Maximum Diameter and Number of Tumors as a New Prognostic Indicator of Colorectal Liver Metastases.

PubMed

Yoshimoto, Toshiaki; Morine, Yuji; Imura, Satoru; Ikemoto, Tetsuya; Iwahashi, Syuichi; Saito, Y U; Yamada, Sinichiro; Ishikawa, Daichi; Teraoku, Hiroki; Yoshikawa, Masato; Higashijima, Jun; Takasu, Chie; Shimada, Mitsuo

2017-01-01

Surgical resection is currently considered the only potentially curative option as a treatment strategy of colorectal liver metastases (CRLM). However, the criteria for selection of resectable CRLM are not clear. The aim of this study was to confirm a new prognostic indicator of CRLM after hepatic resection. One hundred thirty nine patients who underwent initial surgical resection from 1994 to 2015 were investigated retrospectively. Prognostic factors of overall survival including the product of maximum diameter and number of metastases (MDN) were analyzed. Primary tumor differentiation, vessel invasion, lymph node (LN) metastasis, non-optimally resectable metastases, H score, grade of liver metastases, resection with non-curative intent and MDN were found to be prognostic factors of overall survival (OS). In multivariate analyses of clinicopathological features associated with OS, MDN and non-curative intent were independent prognostic factors. Patients with MDN ≥30 had shown significantly poorer prognosis than patients with MDN <30 in OS and relapse-free survival (RFS). MDN ≥30 is an independent prognostic factor of survival in patients with CRLM and optimal surgical criterion of hepatectomy for CRLM. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

The curative management of synchronous rectal and prostate cancer

PubMed Central

Kavanagh, Dara O; Martin, Joseph; Small, Cormac; Joyce, Myles R; Faul, Clare M; Kelly, Paul J; O'Riordain, Michael; Gillham, Charles M; Armstrong, John G; Salib, Osama; McNamara, Deborah A; McVey, Gerard; O'Neill, Brian D P

2016-01-01

Objective: Neoadjuvant “long-course” chemoradiation is considered a standard of care in locally advanced rectal cancer. In addition to prostatectomy, external beam radiotherapy and brachytherapy with or without androgen suppression (AS) are well established in prostate cancer management. A retrospective review of ten cases was completed to explore the feasibility and safety of applying these standards in patients with dual pathology. To our knowledge, this is the largest case series of synchronous rectal and prostate cancers treated with curative intent. Methods: Eligible patients had synchronous histologically proven locally advanced rectal cancer (defined as cT3-4Nx; cTxN1-2) and non-metastatic prostate cancer (pelvic nodal disease permissible). Curative treatment was delivered to both sites simultaneously. Follow-up was as per institutional guidelines. Acute and late toxicities were reviewed, and a literature search performed. Results: Pelvic external beam radiotherapy (RT) 45–50.4 Gy was delivered concurrent with 5-fluorouracil (5FU). Prostate total dose ranged from 70.0 to 79.2 Gy. No acute toxicities occurred, excluding AS-induced erectile dysfunction. Nine patients proceeded to surgery, and one was managed expectantly. Three relapsed with metastatic colorectal cancer, two with metastatic prostate cancer. Five patients have no evidence of recurrence, and four remain alive with metastatic disease. With a median follow-up of 2.2 years (range 1.2–6.3 years), two significant late toxicities occurred; G3 proctitis in a patient receiving palliative bevacizumab and a G3 anastomotic stricture precluding stoma reversal. Conclusion: Patients proceeding to synchronous radical treatment of both primary sites should receive 45–50.4 Gy pelvic RT with infusional 5FU. Prostate dose escalation should be given with due consideration to the potential impact of prostate cancer on patient survival, as increasing dose may result in significant late morbidity. Review of published series explores the possibility of prostate brachytherapy as an alternative method of boost delivery. Frequent use of bevacizumab in metastatic rectal cancer may compound late rectal morbidity in this cohort. Advances in knowledge: To our knowledge, this is the largest case series of synchronous rectal and prostate cancers treated with curative intent. This article contributes to the understanding of how best to approach definitive treatment in these patients. PMID:26539631

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

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.

Pancreatic Neuroendocrine Tumors (Islet Cell Tumors) Treatment (PDQ®)—Health Professional Version

Cancer.gov

Pancreatic neuroendocrine tumors (islet cell tumors) treatment includes surgery with curative intent and surgery for metastatic disease. Hormone therapy, chemotherapy and targeted therapy are sometimes used. Get detailed information on the treatment of this disease in this clinician summary.

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.

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.

Surveillance Practice Patterns after Curative Intent Therapy for Stage I Non-Small-Cell Lung Cancer in the Medicare Population.

PubMed

Erb, Christopher T; Su, Kevin W; Soulos, Pamela R; Tanoue, Lynn T; Gross, Cary P

2016-09-01

Recurrence after treatment for non-small cell lung cancer (NSCLC) is common, and routine imaging surveillance is recommended by evidence-based guidelines. Little is known about surveillance patterns after curative intent therapy for early stage NSCLC. We sought to understand recent practice patterns for surveillance of stage I NSCLC in the first two years after curative intent therapy in the Medicare population. Using the Surveillance, Epidemiology, and End Results (SEER)-Medicare linked database we selected patients diagnosed with stage I NSCLC between 1998 and 2008. We studied adherence to surveillance guidelines based on specialty society recommendations for chest radiography and computed tomography (CT) scanning. We also tracked the use of Positron Emission Tomography (PET) scans, which are not recommended for surveillance. We calculated the percent of patients who received guideline-adherent surveillance imaging and used logistic regression to determine associations between patient and provider factors and guideline adherence. Overall, 61.4% of patients received guideline-adherent surveillance during the initial 2 years after treatment. Use of CT scans in the first year after treatment increased from 47.4% in 1998-78.5% in 2008, and PET use increased from 5.8% to 28.9%. Adherence with surveillance imaging was associated with younger age, higher income, more comorbidities, access to primary care, and receipt of SBRT as the primary treatment. Adherence to specialty society guidelines for surveillance after treatment for stage I NSCLC was poor in this population of Medicare beneficiaries, with less than two-thirds of patients receiving recommended imaging, and almost 30% receiving non-recommended PET scans. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

[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.

Population-Based Study of Cardiovascular Mortality Among Patients With Prostate Cancer Treated With Radical External Beam Radiation Therapy With and Without Adjuvant Androgen Deprivation Therapy at the British Columbia Cancer Agency

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

Kim, Julian; Vaid, Moninder; Tyldesley, Scott, E-mail: styldesl@bccancer.bc.ca

2011-07-01

Purpose: There are conflicting studies of the impact of androgen deprivation therapy (ADT) on cardiovascular (CV) mortality among prostate cancer patients receiving curative intent external beam radiation therapy (EBRT). We assessed the impact of ADT on CV mortality in patients treated in British Columbia. Methods and Materials: Provincial pharmacy and radiotherapy databases were linked to the provincial cancer registry, and defined a cohort of patients treated with curative intent EBRT between 1998 and 2005. We determined the duration of ADT and the cumulative incidence of CV death. We compared death from CV disease with and without ADT, and by durationmore » of ADT using competing risk analysis and Fine and Gray multivariant analysis. A total of 600 randomly selected patients were reviewed to determine baseline CV disease, CV risk factors, and Charlson Index. Results: Of 5,948 prostate cancer patients treated with radical intent EBRT, of whom 1,933 were treated without ADT, 674 received ADT for {<=}6 months and 3,341 received > 6 months of ADT. The cumulative CV mortality at 7 years was 2.6% (95% confidence interval [CI] 1.9-3.5%), 2.1% (95% CI = 1.2-3.5%), and 1.4 (95% CI = 1.0-2.0%) for patients with no ADT, {<=}6 months of ADT, and >6 months of ADT, respectively (Gray's p = 0.002). Baseline CV disease and risk factors were more prevalent in the no-ADT group compared with the >6-month ADT group. Conclusions: This study demonstrated a lower CV mortality rate among patients treated with longer durations of ADT than those treated without ADT. These differences likely relate to selection of patients for ADT rather than effect of ADT itself.« less

Using Data From Ontario's Episode-Based Funding Model to Assess Quality of Chemotherapy.

PubMed

Kaizer, Leonard; Simanovski, Vicky; Lalonde, Carlin; Tariq, Huma; Blais, Irene; Evans, William K

2016-10-01

A new episode-based funding model for ambulatory systemic therapy was implemented in Ontario, Canada on April 1, 2014, after a comprehensive knowledge transfer and exchange strategy with providers and administrators. An analysis of the data from the first year of the new funding model provided an opportunity to assess the quality of chemotherapy, which was not possible under the old funding model. Options for chemotherapy regimens given with adjuvant/curative intent or palliative intent were informed by input from disease site groups. Bundles were developed and priced to enable evidence-informed best practice. Analysis of systemic therapy utilization after model implementation was performed to assess the concordance rate of the treatments chosen with recommended practice. The actual number of cycles of treatment delivered was also compared with expert recommendations. Significant improvement compared with baseline was seen in the proportion of adjuvant/curative regimens that aligned with disease site group-recommended options (98% v 90%). Similar improvement was seen for palliative regimens (94% v 89%). However, overall, the number of cycles of adjuvant/curative therapy delivered was lower than recommended best practice in 57.5% of patients. There was significant variation by disease site and between facilities. Linking funding to quality, supported by knowledge transfer and exchange, resulted in a rapid improvement in the quality of systemic treatment in Ontario. This analysis has also identified further opportunities for improvement and the need for model refinement.

Follow-up of colorectal cancer patients after resection with curative intent-the GILDA trial.

PubMed

Grossmann, Erik M; Johnson, Frank E; Virgo, Katherine S; Longo, Walter E; Fossati, Rolando

2004-01-01

Surgery remains the primary treatment of colorectal cancer. Data are lacking to delineate the optimal surveillance strategy following resection. A large-scale multi-center European study is underway to address this issue (Gruppo Italiano di Lavoro per la Diagnosi Anticipata-GILDA). Following primary surgery with curative intent, stratification, and randomization at GILDA headquarters, colon cancer patients are then assigned to a more intensive or less intensive surveillance regimen. Rectal cancer patients undergoing curative resection are similarly randomized, with their follow-up regimens placing more emphasis on detection of local recurrence. Target recruitment for the study will be 1500 patients to achieve a statistical power of 80% (assuming an alpha of 0.05 and a hazard-rate reduction of >24%). Since the trial opened in 1998, 985 patients have been randomized from 41 centers as of February 2004. There were 496 patients randomized to the less intensive regimens, and 489 randomized to the more intensive regimens. The mean duration of follow-up is 14 months. 75 relapses (15%) and 32 deaths (7%) had been observed in the two more intensive follow-up arms, while 64 relapses (13%) and 24 deaths (5%) had been observed in the two less intensive arms as of February 2004. This trial should provide the first evidence based on an adequately powered randomized trial to determine the optimal follow-up strategy for colorectal cancer patients. This trial is open to US centers, and recruitment continues.

Combined Modality Therapy Including Intraoperative Electron Irradiation for Locally Recurrent Colorectal Cancer

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

Haddock, Michael G., E-mail: haddock.michael@mayo.ed; Miller, Robert C.; Nelson, Heidi

2011-01-01

Purpose: To evaluate survival, relapse patterns, and prognostic factors in patients with colorectal cancer relapse treated with curative-intent therapy, including intraoperative electron radiation therapy (IOERT). Methods and Materials: From April 1981 through January 2008, 607 patients with recurrent colorectal cancer received IOERT as a component of treatment. IOERT was preceded or followed by external radiation (median dose, 45.5 Gy) in 583 patients (96%). Resection was classified as R0 in 227 (37%), R1 in 224 (37%), and R2 in 156 (26%). The median IOERT dose was 15 Gy (range, 7.5-30 Gy). Results: Median overall survival was 36 months. Five- and 10-yearmore » survival rates were 30% and 16%, respectively. Survival estimates at 5 years were 46%, 27%, and 16% for R0, R1, and R2 resection, respectively. Multivariate analysis revealed that R0 resection, no prior chemotherapy, and more recent treatment (in the second half of the series) were associated with improved survival. The 3-year cumulative incidence of central, local, and distant relapse was 12%, 23%, and 49%, respectively. Central and local relapse were more common in previously irradiated patients and in those with subtotal resection. Toxicity Grade 3 or higher partially attributable to IOERT was observed in 66 patients (11%). Neuropathy was observed in 94 patients (15%) and was more common with IOERT doses exceeding 12.5 Gy. Conclusions: Long-term survival and disease control was achievable in patients with locally recurrent colorectal cancer. Continued evaluation of curative-intent, combined-modality therapy that includes IOERT is warranted in this high-risk population.« less

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.

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.

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

Genetic Landscape of Human Papillomavirus–Associated Head and Neck Cancer and Comparison to Tobacco-Related Tumors

PubMed Central

Hayes, D. Neil; Van Waes, Carter; Seiwert, Tanguy Y.

2015-01-01

Head and neck cancer is the fifth most common cancer worldwide. It is often amenable to curative intent therapy when localized to the head and neck region, but it carries a poor prognosis when it is recurrent or metastatic. Therefore, initial treatment decisions are critical to improve patient survival. However, multimodality therapy used with curative intent is toxic. The balance between offering intensive versus tolerable and function-preserving therapy has been thrown into sharp relief with the recently described epidemic of human papillomavirus–associated head and neck squamous cell carcinomas characterized by improved clinical outcomes compared with smoking-associated head and neck tumors. Model systems and clinical trials have been slow to address the clinical questions that face the field to date. With this as a background, a host of translational studies have recently reported the somatic alterations in head and neck cancer and have highlighted the distinct genetic and biologic differences between viral and tobacco-associated tumors. This review seeks to summarize the main findings of studies, including The Cancer Genome Atlas, for the clinician scientist, with a goal of leveraging this new knowledge toward the betterment of patients with head and neck cancer. PMID:26351353

The effect of drugs and stimulants on gastric myoelectrical activity

PubMed Central

Kwiecień, Jarosław; Kasicka-Jonderko, Anna; Buschhaus, Magdalena

2014-01-01

Electrogastrography (EGG) is a non-invasive diagnostic method useful for the registration and analysis of gastric myoelectrical activity. Abnormalities within an electrogastrogram were found to correlate with a number of disorders and symptoms, like functional dyspepsia, diabetic gastroparesis and terminal hepatic or renal failure. The EGG is also a valuable diagnostic method enabling the evaluation of the effect of drugs on gastric myoelectrical activity, which can be intentional, as in the case of prokinetics, or can have an adverse character. Our review focuses on drugs with a proven impact on gastric myoelectrical activity and hence on the electrogastrogram. The paper assembles and discusses the results of investigations dealing with changes in the electrogastrograms evoked by various drugs. Moreover, the mechanisms of the influence on the gastric myoelectrical activity of drugs, curative substances and stimulants are presented. PMID:25097708

Stage III Melanoma in the Axilla: Patterns of Regional Recurrence After Surgery With and Without Adjuvant Radiation Therapy

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

Pinkham, Mark B., E-mail: mark.pinkham@health.qld.gov.au; University of Queensland, Brisbane; Foote, Matthew C.

Purpose: To describe the anatomic distribution of regionally recurrent disease in patients with stage III melanoma in the axilla after curative-intent surgery with and without adjuvant radiation therapy. Methods and Materials: A single-institution, retrospective analysis of a prospective database of 277 patients undergoing curative-intent treatment for stage III melanoma in the axilla between 1992 and 2012 was completed. For patients who received radiation therapy and those who did not, patterns of regional recurrence were analyzed, and univariate analyses were performed to assess for potential factors associated with location of recurrence. Results: There were 121 patients who received adjuvant radiation therapymore » because their clinicopathologic features conferred a greater risk of regional recurrence. There were 156 patients who received no radiation therapy. The overall axillary control rate was 87%. There were 37 patients with regional recurrence; 17 patients had received adjuvant radiation therapy (14%), and 20 patients (13%) had not. The likelihood of in-field nodal recurrence was significantly less in the adjuvant radiation therapy group (P=.01) and significantly greater in sites adjacent to the axilla (P=.02). Patients with high-risk clinicopathologic features who did not receive adjuvant radiation therapy also tended to experience in-field failure rather than adjacent-field failure. Conclusions: Patients who received adjuvant radiation therapy were more likely to experience recurrence in the adjacent-field regions rather than in the in-field regions. This may not simply reflect higher-risk pathology. Using this data, it may be possible to improve outcomes by reducing the number of adjacent-field recurrences after adjuvant radiation therapy.« less

Radiation Therapy Noncompliance and Clinical Outcomes in an Urban Academic Cancer Center

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

Ohri, Nitin; Rapkin, Bruce D.; Guha, Chandan

Purpose: To examine associations between radiation therapy (RT) noncompliance and clinical outcomes. Methods and Materials: We reviewed all patients who completed courses of external beam RT with curative intent in our department from the years 2007 to 2012 for cancers of the head and neck, breast, lung, cervix, uterus, or rectum. Patients who missed 2 or more scheduled RT appointments (excluding planned treatment breaks) were deemed noncompliant. Univariate, multivariable, and propensity-matched analyses were performed to examine associations between RT noncompliance and clinical outcomes. Results: Of 1227 patients, 266 (21.7%) were noncompliant. With median follow-up of 50.9 months, 108 recurrences (8.8%) and 228more » deaths (18.6%) occurred. In univariate analyses, RT noncompliance was associated with increased recurrence risk (5-year cumulative incidence 16% vs 7%, P<.001), inferior recurrence-free survival (5-year actuarial rate 63% vs 79%, P<.001), and inferior overall survival (5-year actuarial rate 72% vs 83%, P<.001). In multivariable analyses that were adjusted for disease site and stage, comorbidity score, gender, ethnicity, race, and socioeconomic status (SES), RT noncompliance was associated with inferior recurrence, recurrence-free survival, and overall survival rates. Propensity score–matched models yielded results nearly identical to those seen in univariate analyses. Low SES was associated with RT noncompliance and was associated with inferior clinical outcomes in univariate analyses, but SES was not associated with inferior outcomes in multivariable models. Conclusion: For cancer patients being treated with curative intent, RT noncompliance is associated with inferior clinical outcomes. The magnitudes of these effects demonstrate that RT noncompliance can serve as a behavioral biomarker to identify high-risk patients who require additional interventions. Treatment compliance may mediate the associations that have been observed linking SES and clinical outcomes.« less

Histamine type 2 receptor antagonists as adjuvant treatment for resected colorectal cancer.

