disease when all patients were followed from diagnosis until death (up to 25 years). Of patients in stage M0 at diagnosis, 50% died of PC. However, in patients who survived for more than 10 years the mortality reached 63% (I). The average PC patient needed 27 days of hospital stay (geriatric wards excluded) and 185 patients needed at least one palliative TURP, 103 patients palliative radiation therapy and 55 patients procedures due to upper urinary tract obstruction. The lion's share of these resources was consumed by patients who later succumbed to PC (II). Ninety-five per cent of patients reported none or minor discomfort after TRUS of the prostate and 92% if TRUS was combined with transrectal core biopsies of the prostate. Haematuria for > 2 days occurred in 13%, haematospermia > 2 days in 9% and blood in stool > 2 days in 3% among patients who underwent core biopsies but none of these patients needed active treatment. Overall, 4.1% of biopsied patients experienced urinary tract infection (III). The use of PSADensity with a cut-off value of 0.10 ng/ml/cc rendered both higher sensitivity (75 vs 50%) and positive predictive value (0.33 vs 0.15) for indicating non-palpable PC in symptomatic patients with benign findings on digital rectal examination (IV). Pretreatment with a GnRH-agonist resulted in a significant PSA decrease not explained by changes in tumour volume. Tumour volume reduction was found in 36% of the patients. According to these studies, PC is a progressive disease with considerable mortality and morbidity when managed by non-curative intention. Since new diagnostic and therapeutic methods described in this thesis are well accepted by patients and may increase the chance of radical surgery, it is reasonable to offer younger patients with long life expectancy the chance of early detection and treatment with curative intention.

Potential usefulness of a topic model-based categorization of lung cancers as quantitative CT biomarkers for predicting the recurrence risk after curative resection

NASA Astrophysics Data System (ADS)

Kawata, Y.; Niki, N.; Ohmatsu, H.; Satake, M.; Kusumoto, M.; Tsuchida, T.; Aokage, K.; Eguchi, K.; Kaneko, M.; Moriyama, N.

2014-03-01

In this work, we investigate a potential usefulness of a topic model-based categorization of lung cancers as quantitative CT biomarkers for predicting the recurrence risk after curative resection. The elucidation of the subcategorization of a pulmonary nodule type in CT images is an important preliminary step towards developing the nodule managements that are specific to each patient. We categorize lung cancers by analyzing volumetric distributions of CT values within lung cancers via a topic model such as latent Dirichlet allocation. Through applying our scheme to 3D CT images of nonsmall- cell lung cancer (maximum lesion size of 3 cm) , we demonstrate the potential usefulness of the topic model-based categorization of lung cancers as quantitative CT biomarkers.

Successful control of Epstein-Barr virus (EBV)-infected cells by allogeneic nonmyeloablative stem cell transplantation in a patient with the lethal form of chronic active EBV infection.

PubMed

Uehara, Taeko; Nakaseko, Chiaki; Hara, Satoru; Harima, Akane; Ejiri, Megumi; Yokota, Akira; Saito, Yasushi; Nishimura, Miki

2004-08-01

Chronic active Epstein-Barr virus infection (CAEBV) is a heterogeneous EBV-related disorder, ranging from mild/moderate forms to rapidly lethal disorders. The lethal form of CAEBV is characterized by multiple organ failure, hemophagocytic syndrome, and development of lymphomas. Allogeneic stem cell transplantation is considered as the only potentially curative treatment for the lethal form of CAEBV, but it is not always desirable because of the high incidence of regimen-related toxicities. A 17-year-old female with CAEBV, who was refractory to conventional therapies and considered to be unable to receive a myeloablative regimen because of multiple organ dysfunction, underwent allogeneic nonmyeloablative stem cell transplantation (allo-NST) before developing a hematological malignancy. She has been well without any signs of CAEBV for 27 months after allo-NST, and we confirmed that specific cytotoxic T lymphocyte activity against EBV was reconstituted. This outcome suggests that allo-NST can control CAEBV by reconstituting the host immunity against EBV. Copyright 2004 Wiley-Liss, Inc.

Surgical Resection for Lymph Node Metastasis After Liver Transplantation for Hepatocellular Carcinoma.

PubMed

Ikegami, Toru; Yoshizumi, Tomoharu; Kawasaki, Jyunji; Nagatsu, Akihisa; Uchiyama, Hideaki; Harada, Noboru; Harimoto, Norifumi; Itoh, Shinji; Motomura, Takashi; Soejima, Yuji; Maehara, Yoshihiko

2017-02-01

Treatment strategies for lymph node (LN) metastasis after liver transplantation (LT) for hepatocellular carcinoma (HCC) have not been studied. The treatment modes and outcomes in patients with LN metastasis after LT (n=6) for HCC were reviewed. The mean time from LT to LN recurrence was 2.0±1.3 years, and the locations of the LNs recurrences included the phrenic (n=2), common hepatic artery (n=2), inferior vena cava (n=1) and gastric (n=1) regions. Treatments included surgery alone (n=3), surgery followed by chemoradiation (n=1), radiation followed by chemotherapy (n=1), and chemotherapy, radiation and sorafenib (n=1). Although the patients receiving non-surgical treatments (n=3) died within 1.2 years, those who underwent surgical removal of the metastatic LNs survived 11.2 years, 4.5 years and 0.8 years, respectively, without any signs of re-recurrence. Surgical resection is the only feasible and potentially curative treatment for LN metastasis after LT for HCC. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

Administration Dependent Antioxidant Effect of Carica papaya Seeds Water Extract

PubMed Central

Panzarini, Elisa; Dwikat, Majdi; Mariano, Stefania; Vergallo, Cristian; Dini, Luciana

2014-01-01

Carica papaya is widely used in folk medicine as herbal remedy to prevent, protect against, and cure several diseases. These curative properties are based on the presence in different parts of the plant of phytochemical nutrients with antioxidant effect. Seeds are the less exploited part; thus this study is aimed at assessing the antioxidant activities of the C. papaya seeds water extract against hydrogen peroxide (H2O2) oxidative stress in human skin Detroit 550 fibroblasts. C. papaya seeds water extract is not toxic and acts as a potent free radical scavenger, providing protection to Detroit 550 fibroblasts that underwent H2O2 oxidative stress. Data show that (i) the maximum protective effect is achieved by the simultaneous administration of the extract with 1 mM H2O2; (ii) the extract in presence of an oxidative stress does not increase catalase activity and prevents the release of cytochrome C and the inner mitochondrial transmembrane potential (Δψ m) loss; (iii) the extract is more efficient than vitamin C to hamper the oxidative damage; (iv) the purified subfractions of the seeds water extract exert the same antioxidant effect of whole extract. In conclusion, C. papaya seeds water extract is potentially useful for protection against oxidative stress. PMID:24795765

Role of salvage esophagectomy after definitive chemoradiotherapy.

PubMed

Tachimori, Yuji

2009-02-01

Chemoradiotherapy has become a popular definitive therapy among many patients and oncologists for potentially resectable esophageal carcinoma. Although the complete response rates are high and short-term survival is favorable after chemoradiotherapy, persistent or recurrent locoregional disease is quite frequent. Salvage surgery is the sole curative intent treatment option for this course. As experience with definitive chemoradiotherapy grows, the number of salvage surgeries may increase. Selected articles about salvage esophagectomy after definitive chemoradiotherapy for esophageal carcinoma are reviewed. The number of salvage surgeries was significantly lower than the number of expected candidates. To identify candidates for salvage surgery, patients undergoing definitive chemoradiotherapy should be followed up carefully. Salvage esophagectomy is difficult when dissecting fibrotic masses from irradiated tissues. Patients who underwent salvage esophagectomy had increased morbidity and mortality. Pulmonary complications such as pneumonia and acute respiratory distress syndrome were common. The anastomotic leak rate was significantly increased because of the effects of the radiation administered to the tissues used as conduits. The most significant factor associated with long-term survival appeared to be complete resection. However, precise evaluation of resectability before operation was difficult. Nevertheless, increased morbidity and mortality will be acceptable in exchange for potential long-term survival after salvage esophagectomy. Such treatment should be considered for carefully selected patients at specialized centers.

Outcome of Radiation Monotherapy for High-risk Patients with Stage I Esophageal Cancer.

PubMed

Shirakawa, Yasuhiro; Noma, Kazuhiro; Maeda, Naoaki; Tanabe, Shunsuke; Kuroda, Shinji; Kagawa, Shunsuke; Katsui, Kuniaki; Katayama, Norihisa; Kanazawa, Susumu; Fujiwara, Toshiyoshi

2017-04-01

Currently, chemoradiation is the most widely used nonsurgical treatment for esophageal cancer. However, some patients, particularly the very elderly or those with severe vital organ dysfunction, face difficulty with the chemotherapy component. We therefore examined the outcome of radiation therapy (RT) alone for patients with esophageal cancer at our facility. Between January 2005 and December 2014, 84 patients underwent RT at our hospital, and 78 of these patients received concomitant chemotherapy. The remaining 6 patients underwent RT alone; these patients were considered to be high-risk and to have no lymph node metastasis (stage I). Five of them received irradiation up to a curative dose: 4 showed a complete response (CR) and 1 showed a partial response (PR). Of the patients exhibiting CR, 3 are currently living recurrence-free, whereas 1 patient underwent endoscopic submucosal dissection (ESD) as salvage therapy for local recurrence, with no subsequent recurrence. High-risk stage I esophageal cancer patients can be treated radically with RT alone under certain conditions. In the future, to broaden the indications for RT monotherapy to include some degree of advanced cancers, a novel concurrent therapy should be identified.

Long-term survival benefit of upfront chemotherapy in patients with newly diagnosed borderline resectable pancreatic cancer.

PubMed

Shrestha, Bikram; Sun, Yifei; Faisal, Farzana; Kim, Victoria; Soares, Kevin; Blair, Alex; Herman, Joseph M; Narang, Amol; Dholakia, Avani S; Rosati, Lauren; Hacker-Prietz, Amy; Chen, Linda; Laheru, Daniel A; De Jesus-Acosta, Ana; Le, Dung T; Donehower, Ross; Azad, Nilofar; Diaz, Luis A; Murphy, Adrian; Lee, Valerie; Fishman, Elliot K; Hruban, Ralph H; Liang, Tingbo; Cameron, John L; Makary, Martin; Weiss, Matthew J; Ahuja, Nita; He, Jin; Wolfgang, Christopher L; Huang, Chiung-Yu; Zheng, Lei

2017-07-01

The use of neoadjuvant chemotherapy or radiation for borderline resectable pancreatic adenocarcinoma (BL-PDAC) is increasing. However, the impact of neoadjuvant chemotherapy and radiation therapy on the outcome of BL-PDAC remains to be elucidated. We performed a retrospective analysis of 93 consecutive patients who were diagnosed with BL-PDAC and primarily followed at Johns Hopkins Hospital between February 2007 and December 2012. Among 93 patients, 62% received upfront neoadjuvant chemotherapy followed by chemoradiation, whereas 20% received neoadjuvant chemoradiation alone and 15% neoadjuvant chemotherapy alone. Resectability following all neoadjuvant therapy was 44%. Patients who underwent resection with a curative intent had a median overall survival (mOS) of 25.8 months, whereas those who did not undergo surgery had a mOS of 11.9 months. However, resectability and overall survival were not significantly different between the three types of neoadjuvant therapy. Nevertheless, 22% (95% CI, 0.13-0.36) of the 58 patients who received upfront chemotherapy followed by chemoradiation remained alive for a minimum of 48 months compared to none of the 19 patients who received upfront chemoradiation. Among patients who underwent curative surgical resection, 32% (95% CI, 0.19-0.55) of those who received upfront chemotherapy remained disease free at least 48 months following surgical resection, whereas none of the eight patients who received upfront chemoradiation remained disease free beyond 24 months following surgical resection. Neoadjuvant therapy with upfront chemotherapy may result in long-term survival in a subpopulation of patients with BL-PDAC. © 2017 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

Survival impact of lymphocyte infiltration into the tumor of hepatocellular carcinoma in hepatitis B virus-positive or non-B non-C patients who underwent curative resection.

PubMed

Nakagawa, Shigeki; Umezaki, Naoki; Yamao, Takanobu; Kaida, Takayoshi; Okabe, Hirohisa; Mima, Kosuke; Imai, Katsunori; Hashimoto, Daisuke; Yamashita, Yo-Ichi; Ishiko, Takatoshi; Chikamoto, Akira; Baba, Hideo

2018-02-01

The prognostic value of lymphocyte infiltration into hepatocellular carcinoma (HCC) is still controversial, and it has not been reported in hepatitis B virus (HBV)-positive or non-B non-C (NBNC) HCC. The aim of this study is to assess the prognostic significance of lymphocyte infiltrate in tumor for HBV-positive and NBNC HCC patients. This study investigated 145 HBV-positive or NBNC patients who underwent hepatectomy for HCC between January 2001 and May 2009. Cumulative recurrence rate, overall survival (OS), and clinicopathological parameters were analyzed according to lymphocyte infiltration in tumor. In patients with low lymphocyte infiltration, the 5-year recurrence rate was higher and OS was poor (86.4 and 44.1%, respectively) than that of the patients with high lymphocyte infiltration (55.3 and 83.7%, respectively). Multivariate analyses revealed that independent risk factors for recurrence were low albumin value (hazard ratio [HR] 2.33, P = 0.009), high American Joint Committee on Cancer (AJCC) T stage (HR 2.31, P < 0.0001), high α-fetoprotein (AFP) value (HR 2.06, P = 0.005), and low lymphocyte infiltration (HR 2.50, P = 0.0001). The independent risk factors for OS were low albumin value (HR 3.69, P = 0.003), high AJCC T stage (HR 2.10, P = 0.049), high AFP value (HR 3.98, P < 0.001), and low lymphocyte infiltration (HR 3.47, P = 0.001). Lymphocyte infiltrate in tumor is significantly associated high recurrence rate and poor overall survival. Evaluation of the infiltrating lymphocyte could improve the prediction of prognosis in HCC patients after curative resection. © 2017 The Japan Society of Hepatology.

Diffuse malignant peritoneal mesothelioma: Evaluation of systemic chemotherapy with comprehensive treatment through the RENAPE Database: Multi-Institutional Retrospective Study.

PubMed

Kepenekian, V; Elias, D; Passot, G; Mery, E; Goere, D; Delroeux, D; Quenet, F; Ferron, G; Pezet, D; Guilloit, J M; Meeus, P; Pocard, M; Bereder, J M; Abboud, K; Arvieux, C; Brigand, C; Marchal, F; Classe, J M; Lorimier, G; De Chaisemartin, C; Guyon, F; Mariani, P; Ortega-Deballon, P; Isaac, S; Maurice, C; Gilly, F N; Glehen, O

2016-09-01

Diffuse malignant peritoneal mesothelioma (DMPM) is a severe disease with mainly locoregional evolution. Cytoreductive surgery and hyperthermic intraperitoneal chemotherapy (CRS-HIPEC) is the reported treatment with the longest survival. The aim of this study was to evaluate the impact of perioperative systemic chemotherapy strategies on survival and postoperative outcomes in patients with DMPM treated with curative intent with CRS-HIPEC, using a multi-institutional database: the French RENAPE network. From 1991 to 2014, 126 DMPM patients underwent CRS-HIPEC at 20 tertiary centres. The population was divided into four groups according to perioperative treatment: only neoadjuvant chemotherapy (NA), only adjuvant chemotherapy (ADJ), perioperative chemotherapy (PO) and no chemotherapy before or after CRS-HIPEC (NoC). All groups (NA: n = 42; ADJ: n = 16; PO: n = 16; NoC: n = 48) were comparable regarding clinicopathological data and main DMPM prognostic factors. After a median follow-up of 61 months, the 5-year overall survival (OS) was 40%, 67%, 62% and 56% in NA, ADJ, PO and NoC groups, respectively (P = 0.049). Major complications occurred for 41%, 45%, 35% and 41% of patients from NA, ADJ, PO and NoC groups, respectively (P = 0.299). In multivariate analysis, NA was independently associated with worse OS (hazard ratio, 2.30; 95% confidence interval, 1.07-4.94; P = 0.033). This retrospective study suggests that adjuvant chemotherapy may delay recurrence and improve survival and that NA may impact negatively the survival for patients with DMPM who underwent CRS-HIPEC with curative intent. Upfront CRS and HIPEC should be considered when achievable, waiting for stronger level of scientific evidence. Copyright © 2016 Elsevier Ltd. All rights reserved.

[Lung Resection after Definitive and Neo-Adjuvant Chemoradiation for Stage IIIA/B Locally Advanced Non-Small Cell Lung Cancer: a Retrospective Analysis].

PubMed

Schreiner, Waldemar; Gavrychenkova, Sofiia; Dudek, Wojciech; Lettmaier, Sebastian; Rieker, Ralf; Fietkau, Rainer; Sirbu, Horia

2018-06-01

The outcomes of so called "salvage" resections after definitive chemoradiation vs. curative resections after neoadjuvant chemoradiation therapy (IT-resection) in patients with stage IIIA/B locally advanced non-small cell lung cancer have rarely been compared. The aim of our study was to compare perioperative results, postoperative and recurrence-free survival and to identify relevant prognostic survival factors for both therapy strategies. Between June 2008 and May 2017, 43 patients underwent pulmonary resection following induction therapy (group 1) and 14 patients underwent salvage resection after definitive chemoradiation (group 2). Retrospective analysis was performed of demographic factors, tumour stage and location, initial therapy, preoperative regression status, perioperative morbidity and mortality, postoperative and recurrence-free survival. In group 2, significantly higher radiation dose was applied (p < 0.001) and the interval between chemoradiation and lung resection was significantly longer (p = 0.02). In addition, significantly higher perioperative blood loss and more frequent blood transfusions were noted (p = 0.003 and 0.005, respectively). Perioperative morbidity and mortality were statistically comparable in the two groups (p = 0.72 and 0.395, respectively). Postoperative 5 year survival in group 1 was 55%, in group 2 48% (log-rank p = 0.353). Five year recurrence-free survival in group 1 was 53%, in group 2 42% (log-rank p = 0.180). Diffuse metastasis occurred mostly in group 2, whereas in group 1 oligometastasis was more frequently noted. Postoperative outcome after salvage resection seems statistically comparable to results following curative resection after induction therapy. Diffuse distant metastasis is frequently noted. Careful patient selection is required. Georg Thieme Verlag KG Stuttgart · New York.

Phase II clinical trial of local use of GM-CSF for prevention and treatment of chemotherapy- and concomitant chemoradiotherapy-induced severe oral mucositis in advanced head and neck cancer patients: an evaluation of effectiveness, safety and costs.

PubMed

Mantovani, Giovanni; Massa, Elena; Astara, Giorgio; Murgia, Viviana; Gramignano, Giulia; Lusso, Maria Rita; Camboni, Paolo; Ferreli, Luca; Mocci, Miria; Perboni, Simona; Mura, Loredana; Madeddu, Clelia; Macciò, Antonio

2003-01-01

In the present open non-randomized phase II study we looked for effectiveness, safety, tolerability and costs of locally applied GM-CSF in preventing or treating mucositis in patients receiving chemotherapy or chemoradiotherapy for head and neck cancer. In addition to clinical mucositis scoring system, the effects of treatment with GM-CSF were evaluated by its impact on patient quality of life and by laboratory immunological assays such as serum proinflammatory cytokines, IL-2 and leptin. The trial was designed to assess the effectiveness of local GM-CSF treatment in two different settings: i) prophylaxis of mucositis; ii) treatment of mucositis. Prophylaxis was chosen for chemoradiotherapy treatments of high mucosatoxic potential, while curative treatment was reserved for chemotherapy or chemoradiotherapy treatments of lesser potential of inducing mucositis. From January 1998 to December 2001, 68 patients entered the study. The great majority of patients of both groups had head and neck cancer, were stage IV, PS ECOG 0-1, were habitual smokers and were treated with chemotherapy and concomitant (or sequential) chemoradiotherapy. Forty-six patients were included in the 'prophylactic' setting and 22 patients in the 'curative' setting. The main findings of our study are: only 50% of patients included in the 'prophylactic' setting developed mucositis; the duration of oral mucositis from appearance until complete remission was significantly shorter in the 'prophylactic' than in the 'curative' setting; the mean grade of oral mucositis at baseline, on day 3 of therapy and on day 6 of therapy was significantly lower in the 'prophylactic' than in the 'curative' setting; 24 (55.82%) patients in the 'prophylactic' setting had grade 3/4 oral mucositis at baseline compared to 25 (80.60%) patients in the 'curative' setting (p=0.048). Thirteen (30.23%) patients in the 'prophylactic' setting had grade 3/4 oral mucositis on day 3 of therapy compared to 19 (61.29%) patients in the 'curative' setting (p=0.015); 'prophylactic' setting was able to shorten grade 3/4 oral mucositis to grade 0/1 more effectively than the 'curative' one on day 6 of therapy (p=0.05). The present clinical trial is to date by far the largest study assessing the effectiveness of topical GM-CSF and it is the first study comparing the efficacy of topical GM-CSF in the 'prophylactic' setting, i.e., with the aim to prevent the chemoradiotherapy-induced oral mucositis, with that in the 'curative' treatment, i.e., the therapy for established oral mucositis. The topical application of GM-CSF was demonstrated to be effective for oral mucositis induced by chemotherapy and chemoradiotherapy regimens. Moreover, the 'prophylactic' setting was demonstrated to be more effective than the 'curative' one.

Cost-effectiveness analysis of potentially curative and combination treatments for hepatocellular carcinoma with person-level data in a Canadian setting.

PubMed

Thein, Hla-Hla; Isaranuwatchai, Wanrudee; Qiao, Yao; Wong, Kenny; Sapisochin, Gonzalo; Chan, Kelvin K W; Yoshida, Eric M; Earle, Craig C

2017-09-01

Patients with early-stage hepatocellular carcinoma (HCC) are potential candidates for curative treatments such as radiofrequency ablation (RFA), surgical resection (SR), or liver transplantation (LT), which have demonstrated a significant survival benefit. We aimed to estimate the cost-effectiveness of curative and combination treatment strategies among patients diagnosed with HCC during 2002-2010. This study used Ontario Cancer Registry-linked administrative data to estimate effectiveness and costs (2013 USD) of the treatment strategies from the healthcare payer's perspective. Multiple imputation by logistic regression was used to handle missing data. A net benefit regression approach of baseline important covariates and propensity score adjustment were used to calculate incremental net benefit to generate incremental cost-effectiveness ratio (ICER) and uncertainty measures. Among 2,222 patients diagnosed with HCC, 10.5%, 14.1%, and 10.3% received RFA, SR, and LT monotherapy, respectively; 0.5-3.1% dual treatments; and 0.5% triple treatments. Compared with no treatment (53.2%), transarterial chemoembolization (TACE) + RFA (average $2,465, 95% CI: -$20,000-$36,600/quality-adjusted life years [QALY]) or RFA monotherapy ($15,553, 95% CI: $3,500-$28,500/QALY) appears to be the most cost-effective modality with lowest ICER value. The cost-effectiveness acceptability curve showed that if the relevant threshold was $50,000/QALY, RFA monotherapy and TACE+ RFA would have a cost-effectiveness probability of 100%. Strategies using LT delivered the most additional QALYs and became cost-effective at a threshold of $77,000/QALY. Our findings found that TACE+ RFA dual treatment or RFA monotherapy appears to be the most cost-effective curative treatment for patients with potential early stage of HCC in Ontario. These findings highlight the importance of identifying and measuring differential benefits, costs, and cost-effectiveness of alternative HCC curative treatments in order to evaluate whether they are providing good value for money in the real world. © 2017 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

Association of Hospital Costs With Complications Following Total Gastrectomy for Gastric Adenocarcinoma.

PubMed

Selby, Luke V; Gennarelli, Renee L; Schnorr, Geoffrey C; Solomon, Stephen B; Schattner, Mark A; Elkin, Elena B; Bach, Peter B; Strong, Vivian E

2017-10-01

Postoperative complications are associated with increased hospital costs following major surgery, but the mechanism by which they increase cost and the categories of care that drive this increase are poorly described. To describe the association of postoperative complications with hospital costs following total gastrectomy for gastric adenocarcinoma. This retrospective analysis of a prospectively collected gastric cancer surgery database at a single National Cancer Institute-designated comprehensive cancer center included all patients undergoing curative-intent total gastrectomy for gastric adenocarcinoma between January 2009 and December 2012 and was conducted in 2015 and 2016. Ninety-day normalized postoperative costs. Hospital accounting system costs were normalized to reflect Medicare reimbursement levels using the ratio of hospital costs to Medicare reimbursement and categorized into major cost categories. Differences between costs in Medicare proportional dollars (MP $) can be interpreted as the amount that would be reimbursed to an average hospital by Medicare if it paid differentially based on types and extent of postoperative complications. In total, 120 patients underwent curative-intent total gastrectomy for stage I through III gastric adenocarcinoma between 2009 and 2012. Of these, 79 patients (65.8%) were men, and the median (interquartile range) age was 64 (52-70) years. The 51 patients (42.5%) who underwent an uncomplicated total gastrectomy had a mean (SD) normalized cost of MP $12 330 (MP $2500), predominantly owing to the cost of surgical care (mean [SD] cost, MP $6830 [MP $1600]). The 34 patients (28.3%) who had a major complication had a mean (SD) normalized cost of MP $37 700 (MP $28 090). Surgical care was more expensive in these patients (mean [SD] cost, MP $8970 [MP $2750]) but was a smaller contributor to total cost (24%) owing to increased costs from room and board (mean [SD] cost, MP $11 940 [MP $8820]), consultations (mean [SD] cost, MP $3530 [MP $2410]), and intensive care unit care (mean [SD] cost, MP $7770 [MP $14 310]). Major complications were associated with tripled normalized costs following curative-intent total gastrectomy. Most of the excess costs were related to the treatment of complications. Interventions that decrease the number or severity of postoperative complications could result in substantial cost savings.

GEOMetaCuration: a web-based application for accurate manual curation of Gene Expression Omnibus metadata

PubMed Central

Li, Zhao; Li, Jin; Yu, Peng

2018-01-01

Abstract Metadata curation has become increasingly important for biological discovery and biomedical research because a large amount of heterogeneous biological data is currently freely available. To facilitate efficient metadata curation, we developed an easy-to-use web-based curation application, GEOMetaCuration, for curating the metadata of Gene Expression Omnibus datasets. It can eliminate mechanical operations that consume precious curation time and can help coordinate curation efforts among multiple curators. It improves the curation process by introducing various features that are critical to metadata curation, such as a back-end curation management system and a curator-friendly front-end. The application is based on a commonly used web development framework of Python/Django and is open-sourced under the GNU General Public License V3. GEOMetaCuration is expected to benefit the biocuration community and to contribute to computational generation of biological insights using large-scale biological data. An example use case can be found at the demo website: http://geometacuration.yubiolab.org. Database URL: https://bitbucket.com/yubiolab/GEOMetaCuration PMID:29688376

Missing metastases as a model to challenge current therapeutic algorithms in colorectal liver metastases.

PubMed

Lucidi, Valerio; Hendlisz, Alain; Van Laethem, Jean-Luc; Donckier, Vincent

2016-04-21

In oncosurgical approach to colorectal liver metastases, surgery remains considered as the only potentially curative option, while chemotherapy alone represents a strictly palliative treatment. However, missing metastases, defined as metastases disappearing after chemotherapy, represent a unique model to evaluate the curative potential of chemotherapy and to challenge current therapeutic algorithms. We reviewed recent series on missing colorectal liver metastases to evaluate incidence of this phenomenon, predictive factors and rates of cure defined by complete pathologic response in resected missing metastases and sustained clinical response when they were left unresected. According to the progresses in the efficacy of chemotherapeutic regimen, the incidence of missing liver metastases regularly increases these last years. Main predictive factors are small tumor size, low marker level, duration of chemotherapy, and use of intra-arterial chemotherapy. Initial series showed low rates of complete pathologic response in resected missing metastases and high recurrence rates when unresected. However, recent reports describe complete pathologic responses and sustained clinical responses reaching 50%, suggesting that chemotherapy could be curative in some cases. Accordingly, in case of missing colorectal liver metastases, the classical recommendation to resect initial tumor sites might have become partially obsolete. Furthermore, the curative effect of chemotherapy in selected cases could lead to a change of paradigm in patients with unresectable liver-only metastases, using intensive first-line chemotherapy to intentionally induce missing metastases, followed by adjuvant surgery on remnant chemoresistant tumors and close surveillance of initial sites that have been left unresected.

A report of amelanotic malignant melanoma of the esophagus diagnosed appropriately with novel markers: A case report.

PubMed

Kobayashi, Junya; Fujimoto, Daisuke; Murakami, Makoto; Hirono, Yasuo; Goi, Takanori

2018-06-01

The present case study reported of amelanotic malignant melanoma of the esophagus. A 68-year-old man underwent laparoscopic distal gastrectomy for early gastric cancer diagnosis. After gastrectomy, endoscopic examination revealed a protruded lesion lying adjacent to the melanosis area of the esophagus. Histology of the biopsy specimen suggested malignancy, but the diagnosis could not be made. The patient underwent trans-thoraco-abdominal curative subtotal esophagectomy. Immunohistochemical examination of the resected specimen was negative for HBM-45 and Melan-A. However, immunohistochemical examinations of SOX10 (Sry-related HMg-Box gene 10) and KBA.62, which are not associated with melanosome, were strongly positive, and tyrosinase was notably positive. A diagnosis primary of amelanotic malignant melanoma of the esophagus that consisted of only premelanosomes was made. The present findings suggest that, in the diagnosis of malignant melanoma, SOX10 and KBA.62 may be useful, particularly in diagnosing amelanotic malignant melanoma.

[Twenty-Five Cases of Locally Advanced Rectal Cancer That Underwent Laparoscopic Surgery after Preoperative Chemotherapy].

PubMed

Okuda, Hiroshi; Nakahara, Masahiro; Yano, Takuya; Bekki, Tomoaki; Takechi, Hitomi; Yoshikawa, Toru; Mochizuki, Tetsuya; Abe, Tomoyuki; Fujikuni, Nobuaki; Sasada, Tatsunari; Yamaki, Minoru; Amano, Hironobu; Noriyuki, Toshio

2017-11-01

Several recent reports have described the administration of preoperative chemotherapy for locally advanced rectal cancer. In our hospital, preoperative chemotherapy based on oxaliplatin was administered for locally advanced rectal cancer with a tumor diameter of 5 cm or more and half semicircularity or more, and curative resection with laparoscopic surgery was performed after tumor shrinkage. We have experienced 25 cases that underwent preoperative chemotherapy for local advanced rectal cancer in our hospital from May 2012 to April 2016. No tumor increased in size during preoperative chemotherapy and there were no cases where R0 resection was impossible. In addition, no distant metastasis during chemotherapy was observed. Postoperative complications were observed in 3 cases(12%), and anastomotic leakage was observed in 1 case (4%), but conservative treatment was possible. Multidisciplinary treatment of preoperative chemotherapy and surgery should be considered as a therapeutic strategy for locally advanced rectal cancer, mainly in medical institutions without radiation treatment facilities.

[Neoadjuvant Chemotherapy Using S-1 for Pancreatic Cancer - Mid-Term Results].

PubMed

Homma, Yuki; Honda, Goro; Sakamoto, Katsunori; Kurata, Masanao; Honjo, Masahiko; Hirata, Yoshihiro; Shinya, Satoshi

2016-10-01

Although surgical resection is the only curative strategy for pancreatic cancer, the prognosis of patients with pancreatic cancer remains poor. Recently, neoadjuvant treatment has been frequently employed as a promising treatment. Here, the mid-term results of neoadjuvant chemoradiotherapy(NACRT)using S-1, which has been performed in our hospital since 2008, are reported. Seventy-nine patients with resectable or borderline resectable pancreatic ductal adenocarcinoma, who had been intended to undergo NACRT treatment using S-1, were enrolled. The NACRT comprised radiotherapy( 1.8 Gy×28 days)and full-dose twice-daily oral S-1 given on the same days as the radiotherapy. The results of the NACRT and pancreatectomy and the patients' prognoses were evaluated. Fifty-five patients(69.6%)underwent pancreatectomy, with no case of mortality. The curative resection rate was 94.5%. Postoperative adjuvant chemotherapy was administered in 46 patients(83.6%). The 3-year survival rates of all 79 patients and 55 pancreatectomy patients were 40.1% and 50.4%, respectively. NACRT using S-1 was found to be feasible, and good mid-term outcomes were obtained. However, analysis of the long-term outcomes and comparisons with other novel anti-cancer drugs are still required.

PIK3CA gene mutations in Northwest Chinese esophageal squamous cell carcinoma

PubMed Central

Liu, Shi-Yuan; Chen, Wei; Chughtai, Ehtesham Annait; Qiao, Zhe; Jiang, Jian-Tao; Li, Shao-Min; Zhang, Wei; Zhang, Jin

2017-01-01

AIM To evaluate PIK3CA gene mutational status in Northwest Chinese esophageal squamous cell carcinoma (ESCC) patients, and examine the associations of PIK3CA gene mutations with clinicopathological characteristics and clinical outcome. METHODS A total of 210 patients with ESCC who underwent curative resection were enrolled in this study. Pyrosequencing was applied to investigate mutations in exons 9 and 20 of PIK3CA gene in 210 Northwest Chinese ESCCs. The associations of PIK3CA gene mutations with clinicopathological characteristics and clinical outcome were examined. RESULTS PIK3CA gene mutations in exon 9 were detected in 48 cases (22.9%) of a non-biased database of 210 curatively resected Northwest Chinese ESCCs. PIK3CA gene mutations were not associated with sex, tobacco use, alcohol use, tumor location, stage, or local recurrence. When compared with wild-type PIK3CA gene cases, patients with PIK3CA gene mutations in exons 9 experienced significantly better disease-free survival and overall survival rates. CONCLUSION The results of this study suggest that PIK3CA gene mutations could act as a prognostic biomarker in Northwest Chinese ESCC patients. PMID:28465643

Laryngeal cancer in acquired immunodeficiency syndrome.

PubMed

Shushan, S; Cinamon, U; Levy, D; Sokolov, M; Roth, Y

2009-08-01

With improved survival, more AIDS patients, especially heavy smokers and alcohol abusers, may be confronted with laryngeal squamous cell carcinoma. Since curative treatment may require aggressive combined therapy, these patients, often suffering from immunosupression and poor general condition, present unique therapeutic challenges. The objective of the study was to describe treatment dilemmas. This case report presents a detailed description of an AIDS patient with carcinoma of the larynx. A patient with T3N0M0 laryngeal carcinoma and AIDS underwent tracheotomy and biopsy, followed by severe neck and pulmonary infection. After convalescence, radiotherapy was administered, with no evidence of a disease during a 3.5-year follow-up. During his remaining life, the patient developed severe psychoaffective disorder, his immune state deteriorated until he demised from sepsis. In conclusion, patients with HIV infection, especially having a history of tobacco or alcohol abuse, should be carefully examined for head and neck carcinoma that is likely to be more aggressive. Following surgery, AIDS patients may have worse wound healing and a greater tendency to contract infections. Radiotherapy and especially chemotherapy may cause life-threatening complications. Although early detection may increase survival, curative treatment should involve many disciplines and extra caution.

Socioeconomic and family influences on dental treatment needs among Brazilian underprivileged schoolchildren participating in a dental health program

PubMed Central

2013-01-01

Background The objective of this study was to compare the socioeconomic and family characteristics of underprivileged schoolchildren with and without curative dental needs participating in a dental health program. Methods A random sample of 1411 of 8-to-10 year-old Brazilian schoolchildren was examined and two sample groups were included in the cross-sectional study: 544 presented curative dental needs and the other 867 schoolchildren were without curative dental needs. The schoolchildren were examined for the presence of caries lesions using the DMFT index and their parents were asked to answer questions about socioenvironmental characteristics of their families. Logistic regression models were adjusted estimating the Odds Ratios (OR), their 95% confidence intervals (CI), and significance levels. Results After adjusting for potential confounders, it was found that families earning more than one Brazilian minimum wage, having fewer than four residents in the house, families living in homes owned by them, and children living with both biological parents were protective factors for the presence of dental caries, and consequently, curative dental needs. Conclusions Socioeconomic status and family structure influences the curative dental needs of children from underprivileged communities. In this sense, dental health programs should plan and implement strategic efforts to reduce inequities in oral health status and access to oral health services of vulnerable schoolchildren and their families. PMID:24138683

The BioC-BioGRID corpus: full text articles annotated for curation of protein–protein and genetic interactions

PubMed Central

Kim, Sun; Chatr-aryamontri, Andrew; Chang, Christie S.; Oughtred, Rose; Rust, Jennifer; Wilbur, W. John; Comeau, Donald C.; Dolinski, Kara; Tyers, Mike

2017-01-01

A great deal of information on the molecular genetics and biochemistry of model organisms has been reported in the scientific literature. However, this data is typically described in free text form and is not readily amenable to computational analyses. To this end, the BioGRID database systematically curates the biomedical literature for genetic and protein interaction data. This data is provided in a standardized computationally tractable format and includes structured annotation of experimental evidence. BioGRID curation necessarily involves substantial human effort by expert curators who must read each publication to extract the relevant information. Computational text-mining methods offer the potential to augment and accelerate manual curation. To facilitate the development of practical text-mining strategies, a new challenge was organized in BioCreative V for the BioC task, the collaborative Biocurator Assistant Task. This was a non-competitive, cooperative task in which the participants worked together to build BioC-compatible modules into an integrated pipeline to assist BioGRID curators. As an integral part of this task, a test collection of full text articles was developed that contained both biological entity annotations (gene/protein and organism/species) and molecular interaction annotations (protein–protein and genetic interactions (PPIs and GIs)). This collection, which we call the BioC-BioGRID corpus, was annotated by four BioGRID curators over three rounds of annotation and contains 120 full text articles curated in a dataset representing two major model organisms, namely budding yeast and human. The BioC-BioGRID corpus contains annotations for 6409 mentions of genes and their Entrez Gene IDs, 186 mentions of organism names and their NCBI Taxonomy IDs, 1867 mentions of PPIs and 701 annotations of PPI experimental evidence statements, 856 mentions of GIs and 399 annotations of GI evidence statements. The purpose, characteristics and possible future uses of the BioC-BioGRID corpus are detailed in this report. Database URL: http://bioc.sourceforge.net/BioC-BioGRID.html PMID:28077563

Impact of [18F]fluorodeoxyglucose PET-CT staging on treatment planning in radiotherapy incorporating elective nodal irradiation for non-small-cell lung cancer: a prospective study.

PubMed

Kolodziejczyk, Milena; Kepka, Lucyna; Dziuk, Miroslaw; Zawadzka, Anna; Szalus, Norbert; Gizewska, Agnieszka; Bujko, Krzysztof

2011-07-15

To evaluate prospectively how positron emission tomography (PET) information changes treatment plans for non-small-cell lung cancer (NSCLC) patients receiving or not receiving elective nodal irradiation (ENI). One hundred consecutive patients referred for curative radiotherapy were included in the study. Treatment plans were carried out with CT data sets only. For stage III patients, mediastinal ENI was planned. Then, patients underwent PET-CT for diagnostic/planning purposes. PET/CT was fused with the CT data for final planning. New targets were delineated. For stage III patients with minimal N disease (N0-N1, single N2), the ENI was omitted in the new plans. Patients were treated according to the PET-based volumes and plans. The gross tumor volume (GTV)/planning tumor volume (PTV) and doses for critical structures were compared for both data sets. The doses for areas of potential geographical misses derived with the CT data set alone were compared in patients with and without initially planned ENI. In the 75 patients for whom the decision about curative radiotherapy was maintained after PET/CT, there would have been 20 cases (27%) with potential geographical misses by using the CT data set alone. Among them, 13 patients would receive ENI; of those patients, only 2 patients had the PET-based PTV covered by 90% isodose by using the plans based on CT alone, and the mean of the minimum dose within the missed GTV was 55% of the prescribed dose, while for 7 patients without ENI, it was 10% (p = 0.006). The lung, heart, and esophageal doses were significantly lower for plans with ENI omission than for plans with ENI use based on CT alone. PET/CT should be incorporated in the planning of radiotherapy for NSCLC, even in the setting of ENI. However, if PET/CT is unavailable, ENI may to some extent compensate for an inadequate dose coverage resulting from diagnostic uncertainties. Copyright © 2011 Elsevier Inc. All rights reserved.

Postoperative liver volume was accurately predicted by a medical image three dimensional visualization system in hepatectomy for liver cancer.

PubMed

Cai, Wei; Fan, Yingfang; Hu, Haoyu; Xiang, Nan; Fang, Chihua; Jia, Fucang

2017-06-01

Liver cancer is the second most common cause of cancer death worldwide. The hepatectomy is the most effective and the only potentially curative treatment for patients with resectable neoplasm. Precisely preoperative assessment of remnant liver volume is essential in preventing postoperative liver failure. The aim of our study is to report our experience of using a medical image three dimensional (3D) visualization system (MI-3DVS), which was developed by our team, in assisting hepatectomy for patients with liver cancer. Between January 2010 and June 2016, 69 patients with liver cancer underwent hepatic resection based on the MI-3DVS were enrolled in this study. All patients underwent CT scan 5 days before the surgery and within 5 days after resection. CT images were reconstructed with the MI-3DVS to assist to perform hepatectomy. Simple linear regression, intra-class correlation coefficient (ICC) and Bland-Altman analysis were used to evaluate the relationship and agreement between actual excisional liver volume (AELV) and predicted excisional liver volume (PELV). Among 69 patients in this study, 62(89.85%) of them were diagnosed with hepatocellular carcinoma by histopathologic examination, and 41(59.42%) underwent major hepatectomy. The average AELV was 330.13 cm 3 and the average PELV was 287.67 cm 3 . The simple regression equation is AELV = 1.016 × PELV+30.39(r = 0.966; p < 0.0003). PELV (ICC = 0.964) achieved an excellent agreement with AELV with statistical significance (p < 0.001). 65 of 69 dots are in the range of 95% confidence interval in Bland-Altman analyses. The MI-3DVS has advantages of simple usage and convenient hold. It is accurate in assessment of postoperative liver volume and improve safety in liver resection. Copyright © 2017 Elsevier Ltd. All rights reserved.

Hepatic resection with or without adjuvant iodine-131-lipiodol for hepatocellular carcinoma: a comparative analysis.

PubMed

Chua, Terence C; Saxena, Akshat; Chu, Francis; Butler, S Patrick; Quinn, Richard J; Glenn, Derek; Morris, David L

2011-04-01

Resection of hepatocellular carcinoma (HCC) is potentially curative; however, recurrence is common. To date, few or no effective adjuvant therapies have been adequately investigated. This study evaluates the efficacy of adjuvant iodine-131-lipiodol after hepatic resection through the experience of a single-center hepatobiliary service of managing this disease. All patients who underwent hepatic resection for HCC and received adjuvant iodine-131-lipiodol between January 1991 and August 2009 were selected for inclusion into the experimental group. A group composed of patients treated during the same time period without adjuvant iodine-131-lipiodol was identified through the unit's HCC surgery database for comparison. The endpoints of this study were disease-free survival and overall survival. Forty-one patients who received adjuvant iodine-131-lipiodol after hepatic resection were compared with a matched group of 41 patients who underwent hepatic resection only. The median disease-free and overall survival were 24 versus 10 months (P = 0.032) and 104 versus 19 months (P = 0.001) in the experimental and control groups, respectively. Rates of intrahepatic-only recurrences (73 vs. 37%; P = 0.02) and surgical and nonsurgical treatments for recurrences (84 vs. 56%; P = 0.04) were higher in the experimental group compared to the control group. The finding of this study corroborates the current evidence from randomized and nonrandomized trials that adjuvant iodine-131-lipiodol improves disease-free and overall survival in patients with HCC after hepatic resection. The lengthened disease-free survival after adjuvant iodine-131-lipiodol allows for further disease-modifying treatments to improve the overall survival.

The clinical value of circulating tumour cells (CTCs) in patients undergoing pulmonary metastasectomy for metastatic colorectal cancer.

PubMed

Hashimoto, Masaki; Tanaka, Fumihiro; Yoneda, Kazue; Takuwa, Teruhisa; Kuroda, Ayumi; Matsumoto, Seiji; Okumura, Yoshitomo; Kondo, Nobuyuki; Tsujimura, Tohru; Nakano, Takashi; Hasegawa, Seiki

2018-03-01

Circulating tumour cells (CTCs) are a potential surrogate for distant metastasis and are considered a useful clinical prognostic marker for metastatic colorectal cancer (mCRC). This prospective study evaluated the preoperative CTC count as a prognostic factor for pulmonary metastasectomy in mCRC patients. Seventy-nine mCRC patients who underwent curative-intent pulmonary metastasectomy were included. Preoperatively, 7.5 mL of peripheral blood from each patient was quantitatively evaluated for CTCs with the CellSearch ® system. The clinical significance of CTC count was evaluated according to Kaplan-Meier analyses and log-rank test. Multivariate analyses of the perioperative variables were performed. The distribution of CTC counts were as follows; 0 in 66 patients (83.5%), 1 in eight patients (10.1%), 2 in three patients (3.8%), and 3 and 6 in one patient (1.3%). The patients with multiple CTCs (CTC count ≥2) had significant shorter disease-free survival (DFS) (P=0.005, median DFS; 19.8 vs . 8.6 months) and overall survival (OS) (P=0.035, median DFS; not reached vs. 37.8 months), respectively. Multivariate analysis showed the patients with multiple CTCs had elevated risk of recurrence [hazard ratio (HR), 3.28; 95% confidence interval (CI), 1.24-8.67; P=0.017]. The detected rate of CTCs was quite low in mCRC patients who underwent pulmonary metastasectomy. The patient with multiple CTCs had shorter DFS in this study. The larger prospective clinical study is needed to establish the meaning of CTC in mCRC candidate for pulmonary metastasectomy.

Carcinoma of the ampulla of Vater: patterns of failure following resection and benefit of chemoradiotherapy.

PubMed

Palta, Manisha; Patel, Pretesh; Broadwater, Gloria; Willett, Christopher; Pepek, Joseph; Tyler, Douglas; Zafar, S Yousuf; Uronis, Hope; Hurwitz, Herbert; White, Rebekah; Czito, Brian

2012-05-01

Ampullary carcinoma is a rare malignancy. Despite radical resection, survival rates remain low with high rates of local failure. We performed a single-institution outcomes analysis to define the role of concurrent chemoradiotherapy (CRT) in addition to surgery. A retrospective analysis was performed of all patients undergoing potentially curative pancreaticoduodenectomy for adenocarcinoma of the ampulla of Vater at Duke University Hospitals between 1976 and 2009. Time-to-event analysis was performed comparing all patients who underwent surgery alone to the cohort of patients receiving CRT in addition to surgery. Local control (LC), disease-free survival (DFS), overall survival (OS), and metastases-free survival (MFS) were estimated using the Kaplan-Meier method. A total of 137 patients with ampullary carcinoma underwent Whipple procedure. Of these, 61 patients undergoing resection received adjuvant (n = 43) or neoadjuvant (n = 18) CRT. Patients receiving chemoradiotherapy were more likely to have poorly differentiated tumors (P = .03). Of 18 patients receiving neoadjuvant therapy, 67% were downstaged on final pathology with 28% achieving pathologic complete response (pCR). With a median follow-up of 8.8 years, 3-year local control was improved in patients receiving CRT (88% vs 55%, P = .001) with trend toward 3-year DFS (66% vs 48%, P = .09) and OS (62% vs 46%, P = .074) benefit in patients receiving CRT. Long-term survival rates are low and local failure rates high following radical resection alone. Given patterns of relapse with surgery alone and local control benefit in patients receiving CRT, the use of chemoradiotherapy in selected patients should be considered.

Impact of specialized multi-disciplinary approach and an integrated pathway on outcomes in hilar cholangiocarcinoma.

PubMed

Gomez, D; Patel, P B; Lacasia-Purroy, C; Byrne, C; Sturgess, R P; Palmer, D; Fenwick, S; Poston, G J; Malik, H Z

2014-01-01

To assess the outcomes of patients with hilar cholangiocarcinoma following referral to a specialist multi-disciplinary team. Over an 11-year period, patients referred with hilar cholangiocarcinoma were identified from a prospectively maintained registry. Collated data included demographics, operative findings and histo-pathological data. Survival differences and prognostic factors were determined. 345 patients were referred with hilar cholangiocarcinoma, of which 57 (16.5%) patients had surgery. Prior to 2008, of 143 patients referred, only 17 (11.9%) patients underwent surgery, compared to 40 (19.8%) of 202 patients referred from 2008 onwards (p = 0.051). In the surgery group, the majority of patients underwent left hemi-hepatectomy (n = 19). In addition, portal vein (n = 5), hepatic artery (n = 2) and inferior vena cava (n = 3) resections were performed. The R0 resection rate was 73.7%. The morbidity and mortality rates were 59.6% and 14.0%, respectively. The median disease-free survival was 16 (4-101) months. The presence of lymph node metastasis (p = 0.002) was the only predictor of poorer disease-free survival. The 5-year overall survival was 39.5% and was significantly better than that of the palliative group (p < 0.001). Surgery is the optimal treatment option for patients with hilar cholangiocarcinoma and is associated with better overall survival. Prompt referral to tertiary centres with a core team of clinicians to manage this difficult condition may allow more patients to come to potentially curative surgical resections. Copyright © 2013. Published by Elsevier Ltd.

Outcomes and prognostic factors of multimodality treatment for locally recurrent rectal cancer with curative intent.

PubMed

Bird, Thomas G; Ngan, Samuel Y; Chu, Julie; Kroon, René; Lynch, Andrew C; Heriot, Alexander G

2018-04-01

Radical management of locally recurrent rectal cancer (LRRC) can lead to prolonged survival. This study aims to assess outcomes and identify prognostic factors for patients with LRRC treated using a multimodality treatment protocol. An analysis of a prospectively maintained institutional database of consecutive patients who underwent radical surgical resection for LRRC was performed. Potential prognostic factors were investigated using a Cox proportional hazards model. Ninety-eight patients were included in this study. A multimodality approach was taken in the majority, including preoperative chemoradiation (78%), intraoperative radiation therapy (47%) and adjuvant chemotherapy (41%). Extended resection was performed where required: bone resection (34%) and lateral pelvic sidewall dissection (31%). The rate of R0 resection was 66%. Estimated rates of 5-year overall survival (OS) and progression-free survival (PFS) were 41.8% (95% CI 32.5-53.7) and 22.5% (95% CI 15.3-33.1). On multivariate analysis, stage III disease at initial primary surgery, a positive margin at initial primary surgery, synchronous or previously resected oligometastases, a lateral or sacral invasive-type pelvic recurrence and the requirement for IORT all predicted for inferior PFS (p < 0.05). Eleven percent of patients subsequently underwent further pelvic surgery for pelvic re-recurrence and had an estimated 5-year OS rate of 54.5% (95% CI 29.0-100.0) from repeat surgery. Radical multimodality management of LRRC leads to prolonged survival in approximately 40% of patients. Those with sacral or lateral invasive-type recurrence or oligometastatic disease have inferior outcomes and further research is needed to optimise treatment for these groups.

Lymph node metastases near the celiac trunk should be considered separately from other nodal metastases in patients with cancer of the esophagus or gastroesophageal junction after neoadjuvant treatment and surgery

PubMed Central

Lagarde, Sjoerd M.; Anderegg, Martinus C. J.; Gisbertz, Suzanne S.; Meijer, Sybren L.; Hulshof, Maarten C. C. M.; Bergman, Jacques J. G. H. M.; van Laarhoven, Hanneke W. M.

2018-01-01

Background The aim of the present study is to identify the incidence and prognostic significance of lymph node metastases near the celiac trunk in patients who underwent neoadjuvant chemo(radio)therapy followed by esophagectomy. Methods Between March 1994 and September 2013 a total of 462 consecutive patients with cancer of the esophagus or gastroesophageal junction (GEJ) who underwent potentially curative esophageal resection after neoadjuvant chemotherapy (N=88; 19.0%) or neoadjuvant chemoradiotherapy (CRT) (N=374; 81.0%) were included. Results Seventy one (15.4%) patients had truncal node metastases in the resection specimen. Metastases to these nodes occurred more frequently in male patients with adenocarcinoma and in tumors at the gastro-esophageal junction. A lower response to neoadjuvant treatment, higher ypT and ypN stages and a poorer grade of differentiation were significantly related with truncal node metastases. Patients with tumor positive truncal nodes had a worse median overall survival (17 vs. 55 months). In multivariate analysis, truncal node metastases were independently associated with a worse survival. Only 22 (31.0%) of the 71 patients with tumor positive truncal nodes were identified preoperatively with EUS or CT. In contrast, 37 patients had suspicious truncal nodes on EUS or CT, but metastases in the pathology specimen were absent. Conclusions In the present study, it is demonstrated that positive truncal nodes in the resection specimen after neoadjuvant therapy, are associated with advanced tumor stages and are an independent factor for inferior survival. PMID:29707301

Lymph node metastases near the celiac trunk should be considered separately from other nodal metastases in patients with cancer of the esophagus or gastroesophageal junction after neoadjuvant treatment and surgery.

PubMed

Lagarde, Sjoerd M; Anderegg, Martinus C J; Gisbertz, Suzanne S; Meijer, Sybren L; Hulshof, Maarten C C M; Bergman, Jacques J G H M; van Laarhoven, Hanneke W M; van Berge Henegouwen, Mark I

2018-03-01

The aim of the present study is to identify the incidence and prognostic significance of lymph node metastases near the celiac trunk in patients who underwent neoadjuvant chemo(radio)therapy followed by esophagectomy. Between March 1994 and September 2013 a total of 462 consecutive patients with cancer of the esophagus or gastroesophageal junction (GEJ) who underwent potentially curative esophageal resection after neoadjuvant chemotherapy (N=88; 19.0%) or neoadjuvant chemoradiotherapy (CRT) (N=374; 81.0%) were included. Seventy one (15.4%) patients had truncal node metastases in the resection specimen. Metastases to these nodes occurred more frequently in male patients with adenocarcinoma and in tumors at the gastro-esophageal junction. A lower response to neoadjuvant treatment, higher ypT and ypN stages and a poorer grade of differentiation were significantly related with truncal node metastases. Patients with tumor positive truncal nodes had a worse median overall survival (17 vs. 55 months). In multivariate analysis, truncal node metastases were independently associated with a worse survival. Only 22 (31.0%) of the 71 patients with tumor positive truncal nodes were identified preoperatively with EUS or CT. In contrast, 37 patients had suspicious truncal nodes on EUS or CT, but metastases in the pathology specimen were absent. In the present study, it is demonstrated that positive truncal nodes in the resection specimen after neoadjuvant therapy, are associated with advanced tumor stages and are an independent factor for inferior survival.

Response to preoperative chemotherapy predicts survival in patients undergoing hepatectomy for liver metastases from gastric and esophageal cancer.

PubMed

Andreou, Andreas; Viganò, Luca; Zimmitti, Giuseppe; Seehofer, Daniel; Dreyer, Martin; Pascher, Andreas; Bahra, Marcus; Schoening, Wenzel; Schmitz, Volker; Thuss-Patience, Peter C; Denecke, Timm; Puhl, Gero; Vauthey, Jean-Nicolas; Neuhaus, Peter; Capussotti, Lorenzo; Pratschke, Johann; Schmidt, Sven-Christian

2014-11-01

The role of hepatectomy for patients with liver metastases from gastric and esophageal cancer (GELM) is not well defined. The present study examined the morbidity, mortality, and long-term survivals after liver resection for GELM. Clinicopathological data of patients who underwent hepatectomy for GELM between 1995 and 2012 at two European high-volume hepatobiliary centers were assessed, and predictors of overall survival (OS) were identified. In addition, the impact of preoperative chemotherapy for GELM on OS was evaluated. Forty-seven patients underwent hepatectomy for GELM. The primary tumor was located in the stomach, cardia, and distal esophagus in 27, 16, and 4 cases, respectively. Twenty patients received preoperative chemotherapy before hepatectomy. After a median follow-up time of 76 months, 1-, 3-, and 5-year OS rates were 70, 37, and 24%, respectively. Postoperative morbidity and mortality rates were 32 and 4%, respectively. Outcomes were comparable between the two centers. Preoperative chemotherapy for GELM (5-year OS: 45 vs 9%, P = .005) and the lack of posthepatectomy complications (5-year OS: 34 vs 0%, P < .0001) were significantly associated with improved OS in univariate and multivariate analyses. When stratifying OS by radiologic response of GELM to preoperative chemotherapy, patients with progressive disease despite preoperative treatment had significantly worse OS (5-year OS: 0 vs 70%, P = .045). For selected patients with GELM, liver resection is safe and should be regarded as a potentially curative approach. A multimodal treatment strategy including systemic therapy may provide better patient selection resulting in prolonged survival in patients with GELM undergoing hepatectomy.

A CTD–Pfizer collaboration: manual curation of 88 000 scientific articles text mined for drug–disease and drug–phenotype interactions

PubMed Central

Davis, Allan Peter; Wiegers, Thomas C.; Roberts, Phoebe M.; King, Benjamin L.; Lay, Jean M.; Lennon-Hopkins, Kelley; Sciaky, Daniela; Johnson, Robin; Keating, Heather; Greene, Nigel; Hernandez, Robert; McConnell, Kevin J.; Enayetallah, Ahmed E.; Mattingly, Carolyn J.

2013-01-01

Improving the prediction of chemical toxicity is a goal common to both environmental health research and pharmaceutical drug development. To improve safety detection assays, it is critical to have a reference set of molecules with well-defined toxicity annotations for training and validation purposes. Here, we describe a collaboration between safety researchers at Pfizer and the research team at the Comparative Toxicogenomics Database (CTD) to text mine and manually review a collection of 88 629 articles relating over 1 200 pharmaceutical drugs to their potential involvement in cardiovascular, neurological, renal and hepatic toxicity. In 1 year, CTD biocurators curated 2 54 173 toxicogenomic interactions (1 52 173 chemical–disease, 58 572 chemical–gene, 5 345 gene–disease and 38 083 phenotype interactions). All chemical–gene–disease interactions are fully integrated with public CTD, and phenotype interactions can be downloaded. We describe Pfizer’s text-mining process to collate the articles, and CTD’s curation strategy, performance metrics, enhanced data content and new module to curate phenotype information. As well, we show how data integration can connect phenotypes to diseases. This curation can be leveraged for information about toxic endpoints important to drug safety and help develop testable hypotheses for drug–disease events. The availability of these detailed, contextualized, high-quality annotations curated from seven decades’ worth of the scientific literature should help facilitate new mechanistic screening assays for pharmaceutical compound survival. This unique partnership demonstrates the importance of resource sharing and collaboration between public and private entities and underscores the complementary needs of the environmental health science and pharmaceutical communities. Database URL: http://ctdbase.org/ PMID:24288140

A CTD-Pfizer collaboration: manual curation of 88,000 scientific articles text mined for drug-disease and drug-phenotype interactions.

PubMed

Davis, Allan Peter; Wiegers, Thomas C; Roberts, Phoebe M; King, Benjamin L; Lay, Jean M; Lennon-Hopkins, Kelley; Sciaky, Daniela; Johnson, Robin; Keating, Heather; Greene, Nigel; Hernandez, Robert; McConnell, Kevin J; Enayetallah, Ahmed E; Mattingly, Carolyn J

2013-01-01

Improving the prediction of chemical toxicity is a goal common to both environmental health research and pharmaceutical drug development. To improve safety detection assays, it is critical to have a reference set of molecules with well-defined toxicity annotations for training and validation purposes. Here, we describe a collaboration between safety researchers at Pfizer and the research team at the Comparative Toxicogenomics Database (CTD) to text mine and manually review a collection of 88,629 articles relating over 1,200 pharmaceutical drugs to their potential involvement in cardiovascular, neurological, renal and hepatic toxicity. In 1 year, CTD biocurators curated 254,173 toxicogenomic interactions (152,173 chemical-disease, 58,572 chemical-gene, 5,345 gene-disease and 38,083 phenotype interactions). All chemical-gene-disease interactions are fully integrated with public CTD, and phenotype interactions can be downloaded. We describe Pfizer's text-mining process to collate the articles, and CTD's curation strategy, performance metrics, enhanced data content and new module to curate phenotype information. As well, we show how data integration can connect phenotypes to diseases. This curation can be leveraged for information about toxic endpoints important to drug safety and help develop testable hypotheses for drug-disease events. The availability of these detailed, contextualized, high-quality annotations curated from seven decades' worth of the scientific literature should help facilitate new mechanistic screening assays for pharmaceutical compound survival. This unique partnership demonstrates the importance of resource sharing and collaboration between public and private entities and underscores the complementary needs of the environmental health science and pharmaceutical communities. Database URL: http://ctdbase.org/

Sharing and community curation of mass spectrometry data with GNPS

PubMed Central

Nguyen, Don Duy; Watrous, Jeramie; Kapono, Clifford A; Luzzatto-Knaan, Tal; Porto, Carla; Bouslimani, Amina; Melnik, Alexey V; Meehan, Michael J; Liu, Wei-Ting; Crüsemann, Max; Boudreau, Paul D; Esquenazi, Eduardo; Sandoval-Calderón, Mario; Kersten, Roland D; Pace, Laura A; Quinn, Robert A; Duncan, Katherine R; Hsu, Cheng-Chih; Floros, Dimitrios J; Gavilan, Ronnie G; Kleigrewe, Karin; Northen, Trent; Dutton, Rachel J; Parrot, Delphine; Carlson, Erin E; Aigle, Bertrand; Michelsen, Charlotte F; Jelsbak, Lars; Sohlenkamp, Christian; Pevzner, Pavel; Edlund, Anna; McLean, Jeffrey; Piel, Jörn; Murphy, Brian T; Gerwick, Lena; Liaw, Chih-Chuang; Yang, Yu-Liang; Humpf, Hans-Ulrich; Maansson, Maria; Keyzers, Robert A; Sims, Amy C; Johnson, Andrew R.; Sidebottom, Ashley M; Sedio, Brian E; Klitgaard, Andreas; Larson, Charles B; P., Cristopher A Boya; Torres-Mendoza, Daniel; Gonzalez, David J; Silva, Denise B; Marques, Lucas M; Demarque, Daniel P; Pociute, Egle; O'Neill, Ellis C; Briand, Enora; Helfrich, Eric J. N.; Granatosky, Eve A; Glukhov, Evgenia; Ryffel, Florian; Houson, Hailey; Mohimani, Hosein; Kharbush, Jenan J; Zeng, Yi; Vorholt, Julia A; Kurita, Kenji L; Charusanti, Pep; McPhail, Kerry L; Nielsen, Kristian Fog; Vuong, Lisa; Elfeki, Maryam; Traxler, Matthew F; Engene, Niclas; Koyama, Nobuhiro; Vining, Oliver B; Baric, Ralph; Silva, Ricardo R; Mascuch, Samantha J; Tomasi, Sophie; Jenkins, Stefan; Macherla, Venkat; Hoffman, Thomas; Agarwal, Vinayak; Williams, Philip G; Dai, Jingqui; Neupane, Ram; Gurr, Joshua; Rodríguez, Andrés M. C.; Lamsa, Anne; Zhang, Chen; Dorrestein, Kathleen; Duggan, Brendan M; Almaliti, Jehad; Allard, Pierre-Marie; Phapale, Prasad; Nothias, Louis-Felix; Alexandrov, Theodore; Litaudon, Marc; Wolfender, Jean-Luc; Kyle, Jennifer E; Metz, Thomas O; Peryea, Tyler; Nguyen, Dac-Trung; VanLeer, Danielle; Shinn, Paul; Jadhav, Ajit; Müller, Rolf; Waters, Katrina M; Shi, Wenyuan; Liu, Xueting; Zhang, Lixin; Knight, Rob; Jensen, Paul R; Palsson, Bernhard O; Pogliano, Kit; Linington, Roger G; Gutiérrez, Marcelino; Lopes, Norberto P; Gerwick, William H; Moore, Bradley S; Dorrestein, Pieter C; Bandeira, Nuno

2017-01-01

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry techniques are well-suited to high-throughput characterization of natural products, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social molecular networking (GNPS, http://gnps.ucsd.edu), an open-access knowledge base for community wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of ‘living data’ through continuous reanalysis of deposited data. PMID:27504778

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.

PubMed

Wang, Mingxun; Carver, Jeremy J; Phelan, Vanessa V; Sanchez, Laura M; Garg, Neha; Peng, Yao; Nguyen, Don Duy; Watrous, Jeramie; Kapono, Clifford A; Luzzatto-Knaan, Tal; Porto, Carla; Bouslimani, Amina; Melnik, Alexey V; Meehan, Michael J; Liu, Wei-Ting; Crüsemann, Max; Boudreau, Paul D; Esquenazi, Eduardo; Sandoval-Calderón, Mario; Kersten, Roland D; Pace, Laura A; Quinn, Robert A; Duncan, Katherine R; Hsu, Cheng-Chih; Floros, Dimitrios J; Gavilan, Ronnie G; Kleigrewe, Karin; Northen, Trent; Dutton, Rachel J; Parrot, Delphine; Carlson, Erin E; Aigle, Bertrand; Michelsen, Charlotte F; Jelsbak, Lars; Sohlenkamp, Christian; Pevzner, Pavel; Edlund, Anna; McLean, Jeffrey; Piel, Jörn; Murphy, Brian T; Gerwick, Lena; Liaw, Chih-Chuang; Yang, Yu-Liang; Humpf, Hans-Ulrich; Maansson, Maria; Keyzers, Robert A; Sims, Amy C; Johnson, Andrew R; Sidebottom, Ashley M; Sedio, Brian E; Klitgaard, Andreas; Larson, Charles B; P, Cristopher A Boya; Torres-Mendoza, Daniel; Gonzalez, David J; Silva, Denise B; Marques, Lucas M; Demarque, Daniel P; Pociute, Egle; O'Neill, Ellis C; Briand, Enora; Helfrich, Eric J N; Granatosky, Eve A; Glukhov, Evgenia; Ryffel, Florian; Houson, Hailey; Mohimani, Hosein; Kharbush, Jenan J; Zeng, Yi; Vorholt, Julia A; Kurita, Kenji L; Charusanti, Pep; McPhail, Kerry L; Nielsen, Kristian Fog; Vuong, Lisa; Elfeki, Maryam; Traxler, Matthew F; Engene, Niclas; Koyama, Nobuhiro; Vining, Oliver B; Baric, Ralph; Silva, Ricardo R; Mascuch, Samantha J; Tomasi, Sophie; Jenkins, Stefan; Macherla, Venkat; Hoffman, Thomas; Agarwal, Vinayak; Williams, Philip G; Dai, Jingqui; Neupane, Ram; Gurr, Joshua; Rodríguez, Andrés M C; Lamsa, Anne; Zhang, Chen; Dorrestein, Kathleen; Duggan, Brendan M; Almaliti, Jehad; Allard, Pierre-Marie; Phapale, Prasad; Nothias, Louis-Felix; Alexandrov, Theodore; Litaudon, Marc; Wolfender, Jean-Luc; Kyle, Jennifer E; Metz, Thomas O; Peryea, Tyler; Nguyen, Dac-Trung; VanLeer, Danielle; Shinn, Paul; Jadhav, Ajit; Müller, Rolf; Waters, Katrina M; Shi, Wenyuan; Liu, Xueting; Zhang, Lixin; Knight, Rob; Jensen, Paul R; Palsson, Bernhard O; Pogliano, Kit; Linington, Roger G; Gutiérrez, Marcelino; Lopes, Norberto P; Gerwick, William H; Moore, Bradley S; Dorrestein, Pieter C; Bandeira, Nuno

2016-08-09

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

TREATING HEMOGLOBINOPATHIES USING GENE CORRECTION APPROACHES: PROMISES AND CHALLENGES

PubMed Central

Cottle, Renee N.; Lee, Ciaran M.; Bao, Gang

2016-01-01

Hemoglobinopathies are genetic disorders caused by aberrant hemoglobin expression or structure changes, resulting in severe mortality and health disparities worldwide. Sickle cell disease (SCD) and β-thalassemia, the most common forms of hemoglobinopathies, are typically treated using transfusions and pharmacological agents. Allogeneic hematopoietic stem cell transplantation is the only curative therapy, but has limited clinical applicability. Although gene therapy approaches have been proposed based on the insertion and forced expression of wild-type or anti-sickling β-globin variants, safety concerns may impede their clinical application. A novel curative approach is nuclease-based gene correction, which involves the application of precision genome editing tools to correct the disease-causing mutation. This review describes the development and potential application of gene therapy and precision genome editing approaches for treating SCD and β-thalassemia. The opportunities and challenges in advancing a curative therapy for hemoglobinopathies are also discussed. PMID:27314256

Pathological response to neoadjuvant chemotherapy: a new prognosis tool for the curative management of peritoneal colorectal carcinomatosis.

PubMed

Passot, Guillaume; You, Benoît; Boschetti, Gilles; Fontaine, Juliette; Isaac, Sylvie; Decullier, Evelyne; Maurice, Christele; Vaudoyer, Delphine; Gilly, François-Noël; Cotte, Eddy; Glehen, Olivier

2014-08-01

The primary objective of this study was to determine the incidence rate of pathological complete responses (pCRs) following neoadjuvant systemic chemotherapy for the treatment of peritoneal carcinomatosis (PC) of colorectal origin. The secondary objective was to evaluate whether pathological response assessments predict survival of patients treated with curative intent by complete cytoreductive surgery (CRS). A retrospective review was performed of 115 patients who underwent preoperative irinotecan- or oxaliplatin-based chemotherapy, followed by 124 procedures of complete CRS alone or combined with hyperthermic intraperitoneal chemotherapy (HIPEC). The pathological response was defined as the mean percentage of cancer cells remaining within all specimens. Univariate and multivariate analyses were performed to identify predictors of survival and pathological response outcome. Twelve procedures (9.7 %) resulted in pCRs, defined as no residual cancer cells in all specimens, 25 (20.2 %) resulted in major responses (1 to 49 % residual cancer cells), and 87 (70.1 %) resulted in minor or no responses (>50 % residual cancer cells). The cumulative 5-year survival rates were 75 and 57 % for patients with pCR and major responses, respectively. Using multivariate analysis, pathological response was the only independent predictor of survival (P = 0.01; major response: hazard ratio [HR] = 4.91; minor response: HR = 13.46). No significant predictor of pathological response was identified. Pathological complete response can be achieved with preoperative systemic chemotherapy for patients with PC of colorectal origin. The degree of pathological response can be assessed and represented as a new outcome for prognosis following treatment with curative intent.

Psychological morbidities in adolescent and young adult blood cancer patients during curative-intent therapy and early survivorship.