PubMed

Deva, Sanjeev; Jameson, Michael

2012-08-15

Anecdotal reports of tumour regression with histamine type 2 receptor antagonists (H(2)RAs) have lead to a series of trials with this class of drug as adjuvant therapy to try and improve outcomes in patients with resected colorectal cancers. There was a plausible scientific rationale suggesting merit in this strategy. This included improved immune surveillance (by way of increasing tumour infiltrating lymphocytes), inhibiting the direct proliferative effect of histamine as a growth factor for colorectal cancer and, in the case of cimetidine, inhibiting endothelial expression of E-selectin (a cell adhesion molecule thought to be critical for metastatic spread). To determine if H(2)RAs improve overall survival when used as pre- and/or postoperative therapy in colorectal cancer patients who have had surgical resection with curative intent. We also stratified the results to see if there was an improvement in overall survival in terms of the specific H(2)RA used. Randomised controlled trials were identified using a sensitive search strategy in the following databases: MEDLINE (1964 to present), the Cochrane Central Register of Controlled Trials (CENTRAL, The Cochrane Library 2009), EMBASE (1980 to present) and Cancerlit (1983 to present). Criteria for study selection included: patients with colorectal cancer surgically resected with curative intent; H(2)RAs used i) at any dose, ii) for any length of time, iii) with any other treatment modality and iv) in the pre-, peri- or post-operative period. The results were stratified for the H(2)RA used. The literature search retrieved 142 articles. There were six studies included in the final analysis, published from 1995 to 2007, including a total of 1229 patients. All patients were analysed by intention to treat according to their initial allocation. Log hazard ratios and standard errors of treatment effects (on overall survival) were calculated using the Cochrane statistical package RevMan Version 5. Hazard ratios and standard errors were recorded from trial publications or, if not provided, were estimated from published actuarial survival curves using a spreadsheet designed for this purpose (http://www.biomedcentral.com/content/supplementary/1745-6215-8-16-S1.xls). Of the six identified trials, five used cimetidine as the experimental H(2)RA, whereas one used ranitidine. There was a trend towards improved survival when H(2)RAs were utilised as adjuvant therapy in patients having curative-intent surgery for colorectal cancer (HR 0.70; 95% CI 0.48-1.03, P = 0.07). Analysis of the five cimetidine trials (n = 421) revealed a statistically significant improvement in overall survival (HR 0.53; 95% CI 0.32 to 0.87). Of the H(2)RAs evaluated cimetidine appears to confer a survival benefit when given as an adjunct to curative surgical resection of colorectal cancers. The trial designs were heterogeneous and adjuvant therapy has evolved since these trials were performed. Further prospective randomised studies are warranted.

Sample Handling Considerations for a Europa Sample Return Mission: An Overview

NASA Technical Reports Server (NTRS)

Fries, M. D.; Calaway, M. L.; Evans, C. A.; McCubbin, F. M.

2015-01-01

The intent of this abstract is to provide a basic overview of mission requirements for a generic Europan plume sample return mission, based on NASA Curation experience in NASA sample return missions ranging from Apollo to OSIRIS-REx. This should be useful for mission conception and early stage planning. We will break the mission down into Outbound and Return legs and discuss them separately.

[Overall treatment time assessment of radiotherapy delivered in a curative intent: A prospective study].

PubMed

Petit, C; Suissa, A; Finet, A; Comte, A; Soltys, B; Daveau, C; Ali, D; Dessard-Diana, B; Giraud, P; Housset, M; Durdux, C

2015-12-01

To assess the overall treatment time of radiotherapy delivered with curative intent in a cohort of 185 consecutive patients and the causes of this possible delay. If delay, to propose corrective actions. We report a single-center prospective study including all consecutive patients receiving a radiation therapy with curative intent, from 1st December 2013 to 28th February 2014, on the three linear accelerators of the radiotherapy department. For each fraction missed, the causes of non-completion were prospectively collected. This analysis took into account the following parameters: age, sex, occupation, transport type and duration, tumour localization, radiation dose, concomitant chemotherapy, hospitalization, type of linear accelerator. One hundred and fifty-five patients were included in the study (183 evaluable, two did not complete treatment). The overall treatment time was respected for 31 patients (17%). It was lengthened on 4.6 days (d) (0-29 d; median: 3d). The mean number of delayed fractions was 3.4 (0-17; median: 2). The reasons of delay were: breakdown 32.2%; maintenance 29.3%; holiday 11%; treatment toxicity 9.4%; inadequate planning 8.6%; other disease 3.9%; treatment refusal 2.1%; unspecified personal reasons 1.5%; refusal to wait 0.8%; transportation 0.3%; error of communication 0.3%; other 0.6%. Two parameters had a significant impact on the overall treatment time: the type of linear accelerator in relation to breakdown occurrence (P<0.001) and transportation duration (more or less than 40 min, P=0.022). One hundred and thirty-eight patients (75%) and 79 patients (43%) were treated on one or more than two Saturdays. Treatment on Saturday significantly reduced the overall treatment time (median, 1.9 d; P<0.001). The overall treatment time was globally respected excluding break down and maintenance. Their impact on the overall treatment time is minimized by the systematic opening of the department on Saturdays. Copyright © 2015 Société française de radiothérapie oncologique (SFRO). Published by Elsevier SAS. All rights reserved.

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

The Role of GIS and Data Librarians in Cyber-infrastructure Support and Governance

NASA Astrophysics Data System (ADS)

Branch, B. D.

2012-12-01

A governance road-map for cyber-infrastructure in the geosciences will include an intentional librarian core capable of technical skills that include GIS and open source support for data curation that involves all aspects of data life cycle management. Per Executive Order 12906 and other policy; spatial data, literacy, and curation are critical cyber-infrastructure needs in the near future. A formal earth science and space informatics librarian may be an outcome of such development. From e-science to e-research, STEM pipelines need librarians as critical data intermediaries in technical assistance and collaboration efforts with scientists' data and outreach needs. Future training concerns should advocate trans-disciplinary data science and policy skills that will be necessary for data management support and procurement.

Chemoradiotherapy in tumours of the oesophagus and gastro-oesophageal junction.

PubMed

Hulshof, M C C M; van Laarhoven, H W M

2016-08-01

Oesophageal cancer remains a malignancy with a poor prognosis. However, in the recent 10-15 years relevant progress has been made by the introduction of chemoradiotherapy (CRT) for tumours of the oesophagus or gastro-oesophageal junction. The addition of neo-adjuvant CRT to surgery has significantly improved survival and locoregional control, for both adenocarcinoma and squamous cell carcinoma. For irresectable or medically inoperable patients, definitive CRT has changed the treatment intent from palliative to curative. Definitive CRT is a good alternative for radical surgery in responding patients with squamous cell carcinoma and those running a high risk of surgical morbidity and mortality. For patients with an out-of-field solitary locoregional recurrence after primary curative treatment, definitive CRT can lead to long term survival. Copyright © 2016. Published by Elsevier Ltd.

Impact of time from diagnosis to initiation of curative chemotherapy on survival of patients with diffuse large B-cell lymphoma.

PubMed

Hay, Kevin; Lee, Benny; Goktepe, Ozge; Connors, Joseph M; Sehn, Laurie H; Savage, Kerry J; Klasa, Richard; Shenkier, Tamara; Gerrie, Alina; Villa, Diego

2015-06-19

Although it is generally regarded appropriate to start chemotherapy promptly after a diagnosis of diffuse large B-cell lymphoma (DLBCL), the optimal time from diagnosis to treatment (TDT) is unknown. A total of 689 patients diagnosed with DLBCL and treated with ≥ 1 cycle of CHOP-R with curative intent during 2003-2008 in British Columbia were identified: 347 (50%) TDT ≤ 4 weeks, 277 (40%) TDT 5-8 weeks, 65 (10%) TDT > 8 weeks. For the respective TDT groups, 5-year OS estimates were 61%, 74%, 63% (p = 0.006); 5-year PFS 57%, 70%, 61% (p = 0.006); and 5-year DSS 64%, 80%, 77% (p <0.001). In multivariate analysis, TDT >8 weeks was associated with worse OS (HR 1.20 (95% CI 1.03, 1.41), p = 0.020), PFS (HR 1.33 (95% CI 1.15, 1.54), p < 0.001), and DSS (HR 1.40 (95% CI 1.10, 1.78), p = 0.006). Clinicians should endeavor to initiate curative chemotherapy as soon as possible after a diagnosis of DLBCL is established.

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.

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)

[Radiofrequency ablation of hepatocellular carcinoma].

PubMed

Widmann, Gerlig; Schullian, Peter; Bale, Reto

2013-03-01

Percutaneous radiofrequency ablation (RFA) is well established in the treatment of hepatocellular carcinoma (HCC). Due to its curative potential, it is the method of choice for non resectable BCLC (Barcelona Liver Clinic) 0 and A. RFA challenges surgical resection for small HCC and is the method of choice in bridging for transplantation and recurrence after resection or transplantation. The technical feasibility of RFA depends on the size and location of the HCC and the availability of ablation techniques (one needle techniques, multi-needle techniques). More recently, stereotactic multi-needle techniques with 3D trajectory planning and guided needle placement substantially improve the spectrum of treatable lesions including large volume tumors. Treatment success depends on the realization of ablations with large intentional margins of tumor free tissue (A0 ablation in analogy to R0 resection), which has to be documented by fusion of post- with pre-ablation images, and confirmed during follow-up imaging.

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…

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.

Identification of Distress in Oncology Patients: A Comparison of the Hospital Anxiety and Depression Scale and a Thorough Clinical Assessment.

PubMed

Thalén-Lindström, Annika M; Glimelius, Bengt G; Johansson, Birgitta B

2016-01-01

Screening is recommended to identify cancer patients with distress, anxiety, and depression. The ability of current methods to identify distress in oncology patients is of high importance. We compared the Hospital Anxiety and Depression Scale (HADS) with a thorough clinical assessment. Furthermore, we explored the agreement of HADS with clinical assessment outcomes as a function of age, sex, and treatment intention. One hundred forty-six oncology patients, representing both sexes, different ages (<65/≥ 65 years), and treatment intention (curative/palliative), completed the HADS before the clinical assessment. Two study team members (blind to the HADS results) completed clinical assessments of anxiety, depression, and distress analogous to categories used in the HADS. The HADS identified 49 participants and the clinical assessment 71 participants as having anxiety, depression, or distress. The overall agreement between the HADS and the clinical assessment was moderate. The greatest differences were found to be a function of participant sex and age. Agreement between the methods was better for females than for males in relation to distress and anxiety and better for the older (≥ 65 years) than younger participants in relation to depression. By treatment intention, agreement was equal for all domains. Especially male and young participants appear to have potential problems that the HADS fails to identify. When the HADS is used for screening, nurses must be aware of psychosocial problems perceived by patients that are not covered by the HADS. Many patients identified as having distress have resources to manage problems without additional support.

Mortality among men with locally advanced prostate cancer managed with noncurative intent: a nationwide study in PCBaSe Sweden.

PubMed

Akre, Olof; Garmo, Hans; Adolfsson, Jan; Lambe, Mats; Bratt, Ola; Stattin, Pär

2011-09-01

There are limited prognostic data for locally advanced prostate cancer PCa to guide in the choice of treatment. To assess mortality in different prognostic categories among men with locally advanced PCa managed with noncurative intent. We conducted a register-based nationwide cohort study within the Prostate Cancer DataBase Sweden. The entire cohort of locally advanced PCa included 14 908 men. After the exclusion of 2724 (18%) men treated with curative intent, 12 184 men with locally advanced PCa either with local clinical stage T3 or T4 or with T2 with serum levels of prostate-specific antigen (PSA) between 50 and 99 ng/ml and without signs of metastases remained for analysis. We followed up the patient cohort in the Cause of Death Register for ≤ 11 yr and assessed cumulative incidence of PCa -specific death stratified by age and clinical characteristics. The PCa -specific mortality at 8 yr of follow-up was 28% (95% confidence interval [CI], 25-32%) for Gleason score (GS) 2-6, 41% (95% CI, 38-44%) for GS 7, 52% (95% CI, 47-57%) for GS 8, and 64% (95% CI, 59-69%) for GS 9-10. Even for men aged >85 yr at diagnosis with GS 8-10, PCa was a major cause of death: 42% (95% CI, 37-47%). Men with locally advanced disease and a PSA<4 ng/ml at diagnosis were at particularly increased risk of dying from PCa. One important limitation is the lack of bone scans in 42% of the patient cohort, but results remained after exclusion of patients with unknown metastasis status. The PCa-specific mortality within 8 yr of diagnosis is high in locally advanced PCa, suggesting undertreatment, particularly among men in older age groups. Our results underscore the need for more studies of treatment with curative intent for locally advanced tumors. Copyright © 2011 European Association of Urology. Published by Elsevier B.V. All rights reserved.

Curative Chemoradiotherapy in Patients With Stage IVB Cervical Cancer Presenting With Paraortic and Left Supraclavicular Lymph Node Metastases

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

Kim, Ji-Yoon; Kim, Joo-Young; Kim, Jin Hee

2012-11-01

Purpose: To evaluate the efficacy and toxicity of concurrent chemoradiotherapy (CCRT) with curative intent in patients with stage IVB cervical cancer initially presenting with paraortic and left supraclavicular lymph node metastases. Methods and Materials: The medical records of 25 patients with both paraortic and left supraclavicular lymph nodal metastases (group I) were reviewed and compared with those of 101 women with paraortic lymph node metastases alone (group II). Group I received a mean 59.4 Gy to the paraortic and left supraclavicular areas and 50.4 Gy to the pelvis, followed by 30 Gy of high-dose-rate brachytherapy in 6 fractions. Group IImore » received the same dose to the paraortic area and pelvis followed by intracavitary brachytherapy. All patients received platinum-based chemotherapy simultaneously. Results: Of the 25 patients in group I, 16 (64%) experienced acute grade 3-4 hematologic toxicities, and 1 had a late grade 3 genitourinary toxicity. Complete responses, including the primary mass and pelvic, paraortic, and left supraclavicular lymph nodes, were observed in 13 patients (52%). At a median follow-up of 32 months for surviving patients, 3 experienced in-field failure, 6 showed distant failure, and 9 showed both. The 3-year overall and disease-free survival rates were 49% and 33%, respectively. In comparison, of the 101 patients in group II, 16 showed in-field failure, 14 experienced distant failure, and 11 showed both. The 3-year overall and disease-free survival rates were 69% and 57%, respectively. Conclusions: Curative CCRT is feasible in patients with stage IVB cervical cancer presenting with paraortic and left supraclavicular lymph nodal metastases, with acceptable late toxicity and high response rates, despite high rates of acute hematologic toxicity.« less

State of Melanoma: An Historic Overview of a Field in Transition

PubMed Central

Gorantla, Vikram C.; Kirkwood, John M.

2014-01-01

The last 30 years has seen a revolution in the field of melanoma. Fundamental elements of the surgical, adjuvant medical, and systemic therapy of the disease have been significantly altered toward improved management and better outcomes. The intent of this article is to reflect on past efforts and research in the field of melanoma and the current landscape of treatment of melanoma. We also hope to capture the excitement currently rippling through the field and the hope for a cure. The intent of treatment for advanced melanoma which was once considered incurable, has changed from palliative to potentially curative. Outcomes from research in the fields of immunotherapy and driver mutations in the following decade will hopefully make this goal a reality. PMID:24880939

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.

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.

Dose and Fractionation in Radiation Therapy of Curative Intent for Non-Small Cell Lung Cancer: Meta-Analysis of Randomized Trials

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

Ramroth, Johanna; Cutter, David J.; Darby, Sarah C.

Purpose: The optimum dose and fractionation in radiation therapy of curative intent for non-small cell lung cancer remains uncertain. We undertook a published data meta-analysis of randomized trials to examine whether radiation therapy regimens with higher time-corrected biologically equivalent doses resulted in longer survival, either when given alone or when given with chemotherapy. Methods and Materials: Eligible studies were randomized comparisons of 2 or more radiation therapy regimens, with other treatments identical. Median survival ratios were calculated for each comparison and pooled. Results: 3795 patients in 25 randomized comparisons of radiation therapy dose were studied. The median survival ratio, highermore » versus lower corrected dose, was 1.13 (95% confidence interval [CI] 1.04-1.22) when radiation therapy was given alone and 0.83 (95% CI 0.71-0.97) when it was given with concurrent chemotherapy (P for difference=.001). In comparisons of radiation therapy given alone, the survival benefit increased with increasing dose difference between randomized treatment arms (P for trend=.004). The benefit increased with increasing dose in the lower-dose arm (P for trend=.01) without reaching a level beyond which no further survival benefit was achieved. The survival benefit did not differ significantly between randomized comparisons where the higher-dose arm was hyperfractionated and those where it was not. There was heterogeneity in the median survival ratio by geographic region (P<.001), average age at randomization (P<.001), and year trial started (P for trend=.004), but not for proportion of patients with squamous cell carcinoma (P=.2). Conclusions: In trials with concurrent chemotherapy, higher radiation therapy doses resulted in poorer survival, possibly caused, at least in part, by high levels of toxicity. Where radiation therapy was given without chemotherapy, progressively higher radiation therapy doses resulted in progressively longer survival, and no upper dose level was found above which there was no further benefit. These findings support the consideration of further radiation therapy dose escalation trials, making use of modern treatment methods to reduce toxicity.« less

Dosimetric evaluation of 4 different treatment modalities for curative-intent stereotactic body radiation therapy for isolated thoracic spinal metastases

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

Yang, Jun; Department of Oncology, First Affiliated Hospital of Xinxiang Medical University, 88 Jiankang Road, Weihui, Henan, 453100; Ma, Lin

2016-07-01

To investigate the dosimetric characteristics of 4 SBRT-capable dose delivery systems, CyberKnife (CK), Helical TomoTherapy (HT), Volumetric Modulated Arc Therapy (VMAT) by Varian RapidArc (RA), and segmental step-and-shoot intensity-modulated radiation therapy (IMRT) by Elekta, on isolated thoracic spinal lesions. CK, HT, RA, and IMRT planning were performed simultaneously for 10 randomly selected patients with 6 body types and 6 body + pedicle types with isolated thoracic lesions. The prescription was set with curative intent and dose of either 33 Gy in 3 fractions (3F) or 40 Gy in 5F to cover at least 90% of the planning target volume (PTV),more » correspondingly. Different dosimetric indices, beam-on time, and monitor units (MUs) were evaluated to compare the advantages/disadvantages of each delivery modality. In ensuring the dose-volume constraints for cord and esophagus of the premise, CK, HT, and RA all achieved a sharp conformity index (CI) and a small penumbra volume compared to IMRT. RA achieved a CI comparable to those from CK, HT, and IMRT. CK had a heterogeneous dose distribution in the target as its radiosurgical nature with less dose uniformity inside the target. CK had the longest beam-on time and the largest MUs, followed by HT and RA. IMRT presented the shortest beam-on time and the least MUs delivery. For the body-type lesions, CK, HT, and RA satisfied the target coverage criterion in 6 cases, but the criterion was satisfied in only 3 (50%) cases with the IMRT technique. For the body + pedicle-type lesions, HT satisfied the criterion of the target coverage of ≥90% in 4 of the 6 cases, and reached a target coverage of 89.0% in another case. However, the criterion of the target coverage of ≥90% was reached in 2 cases by CK and RA, and only in 1 case by IMRT. For curative-intent SBRT of isolated thoracic spinal lesions, RA is the first choice for the body-type lesions owing to its delivery efficiency (time); the second choice is CK or HT; HT is the preferential choice for the body + pedicle-type lesions. This study suggests further clinical investigations with longer follow-up for these studied cases.« less

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.

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.

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.

Progression following neoadjuvant systemic chemotherapy may not be a contraindication to a curative approach for colorectal carcinomatosis.

PubMed

Passot, Guillaume; Vaudoyer, Delphine; Cotte, Eddy; You, Benoit; Isaac, Sylvie; Noël Gilly, François; Mohamed, Faheez; Glehen, Olivier

2012-07-01

The objective of this retrospective study was to evaluate the influence of neoadjuvant systemic chemotherapy on patients with colorectal carcinomatosis before a curative procedure. Peritoneal carcinomatosis (PC) from colorectal cancer may be treated with a curative intent by cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC). The role of perioperative systemic chemotherapy for this particular metastatic disease remains unclear. One hundred twenty patients with PC from colorectal cancer were consecutively treated by 131 procedures combining CRS with HIPEC. The response to neoadjuvant systemic chemotherapy was assessed on data from previous explorative surgery and/or radiological imaging. Ninety patients (75%) were treated with neoadjuvant systemic chemotherapy in whom 32 (36%) were considered to have responded, 19 (21%) had stable disease, and 19 (21%) developed diseases progression. Response could not be evaluated in 20 patients (22%). On univariate analysis, the use of neoadjuvant systemic chemotherapy had a significant positive prognostic influence (P = 0.042). On multivariate analysis, the completeness of CRS and the use of adjuvant systemic chemotherapy were the only significant prognostic factors (P < 0.001 and P = 0.049, respectively). Response to neoadjuvant systemic chemotherapy had no significant prognostic impact with median survival of 31.4 months in patients showing disease progression. In patients with PC from colorectal cancer without extraperitoneal metastases, failure of neoadjuvant systemic chemotherapy should not constitute an absolute contraindication to a curative procedure combining CRS and HIPEC.

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

External beam radiation therapy for advanced/unresectable malignant paraganglioma and pheochromocytoma.

PubMed

Breen, William; Bancos, Irina; Young, William F; Bible, Keith C; Laack, Nadia N; Foote, Robert L; Hallemeier, Christopher L

2018-01-01

To evaluate the role of external beam radiation therapy (EBRT) for treatment of malignant paraganglioma (PGL) and pheochromocytoma (PCC). A retrospective review was performed of all patients with malignant PGL/PCC treated with EBRT at our institution between 1973 and 2015. Local control (LC) per treated lesion and overall survival were estimated using the Kaplan-Meier method. Toxicities were scored using the Common Toxicity Criteria for Adverse Events (AE), version 4. The cohort included 41 patients with 107 sites treated. Median (range) age at EBRT was 33 (11-80) years. Treatment intention was curative in 20 patients (30 lesions) and palliative in 21 patients (77 lesions). The primary tumor was PGL (63%) and PCC (37%). Previous local therapies were surgical resection (90%) and percutaneous ablation (19%). Indications for EBRT were local control (66%), pain (22%), or spinal cord compression (12%). Treatment site included bone (69%), soft tissue (30%), and liver (1%). Median (range) EBRT dose was 40 (6.5-70) Gy. Median biologic effective dose using α/β = 10 (BED 10 ) was 53 (9-132). Median follow-up was 3.8 years (0.04-41.5), and mean follow-up was 9.7 years. Overall survival at 5 years was 65%: 79% for curative- and 50% for palliative-intention patients ( P  = .028). LC at 5 years was 81% for all lesions; 91% for lesions receiving BED 10 ≥53, and 62% for lesions receiving BED 10 <53 ( P  = .001). All 11 lesions treated with stereotactic body RT or radiosurgery had LC at a median of 3.0 (0.2-5.4) years. For the symptomatic lesions, symptoms improved in 94%. There were no acute grade ≥3 treatment-related AEs, including no hypertensive crises. Two patients developed a late grade ≥3 AE. EBRT is a useful treatment modality for malignant PGL and PCC. Higher RT dose was associated with improved LC.

Defining the Chance of Statistical Cure Among Patients with Extrahepatic Biliary Tract Cancer

PubMed Central

Spolverato, Gaya; Bagante, Fabio; Ethun, Cecilia G.; Poultsides, George; Tran, Thuy; Idrees, Kamran; Isom, Chelsea A.; Fields, Ryan C.; Krasnick, Bradley; Winslow, Emily; Cho, Clifford; Martin, Robert C. G.; Scoggins, Charles R.; Shen, Perry; Mogal, Harveshp D.; Schmidt, Carl; Beal, Eliza; Hatzaras, Ioannis; Shenoy, Rivfka; Maithel, Shishir K.; Pawlik, Timothy M.

2017-01-01

Background While surgery offers the best curative-intent treatment, many patients with biliary tract malignancies have poor long-term outcomes. We sought to apply a non-mixture cure model to calculate the cure fraction and the time to cure after surgery of patients with peri-hilar cholangiocarcinoma (PHCC) or gallbladder cancer (GBC). Methods Using the Extrahepatic Biliary Malignancy Consortium, 576 patients who underwent curative-intent surgery for gallbladder carcinoma or peri-hilar cholangiocarcinoma between 1998 and 2014 at 10 major hepatobiliary institutions were identified and included in the analysis. A non-mixture cure model was adopted to compare mortality after surgery to the mortality expected for the general population matched by sex and age. Results The median and 5-year overall survival (OS) were 1.9 years (IQR, 0.9–4.9) and 23.9 % (95 % CI, 19.6–28.6). Among all patients with PHCC or GBC, the probability of being cured after surgery was 14.5 % (95 % CI, 8.7–23.2); the time to cure was 9.7 years and the median survival of uncured patients was 1.8 years. Determinants of cure probabilities included lymph node metastasis and CA 19.9 level (p ≤ 0.05). The cure fraction for patients with a CA 19.9 < 50 U/ml and no lymph nodes metastases were 39.0 % versus only 5.1 % among patients with a CA 19.9 ≥ 50 who also had lymph node metastasis. Conclusions Examining an “all comer” cohort, <15 % of patients with PHCC or GBC could be considered cured after surgery. Factors such CA 19.9 level and lymph node metastasis independently predicted long-term outcome. Estimating the odds of statistical cure following surgery for biliary tract cancer can assist in decision-making as well as inform discussions around survivorship. PMID:27549595

Outcomes of Rehepatectomy for Colorectal Liver Metastases: A Contemporary Multi-Institutional Analysis from the French Surgical Association Database.

PubMed

Hallet, Julie; Cunha, Antonio Sa; Adam, Rene; Goéré, Diane; Azoulay, Daniel; Mabrut, Jean-Yves; Muscari, Fabrice; Laurent, Christophe; Navarro, Francis; Pessaux, Patrick

2016-12-01

Recurrence remains frequent after curative-intent hepatectomy for colorectal liver metastases (CRLM). We sought to define short- and long-term outcomes, and identify prehepatectomy factors associated with survival, following rehepatectomy (RH) for recurrence. We conducted a multi-institutional cohort study of hepatectomy for CRLM over 2006-2013. Second-stage resections were excluded. Primary outcomes were overall survival (OS) and recurrence-free survival (RFS) assessed using Kaplan-Meier methods. Secondary outcomes included 30-day overall morbidity and mortality, and survival from recurrence. Outcomes of RH and initial hepatectomy (IH) were compared. Of 2771 hepatectomies included in the study, 447 were RH. Median operative time, 30-day morbidity, mortality, and median length of stay did not differ for RH and IH. Five-year OS did not statistically differ, i.e. 56.5 % from RH and 67.6 % from IH [adjusted hazard ratio (HR) 0.9, 95 % confidence interval (CI) 0.5-1.7], and 5-year RFS was inferior after RH (18.5 vs. 28.8 %; adjusted HR 1.3, 95 % CI 1.0-1.7). In patients who eventually recurred, 5-year survival from the time of recurrence did not differ whether it was after RH (46.5 %) or after IH (60.3 %) (adjusted HR 1.1, 95  % CI 0.8-1.8). Rectal primary tumor (HR 1.4, 95 % CI 1.0-2.1) and metastasis ≥3 cm (HR 1.3, 95 % CI 1.1-2.7) were independently associated with RFS, but not OS, after RH. Short-term outcomes of RH did not differ from IH. While recurrence was more frequent after RH than IH, it did not impact OS. Survival from the time of recurrence did not differ whether recurrence occurred after RH or after IH. CRLM recurrence can be treated with curative intent with excellent long-term outcomes.

[Rectal squamous cell carcinoma treatment: Retrospective experience in two French university hospitals, review and proposals].

PubMed

Schernberg, A; Servagi-Vernat, S; Loganadane, G; Touboul, E; Bosset, J-F; Huguet, F

2016-12-01

After publishing a retrospective series of 23 patients treated for a rectal squamous cell carcinoma with exclusive curative and conservative intent chemoradiation, we aim to propose a review of the literature about this rare tumour. We identified 11 retrospective studies, on 106 patients, treated between 2007 and 2016. Treatment of rectal squamous cell carcinoma should be similar to anal carcinoma, based on exclusive chemoradiation, displaying a 5-year overall survival rate over 80%, while it was 32% in surgical series. Baseline explorations should be similar as for anal carcinoma, with an interest in PET-CT at diagnosis and monitoring, after a delay over 6 weeks after chemoradiation. Intensity-modulated radiotherapy is legitimate, to a prophylactic dose between 36 and 45Gy, and over 54Gy to the tumour. Concomitant chemotherapy should combine an antimetabolite (5-fluorouracil or capecitabine) and mitomycin C, or cisplatin. This treatment seems well tolerated, associated with grade 2 or above toxicity below 30%. Follow-up should be established on anal squamous cell carcinoma schedule, with endoscopic ultrasonography and PET-CT. Rectal squamous cell carcinoma is a rare tumour; it management should be based on anal curative and conservative intent chemoradiation. Copyright © 2016 Société française de radiothérapie oncologique (SFRO). Published by Elsevier SAS. All rights reserved.

PITX2 and PANCR DNA methylation predicts overall survival in patients with head and neck squamous cell carcinoma.

PubMed

Sailer, Verena; Holmes, Emily Eva; Gevensleben, Heidrun; Goltz, Diane; Dröge, Freya; de Vos, Luka; Franzen, Alina; Schröck, Friederike; Bootz, Friedrich; Kristiansen, Glen; Schröck, Andreas; Dietrich, Dimo

2016-11-15

Squamous cell carcinoma of the head and neck region (HNSCC) is a common malignant disease accompanied by a high risk of local or distant recurrence after curative-intent treatment. Biomarkers that allow for the prediction of disease outcome can guide clinicians with respect to treatment and surveillance strategies. Here, the methylation status of PITX2 and an adjacent lncRNA (PANCR) were evaluated for their ability to predict overall survival in HNSCC patients. PITX2 hypermethylation was associated with a better overall survival (hazard ratio, HR = 0.51, 95%CI: 0.35-0.74, p<0.001), while PANCR hypermethylation was significantly associated with an increased risk of death (HR = 1.64, 95%CI: 1.12-2.39, p=0.010). Quantitative, methylation-specific real-time PCR assays for PITX2 and PANCR were employed to measure bisulfite-converted DNA from formalin-fixed, paraffin-embedded (FFPE) tissues in a cohort of 399 patients with localized or locally advanced HNSCC who received curative-intent treatment (surgery with optional adjuvant radiochemotherapy or definite radiochemotherapy). PITX2 and PANCR methylation status were shown to be independent predictors for overall survival in HNSCC patients. Tissue-based methylation testing could therefore potentially be employed to identify patients with a high risk for death who might benefit from a more radical or alternative treatment.

Advanced Age is Not a Contraindication for Treatment With Curative Intent in Esophageal Cancer.

PubMed

Voncken, Francine E M; van der Kaaij, Rosa T; Sikorska, Karolina; van Werkhoven, Erik; van Dieren, Jolanda M; Grootscholten, Cecile; Snaebjornsson, Petur; van Sandick, Johanna W; Aleman, Berthe M P

2017-07-31

The objective of this study is to compare long-term outcomes between younger and older (70 y and above) esophageal cancer patients treated with curative intent. Overall survival (OS), disease-free survival (DFS), and locoregional recurrence-free interval were compared between older (70 y and above) and younger (below 70 y) esophageal cancer patients treated between 1998 and 2013. Treatment consisted of neoadjuvant chemoradiotherapy with surgery or definitive chemoradiotherapy: 36 to 50.4 Gy in 18 to 28 fractions combined with 5-fluorouracil/cisplatin or carboplatin/paclitaxel. The study comprised 253 patients, of whom 76 were 70 years and older. Median age was 64 years (range, 41 to 83). Most patients had stage II-IIIA disease (83%). Planned treatment was neoadjuvant chemoradiotherapy with surgery for 169 patients (41 patients aged 70 y and older) and definitive chemoradiotherapy for 84 patients (31 patients aged 70 y and older). The compliance to radiotherapy was 92%, with no difference between older and younger patients. In 33 patients (13 patients aged 70 y and older) planned surgery was not performed. Median follow-up was 4.9 years. Three-year OS was 42%. The multivariable analysis showed no statistical difference in OS or in DFS comparing older and younger patients: OS (hazard ratio [HR], 0.88; 95% confidence interval [CI], 0.61-1.28), DFS (HR, 0.87; 95% CI, 0.60-1.25). Elderly showed a longer locoregional recurrence-free interval; HR, 0.53 (95% CI, 0.30-0.92; P=0.02) and a higher pathologic complete response rate (50% vs. 25%; P=0.02). Long-term outcomes of older esophageal cancer patients (70 y and above) selected for treatment with neoadjuvant chemoradiotherapy followed by surgery or definitive chemoradiotherapy were comparable with the outcomes of their younger counterparts. Advanced age alone should not be a contraindication for potentially curative chemoradiotherapy-based treatment in esophageal cancer patients.

Long-term follow-up after transoral laser microsurgery and adjuvant radiotherapy for advanced recurrent squamous cell carcinoma of the head and neck

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

Christiansen, Hans; Hermann, Robert Michael; Martin, Alexios

Purpose: The aim of this study was to evaluate the efficacy of adjuvant radiotherapy after transoral laser microsurgery for advanced recurrent head-and-neck squamous cell carcinoma (HNSCC). Patients and Methods: Between 1988 and 2000, 37 patients with advanced local recurrences (23 local and 14 locoregional recurrences) of HNSCC without distant metastases were treated in curative intent with organ-preserving transoral laser microsurgery and adjuvant radiotherapy (before 1994 split-course radiotherapy with carboplatinum, after 1994 conventional radiotherapy). Initial therapy of the primary (8.1% oral cavity, 35.1% oropharynx, 13.5% hypopharynx, and 43.3% larynx) before relapse was organ-preserving transoral laser microsurgery without any adjuvant therapy. Results:more » After a median follow-up of 124 months, the 5-year overall survival rate was 21.3%, the loco-regional control rate 48.3%, respectively. In multivariate analysis, stage of original primary tumor (Stage I/II vs. Stage III/IV), and patient age (<58 years vs. {>=}58 years) showed statistically significant impact on prognosis. In laryngeal cancer, larynx preservation rate after treatment for recurrent tumor was 50% during follow-up. Conclusion: Our data show that organ-preserving transoral laser microsurgery followed by adjuvant radiotherapy is a curative option for patients who have advanced recurrence after transoral laser surgery and is an alternative to radical treatment.« less

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.

Resection of isolated pelvic recurrences after colorectal surgery: long-term results and predictors of improved clinical outcome.

PubMed

Henry, Leonard R; Sigurdson, Elin; Ross, Eric A; Lee, John S; Watson, James C; Cheng, Jonathan D; Freedman, Gary M; Konski, Andre; Hoffman, John P

2007-07-01

Recurrence in the pelvis after resection of a rectal or rectosigmoid cancer presents a dilemma. Resection offers the only reasonable probability for cure, but at the cost of perioperative morbidity and potential mortality. Clinical decision making remains difficult. Patients resected with curative intent for isolated pelvic recurrences after curative colorectal surgery from 1988 through 2003 were reviewed retrospectively. Clinical and pathologic factors, salvage operations, and complications were recorded. The primary measured outcome was overall survival. Univariate and multivariate analyses were conducted to identify prognostic factors of improved outcome. Ninety patients underwent an attempt at curative resection of a pelvic recurrence with median follow-up of 31 months. Complications occurred in 53% of patients. Operative mortality was 4.4% (4 of 90). Median overall survival was 38 months, and estimated 5-year survival was 40%. A total of 51 of 86 patients had known recurrences (15 local, 16 distant, 20 both). Multivariate analysis revealed that preoperative carcinoembryonic antigen level and final margin status were statistically significant predictors of outcome. The resection of pelvic recurrences after colorectal surgery for cancer can be performed with low mortality and good long-term outcome; however, morbidity from such procedures is high. Low preoperative carcinoembryonic antigen and negative margin of resection predict improved survival.

Resection of isolated pelvic recurrences after colorectal surgery: long-term results and predictors of improved clinical outcome.

PubMed

Henry, Leonard R; Sigurdson, Elin; Ross, Eric A; Lee, John S; Watson, James C; Cheng, Jonathan D; Freedman, Gary M; Konski, Andre; Hoffman, John P

2007-03-01

Recurrence in the pelvis after resection of a rectal or rectosigmoid cancer presents a dilemma. Resection offers the only reasonable probability for cure, but at the cost of marked perioperative morbidity and potential mortality. Clinical decision making remains difficult. Patients who underwent resection with curative intent for isolated pelvic recurrences after curative colorectal surgery from 1988 through 2003 were reviewed retrospectively. Clinical and pathological factors, salvage operations, and complications were recorded. The primary measured outcome was overall survival. Univariate and multivariate analyses were conducted to identify prognostic factors of improved outcome. Ninety patients underwent an attempt at curative resection of a pelvic recurrence; median follow-up was 31 months. Complications occurred in 53% of patients. Operative mortality occurred in 4 (4.4%) of 90 patients. Median overall survival was 38 months, and estimated 5-year survival was 40%. A total of 51 of 86 patients had known recurrences (15 local, 16 distant, 20 both). Multivariate analysis revealed that preoperative carcinoembryonic antigen level and final margin status were statistically significant predictors of outcome. The resection of pelvic recurrences after colorectal surgery for cancer can be performed with low mortality and good long-term outcome; however, morbidity from such procedures is high. Low preoperative carcinoembryonic antigen and negative margin of resection predict improved survival.

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.

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.

Company Profile: Selventa, Inc.