PubMed

Muffly, Lori S; Hlubocky, Fay J; Khan, Niloufer; Wroblewski, Kristen; Breitenbach, Katherine; Gomez, Joseline; McNeer, Jennifer L; Stock, Wendy; Daugherty, Christopher K

2016-03-15

Adolescents and young adults (AYAs) with cancer face unique psychosocial challenges. This pilot study was aimed at describing the prevalence of psychological morbidities among AYAs with hematologic malignancies during curative-intent therapy and early survivorship and at examining provider perceptions of psychological morbidities in their AYA patients. Patients aged 15 to 39 years with acute leukemia, non-Hodgkin lymphoma, or Hodgkin lymphoma who were undergoing curative-intent therapy (on-treatment group) or were in remission within 2 years of therapy completion (early survivors) underwent a semistructured interview that incorporated measures of anxiety, depression, and posttraumatic stress (PTS). A subset of providers (n = 15) concomitantly completed a survey for each of the first 30 patients enrolled that evaluated their perception of each subject's anxiety, depression, and PTS. Sixty-one of 77 eligible AYAs participated. The median age at diagnosis was 26 years (range, 15-39 years), 64% were male, and 59% were non-Hispanic white. On-treatment demographics differed significantly from early-survivor demographics only in the median time from diagnosis to interview. Among the 61 evaluable AYAs, 23% met the criteria for anxiety, 28% met the criteria for depression, and 13% met the criteria for PTS; 46% demonstrated PTS symptomatology. Thirty-nine percent were impaired in 1 or more psychological domains. Psychological impairments were as frequent among early survivors as AYAs on treatment. Provider perceptions did not significantly correlate with patient survey results. AYAs with hematologic malignancies experience substantial psychological morbidities while they are undergoing therapy and during early survivorship, with more than one-third of the patients included in this study meeting the criteria for anxiety, depression, or traumatic stress. This psychological burden may not be accurately identified by their oncology providers. © 2016 American Cancer Society.

CpG island methylator phenotype is an independent predictor of survival after curative resection for colorectal cancer: A prospective cohort study.

PubMed

Kim, Chang Hyun; Huh, Jung Wook; Kim, Hyeong Rok; Kim, Young Jin

2017-08-01

The CpG island methylator phenotype (CIMP) is found in approximately 30% of colorectal cancer (CRC) cases. However, the role of CIMP status in predicting oncologic outcomes in curatively resected CRC is still unclear. Between January 2006 and December 2006, we retrospectively reviewed 157 consecutive patients who underwent curative surgery for CRC. Prognostic significance of CIMP status was evaluated using reverse transcriptase-polymerase chain reaction. CIMP-high (H) and CIMP-none/low (N/L) tumors were found in 50 cases (31.8%) and 107 cases (68.2%), respectively. CIMP-H tumors were significantly associated with female sex, colonic location, poorly/mucinous histologic type, higher T category, perineural invasion, and MSI-high status (P = 0.001). During a median of 64.5 months, tumor recurrence developed in 47 (29.9%) patients. The 5-year disease-free survival for CIMP-H and CIMP-N/L was 61.4% and 76.3% (P = 0.018). In addition, multivariate analysis showed that CIMP-H was also a significant prognostic factor (P = 0.042). When analysis was performed according to anatomical location, more marked survival differences were observed in patients with colon cancer (P = 0.026) than in patients with rectal cancer (P = 0.210). Similarly, the role of CIMP status as a prognostic indicator was more prominent in patients with stage I/II (P = 0.006) than in patients with stage III/IV CRC (P = 0.65). DNA methylation status can be considered as a useful predictor of survival after CRC surgery, particularly for patients with stage I/II disease or colon cancer. © 2017 Journal of Gastroenterology and Hepatology Foundation and John Wiley & Sons Australia, Ltd.

Distant Metastasis Risk Stratification for Patients Undergoing Curative Resection Followed by Adjuvant Chemoradiation for Extrahepatic Bile Duct Cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Kyubo; Chie, Eui Kyu, E-mail: ekchie93@snu.ac.kr; Jang, Jin-Young

2012-09-01

Purpose: To analyze the prognostic factors predicting distant metastasis in patients undergoing adjuvant chemoradiation for extrahepatic bile duct (EHBD) cancer. Methods and Materials: Between January 1995 and August 2006, 166 patients with EHBD cancer underwent resection with curative intent, followed by adjuvant chemoradiation. There were 120 males and 46 females, and median age was 61 years (range, 34-86). Postoperative radiotherapy was delivered to tumor bed and regional lymph nodes (median dose, 40 Gy; range, 34-56 Gy). A total of 157 patients also received fluoropyrimidine chemotherapy as a radiosensitizer, and fluoropyrimidine-based maintenance chemotherapy was administered to 127 patients. Median follow-up durationmore » was 29 months. Results: The treatment failed for 97 patients, and the major pattern of failure was distant metastasis (76 patients, 78.4%). The 5-year distant metastasis-free survival rate was 49.4%. The most common site of distant failure was the liver (n = 36). On multivariate analysis, hilar tumor, tumor size {>=}2 cm, involved lymph node, and poorly differentiated tumor were associated with inferior distant metastasis-free survival (p = 0.0348, 0.0754, 0.0009, and 0.0078, respectively), whereas T stage was not (p = 0.8081). When patients were divided into four groups based on these risk factors, the 5-year distant metastasis-free survival rates for patients with 0, 1, 2, and 3 risk factors were 86.4%, 59.9%, 32.5%, and 0%, respectively (p < 0.0001). Conclusion: Despite maintenance chemotherapy, distant metastasis was the major pattern of failure in patients undergoing adjuvant chemoradiation for EHBD cancer after resection with curative intent. Intensified chemotherapy is warranted to improve the treatment outcome, especially in those with multiple risk factors.« less

Advanced Curation Preparation for Mars Sample Return and Cold Curation

NASA Technical Reports Server (NTRS)

Fries, M. D.; Harrington, A. D.; McCubbin, F. M.; Mitchell, J.; Regberg, A. B.; Snead, C.

2017-01-01

NASA Curation is tasked with the care and distribution of NASA's sample collections, such as the Apollo lunar samples and cometary material collected by the Stardust spacecraft. Curation is also mandated to perform Advanced Curation research and development, which includes improving the curation of existing collections as well as preparing for future sample return missions. Advanced Curation has identified a suite of technologies and techniques that will require attention ahead of Mars sample return (MSR) and missions with cold curation (CCur) requirements, perhaps including comet sample return missions.

Curating NASA's Past, Present, and Future Extraterrestrial Sample Collections

NASA Technical Reports Server (NTRS)

McCubbin, F. M.; Allton, J. H.; Evans, C. A.; Fries, M. D.; Nakamura-Messenger, K.; Righter, K.; Zeigler, R. A.; Zolensky, M.; Stansbery, E. K.

2016-01-01

The Astromaterials Acquisition and Curation Office (henceforth referred to herein as NASA Curation Office) at NASA Johnson Space Center (JSC) is responsible for curating all of NASA's extraterrestrial samples. Under the governing document, NASA Policy Directive (NPD) 7100.10E "Curation of Extraterrestrial Materials", JSC is charged with "...curation of all extra-terrestrial material under NASA control, including future NASA missions." The Directive goes on to define Curation as including "...documentation, preservation, preparation, and distribution of samples for research, education, and public outreach." Here we describe some of the past, present, and future activities of the NASA Curation Office.

Potential treatments for genetic hearing loss in humans: current conundrums.

PubMed

Minoda, R; Miwa, T; Ise, M; Takeda, H

2015-08-01

Genetic defects are a major cause of hearing loss in newborns. Consequently, hearing loss has a profound negative impact on human daily living. Numerous causative genes for genetic hearing loss have been identified. However, presently, there are no truly curative treatments for this condition. There have been several recent reports on successful treatments in mice using embryonic gene therapy, neonatal gene therapy and neonatal antisense oligonucleotide therapy. Herein, we describe state-of-the-art research on genetic hearing loss treatment through gene therapy and discuss the obstacles to overcome in curative treatments of genetic hearing loss in humans.

Outcomes after resection of occupational cholangiocarcinoma.

PubMed

Kubo, Shoji; Takemura, Shigekazu; Tanaka, Shogo; Shinkawa, Hiroji; Kinoshita, Masahiko; Hamano, Genya; Ito, Tokuji; Koda, Masaki; Aota, Takanori; Yamamoto, Takatsugu; Terajima, Hiroaki; Tachiyama, Gorou; Yamada, Terumasa; Nakamori, Shoji; Arimoto, Akira; Fujikawa, Masahiro; Tomimaru, Yoshito; Sugawara, Yasuhiko; Nakagawa, Kei; Unno, Michiaki; Mizuguchi, Toru; Takenaka, Kenji; Kimura, Koichi; Shirabe, Ken; Saiura, Akio; Uesaka, Katsuhiko; Taniguchi, Hiroki; Fukuda, Akira; Chong, Ja-Mun; Kuwae, Yuko; Ohsawa, Masahiko; Sato, Yasunori; Nakanuma, Yasuni

2016-09-01

Cholangiocarcinoma caused by exposure to 1,2-dichloropropane and/or dichloromethane is recognized as occupational cholangiocarcinoma. The aim of this study was to investigate the outcomes after resection of occupational cholangiocarcinoma to establish a treatment strategy for this disease. Clinicopathological findings and outcomes after surgical intervention in 20 patients with occupational cholangiocarcinoma were investigated. Of 20 the patients, curative resection was performed in 16 patients. Three patients underwent radiation at the stump of the bile ducts. Adjuvant chemotherapy was performed in 12 patients. Biliary intraepithelial neoplasia, intraductal papillary neoplasm of the bile duct, and/or chronic bile duct injury was detected in most subjects. Intraabdominal infection developed after surgery in nine patients. Cholangiocarcinoma recurred in 12 of the 20 patients. The recurrent tumors in five patients developed at a different part of the bile duct from the primary tumor and a second resection was performed in four of these five patients. The incidence of postoperative complications including intraabdominal infection was high in patients with occupational cholangiocarcinoma. Multicentric recurrence occurred not infrequently after surgery because the bile ducts had a high potential for the development of carcinoma. The aggressive treatment including second resection for the multicentric recurrence appeared to be effective. © 2016 Japanese Society of Hepato-Biliary-Pancreatic Surgery.

Electrolytic ablation as an adjunct to liver resection: Safety and efficacy in patients.

PubMed

Wemyss-Holden, Simon A; Berry, David P; Robertson, Gavin S M; Dennison, Ashley R; De La M Hall, Pauline; Maddern, Guy J

2002-08-01

Electrolytic ablation is a relatively new method for the local destruction of colorectal liver metastases. Experimental work in animal models has shown this method to be safe and efficacious. However, before proceeding to clinical trials it was necessary to confirm these findings in a pilot study of five patients. Five patients with colorectal liver metastases were studied prospectively. Each patient underwent a potentially curative liver resection. One of the metastases to be removed was treated using electrolysis before resection. Each patient was monitored closely during and after electrolysis to determine any morbidity associated with the treatment. Once resected, the metastases were examined histologically for completeness of ablation. All patients tolerated the electrolysis well; there were no deaths or complications related to the treatment. Histological examination of the resected metastases which had been treated electrolytically showed complete tissue destruction with no viable malignant cells remaining at the site of treatment. This pilot study of electrolytic ablation of liver metastases in five patients showed the treatment to be well tolerated and safe. Additionally, it demonstrated total destruction of the malignant tissue at the site of electrolysis. Based on these encouraging results, clinical trials can now begin.

Prediction of early postoperative infections in pediatric liver transplantation by logistic regression

NASA Astrophysics Data System (ADS)

Uzunova, Yordanka; Prodanova, Krasimira; Spassov, Lubomir

2016-12-01

Orthotopic liver transplantation (OLT) is the only curative treatment for end-stage liver disease. Early diagnosis and treatment of infections after OLT are usually associated with improved outcomes. This study's objective is to identify reliable factors that can predict postoperative infectious morbidity. 27 children were included in the analysis. They underwent liver transplantation in our department. The correlation between two parameters (the level of blood glucose at 5th postoperative day and the duration of the anhepatic phase) and postoperative infections was analyzed, using univariate analysis. In this analysis, an independent predictive factor was derived which adequately identifies patients at risk of infectious complications after a liver transplantation.

Presenting symptoms of giant fibrovascular polyp of the oesophagus: case report and literature review.

PubMed

Sestini, S; Gisabella, M; Pastorino, U; Billé, A

2016-05-01

Lipomas of the gastrointestinal tract are rare, slow-growing lesions that comprise 0.4% of all gastrointestinal neoplasms. They can cause dysphagia, dyspnoea or sudden choking. Due to rarity of this condition and its uncommon presentation, a literature review was carried out (PubMed). This search revealed 290 articles, of which 74 were considered pertinent and were evaluated. We report a case of a 13cm pedunculated oesophageal lipoma that presented with increasing dysphagia and two episodes of suffocation. The patient underwent curative resection through a cervical approach. Resection is recommended for large (>5 cm) or symptomatic polyps. Outcomes are excellent given that lesions are universally benign and oesophageal resection is not required.

Gallbladder Cancer Presenting with Jaundice: Uniformly Fatal or Still Potentially Curable?

PubMed

Tran, Thuy B; Norton, Jeffrey A; Ethun, Cecilia G; Pawlik, Timothy M; Buettner, Stefan; Schmidt, Carl; Beal, Eliza W; Hawkins, William G; Fields, Ryan C; Krasnick, Bradley A; Weber, Sharon M; Salem, Ahmed; Martin, Robert C G; Scoggins, Charles R; Shen, Perry; Mogal, Harveshp D; Idrees, Kamran; Isom, Chelsea A; Hatzaras, Ioannis; Shenoy, Rivfka; Maithel, Shishir K; Poultsides, George A

2017-08-01

Jaundice as a presenting symptom of gallbladder cancer has traditionally been considered to be a sign of advanced disease, inoperability, and poor outcome. However, recent studies have demonstrated that a small subset of these patients can undergo resection with curative intent. Patients with gallbladder cancer managed surgically from 2000 to 2014 in 10 US academic institutions were stratified based on the presence of jaundice at presentation (defined as bilirubin ≥4 mg/ml or requiring preoperative biliary drainage). Perioperative morbidity, mortality, and overall survival were compared between jaundiced and non-jaundiced patients. Of 400 gallbladder cancer patients with available preoperative data, 108 (27%) presented with jaundice while 292 (73%) did not. The fraction of patients who eventually underwent curative-intent resection was much lower in the presence of jaundice (n = 33, 30%) than not (n = 218, 75%; P < 0.001). Jaundiced patients experienced higher perioperative morbidity (69 vs. 38%; P = 0.002), including a much higher need for reoperation (12 vs. 1%; P = 0.003). However, 90-day mortality (6.5 vs. 3.6%; P = 0.35) was not significantly higher. Overall survival after resection was worse in jaundiced patients (median 14 vs. 32 months; P < 0.001). Further subgroup analysis within the jaundiced patients revealed a more favorable survival after resection in the presence of low CA19-9 < 50 (median 40 vs. 12 months; P = 0.003) and in the absence of lymphovascular invasion (40 vs. 14 months; P = 0.014). Jaundice is a powerful preoperative clinical sign of inoperability and poor outcome among gallbladder cancer patients. However, some of these patients may still achieve long-term survival after resection, especially when preoperative CA19-9 levels are low and no lymphovascular invasion is noted pathologically.

Clinicopathological features of alpha-fetoprotein producing early gastric cancer with enteroblastic differentiation.

PubMed

Matsumoto, Kohei; Ueyama, Hiroya; Matsumoto, Kenshi; Akazawa, Yoichi; Komori, Hiroyuki; Takeda, Tsutomu; Murakami, Takashi; Asaoka, Daisuke; Hojo, Mariko; Tomita, Natsumi; Nagahara, Akihito; Kajiyama, Yoshiaki; Yao, Takashi; Watanabe, Sumio

2016-09-28

To investigate clinicopathological features of early stage gastric cancer with enteroblastic differentiation (GCED). We retrospectively investigated data on 6 cases of early stage GCED and 186 cases of early stage conventional gastric cancer (CGC: well or moderately differentiated adenocarcinoma) who underwent endoscopic submucosal dissection or endoscopic mucosal resection from September 2011 to February 2015 in our hospital. GCED was defined as a tumor having a primitive intestine-like structure composed of cuboidal or columnar cells with clear cytoplasm and immunohistochemical positivity for either alpha-fetoprotein, Glypican 3 or SALL4. The following were compared between GCED and CGC: age, gender, location and size of tumor, macroscopic type, ulceration, depth of invasion, lymphatic and venous invasion, positive horizontal and vertical margin, curative resection rate. Six cases (5 males, 1 female; mean age 75.7 years; 6 lesions) of early gastric cancer with a GCED component and 186 cases (139 males, 47 females; mean age 72.7 years; 209 lesions) of early stage CGC were investigated. Mean tumor diameters were similar but rates of submucosal invasion, lymphatic invasion, venous invasion, and non-curative resection were higher in GCED than CGC (66.6% vs 11.4%, 33.3% vs 2.3%, 66.6% vs 0.4%, 83.3% vs 11% respectively, P < 0.01). Deep submucosal invasion was not revealed endoscopically or by preoperative biopsy. Histologically, in GCED the superficial mucosal layer was covered with a CGC component. The GCED component tended to exist in the deeper part of the mucosa to the submucosa by lymphatic and/or venous invasion, without severe stromal reaction. In addition, Glypican 3 was the most sensitive marker for GCED (positivity, 83.3%), immunohistochemically. Even in the early stage GCED has high malignant potential, and preoperative diagnosis is considered difficult. Endoscopists and pathologists should know the clinicopathological features of this highly malignant type of cancer.

Can oesophagectomy be performed for patients with oesophageal carcinoma and concomitant liver cirrhosis? A retrospective study based on a propensity-matched cohort.

PubMed

Wang, Zhi-Qiang; Deng, Han-Yu; Yang, Yu-Shang; Wang, Yun; Hu, Yang; Yuan, Yong; Wang, Wen-Ping; Chen, Long-Qi

2017-09-01

For patients with oesophageal carcinoma and concomitant liver cirrhosis, the safety profile and postoperative prognosis of oesophagectomy are not clearly established due to the lack of relevant studies with large sample sizes. Our objective was to explore the surgical indications and postoperative prognosis in patients with oesophageal carcinoma and liver cirrhosis. A total of 2226 patients with oesophageal carcinoma underwent curative oesophagectomy (37 with liver cirrhosis and 2189 without) in our department from April 2008 to September 2013. Overall, 37 patients with liver cirrhosis (30 Child-Pugh Grade A and 7 Child-Pugh Grade B) and a propensity-matched cohort of 74 patients without cirrhosis were analysed. We compared the rates of postoperative complications and 5-year survival in these 2 groups. In addition, we performed an analysis of any potential risk factors for death, including patient demographic information and of operation performed. A higher operative mortality rate was observed in patients with oesophageal carcinoma and liver cirrhosis compared to patients with oesophageal carcinoma but without cirrhosis (11 vs 1%, P = 0.042). Patients with cirrhosis included those with Child-Pugh Grade B (43%), preoperative moderate ascites (100%), a prothrombin time of ≥ 4 s (75%) and greater weight loss. Although the rates of surgical death and postoperative hydrothorax were significantly higher in patients with liver cirrhosis, the rates of other major complications and 5-year overall survival were not significantly different compared to patients without cirrhosis. Curative oesophagectomy is a feasible, beneficial treatment option for patients with oesophageal carcinoma and liver cirrhosis, with a higher perioperative risk but reasonable longer term survival compared to patients without cirrhosis. © The Author 2017. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

Canto: an online tool for community literature curation.

PubMed

Rutherford, Kim M; Harris, Midori A; Lock, Antonia; Oliver, Stephen G; Wood, Valerie

2014-06-15

Detailed curation of published molecular data is essential for any model organism database. Community curation enables researchers to contribute data from their papers directly to databases, supplementing the activity of professional curators and improving coverage of a growing body of literature. We have developed Canto, a web-based tool that provides an intuitive curation interface for both curators and researchers, to support community curation in the fission yeast database, PomBase. Canto supports curation using OBO ontologies, and can be easily configured for use with any species. Canto code and documentation are available under an Open Source license from http://curation.pombase.org/. Canto is a component of the Generic Model Organism Database (GMOD) project (http://www.gmod.org/). © The Author 2014. Published by Oxford University Press.

Curating NASA's Extraterrestrial Samples - Past, Present, and Future

NASA Technical Reports Server (NTRS)

Allen, Carlton; Allton, Judith; Lofgren, Gary; Righter, Kevin; Zolensky, Michael

2011-01-01

Curation of extraterrestrial samples is the critical interface between sample return missions and the international research community. The Astromaterials Acquisition and Curation Office at the NASA Johnson Space Center (JSC) is responsible for curating NASA s extraterrestrial samples. Under the governing document, NASA Policy Directive (NPD) 7100.10E "Curation of Extraterrestrial Materials", JSC is charged with ". . . curation of all extraterrestrial material under NASA control, including future NASA missions." The Directive goes on to define Curation as including "documentation, preservation, preparation, and distribution of samples for research, education, and public outreach."

Curating NASA's Extraterrestrial Samples - Past, Present, and Future

NASA Technical Reports Server (NTRS)

Allen, Carlton; Allton, Judith; Lofgren, Gary; Righter, Kevin; Zolensky, Michael

2010-01-01

Curation of extraterrestrial samples is the critical interface between sample return missions and the international research community. The Astromaterials Acquisition and Curation Office at the NASA Johnson Space Center (JSC) is responsible for curating NASA's extraterrestrial samples. Under the governing document, NASA Policy Directive (NPD) 7100.10E "Curation of Extraterrestrial Materials," JSC is charged with ". . . curation of all extraterrestrial material under NASA control, including future NASA missions." The Directive goes on to define Curation as including documentation, preservation, preparation, and distribution of samples for research, education, and public outreach.

Southern African Treatment Resistance Network (SATuRN) RegaDB HIV drug resistance and clinical management database: supporting patient management, surveillance and research in southern Africa

PubMed Central

Manasa, Justen; Lessells, Richard; Rossouw, Theresa; Naidu, Kevindra; Van Vuuren, Cloete; Goedhals, Dominique; van Zyl, Gert; Bester, Armand; Skingsley, Andrew; Stott, Katharine; Danaviah, Siva; Chetty, Terusha; Singh, Lavanya; Moodley, Pravi; Iwuji, Collins; McGrath, Nuala; Seebregts, Christopher J.; de Oliveira, Tulio

2014-01-01

Abstract Substantial amounts of data have been generated from patient management and academic exercises designed to better understand the human immunodeficiency virus (HIV) epidemic and design interventions to control it. A number of specialized databases have been designed to manage huge data sets from HIV cohort, vaccine, host genomic and drug resistance studies. Besides databases from cohort studies, most of the online databases contain limited curated data and are thus sequence repositories. HIV drug resistance has been shown to have a great potential to derail the progress made thus far through antiretroviral therapy. Thus, a lot of resources have been invested in generating drug resistance data for patient management and surveillance purposes. Unfortunately, most of the data currently available relate to subtype B even though >60% of the epidemic is caused by HIV-1 subtype C. A consortium of clinicians, scientists, public health experts and policy markers working in southern Africa came together and formed a network, the Southern African Treatment and Resistance Network (SATuRN), with the aim of increasing curated HIV-1 subtype C and tuberculosis drug resistance data. This article describes the HIV-1 data curation process using the SATuRN Rega database. The data curation is a manual and time-consuming process done by clinical, laboratory and data curation specialists. Access to the highly curated data sets is through applications that are reviewed by the SATuRN executive committee. Examples of research outputs from the analysis of the curated data include trends in the level of transmitted drug resistance in South Africa, analysis of the levels of acquired resistance among patients failing therapy and factors associated with the absence of genotypic evidence of drug resistance among patients failing therapy. All these studies have been important for informing first- and second-line therapy. This database is a free password-protected open source database available on www.bioafrica.net. Database URL: http://www.bioafrica.net/regadb/ PMID:24504151

Evolving role of FDG-PET/CT in prognostic evaluation of resectable gastric cancer

PubMed Central

De Raffele, Emilio; Mirarchi, Mariateresa; Cuicchi, Dajana; Lecce, Ferdinando; Cola, Bruno

2017-01-01

Gastric cancer (GC) remains a leading cause of cancer death worldwide. Radical gastrectomy is the only potentially curative treatment, and perioperative adjuvant therapies may improve the prognosis after curative resection. Prognosis largely depends on the tumour stage and histology, but the host systemic inflammatory response (SIR) to GC may contribute as well, as has been determined for other malignancies. In GC patients, the potential utility of positron emission tomography/computed tomography (PET/CT) with the imaging radiopharmaceutical 18F-fluorodeoxyglucose (FDG) is still debated, due to its lower sensitivity in diagnosing and staging GC compared to other imaging modalities. There is, however, growing evidence that FDG uptake in the primary tumour and regional lymph nodes may be efficient for predicting prognosis of resected patients and for monitoring tumour response to perioperative treatments, having prognostic value in that it can change therapeutic strategies. Moreover, FDG uptake in bone marrow seems to be significantly associated with SIR to GC and to represent an efficient prognostic factor after curative surgery. In conclusion, PET/CT technology is efficient in GC patients, since it is useful to integrate other imaging modalities in staging tumours and may have prognostic value that can change therapeutic strategies. With ongoing improvements, PET/CT imaging may gain further importance in the management of GC patients. PMID:29097864

Curating NASA's Future Extraterrestrial Sample Collections: How Do We Achieve Maximum Proficiency?

NASA Technical Reports Server (NTRS)

McCubbin, Francis; Evans, Cynthia; Zeigler, Ryan; Allton, Judith; Fries, Marc; Righter, Kevin; Zolensky, Michael

2016-01-01

The Astromaterials Acquisition and Curation Office (henceforth referred to herein as NASA Curation Office) at NASA Johnson Space Center (JSC) is responsible for curating all of NASA's extraterrestrial samples. Under the governing document, NASA Policy Directive (NPD) 7100.10E "Curation of Extraterrestrial Materials", JSC is charged with "The curation of all extraterrestrial material under NASA control, including future NASA missions." The Directive goes on to define Curation as including "... documentation, preservation, preparation, and distribution of samples for research, education, and public outreach." Here we describe some of the ongoing efforts to ensure that the future activities of the NASA Curation Office are working towards a state of maximum proficiency.

Worm Proteins of Schistosoma mansoni Reduce the Severity of Experimental Chronic Colitis in Mice by Suppressing Colonic Proinflammatory Immune Responses

PubMed Central

Heylen, Marthe; Ruyssers, Nathalie E.; De Man, Joris G.; Timmermans, Jean-Pierre; Pelckmans, Paul A.; Moreels, Tom G.; De Winter, Benedicte Y.

2014-01-01

Although helminthic therapy as a possible new option to treat inflammatory bowel disease is a well-established concept by now, the search for immunomodulatory helminth-derived compounds and their mechanisms of action is still ongoing. We investigated the therapeutic potential and the underlying immunological mechanisms of Schistosoma mansoni soluble worm proteins (SmSWP) in an adoptive T cell transfer mouse model of chronic colitis. Both a curative and a preventive treatment protocol were included in this study. The curative administration of SmSWP (started when colitis was established), resulted in a significant improvement of the clinical disease score, colonoscopy, macroscopic and microscopic inflammation score, colon length and myeloperoxidase activity. The therapeutic potential of the preventive SmSWP treatment (started before colitis was established), was less pronounced compared with the curative SmSWP treatment but still resulted in an improved clinical disease score, body weight loss, colon length and microscopic inflammation score. Both the curative and preventive SmSWP treatment downregulated the mRNA expression of the proinflammatory cytokines IFN-γ and IL-17A and upregulated the mRNA expression of the anti-inflammatory cytokine IL-4 in the colon at the end of the experiment. This colonic immunomodulatory effect of SmSWP could not be confirmed at the protein level. Moreover, the effect of SmSWP appeared to be a local colonic phenomenon, since the flow cytometric T cell characterization of the mesenteric lymph nodes and the cytokine measurements in the serum did not reveal any effect of SmSWP treatment. In conclusion, SmSWP treatment reduced the severity of colitis in the adoptive transfer mouse model via the suppression of proinflammatory cytokines and the induction of an anti-inflammatory response in the colon. PMID:25313594

[A case of cytology-positive, stage IV gastric cancer, alive with no recurrence for 4 years, curatively treated with combination chemotherapy using S-1, CPT-11 and subsequent total gastrectomy].

PubMed

Kubo, Naoshi; Nobuhara, Yasuyuki; Kanemura, Mizuyuki; Sunami, Takeshi; Nishimura, Shigehiko; Ako, Eiji; Yo, Taiho

2007-11-01

A 68-year-old man was admitted to another hospital because of progressive weight decrease and appetite loss. Endoscopic examination revealed type 4 advanced gastric cancer at the upper body of the stomach. In February, 2003, he patient had probe laparotomy because there was a small amount of ascites in his peritoneal cavity, and intraoperative washing cytology revealed cancer cells in ascites.Subsequently, we started chemotherapy using S-1 and CPT-11. S-1 at a dose of 100 mg/day was orally administered for 2 weeks, and CPT-11 at a dose of 90 mg/body was intravenously administered once a week for 2 weeks followed by a 2-week drug-free period as 1 course. After 7 courses of the chemotherapy, the main lesion endoscopically vanished.Subsequently, the patient underwent curative total gastrectomy together with D2 lymph node dissection. Intraoperative cytology revealed no cancer cells, and histological examination of the primary lesion showed cancer cells invading the subserosa with no metastasis to any dissected lymph nodes. This therapy induced Grade 2 effect on cancer cells.Postoperatively, only S-1 was administered to the patient, who has remained alive with no recurrence for 4 years as of January, 2007.

An Analysis of Surgical Treatment for the Spontaneous Rupture of Hepatocellular Carcinoma.

PubMed

Sada, Haruki; Ohira, Masahiro; Kobayashi, Tsuyoshi; Tashiro, Hirotaka; Chayama, Kazuaki; Ohdan, Hideki

2016-01-01

The prognosis of spontaneous rupture of hepatocellular carcinoma (HCC) remains unclear. We investigated the prognosis of patients with ruptured HCC based on the treatments and prognostic factors associated with long-term survival. The prognoses of 64 consecutive patients treated for ruptured HCC from 1986 to 2013 were analyzed according to their methods of treatment. The prognostic factors of 16 surgical patients were identified, and their overall survival (OS) and recurrence rates were compared to 1,157 surgical patients who underwent surgery for non-ruptured HCC. The surgical outcomes were also compared using a propensity score matching method. Surgery was associated with a better OS. Curative resection was the only independent prognostic factor in surgical patients with ruptured HCC (p = 0.040). Although the OS of surgical patients with non-ruptured HCC was found to be significantly better than that of the patients with ruptured HCC, no significant difference in OS was observed after propensity score matching. A curative resection should be the objective of treatment, assuming the suitability of the patient's clinical condition. When the liver function reserve and tumor extension of patients with ruptured and non-ruptured HCC are similar, then their surgical outcomes may not be significantly different. © 2015 S. Karger AG, Basel.

Institutional Experience in the Management of Hilar Liver Obstruction- A Series of 13 Cases.

PubMed

Pathanki, Adithya Malolan; Naragund, Adithya V; Mahadevappa, Basant

2016-12-01

Neoplastic hilar obstruction to the liver outflow presents a unique challenge to the surgeon, wherein, the balance between a curative and possibly larger resection has to be achieved against a more conservative local resection. These are often technically demanding and have thus, far produced equivocal outcomes on both ends. The present case series is on 13 patients who presented with hilar obstruction. They all underwent resections with possible curative intent. The focus of our review is on the technical nuances and the strategies we used, intra- and peri-operatively to make resections possible in these patients, who at first look were deemed inoperable. Among the 13, 10 had hilar cholangiocarcinoma (CCA) while the others had a more benign diagnosis e.g., Hydatid disease. We did not encounter any peri-operative mortality in our series. Two of our patients had to be re-explored for intra-abdominal complications. Among the 13, we encountered two deaths. The rest of the patients are still on follow-up as of April 2016. Hilar CCA continue to be rare and challenging tumours for the Hepato Pancreato Biliary (HPB) surgeon to manage. Outlooks are currently changing as we try to resect bigger and more complicated hilar liver tumours with better results.

Combined evaluation of the Glasgow prognostic score and carcinoembryonic antigen concentration prior to hepatectomy predicts postoperative outcomes in patients with liver metastasis from colorectal cancer.

PubMed

Kobayashi, Takashi; Kawakamil, Masayo; Hara, Yoshiaki; Shioiri, Sadaaki; Yasuno, Masamichi; Teruya, Masanori; Kaminishi, Michio

2014-01-01

Little is known about the ability of the inflammation-based Glasgow prognostic score (GPS). 106 patients who underwent curative resection for colorectal liver metastasis (CRLM) were analyzed. Patients with an elevated Creactive protein concentration (>10 mg/L) and hypoalbuminemia (<35 g/L) at admission were assigned a GPS 2, those with only 1 of these biochemical abnormalities were assigned a GPS 1, and those without either abnormality were assigned a GPS 0. Multivariate analysis showed that 2 variables, carcinoembryonic antigen (CEA) concentration > 30 ng/mL and a GPS 1 or 2, were independently prognostic of survival. Patients were classified into 3 groups on the basis of these 2 variables. Patients with GPS 1 or 2 and CEA concentration > 30 ng/mL were assigned a new score of 2, those with either 1 factor were assigned a new score of 1, and those with neither factors were assigned a new score of 0. The 5-year overall survival rates of new scores of 0, 1, 2 were 71.5%, 31.6%, and 0%, respectively (P < 0.0001). This simple staging system may be able to identify a subgroup of patients who are eligible for curative resection but show poor prognosis.

Artificial pneumothorax: a safe and simple method to relieve pain during microwave ablation of subpleural lung malignancy.

PubMed

Hou, Xiaowei; Zhuang, Xingjun; Zhang, Haiwen; Wang, Kai; Zhang, Yuanxin

2017-08-01

Microwave ablation has been extensively used for eliminating pulmonary tumors; however, it is usually associated with severe pain under local anesthesia. Decreasing the power and shortening the ablation time can help to relieve the pain; however, this leads to incomplete ablation and an increasing recurrence rate. This research aims to employ an artificial pneumothorax to increase both the curative effect and pain relief during the ablation procedure. From July 2013 to January 2015, nine patients presenting with 10 subpleural lung tumors (age: 44-78 years) with a high possibility of severe pain underwent the artificial pneumothorax during microwave ablation. The pain assessment scores and complications induced by the artificial pneumothorax were recorded and analyzed by a CT scan follow-up. The tumors of the nine patients were eliminated successfully using microwave ablation with artificial pneumothorax under local anesthesia. The pain caused by the ablation was relieved to a great extent with an average rate of 94.66% (range: 63.3%-100%) and all tumors were ablated completely. No severe complications occurred after the operation. The artificial pneumothorax is a reliable therapy to improve the curative effect of microwave ablation under local anesthesia by relieving the pain of the patients.

Lymph node metastasis after endoscopic submucosal dissection of a differentiated gastric cancer confined to the mucosa with an ulcer smaller than 30 mm.

PubMed

Fujii, Hiroyuki; Ishii, Eiji; Tochitani, Shinako; Nakaji, So; Hirata, Nobuto; Kusanagi, Hiroshi; Narita, Makoto

2015-01-01

In the expanded indications for endoscopic resection, Japanese guidelines for gastric cancer include differentiated cancers confined to the mucosa with an ulcer <30 mm. We describe a patient with lymph node metastasis after curative endoscopic submucosal dissection (ESD) for a tumor of this indication. The patient was a 70-year-old man with chronic hepatitis C. He underwent ESD for early gastric cancer in May 2010. Pathology revealed a moderately differentiated adenocarcinoma, 22 × 17 mm in size, that was confined to the mucosa with an ulcer. The horizontal and vertical margins were negative for the tumor. We diagnosed thiscase as curative resection of expanded indication and followed this patient with endoscopy, abdominal ultrasonography (AUS) or enhanced computed tomography (CT) approximately every 6 months. After 17 months, lymph node metastasis was detected with AUS and CT and diagnosed by endoscopic ultrasound-guided fine-needle aspiration biopsy in August 2011. Distal gastrectomy with D2 dissection was carried out in December 2011. Although it is low, the possibility of recurrence should be borne in mind after endoscopic treatment of early gastric cancer, despite its inclusion in the expanded indications for endoscopic resection. © 2014 The Authors. Digestive Endoscopy © 2014 Japan Gastroenterological Endoscopy Society.

A Novel Approach for Hepatic Arterial Reconstruction after Total Pancreatectomy with Common Hepatic Artery Resection Using Inferior Phrenic Artery.

PubMed

Matsumoto, Takatsugu; Kubota, Keiichi; Aoki, Taku; Shimizu, Takayuki; Mori, Shozo; Kato, Masato; Asato, Hirotaka

2018-02-07

Because of the anatomical characteristics, pancreatic cancers (PC) can easily invade to visceral vessels such as celiac artery, superior mesenteric artery, common hepatic artery (CHA) and portal vein, which makes curative resection difficult. In this study, we report an R0 resection for locally advanced PC by total pancreatectomy, combined resection of CHA, and reconstruction of hepatic artery using autologous left inferior phrenic artery (IPA). A 47-year-old woman with complaints of low back pain was referred to our department. Contrast-enhanced computed tomography revealed a hypo-attenuation tumor of the pancreatic body measuring 70 mm, which completely encased the CHA. When unresectable locally advanced PC was diagnosed, systematic chemotherapy was administrated. After downstaging, she underwent surgery with curative intent. The tumor completely infiltrated the peripheral part of the CHA and gastroduodenal artery. As the tumor also extended to the head of the pancreas, total pancreatectomy and combined resection of CHA were performed. Then the exposed left IPA and proper hepatic artery were anastomosed with a microvascular technique. R0 resection was performed for restoring hepatic arterial flow and the postoperative course was uneventful without any postoperative morbidity. Hepatic artery reconstruction using IPA is a simple and safe procedure in selected patients. © 2018 S. Karger AG, Basel.

Sarcopenia predicts 1-year mortality in elderly patients undergoing curative gastrectomy for gastric cancer: a prospective study.

PubMed

Huang, Dong-Dong; Chen, Xiao-Xi; Chen, Xi-Yi; Wang, Su-Lin; Shen, Xian; Chen, Xiao-Lei; Yu, Zhen; Zhuang, Cheng-Le

2016-11-01

One-year mortality is vital for elderly oncologic patients undergoing surgery. Recent studies have demonstrated that sarcopenia can predict outcomes after major abdominal surgeries, but the association of sarcopenia and 1-year mortality has never been investigated in a prospective study. We conducted a prospective study of elderly patients (≥65 years) who underwent curative gastrectomy for gastric cancer from July 2014 to July 2015. Sarcopenia was determined by the measurements of muscle mass, handgrip strength, and gait speed. Univariate and multivariate analyses were used to identify the risk factors associated with 1-year mortality. A total of 173 patients were included, in which 52 (30.1 %) patients were identified as having sarcopenia. Twenty-four (13.9 %) patients died within 1 year of surgery. Multivariate analysis showed that sarcopenia was an independent risk factor for 1-year mortality. Area under the receiver operating characteristic curve demonstrated an increased predictive power for 1-year mortality with the inclusion of sarcopenia, from 0.835 to 0.868. Solely low muscle mass was not predictive of 1-year mortality in the multivariate analysis. Sarcopenia is predictive of 1-year mortality in elderly patients undergoing gastric cancer surgery. The measurement of muscle function is important for sarcopenia as a preoperative assessment tool.

The Role of Community-Driven Data Curation for Enterprises

NASA Astrophysics Data System (ADS)

Curry, Edward; Freitas, Andre; O'Riáin, Sean

With increased utilization of data within their operational and strategic processes, enterprises need to ensure data quality and accuracy. Data curation is a process that can ensure the quality of data and its fitness for use. Traditional approaches to curation are struggling with increased data volumes, and near real-time demands for curated data. In response, curation teams have turned to community crowd-sourcing and semi-automatedmetadata tools for assistance. This chapter provides an overview of data curation, discusses the business motivations for curating data and investigates the role of community-based data curation, focusing on internal communities and pre-competitive data collaborations. The chapter is supported by case studies from Wikipedia, The New York Times, Thomson Reuters, Protein Data Bank and ChemSpider upon which best practices for both social and technical aspects of community-driven data curation are described.

Current trends in multimodality treatment of esophageal and gastroesophageal junction cancer - Review article.

PubMed

Klevebro, Fredrik; Ekman, Simon; Nilsson, Magnus

2017-09-01

Multimodality treatment has now been widely introduced in the curatively intended treatment of esophageal and gastroesophageal junction cancer. We aim to give an overview of the scientific evidence for the available treatment strategies and to describe which trends that are currently developing. We conducted a review of the scientific evidence for the different curatively intended treatment strategies that are available today. Relevant articles of randomized controlled trials, cohort studies, and meta analyses were included. After a systematic search of relevant papers we have included 64 articles in the review. The results show that adenocarcinomas and squamous cell carcinomas of the esophagus and gastroesophageal junction are two separate entities and should be analysed and studied as two different diseases. Neoadjuvant treatment followed by surgical resection is the gold standard of the curatively intended treatment today. There is no scientific evidence to support the use of chemoradiotherapy over chemotherapy in the neoadjuvant setting for esophageal or junctional adenocarcinoma. There is reasonable evidence to support definitive chemoradiotherapy as a treatment option for squamous cell carcinoma of the esophagus. The evidence base for curatively intended treatments of esophageal and gastroesophageal junction cancer is not very strong. Several on-going trials have the potential to change the gold standard treatments of today. Copyright © 2017 Elsevier Ltd. All rights reserved.

Formalizing An Approach to Curate the Global Change Master Directory (GCMD)'s Controlled Vocabularies (Keywords) Through a Keyword Governance Process and Community Involvement

NASA Astrophysics Data System (ADS)

Stevens, T.

2016-12-01

NASA's Global Change Master Directory (GCMD) curates a hierarchical set of controlled vocabularies (keywords) covering Earth sciences and associated information (data centers, projects, platforms, and instruments). The purpose of the keywords is to describe Earth science data and services in a consistent and comprehensive manner, allowing for precise metadata search and subsequent retrieval of data and services. The keywords are accessible in a standardized SKOS/RDF/OWL representation and are used as an authoritative taxonomy, as a source for developing ontologies, and to search and access Earth Science data within online metadata catalogs. The keyword curation approach involves: (1) receiving community suggestions; (2) triaging community suggestions; (3) evaluating keywords against a set of criteria coordinated by the NASA Earth Science Data and Information System (ESDIS) Standards Office; (4) implementing the keywords; and (5) publication/notification of keyword changes. This approach emphasizes community input, which helps ensure a high quality, normalized, and relevant keyword structure that will evolve with users' changing needs. The Keyword Community Forum, which promotes a responsive, open, and transparent process, is an area where users can discuss keyword topics and make suggestions for new keywords. Others could potentially use this formalized approach as a model for keyword curation.

Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers

PubMed Central

Ning, Shangwei; Zhang, Jizhou; Wang, Peng; Zhi, Hui; Wang, Jianjian; Liu, Yue; Gao, Yue; Guo, Maoni; Yue, Ming; Wang, Lihua; Li, Xia

2016-01-01

Lnc2Cancer (http://www.bio-bigdata.net/lnc2cancer) is a manually curated database of cancer-associated long non-coding RNAs (lncRNAs) with experimental support that aims to provide a high-quality and integrated resource for exploring lncRNA deregulation in various human cancers. LncRNAs represent a large category of functional RNA molecules that play a significant role in human cancers. A curated collection and summary of deregulated lncRNAs in cancer is essential to thoroughly understand the mechanisms and functions of lncRNAs. Here, we developed the Lnc2Cancer database, which contains 1057 manually curated associations between 531 lncRNAs and 86 human cancers. Each association includes lncRNA and cancer name, the lncRNA expression pattern, experimental techniques, a brief functional description, the original reference and additional annotation information. Lnc2Cancer provides a user-friendly interface to conveniently browse, retrieve and download data. Lnc2Cancer also offers a submission page for researchers to submit newly validated lncRNA-cancer associations. With the rapidly increasing interest in lncRNAs, Lnc2Cancer will significantly improve our understanding of lncRNA deregulation in cancer and has the potential to be a timely and valuable resource. PMID:26481356

A curative regimen would decrease HIV prevalence but not HIV incidence unless targeted to an ART-naïve population.

PubMed

Dimitrov, Dobromir T; Kiem, Hans-Peter; Jerome, Keith R; Johnston, Christine; Schiffer, Joshua T

2016-02-24

HIV curative strategies currently under development aim to eradicate latent provirus, or prevent viral replication, progression to AIDS, and transmission. The impact of implementing curative programs on HIV epidemics has not been considered. We developed a mathematical model of heterosexual HIV transmission to evaluate the independent and synergistic impact of ART, HIV prevention interventions and cure on HIV prevalence and incidence. The basic reproduction number was calculated to study the potential for the epidemic to be eliminated. We explored scenarios with and without the assumption that patients enrolled into HIV cure programs need to be on antiretroviral treatment (ART). In our simulations, curative regimes had limited impact on HIV incidence if only ART patients were eligible for cure. Cure implementation had a significant impact on HIV incidence if ART-untreated patients were enrolled directly into cure programs. Concurrent HIV prevention programs moderately decreased the percent of ART treated or cured patients needed to achieve elimination. We project that widespread implementation of HIV cure would decrease HIV prevalence under all scenarios but would only lower rate of new infections if ART-untreated patients were targeted. Current efforts to identify untreated HIV patients will gain even further relevance upon availability of an HIV cure.

Pretreatment maximum standardized uptake value of (18)F-fluorodeoxyglucose positron emission tomography as a predictor of distant metastasis in adenoid cystic carcinoma of the head and neck.

PubMed

Kim, Donghyun; Kim, Wontaek; Lee, Joohye; Ki, Yongkan; Lee, Byungjoo; Cho, Kyusup; Kim, Seongjang; Nam, Jiho; Lee, Jinchoon; Kim, Dongwon

2016-05-01

The purpose of this study was to determine whether the maximum standardized uptake value (SUVmax) of the primary tumor on pretreatment (18)F-fluorodeoxyglucose positron emission tomography ((18)F-FDG PET) has prognostic significance in patients with adenoid cystic carcinoma (ACC) of the head and neck. A retrospective review was carried out on 34 patients with ACC of the head and neck who underwent pretreatment (18)F-FDG PET imaging from June 2005 through July 2009. All patients underwent surgery with curative intent, and 26 of them received adjuvant radiotherapy (RT). When subjects were stratified into 2 groups according to a cutoff value for SUVmax of 4.15, the risk of distant metastasis was significantly high in patients with high SUVmax (p = .014). Multivariate analysis showed that high SUVmax and histologic grade 3 were independent poor prognostic factors for distant metastasis-free and disease-free survival. Pretreatment SUVmax of the primary tumor is an independent prognostic factor in patients with ACC of the head and neck. © 2015 Wiley Periodicals, Inc.

Long-term Survival Outcomes by Smoking Status in Surgical and Nonsurgical Patients With Non-small Cell Lung Cancer

PubMed Central

Meguid, Robert A.; Hooker, Craig M.; Harris, James; Xu, Li; Westra, William H.; Sherwood, J. Timothy; Sussman, Marc; Cattaneo, Stephen M.; Shin, James; Cox, Solange; Christensen, Joani; Prints, Yelena; Yuan, Nance; Zhang, Jennifer; Yang, Stephen C.

2010-01-01

Background: Survival outcomes of never smokers with non-small cell lung cancer (NSCLC) who undergo surgery are poorly characterized. This investigation compared surgical outcomes of never and current smokers with NSCLC. Methods: This investigation was a single-institution retrospective study of never and current smokers with NSCLC from 1975 to 2004. From an analytic cohort of 4,546 patients with NSCLC, we identified 724 never smokers and 3,822 current smokers. Overall, 1,142 patients underwent surgery with curative intent. For survival analysis by smoking status, hazard ratios (HRs) were estimated using Cox proportional hazard modeling and then further adjusted by other covariates. Results: Never smokers were significantly more likely than current smokers to be women (P < .01), older (P < .01), and to have adenocarcinoma (P < .01) and bronchioloalveolar carcinoma (P < .01). No statistically significant differences existed in stage distribution at presentation for the analytic cohort (P = .35) or for the subgroup undergoing surgery (P = .24). The strongest risk factors of mortality among patients with NSCLC who underwent surgery were advanced stage (adjusted hazard ratio, 3.43; 95% CI, 2.32-5.07; P < .01) and elevated American Society of Anesthesiologists classification (adjusted hazard ratio, 2.18; 95% CI, 1.40-3.40; P < .01). The minor trend toward an elevated risk of death on univariate analysis for current vs never smokers in the surgically treated group (hazard ratio, 1.20; 95% CI, 0.98-1.46; P = .07) was completely eliminated when the model was adjusted for covariates (P = .97). Conclusions: Our findings suggest that smoking status at time of lung cancer diagnosis has little impact on the long-term survival of patients with NSCLC, especially after curative surgery. Despite different etiologies between lung cancer in never and current smokers the prognosis is equally dismal. PMID:20507946

Clinical usefulness of extending the proximal margin in total gastrectomies for gastric adenocarcinoma.

PubMed

Clemente-Gutiérrez, U; Sánchez-Morales, G; Santes, O; Medina-Franco, H

2018-05-09

Surgical resection with negative margins is part of the curative treatment of gastric adenocarcinoma. Positive surgical margins are associated with worse outcome. The aim of the present study was to determine the clinical usefulness of extending the proximal surgical margin in patients undergoing total gastrectomy for gastric adenocarcinoma. A retrospective analysis of patients that underwent total gastrectomy within the time frame of 2002 and 2017 was conducted. Patients diagnosed with adenocarcinoma that underwent curative surgery were included. Patients were divided into three groups, depending on proximal surgical margin status: negative margin (R0), positive margin with additional resection to achieve negative margin (R1-R0), and positive margin (R1). Demographic and clinical variables were analyzed. The outcome measures to evaluate were recurrence, disease-free survival, and overall survival. Forty-eight patients were included in the study. Thirty-seven were classified as R0, 9 as R1-R0, and 2 as R1. Fifty-two percent of the patients had clinical stage III disease. The overall surgical mortality rate was 2% and the morbidity rate was higher than 29%. The local recurrence rate was 0% in the R1-R0 group vs. 50% in the R1 group (p = 0.02). Disease-free survival was 49 months in the R1-R0 group vs. 32 months in the R1 group (p = 0.6). Overall survival was 51 months for the R1-R0 group vs. 35 months for the R1 group (p = 0.5). Intraoperative extension of the positive surgical margin improved the local recurrence rate but was not associated with improvement in overall survival or disease-free survival and could possibly increase postoperative morbidity. Copyright © 2018 Asociación Mexicana de Gastroenterología. Publicado por Masson Doyma México S.A. All rights reserved.

Studying a Rare Disease Using Multi-Institutional Research Collaborations vs Big Data: Where Lies the Truth?

PubMed

Johnson, Aileen C; Ethun, Cecilia G; Liu, Yuan; Lopez-Aguiar, Alexandra G; Tran, Thuy B; Poultsides, George; Grignol, Valerie; Howard, J Harrison; Bedi, Meena; Gamblin, T Clark; Tseng, Jennifer; Roggin, Kevin K; Chouliaras, Konstantinos; Votanopoulos, Konstantinos; Cullinan, Darren; Fields, Ryan C; Delman, Keith A; Wood, William C; Cardona, Kenneth; Maithel, Shishir K

2018-06-12

Multi-institutional collaborations provide granularity lacking in epidemiologic datasets to enable in-depth study of rare diseases. For pts with superficial, high-grade soft tissue sarcomas (STS) of the trunk/extremity, the value of radiation therapy (RT) is not clear. We aimed to utilize the 7-institution US-Sarcoma-Collaborative (USSC) and the National Cancer Database (NCDB) to investigate this issue. All adult pts with superficial truncal/extremity high-grade STS who underwent primary curative-intent resection from 2000-2016 at USSC institutions or were included in the NCDB from 2004-2013 were analyzed. Propensity-score matching was performed. Endpoints were locoregional recurrence-free survival(LRFS), overall-survival(OS), and disease-specific survival(DSS). Of 4,153pts in the USSC, 169pts with superficial high-grade tumors underwent primary curative-intent resection, of whom 38% received RT. On multivariable Cox-regression analysis, RT was not associated with improved LRFS(p=0.56), OS(p=0.31), or DSS(p=0.20). On analysis of 51 propensity-score matched-pairs, RT was still not associated with increased LRFS, OS, or DSS. Analysis of 631 propensity-score matched-pairs in the NCDB demonstrated improved 5-yr OS associated with RT (80%vs70%;p=0.02). LRFS and DSS were not evaluable. Granular data afforded by collaborative research enables in-depth analysis of patient outcomes. The NCDB, although powered with large numbers, cannot assess many relevant outcomes (recurrence, DSS, or complications). In this study, the approaches yielded conflicting results. USSC data suggested no value of radiation while the NCDB demonstrated improved overall survival, contradicting all randomized-controlled trials in sarcoma. The pros/cons of either approach must be considered when applying results to clinical practice, and underscore the importance of randomized-controlled trials. Copyright © 2018. Published by Elsevier Inc.

BioModels: expanding horizons to include more modelling approaches and formats

PubMed Central

Nguyen, Tung V N; Graesslin, Martin; Hälke, Robert; Ali, Raza; Schramm, Jochen; Wimalaratne, Sarala M; Kothamachu, Varun B; Rodriguez, Nicolas; Swat, Maciej J; Eils, Jurgen; Eils, Roland; Laibe, Camille; Chelliah, Vijayalakshmi

2018-01-01

Abstract BioModels serves as a central repository of mathematical models representing biological processes. It offers a platform to make mathematical models easily shareable across the systems modelling community, thereby supporting model reuse. To facilitate hosting a broader range of model formats derived from diverse modelling approaches and tools, a new infrastructure for BioModels has been developed that is available at http://www.ebi.ac.uk/biomodels. This new system allows submitting and sharing of a wide range of models with improved support for formats other than SBML. It also offers a version-control backed environment in which authors and curators can work collaboratively to curate models. This article summarises the features available in the current system and discusses the potential benefit they offer to the users over the previous system. In summary, the new portal broadens the scope of models accepted in BioModels and supports collaborative model curation which is crucial for model reproducibility and sharing. PMID:29106614

Hematopoietic Stem Cell Transplant in Adolescent and Young Adults With Fanconi Anemia Is Feasible With Acceptable Toxicity, With Those Surviving 100 Days Posttransplant Having Excellent Outcomes.

PubMed

Alhuraiji, Ahmad; Alzahrani, Hazza; Al Mohareb, Fahad; Chaudhri, Naeem; Alsharif, Fahad; Mohamed, Said; Rasheed, Walid; Aldawsari, Ghuzayel; Ahmed, Syed Osman; Aljurf, Mahmoud

2016-12-01

Fanconi anemia is a congenital bone marrow failure syndrome that is associated with congenital anomalies and increased risk of cancer. Hematopoietic stem cell transplant is a potentially curative modality for bone marrow failure in Fanconi anemia patients. Here, we report our center's experience regarding adolescent and young adult patients with Fanconi anemia and hematopoietic stem cell transplant. We conducted a retrospective patient record analyses of patients who presented at our center from 1988 to 2014. We included patients greater than 14 years old with confirmed Fanconi anemia based on positive chromosome breakage study and who underwent hematopoietic stem cell transplant at our institution. Our study group comprised 12 patients with Fanconi anemia who underwent hematopoietic stem cell transplant at our institution. The median age was 20 years (range, 14-31 y) with a female predominance of 83%. Low-dose cyclophosphamide (20-80 mg/kg)-based conditioning regimens were used with different combinations that included fludarabine, antithymocyte globulin, or total body irradiation. All patients had HLA-matched sibling grafts. In all patients, stem cell source was the bone marrow. All patients showed engraftment. Four patients (33%) developed acute graft-versus-host disease. Three patients (25%) died early before day 100 after hematopoietic stem cell transplant due to infectious complications, with 1 patient having steroid refractory acute graft-versus-host disease. Overall survival was 75% at a median follow-up of 43 months. All patients who survived are well and remained transfusion independent without evidence of secondary malignancy. Our findings support the feasibility of reduced intensity conditioning allogeneic hematopoietic stem cell transplant in older and more heavily pretreated patients with Fanconi anemia, especially for those who are engrafted.

Predictors of CD34+ cell mobilization and collection in adult men with germ cell tumors: implications for the salvage treatment strategy.

PubMed

Necchi, Andrea; Miceli, Rosalba; Pedrazzoli, Paolo; Giannatempo, Patrizia; Secondino, Simona; Di Nicola, Massimo; Farè, Elena; Raggi, Daniele; Magni, Michele; Matteucci, Paola; Longoni, Paolo; Milanesi, Marco; Paternò, Emanuela; Ravagnani, Fernando; Arienti, Flavio; Nicolai, Nicola; Salvioni, Roberto; Carlo-Stella, Carmelo; Gianni, Alessandro M

2014-06-01

High-dose chemotherapy with tandem or triple carboplatin and etoposide course is currently the first curative choice for relapsing GCT. The collection of an adequate amount of hematopoietic (CD34(+)) stem cells is a priority. We analyzed data of patients who underwent HDCT at 2 referral institutions. Chemotherapy followed by myeloid growth factors was applied in all cases. Uni- and multivariable models were used to evaluate the association between 2 prespecified variables and mobilization parameters. Analyses included only the first mobilizing course of chemotherapy and mobilization failures. A total of 116 consecutive patients underwent a mobilization attempt from December 1995 to November 2012. Mobilizing regimens included cyclophosphamide (CTX) 7 gr/m(2) (n = 39), cisplatin, etoposide, and ifosfamide (PEI) (n = 42), paclitaxel, cisplatin, and gemcitabine (TPG) (n = 11), and mixed regimens (n = 24). Thirty-seven percent were treated in first-line, 50% (n = 58) in second-line, 9.5% (n = 11) and 3.4% (n = 4) in third- and fourth-line settings, respectively. Six patients did not undergo HDCT because they were poor mobilizers, 2 in first- and second-line (1.9%), and 4 beyond the second-line (26.7%). In the multivariable model, third-line or later setting was associated with a lower CD34(+) cell peak/μL (P = .028) and a lower total CD34(+)/kg collected (P = .008). The latter was also influenced by the type of mobilizing regimen (P < .001). A decline in significant mobilization parameters was found, primarily depending on the pretreatment load. Results lend support to the role of CD34(+) cell mobilization in the therapeutic algorithm of relapsing GCT, for whom multiple HDCT courses are still an option, and potentially a cure. Copyright © 2014 Elsevier Inc. All rights reserved.

Analysis of survival after pancreatic resection for oncological pathologies.

PubMed

Benzoni, Enrico; Rossit, Luca; Cojutti, Alessandro; Favero, Alessandro; Saccomano, Enrico; Zompicchiatti, Aron; Noce, Luigi; Bresadola, Fabrizio; Intini, Sergio

2007-01-01

Surgical treatment of pancreatic cancer is to date the only modality that offers a chance of long-term survival. Potentially curative surgery is an option for only about 15% of patients with pancreatic adenocarcinoma. The aim of this study was to determine the survival and to assess the association of clinical, pathological, and treatment features with survival of patients who underwent resection of pancreatic cancer at the Department of Surgery of Udine University Hospital. From November 1989 to December 2005, 137 consecutive patients, who underwent surgical procedures for pancreatic cancer, were followed in our department. We performed 76 pancreatico-duodenectomy, 26 distal pancreatectomies and 35 total pancreatectomies. The surgical reconstruction after pancreatico-duodenectomy was as follows: 11 closures of the main duct with manual nonabsorbable stitches, 24 closures of the main duct with a linear stapler, 17 occlusions of the main duct with neoprene glue and 24 duct-to-mucosa anastomoses. Mean survival time was 27.7 +/- 26.93 months (mean +/- SD) and mean disease-free survival time was 25.4 +/- 23.06 months (mean +/- SD). 1, 3, 5, 7 and 9-year survival rates were 63.9, 33.7, 21.17, 12.7 and 10.2%, respectively. Significant differences in survival were recorded by the Log-rank test for age > 70 (p = 0.001), surgical procedures (p = 0.00046) and presence of metastases (p = 0.0055) The treatment of pancreatic cancer is undertaken with two different aims. The first is radical surgery for patients with early-stage disease, mainly stage I and partly stage II. In all other cases, the aim of treatment is the palliation of the several distressing symptoms related to this cancer. The standard treatment option for resectable tumours is radical pancreatic resection according to the Whipple procedure or total pancreatectomy.

Organ Preservation With Concurrent Chemoradiation for Advanced Laryngeal Cancer: Are We Succeeding?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lambert, Louise, E-mail: louise.lambert@gmail.co; Fortin, Bernard; Soulieres, Denis

2010-02-01

Purpose: To determine the rates of organ preservation and function in patients with advanced laryngeal and hypopharyngeal carcinomas treated with concurrent chemoradiotherapy (CRT). Methods and Materials: Between April 1999 and September 2005, 82 patients with advanced laryngeal (67%) and hypopharyngeal carcinomas (33%) underwent conventional radiotherapy and concurrent platinum-based chemotherapy with curative intent. Sixty-two patients were male (75.6%). The median age was 59 years. Eighteen patients (22%) were in Stage III and 64 (78%) were in Stage IV. The median radiation dose was 70 Gy. The median potential follow-up was 3.9 years. Results: Overall survival and disease-free survival were respectively 63%more » and 73% at 3 years. Complete response rate from CRT was 75%. Nineteen patients (23%) experienced significant long-term toxicity after CRT: 6 (7.3%) required a percutaneous endoscopic gastrostomy, 5 (6%) had persistent Grade 2 or 3 dysphagia, 2 (2.4%) had pharyngoesophageal stenosis requiring multiple dilations, 2 (2.4%) had chronic lung aspiration, and 7 (8.5%) required a permanent tracheostomy. Four patients (4.9%) underwent laryngectomy without pathologic evidence of disease. At last follow-up, 5 (6%) patients were still dependent on a gastrostomy. Overall, 42 patients (52%) were alive, in complete response, with a functional larynx and no other major complications. Conclusions: In our institution, CRT for advanced hypopharyngeal and laryngeal carcinoma has provided good overall survival and locoregional control in the majority of patients, but a significant proportion did not benefit from this approach because of either locoregional failure or late complications. Better organ preservation approaches are necessary to improve locoregional control and to reduce long-term toxicities.« less

Submucosal invasion and risk of lymph node invasion in early Barrett’s cancer: potential impact of different classification systems on patient management

PubMed Central

Fotis, Dimitrios; Doukas, Michael; Wijnhoven, Bas PL; Didden, Paul; Biermann, Katharina; Bruno, Marco J

2015-01-01

Background Due to the high mortality and morbidity rates of esophagectomy, endoscopic mucosal resection (EMR) is increasingly used for the curative treatment of early low risk Barrett’s adenocarcinoma. Objective This retrospective cohort study aimed to assess the prevalence of lymph node metastases (LNM) in submucosal (T1b) esophageal adenocarcinomas (EAC) in relation to the absolute depth of submucosal tumor invasion and demonstrate the efficacy of EMR for low risk (well and moderately differentiated without lymphovascular invasion) EAC with sm1 invasion (submucosal invasion ≤500 µm) according to the Paris classification. Methods The pathology reports of patients undergoing endoscopic resection and surgery from January 1994 until December 2013 at one center were reviewed and 54 patients with submucosal invasion were included. LNM were evaluated in surgical specimens and by follow up examinations in case of EMR. Results No LNM were observed in 10 patients with sm1 adenocarcinomas that underwent endoscopic resection. Three of them underwent supplementary endoscopic eradication therapy with a median follow up of 27 months for patients with sm1 tumors. In the surgical series two patients (29%) with sm1 invasion according to the pragmatic classification (subdivision of the submucosa into three equal thirds), staged as sm2-3 in the Paris classification, had LNM. The rate of LNM for surgical patients with low risk sm1 tumors was 10% according to the pragmatic classification and 0% according to Paris classification. Conclusion Different classifications of the tumor invasion depth lead to different LNM risks and treatment strategies for sm1 adenocarcinomas. Patients with low risk sm1 adenocarcinomas appear to be suitable candidates for EMR. PMID:26668743

Operability assessment in CTEPH: Lessons from the CHEST-1 study.

PubMed

Jenkins, David P; Biederman, Andrzej; D'Armini, Andrea M; Dartevelle, Philippe G; Gan, Hui-Li; Klepetko, Walter; Lindner, Jaroslav; Mayer, Eckhard; Madani, Michael M

2016-09-01

Pulmonary endarterectomy is the gold standard treatment for chronic thromboembolic pulmonary hypertension and is potentially curative, although some patients are unsuitable for pulmonary endarterectomy and require alternative management. Lack of standardized assessment of pulmonary endarterectomy eligibility risks suboptimal treatment in some patients. We discuss the implications for future clinical trials and practice of a unique operability assessment in patients who have chronic thromboembolic pulmonary hypertension and were initially screened for inclusion in the CHEST-1 (Chronic Thromboembolic Pulmonary Hypertension Soluble Guanylate Cyclase Stimulator Trial-1) study. The CHEST-1 study evaluated riociguat for the treatment of inoperable chronic thromboembolic pulmonary hypertension (CTEPH) or persistent/recurrent pulmonary hypertension after pulmonary endarterectomy. Screened patients who were initially considered "inoperable" underwent central independent adjudication by a committee of experienced surgeons, or local adjudication in collaboration with an experienced surgeon. Operability decisions were based on accessibility of thrombi and the association between pulmonary vascular resistance (PVR) and the extent of obstruction, using pulmonary angiography/computed tomography with ventilation/perfusion scintigraphy as the minimum diagnostic tests. Of 446 patients screened for CHEST-1, a total of 188 and 124 underwent central and local adjudication, respectively, after being initially considered to be "inoperable." After a second assessment by an experienced surgeon, 69 of these 312 "inoperable" patients were deemed operable. Rigorous measures in CHEST-1 guaranteed that only technically inoperable patients, or patients who had persistent/recurrent pulmonary hypertension, were enrolled, thus ensuring that only patients for whom surgery was not an option were enrolled. This study design sets new standards for future clinical trials and practice in CTEPH, helping to ensure that patients who have CTEPH receive optimal treatment. Copyright © 2016 The American Association for Thoracic Surgery. Published by Elsevier Inc. All rights reserved.

Data Curation Is for Everyone! The Case for Master's and Baccalaureate Institutional Engagement with Data Curation

ERIC Educational Resources Information Center

Shorish, Yasmeen

2012-01-01

This article describes the fundamental challenges to data curation, how these challenges may be compounded for smaller institutions, and how data management is an essential and manageable component of data curation. Data curation is often discussed within the confines of large research universities. As a result, master's and baccalaureate…

Primary nodal hemangiosarcoma in four dogs.

PubMed

Chan, Catherine M; Zwahlen, Courtney H; de Lorimier, Louis-Philippe; Yeomans, Stephen M; Hoffmann, Karon L; Moore, Antony S

2016-11-01

CASE DESCRIPTION 4 dogs with a slow-growing mass in the cervical region were evaluated. CLINICAL FINDINGS All dogs had no clinical signs at the time of the evaluation. There was no apparent evidence of visceral metastases or other primary tumor based on available CT or MRI data for any dog. TREATMENT AND OUTCOME For each dog, surgery to remove the mass was performed. Histologic examination of the excised tissue revealed a completely excised grade 1 or 2 lymph node hemangiosarcoma. All dogs received adjuvant chemotherapy; 2 dogs underwent curative intent chemotherapy, 1 dog underwent metronomic treatment with cyclophosphamide, and 1 dog underwent metronomic treatment with chlorambucil. The survival time was 259 days in 1 dog; 3 dogs were still alive 615, 399, and 365 days after surgery. CLINICAL RELEVANCE Primary nodal hemangiosarcoma in dogs is a rare and, to the authors' knowledge, previously undescribed disease that appears to develop in the cervical lymph nodes as a slow-growing mass or masses. Surgical excision and adjunct treatment resulted in long survival times for 3 of the 4 dogs of the present report. Given the aggressive biologic behavior of hemangiosarcomas in other body locations, adjunct chemotherapy should be considered for affected dogs, although its role in the cases described in this report was unclear. Additional clinical information is required to further characterize the biologic behavior of this tumor type and determine the expected survival times and associated risk factors in dogs.

Outcome of Laparoscopic Versus Open Resection for Transverse Colon Cancer.

PubMed

Zeng, Wei-Gen; Liu, Meng-Jia; Zhou, Zhi-Xiang; Hou, Hui-Rong; Liang, Jian-Wei; Wang, Zheng; Zhang, Xing-Mao; Hu, Jun-Jie

2015-10-01

Laparoscopic resection for transverse colon cancer remains controversial. The aim of this study is to investigate the short- and long-term outcomes of laparoscopic surgery for transverse colon cancer. A total of 278 patients with transverse colon cancer from a single institution were included. All patients underwent curative surgery, 156 patients underwent laparoscopic resection (LR), and 122 patients underwent open resection (OR). The short- and long-term results were compared between two groups. Baseline demographic and clinical characteristics were comparable between two groups. Conversions were required in eight (5.1 %) patients. LR group was associated with significantly longer median operating time (180 vs. 140 min; P < 0.001). Median estimated blood loss was significantly less in LR group (90 vs. 100 ml; P = 0.001). Time to first flatus and oral intake was significantly earlier in LR group. Perioperative mortality and morbidity rate were not significantly different between two groups. Tumor size, number of lymph nodes harvested, length of proximal, and distal resection margin were comparable between two groups. Postoperative hospital stay was significantly shorter in LR group (9 vs. 10d; P < 0.001). Five-year disease-free survival and overall survival rate were similar between two groups. Laparoscopic resection for transverse colon cancer is associated with better short-term outcomes and equivalent long-term oncologic outcomes.

Recommendations for Locus-Specific Databases and Their Curation

PubMed Central

Cotton, R.G.H.; Auerbach, A.D.; Beckmann, J.S.; Blumenfeld, O.O.; Brookes, A.J.; Brown, A.F.; Carrera, P.; Cox, D.W.; Gottlieb, B.; Greenblatt, M.S.; Hilbert, P.; Lehvaslaiho, H.; Liang, P.; Marsh, S.; Nebert, D.W.; Povey, S.; Rossetti, S.; Scriver, C.R.; Summar, M.; Tolan, D.R.; Verma, I.C.; Vihinen, M.; den Dunnen, J.T.

2009-01-01

Expert curation and complete collection of mutations in genes that affect human health is essential for proper genetic healthcare and research. Expert curation is given by the curators of gene-specific mutation databases or locus-specific databases (LSDBs). While there are over 700 such databases, they vary in their content, completeness, time available for curation, and the expertise of the curator. Curation and LSDBs have been discussed, written about, and protocols have been provided for over 10 years, but there have been no formal recommendations for the ideal form of these entities. This work initiates a discussion on this topic to assist future efforts in human genetics. Further discussion is welcome. PMID:18157828

Recommendations for locus-specific databases and their curation.