PubMed

Fryburg, David A; Latino, Louis J; Tagliamonte, John; Kenney, Renee D; Song, Diane H; Levine, Arnold J; de Graaf, David

2012-08-01

Selventa, Inc. (MA, USA) is a biomarker discovery company that enables personalized healthcare. Originally founded as Genstruct, Inc., Selventa has undergone significant evolution from a technology-based service provider to an active partner in the development of diagnostic tests, functioning as a molecular dashboard of disease activity using a unique platform. As part of that evolution, approximately 2 years ago the company was rebranded as Selventa to reflect its new identity and mission. The contributions to biomedical research by Selventa are based on in silico, reverse-engineering methods to determine biological causality. That is, given a set of in vitro or in vivo biological observations, which biological mechanisms can explain the measured results? Facilitated by a large and carefully curated knowledge base, these in silico methods generated new insights into the mechanisms driving a disease. As Selventa's methods would enable biomarker discovery and be directly applicable to generating novel diagnostics, the scientists at Selventa have focused on the development of predictive biomarkers of response in autoimmune and oncologic diseases. Selventa is presently building a portfolio of independent, as well as partnered, biomarker projects with the intention to create diagnostic tests that predict response to therapy.

Perioperative and long-term outcome of intrahepatic cholangiocarcinoma involving the hepatic hilus after curative-intent resection: comparison with peripheral intrahepatic cholangiocarcinoma and hilar cholangiocarcinoma.

PubMed

Zhang, Xu-Feng; Bagante, Fabio; Chen, Qinyu; Beal, Eliza W; Lv, Yi; Weiss, Matthew; Popescu, Irinel; Marques, Hugo P; Aldrighetti, Luca; Maithel, Shishir K; Pulitano, Carlo; Bauer, Todd W; Shen, Feng; Poultsides, George A; Soubrane, Olivier; Martel, Guillaume; Koerkamp, B Groot; Guglielmi, Alfredo; Itaru, Endo; Pawlik, Timothy M

2018-05-01

Intrahepatic cholangiocarcinoma with hepatic hilus involvement has been either classified as intrahepatic cholangiocarcinoma or hilar cholangiocarcinoma. The present study aimed to investigate the clinicopathologic characteristics and short- and long-term outcomes after curative resection for hilar type intrahepatic cholangiocarcinoma in comparison with peripheral intrahepatic cholangiocarcinoma and hilar cholangiocarcinoma. A total of 912 patients with mass-forming peripheral intrahepatic cholangiocarcinoma, 101 patients with hilar type intrahepatic cholangiocarcinoma, and 159 patients with hilar cholangiocarcinoma undergoing curative resection from 2000 to 2015 were included from two multi-institutional databases. Clinicopathologic characteristics and short- and long-term outcomes were compared among the 3 groups. Patients with hilar type intrahepatic cholangiocarcinoma had more aggressive tumor characteristics (eg, higher frequency of vascular invasion and lymph nodes metastasis) and experienced more extensive resections in comparison with either peripheral intrahepatic cholangiocarcinoma or hilar cholangiocarcinoma patients. The odds of lymphadenectomy and R0 resection rate among patients with hilar type intrahepatic cholangiocarcinoma were comparable with hilar cholangiocarcinoma patients, but higher than peripheral intrahepatic cholangiocarcinoma patients (lymphadenectomy incidence, 85.1% vs 42.5%, P < .001; R0 rate, 75.2% vs 88.8%, P < .001). After curative surgery, patients with hilar type intrahepatic cholangiocarcinoma experienced a higher rate of technical-related complications compared with peripheral intrahepatic cholangiocarcinoma patients. Of note, hilar type intrahepatic cholangiocarcinoma was associated with worse disease-specific survival and recurrence-free survival after curative resection versus peripheral intrahepatic cholangiocarcinoma (median disease-specific survival, 26.0 vs 54.0 months, P < .001; median recurrence-free survival, 13.0 vs 18.0 months, P = .021) and hilar cholangiocarcinoma (median disease-specific survival, 26.0 vs 49.0 months, P = .003; median recurrence-free survival, 13.0 vs 33.4 months, P < .001). Mass-forming intrahepatic cholangiocarcinoma with hepatic hilus involvement is a more aggressive type of cholangiocarcinoma, which showed distinct clinicopathologic characteristics, worse long-term outcomes after curative resection, in comparison with peripheral intrahepatic cholangiocarcinoma and hilar cholangiocarcinoma. Copyright © 2018 Elsevier Inc. All rights reserved.

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.

Clinical outcome of elderly patients (≥ 70 years) with esophageal cancer undergoing definitive or neoadjuvant radio(chemo)therapy: a retrospective single center analysis.

PubMed

Walter, Franziska; Böckle, David; Schmidt-Hegemann, Nina-Sophie; Köpple, Rebecca; Gerum, Sabine; Boeck, Stefan; Angele, Martin; Belka, Claus; Roeder, Falk

2018-05-16

To analyse the outcome of elderly patients (≥70 years) with esophageal cancer treated with curative intent radio(chemo)therapy. Fifty five patients (median 75 years) receiving curative intent radio(chemo)therapy for esophageal cancer from 1999 to 2015 were retrospectively analyzed. Most patients showed locally advanced disease (T3/4:78%, N+:58%) with squamous cell histology (74%). Charlson comorbidity score was > 1 in 27%. 48 patients (87%) received definitive treatment while 7 patients were treated neoadjuvantly. RT was carried out as 3D-conformal treatment or IMRT. Concurrent chemotherapy was applied in 85%, mainly cisplatin/5-FU or mitomycin/5-FU. 18 FDG-PET/CT staging was used in 65%. Median follow-up was 11 months (1-68) and 21 months in survivors. 1- and 2-year rates of LRC, DC, FFTF and OS were 60%/45, 81%/72, 55%/41 and 46%/26% for the entire cohort. In univariate analysis, addition of surgery was associated with improved LRC and FFTF, nodal involvement with improved DC and lower T stage, lower Charlson score and use of PET-CT with improved OS. In multivariate analysis, lower T stage and lower Charlson score remained significant for OS. Patients treated after 2008 showed a significantly improved FFTF (1-year FFTF 64% vs 35%) and OS (1-year OS 66% vs 24%). Maximum (chemo)radiation related grade3+ toxicity was observed in 80% including 7 deaths (13%). Grade5 toxicity was significantly associated with Charlson score (CS > 1:33% vs CS ≤ 1:5%) and treatment period (24% before vs 3% after 2008). The patients treated after 2008 included significantly more SCCs, less T4 stages, had a higher percentage of PET-CT staging and were treated with smaller field lengths. Trends were also observed for lower Charlson scores and increased use of IMRT. Curative intent (chemo)radiation of elderly patients with esophageal cancer may result in considerable toxicity and unfavorable outcome. However, a clear improvement over time was observed in our cohort, probably based on improved patient selection. In patients with less advanced stages and lower comorbidity similar results as in younger cohorts seem achievable with modern staging and treatment approaches. Age per se should not be a decisive factor, but careful attention should be paid regarding patient selection including a structured and tight follow-up strategy.

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.

[Peculiarities of laparoscopic diagnosis of the closed hepatic traumatic damage].

PubMed

Kapshitar', A A; Kapshitar', A V; Syrbu, I F

2008-01-01

Diagnostic possibilities of laparoscopy were studied in 24 injured persons, suffering closed hepatic damage in noninformity of results of clinical, laboratory-biochemical, roentgenologic, ultrasound investigations and diagnostic peritoneal lavage as well, were studied. Isolated trauma was revealed in 8 injured persons, the multiple one in 7 and the combined--in 9. Open operation was performed in 21 patients, relaparotomy--in 3, laparoscopic intervention with curative intent--in 3 hepatic wound tamponade, using hemostatic sponge with ambene, lubricated by dicinon. Three patients died due to severe combined trauma.

Localized prostate cancer in elderly men aged 80-89, findings from a population-based registry.

PubMed

Vatandoust, S; Kichenadasse, G; O'Callaghan, M; Vincent, A D; Kopsaftis, T; Walsh, S; Borg, M; Karapetis, C S; Moretti, K

2018-03-30

To investigate the rate of death due to Prostate Cancer (PCa) and disease characteristics in patients diagnosed with Localized Prostate Cancer (LPCa) at age 80-89 years in comparison with men diagnosed at age 70-79. This is a retrospective study of data from the South Australian Prostate Cancer Clinical Outcomes Collaborative (SA-PCCOC). Included were men diagnosed between 2005 and 2014, aged ≥70 with no evidence of metastatic disease at presentation. Propensity score matching and competing risk Fine and Grey regression were used to assess the chance of treatment (curative v non-curative) and treatment effect on PCa specific-mortality. Of the 1951 eligible patients, 1428 (76%) aged 70-79, and 460 (24%) aged 80-89 yr at diagnosis (median age of 74 (IQR=72-76) and 83 (IQR=81-85) respectively). The 80-89 group had higher Gleason scores and PSA values (all p<0.001) in comparison with the younger group. The 80-89 group were less likely to be treated with curative treatment (OR=0.12, 95CI=[0.09, 0.16], p < 0.001). Proportion of deaths attributable to PCa was similar in both groups: 73 of 263 deaths (28%) in the 80-89 group vs 97 of 310 deaths (31%) in the 70-79 group. The risk of PCa mortality in individuals treated with curative intent was reduced in both groups. The proportion of PCa deaths was similar in both groups. These findings support carefully selected individualized management of elderly patients diagnosed with localized PCa. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Chemoradiotherapy of Anal Carcinoma: Survival and Recurrence in an Unselected National Cohort

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

Bentzen, Anne Gry, E-mail: anne.gry.bentzen@unn.no; Institute of Clinical Medicine, University of Tromso, Tromso; Guren, Marianne G.

2012-06-01

Purpose: To evaluate treatment results, elucidate whether national guidelines were followed, and identify areas demanding further treatment optimization. Methods and Material: Between July 2000 and June 2007, 328 patients were treated with curatively intended chemoradiotherapy (CRT) for nonmetastatic squamous cell carcinoma of the anal region, according to national treatment guidelines based on tumor stage. Results: Complete response after CRT was obtained in 87% of patients, rising to 93% after salvage surgery. Chemotherapy, elective irradiation of the groin and salvage surgery were performed to a lesser extent in elderly patients, mainly because of frailty and comorbidity. Recurrence occurred in 24% ofmore » the patients, resulting in a 3- and 5-year recurrence-free survival (RFS) of 79% and 74%, respectively. Locoregional recurrences dominated, most commonly in the primary tumor site. Recurrence was treated with curative intent in 45% of the cases. The 3- and 5-year overall survival were 79% and 66%, and cancer-specific survival (CSS) were 84% and 75%, respectively. The risk of adverse outcome increased significantly with more locally advanced tumors and for male gender in multivariable analyses for RFS and CSS. Conclusions: The treatment results are in accordance with similar cohorts. The primary treatment control rate was high, but there was a significant risk of locoregional recurrence in advanced tumors. The loyalty to national guidelines was broad, although individual adjustments occurred. However, caution to avoid toxicity must not lead to inadequate treatment. Male gender seems to have inferior outcome.« less

Radiotherapy in the elderly: a multicentric prospective study on 2060 patients referred to 37 Italian radiation therapy centers.

PubMed

Olmi, P; Ausili-Cefaro, G

1997-01-01

60-70% of all cancers will develop in the year 2000 in persons aged 65 and over. Radiation therapy will play a major role in the treatment of cancer, especially in the elderly. The Italian "Geriatric Radiation Oncology Group" (GROG) performed in 1994 a prospective study, in order to assess the characteristics of any old cancer patient referred to radiation oncology centers (age, gender performance status, comorbidity, activities of daily living, family status) and the main features of the tumor in that patient. In about 6 months 2060 patients aged 70 and over entered the study, of whom 1809 were treated with radiotherapy alone, with curative intent in 563 patients, in combination with surgery and/or chemotherapy in 476 and with palliative intent in 769 patients. Most patients had grade 0-1 acute toxicity.

Impact of Increasing Age on Cause-Specific Mortality and Morbidity in Patients With Stage I Non-Small-Cell Lung Cancer: A Competing Risks Analysis.

PubMed

Eguchi, Takashi; Bains, Sarina; Lee, Ming-Ching; Tan, Kay See; Hristov, Boris; Buitrago, Daniel H; Bains, Manjit S; Downey, Robert J; Huang, James; Isbell, James M; Park, Bernard J; Rusch, Valerie W; Jones, David R; Adusumilli, Prasad S

2017-01-20

Purpose To perform competing risks analysis and determine short- and long-term cancer- and noncancer-specific mortality and morbidity in patients who had undergone resection for stage I non-small-cell lung cancer (NSCLC). Patients and Methods Of 5,371 consecutive patients who had undergone curative-intent resection of primary lung cancer at our institution (2000 to 2011), 2,186 with pathologic stage I NSCLC were included in the analysis. All preoperative clinical variables known to affect outcomes were included in the analysis, specifically, Charlson comorbidity index, predicted postoperative (ppo) diffusing capacity of the lung for carbon monoxide, and ppo forced expiratory volume in 1 second. Cause-specific mortality analysis was performed with competing risks analysis. Results Of 2,186 patients, 1,532 (70.1%) were ≥ 65 years of age, including 638 (29.2%) ≥ 75 years of age. In patients < 65, 65 to 74, and ≥ 75 years of age, 5-year lung cancer-specific cumulative incidence of death (CID) was 7.5%, 10.7%, and 13.2%, respectively (overall, 10.4%); noncancer-specific CID was 1.8%, 4.9%, and 9.0%, respectively (overall, 5.3%). In patients ≥ 65 years of age, for up to 2.5 years after resection, noncancer-specific CID was higher than lung cancer-specific CID; the higher noncancer-specific, early-phase mortality was enhanced in patients ≥ 75 years of age than in those 65 to 74 years of age. Multivariable analysis showed that low ppo diffusing capacity of lung for carbon monoxide was an independent predictor of severe morbidity ( P < .001), 1-year mortality ( P < .001), and noncancer-specific mortality ( P < .001), whereas low ppo forced expiratory volume in 1 second was an independent predictor of lung cancer-specific mortality ( P = .002). Conclusion In patients who undergo curative-intent resection of stage I NSCLC, noncancer-specific mortality is a significant competing event, with an increasing impact as patient age increases.

18F-FDG PET/CT has a high impact on patient management and provides powerful prognostic stratification in the primary staging of esophageal cancer: a prospective study with mature survival data.

PubMed

Barber, Thomas W; Duong, Cuong P; Leong, Trevor; Bressel, Mathias; Drummond, Elizabeth G; Hicks, Rodney J

2012-06-01

The aim of this study is to evaluate the incremental staging information, management impact, and prognostic stratification of PET/CT in the primary staging of esophageal cancer in a cohort of patients with mature survival data. Between July 2002 and June 2005, 139 consecutive patients with newly diagnosed esophageal cancer underwent conventional staging investigations (CSI), followed by PET/CT. Disease stage was classified according to the American Joint Committee on Cancer staging system (6th edition) and grouped as stage I-IIA, stage IIB-III, and stage IV reflecting broad groupings that determine therapeutic choice. Validation of results was performed when PET/CT and CSI stage groups were discordant and in those patients where PET/CT changed management. Management impact was determined by comparing prospectively recorded pre-PET/CT management plans with post-PET/CT management plans. Survival after follow-up of at least 5 y in patients was analyzed using the Kaplan-Meier product limit method and the Cox proportional hazards regression model. PET/CT changed the stage group in 56 of 139 (40%) patients and changed management in 47 of 139 (34%) patients. In 22 patients, therapy was changed from curative to palliative and in 3 from palliative to curative; in 11, treatment modality was changed without a change in treatment intent, and in 11 the delivery of therapy or diagnostic procedure was changed. Of the 47 patients with management change, imaging results could be validated in 31 patients, and PET/CT correctly changed management in 26 (84%) of these. Of the remaining 5 patients, CSI stage was also incorrect in 4 and correct in 1. Median survival was 23 mo. PET/CT stages I-IIA, IIB-III, and IV had a 5-y survival of 40%, 38%, and 6%, respectively. Post-PET/CT stage group and treatment intent were both strongly associated with survival (P < 0.001). PET/CT provides incremental staging information compared with CSI, changes management in one third of patients, and has powerful prognostic stratification in the primary staging of esophageal cancer.

The use of TCP based EUD to rank and compare lung radiotherapy plans: in-silico study to evaluate the correlation between TCP with physical quality indices.

PubMed

Chaikh, Abdulhamid; Balosso, Jacques

2017-06-01

To apply the equivalent uniform dose (EUD) radiobiological model to estimate the tumor control probability (TCP) scores for treatment plans using different radiobiological parameter settings, and to evaluate the correlation between TCP and physical quality indices of the treatment plans. Ten radiotherapy treatment plans for lung cancer were generated. The dose distributions were calculated using anisotropic analytical algorithm (AAA). Dose parameters and quality indices derived from dose volume histograms (DVH) for target volumes were evaluated. The predicted TCP was computed using EUD model with tissue-specific parameter (a=-10). The assumed radiobiological parameter setting for adjuvant therapy [tumor dose to control 50% of the tumor (TCD 50 ) =36.5 Gy and γ 50 =0.72] and curative intent (TCD 50 =51.24 Gy and γ 50 =0.83) were used. The bootstrap method was used to estimate the 95% confidence interval (95% CI). The coefficients (ρ) from Spearman's rank test were calculated to assess the correlation between quality indices with TCP. Wilcoxon paired test was used to calculate P value. The 95% CI of TCP were 70.6-81.5 and 46.6-64.7, respectively, for adjuvant radiotherapy and curative intent. The TCP outcome showed a positive and good correlation with calculated dose to 95% of the target volume (D95%) and minimum dose (Dmin). Consistently, TCP correlate negatively with heterogeneity indices. This study confirms that more relevant and robust radiobiological parameters setting should be integrated according to cancer type. The positive correlation with quality indices gives chance to improve the clinical out-come by optimizing the treatment plans to maximize the Dmin and D95%. This attempt to increase the TCP should be carried out with the respect of dose constraints for organs at risks. However, the negative correlation with heterogeneity indices shows that the optimization of beam arrangements could be also useful. Attention should be paid to obtain an appropriate optimization of initial plans, when comparing and ranking radiotherapy plans using TCP models, to avoid over or underestimated for TCP outcome.

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

Survival times for canine intranasal sarcomas treated with radiation therapy: 86 cases (1996-2011).

PubMed

Sones, Evan; Smith, Annette; Schleis, Stephanie; Brawner, William; Almond, Gregory; Taylor, Kathryn; Haney, Siobhan; Wypij, Jackie; Keyerleber, Michele; Arthur, Jennifer; Hamilton, Terrance; Lawrence, Jessica; Gieger, Tracy; Sellon, Rance; Wright, Zack

2013-01-01

Sarcomas comprise approximately one-third of canine intranasal tumors, however few veterinary studies have described survival times of dogs with histologic subtypes of sarcomas separately from other intranasal tumors. One objective of this study was to describe median survival times for dogs treated with radiation therapy for intranasal sarcomas. A second objective was to compare survival times for dogs treated with three radiation therapy protocols: daily-fractionated radiation therapy; Monday, Wednesday, and Friday fractionated radiation therapy; and palliative radiation therapy. Medical records were retrospectively reviewed for dogs that had been treated with radiation therapy for confirmed intranasal sarcoma. A total of 86 dogs met inclusion criteria. Overall median survival time for included dogs was 444 days. Median survival time for dogs with chondrosarcoma (n = 42) was 463 days, fibrosarcoma (n = 12) 379 days, osteosarcoma (n = 6) 624 days, and undifferentiated sarcoma (n = 22) 344 days. Dogs treated with daily-fractionated radiation therapy protocols; Monday, Wednesday and Friday fractionated radiation therapy protocols; and palliative radiation therapy protocols had median survival times of 641, 347, and 305 days, respectively. A significant difference in survival time was found for dogs receiving curative intent radiation therapy vs. palliative radiation therapy (P = 0.032). A significant difference in survival time was also found for dogs receiving daily-fractionated radiation therapy vs. Monday, Wednesday and Friday fractionated radiation therapy (P = 0.0134). Findings from this study support the use of curative intent radiation therapy for dogs with intranasal sarcoma. Future prospective, randomized trials are needed for confirmation of treatment benefits. © 2012 Veterinary Radiology & Ultrasound.

Age at death of patients with colorectal cancer and the effect of lead-time bias on survival in elective vs emergency surgery.

PubMed

MacDonald, A J; McEwan, H; McCabe, M; Macdonald, A

2011-05-01

Colorectal cancer survival depends on stage at presentation, and current strategies aim for improvements through early detection. Previous studies have demonstrated improved survival from diagnosis but not increased life expectancy. While lead-time bias may account for variations in known prognostic indicators and also influence screening programmes, only age at death provides a true representation of the effectiveness of an intervention. We aimed to compare age at death for patients with colorectal cancer presenting on an emergency or elective basis. Patients presenting with colorectal cancer (2000-2006) were entered into a prospective database (analysis 1 December 2008). Fields included age at death, emergency/elective presentation, palliative/curative intent and disease stage. One thousand six hundred and fifty patients (922 men) were identified. Elective patients presented younger than emergency patients (67.9 vs 70.6 years; P < 0.005). Dukes B patients presented older than Dukes D (P = 0.02). Mortality was 41% at time of analysis; no difference was seen in mean age at death between emergency and elective presentation (72.8 vs 72.0 years; P = 0.379) or palliative and curative intent (72.0 vs 72.5 years; P = 0.604). Colorectal cancer is common in a population where actuarial life expectancy is limited. Current colorectal cancer early detection strategies may improve cancer-specific survival by increasing lead-time bias but do not influence overall life expectancy. © 2011 The Authors. Colorectal Disease © 2011 The Association of Coloproctology of Great Britain and Ireland.

Australian contemporary management of synchronous metastatic colorectal cancer.

PubMed

Malouf, Phillip; Gibbs, Peter; Shapiro, Jeremy; Sockler, Jim; Bell, Stephen

2018-01-01

This article outlines the current Australian multidisciplinary treatment of synchronous metastatic colorectal adenocarcinoma and assesses the factors that influence patient outcome. This is a retrospective analysis of the prospective 'Treatment of Recurrent and Advanced Colorectal Cancer' registry, describing the patient treatment pathway and documenting the extent of disease, resection of the colorectal primary and metastases, chemotherapy and biological therapy use. Cox regression models for progression-free and overall survival were constructed with a comprehensive set of clinical variables. Analysis was intentionn-ton-treat, quantifying the effect of treatment intent decided at the multidisciplinary team meeting (MDT). One thousand one hundred and nine patients presented with synchronous metastatic disease between July 2009 and November 2015. Median follow-up was 15.8 months; 4.4% (group 1) had already curative resections of primary and metastases prior to MDT, 22.2% (group 2) were considered curative but were referred to MDT for opinion and/or medical oncology treatment prior to resection and 70.2% were considered palliative at MDT (group 3). Overall, 83% received chemotherapy, 55% had their primary resected and 23% had their metastases resected; 13% of resections were synchronous, 20% were staged with primary resected first and 62% had only the colorectal primary managed surgically. Performance status, metastasis resection (R0 versus R1 versus R2 versus no resection), resection of the colorectal primary and treatment intent determined at MDT were the most significant factors for progression-free and overall survival. This is the largest Australian series of synchronous metastatic colorectal adenocarcinoma and offers insight into the nature and utility of contemporary practice. © 2016 Royal Australasian College of Surgeons.

A theoretical framework to describe communication processes during medical disability assessment interviews

PubMed Central

van Rijssen, H Jolanda; Schellart, Antonius JM; Anema, Johannes R; van der Beek, Allard J

2009-01-01

Background Research in different fields of medicine suggests that communication is important in physician-patient encounters and influences satisfaction with these encounters. It is argued that this also applies to the non-curative tasks that physicians perform, such as sickness certification and medical disability assessments. However, there is no conceptualised theoretical framework that can be used to describe intentions with regard to communication behaviour, communication behaviour itself, and satisfaction with communication behaviour in a medical disability assessment context. Objective The objective of this paper is to describe the conceptualisation of a model for the communication behaviour of physicians performing medical disability assessments in a social insurance context and of their claimants, in face-to-face encounters during medical disability assessment interviews and the preparation thereof. Conceptualisation The behavioural model, based on the Theory of Planned Behaviour (TPB), is conceptualised for the communication behaviour of social insurance physicians and claimants separately, but also combined during the assessment interview. Other important concepts in the model are the evaluation of communication behaviour (satisfaction), intentions, attitudes, skills, and barriers for communication. Conclusion The conceptualisation of the TPB-based behavioural model will help to provide insight into the communication behaviour of social insurance physicians and claimants during disability assessment interviews. After empirical testing of the relationships in the model, it can be used in other studies to obtain more insight into communication behaviour in non-curative medicine, and it could help social insurance physicians to adapt their communication behaviour to their task when performing disability assessments. PMID:19807905

Long-term medical costs and life expectancy of acute myeloid leukemia: a probabilistic decision model.

PubMed

Wang, Han-I; Aas, Eline; Howell, Debra; Roman, Eve; Patmore, Russell; Jack, Andrew; Smith, Alexandra

2014-03-01

Acute myeloid leukemia (AML) can be diagnosed at any age and treatment, which can be given with supportive and/or curative intent, is considered expensive compared with that for other cancers. Despite this, no long-term predictive models have been developed for AML, mainly because of the complexities associated with this disease. The objective of the current study was to develop a model (based on a UK cohort) to predict cost and life expectancy at a population level. The model developed in this study combined a decision tree with several Markov models to reflect the complexity of the prognostic factors and treatments of AML. The model was simulated with a cycle length of 1 month for a time period of 5 years and further simulated until age 100 years or death. Results were compared for two age groups and five different initial treatment intents and responses. Transition probabilities, life expectancies, and costs were derived from a UK population-based specialist registry-the Haematological Malignancy Research Network (www.hmrn.org). Overall, expected 5-year medical costs and life expectancy ranged from £8,170 to £81,636 and 3.03 to 34.74 months, respectively. The economic and health outcomes varied with initial treatment intent, age at diagnosis, trial participation, and study time horizon. The model was validated by using face, internal, and external validation methods. The results show that the model captured more than 90% of the empirical costs, and it demonstrated good fit with the empirical overall survival. Costs and life expectancy of AML varied with patient characteristics and initial treatment intent. The robust AML model developed in this study could be used to evaluate new diagnostic tools/treatments, as well as enable policy makers to make informed decisions. Copyright © 2014 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

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

Diagnostic accuracy of laparoscopy following computed tomography (CT) scanning for assessing the resectability with curative intent in pancreatic and periampullary cancer.

PubMed

Allen, Victoria B; Gurusamy, Kurinchi Selvan; Takwoingi, Yemisi; Kalia, Amun; Davidson, Brian R

2016-07-06

Surgical resection is the only potentially curative treatment for pancreatic and periampullary cancer. A considerable proportion of patients undergo unnecessary laparotomy because of underestimation of the extent of the cancer on computed tomography (CT) scanning. Laparoscopy can detect metastases not visualised on CT scanning, enabling better assessment of the spread of cancer (staging of cancer). This is an update to a previous Cochrane Review published in 2013 evaluating the role of diagnostic laparoscopy in assessing the resectability with curative intent in people with pancreatic and periampullary cancer. To determine the diagnostic accuracy of diagnostic laparoscopy performed as an add-on test to CT scanning in the assessment of curative resectability in pancreatic and periampullary cancer. We searched the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE via PubMed, EMBASE via OvidSP (from inception to 15 May 2016), and Science Citation Index Expanded (from 1980 to 15 May 2016). We included diagnostic accuracy studies of diagnostic laparoscopy in people with potentially resectable pancreatic and periampullary cancer on CT scan, where confirmation of liver or peritoneal involvement was by histopathological examination of suspicious (liver or peritoneal) lesions obtained at diagnostic laparoscopy or laparotomy. We accepted any criteria of resectability used in the studies. We included studies irrespective of language, publication status, or study design (prospective or retrospective). We excluded case-control studies. Two review authors independently performed data extraction and quality assessment using the QUADAS-2 tool. The specificity of diagnostic laparoscopy in all studies was 1 because there were no false positives since laparoscopy and the reference standard are one and the same if histological examination after diagnostic laparoscopy is positive. The sensitivities were therefore meta-analysed using a univariate random-effects logistic regression model. The probability of unresectability in people who had a negative laparoscopy (post-test probability for people with a negative test result) was calculated using the median probability of unresectability (pre-test probability) from the included studies, and the negative likelihood ratio derived from the model (specificity of 1 assumed). The difference between the pre-test and post-test probabilities gave the overall added value of diagnostic laparoscopy compared to the standard practice of CT scan staging alone. We included 16 studies with a total of 1146 participants in the meta-analysis. Only one study including 52 participants had a low risk of bias and low applicability concern in the patient selection domain. The median pre-test probability of unresectable disease after CT scanning across studies was 41.4% (that is 41 out of 100 participants who had resectable cancer after CT scan were found to have unresectable disease on laparotomy). The summary sensitivity of diagnostic laparoscopy was 64.4% (95% confidence interval (CI) 50.1% to 76.6%). Assuming a pre-test probability of 41.4%, the post-test probability of unresectable disease for participants with a negative test result was 0.20 (95% CI 0.15 to 0.27). This indicates that if a person is said to have resectable disease after diagnostic laparoscopy and CT scan, there is a 20% probability that their cancer will be unresectable compared to a 41% probability for those receiving CT alone.A subgroup analysis of people with pancreatic cancer gave a summary sensitivity of 67.9% (95% CI 41.1% to 86.5%). The post-test probability of unresectable disease after being considered resectable on both CT and diagnostic laparoscopy was 18% compared to 40.0% for those receiving CT alone. Diagnostic laparoscopy may decrease the rate of unnecessary laparotomy in people with pancreatic and periampullary cancer found to have resectable disease on CT scan. On average, using diagnostic laparoscopy with biopsy and histopathological confirmation of suspicious lesions prior to laparotomy would avoid 21 unnecessary laparotomies in 100 people in whom resection of cancer with curative intent is planned.

[Thoracoscopic diagnosis and treatment of postoperative residual cavities].

PubMed

Ioffe, D Ts; Dashiev, V A; Amanov, S A

1987-03-01

Investigations performed in 41 patients with postoperative residual cavities after surgical interventions of different volume have shown high value of thoracoscopy as an additional diagnostic and curative method. The endoscopy findings determinate further curative tactics--surgery or conservative therapy.

BCL2 Inhibition by Venetoclax: Targeting the Achilles' Heel of the Acute Myeloid Leukemia Stem Cell?

PubMed

Pullarkat, Vinod A; Newman, Edward M

2016-10-01

Venetoclax is an oral drug with an excellent side-effect profile that has the potential to revolutionize acute myeloid leukemia (AML) therapy in two areas. Venetoclax-based combination therapies could be a bridge to hematopoietic cell transplant with curative intent for patients with refractory/relapsed AML, and venetoclax-based therapy could provide meaningful survival prolongation for older patients with AML who are not candidates for more aggressive therapies. Cancer Discov; 6(10); 1082-3. ©2016 AACR.See related article by Konopleva and colleagues, p. 1106. ©2016 American Association for Cancer Research.

Biological Databases for Behavioral Neurobiology

PubMed Central

Baker, Erich J.

2014-01-01

Databases are, at their core, abstractions of data and their intentionally derived relationships. They serve as a central organizing metaphor and repository, supporting or augmenting nearly all bioinformatics. Behavioral domains provide a unique stage for contemporary databases, as research in this area spans diverse data types, locations, and data relationships. This chapter provides foundational information on the diversity and prevalence of databases, how data structures support the various needs of behavioral neuroscience analysis and interpretation. The focus is on the classes of databases, data curation, and advanced applications in bioinformatics using examples largely drawn from research efforts in behavioral neuroscience. PMID:23195119

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.

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.

Middle-preserving pancreatectomy for advanced transverse colon cancer invading the duodenun and non-functioning endocrine tumor in the pancreatic tail.

PubMed

Noda, Hiroshi; Kato, Takaharu; Kamiyama, Hidenori; Toyama, Nobuyuki; Konishi, Fumio

2011-02-01

A 73-year-old female was referred to our hospital with a diagnosis of advanced transverse colon cancer with severe anemia and body weight loss. Preoperative evaluations, including colonoscopy, gastroduodenoscopy, and computed tomography, revealed not only a transverse colon cancer massively invading the duodenum, but also a non-functioning endocrine tumor in the pancreatic tail. We performed middle-preserving pancreatectomy (MPP) with right hemicolectomy for these tumors with a curative intent. After the resection, about 6 cm of the body of the pancreas was preserved, and signs of diabetes mellitus have not appeared. The postoperative course was complicated by a grade B pancreatic fistula, but this was successfully treated with conservative management. After a 33-day hospital stay, the patient returned to daily life without signs of pancreatic exocrine insufficiency. Although the long-term follow-up of the patient is indispensable, in this case, MPP might be able to lead to the curative resection of transverse colon cancer massively invading the duodenum and non-functioning endocrine tumor in the pancreatic tail with preservation of pancreatic function.

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.

Hematopoietic stem cell transplantation for myelofibrosis: where are we now?

PubMed

Fleischman, Angela G; Maziarz, Richard T

2013-03-01

A succinct yet comprehensive review of the biology of myeloproliferative neoplasms and therapeutic options with a focus on rational decision making for hematopoietic stem cell transplantation. The introduction of Janus kinase inhibitors for myelofibrosis have ushered in a new era for treatment of constitutional symptoms and splenomegaly in myelofibrosis, but the effect of these agents on the natural history of the disease has yet to be clearly defined. Reduced intensity transplants have emerged as the preferred option with recent evidence suggesting fludarabine and melphalan as the optimal conditioning regimen. Myelofibrosis is a rare hematologic malignancy with limited curative therapeutic options. Significant advances in our understanding of disease pathogenesis have led to new targets and new therapeutic options are forthcoming. Hematopoietic stem cell transplantation is at present the only treatment with curative intent; however, the selection of patients who are likely to be best served by this procedure is difficult. As myelofibrosis is an extremely rare disease, randomized clinical trials specifically investigating the role of transplantation in myelofibrosis are unlikely to occur, thus current decision making processes are best guided by retrospective analyses from registry databases and single institution experiences.

Implementation and assessment of a fast-track programme to improve communication between primary and specialized care in patients with suspected cancer: how to shorten time between initial symptoms of cancer, diagnosis and initiation of treatment.

PubMed

Martínez, M T; González, I; Tarazona, N; Roselló, S; Saiz, R; Sanmartín, A; Martínez-Agulló, Á; Caballero, A; Mas, P; Franco, J; Martínez-Jabaloyas, J; García-Callejo, J; Martín, V; Navarro, J; Teruel, A; Lluch, A; Chirivella, I

2015-02-01

This study aims to asses a cancer fast-track programme (CFP) to shorten the time since a patient with suspicion of cancer is referred by the primary care (PC) physician to the specialized medical team. Guidelines for main suspected tumours were designed to help PC physicians to detect and rapidly refer cases to the CFP oncology coordinator, who sent them to the appropriate department to accelerate diagnosis, staging and therapy. All patients analysed in this report were referred from June 2009 to July 2012. A total of 897 suspected cancer cases were submitted and finally 705 were studied. In 205 (29 %) a cancer diagnosis was confirmed within 23 days (median). Therapy was initiated within 46 days after referral (median). Early diagnoses with a potential curative approach were made in 166 (82 %). This CFP decreased the waiting time for cancer diagnosis, by improving communication between PC physician and specialized care teams. Most patients included in this program could get therapy with curative intent.

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

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.

Evaluation of prognostic factors on recurrence after curative resections for hepatocellular carcinoma

PubMed Central

Han, Jae Hyun; Kim, Dong Goo; Na, Gun Hyung; Kim, Eun Young; Lee, Soo Ho; Hong, Tae Ho; You, Young Kyoung

2014-01-01

AIM: To select appropriate patients before surgical resection for hepatocellular carcinoma (HCC), especially those with advanced tumors. METHODS: From January 2000 to December 2012, we retrospectively analyzed the medical records of 298 patients who had undergone surgical resections for HCC with curative intent at our hospital. We evaluated preoperative prognostic factors associated with histologic grade of tumor, recurrence and survival, especially the findings of pre-operative imaging studies such as positron emission tomography-computed tomography (PET-CT) and magnetic resonance imaging (MRI). And then, we established a scoring system to predict recurrence and survival after surgery dividing the patients into two groups based on a tumor size of 5 cm. RESULTS: Of the 298 patients, 129 (43.3%) developed recurrence during the follow-up period. The 5 year disease free survival and overall survival were 47.0% and 58.7% respectively. In multivariate analysis, a serum alpha-fetoprotein (AFP) level of > 100 ng/mL and a standardized uptake value (SUV) of PET-CT of > 3.5 were predictive factors for histologic grade of tumor, recurrence, and survival. Tumor size of > 5 cm and a relative enhancement ratio (RER) calculated from preoperative MRI were also significantly associated with prognosis in univariate analysis. We established a scoring system to predict prognosis using AFP, SUV, and RER. In those with tumors of > 5 cm, it showed predicted both recurrence (P = 0.005) and survival (P = 0.001). CONCLUSION: The AFP, tumor size, SUV and RER are useful for prognosis preoperatively. An accurate prediction of prognosis is possible using our scoring system in large size tumors. PMID:25493027

Feasibility and efficacy of salvage lung resection after definitive chemoradiation therapy for Stage III non-small-cell lung cancer.