PubMed

Cotton, R G H; Auerbach, A D; Beckmann, J S; Blumenfeld, O O; Brookes, A J; Brown, A F; Carrera, P; Cox, D W; Gottlieb, B; Greenblatt, M S; Hilbert, P; Lehvaslaiho, H; Liang, P; Marsh, S; Nebert, D W; Povey, S; Rossetti, S; Scriver, C R; Summar, M; Tolan, D R; Verma, I C; Vihinen, M; den Dunnen, J T

2008-01-01

Expert curation and complete collection of mutations in genes that affect human health is essential for proper genetic healthcare and research. Expert curation is given by the curators of gene-specific mutation databases or locus-specific databases (LSDBs). While there are over 700 such databases, they vary in their content, completeness, time available for curation, and the expertise of the curator. Curation and LSDBs have been discussed, written about, and protocols have been provided for over 10 years, but there have been no formal recommendations for the ideal form of these entities. This work initiates a discussion on this topic to assist future efforts in human genetics. Further discussion is welcome. (c) 2007 Wiley-Liss, Inc.

Data Curation: Improving Environmental Health Data Quality.

PubMed

Yang, Lin; Li, Jiao; Hou, Li; Qian, Qing

2015-01-01

With the growing recognition of the influence of climate change on human health, scientists' attention to analyzing the relationship between meteorological factors and adverse health effects. However, the paucity of high quality integrated data is one of the great challenges, especially when scientific studies rely on data-intensive computing. This paper aims to design an appropriate curation process to address this problem. We present a data curation workflow that: (i) follows the guidance of DCC Curation Lifecycle Model; (ii) combines manual curation with automatic curation; (iii) and solves environmental health data curation problem. The workflow was applied to a medical knowledge service system and showed that it was capable of improving work efficiency and data quality.

Digital Curation and Digital Literacy: Evaluating the Role of Curation in Developing Critical Literacies for Participation in Digital Culture

ERIC Educational Resources Information Center

Mihailidis, Paul

2015-01-01

Despite the increased role of digital curation tools and platforms in the daily life of social network users, little research has focused on the competencies and dispositions that young people develop to effectively curate content online. This paper details the results of a mixed method study exploring the curation competencies of young people in…

Systemic Chemotherapy as Salvage Treatment for Locally Advanced Rectal Cancer Patients Who Fail to Respond to Standard Neoadjuvant Chemoradiotherapy.

PubMed

Sclafani, Francesco; Brown, Gina; Cunningham, David; Rao, Sheela; Tekkis, Paris; Tait, Diana; Morano, Federica; Baratelli, Chiara; Kalaitzaki, Eleftheria; Rasheed, Shahnawaz; Watkins, David; Starling, Naureen; Wotherspoon, Andrew; Chau, Ian

2017-06-01

The potential of chemotherapy as salvage treatment after failure of neoadjuvant chemoradiotherapy for locally advanced rectal cancer (LARC) has never been explored. We conducted a single-center, retrospective analysis to address this question. Patients with newly diagnosed LARC who were inoperable or candidates for extensive (i.e., beyond total mesorectal excision [TME]) surgery after long-course chemoradiotherapy and who received salvage chemotherapy were included. The primary objective was to estimate the proportion of patients who became suitable for TME after chemotherapy. Forty-five patients were eligible (39 candidates for extensive surgery and 6 unresectable). Previous radiotherapy was given concurrently with chemotherapy in 43 cases (median dose: 54.0 Gy). Oxaliplatin- and irinotecan-based salvage chemotherapy was administered in 40 (88.9%) and 5 (11.1%) cases, respectively. Eight patients (17.8%) became suitable for TME after chemotherapy, 10 (22.2%) ultimately underwent TME with clear margins, and 2 (4.4%) were managed with a watch and wait approach. Additionally, 13 patients had extensive surgery with curative intent. Three-year progression-free survival and 5-year overall survival in the entire population were 30.0% (95% confidence interval [CI]: 15.0-46.0) and 44.0% (95% CI: 26.0-61.0), respectively. For the curatively resected and "watch and wait" patients, these figures were 52.0% (95% CI: 27.0-73.0) and 67.0% (95% CI: 40.0-84.0), respectively. Systemic chemotherapy may be an effective salvage strategy for LARC patients who fail to respond to chemoradiotherapy and are inoperable or candidates for beyond TME surgery. According to our study, one out of five patients may become resectable or be spared from an extensive surgery after systemic chemotherapy. High-quality evidence to inform the optimal management of rectal cancer patients who are inoperable or candidates for beyond total mesorectal excision surgery following standard chemoradiotherapy is lacking. We show for the first time that systemic chemotherapy may be beneficial and result in one out of five poor prognosis patients becoming resectable or being spared from an extensive surgical approach. Although mores studies are needed to confirm these data, administering salvage systemic chemotherapy in this setting may have the potential to minimize morbidity associated with extensive surgical procedures and improve long-term oncological outcome. © AlphaMed Press 2017.

Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers.

PubMed

Ning, Shangwei; Zhang, Jizhou; Wang, Peng; Zhi, Hui; Wang, Jianjian; Liu, Yue; Gao, Yue; Guo, Maoni; Yue, Ming; Wang, Lihua; Li, Xia

2016-01-04

Lnc2Cancer (http://www.bio-bigdata.net/lnc2cancer) is a manually curated database of cancer-associated long non-coding RNAs (lncRNAs) with experimental support that aims to provide a high-quality and integrated resource for exploring lncRNA deregulation in various human cancers. LncRNAs represent a large category of functional RNA molecules that play a significant role in human cancers. A curated collection and summary of deregulated lncRNAs in cancer is essential to thoroughly understand the mechanisms and functions of lncRNAs. Here, we developed the Lnc2Cancer database, which contains 1057 manually curated associations between 531 lncRNAs and 86 human cancers. Each association includes lncRNA and cancer name, the lncRNA expression pattern, experimental techniques, a brief functional description, the original reference and additional annotation information. Lnc2Cancer provides a user-friendly interface to conveniently browse, retrieve and download data. Lnc2Cancer also offers a submission page for researchers to submit newly validated lncRNA-cancer associations. With the rapidly increasing interest in lncRNAs, Lnc2Cancer will significantly improve our understanding of lncRNA deregulation in cancer and has the potential to be a timely and valuable resource. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Advanced Curation Activities at NASA: Preparing to Receive, Process, and Distribute Samples Returned from Future Missions

NASA Technical Reports Server (NTRS)

McCubbin, Francis M.; Zeigler, Ryan A.

2017-01-01

The Astromaterials Acquisition and Curation Office (henceforth referred to herein as NASA Curation Office) at NASA Johnson Space Center (JSC) is responsible for curating all of NASA's extraterrestrial samples. Under the governing document, NASA Policy Directive (NPD) 7100.10F JSC is charged with curation of all extraterrestrial material under NASA control, including future NASA missions. The Directive goes on to define Curation as including documentation, preservation, preparation, and distribution of samples for research, education, and public outreach. Here we briefly describe NASA's astromaterials collections and our ongoing efforts related to enhancing the utility of our current collections as well as our efforts to prepare for future sample return missions. We collectively refer to these efforts as advanced curation.

Advanced Curation Activities at NASA: Implications for Astrobiological Studies of Future Sample Collections

NASA Technical Reports Server (NTRS)

McCubbin, F. M.; Evans, C. A.; Fries, M. D.; Harrington, A. D.; Regberg, A. B.; Snead, C. J.; Zeigler, R. A.

2017-01-01

The Astromaterials Acquisition and Curation Office (henceforth referred to herein as NASA Curation Office) at NASA Johnson Space Center (JSC) is responsible for curating all of NASA's extraterrestrial samples. Under the governing document, NASA Policy Directive (NPD) 7100.10F JSC is charged with curation of all extraterrestrial material under NASA control, including future NASA missions. The Directive goes on to define Curation as including documentation, preservation, preparation, and distribution of samples for re-search, education, and public outreach. Here we briefly describe NASA's astromaterials collections and our ongoing efforts related to enhancing the utility of our current collections as well as our efforts to prepare for future sample return missions. We collectively refer to these efforts as advanced curation.

Using patient-derived xenograft models of colorectal liver metastases to predict chemosensitivity.

PubMed

Brown, Kai M; Xue, Aiqun; Julovi, Sohel M; Gill, Anthony J; Pavlakis, Nick; Samra, Jaswinder S; Smith, Ross C; Hugh, Thomas J

2018-07-01

Few in vivo models for colorectal cancer have been demonstrated to show external validity by accurately predicting clinical patient outcomes. Patient-derived xenograft (PDX) models of cancer have characteristics that might provide a form of translational research leading to personalized cancer care. The aim of this pilot study was to assess the feasibility of using PDXs as a platform for predicting patient colorectal liver metastases responses, in this case by correlating PDX and patient tumor responses to either folinic acid, fluorouracil plus oxaliplatin or folinic acid, fluorouracil plus irinotecan-based regimens. Sixteen patients underwent potentially curative resection of colorectal liver metastases, and tumors were grafted into NOD.CB17-Prkdc scid /Arc mice. Mice were divided into groups to determine relative tumor growth in response to treatment. Tumors were analyzed by immunohistochemistry for Ki67 and Excision repair cross-complementation group 1. An engraftment rate of 81% was achieved. Overall, there was a 67% positive match rate between eligible patient and PDX chemosensitivity profiles. There was a significant difference in relative decrease in Ki67 expression between sensitive/stable versus resistant PDXs for both treatment regimens. There was no statistically significant correlation between baseline ERCC1 expression and response to Oxaliplatin + 5-Fluorouracil in the PDXs. This pilot study supports the feasibility of using PDX models of advanced colorectal cancer in larger studies to potentially predict patient chemosensitivity profiles. Copyright © 2018 Elsevier Inc. All rights reserved.

Advanced Curation: Solving Current and Future Sample Return Problems

NASA Technical Reports Server (NTRS)

Fries, M.; Calaway, M.; Evans, C.; McCubbin, F.

2015-01-01

Advanced Curation is a wide-ranging and comprehensive research and development effort at NASA Johnson Space Center that identifies and remediates sample related issues. For current collections, Advanced Curation investigates new cleaning, verification, and analytical techniques to assess their suitability for improving curation processes. Specific needs are also assessed for future sample return missions. For each need, a written plan is drawn up to achieve the requirement. The plan draws while upon current Curation practices, input from Curators, the analytical expertise of the Astromaterials Research and Exploration Science (ARES) team, and suitable standards maintained by ISO, IEST, NIST and other institutions. Additionally, new technologies are adopted on the bases of need and availability. Implementation plans are tested using customized trial programs with statistically robust courses of measurement, and are iterated if necessary until an implementable protocol is established. Upcoming and potential NASA missions such as OSIRIS-REx, the Asteroid Retrieval Mission (ARM), sample return missions in the New Frontiers program, and Mars sample return (MSR) all feature new difficulties and specialized sample handling requirements. The Mars 2020 mission in particular poses a suite of challenges since the mission will cache martian samples for possible return to Earth. In anticipation of future MSR, the following problems are among those under investigation: What is the most efficient means to achieve the less than 1.0 ng/sq cm total organic carbon (TOC) cleanliness required for all sample handling hardware? How do we maintain and verify cleanliness at this level? The Mars 2020 Organic Contamination Panel (OCP) predicts that organic carbon, if present, will be present at the "one to tens" of ppb level in martian near-surface samples. The same samples will likely contain wt% perchlorate salts, or approximately 1,000,000x as much perchlorate oxidizer as organic carbon. The chemical kinetics of this reaction are poorly understood at present under the conditions of cached or curated martian samples. Among other parameters, what is the maximum temperature allowed during storage in order to preserve native martian organic compounds for analysis? What is the best means to collect headspace gases from cached martian (and other) samples? This gas will contain not only martian atmosphere but also off-gassed volatiles from the cached solids.

A formulated double-stranded RNA diet for reducing Penaeus monodon densovirus infection in black tiger shrimp.

PubMed

Chimwai, Chaweewan; Tongboonsong, Punnee; Namramoon, Orathai; Panyim, Sakol; Attasart, Pongsopee

2016-02-01

Penaeus monodon densovirus (PmDNV) is one of the major causes of stunted shrimp in the aquaculture industry in Thailand. Significant reductions in levels of PmDNV as assessed by PCR analysis of shrimp hepatopancreas were seen in both prophylactic and curative experiments after feeding shrimp with a formulated diet containing mixed inactivated bacteria harboring dsRNAs corresponding to the PmDNV ns1 and vp genes. Significant reductions of approximately 88% (prophylactic) and 64% (curative) of PmDNV were observed, suggesting that this diet has a high potential for application in commercial aquaculture for reducing PmDNV associated stunted growth of shrimp. Copyright © 2016 Elsevier Inc. All rights reserved.

CoINcIDE: A framework for discovery of patient subtypes across multiple datasets.

PubMed

Planey, Catherine R; Gevaert, Olivier

2016-03-09

Patient disease subtypes have the potential to transform personalized medicine. However, many patient subtypes derived from unsupervised clustering analyses on high-dimensional datasets are not replicable across multiple datasets, limiting their clinical utility. We present CoINcIDE, a novel methodological framework for the discovery of patient subtypes across multiple datasets that requires no between-dataset transformations. We also present a high-quality database collection, curatedBreastData, with over 2,500 breast cancer gene expression samples. We use CoINcIDE to discover novel breast and ovarian cancer subtypes with prognostic significance and novel hypothesized ovarian therapeutic targets across multiple datasets. CoINcIDE and curatedBreastData are available as R packages.

Curation of Frozen Samples

NASA Technical Reports Server (NTRS)

Fletcher, L. A.; Allen, C. C.; Bastien, R.

2008-01-01

NASA's Johnson Space Center (JSC) and the Astromaterials Curator are charged by NPD 7100.10D with the curation of all of NASA s extraterrestrial samples, including those from future missions. This responsibility includes the development of new sample handling and preparation techniques; therefore, the Astromaterials Curator must begin developing procedures to preserve, prepare and ship samples at sub-freezing temperatures in order to enable future sample return missions. Such missions might include the return of future frozen samples from permanently-shadowed lunar craters, the nuclei of comets, the surface of Mars, etc. We are demonstrating the ability to curate samples under cold conditions by designing, installing and testing a cold curation glovebox. This glovebox will allow us to store, document, manipulate and subdivide frozen samples while quantifying and minimizing contamination throughout the curation process.

Marine Curators Gather

ERIC Educational Resources Information Center

McCoy, Floyd W.

1977-01-01

Reports on a recent meeting of marine curators in which data dissemination, standardization of marine curating techniques and methods, responsibilities of curators, funding problems, and sampling equipment were the main areas of discussion. A listing of the major deep sea sample collections in the United States is also provided. (CP)

What is the most accurate lymph node staging method for perihilar cholangiocarcinoma? Comparison of UICC/AJCC pN stage, number of metastatic lymph nodes, lymph node ratio, and log odds of metastatic lymph nodes.

PubMed

Conci, S; Ruzzenente, A; Sandri, M; Bertuzzo, F; Campagnaro, T; Bagante, F; Capelli, P; D'Onofrio, M; Piccino, M; Dorna, A E; Pedrazzani, C; Iacono, C; Guglielmi, A

2017-04-01

We compared the prognostic performance of the International Union Against Cancer/American Joint Committee on Cancer (UICC/AJCC) 7th edition pN stage, number of metastatic LNs (MLNs), LN ratio (LNR), and log odds of MLNs (LODDS) in patients with perihilar cholangiocarcinoma (PCC) undergoing curative surgery in order to identify the best LN staging method. Ninety-nine patients who underwent surgery with curative intent for PCC in a single tertiary hepatobiliary referral center were included in the study. Two approaches were used to evaluate and compare the predictive power of the different LN staging methods: one based on the estimation of variable importance with prediction error rate and the other based on the calculation of the receiver operating characteristic (ROC) curve. LN dissection was performed in 92 (92.9%) patients; 49 were UICC/AJCC pN0 (49.5%), 33 pN1 (33.3%), and 10 pN2 (10.1%). The median number of LNs retrieved was 8. The prediction error rate ranged from 42.7% for LODDS to 47.1% for UICC/AJCC pN stage. Moreover, LODDS was the variable with the highest area under the ROC curve (AUC) for prediction of 3-year survival (AUC = 0.71), followed by LNR (AUC = 0.60), number of MLNs (AUC = 0.59), and UICC/AJCC pN stage (AUC = 0.54). The number of MLNs, LNR, and LODDS appear to better predict survival than the UICC/AJCC pN stage in patients undergoing curative surgery for PCC. Moreover, LODDS seems to be the most accurate and predictive LN staging method. Copyright © 2017 Elsevier Ltd, BASO ~ The Association for Cancer Surgery, and the European Society of Surgical Oncology. All rights reserved.

Circulating CD14+ HLA-DR-/low myeloid-derived suppressor cells predicted early recurrence of hepatocellular carcinoma after surgery.

PubMed

Gao, Xing-Hui; Tian, Lu; Wu, Jiong; Ma, Xiao-Lu; Zhang, Chun-Yan; Zhou, Yan; Sun, Yun-Fan; Hu, Bo; Qiu, Shuang-Jian; Zhou, Jian; Fan, Jia; Guo, Wei; Yang, Xin-Rong

2017-09-01

Myeloid-derived suppressor cells (MDSCs) play an important role in tumor progression. The aim of the present study was to investigate the prognostic value of MDSCs for early recurrence of hepatocellular carcinoma (HCC) in patients undergoing curative resection. Myeloid-derived suppressor cells were measured by flow cytometry. The correlation between MDSCs and tumor recurrence was analyzed using a cohort of 183 patients who underwent curative resection between February 2014 and July 2015. Prognostic significance was further assessed using Kaplan-Meier survival estimates and log-rank tests. In vivo, CD14 + HLA-DR -/low MDSCs inhibit T cell proliferation and secretion. The frequency of CD14 + HLA-DR -/low MDSCs was significantly higher in HCC patients (3.7 ± 5.3%, n = 183) than in chronic hepatitis patients (1.4 ± 0.6%, n = 25) and healthy controls (1.1 ± 0.5%, n = 50). High frequency of MDSCs was significantly correlated with recurrence (time to recurrence) (P < 0.001) and overall survival (P = 0.034). Patients with HCC in the high MDSC group were prone to more vascular invasion (P = 0.018) and high systemic immune-inflammation index (SII) (P = 0.009) than those in the low MDSC group. Scatter-plot analyses revealed a significant positive correlation between the SII level and the frequency of MDSCs (r = 0.188, P = 0.011). Patients with HCC with a high MDSC frequency and high SII level had significantly shorter time to recurrence (P < 0.001) and overall survival (P = 0.028) than those with a low MDSC frequency and low SII. An increased frequency of MDSCs was correlated with early recurrence and predicted the prognosis of patients with HCC undergoing curative resection. The HCC patients with high frequency of MDSCs should be provided more advanced management and frequent monitoring. © 2016 The Japan Society of Hepatology.

Impact of systemic inflammation on gastric cancer outcomes.

PubMed

Liu, Xuechao; Chen, Shangxiang; Liu, Jianjun; Xu, Dazhi; Li, Wei; Zhan, Youqing; Li, Yuanfang; Chen, Yingbo; Zhou, Zhiwei; Sun, Xiaowei

2017-01-01

The prognostic value of neutrophil-lymphocyte ratio (NLR) and Glasgow Prognostic Score (GPS) has been extensively validated in various cancers. We aimed to examine the usefulness of a combination of NLR and GPS (named CNG) for predicting survival outcomes in patients after curative resection for gastric cancer (GC). We retrospectively analyzed the records of 1056 patients who underwent curative resection as initial treatment for GC from October 2000 to September 2012. The preoperative CNG was calculated as follows: patients with hypoalbuminemia (< 35 g/L), elevated C-reactive protein (> 10 mg/L), and elevated NLR (≥ 2) were allocated a score of 3; patients with two, one, or no abnormal values were allocated a score of 2, 1, or 0, respectively. The NLR and GPS were the only inflammatory variables independently associated with overall survival (OS) in multivariate analysis. When they were replaced by CNG in multivariate analysis, CNG was independently associated with OS (hazard ratio [HR] for CNG 1 [1.367, 95% CI: 1.065-1.755; P = 0.014], CNG 2 [1.887, 95% CI: 1.182-3.011; P = 0.008], and CNG 3 [2.224, 95% CI: 1.238-3.997; P = 0.008]; P = 0.020). In stage-matched analysis, the prognostic significance was still maintained in stage I-III (P = 0.002, P = 0.042, and P < 0.001, respectively). In addition, 5-year survival rates ranged from 92% (stage I) to 35% (stage III) and from 65%(CNG 0) to 18%(CNG 3) with tumor-nodes-metastasis (TNM) stage or CNG alone. However, the combination of TNM and CNG stratified 5-year survival rates from 98% (TNM I, CNG 0) to 12% (TNM III, CNG 3). The preoperative CNG is a novel predictor of postoperative survival, and the combination of CNG and TNM effectively stratifies outcomes in patients after curative resection for GC.

Impact of systemic inflammation on gastric cancer outcomes

PubMed Central

Xu, Dazhi; Li, Wei; Zhan, Youqing; Li, Yuanfang; Chen, Yingbo; Zhou, Zhiwei; Sun, Xiaowei

2017-01-01

Background The prognostic value of neutrophil-lymphocyte ratio (NLR) and Glasgow Prognostic Score (GPS) has been extensively validated in various cancers. We aimed to examine the usefulness of a combination of NLR and GPS (named CNG) for predicting survival outcomes in patients after curative resection for gastric cancer (GC). Methods We retrospectively analyzed the records of 1056 patients who underwent curative resection as initial treatment for GC from October 2000 to September 2012. The preoperative CNG was calculated as follows: patients with hypoalbuminemia (< 35 g/L), elevated C-reactive protein (> 10 mg/L), and elevated NLR (≥ 2) were allocated a score of 3; patients with two, one, or no abnormal values were allocated a score of 2, 1, or 0, respectively. Results The NLR and GPS were the only inflammatory variables independently associated with overall survival (OS) in multivariate analysis. When they were replaced by CNG in multivariate analysis, CNG was independently associated with OS (hazard ratio [HR] for CNG 1 [1.367, 95% CI: 1.065–1.755; P = 0.014], CNG 2 [1.887, 95% CI: 1.182–3.011; P = 0.008], and CNG 3 [2.224, 95% CI: 1.238–3.997; P = 0.008]; P = 0.020). In stage-matched analysis, the prognostic significance was still maintained in stage I-III (P = 0.002, P = 0.042, and P < 0.001, respectively). In addition, 5-year survival rates ranged from 92% (stage I) to 35% (stage III) and from 65%(CNG 0) to 18%(CNG 3) with tumor-nodes-metastasis (TNM) stage or CNG alone. However, the combination of TNM and CNG stratified 5-year survival rates from 98% (TNM I, CNG 0) to 12% (TNM III, CNG 3). Conclusion The preoperative CNG is a novel predictor of postoperative survival, and the combination of CNG and TNM effectively stratifies outcomes in patients after curative resection for GC. PMID:28358923

Endoscopic submucosal dissection for early Barrett’s neoplasia

PubMed Central

Barret, Maximilien; Cao, Dalhia Thao; Beuvon, Frédéric; Leblanc, Sarah; Terris, Benoit; Camus, Marine; Coriat, Romain; Chaussade, Stanislas

2015-01-01

Introduction The possible benefit of endoscopic submucosal dissection (ESD) for early neoplasia arising in Barrett’s esophagus remains controversial. We aimed to assess the efficacy and safety of ESD for the treatment of early Barrett’s neoplasia. Methods All consecutive patients undergoing ESD for the resection of a visible lesion in a Barrett’s esophagus, either suspicious of submucosal infiltration or exceeding 10 mm in size, between February 2012 and January 2015 were prospectively included. The primary endpoint was the rate of curative resection of carcinoma, defined as histologically complete resection of adenocarcinomas without poor histoprognostic factors. Results Thirty-five patients (36 lesions) with a mean age of 66.2 ± 12 years, a mean ASA score of 2.1 ± 0.7, and a mean C4M6 Barrett’s segment were included. The mean procedure time was 191 ± 79 mn, and the mean size of the resected specimen was 51.3 ± 23 mm. En bloc resection rate was 89%. Lesions were 12 ± 15 mm in size, and 81% (29/36) were invasive adenocarcinomas, six of which with submucosal invasion. Although R0 resection of carcinoma was 72.4%, the curative resection rate was 66% (19/29). After a mean follow-up of 12.9 ± 9 months, 16 (45.7%) patients had required additional treatment, among whom nine underwent surgical resection, and seven further endoscopic treatments. Metachronous lesions or recurrence of cancer developed during the follow-up period in 17.2% of the patients. The overall complication rate was 16.7%, including 8.3% perforations, all conservatively managed, and no bleeding. The 30-day mortality was 0%. Conclusion In this early experience, ESD yielded a moderate curative resection rate in Barrett’s neoplasia. At present, improvements are needed if ESD is to replace piecemeal endoscopic mucosal resection in the management of Barrett’s neoplasia. PMID:27087948

Endoscopic submucosal dissection for early Barrett's neoplasia.

PubMed

Barret, Maximilien; Cao, Dalhia Thao; Beuvon, Frédéric; Leblanc, Sarah; Terris, Benoit; Camus, Marine; Coriat, Romain; Chaussade, Stanislas; Prat, Frédéric

2016-04-01

The possible benefit of endoscopic submucosal dissection (ESD) for early neoplasia arising in Barrett's esophagus remains controversial. We aimed to assess the efficacy and safety of ESD for the treatment of early Barrett's neoplasia. All consecutive patients undergoing ESD for the resection of a visible lesion in a Barrett's esophagus, either suspicious of submucosal infiltration or exceeding 10 mm in size, between February 2012 and January 2015 were prospectively included. The primary endpoint was the rate of curative resection of carcinoma, defined as histologically complete resection of adenocarcinomas without poor histoprognostic factors. Thirty-five patients (36 lesions) with a mean age of 66.2 ± 12 years, a mean ASA score of 2.1 ± 0.7, and a mean C4M6 Barrett's segment were included. The mean procedure time was 191 ± 79 mn, and the mean size of the resected specimen was 51.3 ± 23 mm. En bloc resection rate was 89%. Lesions were 12 ± 15 mm in size, and 81% (29/36) were invasive adenocarcinomas, six of which with submucosal invasion. Although R0 resection of carcinoma was 72.4%, the curative resection rate was 66% (19/29). After a mean follow-up of 12.9 ± 9 months, 16 (45.7%) patients had required additional treatment, among whom nine underwent surgical resection, and seven further endoscopic treatments. Metachronous lesions or recurrence of cancer developed during the follow-up period in 17.2% of the patients. The overall complication rate was 16.7%, including 8.3% perforations, all conservatively managed, and no bleeding. The 30-day mortality was 0%. In this early experience, ESD yielded a moderate curative resection rate in Barrett's neoplasia. At present, improvements are needed if ESD is to replace piecemeal endoscopic mucosal resection in the management of Barrett's neoplasia.

The status of perineural invasion predicts the outcomes of postoperative radiotherapy in locally advanced esophageal squamous cell carcinoma.

PubMed

Ning, Zhong-Hua; Zhao, Wei; Li, Xiao-Dong; Chen, Lu-Jun; Xu, Bin; Gu, Wen-Dong; Shao, Ying-Jie; Xu, Yun; Huang, Jin; Pei, Hong-Lei; Jiang, Jing-Ting

2015-01-01

Prognosis of locally advanced esophageal squamous cell carcinoma (ESCC) remains dismal even after curative resection and adjuvant radiotherapy. New biomarkers for predicting prognosis and treatment outcomes are needed for improved treatment stratification of patients with locally advanced ESCC. The prognostic and treatment predictive significance of perineural invasion (PNI) in the locally advanced ESCC remains unclear. This study aimed to examine the effect of PNI on the outcomes of locally advanced ESCC patients after curative resection with or without postoperative radiotherapy (PORT). We retrospectively reviewed 262 consecutive locally advanced ESCC patients who underwent curative resection. Tumors sections were re-evaluated for PNI by an independent pathologist blinded to the patients' outcomes. Overall survival (OS) and disease-free survival (DFS) were determined using the Kaplan-Meier method; univariate log-rank test and multivariate Cox proportional hazard model were used to evaluate the prognostic value of PNI. Finally, 243 patients were analyzed and enrolled into this study, of which 132 received PORT. PNI was identified in 22.2% (54/243) of the pathologic sections. The 5-year DFS was favorable for PNI-negative patients versus PNI-positive patients (21.3% vs. 36.7%, respectively; P = 0.005). The 5-year OS was 40.3% for PNI-negative patients versus 21.7% for PNI-positive patients (P < 0.001). On multivariate analysis, PNI was an independent prognostic factor. In a subset analysis for patients received PORT, PNI was evaluated as a prognostic predictor as well (P < 0.05). In contrast to patients without PORT, PORT couldn't improve the disease recurrence and survival in locally advanced ESCC patients with PNI-positive (P > 0.05). PNI could serve as an independent prognostic factor and prognosticate treatment outcomes in locally advanced ESCC patients. The PNI status should be considered when stratifying high-risk locally advanced ESCC patients for adjuvant radiotherapy. Future prospective study is warranted to confirm our results.

Anorectal melanoma: experience from a tertiary cancer care centre in South India.

PubMed

Ranjith, S; Muralee, M; Sajeed, A; Arun, P M; Cherian, K; Nair, C K; Augustine, P; Ahamed, I

2018-03-01

Introduction Mucosal malignant melanoma of the anorectum is a rare and aggressive disease, in which early diagnosis is difficult. The prognosis remains extremely poor, irrespective of the treatment. We share our experience in treating this malignancy at our centre in South India. Methods This study describes a retrospective analysis of 31 cases of anorectal melanoma presented to our centre between January 2001 and December 2013. Results Twenty-two patients (71%) presented with metastasis and had a median overall survival of nine months. None of the 22 patients survived for two years. Nine patients (29%) had curative surgery, in the form of abdominoperineal resection (six patients), abdominoperineal resection with bilateral inguinal node dissection (one patient), abdominoperineal resection with liver resection (one patient) and posterior exenteration (one patient). In patients who underwent curative surgery, the median overall survival was 15 months and disease-free survival was nine months, with a two-year overall survival of 22%. Conclusions Anorectal melanoma is an aggressive disease with a poor prognosis. The majority of patients present with distant metastases. Prognosis depends on stage at presentation. Early diagnosis and surgical resection may improve the overall outcome. Newer modalities such as immunotherapy and targeted therapies such as anti-CTLA4 monoclonal antibody and anti-programmed cell death protein 1 monoclonal antibodies have radically changed the management of mucosal melanoma and may, in the future, improve the overall prognosis of anorectal melanoma.

Outcome of Radiofrequency Catheter Ablation as a non-pharmacological therapy for idiopathic Ventricular Tachycardia.

PubMed

Samore, Naseer Ahmed; Imran Majeed, Syed Muhammad; Kayani, Azhar Mahmud; Bhalli, Muhammad Asif; Shabbir, Muhammad

2009-09-01

To determine the outcome of Radiofrequency Catheter Ablation (RFCA) as a non-pharmacological curative therapy for idiopathic Ventricular Tachycardia (VT) and to identify procedure-related complications. Descriptive study. The Armed Forces Institute of Cardiology and National Institute of Heart Diseases, Rawalpindi, from February 2001 to October 2008. Ninety eight consecutive patients with idiopathic VT, resistant to drug therapy, who underwent Electrophysiology Studies (EPS) radiofrequency catheter ablation were enrolled. Clinical and electrophysiological variables were recorded and a descriptive analysis was done. Out of the 98 patients, 79 were males (80.6%). The mean age was 33.29+11.93 years. Modes of presentation were sustained VT, Repetitive Monomorphic VT (RMVT), Non-sustained VT (NSVT) and Ventricular Premature Beats (VPBs). Right Ventricular Outflow Tract (RVOT) VT was found in 37 patients, 37 had Idiopathic Left Ventricular Tachycardia (ILVT), 20 had Left Ventricular Outflow Tract (LVOT) VT, and Inflow Right Ventricular Tachycardia (IRVT) was found in 7 patients. Other sites of origin of VT were infrequent. Eight patients had dual morphologies of VT. Atrioventricular Nodal Re-entry Tachycardia (AVNRT) was found in 8 patients. RFCA was successful in abolishing inducible VT in 88 patients. One patient developed complete AV block requiring a permanent pacemaker. Results of this study confirm a high degree of success and safety of radiofrequency catheter ablation as curative therapy for idiopathic ventricular tachycardia.

Impact of smoking habit on surgical outcomes in non-B non-C patients with curative resection for hepatocellular carcinoma

PubMed Central

Kai, Keita; Koga, Hiroki; Aishima, Shinichi; Kawaguchi, Atsushi; Yamaji, Koutaro; Ide, Takao; Ueda, Junji; Noshiro, Hirokazu

2017-01-01

AIM To analyzed the correlation between smoking status and surgical outcomes in patients with non-B non-C hepatocellular carcinoma (NBNC-HCC), and we investigated the patients’ clinicopathological characteristics according to smoking status. METHODS We retrospectively analyzed the consecutive cases of 83 NBNC-HCC patients who underwent curative surgical treatment for the primary lesion at Saga University Hospital between 1984 and December 2012. We collected information about possibly carcinogenic factors such as alcohol abuse, diabetes mellitus, obesity and smoking habit from medical records. Smoking habits were subcategorized as never, ex- and current smoker at the time of surgery. The diagnosis of non-alcoholic steatohepatitis (NASH) was based on both clinical information and pathological confirmation. RESULTS Alcohol abuse, diabetes mellitus, obesity and NASH had no significant effect on the surgical outcomes. Current smoking status was strongly correlated with both overall survival (P = 0.0058) and disease-specific survival (P = 0.0105) by multivariate analyses. Subset analyses revealed that the current smokers were significantly younger at the time of surgery (P = 0.0002) and more likely to abuse alcohol (P = 0.0188) and to have multiple tumors (P = 0.023). CONCLUSION Current smoking habit at the time of surgical treatment is a risk factor for poor long-term survival in NBNC-HCC patients. Current smokers tend to have multiple HCCs at a younger age than other patients. PMID:28293086

Impact of smoking habit on surgical outcomes in non-B non-C patients with curative resection for hepatocellular carcinoma.

PubMed

Kai, Keita; Koga, Hiroki; Aishima, Shinichi; Kawaguchi, Atsushi; Yamaji, Koutaro; Ide, Takao; Ueda, Junji; Noshiro, Hirokazu

2017-02-28

To analyzed the correlation between smoking status and surgical outcomes in patients with non-B non-C hepatocellular carcinoma (NBNC-HCC), and we investigated the patients' clinicopathological characteristics according to smoking status. We retrospectively analyzed the consecutive cases of 83 NBNC-HCC patients who underwent curative surgical treatment for the primary lesion at Saga University Hospital between 1984 and December 2012. We collected information about possibly carcinogenic factors such as alcohol abuse, diabetes mellitus, obesity and smoking habit from medical records. Smoking habits were subcategorized as never, ex- and current smoker at the time of surgery. The diagnosis of non-alcoholic steatohepatitis (NASH) was based on both clinical information and pathological confirmation. Alcohol abuse, diabetes mellitus, obesity and NASH had no significant effect on the surgical outcomes. Current smoking status was strongly correlated with both overall survival ( P = 0.0058) and disease-specific survival ( P = 0.0105) by multivariate analyses. Subset analyses revealed that the current smokers were significantly younger at the time of surgery ( P = 0.0002) and more likely to abuse alcohol ( P = 0.0188) and to have multiple tumors ( P = 0.023). Current smoking habit at the time of surgical treatment is a risk factor for poor long-term survival in NBNC-HCC patients. Current smokers tend to have multiple HCCs at a younger age than other patients.

Evaluation of adverse events in atomic bomb survivors receiving curative-intent radiation therapy from 2005 to 2010.

PubMed

Doi, Yoshiko; Murakami, Yuji; Kenjo, Masahiro; Imano, Nobuki; Kimura, Tomoki; Nagata, Yasushi

2016-01-01

To evaluate the safety of radiation therapy (RT) in atomic bomb (A-bomb) survivors (ABS), we evaluated the frequency of RT-associated adverse events (AEs) in ABS. We selected patients who underwent curative external-beam RT (EBRT) at Hiroshima University Hospital between January 2005 and December 2010 and were born before August 1946; the patients were divided into ABS and non-ABS groups, which groups received identical treatments without stratification. We retrospectively reviewed the medical records of 220 ABS and 753 non-ABS patients. The median age was 72 years. The median observation durations were 41 and 37 months for the ABS and non-ABS groups, respectively. The ABS group had higher frequencies of women, breast cancer patients, and concurrent chemotherapy and had a lower incidence of only acute hematological AEs. However this tendency disappeared when breast cancer patients were excluded, and no significant differences were observed between the ABS and non-ABS groups regarding Grade ⩾ 3 other acute and late AEs. The overall cumulative incidence of Grade ⩾ 3 late AEs did not significantly differ between the ABS and non-ABS groups. Notable increases in AEs were not observed during or after RT among ABS. This study clarified that stratification is not required when treating ABS with RT. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Hepatoprotective and curative properties of Kombucha tea against carbon tetrachloride-induced toxicity.

PubMed

Murugesan, G S; Sathishkumar, M; Jayabalan, R; Binupriya, A R; Swaminathan, K; Yun, S E

2009-04-01

Kombucha tea (KT) is sugared black tea fermented with a symbiotic culture of acetic acid bacteria and yeasts, which is said to be tea fungus. KT is claimed to have various beneficial effects on human health, but there is very little scientific evidence available in the literature. In the present study, KT along with black tea (BT) and black tea manufactured with tea fungus enzymes (enzyme-processed tea, ET) was evaluated for hepatoprotective and curative properties against CCl4-induced toxicity, using male albino rats as an experimental model by analyzing aspartate transaminase, alanine transaminase, and alkaline phosphatase in plasma and malondialdehyde content in plasma and liver tissues. Histopathological analysis of liver tissue was also included. Results showed that BT, ET, and KT have the potential to revert the CCl4-induced hepatotoxicity. Among the three types of teas tried, KT was found to be more efficient than BT and ET. Antioxidant molecules produced during the fermentation period could be the reason for the efficient hepatoprotective and curative properties of KT against CCI4-induced hepatotoxicity.

The Role of the Curator in Modern Hospitals: A Transcontinental Perspective.

PubMed

Moss, Hilary; O'Neill, Desmond

2016-12-13

This paper explores the role of the curator in hospitals. The arts play a significant role in every society; however, recent studies indicate a neglect of the aesthetic environment of healthcare. This international study explores the complex role of the curator in modern hospitals. Semi-structured interviews were conducted with ten arts specialists in hospitals across five countries and three continents for a qualitative, phenomenological study. Five themes arose from the data: (1) Patient involvement and influence on the arts programme in hospital (2) Understanding the role of the curator in hospital (3) Influences on arts programming in hospital (4) Types of arts programmes (5) Limitations to effective curation in hospital. Recommendations arising from the research included recognition of the specialised role of the curator in hospitals; building positive links with clinical staff to effect positive hospital arts programmes and increasing formal involvement of patients in arts planning in hospital. Hospital curation can be a vibrant arena for arts development, and the role of the hospital curator is a ground-breaking specialist role that can bring benefits to hospital life. The role of curator in hospital deserves to be supported and developed by both the arts and health sectors.

Curating NASA's Past, Present, and Future Astromaterial Sample Collections

NASA Technical Reports Server (NTRS)

Zeigler, R. A.; Allton, J. H.; Evans, C. A.; Fries, M. D.; McCubbin, F. M.; Nakamura-Messenger, K.; Righter, K.; Zolensky, M.; Stansbery, E. K.

2016-01-01

The Astromaterials Acquisition and Curation Office at NASA Johnson Space Center (hereafter JSC curation) is responsible for curating all of NASA's extraterrestrial samples. JSC presently curates 9 different astromaterials collections in seven different clean-room suites: (1) Apollo Samples (ISO (International Standards Organization) class 6 + 7); (2) Antarctic Meteorites (ISO 6 + 7); (3) Cosmic Dust Particles (ISO 5); (4) Microparticle Impact Collection (ISO 7; formerly called Space-Exposed Hardware); (5) Genesis Solar Wind Atoms (ISO 4); (6) Stardust Comet Particles (ISO 5); (7) Stardust Interstellar Particles (ISO 5); (8) Hayabusa Asteroid Particles (ISO 5); (9) OSIRIS-REx Spacecraft Coupons and Witness Plates (ISO 7). Additional cleanrooms are currently being planned to house samples from two new collections, Hayabusa 2 (2021) and OSIRIS-REx (2023). In addition to the labs that house the samples, we maintain a wide variety of infra-structure facilities required to support the clean rooms: HEPA-filtered air-handling systems, ultrapure dry gaseous nitrogen systems, an ultrapure water system, and cleaning facilities to provide clean tools and equipment for the labs. We also have sample preparation facilities for making thin sections, microtome sections, and even focused ion-beam sections. We routinely monitor the cleanliness of our clean rooms and infrastructure systems, including measurements of inorganic or organic contamination, weekly airborne particle counts, compositional and isotopic monitoring of liquid N2 deliveries, and daily UPW system monitoring. In addition to the physical maintenance of the samples, we track within our databases the current and ever changing characteristics (weight, location, etc.) of more than 250,000 individually numbered samples across our various collections, as well as more than 100,000 images, and countless "analog" records that record the sample processing records of each individual sample. JSC Curation is co-located with JSC's Astromaterials Research Office, which houses a world-class suite of analytical instrumentation and scientists. We leverage these labs and personnel to better curate the samples. Part of the cu-ration process is planning for the future, and we refer to these planning efforts as "advanced curation". Advanced Curation is tasked with developing procedures, technology, and data sets necessary for curating new types of collections as envi-sioned by NASA exploration goals. We are (and have been) planning for future cu-ration, including cold curation, extended curation of ices and volatiles, curation of samples with special chemical considerations such as perchlorate-rich samples, and curation of organically- and biologically-sensitive samples.

PDB data curation.

PubMed

Wang, Yanchao; Sunderraman, Rajshekhar

2006-01-01

In this paper, we propose two architectures for curating PDB data to improve its quality. The first one, PDB Data Curation System, is developed by adding two parts, Checking Filter and Curation Engine, between User Interface and Database. This architecture supports the basic PDB data curation. The other one, PDB Data Curation System with XCML, is designed for further curation which adds four more parts, PDB-XML, PDB, OODB, Protin-OODB, into the previous one. This architecture uses XCML language to automatically check errors of PDB data that enables PDB data more consistent and accurate. These two tools can be used for cleaning existing PDB files and creating new PDB files. We also show some ideas how to add constraints and assertions with XCML to get better data. In addition, we discuss the data provenance that may affect data accuracy and consistency.

NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease.

PubMed

Iyappan, Anandhi; Kawalia, Shweta Bagewadi; Raschka, Tamara; Hofmann-Apitius, Martin; Senger, Philipp

2016-07-08

Neurodegenerative diseases are incurable and debilitating indications with huge social and economic impact, where much is still to be learnt about the underlying molecular events. Mechanistic disease models could offer a knowledge framework to help decipher the complex interactions that occur at molecular and cellular levels. This motivates the need for the development of an approach integrating highly curated and heterogeneous data into a disease model of different regulatory data layers. Although several disease models exist, they often do not consider the quality of underlying data. Moreover, even with the current advancements in semantic web technology, we still do not have cure for complex diseases like Alzheimer's disease. One of the key reasons accountable for this could be the increasing gap between generated data and the derived knowledge. In this paper, we describe an approach, called as NeuroRDF, to develop an integrative framework for modeling curated knowledge in the area of complex neurodegenerative diseases. The core of this strategy lies in the usage of well curated and context specific data for integration into one single semantic web-based framework, RDF. This increases the probability of the derived knowledge to be novel and reliable in a specific disease context. This infrastructure integrates highly curated data from databases (Bind, IntAct, etc.), literature (PubMed), and gene expression resources (such as GEO and ArrayExpress). We illustrate the effectiveness of our approach by asking real-world biomedical questions that link these resources to prioritize the plausible biomarker candidates. Among the 13 prioritized candidate genes, we identified MIF to be a potential emerging candidate due to its role as a pro-inflammatory cytokine. We additionally report on the effort and challenges faced during generation of such an indication-specific knowledge base comprising of curated and quality-controlled data. Although many alternative approaches have been proposed and practiced for modeling diseases, the semantic web technology is a flexible and well established solution for harmonized aggregation. The benefit of this work, to use high quality and context specific data, becomes apparent in speculating previously unattended biomarker candidates around a well-known mechanism, further leveraged for experimental investigations.

Role of phenolics from Spondias pinnata bark in amelioration of iron overload induced hepatic damage in Swiss albino mice.

PubMed

Chaudhuri, Dipankar; Ghate, Nikhil Baban; Panja, Sourav; Mandal, Nripendranath

2016-07-26

Crude Spondias pinnata bark extract was previously assessed for its antioxidant, anticancer and iron chelating potentials. The isolated compounds gallic acid (GA) and methyl gallate (MG) were evaluated for their curative potential against iron overload-induced liver fibrosis and hepatocellular damage. In vitro iron chelation property and in vivo ameliorating potential from iron overload induced liver toxicity of GA and MG was assessed by different biochemical assays and histopathological studies. MG and GA demonstrated excellent reducing power activities but iron chelation potential of MG is better than GA. Oral MG treatment in mice displayed excellent efficacy (better than GA) to significantly restore the levels of liver antioxidants, serum markers and cellular reactive oxygen species in a dose-dependent fashion. Apart from these, MG exceptionally prevented lipid peroxidation and protein oxidation whereas GA demonstrated better activity to reduce collagen content, thereby strengthening its position as an efficient drug against hepatic damage/fibrosis, which was further supported by histopathological studies. Alongside, MG efficiently eliminated the cause of liver damage, i.e., excess iron, by chelating free iron and reducing the ferritin-bound iron. The present study confirmed the curative effect of GA and MG against iron overload hepatic damage via their potent antioxidant and iron-chelating potential.

[The role of elective neck dissection during salvage laryngectomy - a retrospective analysis].

PubMed

Hussain, Timon; Kanaan, Oliver; Höing, Benedikt; Dominas, Nina; Lang, Stephan; Mattheis, Stefan

2018-05-16

Elective neck dissection of the N0-neck is routinely performed during salvage laryngectomy (SLE) for recurrent cancer of the larynx or hypopharynx. The therapeutic benefit of additional neck dissection must be weighed against the risk of increased morbidity. In this retrospective analysis, we assessed oncologic parameters of patients who underwent SLE with concurrent bilateral neck dissection for recurrent laryngeal or hypopharyngeal cancer. We compared these data with patients who underwent primary laryngectomy (LE) with bilateral neck dissection for laryngeal and hypopharyngeal cancer.19 patients who had undergone SLE and 83 patients after LE were included in the analysis. The majority of patients had advanced stage tumors prior to LE or primary radiation therapy, as well as advanced stage recurrent tumors prior to SLE. Prior to SLE, 5 % of all patients (n = 1) had clinically pathologic lymph nodes, compared to 47 % (n = 39) prior to LE. 17 % (n = 14) of patients with LE and bilateral neck dissection had occult lymph node metastases, compared to 5 % (n = 1) of patients who underwent SLE with bilateral neck dissection. Overall, 55 % (n = 44) of patients who underwent LE had positive cervical lymph nodes, compared to 10 % (n = 2) of SLE patients. Lymph node yield was higher in patients with LE than in SLE-patients (37.3 vs. 18.7, p < 0.001). 5-year OS was 50 % after LE and 33 % after SLE. Cervical lymph node metastases are rare in patients who undergo SLE for recurrent cancers of the larynx of hypopharynx. However, occult metastases do occur. Therefore, since SLE is the final curative therapy, additional neck dissection should be taken into consideration. © Georg Thieme Verlag KG Stuttgart · New York.

Comparison of survival outcomes after anatomical resection and non-anatomical resection in patients with hepatocellular carcinoma

PubMed Central

Kim, Seheon; Kim, Seokwhan; Song, Insang

2015-01-01

Backgrounds/Aims Liver resection is a curative procedure performed worldwide for hepatocellular carcinoma (HCC). Deciding on the appropriate resection range for postoperative hepatic function preservation is an important surgical consideration. This study compares survival outcomes of HCC patients who underwent anatomical or non-anatomical resection, to determine which offers the best clinical survival benefit. Methods One hundred and thirty-one patients underwent liver resection with HCC, between January 2007 and February 2015, and were divided into two groups: those who underwent anatomical liver resection (n=88) and those who underwent non-anatomical liver resection (n=43). Kaplan-Meier survival analysis and Cox regressions were used to compare the disease-free survival (DFS) and overall survival (OS) rates between the groups. Results The mean follow-up periods were 27 and 40 months in the anatomical and non-anatomical groups, respectively (p=0.229). The 3- and 5-year DFS rates were 70% and 60% in the anatomical group and 62% and 48% in the non-anatomical group, respectively. The 3 and 5-year OS rates were 94% and 78% in the anatomical group, and 86% and 80% in the non-anatomical group, respectively. The anatomical group tended to show better outcomes, but the findings were not significant. However, a relative risk of OS between the anatomical and non-anatomical group was 0.234 (95% CI, 0.061-0.896; p=0.034), which is statistically significant. Conclusions Although statistical significance was not detected in survival curves, anatomical resection showed better results. In this respect, anatomical resection is more likely to perform in HCC patients with preserve liver function than non-anatomical resection. PMID:26693235

Conversion therapy for inoperable advanced gastric cancer patients by docetaxel, cisplatin, and S-1 (DCS) chemotherapy: a multi-institutional retrospective study.

PubMed

Sato, Yasushi; Ohnuma, Hiroyuki; Nobuoka, Takayuki; Hirakawa, Masahiro; Sagawa, Tamotsu; Fujikawa, Koshi; Takahashi, Yasuo; Shinya, Minami; Katsuki, Shinich; Takahashi, Minoru; Maeda, Masahiro; Okagawa, Yutaka; Naoki, Uemura; Kikuch, Syouhei; Okamoto, Koichi; Miyamoto, Hiroshi; Shimada, Mitsuo; Takemasa, Ichiro; Kato, Junji; Takayama, Tetsuji

2017-05-01

Conversion therapy is an option for unresectable metastatic gastric cancer when distant metastases are controlled by chemotherapy; however, the feasibility and efficacy remain unclear. This study aimed to assess the feasibility and efficacy of conversion therapy in patients with initially unresectable gastric cancer treated with docetaxel, cisplatin, and S-1 (DCS) chemotherapy by evaluating clinical outcomes. One hundred unresectable metastatic gastric cancer patients, enrolled in three DCS chemotherapy clinical trials, were retrospectively evaluated. The patients received oral S-1 (40 mg/m 2 b.i.d.) on days 1-14 and intravenous cisplatin (60 mg/m 2 ) and docetaxel (50-60 mg/m 2 ) on day 8 every 3 weeks. Conversion therapy was defined when the patients could undergo R0 resection post-DCS chemotherapy and were able to tolerate curative surgery. Conversion therapy was achieved in 33/100 patients, with no perioperative mortality. Twenty-eight of the 33 patients (84.8 %) achieved R0 resection, and 78.8 % were defined as histological chemotherapeutic responders. The median overall survival (OS) of patients who underwent conversion therapy was 47.8 months (95 % CI 28.0-88.5 months). Patients who underwent R0 resection had significantly longer OS than those who underwent R1 and R2 resections (P = 0.0002). Of the patients with primarily unresectable metastases, 10 % lived >5 years. Among patients who underwent conversion therapy, multivariate analysis showed that the pathological response was a significant independent predictor for OS. DCS safely induced a high conversion rate, with very high R0 and pathological response rates, and was associated with a good prognosis; these findings warrant further prospective investigations.

Additive endoscopic resection may be sufficient for patients with a positive lateral margin after endoscopic resection of early gastric cancer.

PubMed

Kim, Hae Won; Kim, Jie-Hyun; Park, Jun Chul; Jeon, Mi Young; Lee, Yong Chan; Lee, Sang Kil; Shin, Sung Kwan; Chung, Hyun Soo; Noh, Sung Hoon; Kim, Jong Won; Choi, Seung Ho; Park, Jae Jun; Youn, Young Hoon; Park, Hyojin

2017-11-01

No well-established treatment strategies exist for lateral margin positivity (LM+) alone after endoscopic resection (ER) of early gastric cancer (EGC). Thus, we aimed to clarify a treatment strategy for non-curative resection (non-CR) with LM+ alone after ER in EGC. Among 2065 patients with EGC treated by ER, 76 (3.6%) with only LM+ after non-CR of EGC were reviewed retrospectively. Of these, 28 underwent gastrectomy, 25 underwent argon plasma coagulation (APC), and 23 underwent repeat ER (re-ER). We analyzed the clinicopathologic characteristics of all patients and compared those who underwent additive surgery, APC, or re-ER. Of the 76 patients, 28 (36.8%) fulfilled the absolute criteria and 48 (63.2%) the expanded criteria for ER. Among the latter patients, the proportion undergoing additive surgery was 75.0%, higher than that of patients in the former group (P = .014). Residual cancer cells were observed in 70.6% of patients after additive surgery or re-ER. Residual cancer cells were observed significantly more often in patients with undifferentiated-type than in those with differentiated-type EGC (P = .02). However, no lymph node metastasis was observed in any patient after additive surgery. Our results suggest that endoscopic treatment may be a sufficient additive therapy for patients with LM+ alone after ER, irrespective of whether the absolute or expanded ER criteria are used. However, as complete ablation of remnant cells cannot be guaranteed, re-ER is a better additive treatment than APC. Copyright © 2017 American Society for Gastrointestinal Endoscopy. Published by Elsevier Inc. All rights reserved.

Preparing to Receive and Handle Martian Samples When They Arrive on Earth

NASA Technical Reports Server (NTRS)

McCubbin, Francis M.

2017-01-01

The Astromaterials Acquisition and Curation Office at NASA Johnson Space Center (JSC) is responsible for curating all of NASA's extraterrestrial samples. Under the governing document, NASA Policy Directive (NPD) 7100.10F+ derivative NPR 'Curation of Extraterrestrial Materials', JSC is charged with 'The curation of all extraterrestrial material under NASA control, including future NASA missions. 'The Directive goes on to define Curation as including'...documentation, preservation, preparation, and distribution of samples for research, education, and public outreach."

Difference in Postsurgical Prognostic Factors between Lung Adenocarcinoma and Squamous Cell Carcinoma

PubMed Central

Sakai, Hiroki; Kimura, Hiroyuki; Miyazawa, Tomoyuki; Marushima, Hideki; Saji, Hisashi

2017-01-01

Purpose: The aim of this study was to compare the clinicopathologic prognostic factors between patients who underwent lung resection for adenocarcinoma (AD) and those with squamous cell carcinoma (SQ). Methods: A database of patients with lung AD or SQ who underwent surgery with curative intent in our department from January 2008 to December 2014 was reviewed. Associations between various clinicopathologic factors, postsurgical recurrence-free survival (RFS), and overall survival (OS) were analyzed to find significant prognostic factors. Results: A total of 537 lung cancer patients (AD, 434; SQ, 103) were included in this study. Although RFS was similar in patients with AD and SQ, OS was significantly poorer in those with SQ. Multivariate analysis in patients with AD revealed that age (≥69 vs. <69), lymphatic invasion, and histologic pleural invasion (p0 vs. p1–3) were associated with RFS, while gender and pleural invasion were associated with OS. In SQ, however, smoking, clinical stage, and pulmonary metastasis were associated with RFS in the multivariate analysis. Conclusion: Since significant postoperative prognostic factors are quite different between lung AD and SQ, these two histologic types should be differently analyzed in a clinical study. PMID:28966230

Utilization of surgical treatment for local and locoregional esophageal cancer: Analysis of the National Cancer Data Base.

PubMed

Taylor, Lauren J; Greenberg, Caprice C; Lidor, Anne O; Leverson, Glen E; Maloney, James D; Macke, Ryan A

2017-02-01

Previous studies have suggested that esophagectomy is severely underused for patients with resectable esophageal cancer. The recent expansion of endoscopic local therapies, advances in surgical techniques, and improved postoperative outcomes have changed the therapeutic landscape. The impact of these developments and evolving treatment guidelines on national practice patterns is unknown. Patients diagnosed with clinical stage 0 to III esophageal cancer were identified from the National Cancer Database (2004-2013). The receipt of potentially curative surgical treatment over time was analyzed, and multivariate logistic regression was used to identify factors associated with surgical treatment. The analysis included 52,122 patients. From 2004 to 2013, the overall rate of potentially curative surgical treatment increased from 36.4% to 47.4% (P < .001). For stage 0 disease, the receipt of esophagectomy decreased from 23.8% to 17.9% (P < .001), whereas the use of local therapies increased from 34.3% to 58.8% (P < .001). The use of surgical treatment increased from 43.4% to 61.8% (P < .001), from 36.1% to 45.0% (P < .001), and from 30.8% to 38.6% (P < .001) for patients with stage I, II, and III disease, respectively. In the multivariate analysis, divergent practice patterns and adherence to national guidelines were noted between academic and community facilities. The use of potentially curative surgical treatment has increased for patients with stage 0 to III esophageal cancer. The expansion of local therapies has driven increased rates of surgical treatment for early-stage disease. Although the increased use of esophagectomy for more advanced disease is encouraging, significant variation persists at the patient and facility levels. Cancer 2017;123:410-419. © 2016 American Cancer Society. © 2016 American Cancer Society.

Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts

PubMed Central

Lu, Zhiyong

2012-01-01

Today’s biomedical research has become heavily dependent on access to the biological knowledge encoded in expert curated biological databases. As the volume of biological literature grows rapidly, it becomes increasingly difficult for biocurators to keep up with the literature because manual curation is an expensive and time-consuming endeavour. Past research has suggested that computer-assisted curation can improve efficiency, but few text-mining systems have been formally evaluated in this regard. Through participation in the interactive text-mining track of the BioCreative 2012 workshop, we developed PubTator, a PubMed-like system that assists with two specific human curation tasks: document triage and bioconcept annotation. On the basis of evaluation results from two external user groups, we find that the accuracy of PubTator-assisted curation is comparable with that of manual curation and that PubTator can significantly increase human curatorial speed. These encouraging findings warrant further investigation with a larger number of publications to be annotated. Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/ PMID:23160414

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

PubMed Central

Orchard, Sandra; Ammari, Mais; Aranda, Bruno; Breuza, Lionel; Briganti, Leonardo; Broackes-Carter, Fiona; Campbell, Nancy H.; Chavali, Gayatri; Chen, Carol; del-Toro, Noemi; Duesbury, Margaret; Dumousseau, Marine; Galeota, Eugenia; Hinz, Ursula; Iannuccelli, Marta; Jagannathan, Sruthi; Jimenez, Rafael; Khadake, Jyoti; Lagreid, Astrid; Licata, Luana; Lovering, Ruth C.; Meldal, Birgit; Melidoni, Anna N.; Milagros, Mila; Peluso, Daniele; Perfetto, Livia; Porras, Pablo; Raghunath, Arathi; Ricard-Blum, Sylvie; Roechert, Bernd; Stutz, Andre; Tognolli, Michael; van Roey, Kim; Cesareni, Gianni; Hermjakob, Henning

2014-01-01

IntAct (freely available at http://www.ebi.ac.uk/intact) is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. IntAct has developed a sophisticated web-based curation tool, capable of supporting both IMEx- and MIMIx-level curation. This tool is now utilized by multiple additional curation teams, all of whom annotate data directly into the IntAct database. Members of the IntAct team supply appropriate levels of training, perform quality control on entries and take responsibility for long-term data maintenance. Recently, the MINT and IntAct databases decided to merge their separate efforts to make optimal use of limited developer resources and maximize the curation output. All data manually curated by the MINT curators have been moved into the IntAct database at EMBL-EBI and are merged with the existing IntAct dataset. Both IntAct and MINT are active contributors to the IMEx consortium (http://www.imexconsortium.org). PMID:24234451

Indications for Surgical Management of Hyperparathyroidism: A Review.

PubMed

Stephen, Antonia E; Mannstadt, Michael; Hodin, Richard A

2017-09-01

Primary hyperparathyroidism (pHPT) is a common clinical entity, with approximately 100 000 new cases diagnosed each year in the United States. Most patients with pHPT have a relatively mild form of the disease and present with few if any overt signs or symptoms. This has led to a dilemma regarding which patients should be considered for parathyroid surgery. In this article, we review the established literature on the indications for surgery in asymptomatic pHPT and discuss the most recent consensus conference guidelines. The reviewed literature suggests that there were improved outcomes among patients with asymptomatic pHPT who underwent curative surgery. Most patients with pHPT should be considered for parathyroidectomy. More randomized clinical trials are needed to strongly support a surgical recommendation for all asymptomatic patients with pHPT.

[The survival prediction model of advanced gallbladder cancer based on Bayesian network: a multi-institutional study].

PubMed

Tang, Z H; Geng, Z M; Chen, C; Si, S B; Cai, Z Q; Song, T Q; Gong, P; Jiang, L; Qiu, Y H; He, Y; Zhai, W L; Li, S P; Zhang, Y C; Yang, Y

2018-05-01

Objective: To investigate the clinical value of Bayesian network in predicting survival of patients with advanced gallbladder cancer(GBC)who underwent curative intent surgery. Methods: The clinical data of patients with advanced GBC who underwent curative intent surgery in 9 institutions from January 2010 to December 2015 were analyzed retrospectively.A median survival time model based on a tree augmented naïve Bayes algorithm was established by Bayesia Lab software.The survival time, number of metastatic lymph nodes(NMLN), T stage, pathological grade, margin, jaundice, liver invasion, age, sex and tumor morphology were included in this model.Confusion matrix, the receiver operating characteristic curve and area under the curve were used to evaluate the accuracy of the model.A priori statistical analysis of these 10 variables and a posterior analysis(survival time as the target variable, the remaining factors as the attribute variables)was performed.The importance rankings of each variable was calculated with the polymorphic Birnbaum importance calculation based on the posterior analysis results.The survival probability forecast table was constructed based on the top 4 prognosis factors. The survival curve was drawn by the Kaplan-Meier method, and differences in survival curves were compared using the Log-rank test. Results: A total of 316 patients were enrolled, including 109 males and 207 females.The ratio of male to female was 1.0∶1.9, the age was (62.0±10.8)years.There was 298 cases(94.3%) R0 resection and 18 cases(5.7%) R1 resection.T staging: 287 cases(90.8%) T3 and 29 cases(9.2%) T4.The median survival time(MST) was 23.77 months, and the 1, 3, 5-year survival rates were 67.4%, 40.8%, 32.0%, respectively.For the Bayesian model, the number of correctly predicted cases was 121(≤23.77 months) and 115(>23.77 months) respectively, leading to a 74.86% accuracy of this model.The prior probability of survival time was 0.503 2(≤23.77 months) and 0.496 8(>23.77 months), the importance ranking showed that NMLN(0.366 6), margin(0.350 1), T stage(0.319 2) and pathological grade(0.258 9) were the top 4 prognosis factors influencing the postoperative MST.These four factors were taken as observation variables to get the probability of patients in different survival periods.Basing on these results, a survival prediction score system including NMLN, margin, T stage and pathological grade was designed, the median survival time(month) of 4-9 points were 66.8, 42.4, 26.0, 9.0, 7.5 and 2.3, respectively, there was a statistically significant difference in the different points( P <0.01). Conclusions: The survival prediction model of GBC based on Bayesian network has high accuracy.NMLN, margin, T staging and pathological grade are the top 4 risk factors affecting the survival of patients with advanced GBC who underwent curative resection.The survival prediction score system based on these four factors could be used to predict the survival and to guide the decision making of patients with advanced GBC.

Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II.

PubMed

Lu, Zhiyong; Hirschman, Lynette

2012-01-01

Manual curation of data from the biomedical literature is a rate-limiting factor for many expert curated databases. Despite the continuing advances in biomedical text mining and the pressing needs of biocurators for better tools, few existing text-mining tools have been successfully integrated into production literature curation systems such as those used by the expert curated databases. To close this gap and better understand all aspects of literature curation, we invited submissions of written descriptions of curation workflows from expert curated databases for the BioCreative 2012 Workshop Track II. We received seven qualified contributions, primarily from model organism databases. Based on these descriptions, we identified commonalities and differences across the workflows, the common ontologies and controlled vocabularies used and the current and desired uses of text mining for biocuration. Compared to a survey done in 2009, our 2012 results show that many more databases are now using text mining in parts of their curation workflows. In addition, the workshop participants identified text-mining aids for finding gene names and symbols (gene indexing), prioritization of documents for curation (document triage) and ontology concept assignment as those most desired by the biocurators. DATABASE URL: http://www.biocreative.org/tasks/bc-workshop-2012/workflow/.

On expert curation and scalability: UniProtKB/Swiss-Prot as a case study

PubMed Central

Arighi, Cecilia N; Magrane, Michele; Bateman, Alex; Wei, Chih-Hsuan; Lu, Zhiyong; Boutet, Emmanuel; Bye-A-Jee, Hema; Famiglietti, Maria Livia; Roechert, Bernd; UniProt Consortium, The

2017-01-01

Abstract Motivation Biological knowledgebases, such as UniProtKB/Swiss-Prot, constitute an essential component of daily scientific research by offering distilled, summarized and computable knowledge extracted from the literature by expert curators. While knowledgebases play an increasingly important role in the scientific community, their ability to keep up with the growth of biomedical literature is under scrutiny. Using UniProtKB/Swiss-Prot as a case study, we address this concern via multiple literature triage approaches. Results With the assistance of the PubTator text-mining tool, we tagged more than 10 000 articles to assess the ratio of papers relevant for curation. We first show that curators read and evaluate many more papers than they curate, and that measuring the number of curated publications is insufficient to provide a complete picture as demonstrated by the fact that 8000–10 000 papers are curated in UniProt each year while curators evaluate 50 000–70 000 papers per year. We show that 90% of the papers in PubMed are out of the scope of UniProt, that a maximum of 2–3% of the papers indexed in PubMed each year are relevant for UniProt curation, and that, despite appearances, expert curation in UniProt is scalable. Availability and implementation UniProt is freely available at http://www.uniprot.org/. Contact sylvain.poux@sib.swiss Supplementary information Supplementary data are available at Bioinformatics online. PMID:29036270

The curation of genetic variants: difficulties and possible solutions.

PubMed

Pandey, Kapil Raj; Maden, Narendra; Poudel, Barsha; Pradhananga, Sailendra; Sharma, Amit Kumar

2012-12-01

The curation of genetic variants from biomedical articles is required for various clinical and research purposes. Nowadays, establishment of variant databases that include overall information about variants is becoming quite popular. These databases have immense utility, serving as a user-friendly information storehouse of variants for information seekers. While manual curation is the gold standard method for curation of variants, it can turn out to be time-consuming on a large scale thus necessitating the need for automation. Curation of variants described in biomedical literature may not be straightforward mainly due to various nomenclature and expression issues. Though current trends in paper writing on variants is inclined to the standard nomenclature such that variants can easily be retrieved, we have a massive store of variants in the literature that are present as non-standard names and the online search engines that are predominantly used may not be capable of finding them. For effective curation of variants, knowledge about the overall process of curation, nature and types of difficulties in curation, and ways to tackle the difficulties during the task are crucial. Only by effective curation, can variants be correctly interpreted. This paper presents the process and difficulties of curation of genetic variants with possible solutions and suggestions from our work experience in the field including literature support. The paper also highlights aspects of interpretation of genetic variants and the importance of writing papers on variants following standard and retrievable methods. Copyright © 2012. Published by Elsevier Ltd.

The Curation of Genetic Variants: Difficulties and Possible Solutions

PubMed Central

Pandey, Kapil Raj; Maden, Narendra; Poudel, Barsha; Pradhananga, Sailendra; Sharma, Amit Kumar

2012-01-01

The curation of genetic variants from biomedical articles is required for various clinical and research purposes. Nowadays, establishment of variant databases that include overall information about variants is becoming quite popular. These databases have immense utility, serving as a user-friendly information storehouse of variants for information seekers. While manual curation is the gold standard method for curation of variants, it can turn out to be time-consuming on a large scale thus necessitating the need for automation. Curation of variants described in biomedical literature may not be straightforward mainly due to various nomenclature and expression issues. Though current trends in paper writing on variants is inclined to the standard nomenclature such that variants can easily be retrieved, we have a massive store of variants in the literature that are present as non-standard names and the online search engines that are predominantly used may not be capable of finding them. For effective curation of variants, knowledge about the overall process of curation, nature and types of difficulties in curation, and ways to tackle the difficulties during the task are crucial. Only by effective curation, can variants be correctly interpreted. This paper presents the process and difficulties of curation of genetic variants with possible solutions and suggestions from our work experience in the field including literature support. The paper also highlights aspects of interpretation of genetic variants and the importance of writing papers on variants following standard and retrievable methods. PMID:23317699

The Astromaterials X-Ray Computed Tomography Laboratory at Johnson Space Center

NASA Technical Reports Server (NTRS)

Zeigler, R. A.; Coleff, D. M.; McCubbin, F. M.

2017-01-01

The Astromaterials Acquisition and Curation Office at NASA's Johnson Space Center (hereafter JSC curation) is the past, present, and future home of all of NASA's astromaterials sample collections. JSC curation currently houses all or part of nine different sample collections: (1) Apollo samples (1969), (2) Lunar samples (1972), (3) Antarctic meteorites (1976), (4) Cosmic Dust particles (1981), (5) Microparticle Impact Collection (1985), (6) Genesis solar wind atoms (2004); (7) Stardust comet Wild-2 particles (2006), (8) Stardust interstellar particles (2006), and (9) Hayabusa asteroid Itokawa particles (2010). Each sample collection is housed in a dedicated clean room, or suite of clean rooms, that is tailored to the requirements of that sample collection. Our primary goals are to maintain the long-term integrity of the samples and ensure that the samples are distributed for scientific study in a fair, timely, and responsible manner, thus maximizing the return on each sample. Part of the curation process is planning for the future, and we also perform fundamental research in advanced curation initiatives. Advanced Curation is tasked with developing procedures, technology, and data sets necessary for curating new types of sample collections, or getting new results from existing sample collections [2]. We are (and have been) planning for future curation, including cold curation, extended curation of ices and volatiles, curation of samples with special chemical considerations such as perchlorate-rich samples, and curation of organically- and biologically-sensitive samples. As part of these advanced curation efforts we are augmenting our analytical facilities as well. A micro X-Ray computed tomography (micro-XCT) laboratory dedicated to the study of astromaterials will be coming online this spring within the JSC Curation office, and we plan to add additional facilities that will enable nondestructive (or minimally-destructive) analyses of astromaterials in the near future (micro-XRF, confocal imaging Raman Spectroscopy). These facilities will be available to: (1) develop sample handling and storage techniques for future sample return missions; (2) be utilized by PET for future sample return missions; (3) be used for retroactive PET (Positron Emission Tomography)-style analyses of our existing collections; and (4) for periodic assessments of the existing sample collections. Here we describe the new micro-XCT system, as well as some of the ongoing or anticipated applications of the instrument.

Value of geriatric frailty and nutritional status assessment in predicting postoperative mortality in gastric cancer surgery.

PubMed

Tegels, Juul J W; de Maat, M F G; Hulsewé, K W E; Hoofwijk, A G M; Stoot, J H M B

2014-03-01

This study seeks to evaluate assessment of geriatric frailty and nutritional status in predicting postoperative mortality in gastric cancer surgery. Preoperatively, patients operated for gastric adenocarcinoma underwent assessment of Groningen Frailty Indicator (GFI) and Short Nutritional Assessment Questionnaire (SNAQ). We studied retrospectively whether these scores were associated with in-hospital mortality. From 2005 to September 2012 180 patients underwent surgery with an overall mortality of 8.3%. Patients with a GFI ≥ 3 (n = 30, 24%) had a mortality rate of 23.3% versus 5.2% in the lower GFI group (OR 4.0, 95%CI 1.1-14.1, P = 0.03). For patients who underwent surgery with curative intent (n = 125), this was 27.3% for patients with GFI ≥ 3 (n = 22, 18%) versus 5.7% with GFI < 3 (OR 4.6, 95% CI 1.0-20.9, P = 0.05). SNAQ ≥ 1 (n = 98, 61%) was associated with a mortality rate of 13.3% versus 3.2% in patients with SNAQ =0 (OR 5.1, 95% CI 1.1-23.8, P = 0.04). Given odds ratios are corrected in multivariate analyses for age, neoadjuvant chemotherapy, type of surgery, tumor stage and ASA classification. This study shows a significant relationship between gastric cancer surgical mortality and geriatric frailty as well as nutritional status using a simple questionnaire. This may have implications in preoperative decision making in selecting patients who optimally benefit from surgery.

Post-treatment management options for patients with lung cancer.

PubMed Central

Virgo, K S; McKirgan, L W; Caputo, M C; Mahurin, D M; Chao, L C; Caputo, N A; Naunheim, K S; Flye, M W; Gillespie, K N; Johnson, F E

1995-01-01

OBJECTIVES: The first objective was to identify variations in patient management practice patterns after potentially curative lung cancer surgery. Patient management practice patterns were expected to range from intensive follow-up to no active surveillance. The second objective was to measure whether intensity of follow-up was related to patient outcomes. METHODS: An 18-month retrospective analysis was conducted of 182 patients with low TNM stage (< or = IIIA) lung cancer who were surgically treated with curative intent over the 11-year period from 1982 through 1992 at the St. Louis Department of Veterans Affairs Medical Center. RESULTS: Patients were followed for a mean of 3.3 years, until death or the end of the study. Analyses of diagnostic test and outpatient visit frequency distributions and cluster analyses facilitated the identification of 62 nonintensively followed patients and 120 intensively followed patients. Both groups were comparable at baseline, and there were no significant differences in patient outcomes attributable to intensity of follow-up. Intensively followed patients did, however, live an average of 192 days longer than nonintensively followed patients. CONCLUSIONS: Significant variations in follow-up practice patterns can exist within a single health care facility. In this analysis, variations in test and visit frequency did not result in statistically significant differences in patient outcomes, though the survival difference between groups suggests that some benefit might exist. Only well-designed prospective trials are likely to answer the question of what constitutes optimal follow-up after potentially curative lung cancer treatment. PMID:8526576

Integrating publicly-available data to generate computationally-predicted adverse outcome pathways for hepatic steatosis

EPA Science Inventory

The adverse outcome pathway (AOP) framework provides a way of organizing knowledge related to the key biological events that result in a particular health outcome. For the majority of environmental chemicals, the availability of curated pathways characterizing potential toxicity ...

The role of interventional radiology in the treatment of intrahepatic cholangiocarcinoma.

PubMed

Ierardi, Anna Maria; Angileri, Salvatore Alessio; Patella, Francesca; Panella, Silvia; Lucchina, Natalie; Petre, Elena N; Pinto, Antonio; Franceschelli, Giuseppe; Carrafiello, Gianpaolo; Cornalba, Gianpaolo; Sofocleous, Constantinos T

2017-01-01

Intrahepatic cholangiocarcinoma (ICC) is the second most common primary hepatic malignancy after hepatocellular carcinoma. Complete surgical resection remains the only potentially curative option for patients with ICC. However, until now, early diagnosis with potential surgical intervention has been the exception rather than the rule with only 30% of patients qualifying for attempted surgical cure. Many patients are unresectable because of disease stage, anatomic conditions, medical comorbidities, and small future remnant liver. Interventional radiology procedures are available for these types of patients with intra-arterial therapies and/or ablative treatments both for curative and for palliative treatment. The goals of interventional therapy are to control local tumor growth, to relieve symptoms, and to improve and preserve quality of life. The choice of treatment depends largely on tumor extent and patient performance. No randomized studies exist to compare treatments. The present review describes the current evidence of the interventional treatments in the management of the ICC. Moreover, interventional procedures available to increase the future liver reserve before surgery were analyzed.

Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex.

PubMed

Balhoff, James P; Dahdul, Wasila M; Dececchi, T Alexander; Lapp, Hilmar; Mabee, Paula M; Vision, Todd J

2014-01-01

Phenex (http://phenex.phenoscape.org/) is a desktop application for semantically annotating the phenotypic character matrix datasets common in evolutionary biology. Since its initial publication, we have added new features that address several major bottlenecks in the efficiency of the phenotype curation process: allowing curators during the data curation phase to provisionally request terms that are not yet available from a relevant ontology; supporting quality control against annotation guidelines to reduce later manual review and revision; and enabling the sharing of files for collaboration among curators. We decoupled data annotation from ontology development by creating an Ontology Request Broker (ORB) within Phenex. Curators can use the ORB to request a provisional term for use in data annotation; the provisional term can be automatically replaced with a permanent identifier once the term is added to an ontology. We added a set of annotation consistency checks to prevent common curation errors, reducing the need for later correction. We facilitated collaborative editing by improving the reliability of Phenex when used with online folder sharing services, via file change monitoring and continual autosave. With the addition of these new features, and in particular the Ontology Request Broker, Phenex users have been able to focus more effectively on data annotation. Phenoscape curators using Phenex have reported a smoother annotation workflow, with much reduced interruptions from ontology maintenance and file management issues.

Directly Improving the Quality of Radiation Treatment Through Peer Review: A Cross-sectional Analysis of Cancer Centers Across a Provincial Cancer Program.

PubMed

Rouette, Julie; Gutierrez, Eric; O'Donnell, Jennifer; Reddeman, Lindsay; Hart, Margaret; Foxcroft, Sophie; Mitera, Gunita; Warde, Padraig; Brundage, Michael D

2017-07-01

To describe the outcomes of peer review across all 14 cancer centers in Ontario. We identified all peer-reviewed, curative treatment plans delivered in Ontario within a 3-month study period from 2013 to 2014 using a provincial cancer treatment database and collected additional data on the peer-review outcomes. Considerable variation was found in the proportion of peer-reviewed plans across the centers (average 70.2%, range 40.8%-99.2%). During the study period, 5561 curative plans underwent peer review. Of those, 184 plans (3.3%) had changes recommended. Of the 184 plans, the changes were major (defined as requiring repeat planning or having a major effect on planning or clinical outcomes, or both) in 40.2% and minor in 47.8%. For the remaining 12.0%, data were missing. The proportions of recommended changes varied among disease sites (0.0%-7.0%). The disease sites with the most recommended changes to treatment plans after peer review and with the greatest potential for benefit were the esophagus (7.0%), uterus (6.7%), upper limb (6.3%), cervix and lower limb (both 6.0%), head and neck and bilateral lung (both 5.9%), right supraclavicular lymph nodes (5.7%), rectum (5.3%), and spine (5.0%). Although the heart is an organ at risk in left-sided breast treatment plans, the proportions of recommended changes did not significantly differ between the left breast treatment plans (3.0%, 95% confidence interval 2.0%-4.5%) and right breast treatment plans (2.4%, 95% confidence interval 1.5%-3.8%). The recommended changes were more frequently made when peer review occurred before radiation therapy (3.8%) than during treatment (1.4%-2.8%; P=.0048). The proportion of plans with recommended changes was not significantly associated with patient volume (P=.23), peer-review performance (P=.36), or center academic status (P=.75). Peer review of treatment plans directly affects the quality of care by identifying important clinical and planning changes. Provincial strategies are underway to optimize its conduct in radiation oncology. Copyright © 2016. Published by Elsevier Inc.

A Window to the World: Lessons Learned from NASA's Collaborative Metadata Curation Effort

NASA Astrophysics Data System (ADS)

Bugbee, K.; Dixon, V.; Baynes, K.; Shum, D.; le Roux, J.; Ramachandran, R.

2017-12-01

Well written descriptive metadata adds value to data by making data easier to discover as well as increases the use of data by providing the context or appropriateness of use. While many data centers acknowledge the importance of correct, consistent and complete metadata, allocating resources to curate existing metadata is often difficult. To lower resource costs, many data centers seek guidance on best practices for curating metadata but struggle to identify those recommendations. In order to assist data centers in curating metadata and to also develop best practices for creating and maintaining metadata, NASA has formed a collaborative effort to improve the Earth Observing System Data and Information System (EOSDIS) metadata in the Common Metadata Repository (CMR). This effort has taken significant steps in building consensus around metadata curation best practices. However, this effort has also revealed gaps in EOSDIS enterprise policies and procedures within the core metadata curation task. This presentation will explore the mechanisms used for building consensus on metadata curation, the gaps identified in policies and procedures, the lessons learned from collaborating with both the data centers and metadata curation teams, and the proposed next steps for the future.

Curative control of Scirtothrips dorsalis with biological insecticides, 2011

USDA-ARS?s Scientific Manuscript database

The objective of this study was 1) to evaluate the efficacy of the selected entomopathogens against a new invasive thrips pest, chilli thrips Scirtothrips dorsalis, in pepper, and 2) compare potential of entomopathogens with a chemical standard under greenhouse condition. The trial was conducted at ...

Implications of Pathologic Complete Response Beyond Mediastinal Nodal Clearance With High-Dose Neoadjuvant Chemoradiation Therapy in Locally Advanced, Non-Small Cell Lung Cancer.

PubMed

Vyfhuis, Melissa A L; Burrows, Whitney M; Bhooshan, Neha; Suntharalingam, Mohan; Donahue, James M; Feliciano, Josephine; Badiyan, Shahed; Nichols, Elizabeth M; Edelman, Martin J; Carr, Shamus R; Friedberg, Joseph; Henry, Gavin; Stewart, Shelby; Sachdeva, Ashutosh; Pickering, Edward M; Simone, Charles B; Feigenberg, Steven J; Mohindra, Pranshu

2018-06-01

To determine, in a retrospective analysis of a large cohort of stage III non-small cell lung cancer patients treated with curative intent at our institution, whether having a pathologic complete response (pCR) influenced overall survival (OS) or freedom from recurrence (FFR) in patients who underwent definitive (≥60 Gy) neoadjuvant doses of chemoradiation (CRT). At our institution, 355 patients with locally advanced non-small cell lung cancer were treated with curative intent with definitive CRT (January 2000-December 2013), of whom 111 underwent mediastinal reassessment for possible surgical resection. Ultimately 88 patients received trimodality therapy. Chi-squared analysis was used to compare categorical variables. The Kaplan-Meier analysis was performed to estimate OS and FFR, with Cox regression used to determine the absolute hazards. Using high-dose neoadjuvant CRT, we observed a mediastinal nodal clearance (MNC) rate of 74% (82 of 111 patients) and pCR rate of 48% (37 of 77 patients). With a median follow-up of 34.2 months (range, 3-177 months), MNC resulted in improved OS and FFR on both univariate (OS: hazard ratio [HR] 0.455, 95% confidence interval [CI] 0.272-0.763, P = .004; FFR: HR 0.426, 95% CI 0.250-0.726, P = .002) and multivariate analysis (OS: HR 0.460, 95% CI 0.239-0.699, P = .001; FFR: HR 0.455, 95% CI 0.266-0.778, P = .004). However, pCR did not independently impact OS (P = .918) or FFR (P = .474). Mediastinal nodal clearance after CRT continues to be predictive of improved survival for patients undergoing trimodality therapy. However, a pCR at both the primary and mediastinum did not further improve survival outcomes. Future therapies should focus on improving MNC to encourage more frequent use of surgery and might justify use of preoperative CRT over chemotherapy alone. Copyright © 2018 Elsevier Inc. All rights reserved.

Immunological considerations in in utero hematopoetic stem cell transplantation (IUHCT)

PubMed Central

Loewendorf, Andrea I.; Csete, Marie; Flake, Alan

2014-01-01

In utero hematopoietic stem cell transplantation (IUHCT) is an attractive approach and a potentially curative surgery for several congenital hematopoietic diseases. In practice, this application has succeeded only in the context of Severe Combined Immunodeficiency Disorders. Here, we review potential immunological hurdles for the long-term establishment of chimerism and discuss relevant models and findings from both postnatal hematopoietic stem cell transplantation and IUHCT. PMID:25610396

Curating NASA's future extraterrestrial sample collections: How do we achieve maximum proficiency?

NASA Astrophysics Data System (ADS)

McCubbin, Francis; Evans, Cynthia; Allton, Judith; Fries, Marc; Righter, Kevin; Zolensky, Michael; Zeigler, Ryan

2016-07-01

Introduction: The Astromaterials Acquisition and Curation Office (henceforth referred to herein as NASA Curation Office) at NASA Johnson Space Center (JSC) is responsible for curating all of NASA's extraterrestrial samples. Under the governing document, NASA Policy Directive (NPD) 7100.10E "Curation of Extraterrestrial Materials", JSC is charged with "The curation of all extraterrestrial material under NASA control, including future NASA missions." The Directive goes on to define Curation as including "…documentation, preservation, preparation, and distribution of samples for research, education, and public outreach." Here we describe some of the ongoing efforts to ensure that the future activities of the NASA Curation Office are working to-wards a state of maximum proficiency. Founding Principle: Curatorial activities began at JSC (Manned Spacecraft Center before 1973) as soon as design and construction planning for the Lunar Receiving Laboratory (LRL) began in 1964 [1], not with the return of the Apollo samples in 1969, nor with the completion of the LRL in 1967. This practice has since proven that curation begins as soon as a sample return mission is conceived, and this founding principle continues to return dividends today [e.g., 2]. The Next Decade: Part of the curation process is planning for the future, and we refer to these planning efforts as "advanced curation" [3]. Advanced Curation is tasked with developing procedures, technology, and data sets necessary for curating new types of collections as envisioned by NASA exploration goals. We are (and have been) planning for future curation, including cold curation, extended curation of ices and volatiles, curation of samples with special chemical considerations such as perchlorate-rich samples, curation of organically- and biologically-sensitive samples, and the use of minimally invasive analytical techniques (e.g., micro-CT, [4]) to characterize samples. These efforts will be useful for Mars Sample Return, Lunar South Pole-Aitken Basin Sample Return, and Comet Surface Sample Return, all of which were named in the NRC Planetary Science Decadal Survey 2013-2022. We are fully committed to pushing the boundaries of curation protocol as humans continue to push the boundaries of space exploration and sample return. However, to improve our ability to curate astromaterials collections of the future and to provide maximum protection to any returned samples, it is imperative that curation involvement commences at the time of mission conception. When curation involvement is at the ground floor of mission planning, it provides a mechanism by which the samples can be protected against project-level decisions that could undermine the scientific value of the re-turned samples. A notable example of one of the bene-fits of early curation involvement in mission planning is in the acquisition of contamination knowledge (CK). CK capture strategies are designed during the initial planning stages of a sample return mission, and they are to be implemented during all phases of the mission from assembly, test, and launch operations (ATLO), through cruise and mission operations, to the point of preliminary examination after Earth return. CK is captured by witness materials and coupons exposed to the contamination environment in the assembly labs and on the space craft during launch, cruise, and operations. These materials, along with any procedural blanks and returned flight-hardware, represent our CK capture for the returned samples and serves as a baseline from which analytical results can be vetted. Collection of CK is a critical part of being able to conduct and interpret data from organic geochemistry and biochemistry investigations of returned samples. The CK samples from a given mission are treated as part of the sample collection of that mission, hence they are part of the permanent archive that is maintained by the NASA curation Office. We are in the midst of collecting witness plates and coupons for the OSIRIS-REx mission, and we are in the planning stages for similar activities for the Mars 2020 rover mission, which is going to be the first step in a multi-stage campaign to return martian samples to Earth. Concluding Remarks: The return of every extraterrestrial sample is a scientific investment, and the CK samples and any procedural blanks represent an insurance policy against imperfections in the sample-collection and sample-return process. The curation facilities and personnel are the primary managers of that investment, and the scientific community, at large, is the beneficiary. The NASA Curation Office at JSC has the assigned task of maintaining the long-term integrity of all of NASA's astromaterials and ensuring that the samples are distributed for scientific study in a fair, timely, and responsible manner. It is only through this openness and global collaboration in the study of astromaterials that the return on our scientific investments can be maximized. For information on requesting samples and becoming part of the global study of astromaterials, please visit curator.jsc.nasa.gov References: [1] Mangus, S. & Larsen, W. (2004) NASA/CR-2004-208938, NASA, Washington, DC. [2] Allen, C. et al., (2011) Chemie Der Erde-Geochemistry, 71, 1-20. [3] McCubbin, F.M. et al., (2016) 47th LPSC #2668. [4] Zeigler, R.A. et al., (2014) 45th LPSC #2665.

ETHNOS: A versatile electronic tool for the development and curation of national genetic databases

PubMed Central

2010-01-01

National and ethnic mutation databases (NEMDBs) are emerging online repositories, recording extensive information about the described genetic heterogeneity of an ethnic group or population. These resources facilitate the provision of genetic services and provide a comprehensive list of genomic variations among different populations. As such, they enhance awareness of the various genetic disorders. Here, we describe the features of the ETHNOS software, a simple but versatile tool based on a flat-file database that is specifically designed for the development and curation of NEMDBs. ETHNOS is a freely available software which runs more than half of the NEMDBs currently available. Given the emerging need for NEMDB in genetic testing services and the fact that ETHNOS is the only off-the-shelf software available for NEMDB development and curation, its adoption in subsequent NEMDB development would contribute towards data content uniformity, unlike the diverse contents and quality of the available gene (locus)-specific databases. Finally, we allude to the potential applications of NEMDBs, not only as worldwide central allele frequency repositories, but also, and most importantly, as data warehouses of individual-level genomic data, hence allowing for a comprehensive ethnicity-specific documentation of genomic variation. PMID:20650823

ETHNOS : A versatile electronic tool for the development and curation of national genetic databases.

PubMed

van Baal, Sjozef; Zlotogora, Joël; Lagoumintzis, George; Gkantouna, Vassiliki; Tzimas, Ioannis; Poulas, Konstantinos; Tsakalidis, Athanassios; Romeo, Giovanni; Patrinos, George P

2010-06-01

National and ethnic mutation databases (NEMDBs) are emerging online repositories, recording extensive information about the described genetic heterogeneity of an ethnic group or population. These resources facilitate the provision of genetic services and provide a comprehensive list of genomic variations among different populations. As such, they enhance awareness of the various genetic disorders. Here, we describe the features of the ETHNOS software, a simple but versatile tool based on a flat-file database that is specifically designed for the development and curation of NEMDBs. ETHNOS is a freely available software which runs more than half of the NEMDBs currently available. Given the emerging need for NEMDB in genetic testing services and the fact that ETHNOS is the only off-the-shelf software available for NEMDB development and curation, its adoption in subsequent NEMDB development would contribute towards data content uniformity, unlike the diverse contents and quality of the available gene (locus)-specific databases. Finally, we allude to the potential applications of NEMDBs, not only as worldwide central allele frequency repositories, but also, and most importantly, as data warehouses of individual-level genomic data, hence allowing for a comprehensive ethnicity-specific documentation of genomic variation.

Curating blood: how students' and researchers' drawings bring potential phenomena to light

NASA Astrophysics Data System (ADS)

Hay, D. B.; Pitchford, S.

2016-11-01

This paper explores students and researchers drawings of white blood cell recruitment. The data combines interviews with exhibit of review-type academic images and analyses of student model-drawings. The analysis focuses on the material aspects of bio-scientific data-making and we use the literature of concrete bioscience modelling to differentiate the qualities of students model-making choices: novelty versus reproduction; completeness versus simplicity; and the achievement of similarity towards selected model targets. We show that while drawing on already published images, some third-year undergraduates are able to curate novel, and yet plausible causal channels in their graphic representations, implicating new phenomenal potentials as lead researchers do in their review-type academic publications. Our work links the virtues of drawing to learn to the disclosure of potential epistemic things, involving close attention to the contours of non-linguistic stuff and corresponding sensory perception of substance; space; time; shape and size; position; and force. The paper documents the authority and power students may achieve through making knowledge rather than repeating it. We show the ways in which drawing on the images elicited by others helps to develop physical, sensory, and sometimes affective relations towards the real and concrete world of scientific practice.

Elevated Blood Neutrophil-to-Lymphocyte Ratio: A Readily Available Biomarker Associated with Death due to Disease in High Risk Nonmetastatic Melanoma.

PubMed

Davis, Jeremy L; Langan, Russell C; Panageas, Katherine S; Zheng, Junting; Postow, Michael A; Brady, Mary S; Ariyan, Charlotte; Coit, Daniel G

2017-07-01

Elevated peripheral blood neutrophil-to-lymphocyte ratio (NLR) is associated with poor oncologic outcomes in patients with stage IV melanoma and other solid tumors, but its impact has not been characterized for patients with high-risk, nonmetastatic melanoma. Retrospective review of a melanoma database identified patients with high-risk melanoma who underwent operation with curative intent at a single institution. NLR was calculated from blood samples obtained within 2 weeks before operation. Multiple primary melanomas and concurrent hematologic or other metastatic malignancies were excluded. Cumulative incidence of death due to disease was estimated, and Gray's test was used to examine the effect of NLR on melanoma disease-specific death (DOD). Multivariable competing risks regression models assessed associated factors. Data on 1431 patients with high-risk, nonmetastatic melanoma were analyzed. Median follow-up for survivors was 4 years. High NLR (≥3 or as continuous variable) was associated with older age, male sex, thicker primaries, higher mitotic index, and more advanced nodal status. On multivariate analysis, high NLR (≥3 or as a continuous variable), older age, male sex, ulcerated primary, lymphovascular invasion, and positive nodal status were all independently associated with worse DOD. NLR is a readily available blood test that was independently associated with DOD in patients with high-risk, nonmetastatic melanoma. It is unclear whether high NLR is a passive indicator of poor prognosis or a potential therapeutic target. Further studies to evaluate the prognostic role of NLR to potentially identify those more likely to benefit from adjuvant immunotherapy may prove informative.

Postgraduate Students as OER Capacitators

ERIC Educational Resources Information Center

King, Thomas William

2017-01-01

A comprehensive theoretical, legal and practical basis for OER has been developed over the past fifteen years, supported by the expansion of open source curation platforms and the work of advocacy groups and international bodies. OER's potential has been sufficiently documented; the question remains how best to support, integrate and normalise OER…

Automated Structure Annotation and Curation for MassBank: Potential and Pitfalls

EPA Science Inventory

The European MassBank server (www.massbank.eu) was founded in 2012 by the NORMAN Network (www.norman-network.net) to provide open access to mass spectra of substances of environmental interest contributed by NORMAN members. The automated workflow RMassBank was developed as a part...

Art, Politics, and the Pedagogical Relation

ERIC Educational Resources Information Center

Ruitenberg, Claudia W.

2011-01-01

In recent years the French philosopher Jacques Ranciere has addressed the predicament of artists and curators who, in their eagerness to convey a critical message or engage their viewers in an emancipatory process, end up predetermining the outcomes of the experience, hence blocking its critical or emancipatory potential. In this essay I consider…

DOE Office of Scientific and Technical Information (OSTI.GOV)

Basinger, G.T.; McCullough, D.L.; McLaughlin, A.P.

Eleven patients with urologic cancer had an abnormal /sup 99m/Tc (technetium-99m) bone scan as the sole evidence of metastatic disease. Potentially curative therapy should not be withheld on the basis of a ''positive'' bone scan if such an area is accessible to selected bone biopsy and proves to be negative for tumor histologically.

Diabetes mellitus increases the risk of intrahepatic recurrence of hepatocellular carcinoma after surgical resection.

PubMed

Choi, Yunseon; Choi, YoungKil; Choi, Chang Soo; Lee, Yun-Han

2017-05-12

The relationship between cancer and metabolism has recently been receiving attention. We investigated the prognostic influence of type 2 diabetes mellitus in patients with hepatocellular carcinoma (HCC) treated with curative resection. The records of 58 patients who underwent curative resection for HCC pT1-2N0M0 between 2010 and 2014 were reviewed retrospectively. Fourteen patients (24.1%) had diabetes mellitus at diagnosis. Local control (LC) was defined as time to recurrence in the liver. The median follow-up was 23.3 months. Relapses occurred in 20 patients (34.5%) during the follow-up period; 17 of them developed intrahepatic recurrence, which was associated with diabetes mellitus (p = 0.013) and alpha fetoprotein (AFP) levels >500 ng/mL (p = 0.019). Overall relapses (n = 20) were related to T stage (p = 0.044), AFP level (p = 0.005), and diabetes (p = 0.044). The 3-year local control (intrahepatic control), disease-free survival, and overall survival rates were 56.7%, 50.5%, and 84.3%, respectively. LC was affected by diabetes mellitus (p = 0.046), Barcelona Clinic Liver Cancer staging (p<0.001), Milan criteria for transplantation (p = 0.041), serosal invasion (p = 0.032), and microvascular invasion (p = 0.043). Diabetes was also associated with reduced LC in the subgroup with hepatitis B-related HCC (n = 44, p = 0.028). Diabetes mellitus is correlated with intrahepatic HCC recurrence after surgery. Greater attention should be paid to managing patients with HCC and diabetes mellitus.

Metachronous solitary metastasis to the thyroid gland from squamous cell carcinoma of the lung: a case report and literature review.

PubMed

Gelsomino, Francesco; Lamberti, Giuseppe; Ambrosini, Valentina; Sperandi, Francesca; Agosti, Roberto; Morganti, Alessio G; Ardizzoni, Andrea

2017-11-15

Non-small cell lung cancer presents at an advanced stage at diagnosis in two-thirds of cases. The most frequent metastatic sites are the central nervous system, adrenal glands and bones. By contrast, the thyroid gland is an extremely rare site of dissemination. A 64-year-old Caucasian man previously treated with radiosurgery and brain metastasectomy followed by right middle lobectomy for a squamous cell lung carcinoma had a metachronous solitary metastasis to the thyroid gland, as confirmed by fine-needle aspiration cytology and open biopsy. He underwent curative radiotherapy, with an initial response. At 9 months' follow-up the tumor relapsed both in the thyroid and the lung. Review of the literature confirmed that thyroid metastasis from lung cancer is very uncommon in clinical practice. No data on the role of surgery or curative radiotherapy in thyroid metastasis are available because of the lack of prospective studies addressing the impact on survival of these treatment strategies either alone or in combination. In the case described here, radical treatment with radiotherapy allowed to obtain a modest benefit in terms of relapse-free survival. A diagnosis of metastasis to the thyroid gland should be suspected in patients who present a thyroid nodule or suggestive imaging findings when there is a history of malignancy, including lung cancer. Indeed, an early diagnosis allows to pursue radical treatment that, in selected patients, could lead to long-term survival.

The positive impact of surgeon specialization on survival for gastric cancer patients after surgery with curative intent.

PubMed

Liang, Yuexiang; Wu, Liangliang; Wang, Xiaona; Ding, Xuewei; Liang, Han

2015-10-01

Many studies have affirmed the survival benefit for cancer patients treated by specialized surgeons. A total of 967 patients with gastric cancer (GC) who underwent gastrectomy with curative intent in our center were enrolled. Patients were categorized into two groups based on surgeon specialization: the specialized group (SG) and nonspecialized group (NSG). To overcome bias due to the different distribution of covariates for the two groups, a one-to-one match was applied using propensity score analysis. After matching, prognosis and recurrence data were analyzed. After one-to-one matching, 261 patients in the SG and 261 patients in the NSG had the same characteristics excluding factors associated with surgery. In multivariate analysis for the whole study series, surgeon specialization was an independent prognostic factor for GC patients after surgery. Patients in the SG demonstrated a significantly higher 5-year overall survival than those in the NSG (50.7 vs. 37.2 %, p = 0.001). With the strata analysis, significant prognostic differences between the two groups were only observed in patients at stage IIIa-b or N1-2. The proportion of locoregional recurrence was greater in the NSG than in the SG. GC patients treated by specialized surgeons tended to have a better prognosis and lower locoregional recurrence rate. Surgeon specialization was an independent prognostic factor for GC patients after surgery. GC should be treated by specialized surgeons in large-volume centers.

Combination with CK19 Might Increase the Prognostic Power of Hep Par 1 in Hepatocellular Carcinoma after Curative Resection.

PubMed

Jin, Ye; Liang, Zhi-Yong; Zhou, Wei-Xun; Zhou, Li

2017-07-31

Hepatocyte Paraffin 1 (Hep Par 1) and cytokeratin 19 (CK19) were shown to be associated with post-surgical prognosis of hepatocellular carcinoma (HCC). However, further validation might be needed. Besides, their combined evaluation has not been reported. The present study was designed to address the issues. Expressions of Hep Par 1 and CK19 were detected using tissue microarray-based immunohistochemical staining in 79 patients with HCC underwent curative hepatectomy. Their associations with cliniopathologic variables, overall and recurrence-free survival were analyzed. Hep Par 1 was highly expressed in 61 patients (77.2%), whereas CK19 was positive in 8 patients (10.1%). Moreover, expressions of these two proteins were all associated with tumor-node-metastasis (TNM) stage and vascular invasion. It was found that high Hep Par 1 expression was univariately associated with good overall and recurrence-free survival, while CK19 was marginally prognostic. Also in univariate analyses, combination of the two markers more effectively predicted for long-term prognosis in HCC than Hep Par 1 did. However, neither Hep Par 1 nor Hep Par 1/CK19 was multivariately significant. Finally, Hep Par 1/CK19 combined with TNM stage might obtain more satisfactory outcome prediction, especially for overall survival. Combination of CK19 with Hep Par 1 might have higher prognostic power, which might be further improved by adding TNM stage, than Hep Par 1 alone, in resected HCC. Of course, subsequent confirmation is necessary.

How should the completeness and quality of curated nanomaterial data be evaluated?

NASA Astrophysics Data System (ADS)

Marchese Robinson, Richard L.; Lynch, Iseult; Peijnenburg, Willie; Rumble, John; Klaessig, Fred; Marquardt, Clarissa; Rauscher, Hubert; Puzyn, Tomasz; Purian, Ronit; Åberg, Christoffer; Karcher, Sandra; Vriens, Hanne; Hoet, Peter; Hoover, Mark D.; Hendren, Christine Ogilvie; Harper, Stacey L.

2016-05-01

Nanotechnology is of increasing significance. Curation of nanomaterial data into electronic databases offers opportunities to better understand and predict nanomaterials' behaviour. This supports innovation in, and regulation of, nanotechnology. It is commonly understood that curated data need to be sufficiently complete and of sufficient quality to serve their intended purpose. However, assessing data completeness and quality is non-trivial in general and is arguably especially difficult in the nanoscience area, given its highly multidisciplinary nature. The current article, part of the Nanomaterial Data Curation Initiative series, addresses how to assess the completeness and quality of (curated) nanomaterial data. In order to address this key challenge, a variety of related issues are discussed: the meaning and importance of data completeness and quality, existing approaches to their assessment and the key challenges associated with evaluating the completeness and quality of curated nanomaterial data. Considerations which are specific to the nanoscience area and lessons which can be learned from other relevant scientific disciplines are considered. Hence, the scope of this discussion ranges from physicochemical characterisation requirements for nanomaterials and interference of nanomaterials with nanotoxicology assays to broader issues such as minimum information checklists, toxicology data quality schemes and computational approaches that facilitate evaluation of the completeness and quality of (curated) data. This discussion is informed by a literature review and a survey of key nanomaterial data curation stakeholders. Finally, drawing upon this discussion, recommendations are presented concerning the central question: how should the completeness and quality of curated nanomaterial data be evaluated?Nanotechnology is of increasing significance. Curation of nanomaterial data into electronic databases offers opportunities to better understand and predict nanomaterials' behaviour. This supports innovation in, and regulation of, nanotechnology. It is commonly understood that curated data need to be sufficiently complete and of sufficient quality to serve their intended purpose. However, assessing data completeness and quality is non-trivial in general and is arguably especially difficult in the nanoscience area, given its highly multidisciplinary nature. The current article, part of the Nanomaterial Data Curation Initiative series, addresses how to assess the completeness and quality of (curated) nanomaterial data. In order to address this key challenge, a variety of related issues are discussed: the meaning and importance of data completeness and quality, existing approaches to their assessment and the key challenges associated with evaluating the completeness and quality of curated nanomaterial data. Considerations which are specific to the nanoscience area and lessons which can be learned from other relevant scientific disciplines are considered. Hence, the scope of this discussion ranges from physicochemical characterisation requirements for nanomaterials and interference of nanomaterials with nanotoxicology assays to broader issues such as minimum information checklists, toxicology data quality schemes and computational approaches that facilitate evaluation of the completeness and quality of (curated) data. This discussion is informed by a literature review and a survey of key nanomaterial data curation stakeholders. Finally, drawing upon this discussion, recommendations are presented concerning the central question: how should the completeness and quality of curated nanomaterial data be evaluated? Electronic supplementary information (ESI) available: (1) Detailed information regarding issues raised in the main text; (2) original survey responses. See DOI: 10.1039/c5nr08944a

Some ethical issues in feminist-oriented therapeutic groups for women.

PubMed

Lakin, M

1991-04-01

Review of the origins of group psychotherapy reveals concerns with social as well as with personal "psychopathology." Thus, group processes have been mobilized for curative or change purposes for ideological as well as individual therapeutic goals. Psychopolitical as well as personal change are the goals for some groups. The ethical problem stems from a persistent assumption that the group's processes are inherently benign and curative and beneficial to individual participants. A more sophisticated understanding takes into account their essential neutrality and their potential use (or abuse) for purposes of ideological persuasion that may or may not be personally therapeutic. As in other ethically implicated issues in the psychotherapies, the question becomes one of treatment versus exploitation, or therapy for the individual versus recruitment on behalf of a cause.

Directly e-mailing authors of newly published papers encourages community curation

PubMed Central

Bunt, Stephanie M.; Grumbling, Gary B.; Field, Helen I.; Marygold, Steven J.; Brown, Nicholas H.; Millburn, Gillian H.

2012-01-01

Much of the data within Model Organism Databases (MODs) comes from manual curation of the primary research literature. Given limited funding and an increasing density of published material, a significant challenge facing all MODs is how to efficiently and effectively prioritize the most relevant research papers for detailed curation. Here, we report recent improvements to the triaging process used by FlyBase. We describe an automated method to directly e-mail corresponding authors of new papers, requesting that they list the genes studied and indicate (‘flag’) the types of data described in the paper using an online tool. Based on the author-assigned flags, papers are then prioritized for detailed curation and channelled to appropriate curator teams for full data extraction. The overall response rate has been 44% and the flagging of data types by authors is sufficiently accurate for effective prioritization of papers. In summary, we have established a sustainable community curation program, with the result that FlyBase curators now spend less time triaging and can devote more effort to the specialized task of detailed data extraction. Database URL: http://flybase.org/ PMID:22554788

Radiation treatment in older patients: a framework for clinical decision making.

PubMed

Smith, Grace L; Smith, Benjamin D

2014-08-20

In older patients, radiation treatment plays a vital role in curative and palliative cancer therapy. Radiation treatment recommendations should be informed by a comprehensive, personalized risk-benefit assessment that evaluates treatment efficacy and toxicity. We review several clinical factors that distinctly affect efficacy and toxicity of radiation treatment in older patients. First, locoregional tumor behavior may be more indolent in older patients for some disease sites but more aggressive for other sites. Assessment of expected locoregional relapse risk informs the magnitude and timeframe of expected radiation treatment benefits. Second, assessment of the competing cancer versus noncancer mortality and morbidity risks contextualizes cancer treatment priorities holistically within patients' entire spectrum and time course of health needs. Third, assessment of functional reserve helps predict patients' acute treatment tolerance, differentiating those patients who are unlikely to benefit from treatment or who are at high risk for treatment complications. Potential radiation treatment options include immediate curative treatment, delayed curative treatment, and no treatment, with additional consideration given to altered radiation target, dose, or sequencing with chemotherapy and/or surgery. Finally, when cure is not feasible, palliative radiation therapy remains valuable for managing symptoms and achieving meaningful quality-of-life improvements. Our proposed decision-making framework integrates these factors to help radiation oncologists formulate strategic treatment recommendations within a multidisciplinary context. Future research is still needed to identify how advanced technologies can be judiciously applied in curative and palliative settings to enhance risk-benefit profiles of radiation treatment in older patients and more accurately quantify treatment efficacy in this group. © 2014 by American Society of Clinical Oncology.

The efficacy of adjuvant immunochemotherapy with OK-432 after curative resection of gastric cancer: an individual patient data meta-analysis of randomized controlled trials.

PubMed

Oba, Mari S; Teramukai, Satoshi; Ohashi, Yasuo; Ogawa, Kenji; Maehara, Yoshihiko; Sakamoto, Junichi

2016-04-01

OK-432 has been used as a cancer treatment for 40 years, and the immunostimulatory effects of OK-432 therapy have been intensely investigated in Japan. Recently, it has received attention as a possible booster for cancer vaccine treatments. Our previous meta-analysis based on summary measures revealed a significant improvement in the survival of patients with curatively resected gastric cancer. However, it is impossible to exclude the possibility of bias due to several prognostic factors. We collected individual data for patients with stage III or stage IV gastric cancer after curative resection from 14 trials that were identified in a previous meta-analysis. Immunochemotherapy with OK-432 was compared with treatment with standard chemotherapy on an intention-to-treat basis. The primary end point was overall survival. Stratified survival analyses were performed with the trial as the stratification factor. Subgroup analyses were also performed according to the potential prognostic factors, which included pathological factors, splenectomy, and delayed-type hypersensitivity. There were 796 and 726 patients in the OK-432 and control groups, respectively. The median overall survival was 42.6 months for the OK-432 group and 32.3 months for the control group. The overall hazard ratio was 0.88 (95 % confidence interval 0.77-1.00, p = 0.050). No factor showed a statistically significant interaction in the subgroup analyses. The results suggest that immunochemotherapy treatment with OK-432 could have a borderline significant effect for patients with stage III or stage IV gastric cancer after curative resection.

[A Case of Curatively Resected Locally Advanced Cancer of the Pancreatic Body Treated by Distal Pancreatectomy with En Bloc Celiac Axis Resection after Preoperative Intensive Treatment].

PubMed

Kim, Yongkook; Hoshino, Hiromitsu; Kakita, Naruyasu; Yamasaki, Masaru; Hosoda, Yohei; Nishino, Masaya; Okano, Miho; Kawada, Junji; Okuyama, Masaki; Tsujinaka, Toshimasa

2016-11-01

A 70-year-old woman with locally advanced pancreatic body cancer invading the celiac axis underwent 4 courses of preoperative chemotherapy consisting of gemcitabine(GEM)plus nab-paclitaxel(nab-PTX)on days 1, 8, and 15 every 4 weeks, followed by radiation therapy(CRT; 50.4Gy delivered in 28 daily fractions). The tumor size was greatly diminished and levels of all tumor markers were decreased. R0resection by distal pancreatectomy with en bloc celiac axis resection(DP-CAR)was performed. The histopathologic findings showed that the effect of CRT was grade 2b(Evans' classification), and the surgical margins were histologically clear. After the surgery, S-1 was administered continuously. The patient shows no signs of recurrence 1 year after surgery.

Astromaterials Curation Online Resources for Principal Investigators

NASA Technical Reports Server (NTRS)

Todd, Nancy S.; Zeigler, Ryan A.; Mueller, Lina

2017-01-01

The Astromaterials Acquisition and Curation office at NASA Johnson Space Center curates all of NASA's extraterrestrial samples, the most extensive set of astromaterials samples available to the research community worldwide. The office allocates 1500 individual samples to researchers and students each year and has served the planetary research community for 45+ years. The Astromaterials Curation office provides access to its sample data repository and digital resources to support the research needs of sample investigators and to aid in the selection and request of samples for scientific study. These resources can be found on the Astromaterials Acquisition and Curation website at https://curator.jsc.nasa.gov. To better serve our users, we have engaged in several activities to enhance the data available for astromaterials samples, to improve the accessibility and performance of the website, and to address user feedback. We havealso put plans in place for continuing improvements to our existing data products.

Gene regulation knowledge commons: community action takes care of DNA binding transcription factors

PubMed Central

Tripathi, Sushil; Vercruysse, Steven; Chawla, Konika; Christie, Karen R.; Blake, Judith A.; Huntley, Rachael P.; Orchard, Sandra; Hermjakob, Henning; Thommesen, Liv; Lægreid, Astrid; Kuiper, Martin

2016-01-01

A large gap remains between the amount of knowledge in scientific literature and the fraction that gets curated into standardized databases, despite many curation initiatives. Yet the availability of comprehensive knowledge in databases is crucial for exploiting existing background knowledge, both for designing follow-up experiments and for interpreting new experimental data. Structured resources also underpin the computational integration and modeling of regulatory pathways, which further aids our understanding of regulatory dynamics. We argue how cooperation between the scientific community and professional curators can increase the capacity of capturing precise knowledge from literature. We demonstrate this with a project in which we mobilize biological domain experts who curate large amounts of DNA binding transcription factors, and show that they, although new to the field of curation, can make valuable contributions by harvesting reported knowledge from scientific papers. Such community curation can enhance the scientific epistemic process. Database URL: http://www.tfcheckpoint.org PMID:27270715

Comprehensive annotation of secondary metabolite biosynthetic genes and gene clusters of Aspergillus nidulans, A. fumigatus, A. niger and A. oryzae

PubMed Central

2013-01-01

Background Secondary metabolite production, a hallmark of filamentous fungi, is an expanding area of research for the Aspergilli. These compounds are potent chemicals, ranging from deadly toxins to therapeutic antibiotics to potential anti-cancer drugs. The genome sequences for multiple Aspergilli have been determined, and provide a wealth of predictive information about secondary metabolite production. Sequence analysis and gene overexpression strategies have enabled the discovery of novel secondary metabolites and the genes involved in their biosynthesis. The Aspergillus Genome Database (AspGD) provides a central repository for gene annotation and protein information for Aspergillus species. These annotations include Gene Ontology (GO) terms, phenotype data, gene names and descriptions and they are crucial for interpreting both small- and large-scale data and for aiding in the design of new experiments that further Aspergillus research. Results We have manually curated Biological Process GO annotations for all genes in AspGD with recorded functions in secondary metabolite production, adding new GO terms that specifically describe each secondary metabolite. We then leveraged these new annotations to predict roles in secondary metabolism for genes lacking experimental characterization. As a starting point for manually annotating Aspergillus secondary metabolite gene clusters, we used antiSMASH (antibiotics and Secondary Metabolite Analysis SHell) and SMURF (Secondary Metabolite Unknown Regions Finder) algorithms to identify potential clusters in A. nidulans, A. fumigatus, A. niger and A. oryzae, which we subsequently refined through manual curation. Conclusions This set of 266 manually curated secondary metabolite gene clusters will facilitate the investigation of novel Aspergillus secondary metabolites. PMID:23617571

How should the completeness and quality of curated nanomaterial data be evaluated?†

PubMed Central

Marchese Robinson, Richard L.; Lynch, Iseult; Peijnenburg, Willie; Rumble, John; Klaessig, Fred; Marquardt, Clarissa; Rauscher, Hubert; Puzyn, Tomasz; Purian, Ronit; Åberg, Christoffer; Karcher, Sandra; Vriens, Hanne; Hoet, Peter; Hoover, Mark D.; Hendren, Christine Ogilvie; Harper, Stacey L.

2016-01-01

Nanotechnology is of increasing significance. Curation of nanomaterial data into electronic databases offers opportunities to better understand and predict nanomaterials’ behaviour. This supports innovation in, and regulation of, nanotechnology. It is commonly understood that curated data need to be sufficiently complete and of sufficient quality to serve their intended purpose. However, assessing data completeness and quality is non-trivial in general and is arguably especially difficult in the nanoscience area, given its highly multidisciplinary nature. The current article, part of the Nanomaterial Data Curation Initiative series, addresses how to assess the completeness and quality of (curated) nanomaterial data. In order to address this key challenge, a variety of related issues are discussed: the meaning and importance of data completeness and quality, existing approaches to their assessment and the key challenges associated with evaluating the completeness and quality of curated nanomaterial data. Considerations which are specific to the nanoscience area and lessons which can be learned from other relevant scientific disciplines are considered. Hence, the scope of this discussion ranges from physicochemical characterisation requirements for nanomaterials and interference of nanomaterials with nanotoxicology assays to broader issues such as minimum information checklists, toxicology data quality schemes and computational approaches that facilitate evaluation of the completeness and quality of (curated) data. This discussion is informed by a literature review and a survey of key nanomaterial data curation stakeholders. Finally, drawing upon this discussion, recommendations are presented concerning the central question: how should the completeness and quality of curated nanomaterial data be evaluated? PMID:27143028

Detection of lymph node metastases with ultrasmall superparamagnetic iron oxide (USPIO)-enhanced magnetic resonance imaging in oesophageal cancer: a feasibility study

PubMed Central

van der Jagt, E.J.; van Westreenen, H.L.; van Dullemen, H.M.; Kappert, P.; Groen, H.; Sietsma, J.; Oudkerk, M.; Plukker, J.Th.M.; van Dam, G.M.

2009-01-01

Abstract Aim: In this feasibility study we investigated whether magnetic resonance imaging (MRI) with ultrasmall superparamagnetic iron oxide (USPIO) can be used to identify regional and distant lymph nodes, including mediastinal and celiac lymph node metastases in patients with oesophageal cancer. Patients and methods: Ten patients with a potentially curative resectable cancer of the oesophagus were eligible for this study. All patients included in the study had positive lymph nodes on conventional staging (including endoscopic ultrasound, computed tomography and fluorodeoxyglucose-positron emission tomography). Nine patients underwent MRI + USPIO before surgery. Results were restricted to those patients who had both MRI + USPIO and histological examination. Results were compared with conventional staging and histopathologic findings. Results: One patient was excluded due to expired study time. Five out of 9 patients underwent an exploration; in 1 patient prior to surgery MRI + USPIO diagnosed liver metastases and in 3 patients an oesophageal resection was performed. USPIO uptake in mediastinal lymph nodes was seen in 6 out of 9 patients; in 3 patients non-malignant nodes were not visible. In total, 9 lymph node stations (of 6 patients) were separately analysed; 7 lymph node stations were assessed as positive (N1) on MRI+USPIO compared with 9 by conventional staging. According to histology findings, there was one false-positive and one false-negative result in MRI + USPIO. Also, conventional staging modalities had one false-positive and one false-negative result. MRI + USPIO had surplus value in one patient. Not all lymph node stations could be compared due to unforeseen explorations. No adverse effects occurred after USPIO infusion. Conclusion: MRI+USPIO identified the majority of mediastinal and celiac (suspect) lymph nodes in 9 patients with oesophageal cancer. MRI+USPIO could have an additional value in loco-regional staging; however, more supplementary research is needed. PMID:19414293

Solid Pseudopapillary Tumor of the Pancreas: A Single-center Experience and Review of the Literature

PubMed Central

ANTONIOU, A. EFSTATHIOS; DAMASKOS, CHRISTOS; GARMPIS, NIKOLAOS; SALAKOS, CHRISTOS; MARGONIS, GIORGOS-ANTONIOS; KONTZOGLOU, KONSTANTINOS; LAHANIS, STEFANOS; SPARTALIS, ELEFTHERIOS; PATSOURAS, DIMITRIOS; KYKALOS, STYLIANOS; GARMPI, ANNA; ANDREATOS, NIKOLAOS; PAWLIK, M. TIMOTHY; KOURAKLIS, GREGORY

2017-01-01

Background: Solid pseudopapillary tumors (SPTs) of the pancreas are a rare occurrence, not exceeding 1-2% of all exocrine pancreatic tumors. SPT was first described in 1959 as “papillary tumor of the pancreas, benign or malignant” and affects mainly young women, in their second or third decade of age. These tumors are of low malignant potential, unclear pathogenesis, grow gradually and become considerably large before causing symptoms. A typical clinical presentation is often described by affected patients and, in some cases, an SPT is an incidental finding during the time the patient undergoes medical imaging studies for other health issues. SPT is frequently located at the head or tail of the pancreas. Metastases are rare but, when present, affect predominantly the liver. Patients and Methods: We report a series of five SPT cases in female patients 13-47 years old, presenting with almost identical symptoms of upper abdominal discomfort and non-tender palpable mass. Two out of five patients also reported vomiting, nausea and poor appetite as co-existing non-diagnostic symptoms. Only one patient presented without any symptoms. Tumor location and dimensions varied. One patient underwent a pancreatoduodenectomy (Whipple’s procedure), while the remaining patients underwent distal pancreatectomy with concomitant splenectomy. Results: Perioperative morbidity and mortality was zero. All five patients are disease-free at a follow-up from 3 months to 13 years. Histopathology reports supported the diagnosis of SPT and no metastatic disease was present in any of the patients. Conclusion: The overall prognosis of SPT of the pancreas is excellent due to its favorable biological features, even in the presence of distal metastasis. Although surgical resection is often curative, a close follow-up is advised in order to diagnose a possible local recurrence or distal metastasis and choose the proper therapeutic option for the patients. PMID:28652415

Solid Pseudopapillary Tumor of the Pancreas: A Single-center Experience and Review of the Literature.

PubMed

Antoniou, Efstathios A; Damaskos, Christos; Garmpis, Nikolaos; Salakos, Christos; Margonis, Giorgos-Antonios; Kontzoglou, Konstantinos; Lahanis, Stefanos; Spartalis, Eleftherios; Patsouras, Dimitrios; Kykalos, Stylianos; Garmpi, Anna; Andreatos, Nikolaos; Pawlik, Timothy M; Kouraklis, Gregory

2017-01-01

Solid pseudopapillary tumors (SPTs) of the pancreas are a rare occurrence, not exceeding 1-2% of all exocrine pancreatic tumors. SPT was first described in 1959 as "papillary tumor of the pancreas, benign or malignant" and affects mainly young women, in their second or third decade of age. These tumors are of low malignant potential, unclear pathogenesis, grow gradually and become considerably large before causing symptoms. A typical clinical presentation is often described by affected patients and, in some cases, an SPT is an incidental finding during the time the patient undergoes medical imaging studies for other health issues. SPT is frequently located at the head or tail of the pancreas. Metastases are rare but, when present, affect predominantly the liver. We report a series of five SPT cases in female patients 13-47 years old, presenting with almost identical symptoms of upper abdominal discomfort and non-tender palpable mass. Two out of five patients also reported vomiting, nausea and poor appetite as co-existing non-diagnostic symptoms. Only one patient presented without any symptoms. Tumor location and dimensions varied. One patient underwent a pancreatoduodenectomy (Whipple's procedure), while the remaining patients underwent distal pancreatectomy with concomitant splenectomy. Perioperative morbidity and mortality was zero. All five patients are disease-free at a follow-up from 3 months to 13 years. Histopathology reports supported the diagnosis of SPT and no metastatic disease was present in any of the patients. The overall prognosis of SPT of the pancreas is excellent due to its favorable biological features, even in the presence of distal metastasis. Although surgical resection is often curative, a close follow-up is advised in order to diagnose a possible local recurrence or distal metastasis and choose the proper therapeutic option for the patients. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

Dynamic Risk Stratification of Patient Long-Term Outcome After Pulmonary Endarterectomy: Results From the United Kingdom National Cohort

PubMed Central

Cannon, John E.; Su, Li; Kiely, David G.; Page, Kathleen; Toshner, Mark; Swietlik, Emilia; Treacy, Carmen; Ponnaberanam, Anie; Condliffe, Robin; Sheares, Karen; Taboada, Dolores; Dunning, John; Tsui, Steven; Ng, Choo; Gopalan, Deepa; Screaton, Nicholas; Elliot, Charlie; Gibbs, Simon; Howard, Luke; Corris, Paul; Lordan, James; Johnson, Martin; Peacock, Andrew; MacKenzie-Ross, Robert; Schreiber, Benji; Coghlan, Gerry; Dimopoulos, Kostas; Wort, Stephen J.; Gaine, Sean; Moledina, Shahin; Jenkins, David P.; Pepke-Zaba, Joanna

2018-01-01

Background Chronic thromboembolic pulmonary hypertension results from incomplete resolution of pulmonary emboli. Pulmonary endarterectomy (PEA) is potentially curative, but residual pulmonary hypertension following surgery is common and its impact on long-term outcome is poorly understood. We wanted to identify factors correlated with poor long-term outcome after surgery and specifically define clinically relevant residual pulmonary hypertension post-PEA. Methods and Results Eight hundred eighty consecutive patients (mean age, 57 years) underwent PEA for chronic thromboembolic pulmonary hypertension. Patients routinely underwent detailed reassessment with right heart catheterization and noninvasive testing at 3 to 6 months and annually thereafter with discharge if they were clinically stable at 3 to 5 years and did not require pulmonary vasodilator therapy. Cox regressions were used for survival (time-to-event) analyses. Overall survival was 86%, 84%, 79%, and 72% at 1, 3, 5, and 10 years for the whole cohort and 91% and 90% at 1 and 3 years for the recent half of the cohort. The majority of patient deaths after the perioperative period were not attributable to right ventricular failure (chronic thromboembolic pulmonary hypertension). At reassessment, a mean pulmonary artery pressure of ≥30 mm Hg correlated with the initiation of pulmonary vasodilator therapy post-PEA. A mean pulmonary artery pressure of ≥38 mm Hg and pulmonary vascular resistance ≥425 dynes·s–1·cm–5 at reassessment correlated with worse long-term survival. Conclusions Our data confirm excellent long-term survival and maintenance of good functional status post-PEA. Hemodynamic assessment 3 to 6 months and 12 months post-PEA allows stratification of patients at higher risk of dying of chronic thromboembolic pulmonary hypertension and identifies a level of residual pulmonary hypertension that may guide the long-term management of patients postsurgery. PMID:27052413

Single-stage anterior high sacrectomy for locally recurrent rectal cancer.

PubMed

Fawaz, Khaled; Khaled, Fawaz; Smith, Myles J; Moises, Cukier; Smith, Andrew J; Yee, Albert J M

2014-03-01

A review of prospectively collected data on a consecutive series of patients undergoing single-stage anterior high sacrectomy for locally recurrent rectal carcinoma (LRRC). To determine the clinical outcome of patients who underwent anterior high sacrectomy for LRRC. High sacrectomy for oncological resection remains technically challenging. Surgery has the potential to achieve cure in carefully selected patients. Complete (R0) tumor excision in LRRC may require sacrectomy. High sacral resections (S3 and above) typically require a combined anterior/supine and posterior/prone procedure. We investigated our experience performing single-stage anterior high sacrectomy for LRRC. A consecutive series of patients with LRRC without systemic metastases who underwent resection with curative intent requiring high sacrectomy were identified. A review of a prospectively maintained colorectal and spine cancer database data was performed. An oblique dome high sacral osteotomy was performed during a single-stage anterior procedure. Outcome measures included surgical resection margin status, hospital length of stay, postoperative complications, physical functioning status, and overall survival. Nineteen consecutive patients were treated between 2002 and 2011. High sacrectomy was performed at sacral level S1-S2 in 4 patients, S2-S3 in 9 patients, and through S3 in 6 patients. An R0 resection margin was achieved histologically in all 19 cases. There was 1 early (<30 d) postoperative death (1/19, 5%). At median follow-up of 38 months, 13 patients had no evidence of residual disease, 1 was alive with disease, and 4 had died of disease. Morbidities occurred in 15 of the 19 patients (79%). Although high sacrectomy may require a combined anterior and posterior surgical approach, our series demonstrates the feasibility of performing single-stage anterior high sacrectomy in LRRC, with acceptable risks and outcomes compared with the literature. The procedure described by us for LRRC lessens the need for a simultaneous or staged prone posterior resection, with favorable R0 tumor resections, patient survival, and clinical outcomes. N/A.

Functional Outcomes After Rectal Resection for Deep Infiltrating Pelvic Endometriosis: Long-term Results.

PubMed

Erdem, Suna; Imboden, Sara; Papadia, Andrea; Lanz, Susanne; Mueller, Michael D; Gloor, Beat; Worni, Mathias

2018-06-01

Curative management of deep infiltrating endometriosis requires complete removal of all endometriotic implants. Surgical approach to rectal involvement has become a topic of debate given potential postoperative bowel dysfunction and complications. This study aims to assess long-term postoperative evacuation and incontinence outcomes after laparoscopic segmental rectal resection for deep infiltrating endometriosis involving the rectal wall. This is a retrospective study of prospectively collected data. This single-center study was conducted at the University Hospital of Bern, Switzerland. Patients with deep infiltrating endometriosis involving the rectum undergoing rectal resection from June 2002 to May 2011 with at least 24 months follow-up were included. Aside from endometriosis-related symptoms, detailed symptoms on evacuation (points: 0 (best) to 21 (worst)) and incontinence (0-24) were evaluated by using a standardized questionnaire before and at least 24 months after surgery. Of 66 women who underwent rectal resection, 51 were available for analyses with a median follow-up period of 86 months (range: 26-168). Forty-eight patients (94%) underwent laparoscopic resection (4% converted, 2% primary open), with end-to-end anastomosis in 41 patients (82%). Two patients (4%) had an anastomotic insufficiency; 1 case was complicated by rectovaginal fistula. Dysmenorrhea, nonmenstrual pain, and dyspareunia substantially improved (p < 0.001 for all comparisons). Overall evacuation score increased from a median of 0 (range: 0-11) to 2 points (0-15), p = 0.002. Overall incontinence also increased from 0 (range: 0-9) to 2 points (0-9), p = 0.003. This study was limited by its retrospective nature and moderate number of patients. Laparoscopic segmental rectal resection for the treatment of deep infiltrating endometriosis including the rectal wall is associated with good results in endometriotic-related symptoms, although patients should be informed about possible postoperative impairments in evacuation and incontinence. However, its clinical impact does not outweigh the benefit that can be achieved through this approach. See Video Abstract at http://links.lww.com/DCR/A547.

MET network in PubMed: a text-mined network visualization and curation system.

PubMed

Dai, Hong-Jie; Su, Chu-Hsien; Lai, Po-Ting; Huang, Ming-Siang; Jonnagaddala, Jitendra; Rose Jue, Toni; Rao, Shruti; Chou, Hui-Jou; Milacic, Marija; Singh, Onkar; Syed-Abdul, Shabbir; Hsu, Wen-Lian

2016-01-01

Metastasis is the dissemination of a cancer/tumor from one organ to another, and it is the most dangerous stage during cancer progression, causing more than 90% of cancer deaths. Improving the understanding of the complicated cellular mechanisms underlying metastasis requires investigations of the signaling pathways. To this end, we developed a METastasis (MET) network visualization and curation tool to assist metastasis researchers retrieve network information of interest while browsing through the large volume of studies in PubMed. MET can recognize relations among genes, cancers, tissues and organs of metastasis mentioned in the literature through text-mining techniques, and then produce a visualization of all mined relations in a metastasis network. To facilitate the curation process, MET is developed as a browser extension that allows curators to review and edit concepts and relations related to metastasis directly in PubMed. PubMed users can also view the metastatic networks integrated from the large collection of research papers directly through MET. For the BioCreative 2015 interactive track (IAT), a curation task was proposed to curate metastatic networks among PubMed abstracts. Six curators participated in the proposed task and a post-IAT task, curating 963 unique metastatic relations from 174 PubMed abstracts using MET.Database URL: http://btm.tmu.edu.tw/metastasisway. © The Author(s) 2016. Published by Oxford University Press.

Failure Rates and Patterns of Recurrence in Patients With Resected N1 Non-Small-Cell Lung Cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Varlotto, John M., E-mail: jvarlotto@hmc.psu.edu; Medford-Davis, Laura Nyshel; Recht, Abram

2011-10-01

Purpose: To examine the local and distant recurrence rates and patterns of failure in patients undergoing potentially curative resection of N1 non-small-cell lung cancer. Methods and Materials: The study included 60 consecutive unirradiated patients treated from 2000 to 2006. Median follow-up was 30 months. Failure rates were calculated by the Kaplan-Meier method. A univariate Cox proportional hazard model was used to assess factors associated with recurrence. Results: Local and distant failure rates (as the first site of failure) at 2, 3, and 5 years were 33%, 33%, and 46%; and 26%, 26%, and 32%, respectively. The most common site ofmore » local failure was in the mediastinum; 12 of 18 local recurrences would have been included within proposed postoperative radiotherapy fields. Patients who received chemotherapy were found to be at increased risk of local failure, whereas those who underwent pneumonectomy or who had more positive nodes had significantly increased risks of distant failure. Conclusions: Patients with resected non-small-cell lung cancer who have N1 disease are at substantial risk of local recurrence as the first site of relapse, which is greater than the risk of distant failure. The role of postoperative radiotherapy in such patients should be revisited in the era of adjuvant chemotherapy.« less

High incidence of chronic graft-versus-host disease after myeloablative allogeneic stem cell transplantation for chronic lymphocytic leukemia in Sweden: graft-versus-leukemia effect protects against relapse.

PubMed

Machaczka, Maciej; Johansson, Jan-Erik; Remberger, Mats; Hallböök, Helene; Lazarevic, Vladimir Lj; Wahlin, Björn Engelbrekt; Omar, Hamdy; Wahlin, Anders; Juliusson, Gunnar; Kimby, Eva; Hägglund, Hans

2013-12-01

Allogeneic hematopoietic stem cell transplantation (allo-SCT) is a potentially curative treatment option for eligible patients with chronic lymphocytic leukemia (CLL). However, it is known that cure of CLL is only possible if a graft-versus-leukemia effect is present. Between 1994 and 2007, 48 adults underwent allo-SCT for poor-risk CLL in Sweden. Of these, ten (21%) patients aged 24-53 years (median: 46 years) received myeloablative conditioning (MAC), based on TBI and cyclophosphamide. All MAC patients had refractory, poorly controlled CLL before allo-SCT (partial remission in 9/10 patients and progressive disease in one). The cumulative incidence of acute graft-versus-host disease (GVHD) grades II-IV was 30%. Nine patients developed chronic GVHD; extensive in four. Rates of nonrelapse mortality at 1, 3 and 10 years were 0, 10 and 20%, respectively. Two patients relapsed 36 and 53 months after transplantation. Six patients were still alive after a median follow-up time of 11.5 years (range 5.9-13.7). The probabilities of relapse-free and overall survival from 1, 3 and 5 years after transplantation were 100, 90 and 70%, and 100, 90 and 80%, respectively. Nevertheless, our analysis of long-term outcome after MAC allo-SCT for CLL suggests that younger patients with poorly controlled CLL may benefit from MAC allo-SCT.

VEGF and Ki-67 Overexpression in Predicting Poor Overall Survival in Adenoid Cystic Carcinoma.

PubMed

Park, Seongyeol; Nam, Soo Jeong; Keam, Bhumsuk; Kim, Tae Min; Jeon, Yoon Kyung; Lee, Se-Hoon; Hah, J Hun; Kwon, Tack-Kyun; Kim, Dong-Wan; Sung, Myung-Whun; Heo, Dae Seog; Bang, Yung-Jue

2016-04-01

The purpose of this study was to evaluate potential prognostic factors in patients with adenoid cystic carcinoma (ACC). A total of 68 patients who underwent curative surgery and had available tissue were enrolled in this study. Their medical records and pathologic slides were reviewed and immunohistochemistry for basic fibroblast growth factor, fibroblast growth factor receptor (FGFR) 2, FGFR3, c-kit, Myb proto-oncogene protein, platelet-derived growth factor receptor beta, vascular endothelial growth factor (VEGF), and Ki-67 was performed. Univariate and multivariate analysis was performed for determination of disease-free survival (DFS) and overall survival (OS). In univariate analyses, primary site of nasal cavity and paranasal sinus (p=0.022) and Ki-67 expression of more than 7% (p=0.001) were statistically significant factors for poor DFS. Regarding OS, perineural invasion (p=0.032), high expression of VEGF (p=0.033), and high expression of Ki-67 (p=0.007) were poor prognostic factors. In multivariate analyses, primary site of nasal cavity and paranasal sinus (p=0.028) and high expression of Ki-67 (p=0.004) were independent risk factors for poor DFS, and high expression of VEGF (p=0.011) and Ki-67 (p=0.011) showed independent association with poor OS. High expression of VEGF and Ki-67 were independent poor prognostic factors for OS in ACC.

An automated procedure to identify biomedical articles that contain cancer-associated gene variants.

PubMed

McDonald, Ryan; Scott Winters, R; Ankuda, Claire K; Murphy, Joan A; Rogers, Amy E; Pereira, Fernando; Greenblatt, Marc S; White, Peter S

2006-09-01

The proliferation of biomedical literature makes it increasingly difficult for researchers to find and manage relevant information. However, identifying research articles containing mutation data, a requisite first step in integrating large and complex mutation data sets, is currently tedious, time-consuming and imprecise. More effective mechanisms for identifying articles containing mutation information would be beneficial both for the curation of mutation databases and for individual researchers. We developed an automated method that uses information extraction, classifier, and relevance ranking techniques to determine the likelihood of MEDLINE abstracts containing information regarding genomic variation data suitable for inclusion in mutation databases. We targeted the CDKN2A (p16) gene and the procedure for document identification currently used by CDKN2A Database curators as a measure of feasibility. A set of abstracts was manually identified from a MEDLINE search as potentially containing specific CDKN2A mutation events. A subset of these abstracts was used as a training set for a maximum entropy classifier to identify text features distinguishing "relevant" from "not relevant" abstracts. Each document was represented as a set of indicative word, word pair, and entity tagger-derived genomic variation features. When applied to a test set of 200 candidate abstracts, the classifier predicted 88 articles as being relevant; of these, 29 of 32 manuscripts in which manual curation found CDKN2A sequence variants were positively predicted. Thus, the set of potentially useful articles that a manual curator would have to review was reduced by 56%, maintaining 91% recall (sensitivity) and more than doubling precision (positive predictive value). Subsequent expansion of the training set to 494 articles yielded similar precision and recall rates, and comparison of the original and expanded trials demonstrated that the average precision improved with the larger data set. Our results show that automated systems can effectively identify article subsets relevant to a given task and may prove to be powerful tools for the broader research community. This procedure can be readily adapted to any or all genes, organisms, or sets of documents. Published 2006 Wiley-Liss, Inc.

Linking data repositories - an illustration of agile data curation principles through robust documentation and multiple application programming interfaces

NASA Astrophysics Data System (ADS)

Benedict, K. K.; Servilla, M. S.; Vanderbilt, K.; Wheeler, J.

2015-12-01

The growing volume, variety and velocity of production of Earth science data magnifies the impact of inefficiencies in data acquisition, processing, analysis, and sharing workflows, potentially to the point of impairing the ability of researchers to accomplish their desired scientific objectives. The adaptation of agile software development principles (http://agilemanifesto.org/principles.html) to data curation processes has significant potential to lower barriers to effective scientific data discovery and reuse - barriers that otherwise may force the development of new data to replace existing but unusable data, or require substantial effort to make data usable in new research contexts. This paper outlines a data curation process that was developed at the University of New Mexico that provides a cross-walk of data and associated documentation between the data archive developed by the Long Term Ecological Research (LTER) Network Office (PASTA - http://lno.lternet.edu/content/network-information-system) and UNM's institutional repository (LoboVault - http://repository.unm.edu). The developed automated workflow enables the replication of versioned data objects and their associated standards-based metadata between the LTER system and LoboVault - providing long-term preservation for those data/metadata packages within LoboVault while maintaining the value-added services that the PASTA platform provides. The relative ease with which this workflow was developed is a product of the capabilities independently developed on both platforms - including the simplicity of providing a well-documented application programming interface (API) for each platform enabling scripted interaction and the use of well-established documentation standards (EML in the case of PASTA, Dublin Core in the case of LoboVault) by both systems. These system characteristics, when combined with an iterative process of interaction between the Data Curation Librarian (on the LoboVault side of the process), the Sevilleta LTER Information Manager and the LTER Network Information System developer, yielded a rapid and relatively streamlined process for targeted replication of data and metadata between the two systems - increasing the discoverability and usability of the LTER data assets.

Favorable overall survival in stage III melanoma patients after adjuvant dendritic cell vaccination

PubMed Central

Bol, Kalijn F; Aarntzen, Erik H J G; Hout, Florentien E M in 't; Schreibelt, Gerty; Creemers, Jeroen H A; Lesterhuis, W Joost; Gerritsen, Winald R; Grunhagen, Dirk J; Verhoef, Cornelis; Punt, Cornelis J A; Bonenkamp, Johannes J; de Wilt, Johannes H W; Figdor, Carl G; de Vries, I Jolanda M

2016-01-01

Melanoma patients with regional metastatic disease are at high risk for recurrence and metastatic disease, despite radical lymph node dissection (RLND). We investigated the immunologic response and clinical outcome to adjuvant dendritic cell (DC) vaccination in melanoma patients with regional metastatic disease who underwent RLND with curative intent. In this retrospective study, 78 melanoma patients with regional lymph node metastasis who underwent RLND received autologous DCs loaded with gp100 and tyrosinase and were analyzed for functional tumor-specific T cell responses in skin-test infiltrating lymphocytes. The study shows that adjuvant DC vaccination in melanoma patients with regional lymph node metastasis is safe and induced functional tumor-specific T cell responses in 71% of the patients. The presence of functional tumor-specific T cells was correlated with a better 2-year overall survival (OS) rate. OS was significantly higher after adjuvant DC vaccination compared to 209 matched controls who underwent RLND without adjuvant DC vaccination, 63.6 mo vs. 31.0 mo (p = 0.018; hazard ratio 0.59; 95%CI 0.42–0.84). Five-year survival rate increased from 38% to 53% (p < 0.01). In summary, in melanoma patients with regional metastatic disease, who are at high risk for recurrence and metastatic disease after RLND, adjuvant DC vaccination is well tolerated. It induced functional tumor-specific immune responses in the majority of patients and these were related to clinical outcome. OS was significantly higher compared to matched controls. A randomized clinical trial is needed to prospectively validate the efficacy of DC vaccination in the adjuvant setting. PMID:26942068

Healthy life expectancy of oral squamous cell carcinoma patients aged 75years and older.

PubMed

Yamada, Shin-Ichi; Kurita, Hiroshi; Tomioka, Takahiro; Ohta, Ryousuke; Yoshimura, Nobuhiko; Nishimaki, Fumihiro; Koyama, Yoshihito; Kondo, Eiji; Kamata, Takahiro

2017-01-01

Healthy life expectancy, an extension of the concept of life expectancy, is a summary measure of population health that takes into account the mortality and morbidity of a population. The aim of the present study was to retrospectively analyze the self-reliance survival times of oral squamous cell carcinoma (OSCC) patients. One hundred and twelve patients aged 75years or older with primary OSCC were included and examined at Shinshu University Hospital. To investigate healthy life expectancy, OSCC patients older than 75years were divided into 3 groups: 75-79, 80-84, and older than 85years. The Kaplan-Meier method was used to estimate the median times of healthy life expectancy. The Log-rank test was used to test significant differences between actual curves. The median self-reliance survival times of patients aged 75-79, 80-84, and older than 85years were 5.7, 1.6, and 1.4years, respectively. Most patients with early stage cancers underwent curative treatments and showed a health expectancy of more than 5years. In patients with advanced cancers, health expectancy was poor (less than one year), except among patients aged 75-79years who underwent standard treatments. It seems that in patients with advanced cancers, health expectancy was poor (less than 1year), except among patients aged 75-79years who underwent standard treatments. In elderly patients, healthy life expectancy (self-reliance survival time) may be one of the measures of patient prognosis as well as overall survival times. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Astromaterials X-Ray Computed Tomography Laboratory at Johnson Space Center

NASA Astrophysics Data System (ADS)

Zeigler, R. A.; Blumenfeld, E. H.; Srinivasan, P.; McCubbin, F. M.; Evans, C. A.