PubMed

Shimada, Yoshihisa; Suzuki, Kenji; Okada, Morihito; Nakayama, Haruhiko; Ito, Hiroyuki; Mitsudomi, Tetsuya; Saji, Hisashi; Takamochi, Kazuya; Kudo, Yujin; Hattori, Aritoshi; Mimae, Takahiro; Aokage, Keiju; Nishii, Teppei; Tsuboi, Masahiro; Ikeda, Norihiko

2016-12-01

For highly selected patients with Stage III non-small-cell lung cancer (NSCLC) who relapse or have residual disease after definitive chemoradiotherapy, salvage lung resection is likely to be one of the options for local control and possible better prognosis. However, the long-term benefit has not been verified. We conducted a retrospective study on salvage surgery on a multicentre basis. Patients included in this study met the following criteria: (i) prior treatment of lung cancer with curative-intent radiotherapy (≥60 Gy); (ii) no a priori plans for induction multimodality therapy; (iii) confirmation of loco-regional recurrence or persistent tumour in the irradiated area; (iv) pretherapeutic pathological results of NSCLC and (v) Stage III disease prior to chemoradiotherapy. A total of 18 patients were eligible for evaluation (Stage IIIA/IIIB, 14/4). The prior median radiation therapy dose was 60 Gy (60-74 Gy), and the median time between the last day of radiotherapy and resection was 38 weeks. The indications for surgery were primary tumour regrowth (10 patients) or tumour persistence (8 patients). Surgical procedures included lobectomy in 13 patients and pneumonectomy in 5 patients. Postoperative complications occurred in 5 patients (28%) without perioperative death. Complete resection was shown in 16 patients (89%) and a complete pathological response in 5 patients (28%). The median follow-up time was 1405 days, and the 3-year overall survival and recurrence-free survival rates were 78 and 72%, respectively. In the highly selected Stage III NSCLC after curative-intent chemoradiation therapy, salvage surgery was safely performed and contributed to satisfactory long-term survival. © The Author 2016. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

Cause-specific colostomy rates after radiotherapy for anal cancer: a Danish multicentre cohort study.

PubMed

Sunesen, Kåre G; Nørgaard, Mette; Lundby, Lilli; Havsteen, Hanne; Buntzen, Steen; Thorlacius-Ussing, Ole; Laurberg, Søren

2011-09-10

In anal cancer, colostomy-free survival is a measure of anal sphincter preservation after treatment with radiotherapy or chemoradiotherapy. Failure to control anal cancer and complications of treatment are alternative indications for colostomy. However, no data exist on cause-specific colostomy rates. We examined this in a cohort study. Through national registries and review of medical records, we identified patients with anal cancer diagnosed from 1995 to 2003 who had curative-intent radiotherapy or chemoradiotherapy in four Danish centers. We computed cumulative incidence of tumor-related colostomy and therapy-related colostomy, treating colostomy and death as competing events. Follow-up started at completion of radiotherapy and continued throughout 2008. We used competing risk regression to compute hazard ratios (HRs) to compare the cumulative incidence of cause-specific colostomies between age, sex, tumor size, chemotherapy, and local excision before radiotherapy. We included 235 patients with anal cancer. The 5-year cumulative incidences of tumor-related and therapy-related colostomy were 26% (95% CI, 21% to 32%) and 8% (95% CI, 5% to 12%), respectively. Tumor size greater than 6 cm versus less than 4 cm was a risk factor for tumor-related colostomy (adjusted HR, 3.8; 95% CI, 1.7 to 8.1), and local excision before radiotherapy was a risk factor for therapy-related colostomy (adjusted HR, 4.5; 95% CI, 1.5 to 13.5). After curative-intent radiotherapy or chemoradiotherapy, one third of patients had a colostomy, of which one third were related to therapy. Large tumor size was associated with a higher risk of tumor-related colostomy, whereas history of prior excision was associated with an increased incidence of therapy-related colostomy.

The integrated place of tracheobronchial stents in the multidisciplinary management of large post-pneumonectomy fistulas: our experience using a novel customised conical self-expandable metallic stent.

PubMed

Dutau, Hervé; Breen, David Patrick; Gomez, Carine; Thomas, Pascal Alexandre; Vergnon, Jean-Michel

2011-02-01

Stump dehiscence after pneumonectomy is a cause of morbidity and mortality in patients treated for non-small-cell lung carcinoma. Surgical repair remains the treatment of choice but can be postponed or contraindicated. Bronchoscopic techniques may be an option with curative intent or as a bridge towards definitive surgery. The aim of the study is to evaluate the efficacy and the outcome of a new customised covered conical self-expandable metallic stent in the management of large bronchopleural fistulas complicating pneumonectomies. A case series using chart review of non-operable patients presenting with large bronchopleural fistulas (>6mm) post-pneumonectomies as a definitive treatment with curative intent for non-small-cell lung carcinomas and requiring the use of a dedicated conical shaped stent in two tertiary referral centres. Seven patients presenting large post-pneumonectomy fistulas (between 6 and 12 mm) were included. Cessation of the air leak and clinical improvement was achieved in all the patients after stent placement. Stent-related complications (two migrations and one stent rupture) were successfully managed using bronchoscopic techniques in two patients and surgery in one. Mortality, mainly related to overwhelming sepsis, was 57%. Delayed definitive surgery was achieved successfully in three patients (43%). This case series assesses the short-term clinical efficacy of a new customised covered conical self-expandable metallic stent in the multidisciplinary management of large bronchopleural fistulas complicating pneumonectomies in patients deemed non-operable. Long-term benefits are jeopardised by infectious complications. Copyright © 2010 European Association for Cardio-Thoracic Surgery. Published by Elsevier B.V. All rights reserved.

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.

Curative-intent Surgery for Perihilar Cholangiocarcinoma with and without Portal Vein Resection - A Comparative Analysis of Early and Late Outcomes.

PubMed

Dumitraşcu, Traian; Stroescu, Cezar; Braşoveanu, Vladislav; Herlea, Vlad; Ionescu, Mihnea; Popescu, Irinel

2017-01-01

Introduction: The safety of portal vein resection (PVR) during surgery for perihilar cholangiocarcinoma (PHC) has been demonstrated in Asia, America, and Western Europe. However, no data about this topic are reported from Eastern Europe. The aim of the present study is to comparatively assess the early and long-term outcomes after resection for PHC with and without PVR. The data of 21 patients with PVR were compared with those of 102 patients with a curative-intent surgery for PHC without PVR. The appropriate statistical tests were used to compare different variables between the groups. Results: A PVR was performed in 17% of the patients. In the PVR group, significantly more right trisectionectomies (p=0.031) and caudate lobectomies (0.049) were performed and, as expected, both the operative time (p=0.015) and blood loss (p=0.002) were significantly higher. No differences between the groups were observed regarding the severe postoperative morbidity and mortality rates, and completion of adjuvant therapy. However, in the PVR group the postoperative clinicallyrelevant liver failure rate was significantly higher (p=0.001). No differences between the groups were observed for the median overall survival times (34 vs. 26 months, p = 0.566). A histological proof of the venous tumor invasion was observed in 52% of the patients with a PVR and was associated with significantly worse survival (p=0.027). A PVR can be safely performed during resection for PHC, without significant added severe morbidity or mortality rates. However, clinically-relevant liver failure rates are significantly higher when a PVR is performed. Furthermore, increased operative times and blood loss should be expected when a PVR is performed. Histological tumor invasion of the portal vein is associated with significantly worse survival. Celsius.

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.

[Curative effect of ozone hydrotherapy for pemphigus].

PubMed

Jiang, Fuqiong; Deng, Danqi; Li, Xiaolan; Wang, Wenfang; Xie, Hong; Wu, Yongzhuo; Luan, Chunyan; Yang, Binbin

2018-02-28

To determine clinical curative effects of ozone therapy for pemphigus vulgaris.
 Methods: Ozone hydrotherapy was used as an aid treatment for 32 patients with pemphigus vulgaris. The hydropathic compression of potassium permanganate solution for 34 patients with pemphigus vulgaris served as a control. The main treatment for both groups were glucocorticoids and immune inhibitors. The lesions of patients, bacterial infection, usage of antibiotics, patient's satisfaction, and clinical curative effect were evaluated in the 2 groups.
 Results: There was no significant difference in the curative effect and the average length of staying at hospital between the 2 groups (P>0.05). But rate for the usage of antibiotics was significantly reduced in the group of ozone hydrotherapy (P=0.039). The patients were more satisfied in using ozone hydrotherapy than the potassium permanganate solution after 7-day therapy (P>0.05).
 Conclusion: Ozone hydrotherapy is a safe and effective aid method for pemphigus vulgaris. It can reduce the usage of antibiotics.

Exploring Best Practices for Research Data Management in Earth Science through Collaborating with University Libraries

NASA Astrophysics Data System (ADS)

Wang, T.; Branch, B. D.

2013-12-01

Earth Science research data, its data management, informatics processing and its data curation are valuable in allowing earth scientists to make new discoveries. But how to actively manage these research assets to ensure them safe and secure, accessible and reusable for long term is a big challenge. Nowadays, the data deluge makes this challenge become even more difficult. To address the growing demand for managing earth science data, the Council on Library and Information Resources (CLIR) partners with the Library and Technology Services (LTS) of Lehigh University and Purdue University Libraries (PUL) on hosting postdoctoral fellows in data curation activity. This inter-disciplinary fellowship program funded by the SLOAN Foundation innovatively connects university libraries and earth science departments and provides earth science Ph.D.'s opportunities to use their research experiences in earth science and data curation trainings received during their fellowship to explore best practices for research data management in earth science. In the process of exploring best practices for data curation in earth science, the CLIR Data Curation Fellows have accumulated rich experiences and insights on the data management behaviors and needs of earth scientists. Specifically, Ting Wang, the postdoctoral fellow at Lehigh University has worked together with the LTS support team for the College of Arts and Sciences, Web Specialists and the High Performance Computing Team, to assess and meet the data management needs of researchers at the Department of Earth and Environmental Sciences (EES). By interviewing the faculty members and graduate students at EES, the fellow has identified a variety of data-related challenges at different research fields of earth science, such as climate, ecology, geochemistry, geomorphology, etc. The investigation findings of the fellow also support the LTS for developing campus infrastructure for long-term data management in the sciences. Likewise, Benjamin D. Branch, the postdoctoral fellow at PUL conducted GIS (Geographic Information Systems) data curation interviews and worked closely with the GIS Information Specialist towards GIS-related instructional programs in order to recognize the data management needs in GIS research. Conceptually, the research implemented grounded theory approach of campus wide interviews for spatial GIS inquiry. To date, research analysis of a subset of 32 individual interviews with faculty, graduate students, or geospatial staff users is underway with the intent of publication. Collectively, CLIR fellowship program should work to expand the capacity and job resiliency of the library as necessary vehicle of institutional competitiveness via its prominence in data services for future consideration in the areas of data science, data curation, data rescue and collaborative support of the scientific community. In addition, the digital data service aspects of library transformation may be showcased in the results of the fellows' accomplishments.

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.

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.

Lifestyle changes in cancer patients undergoing curative or palliative chemotherapy: is it feasible?

PubMed

Vassbakk-Brovold, Karianne; Berntsen, Sveinung; Fegran, Liv; Lian, Henrik; Mjåland, Odd; Mjåland, Svein; Nordin, Karin; Seiler, Stephen; Kersten, Christian

2017-12-14

This study aimed to explore the feasibility of an individualized comprehensive lifestyle intervention in cancer patients undergoing curative or palliative chemotherapy. At one cancer center, serving a population of 180,000, 100 consecutive of 161 eligible newly diagnosed cancer patients starting curative or palliative chemotherapy entered a 12-month comprehensive, individualized lifestyle intervention. Participants received a grouped startup course and monthly counseling, based on self-reported and electronically evaluated lifestyle behaviors. Patients with completed baseline and end of study measurements are included in the final analyses. Patients who did not complete end of study measurements are defined as dropouts. More completers (n = 61) vs. dropouts (n = 39) were married or living together (87 vs. 69%, p = .031), and significantly higher baseline physical activity levels (960 vs. 489 min . wk -1 , p = .010), more healthy dietary choices (14 vs 11 points, p = .038) and fewer smokers (8 vs. 23%, p = .036) were observed among completers vs. dropouts. Logistic regression revealed younger (odds ratios (OR): 0.95, 95% confidence interval (CI): 0.91, 0.99) and more patients diagnosed with breast cancer vs. more severe cancer types (OR: 0.16, 95% CI: 0.04, 0.56) among completers vs. dropouts. Improvements were observed in completers healthy (37%, p < 0.001) and unhealthy dietary habits (23%, p = .002), and distress (94%, p < .001). No significant reductions were observed in physical activity levels. Patients treated with palliative intent did not reduce their physical activity levels while healthy dietary habits (38%, p = 0.021) and distress (104%, p = 0.012) was improved. Favorable and possibly clinical relevant lifestyle changes were observed in cancer patients undergoing curative or palliative chemotherapy after a 12-month comprehensive and individualized lifestyle intervention. Palliative patients were able to participate and to improve their lifestyle behaviors.

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.

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.

[Skin symptoms associated with human immunodeficiency virus infection].

PubMed

Tamási, Béla; Marschalkó, Márta; Kárpáti, Sarolta

2015-01-04

The recently observed accelerated increase of human immunodeficiency virus infection in Hungary poses a major public concern for the healthcare system. Given the effective only but not the curative therapy, prevention should be emphasized. Current statistics estimate that about 50% of the infected persons are not aware of their human immunodeficiency virus-positivity. Thus, early diagnosis of the infection by serological screening and timely recognition of the disease-associated symptoms are crucial. The authors' intention is to facilitate early infection detection with this review on human immunodeficiency virus-associated skin symptoms, and highlight the significance of human immunodeficiency virus care in the everyday medical practice.

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

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

Surgery for malignant pleural mesothelioma: an international guidelines review

PubMed Central

Cardillo, Giuseppe; Zirafa, Carmelina Cristina; Carleo, Francesco; Facciolo, Francesco; Fontanini, Gabriella; Mutti, Luciano; Melfi, Franca

2018-01-01

Currently there is no universally accepted surgical therapy for malignant pleural mesothelioma (MPM). The goal of surgery in this dismal disease is a macroscopic complete resection (MCR) and there are two types of intervention with a curative intent. At one side, there is the extrapleural pneumonectomy (EPP) which consists in an en-bloc resection of the lung, pleura, pericardium and diaphragm and at the other side, there is pleurectomy/decortication (P/D) a lung-sparing surgery. Initially, EPP was considered the only surgical option with a curative aim, but during the decades P/D have acquired a role of increasing importance in MPM therapy. Several randomized prospective trials are required to establish the best strategy in the treatment of pleural mesothelioma. Although which is the best surgical option remains unclear, the International Mesothelioma Interest Group (IMIG), recently have stated that the type of surgery depends on clinical factors and on individual surgical judgment and expertise. Moreover, according to the current evidence, the surgery should be performed in high-volume centres within multimodality protocols. The aim of this study is to examine the currently available international guidelines in the surgical diagnosis and treatment of MPM. PMID:29507797

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.

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

OpenTrials: towards a collaborative open database of all available information on all clinical trials.

PubMed

Goldacre, Ben; Gray, Jonathan

2016-04-08

OpenTrials is a collaborative and open database for all available structured data and documents on all clinical trials, threaded together by individual trial. With a versatile and expandable data schema, it is initially designed to host and match the following documents and data for each trial: registry entries; links, abstracts, or texts of academic journal papers; portions of regulatory documents describing individual trials; structured data on methods and results extracted by systematic reviewers or other researchers; clinical study reports; and additional documents such as blank consent forms, blank case report forms, and protocols. The intention is to create an open, freely re-usable index of all such information and to increase discoverability, facilitate research, identify inconsistent data, enable audits on the availability and completeness of this information, support advocacy for better data and drive up standards around open data in evidence-based medicine. The project has phase I funding. This will allow us to create a practical data schema and populate the database initially through web-scraping, basic record linkage techniques, crowd-sourced curation around selected drug areas, and import of existing sources of structured and documents. It will also allow us to create user-friendly web interfaces onto the data and conduct user engagement workshops to optimise the database and interface designs. Where other projects have set out to manually and perfectly curate a narrow range of information on a smaller number of trials, we aim to use a broader range of techniques and attempt to match a very large quantity of information on all trials. We are currently seeking feedback and additional sources of structured data.

[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.

Immunotherapy (excluding checkpoint inhibitors) for stage I to III non-small cell lung cancer treated with surgery or radiotherapy with curative intent.

PubMed

Zhu, Jianwei; Li, Rui; Tiselius, Eva; Roudi, Raheleh; Teghararian, Olivia; Suo, Chen; Song, Huan

2017-12-16

Non-small cell lung cancer (NSCLC) is the most common lung cancer, accounting for approximately 80% to 85% of all cases. For patients with localised NSCLC (stages I to III), it has been speculated that immunotherapy may be helpful for reducing postoperative recurrence rates, or improving the clinical outcomes of current treatment for unresectable tumours. While several new agents have now entered phase III clinical trials, we felt a systematic review was needed to address the question of the effectiveness and safety of immunotherapy in patients with stages I to III NSCLC. To evaluate the effectiveness and safety of immunotherapy (excluding checkpoint inhibitors) in patients with localised NSCLC (stages I to III) who received surgery or radiotherapy with curative intent. We searched the following databases (from inception to 20 January 2017): CENTRAL, MEDLINE, Embase, and CINAHL, and five trial registers. We also manually checked abstracts or reports from relevant conference proceedings and the reference lists of included trials. We searched for randomised controlled trials (RCTs) in adults (≥ 18 years) with histologically-confirmed early-stage (stages I to III) NSCLC after surgical resection, and those with unresectable locally advanced stage III NSCLC who had received radiotherapy with curative intent. For patients who had received primary surgical treatment, postoperative radiotherapy or chemoradiotherapy was allowed if it was used for both experimental and control groups. Two review authors independently selected eligible trials, assessed risk of bias, and extracted data. We used survival analysis to pool time-to-event data, expressing the intervention effect as a hazard ratio (HR). We calculated risk ratios (RR) for dichotomous data, and mean differences for continuous data, with 95% confidence intervals (CI). Due to clinical heterogeneity (immunotherapeutic agents with different underlying mechanisms), we used random-effects models for our meta-analyses. We identified nine eligible trials that randomised 4940 participants, who had received surgical resection or curative radiotherapy, to either an immunotherapy group or a control group. Included immunological interventions were active immunotherapy (i.e. Bacillus Calmette-Guérin (BCG)), adoptive cell transfer (i.e. transfer factor (TF), tumour-infiltrating lymphocytes (TIL), dendritic cell-cytokine induced killer (DC-CIK), and antigen-specific cancer vaccines (melanoma-associated antigen 3 (MAGE-A3) and L-BLP25). Except for one small trial, which provided insufficient information for risk assessment, we assessed five studies at high risk of bias for at least one of the seven biases studied; we considered the risk of bias in the other three trials to be low. We included data from seven of the nine trials in the meta-analyses (4695 participants). We pooled data from 3693 participants from the three high quality RCTs to evaluate overall survival (OS) and progression-free survival (PFS). We found a small, but not statistically significant, improvement in OS (HR 0.94, 95% CI 0.83 to 1.06; P = 0.35), and PFS (HR 0.93, 95% CI 0.81 to 1.07; P = 0.19; high-quality evidence). The addition of immunotherapy resulted in a small, but not statistically significant, increased risk of having any adverse event (RR 1.15, 95% CI 0.97 to 1.37; P = 0.11, three trials, 3955 evaluated participants, moderate-quality evidence), or severe adverse events (RR 1.10, 95% CI 0.88 to 1.39; four trials, 4362 evaluated participants; low-quality evidence).We analysed data from six studies for one-, two-, and three-year survival rates (4265 participants), and from six studies for five-year survival rates (4234 participants). We observed no clear between-group differences (low-quality evidence for one- and two-year survival rates, and moderate-quality evidence for three- and five-year survival rate).No trial reported the overall response rates; only one trial provided health-related quality of life results. The current literature does not provide evidence that suggests a survival benefit from adding immunotherapy (excluding checkpoint inhibitors) to conventional curative surgery or radiotherapy, for patients with localised NSCLC (stages I to III). The addition of vaccine-based immunotherapy might increase the risk of adverse events. Several ongoing trials with immune checkpoints inhibitors (PD-1/PD-L1) might bring new insights for role of immunotherapy for patients with stages I to III NSCLC.