2018-04-01

The Astromaterials Curation Office has recently begun incorporating X-ray CT data into the curation processes for lunar and meteorite samples, and long-term curation of that data and serving it to the public represent significant technical challenges.

Elective bladder-sparing treatment for muscle invasive bladder cancer.

PubMed

Lendínez-Cano, G; Rico-López, J; Moreno, S; Fernández Parra, E; González-Almeida, C; Camacho Martínez, E

2014-01-01

Radical cystectomy is the standard treatment for localised muscle invasive bladder cancer (MIBC). We offer a bladder-sparing treatment with TURB +/- Chemotherapy+Radiotherapy to selected patients as an alternative. We analyze, retrospectively, 30 patients diagnosed with MIBC from March 1991 to October 2010. The mean age was 62.7 years (51-74). All patients were candidates for a curative treatment, and underwent strict selection criteria: T2 stage, primary tumor, solitary lesion smaller than 5cm with a macroscopic disease-free status after TURB, negative random biopsy without hydronephrosis. Staging CT evaluation was normal. Restaging TURB or tumor bed biopsy showed a disease-free status or microscopic muscle invasion. 14 patients underwent TURB alone, 13 TURB+Chemotherapy and 3 TURB+Chemotherapy+Radiotherapy. The mean follow up was 88.7 months (19-220). 14 patients remained disease free (46.6%), 10 had recurrent non-muscle invasive bladder cancer (33%). 81.3% complete clinical response. 71% bladder preserved at 5-years. Overall, 5-years survival rate was 79% and 85% cancer-specific survival rate. Although radical cystectomy is the standard treatment for localised MIBC, in strictly selected cases, bladder-sparing treatment offers an alternative with good long term results. Copyright © 2013 AEU. Published by Elsevier Espana. All rights reserved.

Emergency pancreatoduodenectomy (whipple procedure) for massive upper gastrointestinal bleeding caused by a diffuse B-cell lymphoma of the duodenum: report of a case.

PubMed

Stratigos, Panagiotis; Kouskos, Efstratios; Kouroglou, Maria; Chrisafis, Ioannis; Fois, Lucia; Mavrogiorgis, Anastasios; Axiotis, Efthimios; Zamtrakis, Sotirios

2007-01-01

We herein report a rare case of a massive upper gastrointestinal (GI) bleeding, caused by high-grade diffuse B-cell lymphoma of the duodenum, secondary to immunoproliferative small intestinal disease (IPSID) and treated with an emergency partial pancreatoduodenectomy. A 42-year-old man was admitted to our hospital because of hematemesis. Upper GI endoscopy was unrevealing because of the copious bleeding. Initially, the patient underwent conservative treatment, thus resulting in the temporary cessation of the bleeding. Later, the hemorrhage massively relapsed. An urgent abdominal ultrasound raised the suspicion of a large, possibly bleeding, neoplasm of the duodenum, which was finally confirmed by abdominal computed tomography. The patient underwent an emergency laparotomy, during which a partial pancreatoduodenectomy was performed (Whipple procedure). Histologically, the tumor was a high-grade B-cell lymphoma of the duodenum. The nearby small intestinal mucosa was suggestive of IPSID. A massive upper GI hemorrhage from a high-grade B-cell non-Hodgkin lymphoma of the duodenum, which develops secondary to IPSID, is a very rare clinical demonstration of this disease. Our case is one of the few reports in the English literature, for which the Whipple procedure has been performed as a curative treatment.

A pilot study about the oncologic safety of colonic self-expandable metal stents (SEMS) in obstructive colon cancer: is occlusion always better than "silent" perforation?

PubMed

Zanghì, A; Piccolo, G; Cavallaro, A; Pulvirenti, E; Lo Menzo, E; Cardì, F; Di Vita, M; Cappellani, A

2016-12-01

To evaluate the oncologic safety of colonic self-expandable metal stents (SEMS) in obstructive colon cancer. We retrospectively reviewed all the patients who were treated with endoscopic placement of a self-expandable metallic stent (SEMS) at our institution. A total of 26 patients were identified during the study period, of which 24 patients (92.30%) were treated with SEMS as a bridge-to-surgery and 2 (7.69%) as palliation. In 22 cases (80.76%), the stenosis was localized to the left side. Clinical success with resolution of bowel obstructions was achieved in 22 (84.61%) patients within a short period of time. Among patients treated successfully with SEMS insertion as bridge to surgery (n = 22), 20 (90.9%) underwent one-stage surgery with primary anastomosis while 2 patients (9.09%) underwent colostomy due to intraoperative evidence of a covered perforation by cancer tissue in the pelvis. Patients with subclinical perforation developed an early peritoneal carcinomatosis, 10 patients treated with curative intent subsequently developed liver metastasis after 24 months. We reported an overall poor outcome among patients treated with the insertion of SEMS. This led us to think that, in some cases, occlusion may be better than a "silent" perforation.

Natural Language Processing in aid of FlyBase curators

PubMed Central

Karamanis, Nikiforos; Seal, Ruth; Lewin, Ian; McQuilton, Peter; Vlachos, Andreas; Gasperin, Caroline; Drysdale, Rachel; Briscoe, Ted

2008-01-01

Background Despite increasing interest in applying Natural Language Processing (NLP) to biomedical text, whether this technology can facilitate tasks such as database curation remains unclear. Results PaperBrowser is the first NLP-powered interface that was developed under a user-centered approach to improve the way in which FlyBase curators navigate an article. In this paper, we first discuss how observing curators at work informed the design and evaluation of PaperBrowser. Then, we present how we appraise PaperBrowser's navigational functionalities in a user-based study using a text highlighting task and evaluation criteria of Human-Computer Interaction. Our results show that PaperBrowser reduces the amount of interactions between two highlighting events and therefore improves navigational efficiency by about 58% compared to the navigational mechanism that was previously available to the curators. Moreover, PaperBrowser is shown to provide curators with enhanced navigational utility by over 74% irrespective of the different ways in which they highlight text in the article. Conclusion We show that state-of-the-art performance in certain NLP tasks such as Named Entity Recognition and Anaphora Resolution can be combined with the navigational functionalities of PaperBrowser to support curation quite successfully. PMID:18410678

Practices of research data curation in institutional repositories: A qualitative view from repository staff

PubMed Central

Stvilia, Besiki

2017-01-01

The importance of managing research data has been emphasized by the government, funding agencies, and scholarly communities. Increased access to research data increases the impact and efficiency of scientific activities and funding. Thus, many research institutions have established or plan to establish research data curation services as part of their Institutional Repositories (IRs). However, in order to design effective research data curation services in IRs, and to build active research data providers and user communities around those IRs, it is essential to study current data curation practices and provide rich descriptions of the sociotechnical factors and relationships shaping those practices. Based on 13 interviews with 15 IR staff members from 13 large research universities in the United States, this paper provides a rich, qualitative description of research data curation and use practices in IRs. In particular, the paper identifies data curation and use activities in IRs, as well as their structures, roles played, skills needed, contradictions and problems present, solutions sought, and workarounds applied. The paper can inform the development of best practice guides, infrastructure and service templates, as well as education in research data curation in Library and Information Science (LIS) schools. PMID:28301533

Practices of research data curation in institutional repositories: A qualitative view from repository staff.

PubMed

Lee, Dong Joon; Stvilia, Besiki

2017-01-01

The importance of managing research data has been emphasized by the government, funding agencies, and scholarly communities. Increased access to research data increases the impact and efficiency of scientific activities and funding. Thus, many research institutions have established or plan to establish research data curation services as part of their Institutional Repositories (IRs). However, in order to design effective research data curation services in IRs, and to build active research data providers and user communities around those IRs, it is essential to study current data curation practices and provide rich descriptions of the sociotechnical factors and relationships shaping those practices. Based on 13 interviews with 15 IR staff members from 13 large research universities in the United States, this paper provides a rich, qualitative description of research data curation and use practices in IRs. In particular, the paper identifies data curation and use activities in IRs, as well as their structures, roles played, skills needed, contradictions and problems present, solutions sought, and workarounds applied. The paper can inform the development of best practice guides, infrastructure and service templates, as well as education in research data curation in Library and Information Science (LIS) schools.

Curating Blood: How Students' and Researchers' Drawings Bring Potential Phenomena to Light

ERIC Educational Resources Information Center

Hay, D. B.; Pitchford, S.

2016-01-01

This paper explores students and researchers drawings of white blood cell recruitment. The data combines interviews with exhibit of review-type academic images and analyses of student model-drawings. The analysis focuses on the material aspects of bioscientific data-making and we use the literature of concrete bioscience modelling to differentiate…

Chemical-gene interaction networks and causal reasoning for biological effects prediction and prioritization of contaminants for environmental monitoring and surveillance (poster)

EPA Science Inventory

Product Description:Evaluation of the potential effects of complex mixtures of chemicals in the environment is challenged by the lack of extensive toxicity data for many chemicals. However, there are growing sources of online information that curate and compile literature reports...

The impact of comorbidity on cancer and its treatment.

PubMed

Sarfati, Diana; Koczwara, Bogda; Jackson, Christopher

2016-07-01

Answer questions and earn CME/CNE Comorbidity is common among cancer patients and, with an aging population, is becoming more so. Comorbidity potentially affects the development, stage at diagnosis, treatment, and outcomes of people with cancer. Despite the intimate relationship between comorbidity and cancer, there is limited consensus on how to record, interpret, or manage comorbidity in the context of cancer, with the result that patients who have comorbidity are less likely to receive treatment with curative intent. Evidence in this area is lacking because of the frequent exclusion of patients with comorbidity from randomized controlled trials. There is evidence that some patients with comorbidity have potentially curative treatment unnecessarily modified, compromising optimal care. Patients with comorbidity have poorer survival, poorer quality of life, and higher health care costs. Strategies to address these issues include improving the evidence base for patients with comorbidity, further development of clinical tools to assist decision making, improved integration and coordination of care, and skill development for clinicians. CA Cancer J Clin 2016;66:337-350. © 2016 American Cancer Society. © 2016 American Cancer Society, Inc.

[Care pathway of patients with hepatocellular carcinoma in France: State of play in 2017].

PubMed

Costentin, Charlotte; Ganne-Carrié, Nathalie; Rousseau, Benoit; Gérolami, René; Barbare, Jean-Claude

2017-09-01

Hepatocellular carcinoma is a major public health problem with one of the highest overall mortality compared to other cancers. The median overall survival in France in a hospital population with hepatocellular carcinoma is 9.4 months. Several publications reported a positive impact of hepatocellular carcinoma screening on diagnosis at an early-stage, eligibility for curative treatment and overall survival. However, the identification of patients to be included in a hepatocellular carcinoma screening program and the application of screening recommendations are not optimal. Other studies suggest a potentially negative impact of delayed diagnosis or treatment initiation on the patient's prognosis. Finally, marked variations between French regions and departments have been described in terms of access to curative treatment and overall survival. In this review article, we propose a state of play of the hepatocellular carcinoma patient's care pathway in France with the aim of identifying potential breaking points with negative impact on prognosis and of developing proposals for improvement. Copyright © 2017 Société Française du Cancer. Published by Elsevier Masson SAS. All rights reserved.

Improving the Acquisition and Management of Sample Curation Data

NASA Technical Reports Server (NTRS)

Todd, Nancy S.; Evans, Cindy A.; Labasse, Dan

2011-01-01

This paper discusses the current sample documentation processes used during and after a mission, examines the challenges and special considerations needed for designing effective sample curation data systems, and looks at the results of a simulated sample result mission and the lessons learned from this simulation. In addition, it introduces a new data architecture for an integrated sample Curation data system being implemented at the NASA Astromaterials Acquisition and Curation department and discusses how it improves on existing data management systems.

Text Mining Effectively Scores and Ranks the Literature for Improving Chemical-Gene-Disease Curation at the Comparative Toxicogenomics Database

PubMed Central

Johnson, Robin J.; Lay, Jean M.; Lennon-Hopkins, Kelley; Saraceni-Richards, Cynthia; Sciaky, Daniela; Murphy, Cynthia Grondin; Mattingly, Carolyn J.

2013-01-01

The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) is a public resource that curates interactions between environmental chemicals and gene products, and their relationships to diseases, as a means of understanding the effects of environmental chemicals on human health. CTD provides a triad of core information in the form of chemical-gene, chemical-disease, and gene-disease interactions that are manually curated from scientific articles. To increase the efficiency, productivity, and data coverage of manual curation, we have leveraged text mining to help rank and prioritize the triaged literature. Here, we describe our text-mining process that computes and assigns each article a document relevancy score (DRS), wherein a high DRS suggests that an article is more likely to be relevant for curation at CTD. We evaluated our process by first text mining a corpus of 14,904 articles triaged for seven heavy metals (cadmium, cobalt, copper, lead, manganese, mercury, and nickel). Based upon initial analysis, a representative subset corpus of 3,583 articles was then selected from the 14,094 articles and sent to five CTD biocurators for review. The resulting curation of these 3,583 articles was analyzed for a variety of parameters, including article relevancy, novel data content, interaction yield rate, mean average precision, and biological and toxicological interpretability. We show that for all measured parameters, the DRS is an effective indicator for scoring and improving the ranking of literature for the curation of chemical-gene-disease information at CTD. Here, we demonstrate how fully incorporating text mining-based DRS scoring into our curation pipeline enhances manual curation by prioritizing more relevant articles, thereby increasing data content, productivity, and efficiency. PMID:23613709

Individualized Mutation Detection in Circulating Tumor DNA for Monitoring Colorectal Tumor Burden Using a Cancer-Associated Gene Sequencing Panel.

PubMed

Sato, Kei A; Hachiya, Tsuyoshi; Iwaya, Takeshi; Kume, Kohei; Matsuo, Teppei; Kawasaki, Keisuke; Abiko, Yukito; Akasaka, Risaburo; Matsumoto, Takayuki; Otsuka, Koki; Nishizuka, Satoshi S

2016-01-01

Circulating tumor DNA (ctDNA) carries information on tumor burden. However, the mutation spectrum is different among tumors. This study was designed to examine the utility of ctDNA for monitoring tumor burden based on an individual mutation profile. DNA was extracted from a total of 176 samples, including pre- and post-operational plasma, primary tumors, and peripheral blood mononuclear cells (PBMC), from 44 individuals with colorectal tumor who underwent curative resection of colorectal tumors, as well as nine healthy individuals. Using a panel of 50 cancer-associated genes, tumor-unique mutations were identified by comparing the single nucleotide variants (SNVs) from tumors and PBMCs with an Ion PGM sequencer. A group of the tumor-unique mutations from individual tumors were designated as individual marker mutations (MMs) to trace tumor burden by ctDNA using droplet digital PCR (ddPCR). From these experiments, three major objectives were assessed: (a) Tumor-unique mutations; (b) mutation spectrum of a tumor; and (c) changes in allele frequency of the MMs in ctDNA after curative resection of the tumor. A total of 128 gene point mutations were identified in 27 colorectal tumors. Twenty-six genes were mutated in at least 1 sample, while 14 genes were found to be mutated in only 1 sample, respectively. An average of 2.7 genes were mutated per tumor. Subsequently, 24 MMs were selected from SNVs for tumor burden monitoring. Among the MMs found by ddPCR with > 0.1% variant allele frequency in plasma DNA, 100% (8 out of 8) exhibited a decrease in post-operation ctDNA, whereas none of the 16 MMs found by ddPCR with < 0.1% variant allele frequency in plasma DNA showed a decrease. This panel of 50 cancer-associated genes appeared to be sufficient to identify individual, tumor-unique, mutated ctDNA markers in cancer patients. The MMs showed the clinical utility in monitoring curatively-treated colorectal tumor burden if the allele frequency of MMs in plasma DNA is above 0.1%.

The Nanomaterial Data Curation Initiative: A Collaborative Approach to Assessing, Evaluating, and Advancing the State of the Field

EPA Science Inventory

The Nanomaterial Data Curation Initiative (NDCI) explores the critical aspect of data curation within the development of informatics approaches to understanding nanomaterial behavior. Data repositories and tools for integrating and interrogating complex nanomaterial datasets are...

The art and science of data curation: Lessons learned from constructing a virtual collection

NASA Astrophysics Data System (ADS)

Bugbee, Kaylin; Ramachandran, Rahul; Maskey, Manil; Gatlin, Patrick

2018-03-01

A digital, or virtual, collection is a value added service developed by libraries that curates information and resources around a topic, theme or organization. Adoption of the virtual collection concept as an Earth science data service improves the discoverability, accessibility and usability of data both within individual data centers but also across data centers and disciplines. In this paper, we introduce a methodology for systematically and rigorously curating Earth science data and information into a cohesive virtual collection. This methodology builds on the geocuration model of searching, selecting and synthesizing Earth science data, metadata and other information into a single and useful collection. We present our experiences curating a virtual collection for one of NASA's twelve Distributed Active Archive Centers (DAACs), the Global Hydrology Resource Center (GHRC), and describe lessons learned as a result of this curation effort. We also provide recommendations and best practices for data centers and data providers who wish to curate virtual collections for the Earth sciences.

Improving the Discoverability and Availability of Sample Data and Imagery in NASA's Astromaterials Curation Digital Repository Using a New Common Architecture for Sample Databases

NASA Technical Reports Server (NTRS)

Todd, N. S.; Evans, C.

2015-01-01

The Astromaterials Acquisition and Curation Office at NASA's Johnson Space Center (JSC) is the designated facility for curating all of NASA's extraterrestrial samples. The suite of collections includes the lunar samples from the Apollo missions, cosmic dust particles falling into the Earth's atmosphere, meteorites collected in Antarctica, comet and interstellar dust particles from the Stardust mission, asteroid particles from the Japanese Hayabusa mission, and solar wind atoms collected during the Genesis mission. To support planetary science research on these samples, NASA's Astromaterials Curation Office hosts the Astromaterials Curation Digital Repository, which provides descriptions of the missions and collections, and critical information about each individual sample. Our office is implementing several informatics initiatives with the goal of better serving the planetary research community. One of these initiatives aims to increase the availability and discoverability of sample data and images through the use of a newly designed common architecture for Astromaterials Curation databases.

ECTFE (HALAR) as a New Material for Primary Sample Containment of Astromaterials

NASA Technical Reports Server (NTRS)

Calaway, Michael J.; McConnell, J.T.

2014-01-01

Fluoropolymers, such as Teflon® (PTFE, PFA, FEP) and Viton® (FKM), have been used for over 40 years in curating astromaterials at NASA JSC. In general, fluoropolymers have low outgassing and particle shedding properties that reduce cross-contamination to curated samples. Ethylene - Chlorotrifluoroethylene (ECTFE), commonly called Halar® (trademark of Solvay Solexis), is a partially fluorinated semi-crystalline copolymer in the same class of fluoropolymers with superior abrasion resistance and extremely low permeability to liquids, gases, and vapors than any other fluoropolymer (fig. 1). ECTFE coatings are becoming more popular in the nuclear, semiconductor, and biomedical industry for lining isolation containment gloveboxes and critical piping as well as other clean room applications. A study was conducted at NASA JSC to evaluate the potential use of Halar on future sample return missions as a material for primary sample containment.

Auditing the Assignments of Top-Level Semantic Types in the UMLS Semantic Network to UMLS Concepts

PubMed Central

He, Zhe; Perl, Yehoshua; Elhanan, Gai; Chen, Yan; Geller, James; Bian, Jiang

2018-01-01

The Unified Medical Language System (UMLS) is an important terminological system. By the policy of its curators, each concept of the UMLS should be assigned the most specific Semantic Types (STs) in the UMLS Semantic Network (SN). Hence, the Semantic Types of most UMLS concepts are assigned at or near the bottom (leaves) of the UMLS Semantic Network. While most ST assignments are correct, some errors do occur. Therefore, Quality Assurance efforts of UMLS curators for ST assignments should concentrate on automatically detected sets of UMLS concepts with higher error rates than random sets. In this paper, we investigate the assignments of top-level semantic types in the UMLS semantic network to concepts, identify potential erroneous assignments, define four categories of errors, and thus provide assistance to curators of the UMLS to avoid these assignments errors. Human experts analyzed samples of concepts assigned 10 of the top-level semantic types and categorized the erroneous ST assignments into these four logical categories. Two thirds of the concepts assigned these 10 top-level semantic types are erroneous. Our results demonstrate that reviewing top-level semantic type assignments to concepts provides an effective way for UMLS quality assurance, comparing to reviewing a random selection of semantic type assignments. PMID:29375930

Auditing the Assignments of Top-Level Semantic Types in the UMLS Semantic Network to UMLS Concepts.

PubMed

He, Zhe; Perl, Yehoshua; Elhanan, Gai; Chen, Yan; Geller, James; Bian, Jiang

2017-11-01

The Unified Medical Language System (UMLS) is an important terminological system. By the policy of its curators, each concept of the UMLS should be assigned the most specific Semantic Types (STs) in the UMLS Semantic Network (SN). Hence, the Semantic Types of most UMLS concepts are assigned at or near the bottom (leaves) of the UMLS Semantic Network. While most ST assignments are correct, some errors do occur. Therefore, Quality Assurance efforts of UMLS curators for ST assignments should concentrate on automatically detected sets of UMLS concepts with higher error rates than random sets. In this paper, we investigate the assignments of top-level semantic types in the UMLS semantic network to concepts, identify potential erroneous assignments, define four categories of errors, and thus provide assistance to curators of the UMLS to avoid these assignments errors. Human experts analyzed samples of concepts assigned 10 of the top-level semantic types and categorized the erroneous ST assignments into these four logical categories. Two thirds of the concepts assigned these 10 top-level semantic types are erroneous. Our results demonstrate that reviewing top-level semantic type assignments to concepts provides an effective way for UMLS quality assurance, comparing to reviewing a random selection of semantic type assignments.

IMPPAT: A curated database of Indian Medicinal Plants, Phytochemistry And Therapeutics.

PubMed

Mohanraj, Karthikeyan; Karthikeyan, Bagavathy Shanmugam; Vivek-Ananth, R P; Chand, R P Bharath; Aparna, S R; Mangalapandi, Pattulingam; Samal, Areejit

2018-03-12

Phytochemicals of medicinal plants encompass a diverse chemical space for drug discovery. India is rich with a flora of indigenous medicinal plants that have been used for centuries in traditional Indian medicine to treat human maladies. A comprehensive online database on the phytochemistry of Indian medicinal plants will enable computational approaches towards natural product based drug discovery. In this direction, we present, IMPPAT, a manually curated database of 1742 Indian Medicinal Plants, 9596 Phytochemicals, And 1124 Therapeutic uses spanning 27074 plant-phytochemical associations and 11514 plant-therapeutic associations. Notably, the curation effort led to a non-redundant in silico library of 9596 phytochemicals with standard chemical identifiers and structure information. Using cheminformatic approaches, we have computed the physicochemical, ADMET (absorption, distribution, metabolism, excretion, toxicity) and drug-likeliness properties of the IMPPAT phytochemicals. We show that the stereochemical complexity and shape complexity of IMPPAT phytochemicals differ from libraries of commercial compounds or diversity-oriented synthesis compounds while being similar to other libraries of natural products. Within IMPPAT, we have filtered a subset of 960 potential druggable phytochemicals, of which majority have no significant similarity to existing FDA approved drugs, and thus, rendering them as good candidates for prospective drugs. IMPPAT database is openly accessible at: https://cb.imsc.res.in/imppat .

Protective and Curative Effects of the Sea Cucumber Holothuria atra Extract against DMBA-Induced Hepatorenal Diseases in Rats

PubMed Central

Dakrory, Ahmed I.; Fahmy, Sohair R.; Soliman, Amel M.; Mohamed, Ayman S.; Amer, Sayed A. M.

2015-01-01

Oxidative stress is a common mechanism contributing to the initiation and progression of hepatic damage. Hence there is a great demand for the development of agents with potent antioxidant effect. The aim of the present study is to evaluate the efficacy of Holothuria atra extract (HaE) as an antioxidant against 7,12-dimethylbenz[a]anthracene- (DMBA-) induced hepatorenal dysfunction. Experimental animals were divided into two main groups: protective and curative. Each group was then divided into five subgroups pre- or posttreated either with distilled water (DMBA subgroups) or with HaE (200 mg/kg body weight) for seven and fourteen days. Single oral administration of DMBA (15 mg/kg body weight) to Wistar rats resulted in a significant increase in the serum liver enzymes and kidney function's parameters. DMBA increased level of liver malondialdehyde (MDA), decreased levels of reduced glutathione (GSH), glutathione-S-transferase (GST), superoxide dismutase (SOD), and catalase (CAT) in the liver tissue, and induced liver histopathological alterations. Pre- or posttreatment with HaE orally for 14 days significantly reversed the hepatorenal alterations induced following DMBA administration. In conclusion, HaE exhibits good hepatoprotective, curative, and antioxidant potential against DMBA-induced hepatorenal dysfunction in rats that might be due to decreased free radical generation. PMID:25821811

Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community

PubMed Central

Hosmani, Prashant S.; Villalobos-Ayala, Krystal; Miller, Sherry; Shippy, Teresa; Flores, Mirella; Rosendale, Andrew; Cordola, Chris; Bell, Tracey; Mann, Hannah; DeAvila, Gabe; DeAvila, Daniel; Moore, Zachary; Buller, Kyle; Ciolkevich, Kathryn; Nandyal, Samantha; Mahoney, Robert; Van Voorhis, Joshua; Dunlevy, Megan; Farrow, David; Hunter, David; Morgan, Taylar; Shore, Kayla; Guzman, Victoria; Izsak, Allison; Dixon, Danielle E.; Cridge, Andrew; Cano, Liliana; Cao, Xiaolong; Jiang, Haobo; Leng, Nan; Johnson, Shannon; Cantarel, Brandi L.; Richards, Stephen; English, Adam; Shatters, Robert G.; Childers, Chris; Chen, Mei-Ju; Hunter, Wayne; Cilia, Michelle; Mueller, Lukas A.; Munoz-Torres, Monica; Nelson, David; Poelchau, Monica F.; Benoit, Joshua B.; Wiersma-Koch, Helen; D’Elia, Tom; Brown, Susan J.

2017-01-01

Abstract The Asian citrus psyllid (Diaphorina citri Kuwayama) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the pathogen associated with citrus Huanglongbing (HLB, citrus greening). HLB threatens citrus production worldwide. Suppression or reduction of the insect vector using chemical insecticides has been the primary method to inhibit the spread of citrus greening disease. Accurate structural and functional annotation of the Asian citrus psyllid genome, as well as a clear understanding of the interactions between the insect and CLas, are required for development of new molecular-based HLB control methods. A draft assembly of the D. citri genome has been generated and annotated with automated pipelines. However, knowledge transfer from well-curated reference genomes such as that of Drosophila melanogaster to newly sequenced ones is challenging due to the complexity and diversity of insect genomes. To identify and improve gene models as potential targets for pest control, we manually curated several gene families with a focus on genes that have key functional roles in D. citri biology and CLas interactions. This community effort produced 530 manually curated gene models across developmental, physiological, RNAi regulatory and immunity-related pathways. As previously shown in the pea aphid, RNAi machinery genes putatively involved in the microRNA pathway have been specifically duplicated. A comprehensive transcriptome enabled us to identify a number of gene families that are either missing or misassembled in the draft genome. In order to develop biocuration as a training experience, we included undergraduate and graduate students from multiple institutions, as well as experienced annotators from the insect genomics research community. The resulting gene set (OGS v1.0) combines both automatically predicted and manually curated gene models. Database URL: https://citrusgreening.org/ PMID:29220441

Curation of inhibitor-target data: process and impact on pathway analysis.

PubMed

Devidas, Sreenivas

2009-01-01

The past decade has seen a significant emergence in the availability and use of pathway analysis tools. The workflow that is supported by most of the pathway analysis tools is limited to either of the following: a. a network of genes based on the input data set, or b. the resultant network filtered down by a few criteria such as (but not limited to) i. disease association of the genes in the network; ii. targets known to be the target of one or more launched drugs; iii. targets known to be the target of one or more compounds in clinical trials; and iv. targets reasonably known to be potential candidate or clinical biomarkers. Almost all the tools in use today are biased towards the biological side and contain little, if any, information on the chemical inhibitors associated with the components of a given biological network. The limitation resides as follows: The fact that the number of inhibitors that have been published or patented is probably several fold (probably greater than 10-fold) more than the number of published protein-protein interactions. Curation of such data is both expensive and time consuming and could impact ROI significantly. The non-standardization associated with protein and gene names makes mapping reasonably non-straightforward. The number of patented and published inhibitors across target classes increases by over a million per year. Therefore, keeping the databases current becomes a monumental problem. Modifications required in the product architectures to accommodate chemistry-related content. GVK Bio has, over the past 7 years, curated the compound-target data that is necessary for the addition of such compound-centric workflows. This chapter focuses on identification, curation and utility of such data.

Total gastrectomy increases the incidence of grade III and IV toxicities in patients with gastric cancer receiving adjuvant TS-1 treatment.

PubMed

Chou, Wen-Chi; Chang, Chia-Lun; Liu, Keng-Hao; Hsu, Jun-Te; Cheng, Wei Hong; Hsu, Hung-Chih; Shen, Wen-Chi; Hung, Yu-Shin; Chen, Jen-Shi

2013-11-01

We aimed to evaluate the safety and efficacy of TS-1 adjuvant chemotherapy in Taiwanese patients with gastric cancer. We included in this study patients with locally advanced gastric cancer who received adjuvant TS-1 or 5-fluorouracil chemotherapy after curative surgery and extended lymph node dissection between 1 June 2008 and 31 December 2012 at Chang Gung Memorial Hospital. Patient characteristics, tumor features, safety profiles and compliance with TS-1 treatment were retrospectively analyzed from medical charts. Forty patients received adjuvant chemotherapy with TS-1 and 193 with 5-fluorouracil within the study period. The 1- and 2-year overall survival rates were 90.6% and 87% in the TS-1 group and 95.4% and 86.8% in the 5-fluorouracil group (P = 0.34). The 1- and 2-year disease-free survival rates were 90.6% and 74.7% in the TS-1 group and 88% and 75.7% in the 5-fluorouracil group (P = 0.66). In the TS-1 group, tumor recurrence was more frequent in those with >15 metastatic lymph nodes than ≤15. Overall, 78.9%, 74.3%, 62.1% and 56% of patients underwent TS-1 treatment for at least 3, 6, 9 and 12 months, respectively. The most common adverse events of TS-1 were skin hyperpigmentation (55%), diarrhea (27.5%), dizziness (27.5%) and leucopenia (20%). Severe adverse events (SAEs; grade III or IV toxicity) were diarrhea (7.5%), stomatitis (7.5%), leukopenia (5%), vomiting (2.5%), anorexia (2.5%) and dizziness (2.5%). Patients who underwent total gastrectomy had a significantly greater risk of TS-1-related SAEs than patients who underwent subtotal gastrectomy (40% versus 8%, P = 0.014). The incidence of SAEs during TS-1 therapy was more common in Taiwanese patients with gastric cancer who underwent total gastrectomy compared with those who underwent subtotal gastrectomy. Clinicians must be aware of and able to manage these SAEs to maximize patient compliance with adjuvant TS-1.

JSC Advanced Curation: Research and Development for Current Collections and Future Sample Return Mission Demands

NASA Technical Reports Server (NTRS)

Fries, M. D.; Allen, C. C.; Calaway, M. J.; Evans, C. A.; Stansbery, E. K.

2015-01-01

Curation of NASA's astromaterials sample collections is a demanding and evolving activity that supports valuable science from NASA missions for generations, long after the samples are returned to Earth. For example, NASA continues to loan hundreds of Apollo program samples to investigators every year and those samples are often analyzed using instruments that did not exist at the time of the Apollo missions themselves. The samples are curated in a manner that minimizes overall contamination, enabling clean, new high-sensitivity measurements and new science results over 40 years after their return to Earth. As our exploration of the Solar System progresses, upcoming and future NASA sample return missions will return new samples with stringent contamination control, sample environmental control, and Planetary Protection requirements. Therefore, an essential element of a healthy astromaterials curation program is a research and development (R&D) effort that characterizes and employs new technologies to maintain current collections and enable new missions - an Advanced Curation effort. JSC's Astromaterials Acquisition & Curation Office is continually performing Advanced Curation research, identifying and defining knowledge gaps about research, development, and validation/verification topics that are critical to support current and future NASA astromaterials sample collections. The following are highlighted knowledge gaps and research opportunities.

[Application of the xenogenic acellular dermal matrix membrane application used in the postoperative tissue shortage repair].

PubMed

Bai, Yanxia; Yan, Liying; Zhang, Shaoqiang; Shao, Yuan; Yao, Xiaobao; Li, Honghui; Zhao, Ruimin; Zhao, Qian; Zhang, Pengfei; Yang, Qi

2014-09-01

To observe the short-term and long-term curative effect of the xenogenic acellular dermal matrix membrane (or joint muscle flap transfer) application used in the 82 cases postoperative tissue shortage repair that after the head neck carcinoma resection. To held the 82 cases head neck carcinoma postoperative mucosa shortage repaired after resection by the xenogenic acellular dermal matrix membrane (or joint muscle flap transfer), 65 cases mucosa shortage wound be directly covered by the repair membrane and the other 17 cases mucosa shortage wound be repaired by the tranfered muscle tissue flap with the repair membrane covered; 53 cases underwent additional postoperative radiotherapy between 2-4 weeks and follow-up in 1, 3, 6, 12, 18, 24, 30, 36, 48, 60 months and observed the operation site repair process through the electronic laryngoscope, observed the patients respiration, swallow, phonation function. Seventy-seven cases patients operation incision reached I phase healing standard, another 5 cases patients operation incision reached II phase healing standard because of the wound infection and fully-recovered through the local wound drainage,dressing process. All the patients tracheal cannula,the stomach tube be extubated successfully and without the local cicatricial constriction occurred. Seventy-eight cases follow up period reached 1 year including 53 cases who underwent postoperative radiotherapy, 49 cases follow up period reached 3 years including 32 cases who underwent postoperative radiotherapy, 14 cases follow up period reached 5 years including 12 cases who underwent postoperative radiotherapy. The patients with static local lesions discovered no reaction such as exclusion, allergy. The application of xenogenic acellular dermal matrix membrane (or joint muscle flap transfer used in in the postoperative tissue shortage repair that after the head neck carcinoma resection have several advantage such as comparatively easily implementation, operation safety edge enough,well preserved organ function, comparatively low incidence about the laryngeal stenosis, the short-term and long-term repair effect are all exact.

Intrinsic Limitations to Unilateral Parathyroid Exploration

PubMed Central

Moore, Francis D.; Mannting, Finn; Tanasijevic, Milenko

1999-01-01

Objective To evaluate a method of limited parathyroid exploration for primary hyperparathyroidism. Summary Background Data Although preoperative localization of parathyroid adenomas has become sensitive enough for clinical practice, it has not achieved success as the basis for limited parathyroid exploration, because multiglandular disease is routinely underdiagnosed. The rapid intraoperative parathyroid hormone assay is sensitive for multiglandular disease, because hormone levels will not fall within 10 minutes of adenoma removal if additional abnormal tissue is present. A combination technique in which the exploration is limited according to the localization studies and the success is confirmed with the parathyroid hormone assay has promise for producing a high rate of curative limited parathyroid explorations. Methods Forty-eight consecutive patients with primary hyperparathyroidism and indications for surgery underwent preoperative localization. After tests, 45 patients underwent unilateral parathyroid exploration and confirmation of the success of unilateral exploration during surgery using the rapid parathyroid hormone assay. The intraoperative management of these patients and their follow-up to 3 months was recorded. Results Thirty-two of the 48 patients (67%) had successful unilateral exploration as gauged by a marked drop in parathyroid hormone levels during the procedure and by 3-month clinical follow-up. Of the 16 patients who ultimately underwent bilateral exploration, 7 had parathyroid hormone levels that did not fall after adenoma removal. Of these seven, five were found to have a second adenoma and two had slow metabolism of hormone with no additional abnormal tissue found. In 5 of the 16 patients, bilateral exploration was performed for erroneous localization. Four additional patients underwent bilateral exploration for improved exposure or negative results on localization tests. Conclusions These results show that unilateral parathyroid exploration is limited by the intrinsic 15% rate of multiglandular primary hyperparathyroidism, combined with the imperfections of preoperative localizing techniques. Although an 85% rate of unilateral exploration can theoretically be obtained for unselected cases, the other vagaries of the technique make a 70% rate a more reasonable expectation. PMID:10493485

Curating NASA's Astromaterials Collections: Past, Present, and Future

NASA Technical Reports Server (NTRS)

Zeigler, Ryan

2015-01-01

Planning for the curation of samples from future sample return missions must begin during the initial planning stages of a mission. Waiting until the samples have been returned to Earth, or even when you begin to physically build the spacecraft is too late. A lack of proper planning could lead to irreversible contamination of the samples, which in turn would compromise the scientific integrity of the mission. For example, even though the Apollo missions first returned samples in 1969, planning for the curation facility began in the early 1960s, and construction of the Lunar Receiving Laboratory was completed in 1967. In addition to designing the receiving facility and laboratory that the samples will be characterized and stored in, there are many aspects of contamination that must be addressed during the planning and building of the spacecraft: planetary protection (both outbound and inbound); cataloging, documenting, and preserving the materials used to build spacecraft (also known as coupons); near real-time monitoring of the environment in which the spacecraft is being built using witness plates for critical aspects of contamination (known as contamination control); and long term monitoring and preservation of the environment in which the spacecraft is being built for most aspects of potential contamination through the use of witness plates (known as contamination knowledge). The OSIRIS REx asteroid sample return mission, currently being built, is dealing with all of these aspects of contamination in order to ensure they return the best preserved sample possible. Coupons and witness plates from OSIRIS REx are currently being studied and stored (for future studies) at the Johnson Space Center. Similarly, planning for the clean room facility at Johnson Space Center to house the OSIRIS-REx samples is well advanced, and construction of the facility should begin in early 2017 (despite a nominal 2023 return date for OSIRIS-REx samples). Similar development is being done, in concert with JAXA, for the return of Hayabusa 2 samples (nominally in 2020). We are also actively developing advanced techniques like cold curation and organically clean curation in anticipation of future sample return missions such as comet nucleus sample return and Mars sample return.

Argo: enabling the development of bespoke workflows and services for disease annotation.

PubMed

Batista-Navarro, Riza; Carter, Jacob; Ananiadou, Sophia

2016-01-01

Argo (http://argo.nactem.ac.uk) is a generic text mining workbench that can cater to a variety of use cases, including the semi-automatic annotation of literature. It enables its technical users to build their own customised text mining solutions by providing a wide array of interoperable and configurable elementary components that can be seamlessly integrated into processing workflows. With Argo's graphical annotation interface, domain experts can then make use of the workflows' automatically generated output to curate information of interest.With the continuously rising need to understand the aetiology of diseases as well as the demand for their informed diagnosis and personalised treatment, the curation of disease-relevant information from medical and clinical documents has become an indispensable scientific activity. In the Fifth BioCreative Challenge Evaluation Workshop (BioCreative V), there was substantial interest in the mining of literature for disease-relevant information. Apart from a panel discussion focussed on disease annotations, the chemical-disease relations (CDR) track was also organised to foster the sharing and advancement of disease annotation tools and resources.This article presents the application of Argo's capabilities to the literature-based annotation of diseases. As part of our participation in BioCreative V's User Interactive Track (IAT), we demonstrated and evaluated Argo's suitability to the semi-automatic curation of chronic obstructive pulmonary disease (COPD) phenotypes. Furthermore, the workbench facilitated the development of some of the CDR track's top-performing web services for normalising disease mentions against the Medical Subject Headings (MeSH) database. In this work, we highlight Argo's support for developing various types of bespoke workflows ranging from ones which enabled us to easily incorporate information from various databases, to those which train and apply machine learning-based concept recognition models, through to user-interactive ones which allow human curators to manually provide their corrections to automatically generated annotations. Our participation in the BioCreative V challenges shows Argo's potential as an enabling technology for curating disease and phenotypic information from literature.Database URL: http://argo.nactem.ac.uk. © The Author(s) 2016. Published by Oxford University Press.

Argo: enabling the development of bespoke workflows and services for disease annotation

PubMed Central

Batista-Navarro, Riza; Carter, Jacob; Ananiadou, Sophia

2016-01-01

Argo (http://argo.nactem.ac.uk) is a generic text mining workbench that can cater to a variety of use cases, including the semi-automatic annotation of literature. It enables its technical users to build their own customised text mining solutions by providing a wide array of interoperable and configurable elementary components that can be seamlessly integrated into processing workflows. With Argo's graphical annotation interface, domain experts can then make use of the workflows' automatically generated output to curate information of interest. With the continuously rising need to understand the aetiology of diseases as well as the demand for their informed diagnosis and personalised treatment, the curation of disease-relevant information from medical and clinical documents has become an indispensable scientific activity. In the Fifth BioCreative Challenge Evaluation Workshop (BioCreative V), there was substantial interest in the mining of literature for disease-relevant information. Apart from a panel discussion focussed on disease annotations, the chemical-disease relations (CDR) track was also organised to foster the sharing and advancement of disease annotation tools and resources. This article presents the application of Argo’s capabilities to the literature-based annotation of diseases. As part of our participation in BioCreative V’s User Interactive Track (IAT), we demonstrated and evaluated Argo’s suitability to the semi-automatic curation of chronic obstructive pulmonary disease (COPD) phenotypes. Furthermore, the workbench facilitated the development of some of the CDR track’s top-performing web services for normalising disease mentions against the Medical Subject Headings (MeSH) database. In this work, we highlight Argo’s support for developing various types of bespoke workflows ranging from ones which enabled us to easily incorporate information from various databases, to those which train and apply machine learning-based concept recognition models, through to user-interactive ones which allow human curators to manually provide their corrections to automatically generated annotations. Our participation in the BioCreative V challenges shows Argo’s potential as an enabling technology for curating disease and phenotypic information from literature. Database URL: http://argo.nactem.ac.uk PMID:27189607

Hemangiopericytoma of the spleen.

PubMed

Illuminati, Giulio; Pizzardi, Giulia; Calio, Francesco; Pacilè, Maria A; Carboni, Fabio; Palumbo, Piergaspare; Vietri, Francesco

2015-03-01

Hemangiopericytoma of the spleen is a very rare tumor, with 14 isolated reports. It was our aim to review our experience and compare it with all the reported cases in an attempt to standardize surgical treatment, adjuvant treatment and follow-up protocol of this infrequent condition. A consecutive case series study, with a mean follow-up of 44 months. Five patients (mean age, 49 years) underwent simple splenectomy for hemangiopericytoma limited to the spleen followed by adriamycin-based chemotherapy in one patient. All the patients are alive and free from disease. For tumors confined to the spleen, simple splenectomy can be considered curative, without any need for further adjuvant treatment. On review of the medical literature, cure can still be achieved with complete resection of recurrences, when feasible, with adjuvant chemotherapy being also indicated. The slow-growing pattern of the tumor suggests a 10-year follow-up. Copyright © 2015 Surgical Associates Ltd. Published by Elsevier Ltd. All rights reserved.

[An Analysis of Perforated Gastric Cancer with Acute Peritonitis in Our Hospital].

PubMed

Adachi, Shinichi; Endo, Shunji; Chinen, Yoshinao; Itakura, Hiroaki; Takayama, Hirotoshi; Tsuda, Yujiro; Ueda, Masami; Nakashima, Shinsuke; Ohta, Katsuya; Ikenaga, Masakazu; Yamada, Terumasa

2018-01-01

Perforated gastric cancer is relatively rare and the incidence is reported about 1% of all the cases of gastric cancer. We retrospectively analyzed the clinical data of the consecutive 12 patients with perforated gastric cancer who underwent operation in our hospital between January 2005 and December 2016. There were 5 men and 7 women, with an average age of 65.8 years old(34-87). Perforated gastric cancer occurred in the region U(1 cases), M(6 cases), L(5 cases). There were 11 cases with distant metastasis. We could successfully diagnosed as perforated gastric cancer in 8 cases before emergency operation. Gastrectomy was performed in 5 cases. However, the curative resection was performed only 1 case. Prognosis of perforated gastric cancer is poor. We considered as an appropriate two-step surgical strategy that the first step of surgery is an acute peritonitis treatment followed by radical gastrectomy with lymphadenectomy.

Impact of infectious complications on gastric cancer recurrence.

PubMed

Hayashi, Tsutomu; Yoshikawa, Takaki; Aoyama, Toru; Hasegawa, Shinichi; Yamada, Takanobu; Tsuchida, Kazuhito; Fujikawa, Hirohito; Sato, Tsutomu; Ogata, Takashi; Cho, Haruhiko; Oshima, Takashi; Rino, Yasushi; Masuda, Munetaka

2015-04-01

Postoperative infectious complications increase disease recurrence in colorectal cancer patients. We herein investigated the impact of infectious complications on gastric cancer recurrence after curative surgery. In total, 502 patients who underwent R0 resection for gastric cancer were reviewed. Patients were classified into those with infectious complications (IC group) and those without infectious complications (NO group). The risk factors for recurrence-free survival (RFS) were identified. Infectious complications, which occurred in 52 patients (10.4%), included pneumonia, ileus with a systemic inflammatory reaction, anastomotic leakage, and intraperitoneal abscess. The overall 5-year RFS rate was 83% in the NO group and 58% in the IC group (p = 0.000). Multivariate analysis demonstrated that age, ASA score, stage, and infectious complications were significant predictors of RFS. Infectious complications were a risk factor for gastric cancer recurrence. To avoid causing infectious complications, the surgical procedure, surgical strategy, and perioperative care should be carefully planned.

Short-Term Outcomes of Simultaneous Laparoscopic Colectomy and Hepatectomy for Primary Colorectal Cancer With Synchronous Liver Metastases

PubMed Central

Inoue, Akira; Uemura, Mamoru; Yamamoto, Hirofumi; Hiraki, Masayuki; Naito, Atsushi; Ogino, Takayuki; Nonaka, Ryoji; Nishimura, Junichi; Wada, Hiroshi; Hata, Taishi; Takemasa, Ichiro; Eguchi, Hidetoshi; Mizushima, Tsunekazu; Nagano, Hiroaki; Doki, Yuichiro; Mori, Masaki

2014-01-01

Although simultaneous resection of primary colorectal cancer and synchronous liver metastases is reported to be safe and effective, the feasibility of a laparoscopic approach remains controversial. This study evaluated the safety, feasibility, and short-term outcomes of simultaneous laparoscopic surgery for primary colorectal cancer with synchronous liver metastases. From September 2008 to December 2013, 10 patients underwent simultaneous laparoscopic resection of primary colorectal cancer and synchronous liver metastases with curative intent at our institute. The median operative time was 452 minutes, and the median estimated blood loss was 245 mL. Median times to discharge from the hospital and adjuvant chemotherapy were 13.5 and 44 postoperative days, respectively. Negative resection margins were achieved in all cases, with no postoperative mortality or major morbidity. Simultaneous laparoscopic colectomy and hepatectomy for primary colorectal cancer with synchronous liver metastases appears feasible with low morbidity and favorable outcomes. PMID:25058762

Management and prognosis of locally recurrent rectal cancer - A national population-based study.

PubMed

Westberg, Karin; Palmer, Gabriella; Hjern, Fredrik; Johansson, Hemming; Holm, Torbjörn; Martling, Anna

2018-01-01

The rate of local recurrence of rectal cancer (LRRC) has decreased but the condition remains a therapeutic challenge. This study aimed to examine treatment and prognosis in patients with LRRC in Sweden. Special focus was directed towards potential differences between geographical regions and time periods. All patients with LRRC as first event, following primary surgery for rectal cancer performed during the period 1995-2002, were included in this national population-based cohort-study. Data were collected from the Swedish Colorectal Cancer Registry and from medical records. The cohort was divided into three time periods, based on the date of diagnosis of the LRRC. In total, 426 patients fulfilled the inclusion criteria. Treatment with curative intent was performed in 149 patients (35%), including 121 patients who had a surgical resection of the LRRC. R0-resection was achieved in 64 patients (53%). Patients with a non-centrally located tumour were more likely to have positive resection margins (R1/R2) (OR 5.02, 95% CI:2.25-11.21). Five-year survival for patients resected with curative intent was 43% after R0-resection and 14% after R1-resection. There were no significant differences in treatment intention or R0-resection rate between time periods or regions. The risk of any failure was significantly higher in R1-resected patients compared with R0-resected patients (HR 2.04, 95% CI:1.22-3.40). A complete resection of the LRRC is essential for potentially curative treatment. Time period and region had no influence on either margin status or prognosis. Copyright © 2017 Elsevier Ltd, BASO ~ The Association for Cancer Surgery, and the European Society of Surgical Oncology. All rights reserved.

SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases

PubMed Central

Foerster, Hartmut; Bombarely, Aureliano; Battey, James N D; Sierro, Nicolas; Ivanov, Nikolai V; Mueller, Lukas A

2018-01-01

Abstract SolCyc is the entry portal to pathway/genome databases (PGDBs) for major species of the Solanaceae family hosted at the Sol Genomics Network. Currently, SolCyc comprises six organism-specific PGDBs for tomato, potato, pepper, petunia, tobacco and one Rubiaceae, coffee. The metabolic networks of those PGDBs have been computationally predicted by the pathologic component of the pathway tools software using the manually curated multi-domain database MetaCyc (http://www.metacyc.org/) as reference. SolCyc has been recently extended by taxon-specific databases, i.e. the family-specific SolanaCyc database, containing only curated data pertinent to species of the nightshade family, and NicotianaCyc, a genus-specific database that stores all relevant metabolic data of the Nicotiana genus. Through manual curation of the published literature, new metabolic pathways have been created in those databases, which are complemented by the continuously updated, relevant species-specific pathways from MetaCyc. At present, SolanaCyc comprises 199 pathways and 29 superpathways and NicotianaCyc accounts for 72 pathways and 13 superpathways. Curator-maintained, taxon-specific databases such as SolanaCyc and NicotianaCyc are characterized by an enrichment of data specific to these taxa and free of falsely predicted pathways. Both databases have been used to update recently created Nicotiana-specific databases for Nicotiana tabacum, Nicotiana benthamiana, Nicotiana sylvestris and Nicotiana tomentosiformis by propagating verifiable data into those PGDBs. In addition, in-depth curation of the pathways in N.tabacum has been carried out which resulted in the elimination of 156 pathways from the 569 pathways predicted by pathway tools. Together, in-depth curation of the predicted pathway network and the supplementation with curated data from taxon-specific databases has substantially improved the curation status of the species–specific N.tabacum PGDB. The implementation of this strategy will significantly advance the curation status of all organism-specific databases in SolCyc resulting in the improvement on database accuracy, data analysis and visualization of biochemical networks in those species. Database URL https://solgenomics.net/tools/solcyc/ PMID:29762652

Automated PDF highlighting to support faster curation of literature for Parkinson's and Alzheimer's disease.

PubMed

Wu, Honghan; Oellrich, Anika; Girges, Christine; de Bono, Bernard; Hubbard, Tim J P; Dobson, Richard J B

2017-01-01

Neurodegenerative disorders such as Parkinson's and Alzheimer's disease are devastating and costly illnesses, a source of major global burden. In order to provide successful interventions for patients and reduce costs, both causes and pathological processes need to be understood. The ApiNATOMY project aims to contribute to our understanding of neurodegenerative disorders by manually curating and abstracting data from the vast body of literature amassed on these illnesses. As curation is labour-intensive, we aimed to speed up the process by automatically highlighting those parts of the PDF document of primary importance to the curator. Using techniques similar to those of summarisation, we developed an algorithm that relies on linguistic, semantic and spatial features. Employing this algorithm on a test set manually corrected for tool imprecision, we achieved a macro F 1 -measure of 0.51, which is an increase of 132% compared to the best bag-of-words baseline model. A user based evaluation was also conducted to assess the usefulness of the methodology on 40 unseen publications, which reveals that in 85% of cases all highlighted sentences are relevant to the curation task and in about 65% of the cases, the highlights are sufficient to support the knowledge curation task without needing to consult the full text. In conclusion, we believe that these are promising results for a step in automating the recognition of curation-relevant sentences. Refining our approach to pre-digest papers will lead to faster processing and cost reduction in the curation process. https://github.com/KHP-Informatics/NapEasy. © The Author(s) 2017. Published by Oxford University Press.

Automated PDF highlighting to support faster curation of literature for Parkinson’s and Alzheimer’s disease

PubMed Central

Oellrich, Anika; Girges, Christine; de Bono, Bernard; Hubbard, Tim J.P.; Dobson, Richard J.B.

2017-01-01

Abstract Neurodegenerative disorders such as Parkinson’s and Alzheimer’s disease are devastating and costly illnesses, a source of major global burden. In order to provide successful interventions for patients and reduce costs, both causes and pathological processes need to be understood. The ApiNATOMY project aims to contribute to our understanding of neurodegenerative disorders by manually curating and abstracting data from the vast body of literature amassed on these illnesses. As curation is labour-intensive, we aimed to speed up the process by automatically highlighting those parts of the PDF document of primary importance to the curator. Using techniques similar to those of summarisation, we developed an algorithm that relies on linguistic, semantic and spatial features. Employing this algorithm on a test set manually corrected for tool imprecision, we achieved a macro F1-measure of 0.51, which is an increase of 132% compared to the best bag-of-words baseline model. A user based evaluation was also conducted to assess the usefulness of the methodology on 40 unseen publications, which reveals that in 85% of cases all highlighted sentences are relevant to the curation task and in about 65% of the cases, the highlights are sufficient to support the knowledge curation task without needing to consult the full text. In conclusion, we believe that these are promising results for a step in automating the recognition of curation-relevant sentences. Refining our approach to pre-digest papers will lead to faster processing and cost reduction in the curation process. Database URL: https://github.com/KHP-Informatics/NapEasy PMID:28365743

The Library as Partner in University Data Curation: A Case Study in Collaboration

ERIC Educational Resources Information Center

Latham, Bethany; Poe, Jodi Welch

2012-01-01

Data curation is a concept with many facets. Curation goes beyond research-generated data, and its principles can support the preservation of institutions' historical data. Libraries are well-positioned to bring relevant expertise to such problems, especially those requiring collaboration, because of their experience as neutral caretakers and…

Curating the Shelves

ERIC Educational Resources Information Center

Schiano, Deborah

2013-01-01

Curation: to gather, organize, and present resources in a way that meets information needs and interests, makes sense for virtual as well as physical resources. A Northern New Jersey middle school library made the decision to curate its physical resources according to the needs of its users, and, in so doing, created a shelving system that is,…

Data Curation

ERIC Educational Resources Information Center

Mallon, Melissa, Ed.

2012-01-01

In their Top Trends of 2012, the Association of College and Research Libraries (ACRL) named data curation as one of the issues to watch in academic libraries in the near future (ACRL, 2012, p. 312). Data curation can be summarized as "the active and ongoing management of data through its life cycle of interest and usefulness to scholarship,…

Health Care Reform and Concurrent Curative Care for Terminally Ill Children: A Policy Analysis

PubMed Central

Lindley, Lisa C.

2012-01-01

Within the Patient Protection and Affordable Care Act of 2010 or health care reform, is a relatively small provision about concurrent curative care that significantly affects terminally ill children. Effective on March 23, 2010, terminally ill children, who are enrolled in a Medicaid or state Children’s Health Insurance Plans (CHIP) hospice benefit, may concurrently receive curative care related to their terminal health condition. The purpose of this article was to conduct a policy analysis of the concurrent curative care legislation by examining the intended goals of the policy to improve access to care and enhance quality of end of life care for terminally ill children. In addition, the policy analysis explored the political feasibility of implementing concurrent curative care at the state-level. Based on this policy analysis, the federal policy of concurrent curative care for children would generally achieve its intended goals. However, important policy omissions focus attention on the need for further federal end of life care legislation for children. These findings have implications nurses. PMID:22822304

Distilling Design Patterns From Agile Curation Case Studies

NASA Astrophysics Data System (ADS)

Benedict, K. K.; Lenhardt, W. C.; Young, J. W.

2016-12-01

In previous work the authors have argued that there is a need to take a new look at the data management lifecycle. Our core argument is that the data management lifecycle needs to be in essence deconstructed and rebuilt. As part of this process we also argue that much can be gained from applying ideas, concepts, and principles from agile software development methods. To be sure we are not arguing for a rote application of these agile software approaches, however, given various trends related to data and technology, it is imperative to update our thinking about how to approach the data management lifecycle, recognize differing project scales, corresponding variations in structure, and alternative models for solving the problems of scientific data curation. In this paper we will describe what we term agile curation design patterns, borrowing the concept of design patterns from the software world and we will present some initial thoughts on agile curation design patterns as informed by a sample of data curation case studies solicited from participants in agile data curation meeting sessions conducted in 2015-16.

[Neoadjuvant Radiochemotherapy Followed by Curative Resection in Patients with Advanced Non-Small Cell Lung Cancer in Stage IIIA/IIIB: Prognostic Factors and Results].

PubMed

Schreiner, W; Dudek, W; Lettmaier, S; Gavrychenkova, S; Rieker, R; Fietkau, R; Sirbu, H

2016-06-01

The role of surgical lung resection following neo-adjuvant radio-chemotherapy (RCT) in patients with locally advanced non-small cell lung cancer (NSCLC) is yet not clearly defined. The aim of our study was to analyze the postoperative survival and to identify relevant prognostic factors. 46 patients underwent curative resections after neo-adjuvant RCT for locally advanced NSCLC (IIIA/IIIB) between February 2008 and February 2015. A retrospective data analysis regarding preoperative regression status, perioperative mortality, postoperative survival, patho-histological remission, relapse pattern and other prognostic factors was performed. A neo-adjuvant RCT with a median radiation dose of 50.4 [range, 45-60] Gy was performed in 44 (96 %) patients. Partial and/or complete regression was observed in 32 (70 %) patients. R0-resection was achieved in 44 (96 %) patients. The 30-day mortality was 4 % and the perioperative morbidity was 37 %. The overall and progression free 5-year survival rate was 47 % and respectively 45 % [in median 58 months]. The 5-year survival rate of 64 % in the "responder"-group was significantly better when compared with 24 % in the "non-responder"-group (p = 0.038). The tri-modality therapy improved the prognosis in patients with locally advanced NSCLC (stage IIIA/IIIB). The complete patho-histological remission is an important prognostic factor for better long term survival. Dividing the patients in "responder" and "non-responder" after neo-adjuvant RCT may have large therapeutically consequences in the future. Georg Thieme Verlag KG Stuttgart · New York.

Significance of coexistent granulomatous inflammation and lung cancer

PubMed Central

Dagaonkar, Rucha S; Choong, Caroline V; Asmat, Atasha Binti; Ahmed, Dokeu Basheer A; Chopra, Akhil; Lim, Albert Y H; Tai, Dessmon Y H; Kor, Ai Ching; Goh, Soon Keng; Abisheganaden, John; Verma, Akash

2017-01-01

Aims Coexistence of lung cancer and granulomatous inflammation in the same patient confuses clinicians. We aimed to document the prevalence, clinicopathological features, treatment outcomes and prognosis in patients with coexisting granulomatous inflammation undergoing curative lung resection for lung cancer, in a tuberculosis (TB)-endemic country. Methods An observational cohort study of patients with lung cancer undergoing curative resection between 2012 and 2015 in a tertiary centre in Singapore. Results One hundred and twenty-seven patients underwent lung resection for cancer, out of which 19 (14.9%) had coexistent granulomatous inflammation in the resected specimen. Median age was 68 years and 58.2% were males. Overall median (range) survival was 451 (22–2452) days. Eighteen (14%) patients died at median duration of 271 days after surgery. The postsurgery median survival for those alive was 494 (29–2452) days in the whole group. Subgroup analysis did not reveal any differences in age, gender, location of cancer, radiological features, type of cancer, chemotherapy, history of TB or survival in patients with or without coexistent granulomatous inflammation. Conclusions Incidental detection of granulomatous inflammation in patients undergoing lung resection for cancer, even in a TB-endemic country, may not require any intervention. Such findings may be due to either mycobacterial infection in the past or ‘sarcoid reaction’ to cancer. Although all patients should have their resected specimen sent for acid-fast bacilli culture and followed up until the culture results are reported, the initiation of the management of such patients as per existing lung cancer management guidelines does not affect their outcome adversely. PMID:27646525

Patient navigation for American Indians undergoing cancer treatment: utilization and impact on care delivery in a regional healthcare center.

PubMed

Guadagnolo, B Ashleigh; Boylan, Amy; Sargent, Michele; Koop, David; Brunette, Deb; Kanekar, Shalini; Shortbull, Vanessa; Molloy, Kevin; Petereit, Daniel G

2011-06-15

A study was undertaken to assess patient navigation utilization and its impact on treatment interruptions and clinical trial enrollment among American Indian cancer patients. Between February 2004 and September 2009, 332 American Indian cancer patients received patient navigation services throughout cancer treatment. The patient navigation program provided culturally competent navigators to assist patients with navigating cancer therapy, obtaining medications, insurance issues, communicating with medical providers, and travel and lodging logistics. Data on utilization and trial enrollment were prospectively collected. Data for a historical control group of 70 American Indian patients who did not receive patient navigation services were used to compare treatment interruptions among those undergoing patient navigation during curative radiation therapy (subgroup of 123 patients). The median number of contacts with a navigator was 12 (range, 1-119). The median time spent with the navigator at first contact was 40 minutes (range, 10-250 minutes), and it was 15 minutes for subsequent contacts. Patients treated with radiation therapy with curative intent who underwent patient navigation had fewer days of treatment interruption (mean, 1.7 days; 95% confidence interval [CI], 1.1-2.2 days) than historical controls who did not receive patient navigation services (mean, 4.9 days; 95% CI, 2.9-6.9 days). Of the 332 patients, 72 (22%; 95% CI, 17%-26%) were enrolled on a clinical treatment trial or cancer control protocol. Patient navigation was associated with fewer treatment interruptions and relatively high rates of clinical trial enrollment among American Indian cancer patients compared with national reports. Copyright © 2010 American Cancer Society.

Symptomatic osteonecrosis of the femoral head after adult orthotopic liver transplantation.

PubMed

Li, Hua; Zhang, Jian; He, Ji-Wen; Wang, Kun; Wang, Gen-Shu; Jiang, Nan; Fu, Bin-Sheng; Wang, Guo-Ying; Yang, Yang; Chen, Gui-Hua

2012-07-01

With the increase of survival in liver transplantation recipients, more patients are at a high risk of developing osteonecrosis, especially in the femoral head, due to immunosuppressive treatment. The purpose of this study was to report the incidence, possible risk factors, and outcome of symptomatic osteonecrosis of the femoral head (ONFH) in adult patients with current immunosuppressive agents and individual protocol after liver transplantation in China. A retrospective analysis was performed on 226 adult patients who underwent orthotopic liver transplantation (OLT) at a single liver transplantation institution between January 2004 and December 2008. The posttransplant survival time (or pre-retransplantation survival time) of all the patients were more than 24 months. The possible pre- and post-transplantation risk factors of symptomatic ONFH were investigated and the curative effects of the treatment were also reported. The incidence of ONFH was 1.33% in patients after OLT. ONFH occurred at a mean of (14 ± 6) months (range, 10 - 21 months) after transplantation. Male patients more often presented with osteonecrosis as a complication than female patients. The patients with lower pre-transplantation total bilirubin and direct bilirubin levels (P < 0.05). There was no difference in the cumulative dose of corticosteroids or tacrolimus between the patients with or without symptomatic ONFH. Patients were treated either pharmacologically or surgically. All patients showed a nice curative effect without major complications during the 18 - 63 months post-treatment follow up. The symptomatic ONFH does not occur commonly after adult OLT in the current individual immunosuppressive protocol in China.

Efficacy of a Self-Expandable Porous Stent as the Sole Curative Treatment for Extracranial Carotid Pseudoaneurysms.

PubMed

Chen, Peng Roc; Edwards, Nancy J; Sanzgiri, Aditya; Day, Arthur L

2016-04-01

Extracranial carotid pseudoaneurysms are uncommon vascular lesions. Even with conservative management complications can happen, such as delayed cerebral embolization or symptoms due to flow limitation. Although endovascular therapy can be curative, literature demonstrating a preferred technique is scant. Our goal was to evaluate the use of 1 technique only-the deployment of overlapping self-expandable porous stents-to treat a series of extracranial carotid pseudoaneurysms. From 2008 to 2014, 14 consecutive cases of symptomatic extracranial carotid pseudoaneurysms were managed with single or multilayer porous stents at our institution. Each patient underwent a standardized angiographic follow-up at 6 months. Twelve patients also received a follow-up computed tomography angiogram at 12 months, and yearly thereafter (median radiographic follow-up, 38 months). The total clinical follow-up period ranged between 6 and 69 months (median, 46 months). In our series, each of the extracranial carotid pseudoaneurysms appeared to be the result of carotid artery dissection with associated carotid stenosis at the origin of every pseudoaneurysm. Endovascular treatment consisted of 1-3 layers of self-expandable porous stents placed without balloon angioplasty. Immediately after stenting angiographic images were notable for stagnant opacification of the pseudoaneurysm through the stent(s). All pseudoaneurysms were completely obliterated by the 6-month follow-up angiogram and remained so throughout the radiographic follow-up period. Complications were minimal, consisting of 1 patient developing a mild Horner's syndrome after treatment that resolved during clinical follow-up. Extracranial carotid pseudoaneurysms can be successfully obliterated with the use of porous, self-expandable stents. Copyright © 2016 Elsevier Inc. All rights reserved.

What Is the Ideal Tumor Regression Grading System in Rectal Cancer Patients after Preoperative Chemoradiotherapy?

PubMed Central

Kim, Soo Hee; Chang, Hee Jin; Kim, Dae Yong; Park, Ji Won; Baek, Ji Yeon; Kim, Sun Young; Park, Sung Chan; Oh, Jae Hwan; Yu, Ami; Nam, Byung-Ho

2016-01-01

Purpose Tumor regression grade (TRG) is predictive of therapeutic response in rectal cancer patients after chemoradiotherapy (CRT) followed by curative resection. However, various TRG systems have been suggested, with subjective categorization, resulting in interobserver variability. This study compared the prognostic validity of four different TRG systems in order to identify the most ideal TRG system. Materials and Methods This study included 933 patients who underwent preoperative CRT and curative resection. Primary tumors alone were graded according to the American Joint Committee on Cancer (AJCC), Dworak, and Ryan TRG systems, and both primary tumors and regional lymph nodes were graded according to a modified Dworak TRG system. The ability of each TRG system to predict recurrence-free survival (RFS) and overall survival (OS) was analyzed using chi-square and C statistics. Results All four TRG systems were significantly predictive of both RFS and OS (p < 0.001 each), however none was a better predictor of prognosis than ypStage. Among the four TRGs, the mDworak TRG system was a better predictor of RFS and OS than the AJCC, Dworak, and Ryan TRG systems, and both the chi-square and C statistics were higher for the former, although the differences were not statistically significant. The combination of ypStage and the modified Dworak TRG better predicted RFS and OS than ypStage alone. Conclusion The modified Dworak TRG system for evaluation of entire tumors including regional lymph nodes is a better predictor of survival than current TRG systems for evaluation of the primary tumor alone. PMID:26511803

Endovascular treatment of head and neck arteriovenous malformations.

PubMed

Dmytriw, A A; Ter Brugge, K G; Krings, T; Agid, R

2014-03-01

Head and neck arteriovenous malformations (H&N AVM) are associated with considerable clinical and psychosocial burden and present a significant treatment challenge. We evaluated the presentation, response to treatment, and outcome of patients with H&N AVMs treated by endovascular means at our institution. Patients with H&N AVMs treated by endovascular means from 1984 to 2012 were evaluated retrospectively. These included AVMs involving the scalp, orbit, maxillofacial, and upper neck localizations. Patient's clinical files, radiological images, catheter angiograms, and surgical reports were reviewed. Eighty-nine patients with H&N AVMs (46 females, 43 males; 48 small, 41 large) received endovascular therapy. The goals of treatment were curative (n = 30), palliative (n = 34), or presurgical (n = 25). The total number of endovascular treatment sessions was 244 (average of 1.5 per patient). The goal of treatment was met in 92.1 % of cases. Eventual cure was achieved in 42 patients accounting for 58.4 % (52/89) of all patients who underwent treatment for any goal. Twenty-eight of these patients were cured by embolization alone (28/89, 31.4 %) of which 18 were single-hole AVFs. Twenty-four were cured by planned surgical excision after presurgical embolization (24/89, 27 %). Seven patients (7/89, 7.2 %) suffered transient and two (2/89, 2.2 %) permanent endovascular treatment complications. Endovascular treatment is effective for H&N AVMs and relatively safe. It is particularly effective for symptom palliation and presurgical aid. Embolization is curative mostly in small lesions and single-hole fistulas. In patients with large non-curable H&N AVMs, endovascular therapy is often the only palliative option.

Impact of age on efficacy of postoperative oxaliplatin-based chemotherapy in patients with rectal cancer after neoadjuvant chemoradiotherapy.

PubMed

Huang, Xuan-Zhang; Gao, Peng; Song, Yong-Xi; Sun, Jing-Xu; Chen, Xiao-Wan; Zhao, Jun-Hua; Ma, Bin; Wang, Jun; Wang, Zhen-Ning

2016-04-12

Clinical practice guidelines focusing on age-related adjuvant chemotherapy for rectal cancer are currently limited. The present study aimed to explore the impact of age on the efficacy of adjuvant oxaliplatin-based chemotherapy in patients with rectal cancer after neoadjuvant chemoradiotherapy. We performed a retrospective cohort analysis using data from the Surveillance, Epidemiology, and End Results-Medicare-linked database from 1992-2009. We enrolled patients with yp stages I-III rectal cancer who received neoadjuvant chemoradiotherapy and underwent curative resection. The age-related survival benefit of adding oxaliplatin to adjuvant 5-fluorouracil (5-FU) chemotherapy was evaluated using Kaplan-Meier survival analysis with propensity score-matching and Cox proportional hazards models. Comparing the oxaliplatin group with the 5-FU group, there were significant interactions between age and chemotherapy efficacy in terms of overall survival (OS) (p for interaction = 0.017) among patients with positive lymph nodes (ypN+). Adding oxaliplatin to 5-FU could prolong survival in patients aged < 73 years and ypN+ category, and but did not translate into survival benefits in patients aged ≥ 73 years and ypN+ category. No significant interactions were observed among ypN- patients, and oxaliplatin did not significantly improve OS, regardless of age. In patients with rectal cancer who have already received neoadjuvant chemoradiotherapy and undergone curative resection, adding oxaliplatin to 5-FU could prolong OS in patients aged < 73 years and ypN+ category. However, adding oxaliplatin did not translate into survival benefits in patients age ≥ 73 years and ypN+ category, or in ypN- patients.

Agreement Between Computed Tomography and Pathologic Nodule Counts in Colorectal Lung Metastases.

PubMed

Marron, M Carmen; Lora, David; Gamez, Pablo; Rivas, Juan J; Embun, Raul; Molins, Laureano; de la Cruz, Javier

2016-01-01

Computed tomography is the most common technique used to estimate the number of pulmonary metastases and their resectability. A lack of agreement between radiologic and surgical pathologic findings could potentially lead to incomplete resection or to rejection of patients for potentially curative treatments. The objective of this study was to estimate the disagreement between the number of radiologic lesions and the number of histologically confirmed malignant lesions excised from patients with pulmonary metastases from colorectal cancer. This was a multicenter longitudinal study using a national registry. All patients underwent open surgery for pulmonary metastasectomy. Radiologic unilateral involvement was documented in 345 of 404 patients (85%); 253 (73%) presented with single nodules. The radiologic and malignant pathologic findings were concordant in 316 (78%) patients. The two independent predictors of discordance between computed tomography and the number of pathologic metastases were the bilateral involvement and the number of radiologic nodules. This model explained 28% of the variability in the disagreement frequency and discriminated between agreement and disagreement in 85% of the patients. Discrepancies increased with the nodule count with an odds ratio of 6.17 (95% confidence interval, 4.08 to 9.33) per additional nodule. For similar nodule counts, a lower disagreement frequency was observed among bilateral cases (odds ratio, 0.2; 95% confidence interval, 0.07 to 0.55). Differences between the radiologic and pathologic findings were documented in 1 of every 5 patients. The correlation was very accurate in patients with single radiologic nodules. However, half of the patients with more nodules showed discrepancies. Copyright © 2016 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

Assessment of Impact of HLA Type on Outcomes of Allogeneic Hematopoietic Stem Cell Transplantation for Chronic Lymphocytic Leukemia.

PubMed

Hill, Brian T; Ahn, Kwang Woo; Hu, Zhen-Huan; Aljurf, Mahmoud; Beitinjaneh, Amer; Cahn, Jean-Yves; Cerny, Jan; Kharfan-Dabaja, Mohamed A; Ganguly, Siddhartha; Ghosh, Nilanjan; Grunwald, Michael R; Inamoto, Yoshihiro; Kindwall-Keller, Tamila; Nishihori, Taiga; Olsson, Richard F; Saad, Ayman; Seftel, Matthew; Seo, Sachiko; Szer, Jeffrey; Tallman, Martin; Ustun, Celalettin; Wiernik, Peter H; Maziarz, Richard T; Kalaycio, Matt; Alyea, Edwin; Popat, Uday; Sobecks, Ronald; Saber, Wael

2018-03-01

Chronic lymphocytic leukemia (CLL) is a common hematologic malignancy with many highly effective therapies. Chemorefractory disease, often characterized by deletion of chromosome 17p, has historically been associated with very poor outcomes, leading to the application of allogeneic hematopoietic stem cell transplantation (allo-HCT) for medically fit patients. Although the use of allo-HCT has declined since the introduction of novel targeted therapy for the treatment of CLL, there remains significant interest in understanding factors that may influence the efficacy of allo-HCT, the only known curative treatment for CLL. The potential benefit of transplantation is most likely due to the presence of alloreactive donor T cells that mediate the graft-versus-leukemia (GVL) effect. The recognition of potentially tumor-specific antigens in the context of class I and II major histocompatibility complex on malignant B lymphocytes by donor T cells may be influenced by subtle differences in the highly polymorphic HLA locus. Given previous reports of specific HLA alleles impacting the incidence of CLL and the clinical outcomes of allo-HCT for CLL, we sought to study the overall survival and progression-free survival of a large cohort of patients with CLL who underwent allo-HCT from fully HLA-matched related and unrelated donors at Center for International Blood and Marrow Transplant Research transplantation centers. We found no statistically significant association of allo-HCT outcomes in CLL based on previously reported HLA combinations. Additional study is needed to further define the immunologic features that portend a more favorable GVL effect after allo-HCT for CLL. Copyright © 2017 The American Society for Blood and Marrow Transplantation. Published by Elsevier Inc. All rights reserved.

MicroRNAs as a potential prognostic factor in gastric cancer

PubMed Central

Brenner, Baruch; Hoshen, Moshe B; Purim, Ofer; David, Miriam Ben; Ashkenazi, Karin; Marshak, Gideon; Kundel, Yulia; Brenner, Ronen; Morgenstern, Sara; Halpern, Marisa; Rosenfeld, Nitzan; Chajut, Ayelet; Niv, Yaron; Kushnir, Michal

2011-01-01

AIM: To compare the microRNA (miR) profiles in the primary tumor of patients with recurrent and non-recurrent gastric cancer. METHODS: The study group included 45 patients who underwent curative gastrectomies from 1995 to 2005 without adjuvant or neoadjuvant therapy and for whom adequate tumor content was available. Total RNA was extracted from formalin-fixed paraffin-embedded tumor samples, preserving the small RNA fraction. Initial profiling using miR microarrays was performed to identify potential biomarkers of recurrence after resection. The expression of the differential miRs was later verified by quantitative real-time polymerase chain reaction (qRT-PCR). Findings were compared between patients who had a recurrence within 36 mo of surgery (bad-prognosis group, n = 14, 31%) and those who did not (good-prognosis group, n = 31, 69%). RESULTS: Three miRs, miR-451, miR-199a-3p and miR-195 were found to be differentially expressed in tumors from patients with good prognosis vs patients with bad prognosis (P < 0.0002, 0.0027 and 0.0046 respectively). High expression of each miR was associated with poorer prognosis for both recurrence and survival. Using miR-451, the positive predictive value for non-recurrence was 100% (13/13). The expression of the differential miRs was verified by qRT-PCR, showing high correlation to the microarray data and similar separation into prognosis groups. CONCLUSION: This study identified three miRs, miR-451, miR-199a-3p and miR-195 to be predictive of recurrence of gastric cancer. Of these, miR-451 had the strongest prognostic impact. PMID:22046085

Hospital of diagnosis and probability of having surgical treatment for resectable gastric cancer.

PubMed

van Putten, M; Verhoeven, R H A; van Sandick, J W; Plukker, J T M; Lemmens, V E P P; Wijnhoven, B P L; Nieuwenhuijzen, G A P

2016-02-01

Gastric cancer surgery is increasingly being centralized in the Netherlands, whereas the diagnosis is often made in hospitals where gastric cancer surgery is not performed. The aim of this study was to assess whether hospital of diagnosis affects the probability of undergoing surgery and its impact on overall survival. All patients with potentially curable gastric cancer according to stage (cT1/1b-4a, cN0-2, cM0) diagnosed between 2005 and 2013 were selected from The Netherlands Cancer Registry. Multilevel logistic regression was used to examine the probability of undergoing surgery according to hospital of diagnosis. The effect of variation in probability of undergoing surgery among hospitals of diagnosis on overall survival during the intervals 2005-2009 and 2010-2013 was examined by using Cox regression analysis. A total of 5620 patients with potentially curable gastric cancer, diagnosed in 91 hospitals, were included. The proportion of patients who underwent surgery ranged from 53.1 to 83.9 per cent according to hospital of diagnosis (P < 0.001); after multivariable adjustment for patient and tumour characteristics it ranged from 57.0 to 78.2 per cent (P < 0.001). Multivariable Cox regression showed that patients diagnosed between 2010 and 2013 in hospitals with a low probability of patients undergoing curative treatment had worse overall survival (hazard ratio 1.21; P < 0.001). The large variation in probability of receiving surgery for gastric cancer between hospitals of diagnosis and its impact on overall survival indicates that gastric cancer decision-making is suboptimal. © 2015 BJS Society Ltd Published by John Wiley & Sons Ltd.

Carcinoma of the pancreatic head and periampullary region. Tumor staging with laparoscopy and laparoscopic ultrasonography.

PubMed Central

John, T G; Greig, J D; Carter, D C; Garden, O J

1995-01-01

OBJECTIVE: The authors performed a prospective evaluation of staging laparoscopy with laparoscopic ultrasonography in predicting surgical resectability in patients with carcinomas of the pancreatic head and periampullary region. SUMMARY BACKGROUND DATA: Pancreatic resection with curative intent is possible in a select minority of patients who have carcinomas of the pancreatic head and periampullary region. Patient selection is important to plan appropriate therapy and avoid unnecessary laparotomy in patients with unresectable disease. Laparoscopic ultrasonography is a novel technique that combines the proven benefits of staging laparoscopy with high resolution intraoperative ultrasound of the liver and pancreas, but which has yet to be evaluated critically in the staging of pancreatic malignancy. METHODS: A cohort of 40 consecutive patients referred to a tertiary referral center and with a diagnosis of potentially resectable pancreatic or periampullary cancer underwent staging laparoscopy with laparoscopic ultrasonography. The diagnostic accuracy of staging laparoscopy alone and in conjunction with laparoscopic ultrasonography was evaluated in predicting tumor resectability (absence of peritoneal or liver metastases; absence of malignant regional lymphadenopathy; tumor confined to pancreatic head or periampullary region). RESULTS: "Occult" metastatic lesions were demonstrated by staging laparoscopy in 14 patients (35%). Laparoscopic ultrasonography demonstrated factors confirming unresectable tumor in 23 patients (59%), provided staging information in addition to that of laparoscopy alone in 20 patients (53%), and changed the decision regarding tumor resectability in 10 patients (25%). Staging laparoscopy with laparoscopic ultrasonography was more specific and accurate in predicting tumor resectability than laparoscopy alone (88% and 89% versus 50% and 65%, respectively). CONCLUSIONS: Staging laparoscopy is indispensable in the detection of "occult" intra-abdominal metastases. Laparoscopic ultrasonography improves the accuracy of laparoscopic staging in patients with potentially resectable pancreatic and periampullary carcinomas. Images Figure 1. Figure 2. Figure 3. Figure 4. PMID:7857143

Pelvic radiotherapy in the setting of rheumatoid arthritis: Refining the paradigm.

PubMed

Felefly, T; Mazeron, R; Huertas, A; Canova, C H; Maroun, P; Kordahi, M; Morice, P; Deutsch, É; Haie-Méder, C; Chargari, C

2017-04-01

Conflicting results concerning the toxicity of radiotherapy in the setting of rheumatoid arthritis were reported in literature. This work describes the toxicity profiles of patients with rheumatoid arthritis undergoing pelvic radiotherapy for gynecologic malignancies at our institution. Charts of patients with rheumatoid arthritis who underwent pelvic radiotherapy for cervical or endometrial cancer in a curative intent at the Gustave-Roussy Cancer Campus between 1990 and 2015 were reviewed for treatment-related toxicities. Acute and late effects were graded as per the Common Terminology Criteria for Adverse Events version 4.0 scoring system. Eight patients with cervical cancer and three with endometrial cancer were identified. Median follow-up was 56 months. Median external beam radiotherapy dose was 45Gy. All patients received a brachytherapy boost using either pulse- or low-dose rate technique. Concomitant chemotherapy was used in seven cases. Median time from rheumatoid arthritis diagnosis to external beam radiation therapy was 5 years. No severe acute gastrointestinal or genitourinary toxicity was reported. One patient had grade 3 dermatitis. Any late toxicity occurred in 7 /11 patients, and one patient experienced severe late toxicities. One patient with overt systemic rheumatoid arthritis symptoms at the time of external beam radiation therapy experienced late grade 3 ureteral stenosis, enterocolitis and lumbar myelitis. Pelvic radiotherapy, in the setting of rheumatoid arthritis, appears to be feasible, with potentially slight increase in low grade late events compared to other anatomic sites. Patients with overt systemic rheumatoid arthritis manifestation at the time of radiotherapy might be at risk of potential severe toxicities. Copyright © 2017 Société française de radiothérapie oncologique (SFRO). Published by Elsevier SAS. All rights reserved.

Technical Tension Between Achieving Particulate and Molecular Organic Environmental Cleanliness: Data from Astromaterial Curation Laboratories

NASA Technical Reports Server (NTRS)

Allton, J. H.; Burkett, P. J.

2011-01-01

NASA Johnson Space Center operates clean curation facilities for Apollo lunar, Antarctic meteorite, stratospheric cosmic dust, Stardust comet and Genesis solar wind samples. Each of these collections is curated separately due unique requirements. The purpose of this abstract is to highlight the technical tensions between providing particulate cleanliness and molecular cleanliness, illustrated using data from curation laboratories. Strict control of three components are required for curating samples cleanly: a clean environment; clean containers and tools that touch samples; and use of non-shedding materials of cleanable chemistry and smooth surface finish. This abstract focuses on environmental cleanliness and the technical tension between achieving particulate and molecular cleanliness. An environment in which a sample is manipulated or stored can be a room, an enclosed glovebox (or robotic isolation chamber) or an individual sample container.

EURO-CARES: European Roadmap for a Sample Return Curation Facility and Planetary Protection Implications.

NASA Astrophysics Data System (ADS)

Brucato, John Robert

2016-07-01

A mature European planetary exploration program and evolving sample return mission plans gathers the interest of a wider scientific community. The interest is generated from studying extraterrestrial samples in the laborato-ry providing new opportunities to address fundamental issues on the origin and evolution of the Solar System, on the primordial cosmochemistry, and on the nature of the building blocks of terrestrial planets and on the origin of life. Major space agencies are currently planning for missions that will collect samples from a variety of Solar Sys-tem environments, from primitive (carbonaceous) small bodies, from the Moon, Mars and its moons and, final-ly, from icy moons of the outer planets. A dedicated sample return curation facility is seen as an essential re-quirement for the receiving, assessment, characterization and secure preservation of the collected extraterrestrial samples and potentially their safe distribution to the scientific community. EURO-CARES is a European Commission study funded under the Horizon-2020 program. The strategic objec-tive of EURO-CARES is to create a roadmap for the implementation of a European Extraterrestrial Sample Cu-ration Facility. The facility has to provide safe storage and handling of extraterrestrial samples and has to enable the preliminary characterization in order to achieve the required effectiveness and collaborative outcomes for the whole international scientific community. For example, samples returned from Mars could pose a threat on the Earth's biosphere if any living extraterrestrial organism are present in the samples. Thus planetary protection is an essential aspect of all Mars sample return missions that will affect the retrival and transport from the point of return, sample handling, infrastructure methodology and management of a future curation facility. Analysis of the state of the art of Planetary Protection technology shows there are considerable possibilities to define and develop technical and scientific features in a sample return mission and the infrastructural, procedur-al and legal issues that consequently rely on a curation facility. This specialist facility will be designed with con-sideration drawn from highcontainment laboratories and cleanroom facilities to protect the Earth from contami-nation with potential Martian organisms and the samples from Earth contaminations. This kind of integrated facility does not currently exist and this emphasises the need for an innovative design approach with an integrat-ed and multidisciplinary design to enable the ultimate science goals of such exploration. The issues of how the Planetary Protection considerations impact on the system technologies and scientific meaurements, with a final aim to prioritize outstanding technology needs is presented in the framework of sam-ple return study missions and the Horizon-2020 EURO-CARES project.

The Nanomaterial Data Curation Initiative: A collaborative approach to assessing, evaluating, and advancing the state of the field

PubMed Central

Powers, Christina M; Hoover, Mark D; Harper, Stacey L

2015-01-01

Summary The Nanomaterial Data Curation Initiative (NDCI), a project of the National Cancer Informatics Program Nanotechnology Working Group (NCIP NanoWG), explores the critical aspect of data curation within the development of informatics approaches to understanding nanomaterial behavior. Data repositories and tools for integrating and interrogating complex nanomaterial datasets are gaining widespread interest, with multiple projects now appearing in the US and the EU. Even in these early stages of development, a single common aspect shared across all nanoinformatics resources is that data must be curated into them. Through exploration of sub-topics related to all activities necessary to enable, execute, and improve the curation process, the NDCI will provide a substantive analysis of nanomaterial data curation itself, as well as a platform for multiple other important discussions to advance the field of nanoinformatics. This article outlines the NDCI project and lays the foundation for a series of papers on nanomaterial data curation. The NDCI purpose is to: 1) present and evaluate the current state of nanomaterial data curation across the field on multiple specific data curation topics, 2) propose ways to leverage and advance progress for both individual efforts and the nanomaterial data community as a whole, and 3) provide opportunities for similar publication series on the details of the interactive needs and workflows of data customers, data creators, and data analysts. Initial responses from stakeholder liaisons throughout the nanoinformatics community reveal a shared view that it will be critical to focus on integration of datasets with specific orientation toward the purposes for which the individual resources were created, as well as the purpose for integrating multiple resources. Early acknowledgement and undertaking of complex topics such as uncertainty, reproducibility, and interoperability is proposed as an important path to addressing key challenges within the nanomaterial community, such as reducing collateral negative impacts and decreasing the time from development to market for this new class of technologies. PMID:26425427

Organic Contamination Baseline Study: In NASA JSC Astromaterials Curation Laboratories. Summary Report

NASA Technical Reports Server (NTRS)

Calaway, Michael J.

2013-01-01

In preparation for OSIRIS-REx and other future sample return missions concerned with analyzing organics, we conducted an Organic Contamination Baseline Study for JSC Curation Labsoratories in FY12. For FY12 testing, organic baseline study focused only on molecular organic contamination in JSC curation gloveboxes: presumably future collections (i.e. Lunar, Mars, asteroid missions) would use isolation containment systems over only cleanrooms for primary sample storage. This decision was made due to limit historical data on curation gloveboxes, limited IR&D funds and Genesis routinely monitors organics in their ISO class 4 cleanrooms.

A semi-automated methodology for finding lipid-related GO terms.

PubMed

Fan, Mengyuan; Low, Hong Sang; Wenk, Markus R; Wong, Limsoon

2014-01-01

Although semantic similarity in Gene Ontology (GO) and other approaches may be used to find similar GO terms, there is yet a method to systematically find a class of GO terms sharing a common property with high accuracy (e.g., involving human curation). We have developed a methodology to address this issue and applied it to identify lipid-related GO terms, owing to the important and varied roles of lipids in many biological processes. Our methodology finds lipid-related GO terms in a semi-automated manner, requiring only moderate manual curation. We first obtain a list of lipid-related gold-standard GO terms by keyword search and manual curation. Then, based on the hypothesis that co-annotated GO terms share similar properties, we develop a machine learning method that expands the list of lipid-related terms from the gold standard. Those terms predicted most likely to be lipid related are examined by a human curator following specific curation rules to confirm the class labels. The structure of GO is also exploited to help reduce the curation effort. The prediction and curation cycle is repeated until no further lipid-related term is found. Our approach has covered a high proportion, if not all, of lipid-related terms with relatively high efficiency. http://compbio.ddns.comp.nus.edu.sg/∼lipidgo. © The Author(s) 2014. Published by Oxford University Press.

The curation paradigm and application tool used for manual curation of the scientific literature at the Comparative Toxicogenomics Database

PubMed Central

Davis, Allan Peter; Wiegers, Thomas C.; Murphy, Cynthia G.; Mattingly, Carolyn J.

2011-01-01

The Comparative Toxicogenomics Database (CTD) is a public resource that promotes understanding about the effects of environmental chemicals on human health. CTD biocurators read the scientific literature and convert free-text information into a structured format using official nomenclature, integrating third party controlled vocabularies for chemicals, genes, diseases and organisms, and a novel controlled vocabulary for molecular interactions. Manual curation produces a robust, richly annotated dataset of highly accurate and detailed information. Currently, CTD describes over 349 000 molecular interactions between 6800 chemicals, 20 900 genes (for 330 organisms) and 4300 diseases that have been manually curated from over 25 400 peer-reviewed articles. This manually curated data are further integrated with other third party data (e.g. Gene Ontology, KEGG and Reactome annotations) to generate a wealth of toxicogenomic relationships. Here, we describe our approach to manual curation that uses a powerful and efficient paradigm involving mnemonic codes. This strategy allows biocurators to quickly capture detailed information from articles by generating simple statements using codes to represent the relationships between data types. The paradigm is versatile, expandable, and able to accommodate new data challenges that arise. We have incorporated this strategy into a web-based curation tool to further increase efficiency and productivity, implement quality control in real-time and accommodate biocurators working remotely. Database URL: http://ctd.mdibl.org PMID:21933848

Hayabusa Recovery, Curation and Preliminary Sample Analysis: Lessons Learned from Recent Sample Return Mission

NASA Technical Reports Server (NTRS)

Zolensky, Michael E.

2011-01-01

I describe lessons learned from my participation on the Hayabusa Mission, which returned regolith grains from asteroid Itokawa in 2010 [1], comparing this with the recently returned Stardust Spacecraft, which sampled the Jupiter Family comet Wild 2. Spacecraft Recovery Operations: The mission Science and Curation teams must actively participate in planning, testing and implementing spacecraft recovery operations. The crash of the Genesis spacecraft underscored the importance of thinking through multiple contingency scenarios and practicing field recovery for these potential circumstances. Having the contingency supplies on-hand was critical, and at least one full year of planning for Stardust and Hayabusa recovery operations was necessary. Care must be taken to coordinate recovery operations with local organizations and inform relevant government bodies well in advance. Recovery plans for both Stardust and Hayabusa had to be adjusted for unexpectedly wet landing site conditions. Documentation of every step of spacecraft recovery and deintegration was necessary, and collection and analysis of launch and landing site soils was critical. We found the operation of the Woomera Text Range (South Australia) to be excellent in the case of Hayabusa, and in many respects this site is superior to the Utah Test and Training Range (used for Stardust) in the USA. Recovery operations for all recovered spacecraft suffered from the lack of a hermetic seal for the samples. Mission engineers should be pushed to provide hermetic seals for returned samples. Sample Curation Issues: More than two full years were required to prepare curation facilities for Stardust and Hayabusa. Despite this seemingly adequate lead time, major changes to curation procedures were required once the actual state of the returned samples became apparent. Sample databases must be fully implemented before sample return for Stardust we did not adequately think through all of the possible sub sampling and analytical activities before settling on a database design - Hayabusa has done a better job of this. Also, analysis teams must not be permitted to devise their own sample naming schemes. The sample handling and storage facilities for Hayabusa are the finest that exist, and we are now modifying Stardust curation to take advantage of the Hayabusa facilities. Remote storage of a sample subset is desirable. Preliminary Examination (PE) of Samples: There must be some determination of the state and quantity of the returned samples, to provide a necessary guide to persons requesting samples and oversight committees tasked with sample curation oversight. Hayabusa s sample PE, which is called HASPET, was designed so that late additions to the analysis protocols were possible, as new analytical techniques became available. A small but representative number of recovered grains are being subjected to in-depth characterization. The bulk of the recovered samples are being left untouched, to limit contamination. The HASPET plan takes maximum advantage of the unique strengths of sample return missions

Receptivity to Library Involvement in Scientific Data Curation: A Case Study at the University of Colorado Boulder

ERIC Educational Resources Information Center

Lage, Kathryn; Losoff, Barbara; Maness, Jack

2011-01-01

Increasingly libraries are expected to play a role in scientific data curation initiatives, i.e., "the management and preservation of digital data over the long-term." This case study offers a novel approach for identifying researchers who are receptive toward library involvement in data curation. The authors interviewed researchers at…

Co-Curate: Working with Schools and Communities to Add Value to Open Collections

ERIC Educational Resources Information Center

Cotterill, Simon; Hudson, Martyn; Lloyd, Katherine; Outterside, James; Peterson, John; Coburn, John; Thomas, Ulrike; Tiplady, Lucy; Robinson, Phil; Heslop, Phil

2016-01-01

Co-Curate North East is a cross-disciplinary initiative involving Newcastle University and partner organisations, working with schools and community groups in the North East of England. Co-curation builds on the concept of the "ecomuseum" model for heritage based around a virtual territory, social memory and participative input from the…

Digital Curation as a Core Competency in Current Learning and Literacy: A Higher Education Perspective

ERIC Educational Resources Information Center

Ungerer, Leona M.

2016-01-01

Digital curation may be regarded as a core competency in higher education since it contributes to establishing a sense of metaliteracy (an essential requirement for optimally functioning in a modern media environment) among students. Digital curation is gradually finding its way into higher education curricula aimed at fostering social media…

Surveillance of colorectal cancer: effectiveness of early detection of intraluminal recurrences on prognosis and survival of patients treated for cure.

PubMed

Barillari, P; Ramacciato, G; Manetti, G; Bovino, A; Sammartino, P; Stipa, V

1996-04-01

The authors evaluate the effectiveness of routine colonoscopy and marker evaluation in diagnosis of intraluminal recurrent cancer. Chart review was conducted on 481 patients who underwent curative resection for colorectal cancer between 1980 and 1990. Clinical visits were scheduled and carcinoembryonic antigen evaluation was performed every three months, and colonoscopy was performed preoperatively, 12 to 15 months after surgical treatment, and then with intervals of 12 to 24 months or when symptoms appeared. About 10 percent of patients developed intraluminal recurrences. More than one-half of metachronous lesions arose within the first 24 months, and median time to diagnosis was 25 months. Patients with left-sited tumors in the advanced stage had a higher risk of developing recurrent intraluminal disease. Twenty-nine patients underwent a second surgical operation, of which 17 cases were radical. In this group, the five-year survival was 70.6 percent, although no nonradically treated or nonresected patients survived longer than 31 months. Twenty-two patients were asymptomatic at time of diagnosis of recurrence, and of these, 12 patients underwent radical operation; on the other hand, of the 24 symptomatic patients, only 5 were treated radically. Carcinoembryonic antigen was the first sign of recurrence in eight cases. Colonoscopy must be performed within the first 12 to 15 months after operation, whereas an interval of 24 months between examinations seems sufficient to guarantee early detection of metachronous lesions. Serial tumor marker evaluation is of help in earlier diagnosis of local recurrences. Asymptomatic patients more frequently undergo another operation for cure and thus have a better survival rate.

A novel approach emphasising intra-operative superficial margin enhancement of head-neck tumours with narrow-band imaging in transoral robotic surgery.

PubMed

Vicini, C; Montevecchi, F; D'Agostino, G; DE Vito, A; Meccariello, G

2015-06-01

The primary goal of surgical oncology is to obtain a tumour resection with disease-free margins. Transoral robotic surgery (TORS) for surgical treatment of head-neck cancer is commensurate with standard treatments. However, the likelihood of positive margins after TORS is up to 20.2% in a recent US survey. The aim of this study is to evaluate the efficacy and the feasibility of narrow-band imaging (NBI) during TORS in order to improve the ability to achieve disease-free margins during tumour excision. The present study was conducted at the ENT, Head- Neck Surgery and Oral Surgery Unit, Department of Special Surgery, Morgagni Pierantoni Hospital, Azienda USL Romagna. From March 2008 to January 2015, 333 TORS were carried out for malignant and benign diseases. For the present study, we retrospectively evaluated 58 biopsy-proven squamous cell carcinoma patients who underwent TORS procedures. Patients were divided into 2 groups: (1) 32 who underwent TORS and intra-operative NBI evaluation (NBI-TORS); (2) 21 who underwent TORS with standard intra-operative white-light imaging (WLITORS). Frozen section analysis of margins on surgical specimens showed a higher rate of negative superficial lateral margins in the NBI-TORS group compared with the WLI-TORS group (87.9% vs. 57.9%, respectively, p = 0.02). The sensitivity and specificity of intra-operative use of NBI, respectively, were 72.5% and 66.7% with a negative predictive value of 87.9%. Tumour margin enhancement provided by NBI associated with magnification and 3-dimensional view of the surgical field might increase the capability to achieve an oncologically-safe resection in challenging anatomical areas where minimal curative resection is strongly recommended for function preservation.

Middle meningeal artery: Gateway for effective transarterial Onyx embolization of dural arteriovenous fistulas.

PubMed

Griessenauer, Christoph J; He, Lucy; Salem, Mohamed; Chua, Michelle H; Ogilvy, Christopher S; Thomas, Ajith J

2016-09-01

Curative transarterial embolization of noncavernous sinus dural arteriovenous fistulas (dAVFs) is challenging. We sought to evaluate the role of the middle meningeal artery (MMA) in endovascular treatment of these lesions. We performed a retrospective cohort study on patients who underwent transarterial Onyx embolization of a noncavernous sinus dAVFs with contribution from the MMA at a major academic institution in the United States from January 2009 to January 2015. Twenty consecutive patients who underwent transarterial Onyx embolization of a noncavernous sinus dAVF were identified. One patient was excluded as there was no MMA contribution to the dAVF. All of the remaining 19 patients (61.3 ± 13.8 years of age) underwent transarterial embolization through the MMA. Six patients (31.6%) presented with intraparenchymal or subarachnoid hemorrhage from the dAVF. The overall angiographic cure rate was 73.7% upon last follow up. In 71.4% of successfully treated patients transarterial embolization of the MMA alone was sufficient to achieve angiographic cure. When robust MMA supply was present, MMA embolization resulted in angiographic cure even after embolization of other arterial feeders had failed in 92.9% of patients. A robust contribution of the MMA to the fistula was the single most important predictor for successful embolization (P = 0.00129). We attribute our findings to the fairly straight, non-tortuous course of the MMA that facilitates microcatheter access, navigation, and Onyx penetration. Noncavernous sinus dAVF can be successfully embolized with transarterial Onyx through the MMA, as long as supply is robust. A transvenous approach is rarely necessary. Clin. Anat. 29:718-728, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

PubMed Central

VICINI, C.; MONTEVECCHI, F.; D'AGOSTINO, G.; DE VITO, A.

2015-01-01

SUMMARY The primary goal of surgical oncology is to obtain a tumour resection with disease-free margins. Transoral robotic surgery (TORS) for surgical treatment of head-neck cancer is commensurate with standard treatments. However, the likelihood of positive margins after TORS is up to 20.2% in a recent US survey. The aim of this study is to evaluate the efficacy and the feasibility of narrow-band imaging (NBI) during TORS in order to improve the ability to achieve disease-free margins during tumour excision. The present study was conducted at the ENT, Head- Neck Surgery and Oral Surgery Unit, Department of Special Surgery, Morgagni Pierantoni Hospital, Azienda USL Romagna. From March 2008 to January 2015, 333 TORS were carried out for malignant and benign diseases. For the present study, we retrospectively evaluated 58 biopsy-proven squamous cell carcinoma patients who underwent TORS procedures. Patients were divided into 2 groups: (1) 32 who underwent TORS and intra-operative NBI evaluation (NBI-TORS); (2) 21 who underwent TORS with standard intra-operative white-light imaging (WLITORS). Frozen section analysis of margins on surgical specimens showed a higher rate of negative superficial lateral margins in the NBI-TORS group compared with the WLI-TORS group (87.9% vs. 57.9%, respectively, p = 0.02). The sensitivity and specificity of intra-operative use of NBI, respectively, were 72.5% and 66.7% with a negative predictive value of 87.9%. Tumour margin enhancement provided by NBI associated with magnification and 3-dimensional view of the surgical field might increase the capability to achieve an oncologically-safe resection in challenging anatomical areas where minimal curative resection is strongly recommended for function preservation. PMID:26246659

The preventive-curative conflict in primary health care.

PubMed

De Sa, C

1993-04-01

Approximately 80% of the rural population in developing countries do not have access to appropriate curative care. The primary health care (PHC) approach emphasizes promotive and preventive services. Yet most people in developing countries consider curative care to be more important. Thus, PHC should include curative and rehabilitative care along with preventive and promotive care. The conflict between preventive and curative care is apparent at the community level, among health workers from all levels of the health system, and among policy makers. Community members are sometimes willing to pay for curative services but not preventive services. Further, they believe that they already know enough to prevent illness. Community health workers (CHWs), the mainstays of most PHC projects are trained in preventive efforts, but this hinders their effectiveness, since the community expects curative care. Besides, 66% of villagers' health problems require curative care. Further, CHWs are isolated from health professionals, adding to their inability to effect positive change. Health professionals are often unable to set up a relationship of trust with the community, largely due to their urban-based medical education. They tend not to explain treatment to patients or to simplify explanations in a condescending manner. They also mystify diseases, preventing people from understanding their own bodies and managing their illnesses. National governments often misinterpret national health policies promoting PHC and implement them from a top-down approach rather than from the bottom-up PHC-advocated approach. Nongovernmental organizations (NGOs) and international agencies also interpret PHC in different ways. Still, strong partnerships between government, NGOs, private sector, and international agencies are needed for effective implementation of PHC. Yet, many countries continue to have complex hierarchical social structures, inequitable distribution, and inadequate resources, making it difficult to implement effective PHC.

Lunar and Meteorite Thin Sections for Undergraduate and Graduate Studies

NASA Astrophysics Data System (ADS)

Allen, J.; Allen, C.

2012-12-01

The Johnson Space Center (JSC) has the unique responsibility to curate NASA's extraterrestrial samples from past and future missions. Curation includes documentation, preservation, preparation, and distribution of samples for research, education, and public outreach. Studies of rock and soil samples from the Moon and meteorites continue to yield useful information about the early history of the Moon, the Earth, and the inner solar system. Petrographic Thin Section Packages containing polished thin sections of samples from either the Lunar or Meteorite collections have been prepared. Each set of twelve sections of Apollo lunar samples or twelve sections of meteorites is available for loan from JSC. The thin sections sets are designed for use in domestic college and university courses in petrology. The loan period is very strict and limited to two weeks. Contact Ms. Mary Luckey, Education Sample Curator. Email address: mary.k.luckey@nasa.gov Each set of slides is accompanied by teaching materials and a sample disk of representative lunar or meteorite samples. It is important to note that the samples in these sets are not exactly the same as the ones listed here. This list represents one set of samples. A key education resource available on the Curation website is Antarctic Meteorite Teaching Collection: Educational Meteorite Thin Sections, originally compiled by Bevan French, Glenn McPherson, and Roy Clarke and revised by Kevin Righter in 2010. Curation Websites College and university staff and students are encouraged to access the Lunar Petrographic Thin Section Set Publication and the Meteorite Petrographic Thin Section Package Resource which feature many thin section images and detailed descriptions of the samples, research results. http://curator.jsc.nasa.gov/Education/index.cfm Request research samples: http://curator.jsc.nasa.gov/ JSC-CURATION-EDUCATION-DISKS@mail.nasa.govLunar Thin Sections; Meteorite Thin Sections;

The demand for child curative care in two rural thanas of Bangladesh: effect of income and women's employment.

PubMed

Levin, A; Rahman, M A; Quayyum, Z; Routh, S; Barkat-e-Khuda

2001-01-01

This paper seeks to investigate the determinants of child health care seeking behaviours in rural Bangladesh. In particular, the effects of income, women's access to income, and the prices of obtaining child health care are examined. Data on the use of child curative care were collected in two rural areas of Bangladesh--Abhoynagar Thana of Jessore District and Mirsarai Thana of Chittagong District--in March 1997. In estimating the use of child curative care, the nested multinomial logit specification was used. The results of the analysis indicate that a woman's involvement in a credit union or income generation affected the likelihood that curative child care was used. Household wealth decreased the likelihood that the child had an illness episode and affected the likelihood that curative child care was sought. Among facility characteristics, travel time was statistically significant and was negatively associated with the use of a provider.

Reflections on curative health care in Nicaragua.

PubMed Central

Slater, R G

1989-01-01

Improved health care in Nicaragua is a major priority of the Sandinista revolution; it has been pursued by major reforms of the national health care system, something few developing countries have attempted. In addition to its internationally recognized advances in public health, considerable progress has been made in health care delivery by expanding curative medical services through training more personnel and building more facilities to fulfill a commitment to free universal health coverage. The very uneven quality of medical care is the leading problem facing curative medicine now. Underlying factors include the difficulty of adequately training the greatly increased number of new physicians. Misdiagnosis and mismanagement continue to be major problems. The curative medical system is not well coordinated with the preventive sector. Recent innovations include initiation of a "medicina integral" residency, similar to family practice. Despite its inadequacies and the handicaps of war and poverty, the Nicaraguan curative medical system has made important progress. PMID:2705603

Prognostic factors and long-term outcomes of hilar cholangiocarcinoma: A single-institution experience in China

PubMed Central

Hu, Hai-Jie; Mao, Hui; Shrestha, Anuj; Tan, Yong-Qiong; Ma, Wen-Jie; Yang, Qin; Wang, Jun-Ke; Cheng, Nan-Sheng; Li, Fu-Yu

2016-01-01

AIM: To evaluate the prognostic factors of hilar cholangiocarcinoma in a large series of patients in a single institution. METHODS: Eight hundred and fourteen patients with a diagnosis of hilar cholangiocarcinoma that were evaluated and treated between 1990 and 2014, of which 381 patients underwent curative surgery, were included in this study. Potential factors associated with overall survival (OS) and disease-free survival (DFS) were evaluated by univariate and multivariate analyses. RESULTS: Curative surgery provided the best long-term survival with a median OS of 26.3 mo. The median DFS was 18.1 mo. Multivariate analysis showed that patients with tumor size > 3 cm [hazard ratio (HR) = 1.482, 95%CI: 1.127-1.949; P = 0.005], positive nodal disease (HR = 1.701, 95%CI: 1.346-2.149; P < 0.001), poor differentiation (HR = 2.535, 95%CI: 1.839-3.493; P < 0.001), vascular invasion (HR = 1.542, 95%CI: 1.082-2.197; P = 0.017), and positive margins (HR = 1.798, 95%CI: 1.314-2.461; P < 0.001) had poor OS outcome. The independent factors for DFS were positive nodal disease (HR = 3.383, 95%CI: 2.633-4.348; P < 0.001), poor differentiation (HR = 2.774, 95%CI: 2.012-3.823; P < 0.001), vascular invasion (HR = 2.136, 95%CI: 1.658-3.236; P < 0.001), and positive margins (HR = 1.835, 95%CI: 1.256-2.679; P < 0.001). Multiple logistic regression analysis showed that caudate lobectomy [odds ratio (OR) = 9.771, 95%CI: 4.672-20.433; P < 0.001], tumor diameter (OR = 3.772, 95%CI: 1.914-7.434; P < 0.001), surgical procedures (OR = 10.236, 95%CI: 4.738-22.116; P < 0.001), American Joint Committee On Cancer T stage (OR = 2.010, 95%CI: 1.043-3.870; P = 0.037), and vascular invasion (OR = 2.278, 95%CI: 0.997-5.207; P = 0.051) were independently associated with tumor-free margin, and surgical procedures could indirectly affect survival outcome by influencing the tumor resection margin. CONCLUSION: Tumor margin, tumor differentiation, vascular invasion, and lymph node status were independent factors for OS and DFS. Surgical procedures can indirectly affect survival outcome by influencing the tumor resection margin. PMID:26937148

Efficient in vivo gene editing using ribonucleoproteins in skin stem cells of recessive dystrophic epidermolysis bullosa mouse model.

PubMed

Wu, Wenbo; Lu, Zhiwei; Li, Fei; Wang, Wenjie; Qian, Nannan; Duan, Jinzhi; Zhang, Yu; Wang, Fengchao; Chen, Ting

2017-02-14

The prokaryotic CRISPR/Cas9 system has recently emerged as a powerful tool for genome editing in mammalian cells with the potential to bring curative therapies to patients with genetic diseases. However, efficient in vivo delivery of this genome editing machinery and indeed the very feasibility of using these techniques in vivo remain challenging for most tissue types. Here, we show that nonreplicable Cas9/sgRNA ribonucleoproteins can be used to correct genetic defects in skin stem cells of postnatal recessive dystrophic epidermolysis bullosa (RDEB) mice. We developed a method to locally deliver Cas9/sgRNA ribonucleoproteins into the skin of postnatal mice. This method results in rapid gene editing in epidermal stem cells. Using this method, we show that Cas9/sgRNA ribonucleoproteins efficiently excise exon80, which covers the point mutation in our RDEB mouse model, and thus restores the correct localization of the collagen VII protein in vivo. The skin blistering phenotype is also significantly ameliorated after treatment. This study provides an in vivo gene correction strategy using ribonucleoproteins as curative treatment for genetic diseases in skin and potentially in other somatic tissues.

Data and the Shift in Systems, Services, and Literacy

ERIC Educational Resources Information Center

Mitchell, Erik T.

2012-01-01

This month, the "Journal of Web Librarianship" is exploring the idea of data curation and its uses in libraries. The word "data" is as universal now as the word "cloud" was last year, and it is no accident that libraries are exploring how best to support data curation services. Data curation involves library activities in just about every way,…

Characteristics of Quality OER Textbook Curators: An Analysis of Tullahoma City Schools' Flexbook Curators

ERIC Educational Resources Information Center

Hodge, Zach

2017-01-01

Tullahoma City Schools, a rural district in Middle Tennessee, recently switched from traditional static textbooks to an online, open educational resource platform. As a result of this change the role of curator, a teacher who creates the Flexbook by compiling and organizing content, was created. This research project sought to add to the limited…

Jointly creating digital abstracts: dealing with synonymy and polysemy

PubMed Central

2012-01-01

Background Ideally each Life Science article should get a ‘structured digital abstract’. This is a structured summary of the paper’s findings that is both human-verified and machine-readable. But articles can contain a large variety of information types and contextual details that all need to be reconciled with appropriate names, terms and identifiers, which poses a challenge to any curator. Current approaches mostly use tagging or limited entry-forms for semantic encoding. Findings We implemented a ‘controlled language’ as a more expressive representation method. We studied how usable this format was for wet-lab-biologists that volunteered as curators. We assessed some issues that arise with the usability of ontologies and other controlled vocabularies, for the encoding of structured information by ‘untrained’ curators. We take a user-oriented viewpoint, and make recommendations that may prove useful for creating a better curation environment: one that can engage a large community of volunteer curators. Conclusions Entering information in a biocuration environment could improve in expressiveness and user-friendliness, if curators would be enabled to use synonymous and polysemous terms literally, whereby each term stays linked to an identifier. PMID:23110757

Research Problems in Data Curation: Outcomes from the Data Curation Education in Research Centers Program

NASA Astrophysics Data System (ADS)

Palmer, C. L.; Mayernik, M. S.; Weber, N.; Baker, K. S.; Kelly, K.; Marlino, M. R.; Thompson, C. A.

2013-12-01

The need for data curation is being recognized in numerous institutional settings as national research funding agencies extend data archiving mandates to cover more types of research grants. Data curation, however, is not only a practical challenge. It presents many conceptual and theoretical challenges that must be investigated to design appropriate technical systems, social practices and institutions, policies, and services. This presentation reports on outcomes from an investigation of research problems in data curation conducted as part of the Data Curation Education in Research Centers (DCERC) program. DCERC is developing a new model for educating data professionals to contribute to scientific research. The program is organized around foundational courses and field experiences in research and data centers for both master's and doctoral students. The initiative is led by the Graduate School of Library and Information Science at the University of Illinois at Urbana-Champaign, in collaboration with the School of Information Sciences at the University of Tennessee, and library and data professionals at the National Center for Atmospheric Research (NCAR). At the doctoral level DCERC is educating future faculty and researchers in data curation and establishing a research agenda to advance the field. The doctoral seminar, Research Problems in Data Curation, was developed and taught in 2012 by the DCERC principal investigator and two doctoral fellows at the University of Illinois. It was designed to define the problem space of data curation, examine relevant concepts and theories related to both technical and social perspectives, and articulate research questions that are either unexplored or under theorized in the current literature. There was a particular emphasis on the Earth and environmental sciences, with guest speakers brought in from NCAR, National Snow and Ice Data Center (NSIDC), and Rensselaer Polytechnic Institute. Through the assignments, students constructed dozens of research questions informed by class readings, presentations, and discussions. A technical report is in progress on the resulting research agenda covering: data standards; infrastructure; research context; data reuse; sharing and access; preservation; and conceptual foundations. This presentation will discuss the agenda and its importance for the geosciences, highlighting high priority research questions. It will also introduce the related research to be undertaken by two DCERC doctoral students at NCAR during the 2013-2014 academic year and other data curation research in progress by the doctoral DCERC team.

Low-Dose and Limited-Volume Radiotherapy Alone for Primary Dural Marginal Zone Lymphoma: Treatment Approach and Review of Published Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Puri, Dev R.; Tereffe, Welela; Yahalom, Joachim

2008-08-01

Purpose: Primary dural lymphoma is a rare intracranial lymphoma that almost always has a marginal zone histologic type and immunophenotype and often remains localized and is thus potentially curable with radiotherapy (RT) alone. The unusual location and histologic type of primary dural marginal zone lymphoma (PDMZL) distinguish it from primary central nervous system lymphoma and poses treatment dilemmas of technique, volume, and dose that have not been well addressed. We set out to analyze our recent experience in treating PDMZL and reviewed the limited published data available. Methods and Materials: Between 2002 and 2006, we treated 5 patients with localizedmore » PDMZL. Of these 5 patients, 3 had unilateral and 2 had bilateral/multifocal involvement, and 3 underwent subtotal tumor resection and 2 biopsy only. Whole brain RT was given before involved-field RT (IFRT) in 4 patients and 1 received IFRT alone. The median whole brain RT, IFRT, and total RT dose was 20, 12, and 30 Gy, respectively. The planning computed tomography scan was always fused with the post-gadolinium magnetic resonance imaging scan to assist in the IFRT volume determination. We also analyzed the published data from 27 additional patients. Results: The median follow-up was 34 months (range, 31-52). All obtained lasting local control. One patient developed a relapse in the soft tissue of the flank and additional systemic progression but no central nervous system recurrence. At last follow-up, no significant treatment-related neurotoxicity was detected. Conclusion: The results of our study have demonstrated that a combination of whole brain RT/IFRT or even low-dose IFRT alone provides excellent durable local control of PDMZL. This approach is potentially curative, possibly without significant neurotoxicity. Additional study and longer follow-up are needed to determine the appropriate RT dose and volume parameters for this rare, debilitating, and yet potentially curable lymphoma.« less

PathNER: a tool for systematic identification of biological pathway mentions in the literature

PubMed Central

2013-01-01

Background Biological pathways are central to many biomedical studies and are frequently discussed in the literature. Several curated databases have been established to collate the knowledge of molecular processes constituting pathways. Yet, there has been little focus on enabling systematic detection of pathway mentions in the literature. Results We developed a tool, named PathNER (Pathway Named Entity Recognition), for the systematic identification of pathway mentions in the literature. PathNER is based on soft dictionary matching and rules, with the dictionary generated from public pathway databases. The rules utilise general pathway-specific keywords, syntactic information and gene/protein mentions. Detection results from both components are merged. On a gold-standard corpus, PathNER achieved an F1-score of 84%. To illustrate its potential, we applied PathNER on a collection of articles related to Alzheimer's disease to identify associated pathways, highlighting cases that can complement an existing manually curated knowledgebase. Conclusions In contrast to existing text-mining efforts that target the automatic reconstruction of pathway details from molecular interactions mentioned in the literature, PathNER focuses on identifying specific named pathway mentions. These mentions can be used to support large-scale curation and pathway-related systems biology applications, as demonstrated in the example of Alzheimer's disease. PathNER is implemented in Java and made freely available online at http://sourceforge.net/projects/pathner/. PMID:24555844

Advances in Small Particle Handling of Astromaterials in Preparation for OSIRIS-REx and Hayabusa2: Initial Developments

NASA Technical Reports Server (NTRS)

Snead, C. J.; McCubbin, F. M.; Nakamura-Messenger, K.; Righter, K.

2018-01-01

The Astromaterials Acquisition and Curation office at NASA Johnson Space Center has established an Advanced Curation program that is tasked with developing procedures, technologies, and data sets necessary for the curation of future astromaterials collections as envisioned by NASA exploration goals. One particular objective of the Advanced Curation program is the development of new methods for the collection, storage, handling and characterization of small (less than 100 micrometer) particles. Astromaterials Curation currently maintains four small particle collections: Cosmic Dust that has been collected in Earth's stratosphere by ER2 and WB-57 aircraft, Comet 81P/Wild 2 dust returned by NASA's Stardust spacecraft, interstellar dust that was returned by Stardust, and asteroid Itokawa particles that were returned by the JAXA's Hayabusa spacecraft. NASA Curation is currently preparing for the anticipated return of two new astromaterials collections - asteroid Ryugu regolith to be collected by Hayabusa2 spacecraft in 2021 (samples will be provided by JAXA as part of an international agreement), and asteroid Bennu regolith to be collected by the OSIRIS-REx spacecraft and returned in 2023. A substantial portion of these returned samples are expected to consist of small particle components, and mission requirements necessitate the development of new processing tools and methods in order to maximize the scientific yield from these valuable acquisitions. Here we describe initial progress towards the development of applicable sample handling methods for the successful curation of future small particle collections.

Data Curation Education Grounded in Earth Sciences and the Science of Data

NASA Astrophysics Data System (ADS)

Palmer, C. L.

2015-12-01

This presentation looks back over ten years of experience advancing data curation education at two Information Schools, highlighting the vital role of earth science case studies, expertise, and collaborations in development of curriculum and internships. We also consider current data curation practices and workforce demand in data centers in the geosciences, drawing on studies conducted in the Data Curation Education in Research Centers (DCERC) initiative and the Site-Based Data Curation project. Outcomes from this decade of data curation research and education has reinforced the importance of key areas of information science in preparing data professionals to respond to the needs of user communities, provide services across disciplines, invest in standards and interoperability, and promote open data practices. However, a serious void remains in principles to guide education and practice that are distinct to the development of data systems and services that meet both local and global aims. We identify principles emerging from recent empirical studies on the reuse value of data in the earth sciences and propose an approach for advancing data curation education that depends on systematic coordination with data intensive research and propagation of current best practices from data centers into curriculum. This collaborative model can increase both domain-based and cross-disciplinary expertise among data professionals, ultimately improving data systems and services in our universities and data centers while building the new base of knowledge needed for a foundational science of data.

[Evaluation of upper urinary tract function in patients undergoing autoplastic surgery for hydronphrosis of the intrarenal pelvis].

PubMed

Kurbanaliev, R M; Usupbaev, A Ch; Kolesnichenko, I V; Sadyrbekov, N Zh; Sultanov, B M

2018-05-01

To investigate the functional state of the upper urinary tract in patients undergoing autoplastic surgery for a hydronophrosis of the intrarenal pelvis. The study comprised 78 patients with the intrarenal pelvis and impaired urinary outflow due to stricture of the ureteropelvic junction and vascular conflict (interatrial and arteriovenous narrowing), who underwent pyeloplasty using autologous tunica vaginalis. All patients underwent an incision of ureteropelvic stricture and resection of the parietal layer of the tunica vaginalis which was used to repair the obstruction site and internal stenting of the upper urinary tract. The patients were examined at baseline and during follow-up ranging from 3 months to 3 years. At three months after surgery, there was a decrease in the size of the renal pelvis and calyces with an improvement of all parameters of uro- and hemodynamics. At three years after surgery, the structural and functional parameters of the upper urinary tract were completely restored. Obstructive uropathy, resulting from the intrarenal pelvis, leads to persistently impaired urinary outflow from the upper urinary tract. Surgical intervention is the only curative treatment able to restore the urinary flow. In men with the intrarenal pelvis, the autoplastic surgery of the ureteropelvic junction obstruction using a parietal layer of the tunica vaginalis is an effective surgical modality improving renal pelvis capacity and contributing to the recovery of urinary outflow from the upper urinary tract.

Videothoracoscopy in the treatment of mediastinal cysts

PubMed Central

Brzeziński, Daniel; Kozak, Józef

2014-01-01

Introduction Progress in the development of surgical techniques has led to the growing use of video-assisted thoracoscopic surgery (VATS) techniques in mediastinal cyst treatment. Aim To present our experience of treating mediastinal cysts with the minimally invasive technique. Material and methods Fifty patients with mediastinal cysts were treated from 2001 to 2011. There were 32 women and 18 men. The age of the patients ranged from 17 to 72, the mean age being 42 years. All patients underwent basic preoperative diagnostic tests of the chest: X-ray, computed tomography (CT), bronchoscopy and spirometry; 4 patients underwent endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) and 3 fine needle aspiration biopsy (FNAB) of the described lesions. Results The VATS was performed in each case. Conversion was carried out due to superior mediastinal location in 10 cases and pleural adhesions in 3 cases. The partial resection of a cyst was performed in 3 patients. One patient was treated conservatively due to heart failure. In that patient the transthoracic needle aspiration of a cyst under ultrasound guidance using alcoholisation with 76% ethanol with a good effect was performed twice. Cyst recurrence was observed in 1 case. Conclusions The surgical access depends on the location of a cyst. The VATS resection of a superior mediastinal cyst is not always feasible. Surgery of mediastinal cysts is both diagnostic and curative. PMID:25337163

Gastric cancer perforation: experience from a tertiary care hospital.

PubMed

Kandel, Bishnu Prasad; Singh, Yogendra; Singh, Keshav Prasad; Khakurel, Mahesh

2013-01-01

Gastric cancer perforation can occurs in advanced stage of the disease and is often associated with a high morbidity and mortality. Peritonitis due to perforation needs emergency laparotomy and different surgical procedures can be performed for definitive treatment. Surgical procedures largely depend on the stage of the disease and general condition of the patient. This study was carried out to evaluate the outcome and role of different surgical procedures in gastric cancer perforation. Medical record of patients with gastric perforation, who were treated during ten years period, was reviewed retrospectively. Data regarding clinical presentation, surgical procedures, staging and survival of patients were obtained. Features suggestive of diffuse peritonitis were evident in all cases. The majority of the patients underwent emergency surgery except one who died during resuscitation. The majority of patients were in stage III and stage IV. Surgical procedure includes simple closure and omental patch in five patients, simple closure and gastrojejunostomy in nine patients, gastrectomy in six patients and Devine's antral exclusion in one patient. Surgical site infection was the most common (45.5%) postoperative complication. Four patients died within one month of the surgery. Three patients who underwent gastrectomy survived for one year and one patient survived for five years. Although gastric cancer perforation usually occurs in advanced stage of the disease, curative resection should be considered as far as possible.

Performance of a Nomogram Predicting Disease-Specific Survival After an R0 Resection for Gastric Cancer in Patients Receiving Postoperative Chemoradiation Therapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dikken, Johan L.; Department of Surgery, Leiden University Medical Center, Leiden; Coit, Daniel G.

Purpose: The internationally validated Memorial Sloan-Kettering Cancer Center (MSKCC) gastric carcinoma nomogram was based on patients who underwent curative (R0) gastrectomy, without any other therapy. The purpose of the current study was to assess the performance of this gastric cancer nomogram in patients who received chemoradiation therapy after an R0 resection for gastric cancer. Methods and Materials: In a combined dataset of 76 patients from the Netherlands Cancer Institute (NKI), and 63 patients from MSKCC, who received postoperative chemoradiation therapy (CRT) after an R0 gastrectomy, the nomogram was validated by means of the concordance index (CI) and a calibration plot. Results:more » The concordance index for the nomogram was 0.64, which was lower than the CI of the nomogram for patients who received no adjuvant therapy (0.80). In the calibration plot, observed survival was approximately 20% higher than the nomogram-predicted survival for patients receiving postoperative CRT. Conclusions: The MSKCC gastric carcinoma nomogram significantly underpredicted survival for patients in the current study, suggesting an impact of postoperative CRT on survival in patients who underwent an R0 resection for gastric cancer, which has been demonstrated by randomized controlled trials. This analysis stresses the need for updating nomograms with the incorporation of multimodal strategies.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Denecke, Timm, E-mail: timm.denecke@charite.de; Andreou, Andreas; Podrabsky, Petr

Purpose: Infiltration of the celiac trunk by adenocarcinoma of the pancreatic body has been considered a contraindication for surgical treatment, thus resulting in a very poor prognosis. The concept of distal pancreatectomy with resection of the celiac trunk offers a curative treatment option but implies the risk of relevant hepatic or gastric ischemia. We describe initial experiences in a small series of patients with left celiacopancreatectomy with or without angiographic preconditioning of arterial blood flow to the stomach and the liver. Materials and Methods: Between January 2007 and October 2009, six patients underwent simultaneous resection of the celiac trunk formore » adenocarcinoma of the pancreatic body involving the celiac axis. In four of these cases, angiographic occlusion of the celiac trunk before surgery was performed to enhance collateral flow from the gastroduodenal artery. Radiologic and surgical procedures, findings, and outcome were analyzed retrospectively. Results: Complete tumor removal (R0) succeeded in two patients, whereas four patients underwent R1-tumor resection. After surgery, one of the two patients without angiographic preparation experienced an ischemic stomach perforation 1 week after surgery. The other patient died from severe bleeding from an ischemic gastric ulcer. Of the four patients with celiac trunk embolization, none presented ischemic complications after surgery. Mean survival was 371 days. Conclusion: In this small series, ischemic complications after celiacopancreatectomy occurred only in those patients who did not receive preoperative celiac trunk embolization.« less

Retroperitoneal margin involvement by adenocarcinoma of the caecum and ascending colon: what does it mean?

PubMed

Scott, N; Jamali, A; Verbeke, C; Ambrose, N S; Botterill, I D; Jayne, D G

2008-03-01

Circumferential margin involvement (CRM) is a powerful predictor of local recurrence, distant metastasis and patient survival in rectal cancer. In this study, we aimed to determine the frequency of retroperitoneal margin involvement in right colon cancer and describe its relationship to tumour stage and outcome of surgical treatment. Two hundred and twenty-eight consecutive resections for adenocarcinoma of the ascending colon and caecum were identified between 1998 and 2006. Tumour involvement of the posterior retroperitoneal surgical resection margin (RSRM) was recorded and correlated with tumour stage, grade and clinical outcome. RSRM positive patients were compared with CRM positive rectal tumours resected in the same surgical unit. Nineteen of 228 right hemicolectomies (8.4%) showed tumour involvement of the RSRM (defined as < or = 1 mm). Approximately half of the RSRM positive patients underwent palliative resections because of synchronous distant metastases. Out of nine 'potentially curative' resections where the RSRM was involved, five patients subsequently developed metastatic recurrence and two isolated local recurrence. RSRM positivity was associated with advanced tumour stage and more extensive extramural spread than CRM positive rectal cancers. Retroperitoneal surgical resection margin involvement by caecal and ascending colon carcinoma is a marker of advanced tumour stage and associated with a high incidence of synchronous and metachronous distant metastasis. More aggressive surgery to obtain a clear margin or postoperative radiotherapy to the tumour bed is likely to benefit only a minority of patients.

Potentiation of antimalarial activity of arteether in combination with Vetiver root extract.

PubMed

Dhawan, Sangeeta; Gunjan, Sarika; Pal, Anirban; Tripathi, Renu

2016-05-01

In malaria, development of resistance towards artemisinin derivatives has urged the need for new drugs or new drug combinations to tackle the drug resistant malaria. We studied the fresh root extract of Vetiver zizanioides (Linn.) Nash (VET) with a CDRI-CIMAP antimalarial α/β arteether (ART) together for their antimalarial potential. Our results showed additive to synergistic antimalarial activity of VET and ART with sum fractional inhibitory concentrations Σ FICs 1.02 ± 0.24 and 1.12 ± 0.32 for chloroquine sensitive (CQS) and chloroquine resistant (CQR) strain of Plasmodium falciparum (William H. Welch), respectively. Further, these combinations were explored against multidrug resistant rodent malaria parasite i.e. P. yoelii nigeriensis. Analysis of in vivo interaction of ART and VET showed that 10 mg/kg x 5 days of ART with 1000 mg/kg of VET x 5 days cured 100% mice infected with MDR parasite, while the same dose of ART could produce only up to 30% cure and VET fraction was not curative at all. Synergism/additiveness, found between VET and ART is reported for the first time. The curative dose of ART in the combination was reduced to its one fourth, and thus limits the side effects, if any. Although antimalarial potential of ART was enhanced by VET, action mechanism of later needs to be elucidated in detail.

Astromaterials Acquisition and Curation Office (KT) Overview

NASA Technical Reports Server (NTRS)

Allen, Carlton

2014-01-01

The Astromaterials Acquisition and Curation Office has the unique responsibility to curate NASA's extraterrestrial samples - from past and forthcoming missions - into the indefinite future. Currently, curation includes documentation, preservation, physical security, preparation, and distribution of samples from the Moon, asteroids, comets, the solar wind, and the planet Mars. Each of these sample sets has a unique history and comes from a unique environment. The curation laboratories and procedures developed over 40 years have proven both necessary and sufficient to serve the evolving needs of a worldwide research community. A new generation of sample return missions to destinations across the solar system is being planned and proposed. The curators are developing the tools and techniques to meet the challenges of these new samples. Extraterrestrial samples pose unique curation requirements. These samples were formed and exist under conditions strikingly different from those on the Earth's surface. Terrestrial contamination would destroy much of the scientific significance of extraterrestrial materials. To preserve the research value of these precious samples, contamination must be minimized, understood, and documented. In addition, the samples must be preserved - as far as possible - from physical and chemical alteration. The elaborate curation facilities at JSC were designed and constructed, and have been operated for many years, to keep sample contamination and alteration to a minimum. Currently, JSC curates seven collections of extraterrestrial samples: (a)) Lunar rocks and soils collected by the Apollo astronauts, (b) Meteorites collected on dedicated expeditions to Antarctica, (c) Cosmic dust collected by high-altitude NASA aircraft,t (d) Solar wind atoms collected by the Genesis spacecraft, (e) Comet particles collected by the Stardust spacecraft, (f) Interstellar dust particles collected by the Stardust spacecraft, and (g) Asteroid soil particles collected by the Japan Aerospace Exploration Agency (JAXA) Hayabusa spacecraft Each of these sample sets has a unique history and comes from a unique environment. We have developed specialized laboratories and practices over many years to preserve and protect the samples, not only for current research but for studies that may be carried out in the indefinite future.

Organic Contamination Baseline Study in NASA Johnson Space Center Astromaterials Curation Laboratories

NASA Technical Reports Server (NTRS)

Calaway, Michael J.; Allen, Carlton C.; Allton, Judith H.

2014-01-01

Future robotic and human spaceflight missions to the Moon, Mars, asteroids, and comets will require curating astromaterial samples with minimal inorganic and organic contamination to preserve the scientific integrity of each sample. 21st century sample return missions will focus on strict protocols for reducing organic contamination that have not been seen since the Apollo manned lunar landing program. To properly curate these materials, the Astromaterials Acquisition and Curation Office under the Astromaterial Research and Exploration Science Directorate at NASA Johnson Space Center houses and protects all extraterrestrial materials brought back to Earth that are controlled by the United States government. During fiscal year 2012, we conducted a year-long project to compile historical documentation and laboratory tests involving organic investigations at these facilities. In addition, we developed a plan to determine the current state of organic cleanliness in curation laboratories housing astromaterials. This was accomplished by focusing on current procedures and protocols for cleaning, sample handling, and storage. While the intention of this report is to give a comprehensive overview of the current state of organic cleanliness in JSC curation laboratories, it also provides a baseline for determining whether our cleaning procedures and sample handling protocols need to be adapted and/or augmented to meet the new requirements for future human spaceflight and robotic sample return missions.

Active Science as a Contribution to the Trauma Recovery Process: Preliminary Indications with Orphans from the 1994 Genocide in Rwanda

ERIC Educational Resources Information Center

Perrier, Frederic; Nsengiyumva, Jean-Baptiste

2003-01-01

Constructivist, hands-on, inquiry-based, science activities may have a curative potential that could be valuable in a psychological assistance programme for child victims of violence and war. To investigate this idea, pilot sessions were performed in an orphanage located in Ruhengeri, Rwanda, with seven young adults and two groups of 11 children…

OntoMate: a text-mining tool aiding curation at the Rat Genome Database

PubMed Central

Liu, Weisong; Laulederkind, Stanley J. F.; Hayman, G. Thomas; Wang, Shur-Jen; Nigam, Rajni; Smith, Jennifer R.; De Pons, Jeff; Dwinell, Melinda R.; Shimoyama, Mary

2015-01-01

The Rat Genome Database (RGD) is the premier repository of rat genomic, genetic and physiologic data. Converting data from free text in the scientific literature to a structured format is one of the main tasks of all model organism databases. RGD spends considerable effort manually curating gene, Quantitative Trait Locus (QTL) and strain information. The rapidly growing volume of biomedical literature and the active research in the biological natural language processing (bioNLP) community have given RGD the impetus to adopt text-mining tools to improve curation efficiency. Recently, RGD has initiated a project to use OntoMate, an ontology-driven, concept-based literature search engine developed at RGD, as a replacement for the PubMed (http://www.ncbi.nlm.nih.gov/pubmed) search engine in the gene curation workflow. OntoMate tags abstracts with gene names, gene mutations, organism name and most of the 16 ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. All listed terms are linked both to data entry boxes and a term browser in the curation tool. OntoMate also provides user-activated filters for species, date and other parameters relevant to the literature search. Using the system for literature search and import has streamlined the process compared to using PubMed. The system was built with a scalable and open architecture, including features specifically designed to accelerate the RGD gene curation process. With the use of bioNLP tools, RGD has added more automation to its curation workflow. Database URL: http://rgd.mcw.edu PMID:25619558

A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework.

PubMed

Bandrowski, A E; Cachat, J; Li, Y; Müller, H M; Sternberg, P W; Ciccarese, P; Clark, T; Marenco, L; Wang, R; Astakhov, V; Grethe, J S; Martone, M E

2012-01-01

The breadth of information resources available to researchers on the Internet continues to expand, particularly in light of recently implemented data-sharing policies required by funding agencies. However, the nature of dense, multifaceted neuroscience data and the design of contemporary search engine systems makes efficient, reliable and relevant discovery of such information a significant challenge. This challenge is specifically pertinent for online databases, whose dynamic content is 'hidden' from search engines. The Neuroscience Information Framework (NIF; http://www.neuinfo.org) was funded by the NIH Blueprint for Neuroscience Research to address the problem of finding and utilizing neuroscience-relevant resources such as software tools, data sets, experimental animals and antibodies across the Internet. From the outset, NIF sought to provide an accounting of available resources, whereas developing technical solutions to finding, accessing and utilizing them. The curators therefore, are tasked with identifying and registering resources, examining data, writing configuration files to index and display data and keeping the contents current. In the initial phases of the project, all aspects of the registration and curation processes were manual. However, as the number of resources grew, manual curation became impractical. This report describes our experiences and successes with developing automated resource discovery and semiautomated type characterization with text-mining scripts that facilitate curation team efforts to discover, integrate and display new content. We also describe the DISCO framework, a suite of automated web services that significantly reduce manual curation efforts to periodically check for resource updates. Lastly, we discuss DOMEO, a semi-automated annotation tool that improves the discovery and curation of resources that are not necessarily website-based (i.e. reagents, software tools). Although the ultimate goal of automation was to reduce the workload of the curators, it has resulted in valuable analytic by-products that address accessibility, use and citation of resources that can now be shared with resource owners and the larger scientific community. DATABASE URL: http://neuinfo.org.

A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework

PubMed Central

Bandrowski, A. E.; Cachat, J.; Li, Y.; Müller, H. M.; Sternberg, P. W.; Ciccarese, P.; Clark, T.; Marenco, L.; Wang, R.; Astakhov, V.; Grethe, J. S.; Martone, M. E.

2012-01-01

The breadth of information resources available to researchers on the Internet continues to expand, particularly in light of recently implemented data-sharing policies required by funding agencies. However, the nature of dense, multifaceted neuroscience data and the design of contemporary search engine systems makes efficient, reliable and relevant discovery of such information a significant challenge. This challenge is specifically pertinent for online databases, whose dynamic content is ‘hidden’ from search engines. The Neuroscience Information Framework (NIF; http://www.neuinfo.org) was funded by the NIH Blueprint for Neuroscience Research to address the problem of finding and utilizing neuroscience-relevant resources such as software tools, data sets, experimental animals and antibodies across the Internet. From the outset, NIF sought to provide an accounting of available resources, whereas developing technical solutions to finding, accessing and utilizing them. The curators therefore, are tasked with identifying and registering resources, examining data, writing configuration files to index and display data and keeping the contents current. In the initial phases of the project, all aspects of the registration and curation processes were manual. However, as the number of resources grew, manual curation became impractical. This report describes our experiences and successes with developing automated resource discovery and semiautomated type characterization with text-mining scripts that facilitate curation team efforts to discover, integrate and display new content. We also describe the DISCO framework, a suite of automated web services that significantly reduce manual curation efforts to periodically check for resource updates. Lastly, we discuss DOMEO, a semi-automated annotation tool that improves the discovery and curation of resources that are not necessarily website-based (i.e. reagents, software tools). Although the ultimate goal of automation was to reduce the workload of the curators, it has resulted in valuable analytic by-products that address accessibility, use and citation of resources that can now be shared with resource owners and the larger scientific community. Database URL: http://neuinfo.org PMID:22434839

Patient-reported symptoms during radiotherapy : Clinically relevant symptom burden in patients treated with palliative and curative intent.

PubMed

Körner, Philipp; Ehrmann, Katja; Hartmannsgruber, Johann; Metz, Michaela; Steigerwald, Sabrina; Flentje, Michael; van Oorschot, Birgitt

2017-07-01

The benefits of patient-reported symptom assessment combined with integrated palliative care are well documented. This study assessed the symptom burden of palliative and curative-intent radiation oncology patients. Prior to first consultation and at the end of RT, all adult cancer patients planned to receive fractionated percutaneous radiotherapy (RT) were asked to answer the Edmonton Symptom Assessment Scale (ESAS; nine symptoms from 0 = no symptoms to 10 = worst possible symptoms). Mean values were used for curative vs. palliative and pre-post comparisons, and the clinical relevance was evaluated (symptom values ≥ 4). Of 163 participating patients, 151 patients (90.9%) completed both surveys (116 curative and 35 palliative patients). Before beginning RT, 88.6% of palliative and 72.3% of curative patients showed at least one clinically relevant symptom. Curative patients most frequently named decreased general wellbeing (38.6%), followed by tiredness (35.0%), anxiety (32.4%), depression (30.0%), pain (26.3%), lack of appetite (23.5%), dyspnea (17.8%), drowsiness (8.0%) and nausea (6.1%). Palliative patients most frequently named decreased general wellbeing (62.8%), followed by pain (62.8%), tiredness (60.0%), lack of appetite (40.0%), anxiety (38.0%), depression (33.3%), dyspnea (28.5%), drowsiness (25.7%) and nausea (14.2%). At the end of RT, the proportion of curative and palliative patients with a clinically relevant symptom had increased significantly to 79.8 and 91.4%, respectively; whereas the proportion of patients reporting clinically relevant pain had decreased significantly (42.8 vs. 62.8%, respectively). Palliative patients had significantly increased tiredness. Curative patients reported significant increases in pain, tiredness, nausea, drowsiness, lack of appetite and restrictions in general wellbeing. Assessment of patient-reported symptoms was successfully realized in radiation oncology routine. Overall, both groups showed a high symptom burden. The results prove the need of systematic symptom assessment and programs for early integrated supportive and palliative care in radiation oncology.