A new approach to endoscopic treatment of tumors of the esophagogastric junction with individually designed self-expanding metal stents

PubMed Central

Aymaz, Serhat; Dormann, Arno J

2008-01-01

The incidence of adenocarcinoma of the esophago-gastric junction is constantly increasing. Curative treatment is no longer possible at the time of diagnosis in more than 50% of patients with esophageal carcinoma, and palliative treatment focusing on eliminating dysphagia is required. Endoscopic therapy with stent implantation is an established method of achieving this. It can be carried out quickly, with a low rate of early complications, and leads to fast symptomatic improvement, assessed using the dysphagia score. The relatively high rate of late complications such as stent migration, hemorrhage, and gastroesophageal mucosal prolapse has led to recent debate on the role of metal stents in palliative therapy. We present here a new type of stent design for transcardial application, which is intended to prevent bleeding due to mechanical mucosal lesions caused by the distal end of the stent extending into the stomach. The further intention of this case report is to force the discussion on individually designed nitinol stents in special anatomic conditions. PMID:18609720

Irradiation of nonlymphoproliferative neoplasms of the nasal cavity and paranasal sinuses in 16 cats.

PubMed

Théon, A P; Peaston, A E; Madewell, B R; Dungworth, D L

1994-01-01

Sixteen cats with malignant tumors (10 carcinomas, 6 sarcomas) of the nasal cavity and paranasal sinuses were treated with curative intent by radiotherapy. Clinical stating was based on radiographic findings, using the tumor, node, metastasis classification system of the World Health Organization. Irradiation was done with a telecobalt-60 unit (13 cats) and an orthovoltage unit (3 cats). Fourteen cats were treated with irradiation alone, and 2 cats had incomplete surgical resections prior to radiotherapy. Treatment dose was 48 Gy (minimum tumor dose), administered by use of 4 Gy per fraction on a Monday/Wednesday/Friday basis over 4 weeks. Survival times after treatment ranged from 1 to 36 months. The 1- and 2-year overall survival rates were 44.3 and 16.6%, respectively. Histologic type and clinical stage did not have prognostic value. Most acute radiation reactions were mild and self-limiting. Chronic ocular complications were seen in 3 cats. These treatment responses compared favorably with those previously described in dogs and cats with intranasal neoplasms treated with teletherapy and provided a perspective for comparison of new treatment methods.

Current Status of Percutaneous Transhepatic Biliary Drainage in Palliation of Malignant Obstructive Jaundice: A Review

PubMed Central

Chandrashekhara, SH; Gamanagatti, S; Singh, Anuradha; Bhatnagar, Sushma

2016-01-01

Malignancies leading to obstructive jaundice present too late to perform surgery with a curative intent. Due to inexorably progressing hyperbilirubinemia with its consequent deleterious effects, drainage needs to established even in advanced cases. Percutaneous transhepatic biliary drainage (PTBD) and endoscopic retrograde cholangiopancreatography (ERCP) are widely used palliative procedures each with its own merits and lacunae. With the current state-of-the-art PTBD technique consequent upon procedural and hardware improvement, it is equaling ERCP regarding technical success and complications. In addition, there is a reduction in immediate procedure-related mortality with proven survival benefit. Nonetheless, it is the only imminent lifesaving procedure in cholangitis and sepsis. PMID:27803558

Surgery for Locally Recurrent Rectal Cancer: Tips, Tricks, and Pitfalls.

PubMed

Warrier, Satish K; Heriot, Alexander G; Lynch, Andrew Craig

2016-06-01

Rectal cancer can recur locally in up to 10% of the patients who undergo definitive resection for their primary cancer. Surgical salvage is considered appropriate in the curative setting as well as select cases with palliative intent. Disease-free survival following salvage resection is dependent upon achieving an R0 resection margin. A clear understanding of applied surgical anatomy, appropriate preoperative planning, and a multidisciplinary approach to aggressive soft tissue, bony, and vascular resection with appropriate reconstruction is necessary. Technical tips, tricks, and pitfalls that may assist in managing these cancers are discussed and the roles of additional boost radiation and intraoperative radiation therapy in the management of such cancers are also discussed.

Obstructive ureteropathy following radiation therapy for carcinoma of the cervix

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

Parliament, M.; Genest, P.; Girard, A.

1989-05-01

Between January 1959 and December 1986, 10 of 328 patients (3%) treated with curative intent using primary radiation therapy for carcinoma of the cervix developed obstructive ureteropathy due to fibrosis. The mean age of the patients with obstructive ureteropathy was 45 years and the median time to obstruction was 26 months. The obstruction was unilateral in 8 cases and involved the parametrial portion of the ureter in at least 5 cases. No predisposing risk factor was found to be associated with the development of obstructive ureteropathy. After corrective surgery, renal function remained normal in 8 patients, and resolution of themore » hydronephrosis occurred in 4 patients.« less

Patients' understanding of treatment goals and disease course and their relationship with optimism, hope, and quality of life: a preliminary study among advanced breast cancer outpatients before receiving palliative treatment.

PubMed

Soylu, Cem; Babacan, Taner; Sever, Ali R; Altundag, Kadri

2016-08-01

The aims of this study were to explore advanced breast cancer patients' knowledge of treatment intent and expectation of illness course and to evaluate their relationship with optimism, hope, and quality of life (QoL). Patients with advanced breast cancer (n = 55) who were treated in the ambulatory clinic of the University of Hacettepe were included in the study. They completed Life Orientation Scale, The Hope Scale, and the European Organization for Research and Treatment of Cancer Quality of Life questionnaires. The data regarding the knowledge of illness progression and the perceptions of therapy intent were assessed using self-administered open-ended questionnaires that were answered by the patients. The data revealed that 58.2 % of the patients had an inaccurate perception of treatment intent, believing the aim of treatment was cure, whereas only 38.2 % of the patients had a realistic expectation that their disease may remain stable or may progress over a year. In addition, the awareness of disease progression and perception of goals of treatment was significantly related to hope and optimism scores but not to QoL. A large proportion of patients diagnosed with advanced breast cancer believed that their treatment was "curative", and they would improve within a year. Findings of our study suggest that patients with inaccurate perception of treatment intent and unrealistic expectation of prognosis have higher hope and optimism scores than those who do not, but there were no significant differences in terms of global health status.

Conversion to resection of liver metastases from colorectal cancer with hepatic artery infusion of combined chemotherapy and systemic cetuximab in multicenter trial OPTILIV.

PubMed

Lévi, F A; Boige, V; Hebbar, M; Smith, D; Lepère, C; Focan, C; Karaboué, A; Guimbaud, R; Carvalho, C; Tumolo, S; Innominato, P; Ajavon, Y; Truant, S; Castaing, D; De Baere, T; Kunstlinger, F; Bouchahda, M; Afshar, M; Rougier, P; Adam, R; Ducreux, M

2016-02-01

Systemic chemotherapy typically converts previously unresectable liver metastases (LM) from colorectal cancer to curative intent resection in ∼15% of patients. This European multicenter phase II trial tested whether hepatic artery infusion (HAI) with triplet chemotherapy and systemic cetuximab could increase this rate to 30% in previously treated patients. Participants had unresectable LM from wt KRAS colorectal cancer. Main non-inclusion criteria were advanced extra hepatic disease, prior HAI and grade 3 neuropathy. Irinotecan (180 mg/m(2)), oxaliplatin (85 mg/m(2)) and 5-fluorouracil (2800 mg/m(2)) were delivered via an implanted HAI access port and combined with i.v. cetuximab (500 mg/m(2)) every 14 days. Multidisciplinary decisions to resect LM were taken after every three courses. The rate of macroscopic complete resections (R0 + R1) of LM, progression-free survival (PFS) and overall survival (OS) were computed according to intent to treat. The patient population consisted of 42 men and 22 women, aged 33-76 years, with a median of 10 LM involving a median of six segments. Up to 3 extrahepatic lesions of <1 cm were found in 41% of the patients. A median of six courses was delivered. The primary end point was met, with R0-R1 hepatectomy for 19 of the 64 previously treated patients, 29.7% (95% confidence interval 18.5-40.9). Grade 3-4 neutropenia (42.6%), abdominal pain (26.2%), fatigue (18%) and diarrhea (16.4%) were frequent. Objective response rate was 40.6% (28.6-52.3). Median PFS and OS reached 9.3 (7.8-10.9) and 25.5 months (18.8-32.1) respectively. Those with R0-R1 hepatectomy had a median OS of 35.2 months (32.6-37.8), with 37.4% (23.6-51.2) alive at 4 years. The coordination of liver-specific intensive chemotherapy and surgery had a high curative intent potential that deserves upfront randomized testing. EUDRACT 2007-004632-24, NCT00852228. © The Author 2015. Published by Oxford University Press on behalf of the European Society for Medical Oncology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Conversion in laparoscopic colorectal cancer surgery: impact on short- and long-term outcome.

PubMed

Scheidbach, Hubert; Garlipp, Benjamin; Oberländer, Henrik; Adolf, Daniela; Köckerling, Ferdinand; Lippert, Hans

2011-12-01

Despite the well-documented safety and effectiveness of laparoscopic colorectal surgery in curative intention, the role of conversion and its impact on short- and long-term outcome after resection of a carcinoma are unclear and continue to give rise to controversial discussion. Within the framework of a prospective, multicenter observational study (Laparoscopic Colorectal Surgery Study Group), into which a total of 5,863 patients from 69 hospitals were recruited over a period of 10 years, a subgroup of all patients who had undergone curative resection was analyzed with regard to the effects of conversion. Of the 1409 patients who had undergone curative resection for colorectal carcinoma, conversion had to be performed in 80 (5.7%) cases for the most diverse reasons. The duration of surgery (median: 183 vs. 241 minutes; P<.001) was significantly longer in the conversion group. Perioperatively, significant disadvantages were noted in converted patients in terms of intraoperative blood loss (median: 243 vs. 573 mL, P<.001), need for perioperative blood transfusion (10.8% vs. 33.8%; P<.001), and resumption of bowel movement (median: after 3 vs. 4 days; P<.001). With regard to postoperative morbidity, significant disadvantages were observed in converted patients, in particular in terms of specific surgical complications, including a higher rate of anastomotic insufficiency (5.0% vs. 13.8%; P=.003) and a higher reoperation rate (4.9% vs. 15.0%; P=.001). In the long term, conversion was associated with lower overall survival, but not with poorer disease-free survival. Significantly higher postoperative morbidity was observed in patients after conversion, in particular in terms of specific surgical complications. In addition, conversion is associated with overall lower survival but not with poorer disease-free survival.

Retrospective audit of clinico-pathologic features and treatment outcomes in a cohort of elderly non-Hodgkin's lymphoma patients in a tertiary cancer center.

PubMed

Nair, C K; Patil, V M; Raghavan, V; Babu, S; Nayanar, S

2015-01-01

There is limited data from India regarding elderly non-Hodgkin's lymphomas (NHL) patients. Hence, this audit was planned to study the clinic-pathological features and treatment outcomes in elderly NHL patients. Retrospective analysis of all NHL patients above age of 59 years treated at the author's institute, between December 2010 and December 2013 was done. Case records were reviewed for baseline details, staging details, prognostic factors, treatment delivered, response, toxicity and efficacy. SPSS version 16 (IBM, Newyork) was used for analysis. Descriptive statistics was performed. Kaplan-Meir survival analysis was done for estimation of progression-free survival (PFS) and overall survival (OS). Univariate analysis was done for identifying factors affecting PFS and OS. Out of 141 NHL patients, 67 patients were identified subjected to the inclusion criteria. The median age was 68 years (60-92). Majority were B-cell NHL (86.6%). The commonest subtype in B-cell was diffuse large B-cell lymphoma (55.2%). Fifty-four patients took treatment. The treatment intent was curative in 41 patients (61.2%). Among the patients receiving curative treatment, 16 patients couldn't receive treatment in accordance with NCCN guidelines due to financial issues. Two years PFS was 55%. Two years PFS for B-cell NHL and T-cell NHL were 55% and 50% respectively (P = 0.982). Two years PFS for standard Rx and nonstandard Rx were 62% and 50% respectively, but it didn't reach statistical significance (P = 0.537). Two years OS for the entire cohort was 84%. Standard treatment in accordance with guidelines can be delivered in elderly patients irrespective of age. There is a need for creating financial assistance for patients, so that potentially curative treatments are not denied.

Cost-effectiveness analysis of treatment with non-curative or palliative intent for hepatocellular carcinoma in the real-world setting.

PubMed

Thein, Hla-Hla; Qiao, Yao; Zaheen, Ahmad; Jembere, Nathaniel; Sapisochin, Gonzalo; Chan, Kelvin K W; Yoshida, Eric M; Earle, Craig C

2017-01-01

Hepatocellular carcinoma (HCC) presentation is heterogeneous necessitating a variety of therapeutic interventions with varying efficacies and associated prognoses. Poor prognostic patients often undergo non-curative palliative interventions including transarterial chemoembolization (TACE), sorafenib, chemotherapy, or purely supportive care. The decision to pursue one of many palliative interventions for HCC is complex and an economic evaluation comparing these interventions has not been done. This study evaluates the cost-effectiveness of non-curative palliative treatment strategies such as TACE alone or TACE+sorafenib, sorafenib alone, and non-sorafenib chemotherapy compared with no treatment or best supportive care (BSC) among patients diagnosed with HCC between 2007 and 2010 in a Canadian setting. Using person-level data, we estimated effectiveness in life years and quality-adjusted life years (QALYs) along with total health care costs (2013 US dollars) from the health care payer's perspective (3% annual discount). A net benefit regression approach accounting for baseline covariates with propensity score adjustment was used to calculate incremental net benefit to generate incremental cost-effectiveness ratio (ICER) and uncertainty measures. Among 1,172 identified patients diagnosed with HCC, 4.5%, 7.9%, and 5.6%, received TACE alone or TACE+sorafenib, sorafenib, and non-sorafenib chemotherapy clone, respectively. Compared with no treatment or BSC (81.9%), ICER estimates for TACE alone or TACE+sorafenib was $6,665/QALY (additional QALY: 0.47, additional cost: $3,120; 95% CI: -$18,800-$34,500/QALY). The cost-effectiveness acceptability curve demonstrated that if the relevant threshold was $50,000/QALY, TACE alone or TACE+sorafenib, non-sorafenib chemotherapy, and sorafenib alone, would have a cost-effectiveness probability of 99.7%, 46.6%, and 5.5%, respectively. Covariates associated with the incremental net benefit of treatments are age, sex, comorbidity, and cancer stage. Findings suggest that TACE with or without sorafenib is currently the most cost-effective active non-curative palliative treatment approach to HCC. Further research into new combination treatment strategies that afford the best tumor response is needed.

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.

Clinical outcomes of black vs. non-black patients with locally advanced non-small cell lung cancer.

PubMed

Vyfhuis, Melissa A L; Bhooshan, Neha; Molitoris, Jason; Bentzen, Søren M; Feliciano, Josephine; Edelman, Martin; Burrows, Whitney M; Nichols, Elizabeth M; Suntharalingam, Mohan; Donahue, James; Nagib, Marc; Carr, Shamus R; Friedberg, Joseph; Badiyan, Shahed; Simone, Charles B; Feigenberg, Steven J; Mohindra, Pranshu

2017-12-01

The black population remains underrepresented in clinical trials despite reports suggesting greater incidence and deaths from locally advanced non-small cell lung cancer (NSCLC). We determined outcomes for black and non-black patients in a well-annotated cohort treated with either definitive chemoradiation (CRT; bimodality) or CRT followed by surgery (trimodality therapy). A retrospective analysis of 355 stage III NSCLC patients treated with curative intent at the University of Maryland, Medical Center, between January 2000-December 2013 was performed. The Kaplan-Meier approach and the Cox proportional hazards models were used to analyze overall survival (OS) and freedom-from-recurrence (FFR) in black and non-black patients. The chi-square test was used to compare categorical variables. Black patients comprised 42% of the cohort and were more likely to be younger (p<0.0001), male (p=0.030), single (p<0.0001), reside in lower household income zipcodes (p<0.0001), have an Eastern Cooperative Oncology Group (ECOG) performance status >0 (p<0.001), and less likely to undergo surgery (p<0.0001). With a median follow-up of 15 months for all patients and 89 months for surviving patients (range:1-186 months), median OS times for black and non-black patients were 22 and 24 months, respectively (p=0.698). FFR rates were also comparable between the two groups (p=0.468). Surgery improved OS in both cohorts. Race was not a significant predictor for OS or FFR even when adjusted for other factors. We found similar oncologic outcomes in black and non-black NSCLC patients when treated with curative intent in a comprehensive cancer center setting, despite epidemiologic differences in presentation and receipt of care. Future efforts to improve outcomes in black patients could focus on addressing modifiable social disparities. Copyright © 2017. Published by Elsevier B.V.

What is the significance of a microscopically positive resection margin in the curative-intent treatment of rectal adenocarcinoma? A retrospective study.

PubMed

Fekete, Z; Muntean, A; Irimie, A; Hica, S; Resiga, L; Todor, N; Nagy, V

2013-01-01

The aim of this study was to analyze the characteristics of patients with rectal cancer operated with a microscopic positive margin (R1) and thus avoid these situations or adapt treatment in these particular cases. We reviewed all the pathology data of resected specimens from patients with rectal or recto-sigmoid cancer operated with curative intent at the Institute of Oncology "Prof. Dr. Ion Chiricuta" between 2000-2011 (763 patients in 12 years) and the pathology files of patients from other institutions referred for adjuvant treatment to our hospital (318 patients). We included patients with anterior resection, Hartmann's procedure and abdomino-perineal resection, but we excluded patients with local excision and patients with R2/R1 at first, but R0 after re-resection (56 patients). We have identified 31 patients with R1, but had to exclude one case from analysis because this patient was lost to follow-up. With surgery alone the local relapse (LR) was unavoidable. In the neoadjuvant chemoradiation (CRT) group 85.7% of the patients did not develop LR despite of R1. In the adjuvant CRT cohort 50% of the patients were LR-free at 2 years after conventional radiotherapy (p<0.01). Based on these results it is concluded that a clear resection margin is extremely important for the local control of rectal cancer, because it cannot be always compensated by adjuvant CRT. In R1 cases neoadjuvant CRT seems to offer better prognosis than adjuvant CRT. To avoid R1 and its consequences a good quality control of total mesorectal excision (TME) is needed and CRT should be done before and not after surgery. R1 after primary surgery needs to be compensated by re-resection if possible, otherwise probably high dose radiotherapy with chemotherapy is needed.