Trust, but verify: On the importance of chemical structure curation in cheminformatics and QSAR modeling research

PubMed Central

Fourches, Denis; Muratov, Eugene; Tropsha, Alexander

2010-01-01

Molecular modelers and cheminformaticians typically analyze experimental data generated by other scientists. Consequently, when it comes to data accuracy, cheminformaticians are always at the mercy of data providers who may inadvertently publish (partially) erroneous data. Thus, dataset curation is crucial for any cheminformatics analysis such as similarity searching, clustering, QSAR modeling, virtual screening, etc., especially nowadays when the availability of chemical datasets in public domain has skyrocketed in recent years. Despite the obvious importance of this preliminary step in the computational analysis of any dataset, there appears to be no commonly accepted guidance or set of procedures for chemical data curation. The main objective of this paper is to emphasize the need for a standardized chemical data curation strategy that should be followed at the onset of any molecular modeling investigation. Herein, we discuss several simple but important steps for cleaning chemical records in a database including the removal of a fraction of the data that cannot be appropriately handled by conventional cheminformatics techniques. Such steps include the removal of inorganic and organometallic compounds, counterions, salts and mixtures; structure validation; ring aromatization; normalization of specific chemotypes; curation of tautomeric forms; and the deletion of duplicates. To emphasize the importance of data curation as a mandatory step in data analysis, we discuss several case studies where chemical curation of the original “raw” database enabled the successful modeling study (specifically, QSAR analysis) or resulted in a significant improvement of model's prediction accuracy. We also demonstrate that in some cases rigorously developed QSAR models could be even used to correct erroneous biological data associated with chemical compounds. We believe that good practices for curation of chemical records outlined in this paper will be of value to all scientists working in the fields of molecular modeling, cheminformatics, and QSAR studies. PMID:20572635

Advancing Site-Based Data Curation for Geobiology: The Yellowstone Exemplar (Invited)

NASA Astrophysics Data System (ADS)

Palmer, C. L.; Fouke, B. W.; Rodman, A.; Choudhury, G. S.

2013-12-01

While advances in the management and archiving of scientific digital data are proceeding apace, there is an urgent need for data curation services to collect and provide access to high-value data fit for reuse. The Site-Based Data Curation (SBDC) project is establishing a framework of guidelines and processes for the curation of research data generated at scientifically significant sites. The project is a collaboration among information scientists, geobiologists, data archiving experts, and resource managers at Yellowstone National Park (YNP). Based on our previous work with the Data Conservancy on indicators of value for research data, several factors made YNP an optimal site for developing the SBDC framework, including unique environmental conditions, a permitting process for data collection, and opportunities for geo-located longitudinal data and multiple data sources for triangulation and context. Stakeholder analysis is informing the SBDC requirements, through engagement with geologists, geochemists, and microbiologists conducting research at YNP and personnel from the Yellowstone Center for Resources and other YNP units. To date, results include data value indicators specific to site-based research, minimum and optimal parameters for data description and metadata, and a strategy for organizing data around sampling events. New value indicators identified by the scientists include ease of access to park locations for verification and correction of data, and stable environmental conditions important for controlling variables. Researchers see high potential for data aggregated from the many individual investigators conducting permitted research at YNP, however reuse is clearly contingent on detailed and consistent sampling records. Major applications of SBDC include identifying connections in dynamic systems, spatial temporal synthesis, analyzing variability within and across geological features, tracking site evolution, assessing anomalies, and greater awareness of complementary research and opportunities for collaboration. Moreover, making evident the range of available YNP data will inform what should be explored next, even beyond YNP. Like funding agencies and policy makers, YNP researchers and resource managers are invested in data curation for strategic purposes related to the big picture and efficiency of science. For the scientists, YNP represents an ideal, protected natural system that can serve as an indicator of world events, and SBDC provides the ability to ask and answer broader research questions and leverage an extensive store of highly applicable data. SBDC affords YNP improved coordination and transparency of data collection activities, and easier identification of trends and connections across projects. SBDC capabilities that support broader inquiry and better coordination of scientific effort have clear implications for data curation at other research intensive sites, and may also inform how data systems can provide strategic assistance to science more generally.

The correlation of the morphological changes of ankle point and ankle joint function after surgery on the Ruedi-Allgouer type III Pilon fracture: A case series study.

PubMed

Zhou, Yifei; Cai, Leyi; Lu, Xiaolang; Yu, Yang; Hong, Jianjun

2017-08-01

To analyze the relationship between imaging findings and postoperative curative effect by measuring the morphology of the ankle mortise in patients with the Ruedi-Allgouer type III Pilon fractures. Forty-seven patients with Ruedi-Allgouer type III Pilon fractures who underwent surgical treatment from January 2011 to January 2015 were retrospectively analyzed. At the last follow-up, x-rays of the affected ankle and the healthy side were measured. According to the Kitaoka score of ankle joint function at the last follow-up. All patients were followed up for 18-24 months (mean 21 months). This study demonstrated that compared with the healthy side, the index of the width, depth, and coronal/sagittal angles of the ankle mortise were significantly different (P < 0.05) in the 47 patients except for the index of height (P > 0.05). According to the Kitaoka score, the difference between the affected and the healthy sides of each index of the ankle mortise was compared between the 3 groups. That is, the intraoperative treatment of the width and depth of the ankle mortise as well as the coronal and sagittal angles of the ankle mortise were significantly correlated with the postoperative curative effect. The intraoperative treatment of ankle mortise width, depth, and ankle coronal/sagittal angle in patients with severe Pilon fractures has a significant impact on postoperative efficacy. In order to prevent the occurrence of traumatic arthritis, the anatomical morphology of the ankle should be restored as much as possible in the course of surgery. Copyright © 2017. Published by Elsevier Ltd.

Oncological superiority of hilar en bloc resection for the treatment of hilar cholangiocarcinoma.

PubMed

Neuhaus, Peter; Thelen, Armin; Jonas, Sven; Puhl, Gero; Denecke, Timm; Veltzke-Schlieker, Wilfried; Seehofer, Daniel

2012-05-01

Long-term results after liver resection for hilar cholangiocarcinoma are still not satisfactory. Previously, we described a survival advantage of patients who undergo combined right trisectionectomy and portal vein resection, a procedure termed "hilar en bloc resection." The present study was conducted to analyze its oncological effectiveness compared to conventional hepatectomy. During hilar en bloc resection, the extrahepatic bile ducts were resected en bloc with the portal vein bifurcation, the right hepatic artery, and liver segments 1 and 4 to 8. With this "no-touch" technique, preparation of the hilar vessels in the vicinity of the tumor was avoided. The long-term outcome of 50 consecutive patients who underwent curative (R0) hilar en bloc resection between 1990 and 2004 was compared to that of 50 consecutive patients who received curative conventional major hepatectomy for hilar cholangiocarcinoma (perioperative deaths excluded). The 1-, 3-, and 5-year survival rates after hilar en bloc resection were 87%, 70%, and 58%, respectively, which was significantly higher than after conventional major hepatectomy. In the latter group, 1-, 3-, and 5-year survival rates were 79%, 40%, and 29%, respectively (P = 0.021). Tumor characteristics were comparable in both groups. A high number of pT3 and pT4 tumors and patients with positive regional lymph nodes were present in both groups. Multivariate analysis identified hilar en bloc resection as an independent prognostic factor for long-term survival (P = 0.036). In patients with central bile duct carcinomas, hilar en bloc resection is oncologically superior to conventional major hepatectomy, providing a chance of long-term survival even in advanced tumors.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hata, Masaharu, E-mail: mhata@syd.odn.ne.j; Omura, Motoko; Koike, Izumi

Purpose: Extramammary Paget's disease (EMPD) is a relatively rare malignancy that usually arises in the genital areas. Wide surgical excision remains the standard and most reliable curative treatment of EMPD. However, surgery is sometimes not possible, because many patients are elderly, and complete excision can be difficult owing to the tumor location. We, therefore, performed a review to determine the role of radiotherapy (RT) for EMPD. Methods and Materials: A total of 22 patients with EMPD in their external genitalia (4 men and 18 women, age 52-94 years at RT) underwent RT with curative intent. Nine patients had regional lymphmore » node metastases. A total dose of 45-70.2 Gy (median, 60) was delivered to the pelvis, including the tumors, in 25-39 fractions (median, 33). Results: In all but 3 patients, the irradiated tumors were controlled during a follow-up period of 8-133 months (median, 42). Of the 22 patients, 13 developed recurrences, including local progression within the radiation field in 3 and lymph node and/or distant metastases outside the radiation field in 10, at 3-43 months after treatment. The 2- and 5-year local progression-free rates were 91% and 84%, respectively. Of the 22 patients, 7 patients had died at 33-73 months after RT. The cause of death was tumor progression in 4, infectious pneumonia in 2, and renal failure in 1 patient. The overall and cause-specific survival rates were 100% for both at 2 years and 53% and 73% at 5 years, respectively. No therapy-related Grade 3 or greater toxicity was observed. Conclusions: RT is safe and effective for patients with EMPD. It appears to contribute to prolonged survival as a result of good tumor control.« less

Added prognostic value of CT characteristics and IASLC/ATS/ERS histologic subtype in surgically resected lung adenocarcinomas.

PubMed

Suh, Young Joo; Lee, Hyun-Ju; Kim, Young Tae; Kang, Chang Hyun; Park, In Kyu; Jeon, Yoon Kyung; Chung, Doo Hyun

2018-06-01

Our study investigates the added value of computed tomography (CT) characteristics, histologic subtype classification of the International Association for the Study of Lung Cancer (IASLC)/the American Thoracic Society (ATS)/the European Respiratory Society (ERS), and genetic mutation for predicting postoperative prognoses of patients who received curative surgical resections for lung adenocarcinoma. We retrospectively enrolled 988 patients who underwent curative resection for invasive lung adenocarcinoma between October 2007 and December 2013. Cox's proportional hazard model was used to explore the risk of recurrence-free survival, based on the combination of conventional prognostic factors, CT characteristics, IASLC/ATS/ERS histologic subtype, and epidermal growth factor receptor (EGFR) mutations. Incremental prognostic values of CT characteristics, histologic subtype, and EGFR mutations over conventional risk factors were measured by C-statistics. During median follow-up period of 44.7 months (25th to 75th percentile 24.6-59.7 months), postoperative recurrence occurred in 248 patients (25.1%). In univariate Cox proportion hazard model, female sex, tumor size and stage, CT characteristics, and predominant histologic subtype were associated with tumor recurrence (P < 0.05). In multivariate Cox regression model adjusted for tumor size and stage, both CT characteristics and histologic subtype were independent tumor recurrence predictors (P < 0.05). Cox proportion hazard models combining CT characteristics or histologic subtype with size and tumor stage showed higher C-indices (0.763 and 0.767, respectively) than size and stage-only models (C-index 0.759, P > 0.05). CT characteristics and histologic subtype have relatively limited added prognostic values over tumor size and stage in surgically resected lung adenocarcinomas. Copyright © 2018 Elsevier B.V. All rights reserved.

Impact of epidermal growth factor single-nucleotide polymorphism on recurrence of hepatocellular carcinoma after hepatectomy in patients with chronic hepatitis C virus infection.

PubMed

Yoshiya, Shohei; Fujimoto, Yukiko; Bekki, Yuki; Konishi, Hideyuki; Yamashita, Yo-Ichi; Ikegami, Toru; Yoshizumi, Tomoharu; Shirabe, Ken; Oda, Yoshinao; Maehara, Yoshihiko

2014-06-01

Epidermal growth factor (EGF) gene single-nucleotide polymorphism (SNP) is associated with an increased risk of hepatic tumors. The study aimed to elucidate the impact of EGF SNP and EGF receptor (EGFR) expression on the recurrence of hepatocellular carcinoma (HCC) after hepatectomy. To examine the impact of EGF SNP and EGFR on recurrent HCC, we retrospectively analyzed 141 HCC patients with chronic hepatitis C virus infection who underwent curative hepatectomy. The EGF *61 GG allele was present in 69 patients (48.9%), AG in 56 (39.7%) and AA in 16 (11.4%). The AA group had a significantly lower rate of intrahepatic metastasis (0% vs 16.5%, P = 0.02), lower serum EGF concentration (26.3 ± 15.9 pg/mL vs 43.4 ± 30.5 pg/mL, P = 0.02) and lower proportion of early recurrence (≤2 years; 28.6% vs 71.2%, P = 0.03) than the AG/GG group. The AA group had significantly higher recurrence-free survival than the AG/GG group (P = 0.04), but there was no significant difference in overall survival between these two groups (P = 0.97). High versus low EGFR expression analyzed by immunohistochemical staining in cancer cells was not significantly associated with overall survival (P = 0.37) or recurrence-free survival (P = 0.39). Therefore, EGF *61 AA was associated with a lower risk of recurrence after curative hepatectomy for HCC in patients with hepatitis C virus infection than other genotypes, but EGFR expression in cancer cells was not significantly associated with prognosis. © 2014 The Authors. Cancer Science published by Wiley Publishing Asia Pty Ltd on behalf of Japanese Cancer Association.

Changes in highly sensitive alpha-fetoprotein for the prediction of the outcome in patients with hepatocellular carcinoma after hepatectomy.

PubMed

Toyoda, Hidenori; Kumada, Takashi; Tada, Toshifumi; Ito, Takanori; Maeda, Atsuyuki; Kaneoka, Yuji; Kagebayashi, Chiaki; Satomura, Shinji

2014-06-01

We investigated changes in highly sensitive lens culinaris agglutinin A-reactive fraction of alpha-fetoprotein (hsAFP-L3) measured using a novel method and its predictive ability for prognosis in patients with hepatocellular carcinoma (HCC) who underwent curative hepatectomy, comparing to other HCC tumor markers, that is, AFP, des-gamma-carboxy prothrombin (DCP), and AFP-L3 measured with conventional method (cAFP-L3). AFP, DCP, and AFP-L3 including both cAFP-L3 and hsAFP-L3 were measured before and after curative hepatectomy in 187 patients. The percentage of patients with elevated tumor marker levels pre- and postoperatively was compared, and recurrence-free and overall survival rates were analyzed based on changes in tumor markers. The percentages of patients with elevated AFP, DCP, and cAFP-L3 decreased postoperatively. In contrast, the percentage of patients with elevated hsAFP-L3 did not decrease postoperatively. Both recurrence-free and overall survival rates were significantly lower in patients whose tumor marker levels remained elevated postoperatively than patients without tumor marker elevation postoperatively. Recurrence-free and overall survival rates of patients in whom hsAFP-L3 became elevated postoperatively despite normal preoperative hsAFP-L3 levels were significantly lower than those of patients with normal hsAFP-L3 postoperatively, and were similar to those of patients with persistent elevation. Preoperative elevations of AFP, DCP, and cAFP normalized in many patients postoperatively, but not for hsAFP-L3. The elevation of hsAFP-L3 identifies patients with poor prognosis despite the normalization of AFP and DCP. © 2014 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

Loss of DPC4/SMAD4 expression in primary gastrointestinal neuroendocrine tumors is associated with cancer-related death after resection.

PubMed

Roland, Christina L; Starker, Lee F; Kang, Y; Chatterjee, Deyali; Estrella, Jeannelyn; Rashid, Asif; Katz, Matthew H; Aloia, Thomas A; Lee, Jeffrey E; Dasari, Arvind; Yao, James C; Fleming, Jason B

2017-03-01

Gastrointestinal neuroendocrine tumors have frequent loss of DPC4/SMAD4 expression, a known tumor suppressor. The impact of SMAD4 loss on gastrointestinal neuroendocrine tumors aggressiveness or cancer-related patient outcomes is not defined. We examined the expression of SMAD4 in resected gastrointestinal neuroendocrine tumors and its impact on oncologic outcomes. Patients who underwent complete curative operative resection of gastrointestinal neuroendocrine tumors were identified retrospectively (n = 38). Immunohistochemical staining for SMAD4 expression was scored by a blinded pathologist and correlated with clinicopathologic features and oncologic outcomes. Twenty-nine percent of the gastrointestinal neuroendocrine tumors were SMAD4-negative and 71% SMAD4-positive. Median overall survival was 155 months (95% confidence interval, 102-208 months). Loss of SMAD4 was associated with both decreased median disease-free survival (28 months; 95% confidence interval, 16-40) months compared with 223 months (95% confidence interval, 3-443 months) for SMAD4-positive patients (P = .03) and decreased median disease-specific survival (SMAD4: 137 [95% confidence interval, 81-194] months versus SMAD4-positive: 204 [95% confidence interval, 143-264] months; P = .04). This translated into a decrease in median overall survival (SMAD4-negative: 125 (95% confidence interval, 51-214) months versus SMAD4-positive: 185 (95% confidence interval, 138-232) months; P = .02). Consistent with the known biology of the DPC4/SMAD4 gene, an absence of its protein expression in primary gastrointestinal neuroendocrine tumors was negatively associated with outcomes after curative operative resection. Copyright © 2016 Elsevier Inc. All rights reserved.

Macroscopic appearance of Type IV and giant Type III is a high risk for a poor prognosis in pathological stage II/III advanced gastric cancer with postoperative adjuvant chemotherapy

PubMed Central

Yamashita, Keishi; Ema, Akira; Hosoda, Kei; Mieno, Hiroaki; Moriya, Hiromitsu; Katada, Natsuya; Watanabe, Masahiko

2017-01-01

AIM To evaluate whether a high risk macroscopic appearance (Type IV and giant Type III) is associated with a dismal prognosis after curative surgery, because its prognostic relevance remains elusive in pathological stage II/III (pStage II/III) gastric cancer. METHODS One hundred and seventy-two advanced gastric cancer (defined as pT2 or beyond) patients with pStage II/III who underwent curative surgery plus adjuvant S1 chemotherapy were evaluated, and the prognostic relevance of a high-risk macroscopic appearance was examined. RESULTS Advanced gastric cancers with a high-risk macroscopic appearance were retrospectively identified by preoperative recorded images. A high-risk macroscopic appearance showed a significantly worse relapse free survival (RFS) (35.7%) and overall survival (OS) (34%) than an average risk appearance (P = 0.0003 and P < 0.0001, respectively). A high-risk macroscopic appearance was significantly associated with the 13th Japanese Gastric Cancer Association (JGCA) pT (P = 0.01), but not with the 13th JGCA pN. On univariate analysis for RFS and OS, prognostic factors included 13th JGCA pStage (P < 0.0001) and other clinicopathological factors including macroscopic appearance. A multivariate Cox proportional hazards model for univariate prognostic factors identified high-risk macroscopic appearance (P = 0.036, HR = 2.29 for RFS and P = 0.021, HR = 2.74 for OS) as an independent prognostic indicator. CONCLUSION A high-risk macroscopic appearance was associated with a poor prognosis, and it could be a prognostic factor independent of 13th JGCA stage in pStage II/III advanced gastric cancer. PMID:28451064

RAS mutation status predicts survival and patterns of recurrence in patients undergoing hepatectomy for colorectal liver metastases.

PubMed

Vauthey, Jean-Nicolas; Zimmitti, Giuseppe; Kopetz, Scott E; Shindoh, Junichi; Chen, Su S; Andreou, Andreas; Curley, Steven A; Aloia, Thomas A; Maru, Dipen M

2013-10-01

To determine the impact of RAS mutation status on survival and patterns of recurrence in patients undergoing curative resection of colorectal liver metastases (CLM) after preoperative modern chemotherapy. RAS mutation has been reported to be associated with aggressive tumor biology. However, the effect of RAS mutation on survival and patterns of recurrence after resection of CLM remains unclear. Somatic mutations were analyzed using mass spectroscopy in 193 patients who underwent single-regimen modern chemotherapy before resection of CLM. The relationship between RAS mutation status and survival outcomes was investigated. Detected somatic mutations included RAS (KRAS/NRAS) in 34 (18%), PIK3CA in 13 (7%), and BRAF in 2 (1%) patients. At a median follow-up of 33 months, 3-year overall survival (OS) rates were 81% in patients with wild-type versus 52.2% in patients with mutant RAS (P = 0.002); 3-year recurrence-free survival (RFS) rates were 33.5% with wild-type versus 13.5% with mutant RAS (P = 0.001). Liver and lung recurrences were observed in 89 and 83 patients, respectively. Patients with RAS mutation had a lower 3-year lung RFS rate (34.6% vs 59.3%, P < 0.001) but not a lower 3-year liver RFS rate (43.8% vs 50.2%, P = 0.181). In multivariate analyses, RAS mutation predicted worse OS [hazard ratio (HR) = 2.3, P = 0.002), overall RFS (HR = 1.9, P = 0.005), and lung RFS (HR = 2.0, P = 0.01), but not liver RFS (P = 0.181). RAS mutation predicts early lung recurrence and worse survival after curative resection of CLM. This information may be used to individualize systemic and local tumor-directed therapies and follow-up strategies.

RAS mutation status predicts survival and patterns of recurrence in patients undergoing hepatectomy for colorectal liver metastases

PubMed Central

Vauthey, Jean-Nicolas; Zimmitti, Giuseppe; Kopetz, Scott E.; Shindoh, Junichi; Chen, Su S.; Andreou, Andreas; Curley, Steven A.; Aloia, Thomas A.; Maru, Dipen M.

2013-01-01

Objective To determine the impact of RAS mutation status on survival and patterns of recurrence in patients undergoing curative resection of colorectal liver metastases (CLM) after preoperative modern chemotherapy. Summary Background Data RAS mutation has been reported to be associated with aggressive tumor biology. However, the effect of RAS mutation on survival and patterns of recurrence after resection of CLM remains unclear. Methods Somatic mutations were analyzed using mass spectroscopy in 193 patients who underwent single-regimen modern chemotherapy before resection of CLM. The relationship between RAS mutation status and survival outcomes was investigated. Results Detected somatic mutations included RAS (KRAS/NRAS) in 34 patients (18%), PIK3CA in 13 (7%), and BRAF in 2 (1%). At a median follow-up of 33 months, 3-year overall survival (OS) rates were 81% in patients with wild-type vs 52.2% in patients with mutant RAS (P=0.002); 3-year recurrence-free survival (RFS) rates were 33.5% with wild-type vs 13.5% with mutant RAS (P=0.001). Liver and lung recurrences were observed in 89 and 83 patients, respectively. Patients with RAS mutation had a lower 3-year lung RFS rate (34.6% vs 59.3%, P<0.001), but not a lower 3-year liver RFS rate (43.8% vs 50.2%, P=0.181). In multivariate analyses, RAS mutation predicted worse OS (hazard ratio [HR] 2.3, P=0.002), overall RFS (HR 1.9, P=0.005), and lung RFS (HR 2.0, P=0.01), but not liver RFS (P=0.181). Conclusions RAS mutation predicts early lung recurrence and worse survival after curative resection of CLM. This information may be used to individualize systemic and local tumor-directed therapies and follow-up strategies. PMID:24018645

Tumor location is a strong predictor of tumor progression and survival in T2 gallbladder cancer: an international multicenter study.

PubMed

Shindoh, Junichi; de Aretxabala, Xabier; Aloia, Thomas A; Roa, Juan Carlos; Roa, Ivan; Zimmitti, Giuseppe; Javle, Milind; Conrad, Claudius; Maru, Dipen M; Aoki, Taku; Vigano, Luca; Ribero, Dario; Kokudo, Norihiro; Capussotti, Lorenzo; Vauthey, Jean-Nicolas

2015-04-01

To determine the prognostic impact of tumor location in gallbladder cancer. Depth of tumor is a strong predictor of survival after curative resection of gallbladder cancer. However, the gallbladder has a unique anatomical relationship with the liver, and the clinical significance of tumor location remains unclear. For 437 patients with gallbladder cancer who underwent resection at 4 international institutions, clinicopathologic characteristics and their association with survival were analyzed. Tumor location was defined as "hepatic side" or "peritoneal side," and the prognostic significance of tumor location was evaluated. Among the 252 patients with T2 disease, patients with tumors on the hepatic side (T2h, n = 99) had higher rates of vascular invasion, neural invasion, and nodal metastasis than patients with tumors on the peritoneal side (T2p, n = 153) (51% vs 19%, 33% vs 8%, and 40% vs 17%, respectively; P < 0.01 for all). After a median follow-up of 58.9 months, 3-year and 5-year survival rates were 52.1% and 42.6%, respectively, for T2h tumors and 73.7% and 64.7%, respectively, for T2p tumors (P = 0.0006). No such differences were observed in T1 or T3 tumors. Multivariate analysis confirmed the independent association of hepatic-side location with survival in T2 tumors (hazard ratio, 2.7; 95% confidence interval, 1.7-4.2; P < 0.001). This subclassification of T2 tumors predicted recurrence in the liver (23% vs 3%; P = 0.003) and distant lymph nodes (16% vs 3%; P = 0.019) even after radical resection. After curative resection of T2 gallbladder cancer, tumor location predicts the pattern of recurrence and survival.

Lower body mass index predicts worse cancer-specific prognosis in octogenarians with colorectal cancer.

PubMed

Adachi, Tomohiro; Hinoi, Takao; Kinugawa, Yusuke; Enomoto, Toshiyuki; Maruyama, Satoshi; Hirose, Hajime; Naito, Masanori; Tanaka, Keitaro; Miyake, Yasuhiro; Watanabe, Masahiko

2016-08-01

High body mass index (BMI) is a risk factor for colorectal cancer. However, the prognostic impact of BMI and other factors may differ between elderly and younger colorectal cancer patients. We analyze here prognostic factors in the surgical management of octogenarians with colorectal cancer and clarify the prognostic impact of BMI. Cox regression analysis and propensity score methods were used to retrospectively examine the association of BMI with mortality in 1613 octogenarian patients who underwent curative surgery for stage 0-III colorectal cancer. In the Cox regression analysis, lower BMI (<18.5 kg/m(2); p = 0.001), age ≥83 years (p = 0.008), American Society of Anesthesiology class ≥3: (p = 0.001), performance status ≥2 (p = 0.003), Union for International Cancer Control (UICC) stage ≥III (p = 0.001), and postoperative adverse events (p = 0.001) were independently associated with decreased overall survival. Lower BMI (p = 0.001) and UICC stage ≥III (p = 0.001) were independently associated with decreased cancer-specific survival. After covariate adjustment, lower BMI was a risk factor for overall [hazard ratio (HR) 1.62; 95 % confidence interval (CI) 1.26-2.05; p = 0.0004] and cancer-specific survival (HR 2.00; 95 % CI 1.39-2.87; p = 0.0038) compared with normal BMI (18.5-24.9 kg/m(2)). Lower BMI is significantly and independently associated with increased mortality risk in octogenarians who undergo curative surgery for colorectal cancer. Lower BMI should be used for prognosis assessment in octogenarians with colorectal cancer.

Recovery, Transportation and Acceptance to the Curation Facility of the Hayabusa Re-Entry Capsule

NASA Technical Reports Server (NTRS)

Abe, M.; Fujimura, A.; Yano, H.; Okamoto, C.; Okada, T.; Yada, T.; Ishibashi, Y.; Shirai, K.; Nakamura, T.; Noguchi, T.;

[Efficacy analysis of proximally extended resection for locally advanced rectal cancer after neoadjuvant chemoradiotherapy].

PubMed

Qin, Qiyuan; Kuang, Yingyi; Ma, Tenghui; Wu, Yali; Wang, Huaiming; Pi, Yanna; Wang, Hui; Wang, Lei

2017-11-25

To evaluate the short-term outcomes and perioperative safety of proximally extended resection for locally advanced rectal cancer after neoadjuvant chemoradiotherapy. From colorectal cancer database in The Sixth Affiliated Hospital of Sun Yat-sen University, a cohort of patients who underwent neoadjuvant chemoradiotherapy(1.8-2.0 Gy per day, 25-28 fractions, concurrent fluorouracil-based chemotherapy) followed by curative sphincter-preserving surgery for locally advanced rectal cancer between May 2016 and June 2017 were retrospectively identified. Exclusion criteria were synchronous colon cancer, intraoperatively confirmed distal metastasis, multiple visceral resection, and emergency operation. Thirty-one patients underwent proximal extended resection and two were excluded for incomplete extended resection, then 29 patients were enrolled as the extended group. Using propensity scores matching with 1/1 ration, 29 locally advanced rectal cancer patients who underwent conventional resection after neoadjuvant chemoradiotherapy at the same time were matched as the conventional group. Clinical data of two groups were analyzed, and the baseline characteristics and short-term outcomes were compared using the t test, χ 2 test, or Mann-Whitney U test. Two groups were well balanced with respect to the baseline characteristics after propensity score matching. As compared with conventional group, patients in extended group had longer surgical specimen [(18.8±5.1) cm vs.(11.6±3.4) cm, t=6.314, P=0.000] and longer proximal resection margin [(14.8±5.5) cm vs.(8.2±3.0) cm, t=5.725, P=0.000], but also had longer total operating time [(322.4±100.7) min vs.(254.6±70.3) min, t=2.975, P=0.004] and more intraoperative blood loss [100(225) ml vs. 100(50) ml, Z=-2.403, P=0.016]. No significant differences were observed in the length of distal resection margin, ratio of positive resection margin, number of retrieved lymph node, time of analgesic use, time of draining tube use, time to first flatus, time to first oral diet, and postoperative hospital stay. During the perioperative period of 30 days, the morbidity of complication in extended group and conventional group was 17.2%(5/29) and 34.5% (10/29), respectively (P=0.134). Proximally extended resection is a radical and safe surgical alternative for locally advanced rectal cancer after neoadjuvant chemoradiotherapy, which can potentially reduce the risk of anastomosis complication.

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task

PubMed Central

Arighi, Cecilia N.; Carterette, Ben; Cohen, K. Bretonnel; Krallinger, Martin; Wilbur, W. John; Fey, Petra; Dodson, Robert; Cooper, Laurel; Van Slyke, Ceri E.; Dahdul, Wasila; Mabee, Paula; Li, Donghui; Harris, Bethany; Gillespie, Marc; Jimenez, Silvia; Roberts, Phoebe; Matthews, Lisa; Becker, Kevin; Drabkin, Harold; Bello, Susan; Licata, Luana; Chatr-aryamontri, Andrew; Schaeffer, Mary L.; Park, Julie; Haendel, Melissa; Van Auken, Kimberly; Li, Yuling; Chan, Juancarlos; Muller, Hans-Michael; Cui, Hong; Balhoff, James P.; Chi-Yang Wu, Johnny; Lu, Zhiyong; Wei, Chih-Hsuan; Tudor, Catalina O.; Raja, Kalpana; Subramani, Suresh; Natarajan, Jeyakumar; Cejuela, Juan Miguel; Dubey, Pratibha; Wu, Cathy

2013-01-01

In many databases, biocuration primarily involves literature curation, which usually involves retrieving relevant articles, extracting information that will translate into annotations and identifying new incoming literature. As the volume of biological literature increases, the use of text mining to assist in biocuration becomes increasingly relevant. A number of groups have developed tools for text mining from a computer science/linguistics perspective, and there are many initiatives to curate some aspect of biology from the literature. Some biocuration efforts already make use of a text mining tool, but there have not been many broad-based systematic efforts to study which aspects of a text mining tool contribute to its usefulness for a curation task. Here, we report on an effort to bring together text mining tool developers and database biocurators to test the utility and usability of tools. Six text mining systems presenting diverse biocuration tasks participated in a formal evaluation, and appropriate biocurators were recruited for testing. The performance results from this evaluation indicate that some of the systems were able to improve efficiency of curation by speeding up the curation task significantly (∼1.7- to 2.5-fold) over manual curation. In addition, some of the systems were able to improve annotation accuracy when compared with the performance on the manually curated set. In terms of inter-annotator agreement, the factors that contributed to significant differences for some of the systems included the expertise of the biocurator on the given curation task, the inherent difficulty of the curation and attention to annotation guidelines. After the task, annotators were asked to complete a survey to help identify strengths and weaknesses of the various systems. The analysis of this survey highlights how important task completion is to the biocurators’ overall experience of a system, regardless of the system’s high score on design, learnability and usability. In addition, strategies to refine the annotation guidelines and systems documentation, to adapt the tools to the needs and query types the end user might have and to evaluate performance in terms of efficiency, user interface, result export and traditional evaluation metrics have been analyzed during this task. This analysis will help to plan for a more intense study in BioCreative IV. PMID:23327936

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task.

PubMed

Arighi, Cecilia N; Carterette, Ben; Cohen, K Bretonnel; Krallinger, Martin; Wilbur, W John; Fey, Petra; Dodson, Robert; Cooper, Laurel; Van Slyke, Ceri E; Dahdul, Wasila; Mabee, Paula; Li, Donghui; Harris, Bethany; Gillespie, Marc; Jimenez, Silvia; Roberts, Phoebe; Matthews, Lisa; Becker, Kevin; Drabkin, Harold; Bello, Susan; Licata, Luana; Chatr-aryamontri, Andrew; Schaeffer, Mary L; Park, Julie; Haendel, Melissa; Van Auken, Kimberly; Li, Yuling; Chan, Juancarlos; Muller, Hans-Michael; Cui, Hong; Balhoff, James P; Chi-Yang Wu, Johnny; Lu, Zhiyong; Wei, Chih-Hsuan; Tudor, Catalina O; Raja, Kalpana; Subramani, Suresh; Natarajan, Jeyakumar; Cejuela, Juan Miguel; Dubey, Pratibha; Wu, Cathy

2013-01-01

In many databases, biocuration primarily involves literature curation, which usually involves retrieving relevant articles, extracting information that will translate into annotations and identifying new incoming literature. As the volume of biological literature increases, the use of text mining to assist in biocuration becomes increasingly relevant. A number of groups have developed tools for text mining from a computer science/linguistics perspective, and there are many initiatives to curate some aspect of biology from the literature. Some biocuration efforts already make use of a text mining tool, but there have not been many broad-based systematic efforts to study which aspects of a text mining tool contribute to its usefulness for a curation task. Here, we report on an effort to bring together text mining tool developers and database biocurators to test the utility and usability of tools. Six text mining systems presenting diverse biocuration tasks participated in a formal evaluation, and appropriate biocurators were recruited for testing. The performance results from this evaluation indicate that some of the systems were able to improve efficiency of curation by speeding up the curation task significantly (∼1.7- to 2.5-fold) over manual curation. In addition, some of the systems were able to improve annotation accuracy when compared with the performance on the manually curated set. In terms of inter-annotator agreement, the factors that contributed to significant differences for some of the systems included the expertise of the biocurator on the given curation task, the inherent difficulty of the curation and attention to annotation guidelines. After the task, annotators were asked to complete a survey to help identify strengths and weaknesses of the various systems. The analysis of this survey highlights how important task completion is to the biocurators' overall experience of a system, regardless of the system's high score on design, learnability and usability. In addition, strategies to refine the annotation guidelines and systems documentation, to adapt the tools to the needs and query types the end user might have and to evaluate performance in terms of efficiency, user interface, result export and traditional evaluation metrics have been analyzed during this task. This analysis will help to plan for a more intense study in BioCreative IV.

Income-related inequalities in preventive and curative dental care use among working-age Japanese adults in urban areas: a cross-sectional study.

PubMed

Murakami, Keiko; Aida, Jun; Ohkubo, Takayoshi; Hashimoto, Hideki

2014-09-19

Preventive dental care use remains relatively low in Japan, especially among working-age adults. Universal health insurance in Japan covers curative dental care with an out-of-pocket payment limit, though its coverage of preventive dental care is limited. The aim of this study was to test the hypothesis that income inequality in dental care use is found in preventive, but not curative dental care among working-age Japanese adults. A cross-sectional survey was conducted using a computer-assisted, self-administered format for community residents aged 25-50 years. In all, 4357 residents agreed to participate and complete the questionnaire (valid response rate: 31.3%). Preventive dental care use was measured according to whether the participant had visited a dentist or a dental hygienist during the past year for dental scaling or fluoride or orthodontic treatments. Curative dental care use was assessed by dental visits for other reasons. The main explanatory variable was equivalent household income. Logistic regression analyses with linear trend tests were conducted to determine whether there were significant income-related gradients with curative or preventive dental care use. Among the respondents, 40.0% of men and 41.5% of women had used curative dental care in the past year; 24.1% of men and 34.1% of women had used preventive care. We found no significant income-related gradients of curative dental care among either men or women (p = 0.234 and p = 0.270, respectively). Significant income-related gradients of preventive care were observed among both men and women (p < 0.001 and p = 0.003, respectively). Among women, however, income-related differences were no longer significant (p = 0.126) after adjusting for education and other covariates. Compared with men with the lowest income, the highest-income group had a 1.79-fold significantly higher probability for using preventive dental care. The prevalence of preventive dental care use was lower than that of curative care. The results showed income-related inequality in preventive dental care use among men, though there were no significant income-related gradients of curative dental care use among either men or women. Educational attainment had a positive association with preventive dental care use only among women.

Analysis on curative effects and safety of 2% liranaftate ointment in treating tinea pedis and tinea corporis & cruris.

PubMed

Sulaiman, Akebaier; Wan, Xuefeng; Fan, Junwei; Kasimu, Hadiliya; Dong, Xiaoyang; Wang, Xiaodong; Zhang, Lijuan; Abliz, Paride; Upur, Halmurat

2017-05-01

The paper is intended to analyze and evaluate the specific curative effect and safety of 2% liranaftate ointment in treating patients with tinea pedis and tinea cruris. 1,100 cases of patients with tinea pedis and tinea corporis & cruris were selected as research objects and were divided into two groups according to the random number table method. They were treated with different methods: 550 cases of patients were treated with 2% liranaftate ointment for external use in the observation group and the rest 550 cases of patients were treated with 1% bifonazole cream in the control group. The treatment time was two weeks for patients with tinea corporis & cruris and four weeks for those with tinea pedis respectively. Meanwhile, the one-month follow-up visit was conducted among the patients to compare the curative effects of two groups. After the medication, the curative effectiveness rate was 87.65% (482/550) in the observation group, while that was 84.91% (467/550) in the control group. After the average follow-up visits of (15.5±2.4), the curative effectiveness rate 96.55% (531/550) in the observation group, while that was 91.45% (503/550) in the control group. Two groups of patients recovered well with a low incidence of adverse reactions in the treatment, and the overall curative effect was good with the inter-group difference at P>0.05, so it was without statistical significance. The curative effect of 2% liranaftate ointment is safe and obvious in treating tinea pedis and tinea corporis & cruris, so it is valuable for clinical popularization and application.

The hepatocurative effects of Cynara scolymus L. leaf extract on carbon tetrachloride-induced oxidative stress and hepatic injury in rats.

PubMed

Colak, Emine; Ustuner, Mehmet Cengiz; Tekin, Neslihan; Colak, Ertugrul; Burukoglu, Dilek; Degirmenci, Irfan; Gunes, Hasan Veysi

2016-01-01

Cynara scolymus is a pharmacologically important medicinal plant containing phenolic acids and flavonoids. Experimental studies indicate antioxidant and hepatoprotective effects of C. scolymus but there have been no studies about therapeutic effects of liver diseases yet. In the present study, hepatocurative effects of C. scolymus leaf extract on carbon tetrachloride (CCl4)-induced oxidative stress and hepatic injury in rats were investigated by serum hepatic enzyme levels, oxidative stress indicator (malondialdehyde-MDA), endogenous antioxidants, DNA fragmentation, p53, caspase 3 and histopathology. Animals were divided into six groups: control, olive oil, CCl4, C. scolymus leaf extract, recovery and curative. CCl4 was administered at a dose of 0.2 mL/kg twice daily on CCl4, recovery and curative groups. Cynara scolymus extract was given orally for 2 weeks at a dose of 1.5 g/kg after CCl4 application on the curative group. Significant decrease of serum alanine-aminotransferase (ALT) and aspartate-aminotransferase (AST) levels were determined in the curative group. MDA levels were significantly lower in the curative group. Significant increase of superoxide dismutase (SOD) and catalase (CAT) activity in the curative group was determined. In the curative group, C. scolymus leaf extract application caused the DNA % fragmentation, p53 and caspase 3 levels of liver tissues towards the normal range. Our results indicated that C. scolymus leaf extract has hepatocurative effects of on CCl4-induced oxidative stress and hepatic injury by reducing lipid peroxidation, providing affected antioxidant systems towards the normal range. It also had positive effects on the pathway of the regulatory mechanism allowing repair of DNA damage on CCl4-induced hepatotoxicity.

Automatic reconstruction of a bacterial regulatory network using Natural Language Processing

PubMed Central

Rodríguez-Penagos, Carlos; Salgado, Heladia; Martínez-Flores, Irma; Collado-Vides, Julio

2007-01-01

Background Manual curation of biological databases, an expensive and labor-intensive process, is essential for high quality integrated data. In this paper we report the implementation of a state-of-the-art Natural Language Processing system that creates computer-readable networks of regulatory interactions directly from different collections of abstracts and full-text papers. Our major aim is to understand how automatic annotation using Text-Mining techniques can complement manual curation of biological databases. We implemented a rule-based system to generate networks from different sets of documents dealing with regulation in Escherichia coli K-12. Results Performance evaluation is based on the most comprehensive transcriptional regulation database for any organism, the manually-curated RegulonDB, 45% of which we were able to recreate automatically. From our automated analysis we were also able to find some new interactions from papers not already curated, or that were missed in the manual filtering and review of the literature. We also put forward a novel Regulatory Interaction Markup Language better suited than SBML for simultaneously representing data of interest for biologists and text miners. Conclusion Manual curation of the output of automatic processing of text is a good way to complement a more detailed review of the literature, either for validating the results of what has been already annotated, or for discovering facts and information that might have been overlooked at the triage or curation stages. PMID:17683642

In vivo antiplasmodial activities of ethanolic extract and fractions of Eleucine indica.

PubMed

Ettebong, E O; Nwafor, P A; Okokon, J E

2012-09-01

To evaluate the in vivo antiplasmodial activities of the extract and fractions (n-hexane, chloroform, ethylacetate, butanol, aqueous) of the whole plant in Plasmodium berghei berghei infected mice. Oral administrations of the extract (200, 400, and 600 mg/kg) of Eleucine indica and fractions (400 mg/kg) were screened in the 4-day, repository and curative tests. Chloroquine (5 mg/kg), pyrimethamine (1.2 mg/kg) and artesunate (5 mg/kg) were used as controls. The extract showed significant (P< 0.05-0.001) dose-dependent, antiplasmodial activity in the 4-day, repository and curative tests and increased the survival times of the infected mice. All the fractions exhibited significant antiplasmodial activity with the highest being ethylacetate fraction. Eleucine indica extract and fractions possess antimalarial activity which confirms the ethnobotanical use of this plant as a malarial remedy and opens a new highway to further investigate its potentials in the on-going fight against malaria. Copyright © 2012 Hainan Medical College. Published by Elsevier B.V. All rights reserved.

The MR-Base platform supports systematic causal inference across the human phenome

PubMed Central

Wade, Kaitlin H; Haberland, Valeriia; Baird, Denis; Laurin, Charles; Burgess, Stephen; Bowden, Jack; Langdon, Ryan; Tan, Vanessa Y; Yarmolinsky, James; Shihab, Hashem A; Timpson, Nicholas J; Evans, David M; Relton, Caroline; Martin, Richard M; Davey Smith, George

2018-01-01

Results from genome-wide association studies (GWAS) can be used to infer causal relationships between phenotypes, using a strategy known as 2-sample Mendelian randomization (2SMR) and bypassing the need for individual-level data. However, 2SMR methods are evolving rapidly and GWAS results are often insufficiently curated, undermining efficient implementation of the approach. We therefore developed MR-Base (http://www.mrbase.org): a platform that integrates a curated database of complete GWAS results (no restrictions according to statistical significance) with an application programming interface, web app and R packages that automate 2SMR. The software includes several sensitivity analyses for assessing the impact of horizontal pleiotropy and other violations of assumptions. The database currently comprises 11 billion single nucleotide polymorphism-trait associations from 1673 GWAS and is updated on a regular basis. Integrating data with software ensures more rigorous application of hypothesis-driven analyses and allows millions of potential causal relationships to be efficiently evaluated in phenome-wide association studies. PMID:29846171

Astrolabe: Curating, Linking, and Computing Astronomy’s Dark Data

NASA Astrophysics Data System (ADS)

Heidorn, P. Bryan; Stahlman, Gretchen R.; Steffen, Julie

2018-05-01

Where appropriate repositories are not available to support all relevant astronomical data products, data can fall into darkness: unseen and unavailable for future reference and reuse. Some data in this category are legacy or old data, but newer data sets are also often uncurated and could remain dark. This paper provides a description of the design motivation and development of Astrolabe, a cyberinfrastructure project that addresses a set of community recommendations for locating and ensuring the long-term curation of dark or otherwise at-risk data and integrated computing. This paper also describes the outcomes of the series of community workshops that informed creation of Astrolabe. According to participants in these workshops, much astronomical dark data currently exist that are not curated elsewhere, as well as software that can only be executed by a few individuals and therefore becomes unusable because of changes in computing platforms. Astronomical research questions and challenges would be better addressed with integrated data and computational resources that fall outside the scope of existing observatory and space mission projects. As a solution, the design of the Astrolabe system is aimed at developing new resources for management of astronomical data. The project is based in CyVerse cyberinfrastructure technology and is a collaboration between the University of Arizona and the American Astronomical Society. Overall, the project aims to support open access to research data by leveraging existing cyberinfrastructure resources and promoting scientific discovery by making potentially useful data available to the astronomical community, in a computable format.

Hepatoprotective and antioxidant activity of aqueous extract of Hybanthus enneaspermus against CCl4-induced liver injury in rats.

PubMed

Vuda, Madhusudanarao; D'Souza, Roshan; Upadhya, Suhas; Kumar, Vijay; Rao, Namita; Kumar, Vasanth; Boillat, Colette; Mungli, Prakash

2012-11-01

The hepatoprotective, curative and anti-oxidant properties of aqueous extract of Hybanthus enneaspermus (Violaceae) used against CCl4-induced liver damage in rats were investigated in the present study. Liver damage was induced by CCl4 (1 ml/kg i.p.), and silymarin was used as a standard drug to compare hepatoprotective, curative and antioxidant effects of the extract. Rats were treated with aqueous extract of H. enneaspermus at a dose of either 200 or 400 mg/kg after division into pre-treatment (once daily for 14 days before CCl4 intoxication) and post-treatment (2, 6, 24 and 48 h after CCl4 intoxication) groups. Pre-treatment and post-treatment with aqueous extract of H. enneaspermus showed significant hepatoprotection by reducing the aspartate transaminase, alanine transaminase, and alkaline phosphatase enzymatic activities and total bilirubin levels which had been raised by CCl4 administration. Pre- and post-treatment with aqueous extract significantly decreased hepatic lipid peroxidation as well as producing a corresponding increase in tissue total thiols. Post-treatment with aqueous extract improved ceruloplasmin levels. The histopathological examination of rat liver sections treated with aqueous extract confirms the serum biochemical observations. The present study results demonstrate the protective, curative and anti-oxidant effects of H. enneaspermus aqueous extract used against CCl4-induced hepatotoxicity in rats, and suggest a potential therapeutic use of H. enneaspermus as an alternative for patients with acute liver diseases. Copyright © 2011 Elsevier GmbH. All rights reserved.

MSDD: a manually curated database of experimentally supported associations among miRNAs, SNPs and human diseases

PubMed Central

Yue, Ming; Zhou, Dianshuang; Zhi, Hui; Wang, Peng; Zhang, Yan; Gao, Yue; Guo, Maoni; Li, Xin; Wang, Yanxia

2018-01-01

Abstract The MiRNA SNP Disease Database (MSDD, http://www.bio-bigdata.com/msdd/) is a manually curated database that provides comprehensive experimentally supported associations among microRNAs (miRNAs), single nucleotide polymorphisms (SNPs) and human diseases. SNPs in miRNA-related functional regions such as mature miRNAs, promoter regions, pri-miRNAs, pre-miRNAs and target gene 3′-UTRs, collectively called ‘miRSNPs’, represent a novel category of functional molecules. miRSNPs can lead to miRNA and its target gene dysregulation, and resulting in susceptibility to or onset of human diseases. A curated collection and summary of miRSNP-associated diseases is essential for a thorough understanding of the mechanisms and functions of miRSNPs. Here, we describe MSDD, which currently documents 525 associations among 182 human miRNAs, 197 SNPs, 153 genes and 164 human diseases through a review of more than 2000 published papers. Each association incorporates information on the miRNAs, SNPs, miRNA target genes and disease names, SNP locations and alleles, the miRNA dysfunctional pattern, experimental techniques, a brief functional description, the original reference and additional annotation. MSDD provides a user-friendly interface to conveniently browse, retrieve, download and submit novel data. MSDD will significantly improve our understanding of miRNA dysfunction in disease, and thus, MSDD has the potential to serve as a timely and valuable resource. PMID:29106642

MSDD: a manually curated database of experimentally supported associations among miRNAs, SNPs and human diseases.

PubMed

Yue, Ming; Zhou, Dianshuang; Zhi, Hui; Wang, Peng; Zhang, Yan; Gao, Yue; Guo, Maoni; Li, Xin; Wang, Yanxia; Zhang, Yunpeng; Ning, Shangwei; Li, Xia

2018-01-04

The MiRNA SNP Disease Database (MSDD, http://www.bio-bigdata.com/msdd/) is a manually curated database that provides comprehensive experimentally supported associations among microRNAs (miRNAs), single nucleotide polymorphisms (SNPs) and human diseases. SNPs in miRNA-related functional regions such as mature miRNAs, promoter regions, pri-miRNAs, pre-miRNAs and target gene 3'-UTRs, collectively called 'miRSNPs', represent a novel category of functional molecules. miRSNPs can lead to miRNA and its target gene dysregulation, and resulting in susceptibility to or onset of human diseases. A curated collection and summary of miRSNP-associated diseases is essential for a thorough understanding of the mechanisms and functions of miRSNPs. Here, we describe MSDD, which currently documents 525 associations among 182 human miRNAs, 197 SNPs, 153 genes and 164 human diseases through a review of more than 2000 published papers. Each association incorporates information on the miRNAs, SNPs, miRNA target genes and disease names, SNP locations and alleles, the miRNA dysfunctional pattern, experimental techniques, a brief functional description, the original reference and additional annotation. MSDD provides a user-friendly interface to conveniently browse, retrieve, download and submit novel data. MSDD will significantly improve our understanding of miRNA dysfunction in disease, and thus, MSDD has the potential to serve as a timely and valuable resource. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata

DOE Office of Scientific and Technical Information (OSTI.GOV)

Putman, Tim E.; Lelong, Sebastien; Burgstaller-Muehlbacher, Sebastian

With the advancement of genome-sequencing technologies, new genomes are being sequenced daily. Although these sequences are deposited in publicly available data warehouses, their functional and genomic annotations (beyond genes which are predicted automatically) mostly reside in the text of primary publications. Professional curators are hard at work extracting those annotations from the literature for the most studied organisms and depositing them in structured databases. However, the resources don’t exist to fund the comprehensive curation of the thousands of newly sequenced organisms in this manner. Here, we describe WikiGenomes (wikigenomes.org), a web application that facilitates the consumption and curation of genomicmore » data by the entire scientific community. WikiGenomes is based on Wikidata, an openly editable knowledge graph with the goal of aggregating published knowledge into a free and open database. WikiGenomes empowers the individual genomic researcher to contribute their expertise to the curation effort and integrates the knowledge into Wikidata, enabling it to be accessed by anyone without restriction.« less

[Current status in the commercialization and application of genetically modified plants and their effects on human and livestock health and phytoremediation].

PubMed

Yoshimatsu, Kayo; Kawano, Noriaki; Kawahara, Nobuo; Akiyama, Hiroshi; Teshima, Reiko; Nishijima, Masahiro

2012-01-01

Developments in the use of genetically modified plants for human and livestock health and phytoremediation were surveyed using information retrieved from Entrez PubMed, Chemical Abstracts Service, Google, congress abstracts and proceedings of related scientific societies, scientific journals, etc. Information obtained was classified into 8 categories according to the research objective and the usage of the transgenic plants as 1: nutraceuticals (functional foods), 2: oral vaccines, 3: edible curatives, 4: vaccine antigens, 5: therapeutic antibodies, 6: curatives, 7: diagnostic agents and reagents, and 8: phytoremediation. In total, 405 cases were collected from 2006 to 2010. The numbers of cases were 120 for nutraceuticals, 65 for oral vaccines, 25 for edible curatives, 36 for vaccine antigens, 36 for therapeutic antibodies, 76 for curatives, 15 for diagnostic agents and reagents, and 40 for phytoremediation (sum of each cases was 413 because some reports were related to several categories). Nutraceuticals, oral vaccines and curatives were predominant. The most frequently used edible crop was rice (51 cases), and tomato (28 cases), lettuce (22 cases), potato (18 cases), corn (15 cases) followed.

WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata

DOE PAGES

Putman, Tim E.; Lelong, Sebastien; Burgstaller-Muehlbacher, Sebastian; ...

2017-03-06

With the advancement of genome-sequencing technologies, new genomes are being sequenced daily. Although these sequences are deposited in publicly available data warehouses, their functional and genomic annotations (beyond genes which are predicted automatically) mostly reside in the text of primary publications. Professional curators are hard at work extracting those annotations from the literature for the most studied organisms and depositing them in structured databases. However, the resources don’t exist to fund the comprehensive curation of the thousands of newly sequenced organisms in this manner. Here, we describe WikiGenomes (wikigenomes.org), a web application that facilitates the consumption and curation of genomicmore » data by the entire scientific community. WikiGenomes is based on Wikidata, an openly editable knowledge graph with the goal of aggregating published knowledge into a free and open database. WikiGenomes empowers the individual genomic researcher to contribute their expertise to the curation effort and integrates the knowledge into Wikidata, enabling it to be accessed by anyone without restriction.« less

STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation

PubMed Central

2013-01-01

Background Gene Ontology (GO) enrichment analysis remains one of the most common methods for hypothesis generation from high throughput datasets. However, we believe that researchers strive to test other hypotheses that fall outside of GO. Here, we developed and evaluated a tool for hypothesis generation from gene or protein lists using ontological concepts present in manually curated text that describes those genes and proteins. Results As a consequence we have developed the method Statistical Tracking of Ontological Phrases (STOP) that expands the realm of testable hypotheses in gene set enrichment analyses by integrating automated annotations of genes to terms from over 200 biomedical ontologies. While not as precise as manually curated terms, we find that the additional enriched concepts have value when coupled with traditional enrichment analyses using curated terms. Conclusion Multiple ontologies have been developed for gene and protein annotation, by using a dataset of both manually curated GO terms and automatically recognized concepts from curated text we can expand the realm of hypotheses that can be discovered. The web application STOP is available at http://mooneygroup.org/stop/. PMID:23409969

An Analysis of the Climate Data Initiative's Data Collection

NASA Astrophysics Data System (ADS)

Ramachandran, R.; Bugbee, K.

2015-12-01

The Climate Data Initiative (CDI) is a broad multi-agency effort of the U.S. government that seeks to leverage the extensive existing federal climate-relevant data to stimulate innovation and private-sector entrepreneurship to support national climate-change preparedness. The CDI project is a systematic effort to manually curate and share openly available climate data from various federal agencies. To date, the CDI has curated seven themes, or topics, relevant to climate change resiliency. These themes include Coastal Flooding, Food Resilience, Water, Ecosystem Vulnerability, Human Health, Energy Infrastructure, and Transportation. Each theme was curated by subject matter experts who selected datasets relevant to the topic at hand. An analysis of the entire Climate Data Initiative data collection and the data curated for each theme offers insights into which datasets are considered most relevant in addressing climate resiliency. Other aspects of the data collection will be examined including which datasets were the most visited or popular and which datasets were the most sought after for curation by the theme teams. Results from the analysis of the CDI collection will be presented in this talk.

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

PubMed Central

Jia, Baofeng; Raphenya, Amogelang R.; Alcock, Brian; Waglechner, Nicholas; Guo, Peiyao; Tsang, Kara K.; Lago, Briony A.; Dave, Biren M.; Pereira, Sheldon; Sharma, Arjun N.; Doshi, Sachin; Courtot, Mélanie; Lo, Raymond; Williams, Laura E.; Frye, Jonathan G.; Elsayegh, Tariq; Sardar, Daim; Westman, Erin L.; Pawlowski, Andrew C.; Johnson, Timothy A.; Brinkman, Fiona S.L.; Wright, Gerard D.; McArthur, Andrew G.

2017-01-01

The Comprehensive Antibiotic Resistance Database (CARD; http://arpcard.mcmaster.ca) is a manually curated resource containing high quality reference data on the molecular basis of antimicrobial resistance (AMR), with an emphasis on the genes, proteins and mutations involved in AMR. CARD is ontologically structured, model centric, and spans the breadth of AMR drug classes and resistance mechanisms, including intrinsic, mutation-driven and acquired resistance. It is built upon the Antibiotic Resistance Ontology (ARO), a custom built, interconnected and hierarchical controlled vocabulary allowing advanced data sharing and organization. Its design allows the development of novel genome analysis tools, such as the Resistance Gene Identifier (RGI) for resistome prediction from raw genome sequence. Recent improvements include extensive curation of additional reference sequences and mutations, development of a unique Model Ontology and accompanying AMR detection models to power sequence analysis, new visualization tools, and expansion of the RGI for detection of emergent AMR threats. CARD curation is updated monthly based on an interplay of manual literature curation, computational text mining, and genome analysis. PMID:27789705

Patient-Reported Roles, Preferences, and Expectations Regarding Treatment of Stage I Rectal Cancer in the Cancer Care Outcomes Research and Surveillance Consortium.

PubMed

Tyler Ellis, C; Charlton, Mary E; Stitzenberg, Karyn B

2016-10-01

Historically, stage I rectal cancer was treated with total mesorectal excision. However, there has been growing use of local excision, with and without adjuvant therapy, to treat these early rectal cancers. Little is known about how patients and providers choose among the various treatment approaches. The purpose of this study was to identify patient roles, preferences, and expectations as they relate to treatment decision making for patients with stage I rectal cancer. This is a population-based study. The study included a geographically diverse population and health-system-based cohort. A total of 154 adults with newly diagnosed and surgically treated stage I rectal cancer between 2003 and 2005 were included. We compared patients by surgical treatment groups, including total mesorectal excision and local excision. Clinical, sociodemographic, and health-system factors were assessed for association with patient decision-making preferences and expectations. A total of 80% of patients who underwent total mesorectal excision versus 63% of patients who underwent local excision expected that surgery would be curative (p = 0.04). The total mesorectal excision group was less likely to report that radiation would cure their cancer compared with the local excision group (27% vs 63%; p = 0.004). When asked about their preferred role in decision making, 28% of patients who underwent total mesorectal excision preferred patient-controlled decision making compared with 48% of patients who underwent local excision (p = 0.046). However, with regard to the treatment actually received, 38% of the total mesorectal excision group reported making their own surgical decision compared with 25% of the local excision group (p = 0.18). The study was limited by its sample size. The preferred decision-making role for patients did not match the actual decision-making process. Future efforts should focus on bridging the gap between the decision-making process and patient preferences regarding various treatment approaches. This will be particularly important as newer innovative procedures play a more prominent role in the rectal cancer treatment paradigm.

Anti-NMDA-receptor encephalitis presenting with catatonia and neuroleptic malignant syndrome in patients with intellectual disability and autism.

PubMed

Kiani, Reza; Lawden, Mark; Eames, Penelope; Critchley, Peter; Bhaumik, Sabyasachi; Odedra, Sunita; Gumber, Rohit

2015-02-01

We report anti-N-methyl-d-aspartate (NMDA) receptor encephalitis in two patients with autism and intellectual disability presenting with neuropsychiatric symptoms of catatonia and neuroleptic malignant syndrome. Case reports such as these help raise awareness of this clinical issue. By paving the way for earlier diagnoses they ultimately maximise the potential for curative treatments and prevention of long-term complications.

Regulation and Function of Cytokines That Predict Prostate Cancer Metastasis

DTIC Science & Technology

2013-10-01

role of Stat3 activation and p53 intracellular signaling downstream of these cytokines commonly seem to differentialy regulate invasion and... active surveillance. The issue is an important one given the potential for attempts at local curative therapy (whether it be surgery, radiation or...down regulated in the recurrent population, is critical to the communication with MSC in eliciting anti-tumor activity . However, the goals this year

[Physiotherapy methods in the rehabilitation of patients with cerebral vascular diseases].

PubMed

Ezhov, V V

1996-01-01

The author has examined 650 patients aged 30-65 years with prestroke forms of cerebrovascular diseases. Basing on clinico-neurological, electrophysiological and biochemical data, five new variants of physiotherapy are proposed: transcerebral and segmental dalargin electrophoresis combined with magnetotherapy and manual therapy. Relevant practical recommendations are provided. The author's findings extend the knowledge of curative potential of physical methods and on their mechanism of action in cerebrovascular insufficiency.

Current management of locally advanced head and neck cancer: the combination of chemotherapy with locoregional treatments.

PubMed

Bar-Ad, Voichita; Palmer, Joshua; Yang, Hushan; Cognetti, David; Curry, Joseph; Luginbuhl, Adam; Tuluc, Madalina; Campling, Barbara; Axelrod, Rita

2014-12-01

This review will discuss the evolution of the role of chemotherapy in the treatment of locally advanced head and neck cancer (HNC), over the last few decades. Studies were identified by searching PubMed electronic databases. Surgery followed by radiotherapy (RT) or definitive RT are potentially curative approaches for locally advanced HNC. While chemotherapy itself is not curative, it can improve cure rates when given as an adjunct to RT. The benefit of combining chemotherapy with RT is related to the timing of the chemotherapy. Several prospective randomized trials have demonstrated that concurrent delivery of chemotherapy and RT (CRT) is the most promising approach, given that locoregional recurrence is the leading pattern of failure for patients with locally advanced HNC. Induction chemotherapy before CRT has not been shown to be superior to CRT alone and the added toxicity may negatively impact the compliance with CRT. Sequential chemotherapy administration, in the form of induction chemotherapy followed by RT or CRT, has been successful as a strategy for organ preservation in patients with potentially resectable laryngeal and hypopharyngeal cancer. Systemic chemotherapy delivered concurrently with RT is used as a standard treatment for locally advanced HNC. Copyright © 2014 Elsevier Inc. All rights reserved.

Successful enteral nutrition in the treatment of esophagojejunal fistula after total gastrectomy in gastric cancer patients.

PubMed

Portanova, Michel

2010-08-16

Esophagojejunal fistula is a serious complication after total gastrectomy in gastric cancer patients. This study describes the successful conservative management in 3 gastric cancer patients with esophagojejunal fistula after total gastrectomy using total enteral nutrition. Between January 2004 to December 2008, 588 consecutive patients with a proven diagnosis of gastric cancer were taken to the operation room to try a curative treatment. Of these, 173 underwent total gastrectomy, 9 of them had esophagojejunal fistula (5.2%). In three selected patients a trans-anastomotic naso-enteral feeding tube was placed under fluoroscopic vision when the fistula was clinically detected and a complete polymeric enteral formula was used. The complete closing of the esophagojejunal fistula was obtained in day 8, 14 and 25 respectively. In some selected cases it is possible to make a successful enteral nutrition using a feeding tube distal to the leak area inserted with the help of fluoroscopic vision. The specialized management of a gastric surgery unit and nutritional therapy unit are highlighted.

Hypertensive patients' preferences for complementary and alternative medicine and the influence of these preferences on the adherence to prescribed medication.

PubMed

Lee, Khuan; Mokhtar, Halimatun Halaliah; Krauss, Steven Eric; Ong, Beng Kok

2014-05-01

This study aimed to understand hypertensive patients' perceptions of and adherence to prescribed medication. A qualitative research study based on 23 purposely selected participants from a community health clinic in Malaysia. The participants underwent in-depth semi-structured interviews, and the data were analyzed using qualitative content analysis method. The participants were presented with six types of perceptions of medication. The majority of the participants had negative perceptions of Western medicine (WM), self-adjusted their prescribed medication with complementary and alternative medicine (CAM) and concealed their self-adjusting habits from their doctors. Participants who thought positively of WM took their prescribed medication regularly. Most of the participants perceived the nature of WM as not being curative because of its side effects. Patients have the right to choose their preferred medication when they understand their illness. Local health care systems should provide patients with alternative health services that suit their requests. Copyright © 2014 Elsevier Ltd. All rights reserved.

Prognostic predictors of patients with carcinoma of the gastric cardia.

PubMed

Zhang, Ming; Li, Zhigao; Ma, Yan; Zhu, Guanyu; Zhang, Hongfeng; Xue, Yingwei

2012-05-01

This study gives insight into survival predictors and clinicopathological features of carcinoma of the gastric cardia. The study included 233 patients who underwent operation for carcinoma of the gastric cardia. Clinicopathological prognostic variables were evaluated as predictors of long-term survival by univariate and multivariate analysis. Cox regression was used for multivariate analysis and survival curves were drawn by the Kaplan- Meier method. Carcinoma of the gastric cardia was characterized by positive lymph node metastasis (77.3%), serosal invasion (83.3%) and more stage III or IV tumors (72.5%). Overall 5-year survival rate was 21.9% and median survival period was 24 months. The 5-year survival rate was influenced by tumor size, depth on invasion, lymph node metastasis, extent of lymph node dissection, disease stage, operation methods and resection margin. The absent of serosal invasion and lymph node metastasis, curative resection should be considered to be the favourable predictors of long-term survival of patients with carcinoma of the gastric cardia.

[Black urine or black sclera of the eyes? Consider alkaptonuria].

PubMed

Gubbels, Nanda P; Sijbrand, Merijn H; Onstenk, Ron

2014-01-01

Alkaptonuria is a rare metabolic disorder due to a defect in the gene for homogentisic acid oxidase. This results in an accumulation of homogentisic acid, which leads to the deposit of pigment in the connective tissue in the body. This causes problems and symptoms in various organ systems, such as early artropathy, dark-coloured urine, black sclerae, dark-coloured aortic valves and an increased risk of kidney stones and gall stones. Various specialists may see patients with this disease. The diagnosis is often missed. We describe a 69-year-old woman who underwent surgery due to joint problems, which showed up black cartilage. It turned out that for many years she had also had eye and heart problems. Not until later in life was she diagnosed with alkaptonuria. There is no curative treatment for alkaptonuria at the moment. Early recognition of the disease can increase the quality of life. Preventative check-ups and guidance are also therefore necessary.

Gastric carcinoma originating from the heterotopic submucosal gastric gland treated by laparoscopy and endoscopy cooperative surgery

PubMed Central

Imamura, Taisuke; Komatsu, Shuhei; Ichikawa, Daisuke; Kobayashi, Hiroki; Miyamae, Mahito; Hirajima, Shoji; Kawaguchi, Tsutomu; Kubota, Takeshi; Kosuga, Toshiyuki; Okamoto, Kazuma; Konishi, Hirotaka; Shiozaki, Atsushi; Fujiwara, Hitoshi; Ogiso, Kiyoshi; Yagi, Nobuaki; Yanagisawa, Akio; Ando, Takashi; Otsuji, Eigo

2015-01-01

Gastric carcinoma is derived from epithelial cells in the gastric mucosa. We reported an extremely rare case of submucosal gastric carcinoma originating from the heterotopic submucosal gastric gland (HSG) that was safely diagnosed by laparoscopy and endoscopy cooperative surgery (LECS). A 66-year-old man underwent gastrointestinal endoscopy, which detected a submucosal tumor (SMT) of 1.5 cm in diameter on the lesser-anterior wall of the upper gastric body. The tumor could not be diagnosed histologically, even by endoscopic ultrasound-guided fine-needle aspiration biopsy. Local resection by LECS was performed to confirm a diagnosis. Pathologically, the tumor was an intra-submucosal well differentiated adenocarcinoma invading 5000 μm into the submucosal layer. The resected tumor had negative lateral and vertical margins. Based on the Japanese treatment guidelines, additional laparoscopic proximal gastrectomy was curatively performed. LECS is a less invasive and safer approach for the diagnosis of SMT, even in submucosal gastric carcinoma originating from the HSG. PMID:26306144

Comparison of Outcomes with Hand-sewn Versus Stapler Closure of Pancreatic Stump in Distal Pancreatectomy.

PubMed

Futagawa, Yasuro; Takano, Yuki; Furukawa, Kenei; Kanehira, Masaru; Onda, Shinji; Sakamoto, Taro; Gocho, Takeshi; Shiba, Hiroaki; Yanaga, Katsuhiko

2017-05-01

The optimal method for pancreatic stump closure to prevent postoperative pancreatic fistula (POPF) after distal pancreatectomy (DP), remains controversial though DP is still the only curative treatment for pancreatic cancer and other malignancies located on pancreatic body or tail. A total of 44 patients who consecutively underwent open DP were retrospectively analyzed, dividing them into two groups: group H (hand-sewn; n=24) and group S (stapler closure; n=20). POPFs were encountered in 5 (21%) and 11 (55%) patients in groups H and S, respectively (p=0.02). POPFs of Clavien-Dindo grade IIIa or above were observed in two (8%) and seven (35%) patients in groups H and S, respectively (p=0.03). When indicating stapler closure, caution should be exercised for pancreatic consistency and thickness, device and cartridge type, and pancreatic duct ligation to more effectively control POPF rates. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

Treatment outcomes in locally advanced colorectal carcinoma

PubMed Central

Harish, K; Narayanaswamy, YV; Nirmala, S

2004-01-01

Background Locally advanced colorectal cancers form a distinct subgroup where contiguous organs could be involved without distant metastases and so may be amenable to curative surgical resection. It was our objective to report our experience in treating six such patients with operable locally advanced colorectal carcinomas. Methods We retrospectively reviewed the case notes of 47 patients who were diagnosed with colorectal cancers at M S Ramaiah Medical Teaching Hospital between the years 1996 – 2001. Six patients were identified with T4 lesions, adjacent organ involvement and with no nodal involvement. The treatments and outcomes for these patients were then reviewed. Results Two of three patients with rectal malignancies who underwent pelvic exenteration succumbed to disease recurrence within the first 18 months. One of the three patients with colonic cancers died of non malignant causes. The other two are disease free till date. Conclusions Aggressive multivisceral resections for locally advanced colonic cancers might be appropriate. Rectal cancers when locally advanced may be considered for pelvic exenteration, but a more guarded prognosis may apply. PMID:15527504

Primary carcinoma of the gallbladder--review of 143 cases.

PubMed

Arnaud, J P; Casa, C; Georgeac, C; Serra-Maudet, V; Jacob, J P; Ronceray, J; Bergamaschi, R

1995-01-01

We reviewed a consecutive series of patients with primary cancer of the gallbladder and looked for specific symptoms, signs, laboratory tests, radiological examinations, operative procedures, operative findings and survival. The records of 143 patients with gallbladder carcinoma operatively treated between 1975 and 1990 were retrospectively reviewed. Abdominal pain was the most common symptom and present in 72% of our patients. Jaundice was present in 83 patients (58%) and weight loss in 68 (47.5%). The pre-operative diagnosis was made in only 28.7 per cent of the cases. Surgical procedures included cholecystectomy alone (24 patients), cholecystectomy and resection of the hepatic bed (17 patients), and exploration with biopsy or bypass (20 patients). Only 21.5% of patients underwent curative surgery. Overall five year survival rate was 11%. For patients whose tumor was limited to the gallbladder wall (T1, T2, T3), the acturial 5-year survival rate was respectively 100%, 29% and 23%. For patients with T4 and T5 tumor, the 5 year survival rate was nil.

Payao: a community platform for SBML pathway model curation

PubMed Central

Matsuoka, Yukiko; Ghosh, Samik; Kikuchi, Norihiro; Kitano, Hiroaki

2010-01-01

Summary: Payao is a community-based, collaborative web service platform for gene-regulatory and biochemical pathway model curation. The system combines Web 2.0 technologies and online model visualization functions to enable a collaborative community to annotate and curate biological models. Payao reads the models in Systems Biology Markup Language format, displays them with CellDesigner, a process diagram editor, which complies with the Systems Biology Graphical Notation, and provides an interface for model enrichment (adding tags and comments to the models) for the access-controlled community members. Availability and implementation: Freely available for model curation service at http://www.payaologue.org. Web site implemented in Seaser Framework 2.0 with S2Flex2, MySQL 5.0 and Tomcat 5.5, with all major browsers supported. Contact: kitano@sbi.jp PMID:20371497

50th Anniversary of the World's First Extraterrestrial Sample Receiving Laboratory: The Apollo Program's Lunar Receiving Laboratory

NASA Technical Reports Server (NTRS)

Calaway, M. J.; Allton, J. H.; Zeigler, R. A.; McCubbin, F. M.

2017-01-01

The Apollo program's Lunar Receiving Laboratory (LRL), building 37 at NASA's Manned Spaceflight Center (MSC), now Johnson Space Center (JSC), in Houston, TX, was the world's first astronaut and extraterrestrial sample quarantine facility (Fig. 1). It was constructed by Warrior Construction Co. and Warrior-Natkin-National at a cost of $8.1M be-tween August 10, 1966 and June 26, 1967. In 1969, the LRL received and curated the first collection of extra-terrestrial samples returned to Earth; the rock and soil samples of the Apollo 11 mission. This year, the JSC Astromaterials Acquisition and Curation Office (here-after JSC curation) celebrates 50 years since the opening of the LRL and its legacy of laying the foundation for modern curation of extraterrestrial samples.

Curating and Integrating Data from Multiple Sources to Support Healthcare Analytics.

PubMed

Ng, Kenney; Kakkanatt, Chris; Benigno, Michael; Thompson, Clay; Jackson, Margaret; Cahan, Amos; Zhu, Xinxin; Zhang, Ping; Huang, Paul

2015-01-01

As the volume and variety of healthcare related data continues to grow, the analysis and use of this data will increasingly depend on the ability to appropriately collect, curate and integrate disparate data from many different sources. We describe our approach to and highlight our experiences with the development of a robust data collection, curation and integration infrastructure that supports healthcare analytics. This system has been successfully applied to the processing of a variety of data types including clinical data from electronic health records and observational studies, genomic data, microbiomic data, self-reported data from surveys and self-tracked data from wearable devices from over 600 subjects. The curated data is currently being used to support healthcare analytic applications such as data visualization, patient stratification and predictive modeling.

Curation, Spacecraft Recovery and Preliminary Examination for the Stardust Mission: A Perspective from the Curatorial Facility

NASA Technical Reports Server (NTRS)

Zolensky, Michael; Nakamura-Messenger, Keiko; Fletcher, Lisa; See, Thomas

2008-01-01

We briefly describe some of the challenges to the Stardust mission, curation and sample preliminary analysis, from the perspective of the Curation Office at the Johnson Space Center. Our goal is to inform persons planning future sample returns, so that they may learn from both our successes and challenges (and avoid some of our mistakes). The Curation office played a role in the mission from its inception, most critically assisting in the design and implementation of the spacecraft contamination control plan, and in planning and documenting the recovery of the spacecraft reentry capsule in Utah. A unique class 100 cleanroom was built to maintain the returned comet and interstellar samples in clean comfort, and to permit dissection and allocation of samples for analysis.

Building an efficient curation workflow for the Arabidopsis literature corpus

PubMed Central

Li, Donghui; Berardini, Tanya Z.; Muller, Robert J.; Huala, Eva

2012-01-01

TAIR (The Arabidopsis Information Resource) is the model organism database (MOD) for Arabidopsis thaliana, a model plant with a literature corpus of about 39 000 articles in PubMed, with over 4300 new articles added in 2011. We have developed a literature curation workflow incorporating both automated and manual elements to cope with this flood of new research articles. The current workflow can be divided into two phases: article selection and curation. Structured controlled vocabularies, such as the Gene Ontology and Plant Ontology are used to capture free text information in the literature as succinct ontology-based annotations suitable for the application of computational analysis methods. We also describe our curation platform and the use of text mining tools in our workflow. Database URL: www.arabidopsis.org PMID:23221298

Application of curative therapy in the ward. 1920.

PubMed

Marble, Henry Chase

2009-06-01

This Classic article is a reprint of the original work by Henry Chase Marble, Application of Curative Therapy in the Ward. An accompanying biographical sketch on Henry Chase Marble, MD, is available at DOI 10.1007/s11999-009-0789-7 . The Classic Article is (c)1920 by the Journal of Bone and Joint Surgery, Inc. and is reprinted with permission from Marble HC. Application of curative therapy in the ward. J Bone Joint Surg Am. 1920;2:136-138.

[Determination of barium in natural curative waters by ICP-OES technique. Part I. Waters taken on the area of health resorts in Poland].

PubMed

Garboś, Sławomir; Swiecicka, Dorota

2011-01-01

Maximum admissible concentration level (MACL) of barium in natural mineral waters, natural spring waters and potable waters was set at the level of 1 mg/l, while MACL of this element in natural curative waters intended for drinking therapies and inhalations were set at the levels of 1.0 mg/l and 10.0 mg/l, respectively. Those requirements were related to therapies which are applied longer than one month. Above mentioned maximum admissible concentration levels of barium in consumed waters were established after taking into account actual criteria of World Health Organization which determined the guidelines value for this element in water intended for human consumption at the level of 0.7 mg/l. In this work developed and validated method of determination of barium by inductively coupled plasma emission spectrometry technique was applied for determination of this element in 45 natural curative waters sampled from 24 spa districts situated on the area of Poland. Concentrations of barium determined were in the range from 0.0036 mg/l to 24.0 mg/l. Natural curative waters characterized by concentrations of barium in the ranges of 0.0036 - 0.073 mg/l, 0.0036 - 1.31 mg/l and 0.0036 - 24.0 mg/l, were applied to drinking therapy, inhalations and balneotherapy, respectively (some of waters analyzed were simultaneously applied to drinking therapy, inhalations and balneotherapy). In the cases of 11 natural curative waters exceeding limit of 1 mg/l were observed, however they were classified mainly as waters applied to balneotherapy and in two cases to inhalation therapies (concentrations of barium - 1.08 mg/l and 1.31 mg/l). The procedure of classification of curative waters for adequate therapies based among other things on barium concentrations meets requirements of the Decree of Minister of Health from 13 April 2006 on the range of studies indispensable for establishing medicinal properties of natural curative materials and curative properties of climate, criteria of their assessment and a specimen of certificate confirmed those properties.

neXtA5: accelerating annotation of articles via automated approaches in neXtProt.

PubMed

Mottin, Luc; Gobeill, Julien; Pasche, Emilie; Michel, Pierre-André; Cusin, Isabelle; Gaudet, Pascale; Ruch, Patrick

2016-01-01

The rapid increase in the number of published articles poses a challenge for curated databases to remain up-to-date. To help the scientific community and database curators deal with this issue, we have developed an application, neXtA5, which prioritizes the literature for specific curation requirements. Our system, neXtA5, is a curation service composed of three main elements. The first component is a named-entity recognition module, which annotates MEDLINE over some predefined axes. This report focuses on three axes: Diseases, the Molecular Function and Biological Process sub-ontologies of the Gene Ontology (GO). The automatic annotations are then stored in a local database, BioMed, for each annotation axis. Additional entities such as species and chemical compounds are also identified. The second component is an existing search engine, which retrieves the most relevant MEDLINE records for any given query. The third component uses the content of BioMed to generate an axis-specific ranking, which takes into account the density of named-entities as stored in the Biomed database. The two ranked lists are ultimately merged using a linear combination, which has been specifically tuned to support the annotation of each axis. The fine-tuning of the coefficients is formally reported for each axis-driven search. Compared with PubMed, which is the system used by most curators, the improvement is the following: +231% for Diseases, +236% for Molecular Functions and +3153% for Biological Process when measuring the precision of the top-returned PMID (P0 or mean reciprocal rank). The current search methods significantly improve the search effectiveness of curators for three important curation axes. Further experiments are being performed to extend the curation types, in particular protein-protein interactions, which require specific relationship extraction capabilities. In parallel, user-friendly interfaces powered with a set of JSON web services are currently being implemented into the neXtProt annotation pipeline.Available on: http://babar.unige.ch:8082/neXtA5Database URL: http://babar.unige.ch:8082/neXtA5/fetcher.jsp. © The Author(s) 2016. Published by Oxford University Press.

Variations in Receipt of Curative-Intent Surgery for Early-Stage Non-Small Cell Lung Cancer (NSCLC) by State.

PubMed

Sineshaw, Helmneh M; Wu, Xiao-Cheng; Flanders, W Dana; Osarogiagbon, Raymond Uyiosa; Jemal, Ahmedin

2016-06-01

Previous studies reported racial and socioeconomic disparities in receipt of curative-intent surgery for early-stage non-small cell lung cancer (NSCLC) in the United States. We examined variation in receipt of surgery and whether the racial disparity varies by state. Patients in whom stage I or II NSCLC was diagnosed from 2007 to 2011 were identified from 38 state and the District of Columbia population-based cancer registries compiled by the North American Association of Central Cancer Registries. Percentage of patients receiving curative-intent surgery was calculated for each registry. Adjusted risk ratios were generated by using modified Poisson regression to control for sociodemographic (e.g., age, sex, race, insurance) and clinical (e.g., grade, stage) factors. Non-Hispanic (NH) whites and Massachusetts were used as references for comparisons because they had the lowest uninsured rates. In all registries combined, 66.4% of patients with early-stage NSCLC (73,475 of 110,711) received curative-intent surgery. Receipt of curative-intent surgery for early-stage NSCLC varied substantially by state, ranging from 52.2% to 56.1% in Wyoming, Louisiana, and New Mexico to 75.2% to 77.2% in Massachusetts, New Jersey, and Utah. In a multivariable analysis, the likelihood of receiving curative-intent surgery was significantly lower in all but nine states/registries compared with Massachusetts, ranging from 7% lower in California to 25% lower in Wyoming. Receipt of curative-intent surgery for early-stage NSCLC was lower for NH blacks than for NH whites in every state, although statistically significant in Florida and Texas. Receipt of curative-intent surgery for early-stage NSCLC varies substantially across states in the United States, with northeastern states generally showing the highest rates. Further, receipt of treatment appeared to be lower in NH blacks than in NH whites in every state, although statistically significant in Florida and Texas. Copyright © 2016 International Association for the Study of Lung Cancer. Published by Elsevier Inc. All rights reserved.

Advancing the application of systems thinking in health: why cure crowds out prevention.

PubMed

Bishai, David; Paina, Ligia; Li, Qingfeng; Peters, David H; Hyder, Adnan A

2014-06-16

This paper presents a system dynamics computer simulation model to illustrate unintended consequences of apparently rational allocations to curative and preventive services. A modeled population is subject to only two diseases. Disease A is a curable disease that can be shortened by curative care. Disease B is an instantly fatal but preventable disease. Curative care workers are financed by public spending and private fees to cure disease A. Non-personal, preventive services are delivered by public health workers supported solely by public spending to prevent disease B. Each type of worker tries to tilt the balance of government spending towards their interests. Their influence on the government is proportional to their accumulated revenue. The model demonstrates effects on lost disability-adjusted life years and costs over the course of several epidemics of each disease. Policy interventions are tested including: i) an outside donor rationally donates extra money to each type of disease precisely in proportion to the size of epidemics of each disease; ii) lobbying is eliminated; iii) fees for personal health services are eliminated; iv) the government continually rebalances the funding for prevention by ring-fencing it to protect it from lobbying.The model exhibits a "spend more get less" equilibrium in which higher revenue by the curative sector is used to influence government allocations away from prevention towards cure. Spending more on curing disease A leads paradoxically to a higher overall disease burden of unprevented cases of disease B. This paradoxical behavior of the model can be stopped by eliminating lobbying, eliminating fees for curative services, and ring-fencing public health funding. We have created an artificial system as a laboratory to gain insights about the trade-offs between curative and preventive health allocations, and the effect of indicative policy interventions. The underlying dynamics of this artificial system resemble features of modern health systems where a self-perpetuating industry has grown up around disease-specific curative programs like HIV/AIDS or malaria. The model shows how the growth of curative care services can crowd both fiscal and policy space for the practice of population level prevention work, requiring dramatic interventions to overcome these trends.

A statistical approach to identify, monitor, and manage incomplete curated data sets.

PubMed

Howe, Douglas G

2018-04-02

Many biological knowledge bases gather data through expert curation of published literature. High data volume, selective partial curation, delays in access, and publication of data prior to the ability to curate it can result in incomplete curation of published data. Knowing which data sets are incomplete and how incomplete they are remains a challenge. Awareness that a data set may be incomplete is important for proper interpretation, to avoiding flawed hypothesis generation, and can justify further exploration of published literature for additional relevant data. Computational methods to assess data set completeness are needed. One such method is presented here. In this work, a multivariate linear regression model was used to identify genes in the Zebrafish Information Network (ZFIN) Database having incomplete curated gene expression data sets. Starting with 36,655 gene records from ZFIN, data aggregation, cleansing, and filtering reduced the set to 9870 gene records suitable for training and testing the model to predict the number of expression experiments per gene. Feature engineering and selection identified the following predictive variables: the number of journal publications; the number of journal publications already attributed for gene expression annotation; the percent of journal publications already attributed for expression data; the gene symbol; and the number of transgenic constructs associated with each gene. Twenty-five percent of the gene records (2483 genes) were used to train the model. The remaining 7387 genes were used to test the model. One hundred and twenty-two and 165 of the 7387 tested genes were identified as missing expression annotations based on their residuals being outside the model lower or upper 95% confidence interval respectively. The model had precision of 0.97 and recall of 0.71 at the negative 95% confidence interval and precision of 0.76 and recall of 0.73 at the positive 95% confidence interval. This method can be used to identify data sets that are incompletely curated, as demonstrated using the gene expression data set from ZFIN. This information can help both database resources and data consumers gauge when it may be useful to look further for published data to augment the existing expertly curated information.

neXtA5: accelerating annotation of articles via automated approaches in neXtProt

PubMed Central

Mottin, Luc; Gobeill, Julien; Pasche, Emilie; Michel, Pierre-André; Cusin, Isabelle; Gaudet, Pascale; Ruch, Patrick

2016-01-01

The rapid increase in the number of published articles poses a challenge for curated databases to remain up-to-date. To help the scientific community and database curators deal with this issue, we have developed an application, neXtA5, which prioritizes the literature for specific curation requirements. Our system, neXtA5, is a curation service composed of three main elements. The first component is a named-entity recognition module, which annotates MEDLINE over some predefined axes. This report focuses on three axes: Diseases, the Molecular Function and Biological Process sub-ontologies of the Gene Ontology (GO). The automatic annotations are then stored in a local database, BioMed, for each annotation axis. Additional entities such as species and chemical compounds are also identified. The second component is an existing search engine, which retrieves the most relevant MEDLINE records for any given query. The third component uses the content of BioMed to generate an axis-specific ranking, which takes into account the density of named-entities as stored in the Biomed database. The two ranked lists are ultimately merged using a linear combination, which has been specifically tuned to support the annotation of each axis. The fine-tuning of the coefficients is formally reported for each axis-driven search. Compared with PubMed, which is the system used by most curators, the improvement is the following: +231% for Diseases, +236% for Molecular Functions and +3153% for Biological Process when measuring the precision of the top-returned PMID (P0 or mean reciprocal rank). The current search methods significantly improve the search effectiveness of curators for three important curation axes. Further experiments are being performed to extend the curation types, in particular protein–protein interactions, which require specific relationship extraction capabilities. In parallel, user-friendly interfaces powered with a set of JSON web services are currently being implemented into the neXtProt annotation pipeline. Available on: http://babar.unige.ch:8082/neXtA5 Database URL: http://babar.unige.ch:8082/neXtA5/fetcher.jsp PMID:27374119

Moving receptor redirected adoptive cell therapy toward fine tuning of antitumor responses.

PubMed

Chicaybam, Leonardo; Bonamino, Martin Hernan

2014-10-01

Adoptive cell transfer (ACT) is emerging as a powerful modality of cancer treatment. While ACT has proved able to induce massive clinical responses, genetic modification of T lymphocytes further improved clinical responses obtained. One of the major current limitations of ACT is the inability to discern healthy from malignant cells, leading to on target/off tumor responses that can limit its application. We here discuss some of the approaches currently under development and potential solutions to circumvent these limitations and extend this potentially curative therapy to different tumors by targeting a variety of antigens.

Endovascular Management of Ureteroarterial Fistula: A Rare Potentially Life Threatening Cause of Hematuria

PubMed Central

Copelan, Alexander; Chehab, Monzer; Cash, Charles; Korman, Howard; Dixit, Purushottam

2014-01-01

Ureteroarterial fistula is a rare, potentially life-threatening cause of hematuria characterized by an abnormal channel between a ureter and artery. The rarity of this condition, complexity of predisposing risk factors and intermittence of symptoms may delay or obscure its diagnosis. With a high index of suspicion and careful angiographic evaluation, embarking on this condition is not only possible but sets the stage for curative intervention. We report a case of a ureteroarterial fistula presenting with intermittent hematuria, successfully diagnosed at angiography and managed with endovascular stent graft placement. PMID:25426238

The impact of caudate lobe resection on margin status and outcomes in patients with hilar cholangiocarcinoma: a multi-institutional analysis from the US Extrahepatic Biliary Malignancy Consortium.

PubMed

Bhutiani, Neal; Scoggins, Charles R; McMasters, Kelly M; Ethun, Cecilia G; Poultsides, George A; Pawlik, Timothy M; Weber, Sharon M; Schmidt, Carl R; Fields, Ryan C; Idrees, Kamran; Hatzaras, Ioannis; Shen, Perry; Maithel, Shishir K; Martin, Robert C G

2018-04-01

The objective of this study was to determine the impact of caudate resection on margin status and outcomes during resection of extrahepatic hilar cholangiocarcinoma. A database of 1,092 patients treated for biliary malignancies at institutions of the Extrahepatic Biliary Malignancy Consortium was queried for individuals undergoing curative-intent resection for extrahepatic hilar cholangiocarcinoma. Patients who did versus did not undergo concomitant caudate resection were compared with regard to demographic, baseline, and tumor characteristics as well as perioperative outcomes. A total of 241 patients underwent resection for a hilar cholangiocarcinoma, of whom 85 underwent caudate resection. Patients undergoing caudate resection were less likely to have a final positive margin (P = .01). Kaplan-Meier curve of overall survival for patients undergoing caudate resection indicated no improvement over patients not undergoing caudate resection (P = .16). On multivariable analysis, caudate resection was not associated with improved overall survival or recurrence-free survival, although lymph node positivity was associated with worse overall survival and recurrence-free survival, and adjuvant chemoradiotherapy was associated with improved overall survival and recurrence-free survival. Caudate resection is associated with a greater likelihood of margin-negative resection in patients with extrahepatic hilar cholangiocarcinoma. Precise preoperative imaging is critical to assess the extent of biliary involvement, so that all degrees of hepatic resections are possible at the time of the initial operation. Copyright © 2017 Elsevier Inc. All rights reserved.

Nutritional predictors for postoperative short-term and long-term outcomes of patients with gastric cancer.

PubMed

Kanda, Mitsuro; Mizuno, Akira; Tanaka, Chie; Kobayashi, Daisuke; Fujiwara, Michitaka; Iwata, Naoki; Hayashi, Masamichi; Yamada, Suguru; Nakayama, Goro; Fujii, Tsutomu; Sugimoto, Hiroyuki; Koike, Masahiko; Takami, Hideki; Niwa, Yukiko; Murotani, Kenta; Kodera, Yasuhiro

2016-06-01

Evidence indicates that impaired immunocompetence and nutritional status adversely affect short-term and long-term outcomes of patients with cancer. We aimed to evaluate the clinical significance of preoperative immunocompetence and nutritional status according to Onodera's prognostic nutrition index (PNI) among patients who underwent curative gastrectomy for gastric cancer (GC).This study included 260 patients with stage II/III GC who underwent R0 resection. The predictive values of preoperative nutritional status for postoperative outcome (morbidity and prognosis) were evaluated. Onodera's PNI was calculated as follows: 10 × serum albumin (g/dL) + 0.005 × lymphocyte count (per mm).The mean preoperative PNI was 47.8. The area under the curve for predicting complications was greater for PNI compared with the serum albumin concentration or lymphocyte count. Multivariate analysis identified preoperative PNI < 47 as an independent predictor of postoperative morbidity. Moreover, patients in the PNI < 47 group experienced significantly shorter overall and disease-free survival compared with those in the PNI ≥ 47 group, notably because of a higher prevalence of hematogenous metastasis as the initial recurrence. Subgroup analysis according to disease stage and postoperative adjuvant treatment revealed that the prognostic significance of PNI was more apparent in patients with stage II GC and in those who received adjuvant chemotherapy.Preoperative PNI is easy and inexpensive to determine, and our findings indicate that PNI served as a significant predictor of postoperative morbidity, prognosis, and recurrence patterns of patients with stage II/III GC.

Extended versus peripancreatic lymph node dissection for the treatment of left-sided pancreatic cancer

PubMed Central

Lee, Huisong; Choi, Seong Ho; Choi, Dong Wook

2017-01-01

Purpose The pathways of lymphatic metastases differ according to the tumor location in pancreatic cancer patients. However, it is unclear whether extended lymph node dissection (LND) is essential for all left-sided pancreatic cancer. The aim of this study is to evaluate the survival outcomes according to the extent of LND and tumor location in patients with left-sided pancreatic cancer. Methods January 2005 to December 2013, we retrospectively identified 107 patients who underwent curative intent surgery for left-sided pancreatic cancer. The left-sided pancreatic cancer was defined as a tumor located in pancreatic body or tail. The extent of LND was divided into 2 groups: extended LND and peripancreatic LND. The extended LND group included celiac and superior mesenteric LNs. Results We included 107 patients with left-sided pancreatic cancer; 59 patients with pancreatic body cancer and 48 patients with pancreatic tail cancer. The median follow-up period was 17 months (range, 3–110 months). Fifty patients with pancreatic body cancer and 30 patients with pancreatic tail cancer underwent extended LND. In patients with pancreatic body cancer, extended LND was associated with improved disease-free survival (DFS) (P = 0.010) and overall survival (P = 0.014). However, extended LND was not associated with DFS in patients with pancreatic tail cancer. Conclusion Extended LND could improve survival in patients with pancreatic body cancer. However, extended LND had no survival benefit for the treatment of pancreatic tail cancer. PMID:28580345

Extended versus peripancreatic lymph node dissection for the treatment of left-sided pancreatic cancer.

PubMed

Lee, Huisong; Heo, Jin Seok; Choi, Seong Ho; Choi, Dong Wook

2017-06-01

The pathways of lymphatic metastases differ according to the tumor location in pancreatic cancer patients. However, it is unclear whether extended lymph node dissection (LND) is essential for all left-sided pancreatic cancer. The aim of this study is to evaluate the survival outcomes according to the extent of LND and tumor location in patients with left-sided pancreatic cancer. January 2005 to December 2013, we retrospectively identified 107 patients who underwent curative intent surgery for left-sided pancreatic cancer. The left-sided pancreatic cancer was defined as a tumor located in pancreatic body or tail. The extent of LND was divided into 2 groups: extended LND and peripancreatic LND. The extended LND group included celiac and superior mesenteric LNs. We included 107 patients with left-sided pancreatic cancer; 59 patients with pancreatic body cancer and 48 patients with pancreatic tail cancer. The median follow-up period was 17 months (range, 3-110 months). Fifty patients with pancreatic body cancer and 30 patients with pancreatic tail cancer underwent extended LND. In patients with pancreatic body cancer, extended LND was associated with improved disease-free survival (DFS) (P = 0.010) and overall survival (P = 0.014). However, extended LND was not associated with DFS in patients with pancreatic tail cancer. Extended LND could improve survival in patients with pancreatic body cancer. However, extended LND had no survival benefit for the treatment of pancreatic tail cancer.

Low skeletal muscle mass is associated with increased hospital expenditure in patients undergoing cancer surgery of the alimentary tract.

PubMed

van Vugt, Jeroen L A; Buettner, Stefan; Levolger, Stef; Coebergh van den Braak, Robert R J; Suker, Mustafa; Gaspersz, Marcia P; de Bruin, Ron W F; Verhoef, Cornelis; van Eijck, Casper H C; Bossche, Niek; Groot Koerkamp, Bas; IJzermans, Jan N M

2017-01-01

Low skeletal muscle mass is associated with poor postoperative outcomes in cancer patients. Furthermore, it is associated with increased healthcare costs in the United States. We investigated its effect on hospital expenditure in a Western-European healthcare system, with universal access. Skeletal muscle mass (assessed on CT) and costs were obtained for patients who underwent curative-intent abdominal cancer surgery. Low skeletal muscle mass was defined based on pre-established cut-offs. The relationship between low skeletal muscle mass and hospital costs was assessed using linear regression analysis and Mann-Whitney U-tests. 452 patients were included (median age 65, 61.5% males). Patients underwent surgery for colorectal cancer (38.9%), colorectal liver metastases (27.4%), primary liver tumours (23.2%), and pancreatic/periampullary cancer (10.4%). In total, 45.6% had sarcopenia. Median costs were €2,183 higher in patients with low compared with patients with high skeletal muscle mass (€17,144 versus €14,961; P<0.001). Hospital costs incrementally increased with lower sex-specific skeletal muscle mass quartiles (P = 0.029). After adjustment for confounders, low skeletal muscle mass was associated with a cost increase of €4,061 (P = 0.015). Low skeletal muscle mass was independently associated with increased hospital costs of about €4,000 per patient. Strategies to reduce skeletal muscle wasting could reduce hospital costs in an era of incremental healthcare costs and an increasingly ageing population.

DEMO: ECOTOX Knowledgebase

EPA Science Inventory

The ECOTOXicology Knowledgebase (ECOTOX), is a comprehensive, curated database that summarizes toxicology data fromsingle chemical exposure studies to aquatic life, terrestrial plants, and wildlife. The ECOTOX Knowledgebase currently has curated data from over 47,000 references a...

Ci4SeR--curation interface for semantic resources--evaluation with adverse drug reactions.

PubMed

Souvignet, Julien; Asfari, Hadyl; Declerck, Gunnar; Lardon, Jérémy; Trombert-Paviot, Béatrice; Jaulent, Marie-Christine; Bousquet, Cédric

2014-01-01

Evaluation and validation have become a crucial problem for the development of semantic resources. We developed Ci4SeR, a Graphical User Interface to optimize the curation work (not taking into account structural aspects), suitable for any type of resource with lightweight description logic. We tested it on OntoADR, an ontology of adverse drug reactions. A single curator has reviewed 326 terms (1020 axioms) in an estimated time of 120 hours (2.71 concepts and 8.5 axioms reviewed per hour) and added 1874 new axioms (15.6 axioms per hour). Compared with previous manual endeavours, the interface allows increasing the speed-rate of reviewed concepts by 68% and axiom addition by 486%. A wider use of Ci4SeR would help semantic resources curation and improve completeness of knowledge modelling.

Text mining for the biocuration workflow

PubMed Central

Hirschman, Lynette; Burns, Gully A. P. C; Krallinger, Martin; Arighi, Cecilia; Cohen, K. Bretonnel; Valencia, Alfonso; Wu, Cathy H.; Chatr-Aryamontri, Andrew; Dowell, Karen G.; Huala, Eva; Lourenço, Anália; Nash, Robert; Veuthey, Anne-Lise; Wiegers, Thomas; Winter, Andrew G.

2012-01-01

Molecular biology has become heavily dependent on biological knowledge encoded in expert curated biological databases. As the volume of biological literature increases, biocurators need help in keeping up with the literature; (semi-) automated aids for biocuration would seem to be an ideal application for natural language processing and text mining. However, to date, there have been few documented successes for improving biocuration throughput using text mining. Our initial investigations took place for the workshop on ‘Text Mining for the BioCuration Workflow’ at the third International Biocuration Conference (Berlin, 2009). We interviewed biocurators to obtain workflows from eight biological databases. This initial study revealed high-level commonalities, including (i) selection of documents for curation; (ii) indexing of documents with biologically relevant entities (e.g. genes); and (iii) detailed curation of specific relations (e.g. interactions); however, the detailed workflows also showed many variabilities. Following the workshop, we conducted a survey of biocurators. The survey identified biocurator priorities, including the handling of full text indexed with biological entities and support for the identification and prioritization of documents for curation. It also indicated that two-thirds of the biocuration teams had experimented with text mining and almost half were using text mining at that time. Analysis of our interviews and survey provide a set of requirements for the integration of text mining into the biocuration workflow. These can guide the identification of common needs across curated databases and encourage joint experimentation involving biocurators, text mining developers and the larger biomedical research community. PMID:22513129

Text mining for the biocuration workflow.

PubMed

Hirschman, Lynette; Burns, Gully A P C; Krallinger, Martin; Arighi, Cecilia; Cohen, K Bretonnel; Valencia, Alfonso; Wu, Cathy H; Chatr-Aryamontri, Andrew; Dowell, Karen G; Huala, Eva; Lourenço, Anália; Nash, Robert; Veuthey, Anne-Lise; Wiegers, Thomas; Winter, Andrew G

2012-01-01

Molecular biology has become heavily dependent on biological knowledge encoded in expert curated biological databases. As the volume of biological literature increases, biocurators need help in keeping up with the literature; (semi-) automated aids for biocuration would seem to be an ideal application for natural language processing and text mining. However, to date, there have been few documented successes for improving biocuration throughput using text mining. Our initial investigations took place for the workshop on 'Text Mining for the BioCuration Workflow' at the third International Biocuration Conference (Berlin, 2009). We interviewed biocurators to obtain workflows from eight biological databases. This initial study revealed high-level commonalities, including (i) selection of documents for curation; (ii) indexing of documents with biologically relevant entities (e.g. genes); and (iii) detailed curation of specific relations (e.g. interactions); however, the detailed workflows also showed many variabilities. Following the workshop, we conducted a survey of biocurators. The survey identified biocurator priorities, including the handling of full text indexed with biological entities and support for the identification and prioritization of documents for curation. It also indicated that two-thirds of the biocuration teams had experimented with text mining and almost half were using text mining at that time. Analysis of our interviews and survey provide a set of requirements for the integration of text mining into the biocuration workflow. These can guide the identification of common needs across curated databases and encourage joint experimentation involving biocurators, text mining developers and the larger biomedical research community.

Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE.

PubMed

Névéol, Aurélie; Wilbur, W John; Lu, Zhiyong

2012-01-01

High-throughput experiments and bioinformatics techniques are creating an exploding volume of data that are becoming overwhelming to keep track of for biologists and researchers who need to access, analyze and process existing data. Much of the available data are being deposited in specialized databases, such as the Gene Expression Omnibus (GEO) for microarrays or the Protein Data Bank (PDB) for protein structures and coordinates. Data sets are also being described by their authors in publications archived in literature databases such as MEDLINE and PubMed Central. Currently, the curation of links between biological databases and the literature mainly relies on manual labour, which makes it a time-consuming and daunting task. Herein, we analysed the current state of link curation between GEO, PDB and MEDLINE. We found that the link curation is heterogeneous depending on the sources and databases involved, and that overlap between sources is low, <50% for PDB and GEO. Furthermore, we showed that text-mining tools can automatically provide valuable evidence to help curators broaden the scope of articles and database entries that they review. As a result, we made recommendations to improve the coverage of curated links, as well as the consistency of information available from different databases while maintaining high-quality curation. Database URLs: http://www.ncbi.nlm.nih.gov/PubMed, http://www.ncbi.nlm.nih.gov/geo/, http://www.rcsb.org/pdb/

Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE

PubMed Central

Névéol, Aurélie; Wilbur, W. John; Lu, Zhiyong

2012-01-01

High-throughput experiments and bioinformatics techniques are creating an exploding volume of data that are becoming overwhelming to keep track of for biologists and researchers who need to access, analyze and process existing data. Much of the available data are being deposited in specialized databases, such as the Gene Expression Omnibus (GEO) for microarrays or the Protein Data Bank (PDB) for protein structures and coordinates. Data sets are also being described by their authors in publications archived in literature databases such as MEDLINE and PubMed Central. Currently, the curation of links between biological databases and the literature mainly relies on manual labour, which makes it a time-consuming and daunting task. Herein, we analysed the current state of link curation between GEO, PDB and MEDLINE. We found that the link curation is heterogeneous depending on the sources and databases involved, and that overlap between sources is low, <50% for PDB and GEO. Furthermore, we showed that text-mining tools can automatically provide valuable evidence to help curators broaden the scope of articles and database entries that they review. As a result, we made recommendations to improve the coverage of curated links, as well as the consistency of information available from different databases while maintaining high-quality curation. Database URLs: http://www.ncbi.nlm.nih.gov/PubMed, http://www.ncbi.nlm.nih.gov/geo/, http://www.rcsb.org/pdb/ PMID:22685160

Impact of affected lymph nodes on long-term outcome after surgical therapy of alveolar echinococcosis.

PubMed

Hillenbrand, Andreas; Beck, Annika; Kratzer, Wolfgang; Graeter, Tilmann; Barth, Thomas F E; Schmidberger, Julian; Möller, Peter; Henne-Bruns, Doris; Gruener, Beate

2018-06-16

Alveolar echinococcosis (AE) is a life-threatening helminthic disease. In humans, AE mostly affects the liver; the regional hepatic lymph nodes may be involved, indicating dissemination of AE from the liver. To achieve complete removal of the disease, enlarged hepatic lymph nodes may be resected during surgical treatment. We evaluated the frequency of affected lymph nodes by conventional microscopic and immunohistochemical analyses including detection of small particles of Echinococcus multilocularis (spem). Furthermore, we analyzed the association of resection of enlarged and affected lymph nodes with long-term outcome after surgical therapy of patients who underwent surgery with curative intent. We identified 43 patients who underwent hepatic surgery with curative intent with lymph node resection for AE. We analyzed the cohort for the manifestation of the parasite in the resected lymph nodes by conventional histology and by immunohistochemistry and compared these data with the further course of AE. Microscopically infected lymph nodes (laminar layer visible) were found in 7 out of these 43 patients (16%). In more than three quarters (25/32) of all specimens investigated, lymph nodes showed spems when stained with antibody against Em2G11, a monoclonal antibody specific for the Em2 antigen of the Echinococcus multilocularis metacestode. Most frequently, lymph nodes were resected due to enlargement. The median size of microscopically affected lymph nodes was 2 cm (range, 1.2 to 2.5 cm), the median size of immunohistochemically and non-affected lymph nodes was 1.3 cm each (range, "small" to 2.3 or 2.5 cm, respectively). Median follow-up was 8 years for all patients, 5 years for patients with lymph node resection, and 4 years for patients with infested lymph nodes. Overall, recurrent disease was seen in ten patients (10/109; 9%) after a median period of 1.5 years (range, 4 months to 4 years). None of the seven patients with conventionally microscopically affected lymph nodes suffered from recurrent disease. One patient with negative resected nodes and one patient with spems showed recurrent disease after 4 and 35 months, respectively. Lymph node involvement in AE is frequent, particularly when evaluated by immunohistochemical examination of lymph nodes with the monoclonal antibody Em2G11. Affected lymph nodes tend to be larger in size. Lymph node involvement is not associated with recurrent disease and therefore warrants further analysis of the biological significance of lymph node involvement.

Protected Repository for the Defense of Infrastructure Against Cyber Threats (PREDICT) Dataset Development and Hosting

DTIC Science & Technology

2018-04-01

Creation, curation and hosting of datasets for cybersecurity researchers; • Serving as a “host of convenience” for datasets from PREDICT and IMPACT non...assumptions and preferences, as cybersecurity investigators and proxies for the broader current and potential user communities. No attempt was made to...understand what would have been of use, i.e., cybersecurity researcher needs were known more anecdotally than systematically.[1] We believe that

An Analysis of Blood Utilization for Stem Cell Transplant Patients in a Tertiary Care Hospital.

PubMed

Ali, Natasha

2017-05-30

Haematopoietic stem cell transplant is a potentially curative treatment option in various benign and malignant haematological diseases. Patients undergoing stem cell transplant procedure require blood transfusion on a daily basis. Currently, there is paucity of data from developing countries on transfusion practices. This audit was undertaken to determine the consumption of packed red blood cells (PRBCs) transfusion in the bone marrow transplant unit of the Aga Khan University Hospital. A retrospective audit was conducted for packed red cell transfusion ordering practice over a period from June 2014∼June 2015. All consecutive patients, admitted for stem cell transplant procedure for various underlying diseases were included. Outcome measures used in this study were (i) cross match to transfusion (C: T) ratio and (ii) transfusion trigger. During the study period, n=25 patients underwent haematopoietic stem cell transplant. There were n=19 males and n=6 females. One patient was less than 15 years of age while rests were adults. Median age±SD was 26.5±14.5 years (12∼54 years). The underlying diagnosis included Aplastic anemia (n=8), Thalassemia major (n=3), Multiple Myeloma (n=4), Acute leukemia (n=5), Hodgkin's lymphoma (n=4), PRCA (n=1). Grand total consumption of PRBCs during the study period was 204 while 258 products were crossmatch. The C:T ratio was 1.26. The transfusion trigger was Hb level of less than 8 gms/dl. The results of our BMT unit indicate that the C:T ratio and transfusion trigger is comparable to the international benchmark.

8p11 myeloproliferative syndrome: diagnostic challenges and pitfalls.

PubMed

Antic, Darko A; Vukovic, Vojin M; Milosevic Feenstra, Jelena D; Kralovics, Robert; Bogdanovic, Andrija D; Dencic Fekete, Marija S; Mihaljevic, Biljana S

2016-01-01

8p11 myeloproliferative syndrome (EMS) is a very rare clinicopathological entity which is characterized by the appearance of a myeloproliferative neoplasm in the bone marrow, peripheral lymphadenopathy, usually caused by T or B lymphoblastic lymphoma/leukemia, and a reciprocal translocation involving chromosome 8p11. Herein we describe a 22-year-old male patient with unusual clinical presentation of EMS. Namely, he initially presented with prolonged epistaxis. Complete blood count showed elevated hemoglobin (17.7g/dl), thrombocytopenia (98x109/l) and leukocytosis (57x109/l). Bone marrow aspirate and biopsy findings corresponded with the presence of a myeloproliferative neoplasm while cytogenetic analysis revealed t(8;13)(p11q12). After that ZMYM2-FGFR1 in-frame fusion was confirmed at the molecular level. Immediately after establishing the diagnosis of a myeloproliferative neoplasm (MPN) generalized lymphadenopathy was developed. Histopathologic examination of lymph node sample confirmed the diagnosis of a T cell lymphoblastic lymphoma without bone marrow involvement. Four cycles of Hyper CVAD chemotherapy were administered with complete morphological and cytogenetic remission. Four weeks after evaluation, patient developed peripheral blood monocytosis and eosinophilia without bone marrow criteria for acute leukemia. Cytogenetic analysis showed t(8;13) accompanied by complex numerical and structural aberrations. The patient underwent allogeneic stem cell transplantation (allo-SCT) from HLA matched sister and he subsequently achieved complete remission. In conclusion, patients with MPN and translocations involving chromosome 8 need to be carefully evaluated for EMS. However, having in mind the very aggressive clinical course of EMS allo-SCT is the only potential curative option.

Active surveillance for localized prostate cancer: an analysis of patient contacts and utilization of healthcare resources.

PubMed

Thomsen, Frederik B; Berg, Kasper D; Røder, M Andreas; Iversen, Peter; Brasso, Klaus

2015-02-01

Evidence supports active surveillance (AS) as a means to reduce overtreatment of low-risk prostate cancer (PCa). The consequences of close and long-standing follow-up with regard to outpatient visits, tests and repeated biopsies are widely unknown. This study investigated the trajectory and costs of AS in patients with localized PCa. In total, 317 PCa patients were followed in a prospective, single-arm AS cohort. The primary outcomes were number of patient contacts, prostate-specific antigen (PSA) tests, biopsies, hospital admissions due to biopsy complications and patients eventually undergoing curative treatment. The secondary outcome was cost. The 5 year cumulative incidence of discontinued AS in a competing-risk model was 40%. During the first 5 years of AS patients underwent a median of two biopsy sets, and patients were seen in an outpatient clinic including PSA testing three to four times annually. In total, 38 of the 406 biopsy sessions led to hospital admission and 87 of the 317 patients required treatment for bladder outlet obstruction (BOO). With a median of 3.7 years' follow-up, the total cost of AS was euro (€) 1,240,286. Assuming all patients had otherwise undergone primary radical prostatectomy, the cost difference favoured AS with a net benefit of €662,661 (35% reduction). AS entails a close clinical follow-up with a considerable risk of rebiopsy complication, treatment of BOO and subsequent delayed definitive therapy. This risk should be weighed against a potential economic benefit and reduction in the risk of overtreatment compared to immediate radical treatment.

Outcomes in relapsed Hodgkin's lymphoma treated with autologous and allogeneic hematopoietic cell transplantation at the Pontificia Universidad Católica de Chile

PubMed Central

Ramirez, Pablo; Ocqueteau, Mauricio; Rodriguez, Alejandra; Garcia, Maria Jose; Sarmiento, Mauricio; Ernst, Daniel; Jara, Veronica; Bertin, Pablo

2015-01-01

Introduction Hodgkin's lymphoma is a highly curable disease. Autologous and reduced intensity allogeneic hematopoietic cell transplantations are alternatives to treat relapsed patients. Here, we report on the results of one service using these procedures. Methods All patients who underwent transplantations in our institution between 1996 and 2014 were retrospectively studied and demographics, toxicities and survival rate were analyzed. Results This study evaluated 24 autologous and five reduced intensity allogeneic transplantations: the median ages of the patients were 29 and 32 years, respectively. At the time of autologous transplantation, ten patients were in complete remission, nine had chemosensitive disease but were not in complete remission, three had refractory disease and the status of two is unknown. In the allogeneic group, two were in complete remission and three had chemosensitive disease. The 5-year overall survival after autologous transplantation was 42% (66% patients were in complete remission, 37% had chemosensitive disease with incomplete remission and 0% had refractory disease) and 1-year overall survival after allogeneic transplantation was 80%. Transplant-related mortality was 0% in patients conditioned with the ifosfamide/carboplatin/etoposide (ICE), carmustine/etoposide/cyclophosphamide (BEC) and carmustine/etoposide/cytarabine/melphalan (BEAM) regimens, 37% in patients conditioned with busulfan-based regimens and 20% in allogeneic transplantations. Conclusions Hematopoietic cell transplantation for relapsed Hodgkin's lymphoma is a potentially curative procedure especially in patients in complete remission at the time of autologous transplantations, and possibly after allogeneic transplantations. Further studies are necessary to clarify the role of allogeneic transplantations in the treatment of relapsed Hodgkin's lymphoma. PMID:26041421

Reduced argininosuccinate synthetase is a predictive biomarker for the development of pulmonary metastasis in patients with osteosarcoma.

PubMed

Kobayashi, Eisuke; Masuda, Mari; Nakayama, Robert; Ichikawa, Hitoshi; Satow, Reiko; Shitashige, Miki; Honda, Kazufumi; Yamaguchi, Umio; Shoji, Ayako; Tochigi, Naobumi; Morioka, Hideo; Toyama, Yoshiaki; Hirohashi, Setsuo; Kawai, Akira; Yamada, Tesshi

2010-03-01

Pulmonary metastasis is the most significant prognostic determinant for osteosarcoma, but methods for its prediction and treatment have not been established. Using oligonucleotide microarrays, we compared the global gene expression of biopsy samples between seven osteosarcoma patients who developed pulmonary metastasis within 4 years after neoadjuvant chemotherapy and curative resection, and 12 patients who did not relapse. We identified argininosuccinate synthetase (ASS) as a gene differentially expressed with the highest statistical significance (Welch's t test, P = 2.2 x 10(-5)). Immunohistochemical analysis of an independent cohort of 62 osteosarcoma cases confirmed that reduced expression of ASS protein was significantly correlated with the development of pulmonary metastasis after surgery (log-rank test, P < 0.05). Cox regression analysis revealed that ASS was the sole significant predictive factor (P = 0.039; hazard ratio, 0.319; 95% confidence interval, 0.108-0.945). ASS is one of the enzymes required for the production of a nonessential amino acid, arginine. We showed that osteosarcoma cells lacking ASS expression were auxotrophic for arginine and underwent G(0)-G(1) arrest in arginine-free medium, suggesting that an arginine deprivation therapy could be effective in patients with osteosarcoma. Recently, phase I and II clinical trials in patients with melanoma and hepatocellular carcinoma have shown the safety and efficacy of plasma arginine depletion by stabilized arginine deiminase. Our data indicate that in patients with osteosarcoma, reduced expression of ASS is not only a novel predictive biomarker for the development of metastasis, but also a potential target for pharmacologic intervention.

Long-lasting response to electrochemotherapy in melanoma patients with cutaneous metastasis.

PubMed

Caracò, Corrado; Mozzillo, Nicola; Marone, Ugo; Simeone, Ester; Benedetto, Lucia; Di Monta, Gianluca; Di Cecilia, Maria Luisa; Botti, Gerardo; Ascierto, Paolo Antonio

2013-12-01

Treatment of early and multiple cutaneous unresectable recurrences is a major therapeutic problem with around 80% of patients relapsing within 5 years. For lesions refractory to elective treatments, electrochemotherapy (ECT) involving electroporation combined with antineoplastic drug treatment appears to be a new potential option. This study was undertaken to analyze the short- and long-term responses of lesions treated with ECT with intravenous injection of bleomycin in melanoma patients with in-transit disease or distant cutaneous metastases. Between June 2007 and September 2012, 60 patients with relapsed and refractory cutaneous melanoma metastases or in-transit disease underwent 100 courses of ECT with intravenous injection of bleomycin. Response to treatment was evaluated three months after ECT. A long-lasting response was defined as no cutaneous or in-transit relapse after a minimum of six months. Three months after ECT, a complete response was observed in 29 patients (48.4%), a partial response in 23 patients (38.3%) and no change or progressive disease in 8 patients (13.3%). The objective response rate of all treated lesions was 86.6%. Thirteen patients (44.8% of complete responders) experienced a long-lasting response after one ECT session and were disease-free after a mean duration of follow-up of 27.5 months. The favorable outcome obtained in the present study demonstrates that ECT is a reliable, and effective procedure that provides long-term benefit in terms of curative and palliative treatment for unresectable cutaneous lesions without adversely impacting the quality of life of patients.

Long-lasting response to electrochemotherapy in melanoma patients with cutaneous metastasis

PubMed Central

2013-01-01

Background Treatment of early and multiple cutaneous unresectable recurrences is a major therapeutic problem with around 80% of patients relapsing within 5 years. For lesions refractory to elective treatments, electrochemotherapy (ECT) involving electroporation combined with antineoplastic drug treatment appears to be a new potential option. This study was undertaken to analyze the short- and long-term responses of lesions treated with ECT with intravenous injection of bleomycin in melanoma patients with in-transit disease or distant cutaneous metastases. Methods Between June 2007 and September 2012, 60 patients with relapsed and refractory cutaneous melanoma metastases or in-transit disease underwent 100 courses of ECT with intravenous injection of bleomycin. Response to treatment was evaluated three months after ECT. A long-lasting response was defined as no cutaneous or in-transit relapse after a minimum of six months. Results Three months after ECT, a complete response was observed in 29 patients (48.4%), a partial response in 23 patients (38.3%) and no change or progressive disease in 8 patients (13.3%). The objective response rate of all treated lesions was 86.6%. Thirteen patients (44.8% of complete responders) experienced a long-lasting response after one ECT session and were disease-free after a mean duration of follow-up of 27.5 months. Conclusions The favorable outcome obtained in the present study demonstrates that ECT is a reliable, and effective procedure that provides long-term benefit in terms of curative and palliative treatment for unresectable cutaneous lesions without adversely impacting the quality of life of patients. PMID:24289268

Unicentric study of cell therapy in chronic obstructive pulmonary disease/pulmonary emphysema

PubMed Central

Ribeiro-Paes, João Tadeu; Bilaqui, Aldemir; Greco, Oswaldo T; Ruiz, Milton Artur; Marcelino, Monica Y; Stessuk, Talita; de Faria, Carolina A; Lago, Mario R

2011-01-01

Within the chronic obstructive pulmonary disease (COPD) spectrum, lung emphysema presents, as a primarily histopathologic feature, the destruction of pulmonary parenchyma and, accordingly, an increase in the airflow obstruction distal to the terminal bronchiole. Notwithstanding the significant advances in prevention and treatment of symptoms, no effective or curative therapy has been accomplished. In this context, cellular therapy with stem cells (SCs) arises as a new therapeutic approach, with a wide application potential. The purpose of this study is to evaluate the safety of SCs infusion procedure in patients with advanced COPD (stage IV dyspnea). After selection, patients underwent clinical examination and received granulocyte colony-stimulating factor, immediately prior to the bone marrow harvest. The bone marrow mononuclear cells (BMMC) were isolated and infused into a peripheral vein. The 12-month follow-up showed a significant improvement in the quality of life, as well as a clinical stable condition, which suggest a change in the natural process of the disease. Therefore, the proposed methodology in this study for BMMC cell therapy in sufferers of advanced COPD was demonstrated to be free of significant adverse effects. Although a larger sample and a greater follow-up period are needed, it is possible to infer that BMMC cell therapy introduces an unprecedented change in the course or in the natural history of emphysema, inhibiting or slowing the progression of disease. This clinical trial was registered with ClinicalTrials.gov (NCT01110252) and was approved by the Brazilian National Committee of Ethics in Research (registration no. 14764, CONEP report 233/2009). PMID:21311694

Klatskin tumour: meticulous preoperative work-up and resection rate.

PubMed

Otto, G; Hoppe-Lotichius, M; Bittinger, F; Schuchmann, M; Düber, C

2011-04-01

Surgery represents the only potentially curative treatment of hilar cholangiocarcinoma (hilCC). It may be suggested that meticulous preoperative work-up in Asian countries leads to higher resection rates. One hundred and eighty-two patients treated in our department between 1998 and 2008 were included in an analysis based on our prospectively recorded database. Among them, 75 % had a percutaneous transhepatic cholangiography as part of their diagnostic work-up. A total of 160 patients underwent explorative surgery and 123 patients were resected (77 % of patients undergoing exploration, 68 % of all patients). Ninety-one percent of the patients were diagnosed to have Bismuth III and IV tumours. En-bloc resection of the tumour and the adjacent liver including segment 1 was the standard procedure in 109 of these patients, while hilar resection was performed in 14 patients. Upon tumour resection, hospital mortality was 5.7 %. Five-year survival in patients without surgery or with mere exploration was 0 %, after resection it reached 26 %. Patients with R 1 resection experienced longer survival than patients without resection (p < 0.001). Right and left hemihepatectomies were performed with identical frequency resulting in identical survival. Lymph node involvement proved to be the only significant predictor of prognosis (p = 0.006). Resection should be performed whenever possible since even after palliative resection survival is substantially increased compared to patients without resection. Meticulous preoperative work-up may contribute to a high resection rate in patients with hilCC by providing additional information allowing the surgeon to perform more aggressive approaches. © Georg Thieme Verlag KG Stuttgart · New York.

Pulmonary metastasectomy in colorectal cancer patients with previously resected liver metastasis: pooled analysis.

PubMed

Salah, Samer; Ardissone, Francesco; Gonzalez, Michel; Gervaz, Pascal; Riquet, Marc; Watanabe, Kazuhiro; Zabaleta, Jon; Al-Rimawi, Dalia; Toubasi, Samar; Massad, Ehab; Lisi, Elena; Hamed, Osama H

2015-01-01

Data addressing the outcomes and patterns of recurrence after pulmonary metastasectomy (PM) in patients with colorectal cancer (CRC) and previously resected liver metastasis are limited. We searched the PubMed database for studies assessing PM in CRC and gathered individual data for patients who had PM and a previous curative liver resection. The influence of potential factors on overall survival (OS) was analyzed through univariate and multivariate analysis. Between 1983 and 2009, 146 patients from five studies underwent PM and had previous liver resection. The median interval from resection of liver metastasis until detection of lung metastasis and the median follow-up from PM were 23 and 48 months, respectively. Five-year OS and recurrence-free survival rates calculated from the date of PM were 54.4 and 29.3 %, respectively. Factors predicting inferior OS in univariate analysis included thoracic lymph node (LN) involvement and size of largest lung nodule ≥2 cm. Adjuvant chemotherapy and whether lung metastasis was detected synchronous or metachronous to liver metastasis had no influence on survival. In multivariate analysis, thoracic LN involvement emerged as the only independent factor (hazard ratio 4.86, 95 % confidence interval 1.56-15.14, p = 0.006). PM offers a chance for long-term survival in selected patients with CRC and previously resected liver metastasis. Thoracic LN involvement predicted poor prognosis; therefore, significant efforts should be undertaken for adequate staging of the mediastinum before PM. In addition, adequate intraoperative LN sampling allows proper prognostic stratification and enrollment in novel adjuvant therapy trials.

A Novel Nomogram to Predict the Prognosis of Patients Undergoing Liver Resection for Neuroendocrine Liver Metastasis: an Analysis of the Italian Neuroendocrine Liver Metastasis Database.

PubMed

Ruzzenente, Andrea; Bagante, Fabio; Bertuzzo, Francesca; Aldrighetti, Luca; Ercolani, Giorgio; Giuliante, Felice; Ferrero, Alessandro; Torzilli, Guido; Grazi, Gian Luca; Ratti, Francesca; Cucchetti, Alessandro; De Rose, Agostino M; Russolillo, Nadia; Cimino, Matteo; Perri, Pasquale; Cataldo, Ivana; Scarpa, Aldo; Guglielmi, Alfredo; Iacono, Calogero

2017-01-01

Even though surgery remains the only potentially curative option for patients with neuroendocrine liver metastases, the factors determining a patient's prognosis following hepatectomy are poorly understood. Using a multicentric database including patients who underwent hepatectomy for NELMs at seven tertiary referral hepato-biliary-pancreatic centers between January 1990 and December 2014, we sought to identify the predictors of survival and develop a clinical tool to predict patient's prognosis after liver resection for NELMs. The median age of the 238 patients included in the study was 61.9 years (interquartile range 51.5-70.1) and 55.9 % (n = 133) of patients were men. The number of NELMs (hazard ratio = 1.05), tumor size (HR = 1.01), and Ki-67 index (HR = 1.07) were the predictors of overall survival. These variables were used to develop a nomogram able to predict survival. According to the predicted 5-year OS, patients were divided into three different risk classes: 19.3, 55.5, and 25.2 % of patients were in low (>80 % predicted 5-year OS), medium (40-80 % predicted 5-year OS), and high (<40 % predicted 5-year OS) risk classes. The 10-year OS was 97.0, 55.9, and 20.0 % in the low, medium, and high-risk classes, respectively (p < 0.001). We developed a novel nomogram that accurately (c-index >70 %) staged and predicted the prognosis of patients undergoing liver resection for NELMs.

Clinical impact of endometrial cancer stratified by genetic mutational profiles, POLE mutation, and microsatellite instability.

PubMed

Haruma, Tomoko; Nagasaka, Takeshi; Nakamura, Keiichiro; Haraga, Junko; Nyuya, Akihiro; Nishida, Takeshi; Goel, Ajay; Masuyama, Hisashi; Hiramatsu, Yuji

2018-01-01

The molecular characterization of endometrial cancer (EC) can facilitate identification of various tumor subtypes. Although EC patients with POLE mutations reproducibly demonstrate better prognosis, the outcome of patients with microsatellite instability (MSI) remains controversial. This study attempted to interrogate whether genetic stratification of EC can identify distinct subsets with prognostic significance. A cohort of 138 EC patients who underwent surgical resection with curative intent was enrolled. Sanger sequencing was used to evaluate mutations in the POLE and KRAS genes. MSI analysis was performed using four mononucleotide repeat markers and methylation status of the MLH1 promoter was measured by a fluorescent bisulfite polymerase chain reaction (PCR). Protein expression for mismatch repair (MMR) proteins was evaluated by immunohistochemistry (IHC). Extensive hypermethylation of the MLH1 promoter was observed in 69.6% ECs with MLH1 deficiency and 3.5% with MMR proficiency, but in none of the ECs with loss of other MMR genes (P < .0001). MSI-positive and POLE mutations were found in 29.0% and 8.7% EC patients, respectively. Our MSI analysis showed a sensitivity of 92.7% for EC patients with MMR deficiency, and a specificity of 97.9% for EC patients with MMR proficiency. In univariate and multivariate analyses, POLE mutations and MSI status was significantly associated with progression-free survival (P = 0.0129 and 0.0064, respectively) but not with endometrial cancer-specific survival. This study provides significant evidence that analyses of proofreading POLE mutations and MSI status based on mononucleotide repeat markers are potentially useful biomarkers to identify EC patients with better prognosis.

Standards-based curation of a decade-old digital repository dataset of molecular information.

PubMed

Harvey, Matthew J; Mason, Nicholas J; McLean, Andrew; Murray-Rust, Peter; Rzepa, Henry S; Stewart, James J P

2015-01-01

The desirable curation of 158,122 molecular geometries derived from the NCI set of reference molecules together with associated properties computed using the MOPAC semi-empirical quantum mechanical method and originally deposited in 2005 into the Cambridge DSpace repository as a data collection is reported. The procedures involved in the curation included annotation of the original data using new MOPAC methods, updating the syntax of the CML documents used to express the data to ensure schema conformance and adding new metadata describing the entries together with a XML schema transformation to map the metadata schema to that used by the DataCite organisation. We have adopted a granularity model in which a DataCite persistent identifier (DOI) is created for each individual molecule to enable data discovery and data metrics at this level using DataCite tools. We recommend that the future research data management (RDM) of the scientific and chemical data components associated with journal articles (the "supporting information") should be conducted in a manner that facilitates automatic periodic curation. Graphical abstractStandards and metadata-based curation of a decade-old digital repository dataset of molecular information.

An automated curation procedure for addressing chemical errors and inconsistencies in public datasets used in QSAR modelling.

PubMed

Mansouri, K; Grulke, C M; Richard, A M; Judson, R S; Williams, A J

2016-11-01

The increasing availability of large collections of chemical structures and associated experimental data provides an opportunity to build robust QSAR models for applications in different fields. One common concern is the quality of both the chemical structure information and associated experimental data. Here we describe the development of an automated KNIME workflow to curate and correct errors in the structure and identity of chemicals using the publicly available PHYSPROP physicochemical properties and environmental fate datasets. The workflow first assembles structure-identity pairs using up to four provided chemical identifiers, including chemical name, CASRNs, SMILES, and MolBlock. Problems detected included errors and mismatches in chemical structure formats, identifiers and various structure validation issues, including hypervalency and stereochemistry descriptions. Subsequently, a machine learning procedure was applied to evaluate the impact of this curation process. The performance of QSAR models built on only the highest-quality subset of the original dataset was compared with the larger curated and corrected dataset. The latter showed statistically improved predictive performance. The final workflow was used to curate the full list of PHYSPROP datasets, and is being made publicly available for further usage and integration by the scientific community.

OntoBrowser: a collaborative tool for curation of ontologies by subject matter experts.

PubMed

Ravagli, Carlo; Pognan, Francois; Marc, Philippe

2017-01-01

The lack of controlled terminology and ontology usage leads to incomplete search results and poor interoperability between databases. One of the major underlying challenges of data integration is curating data to adhere to controlled terminologies and/or ontologies. Finding subject matter experts with the time and skills required to perform data curation is often problematic. In addition, existing tools are not designed for continuous data integration and collaborative curation. This results in time-consuming curation workflows that often become unsustainable. The primary objective of OntoBrowser is to provide an easy-to-use online collaborative solution for subject matter experts to map reported terms to preferred ontology (or code list) terms and facilitate ontology evolution. Additional features include web service access to data, visualization of ontologies in hierarchical/graph format and a peer review/approval workflow with alerting. The source code is freely available under the Apache v2.0 license. Source code and installation instructions are available at http://opensource.nibr.com This software is designed to run on a Java EE application server and store data in a relational database. philippe.marc@novartis.com. © The Author 2016. Published by Oxford University Press.

OntoBrowser: a collaborative tool for curation of ontologies by subject matter experts

PubMed Central

Ravagli, Carlo; Pognan, Francois

2017-01-01

Summary: The lack of controlled terminology and ontology usage leads to incomplete search results and poor interoperability between databases. One of the major underlying challenges of data integration is curating data to adhere to controlled terminologies and/or ontologies. Finding subject matter experts with the time and skills required to perform data curation is often problematic. In addition, existing tools are not designed for continuous data integration and collaborative curation. This results in time-consuming curation workflows that often become unsustainable. The primary objective of OntoBrowser is to provide an easy-to-use online collaborative solution for subject matter experts to map reported terms to preferred ontology (or code list) terms and facilitate ontology evolution. Additional features include web service access to data, visualization of ontologies in hierarchical/graph format and a peer review/approval workflow with alerting. Availability and implementation: The source code is freely available under the Apache v2.0 license. Source code and installation instructions are available at http://opensource.nibr.com. This software is designed to run on a Java EE application server and store data in a relational database. Contact: philippe.marc@novartis.com PMID:27605099

Quantitative PCR monitoring of the effect of azoxystrobin treatments on Mycosphaerella graminicola epidemics in the field.

PubMed

Rohel, Eric A; Laurent, Paul; Fraaije, Bart A; Cavelier, Nadine; Hollomon, Derek W

2002-03-01

Quantitative PCR and visual monitoring of Mycosphaerella graminicola epidemics were performed to investigate the effect of curative and preventative applications of azoxystrobin in wheat field crops. A non-systemic protectant and a systemic curative fungicide, chlorothalonil and epoxiconazole, respectively, were used as references. PCR diagnosis detected leaf infection by M graminicola 3 weeks before symptom appearance, thereby allowing a clear distinction between curative and preventative treatments. When applied 1 week after the beginning of infection, azoxystrobin curative activity was intermediate between chlorothalonil (low effect) and epoxiconazole. When applied preventatively, none of the fungicides completely prevented leaf infection. There was some indication that azoxystrobin preventative treatments may delay fungal DNA increase more than epoxiconazole at the beginning of leaf infection. Both curative and preventative treatments increased the time lapse between the earliest PCR detection and the measurement of a 10% necrotic leaf area. Azoxystrobin only slightly decreased the speed of necrotic area increase compared with epoxiconazole. Hence, azoxystrobin activity toward M graminicola mainly resides in lengthening the time lapse between the earliest PCR detection and the measurement of a 10% necrotic leaf area. Information generated in this way is useful for optimal positioning of azoxystrobin treatments on M graminicola.

[Curative Effects of Hydroxyurea on the Patients with β-thalassaemia Intermadia].

PubMed

Huang, Li; Yao, Hong-Xia

2016-06-01

To investigate the clinical features of β-thalassaemia intermediate (TI) patients and the curative effect and side reactions of hydroxyurea therapys. Twenty nine patients with TI were divided into hydroxyurea therapy group and no hydroxyurea therapy group; the curative effect and side reactions in 2 groups were compared; the situation of blood transfusion in the 2 groups was evaluated. In hydroxyurea therapy group, the hemoglobin level increased after treatment for 3 months; the reticulocyte percentage obviously decreased after treatment for 12 months; the serum ferritin had been maintained at a low level; while in no hydroxyurea therapy group, the levels of hemoglobin and reticulocytes were not significantly improved after treatment, the serum ferritin level gradually increased. In hydroxyurea therapy group, 12 cases were out of blood transfusion after treatment for 12 months, effective rate of treatment was 85.71%; while in no hydroxyurea therapy group, the blood transfusion dependency was not improved after treatment. No serious side reactions were found in all the hydroxyurea treated patients. The hydroxyurea shows a better curative effect on TI patients, no serious side reactions occur in all the patients treated with hydroxyurea, but the long-term curative effect and side reactions should be observed continuously.

The role of non-governmental organizations in providing curative health services in North Darfur State, Sudan.

PubMed

Yagub, Abdallah I A; Mtshali, Khondlo

2015-09-01

Conflict in North Darfur state, Western Sudan started in 2003, and the delivering of curative health services was becoming a greater challenge for the country's limited resources. NGOs have played an important role in providing curative health services. To examine the role that Non-Governmental Organizations (NGOs) have played in providing curative health services, as well as to identify the difficulties and challenges that affect NGOs in delivering curative health services. Secondary data was collected from different sources, including government offices and medical organizations in Sudan and in North Darfur state. Primary data was obtained through interviews with government and NGOs representatives. The interviews were conducted with (1) expatriates working for international NGOs (N=15) (2) health professionals and administrators working in health sector (N= 45) in the period from November 2010 to January 2011. The government in North Darfur state spent 70% of its financial budget on security, while it spent it less than 1% on providing health services. The international NGOs have been providing 70% of curative health services to the State's population by contributing 52.9% of the health budget and 1 390 health personnel. Since 2003 NGOs have provided technical assistance to the health staff. As a result, more than fifty nurses have been trained to provide care and treatment, more than twenty-three doctors have been trained in laboratory equipment operation, and approximately six senior doctors and hospital directors have received management training. NGOs have been managing and supporting 89 public health facilities, and established 24 health centres in IDP camps, and 20 health centres across all the districts in North Darfur state. The NGOs have played an important role in providing curative health services and in establishing good health facilities, but a future problem is how the government will run these health facilities after a peaceful settlement has been reached which might cause NGOs to leave the region.

Textpresso Central: a customizable platform for searching, text mining, viewing, and curating biomedical literature.

PubMed

Müller, H-M; Van Auken, K M; Li, Y; Sternberg, P W

2018-03-09

The biomedical literature continues to grow at a rapid pace, making the challenge of knowledge retrieval and extraction ever greater. Tools that provide a means to search and mine the full text of literature thus represent an important way by which the efficiency of these processes can be improved. We describe the next generation of the Textpresso information retrieval system, Textpresso Central (TPC). TPC builds on the strengths of the original system by expanding the full text corpus to include the PubMed Central Open Access Subset (PMC OA), as well as the WormBase C. elegans bibliography. In addition, TPC allows users to create a customized corpus by uploading and processing documents of their choosing. TPC is UIMA compliant, to facilitate compatibility with external processing modules, and takes advantage of Lucene indexing and search technology for efficient handling of millions of full text documents. Like Textpresso, TPC searches can be performed using keywords and/or categories (semantically related groups of terms), but to provide better context for interpreting and validating queries, search results may now be viewed as highlighted passages in the context of full text. To facilitate biocuration efforts, TPC also allows users to select text spans from the full text and annotate them, create customized curation forms for any data type, and send resulting annotations to external curation databases. As an example of such a curation form, we describe integration of TPC with the Noctua curation tool developed by the Gene Ontology (GO) Consortium. Textpresso Central is an online literature search and curation platform that enables biocurators and biomedical researchers to search and mine the full text of literature by integrating keyword and category searches with viewing search results in the context of the full text. It also allows users to create customized curation interfaces, use those interfaces to make annotations linked to supporting evidence statements, and then send those annotations to any database in the world. Textpresso Central URL: http://www.textpresso.org/tpc.

Targeted journal curation as a method to improve data currency at the Comparative Toxicogenomics Database

PubMed Central

Davis, Allan Peter; Johnson, Robin J.; Lennon-Hopkins, Kelley; Sciaky, Daniela; Rosenstein, Michael C.; Wiegers, Thomas C.; Mattingly, Carolyn J.

2012-01-01

The Comparative Toxicogenomics Database (CTD) is a public resource that promotes understanding about the effects of environmental chemicals on human health. CTD biocurators read the scientific literature and manually curate a triad of chemical–gene, chemical–disease and gene–disease interactions. Typically, articles for CTD are selected using a chemical-centric approach by querying PubMed to retrieve a corpus containing the chemical of interest. Although this technique ensures adequate coverage of knowledge about the chemical (i.e. data completeness), it does not necessarily reflect the most current state of all toxicological research in the community at large (i.e. data currency). Keeping databases current with the most recent scientific results, as well as providing a rich historical background from legacy articles, is a challenging process. To address this issue of data currency, CTD designed and tested a journal-centric approach of curation to complement our chemical-centric method. We first identified priority journals based on defined criteria. Next, over 7 weeks, three biocurators reviewed 2425 articles from three consecutive years (2009–2011) of three targeted journals. From this corpus, 1252 articles contained relevant data for CTD and 52 752 interactions were manually curated. Here, we describe our journal selection process, two methods of document delivery for the biocurators and the analysis of the resulting curation metrics, including data currency, and both intra-journal and inter-journal comparisons of research topics. Based on our results, we expect that curation by select journals can (i) be easily incorporated into the curation pipeline to complement our chemical-centric approach; (ii) build content more evenly for chemicals, genes and diseases in CTD (rather than biasing data by chemicals-of-interest); (iii) reflect developing areas in environmental health and (iv) improve overall data currency for chemicals, genes and diseases. Database URL: http://ctdbase.org/ PMID:23221299

Closing the loop: from paper to protein annotation using supervised Gene Ontology classification.

PubMed

Gobeill, Julien; Pasche, Emilie; Vishnyakova, Dina; Ruch, Patrick

2014-01-01

Gene function curation of the literature with Gene Ontology (GO) concepts is one particularly time-consuming task in genomics, and the help from bioinformatics is highly requested to keep up with the flow of publications. In 2004, the first BioCreative challenge already designed a task of automatic GO concepts assignment from a full text. At this time, results were judged far from reaching the performances required by real curation workflows. In particular, supervised approaches produced the most disappointing results because of lack of training data. Ten years later, the available curation data have massively grown. In 2013, the BioCreative IV GO task revisited the automatic GO assignment task. For this issue, we investigated the power of our supervised classifier, GOCat. GOCat computes similarities between an input text and already curated instances contained in a knowledge base to infer GO concepts. The subtask A consisted in selecting GO evidence sentences for a relevant gene in a full text. For this, we designed a state-of-the-art supervised statistical approach, using a naïve Bayes classifier and the official training set, and obtained fair results. The subtask B consisted in predicting GO concepts from the previous output. For this, we applied GOCat and reached leading results, up to 65% for hierarchical recall in the top 20 outputted concepts. Contrary to previous competitions, machine learning has this time outperformed standard dictionary-based approaches. Thanks to BioCreative IV, we were able to design a complete workflow for curation: given a gene name and a full text, this system is able to select evidence sentences for curation and to deliver highly relevant GO concepts. Contrary to previous competitions, machine learning this time outperformed dictionary-based systems. Observed performances are sufficient for being used in a real semiautomatic curation workflow. GOCat is available at http://eagl.unige.ch/GOCat/. http://eagl.unige.ch/GOCat4FT/. © The Author(s) 2014. Published by Oxford University Press.