A survey of radiation treatment planning peer-review activities in a provincial radiation oncology programme: current practice and future directions

PubMed Central

Brundage, Michael; Foxcroft, Sophie; McGowan, Tom; Gutierrez, Eric; Sharpe, Michael; Warde, Padraig

2013-01-01

Objectives To describe current patterns of practice of radiation oncology peer review within a provincial cancer system, identifying barriers and facilitators to its use with the ultimate aim of process improvement. Design A survey of radiation oncology programmes at provincial cancer centres. Setting All cancer centres within the province of Ontario, Canada (n=14). These are community-based outpatient facilities overseen by Cancer Care Ontario, the provincial cancer agency. Participants A delegate from each radiation oncology programme filled out a single survey based on input from their multidisciplinary team. Outcome measures Rated importance of peer review; current utilisation; format of the peer-review process; organisation and timing; case attributes; outcomes of the peer-review process and perceived barriers and facilitators to expanding peer-review processes. Results 14 (100%) centres responded. All rated the importance of peer review as at least 8/10 (10=extremely important). Detection of medical error and improvement of planning processes were the highest rated perceived benefits of peer review (each median 9/10). Six centres (43%) reviewed at least 50% of curative cases; four of these centres (29%) conducted peer review in more than 80% of cases treated with curative intent. Fewer than 20% of cases treated with palliative intent were reviewed in most centres. Five centres (36%) reported usually conducting peer review prior to the initiation of treatment. Five centres (36%) recorded the outcomes of peer review on the medical record. Thirteen centres (93%) planned to expand peer-review activities; a critical mass of radiation oncologists was the most important limiting factor (median 6/10). Conclusions Radiation oncology peer-review practices can vary even within a cancer system with provincial oversight. The application of guidelines and standards for peer-review processes, and monitoring of implementation and outcomes, will require effective knowledge translation activities. PMID:23903814

Operation and Chemotherapy: Prognostic Factors for Lung Cancer With One Synchronous Metastasis.

PubMed

Toffart, Anne-Claire; Duruisseaux, Michaël; Brichon, Pierre-Yves; Pirvu, Augustin; Villa, Julie; Selek, Laurent; Guillem, Pascale; Dumas, Isabelle; Ferrer, Léonie; Levra, Matteo Giaj; Moro-Sibilot, Denis

2018-03-01

Stage IV non-small cell lung cancer (NSCLC) is considered incurable; however, some patients with only few metastases may benefit from treatment with a curative intent. We aimed to identify the prognostic factors for stage IV NSCLC with synchronous solitary M1. A database constructed from our weekly multidisciplinary thoracic oncology meetings was retrospectively screened from 1993 to 2012. Consecutive patients with NSCLC stages I to IV were included. Of the 6,760 patients found, 4,832 patients were studied. Among the 1,592 patients (33%) with stage IV NSCLC, 109 (7%) had a synchronous solitary M1. Metastasis involved the brain in 64% of patients. Median overall survival was significantly longer in synchronous solitary M1 than in other stage IV (18.9 months, interquartile range [IQR]: 9.9 to 34.6 months versus 6.1 months, IQR: 2.3 to 13.7 months], respectively, p < 10 -4 ). Among patients with synchronous solitary M1, 90 (83%) received a local treatment with curative intent at the primary and metastatic sites. Factors independently associated with survival were age older than 63 years (hazard ratio [HR] 1.63, 95% confidence interval [CI]: 1.01 to 2.63), Performance status of 3 or 4 (HR 7.91, 95% CI: 2.23 to 28.03), use of chemotherapy (HR 0.38, 95% CI: 0.23 to 0.64), and operation conducted at both sites (HR 0.35, 95% CI: 0.19 to 0.65). Synchronous solitary M1 treated with chemotherapy and operation at both sites resulted in better survival. Survival of NSCLC with synchronous solitary M1 was more similar to stage III than other stage IV NSCLCs. The eighth TNM classification takes this into account by distinguishing between stages M1b and M1c. Copyright © 2018 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

Defining the Chance of Statistical Cure Among Patients with Extrahepatic Biliary Tract Cancer.

PubMed

Spolverato, Gaya; Bagante, Fabio; Ethun, Cecilia G; Poultsides, George; Tran, Thuy; Idrees, Kamran; Isom, Chelsea A; Fields, Ryan C; Krasnick, Bradley; Winslow, Emily; Cho, Clifford; Martin, Robert C G; Scoggins, Charles R; Shen, Perry; Mogal, Harveshp D; Schmidt, Carl; Beal, Eliza; Hatzaras, Ioannis; Shenoy, Rivfka; Maithel, Shishir K; Pawlik, Timothy M

2017-01-01

While surgery offers the best curative-intent treatment, many patients with biliary tract malignancies have poor long-term outcomes. We sought to apply a non-mixture cure model to calculate the cure fraction and the time to cure after surgery of patients with peri-hilar cholangiocarcinoma (PHCC) or gallbladder cancer (GBC). Using the Extrahepatic Biliary Malignancy Consortium, 576 patients who underwent curative-intent surgery for gallbladder carcinoma or peri-hilar cholangiocarcinoma between 1998 and 2014 at 10 major hepatobiliary institutions were identified and included in the analysis. A non-mixture cure model was adopted to compare mortality after surgery to the mortality expected for the general population matched by sex and age. The median and 5-year overall survival (OS) were 1.9 years (IQR, 0.9-4.9) and 23.9 % (95 % CI, 19.6-28.6). Among all patients with PHCC or GBC, the probability of being cured after surgery was 14.5 % (95 % CI, 8.7-23.2); the time to cure was 9.7 years and the median survival of uncured patients was 1.8 years. Determinants of cure probabilities included lymph node metastasis and CA 19.9 level (p ≤ 0.05). The cure fraction for patients with a CA 19.9 < 50 U/ml and no lymph nodes metastases were 39.0 % versus only 5.1 % among patients with a CA 19.9 ≥ 50 who also had lymph node metastasis. Examining an "all comer" cohort, <15 % of patients with PHCC or GBC could be considered cured after surgery. Factors such CA 19.9 level and lymph node metastasis independently predicted long-term outcome. Estimating the odds of statistical cure following surgery for biliary tract cancer can assist in decision-making as well as inform discussions around survivorship.

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.

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

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.

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.

Solving gap metabolites and blocked reactions in genome-scale models: application to the metabolic network of Blattabacterium cuenoti.

PubMed

Ponce-de-León, Miguel; Montero, Francisco; Peretó, Juli

2013-10-31

Metabolic reconstruction is the computational-based process that aims to elucidate the network of metabolites interconnected through reactions catalyzed by activities assigned to one or more genes. Reconstructed models may contain inconsistencies that appear as gap metabolites and blocked reactions. Although automatic methods for solving this problem have been previously developed, there are many situations where manual curation is still needed. We introduce a general definition of gap metabolite that allows its detection in a straightforward manner. Moreover, a method for the detection of Unconnected Modules, defined as isolated sets of blocked reactions connected through gap metabolites, is proposed. The method has been successfully applied to the curation of iCG238, the genome-scale metabolic model for the bacterium Blattabacterium cuenoti, obligate endosymbiont of cockroaches. We found the proposed approach to be a valuable tool for the curation of genome-scale metabolic models. The outcome of its application to the genome-scale model B. cuenoti iCG238 is a more accurate model version named as B. cuenoti iMP240.

Adjuvant and induction chemotherapy in non-small cell lung cancer.

PubMed

Pirker, R; Malayeri, R; Huber, H

1999-01-01

About 25%-30% of patients with non-small cell lung cancer can be resected with curative intent. However, systemic relapses occur in up to 70% of these patients. Thus, postoperative adjuvant chemotherapy was evaluated in several randomised trials but the results of these trials were inconclusive with a survival benefit only in some trials. Shortcomings of these trials included low number of patients, poor patient compliance and inadequate chemotherapy protocols. A recent meta-analysis suggested an absolute survival benefit of 5% at five years for postoperative cisplatin-based chemotherapy as compared to surgery alone. Thus adjuvant chemotherapy with both improved chemotherapy protocols and improved anti-emetics is currently re-evaluated in several randomised trials on large patient populations.

Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD).

PubMed

Jiang, Xiangying; Ringwald, Martin; Blake, Judith; Shatkay, Hagit

2017-01-01

The Gene Expression Database (GXD) is a comprehensive online database within the Mouse Genome Informatics resource, aiming to provide available information about endogenous gene expression during mouse development. The information stems primarily from many thousands of biomedical publications that database curators must go through and read. Given the very large number of biomedical papers published each year, automatic document classification plays an important role in biomedical research. Specifically, an effective and efficient document classifier is needed for supporting the GXD annotation workflow. We present here an effective yet relatively simple classification scheme, which uses readily available tools while employing feature selection, aiming to assist curators in identifying publications relevant to GXD. We examine the performance of our method over a large manually curated dataset, consisting of more than 25 000 PubMed abstracts, of which about half are curated as relevant to GXD while the other half as irrelevant to GXD. In addition to text from title-and-abstract, we also consider image captions, an important information source that we integrate into our method. We apply a captions-based classifier to a subset of about 3300 documents, for which the full text of the curated articles is available. The results demonstrate that our proposed approach is robust and effectively addresses the GXD document classification. Moreover, using information obtained from image captions clearly improves performance, compared to title and abstract alone, affirming the utility of image captions as a substantial evidence source for automatically determining the relevance of biomedical publications to a specific subject area. www.informatics.jax.org. © The Author(s) 2017. Published by Oxford University Press.

End points for adjuvant therapy trials: has the time come to accept disease-free survival as a surrogate end point for overall survival?

PubMed

Gill, Sharlene; Sargent, Daniel

2006-06-01

The intent of adjuvant therapy is to eradicate micro-metastatic residual disease following curative resection with the goal of preventing or delaying recurrence. The time-honored standard for demonstrating efficacy of new adjuvant therapies is an improvement in overall survival (OS). This typically requires phase III trials of large sample size with lengthy follow-up. With the intent of reducing the cost and time of completing such trials, there is considerable interest in developing alternative or surrogate end points. A surrogate end point may be employed as a substitute to directly assess the effects of an intervention on an already accepted clinical end point such as mortality. When used judiciously, surrogate end points can accelerate the evaluation of new therapies, resulting in the more timely dissemination of effective therapies to patients. The current review provides a perspective on the suitability and validity of disease-free survival (DFS) as an alternative end point for OS. Criteria for establishing surrogacy and the advantages and limitations associated with the use of DFS as a primary end point in adjuvant clinical trials and as the basis for approval of new adjuvant therapies are discussed.

Evidence based radiation oncology with existing technology

PubMed Central

Isa, Nicolas

2013-01-01

Aim To assess the real contribution of modern radiation therapy (RT) technology in the more common tumoral types in Central America, Caribbean and South America. Background RT is an essential tool in the management of cancer. RT can be either palliative or of curative intent. In general, for palliative radiotherapy, major technologies are not needed. Materials and methods We analyzed the contribution of RT technology based on published evidence for breast, lung, gastric, gallbladder, colorectal, prostate and cervix cancer in terms of disease control, survival or toxicity with especial focus on Latin America. Results Findings indicate that three dimensional conformal radiation therapy (3D RT) is the gold standard in most common type of cancer in the studied regions. Prostate cancer is probably the pathology that has more benefits when using new RT technology such as intensity modulated radiation therapy (IMRT) versus 3DRT in terms of toxicity and biochemical progression-free survival. Conclusions In light of the changes in technology, the ever-increasing access of developing countries to such technology, and its current coverage in Latin America, any efforts in this area should be aimed at improving the quality of the radiotherapy departments and centers that are already in place. PMID:25061519

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

Factors Influencing Relapse-Free Survival in Merkel Cell Carcinoma of the Lower Limb-A Review of 60 Cases

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

Poulsen, Michael, E-mail: michael_poulsen@health.qld.gov.a; Round, Caroline; Keller, Jacqui

2010-02-01

Purpose: Factors affecting relapse-free survival (RFS) in patients with Merkel cell carcinoma (MCC) of the lower limb were reviewed. Methods and Materials: The records of 60 patients from 1986 to 2005 with a diagnosis of MCC of the lower limb or buttock were retrospectively reviewed. The patients were treated with curative intent with surgery, radiation, or chemotherapy. Results: The 5-year overall survival, disease-specific survival, and RFS were 53%, 61%, and 20%, respectively. Factors influencing RFS were analyzed using univariate analysis. It appeared that recurrent disease worsened RFS (p = 0.03) and the addition of any radiotherapy improved RFS (p <0.001),more » as did radiotherapy to the inguinal nodes (p = 0.01) or primary site and inguinal nodes (p = 0.003). Age, surgical margins, and stage were not statistically significant. On multivariate analysis, the only significant factor was the addition of radiotherapy (hazard ratio = 0.51 p = 0.03). Conclusion: The addition of radiotherapy improves RFS compared with surgery alone. Elective treatment should be given to the inguinal nodes to reduce the risk of relapse.« 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.

Advanced Curation Protocols for Mars Returned Sample Handling

NASA Astrophysics Data System (ADS)

Bell, M.; Mickelson, E.; Lindstrom, D.; Allton, J.

Introduction: Johnson Space Center has over 30 years experience handling precious samples which include Lunar rocks and Antarctic meteorites. However, we recognize that future curation of samples from such missions as Genesis, Stardust, and Mars S mple Return, will require a high degree of biosafety combined witha extremely low levels of inorganic, organic, and biological contamination. To satisfy these requirements, research in the JSC Advanced Curation Lab is currently focused toward two major areas: preliminary examination techniques and cleaning and verification techniques . Preliminary Examination Techniques : In order to minimize the number of paths for contamination we are exploring the synergy between human &robotic sample handling in a controlled environment to help determine the limits of clean curation. Within the Advanced Curation Laboratory is a prototype, next-generation glovebox, which contains a robotic micromanipulator. The remotely operated manipulator has six degrees-of- freedom and can be programmed to perform repetitive sample handling tasks. Protocols are being tested and developed to perform curation tasks such as rock splitting, weighing, imaging, and storing. Techniques for sample transfer enabling more detailed remote examination without compromising the integrity of sample science are also being developed . The glovebox is equipped with a rapid transfer port through which samples can be passed without exposure. The transfer is accomplished by using a unique seal and engagement system which allows passage between containers while maintaining a first seal to the outside environment and a second seal to prevent the outside of the container cover and port door from becoming contaminated by the material being transferred. Cleaning and Verification Techniques: As part of the contamination control effort, innovative cleaning techniques are being identified and evaluated in conjunction with sensitive cleanliness verification methods. Towards this end, cleaning techniques such as ultrasonication in ultra -pure water (UPW), oxygen (O2) plasma, and carbon dioxide (CO2) "snow" are being used to clean a variety of different contaminants on a variety of different surfaces. Additionally, once cleaned, techniques to directly verify the s rface cleanliness are being developed. Theseu include X ray photoelectron spectroscopy (XPS) quantification, and screening with- contact angle measure ments , which can be correlated with XPS standards. Methods developed in the Advanced Curation Laboratory will determine the extent to which inorganic and biological contamination can be controlled and minimized.

The Pattern of Failure After Reirradiation of Recurrent Squamous Cell Head and Neck Cancer: Implications for Defining the Targets

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

Popovtzer, Aron; Gluck, Iris; Chepeha, Douglas B.

2009-08-01

Purpose: Reirradiation (re-RT) of recurrent head and neck cancer (HNC) may achieve long-term disease control in some patients, at the expense of high rates of late sequelae. Limiting the re-RT targets to the recurrent gross tumor volume (rGTV) would reduce the volumes of reirradiated tissues; however, its effect on tumor recurrence pattern is unknown. Methods and Materials: This is a retrospective review of 66 patients who underwent curative-intent re-RT for nonresectable recurrent or second primary mucosal squamous cell HNC. Treatment was delivered with three-dimensional conformal (3D) RT or intensity-modulated RT (IMRT). The targets in all patients consisted of the rGTVsmore » with tight (0.5-cm) margins, with no intent to treat prophylactically lymph nodes or subclinical disease in the vicinity of the rGTVs. The sites of locoregional failures (LRFs) were determined using imaging at the time of failure and were compared with the rGTVs. Results: Median re-RT dose was 68 Gy. Forty-seven patients (71%) received concomitant chemotherapy, and 31 (47%) received hyperfractionated, accelerated RT. At a median follow-up of 42 months, 16 (23%) were alive and disease-free. Fifty patients (77%) had a third recurrence or persistent disease, including 47 LRFs. All LRFs occurred within the rGTVs except for two (4%) (95% confidence interval, 0-11%). Nineteen patients (29%) had Grade {>=} 3 late complications, mostly dysphagia (12 patients). Conclusions: Almost all LRFs occurred within the reirradiated rGTVs despite avoiding prophylactic RT of tissue at risk of subclinical disease. These results support confining the re-RT targets to the rGTVs to reduce reirradiated tissue volumes.« less

Liver transplantation in the Nordic countries – An intention to treat and post-transplant analysis from The Nordic Liver Transplant Registry 1982–2013

PubMed Central

Fosby, Bjarte; Melum, Espen; Bjøro, Kristian; Bennet, William; Rasmussen, Allan; Andersen, Ina Marie; Castedal, Maria; Olausson, Michael; Wibeck, Christina; Gotlieb, Mette; Gjertsen, Henrik; Toivonen, Leena; Foss, Stein; Makisalo, Heikki; Nordin, Arno; Sanengen, Truls; Bergquist, Annika; Larsson, Marie E.; Soderdahl, Gunnar; Nowak, Greg; Boberg, Kirsten Muri; Isoniemi, Helena; Keiding, Susanne; Foss, Aksel; Line, Pål-Dag; Friman, Styrbjörn; Schrumpf, Erik; Ericzon, Bo-Göran; Höckerstedt, Krister; Karlsen, Tom H.

2015-01-01

Abstract Aim and background. The Nordic Liver Transplant Registry (NLTR) accounts for all liver transplants performed in the Nordic countries since the start of the transplant program in 1982. Due to short waiting times, donor liver allocation has been made without considerations of the model of end-stage liver disease (MELD) score. We aimed to summarize key outcome measures and developments for the activity up to December 2013. Materials and methods. The registry is integrated with the operational waiting-list and liver allocation system of Scandiatransplant (www.scandiatransplant.org) and accounted at the end of 2013 for 6019 patients out of whom 5198 were transplanted. Data for recipient and donor characteristics and relevant end-points retransplantation and death are manually curated on an annual basis to allow for statistical analysis and the annual report. Results. Primary sclerosing cholangitis, acute hepatic failure, alcoholic liver disease, primary biliary cirrhosis and hepatocellular carcinoma are the five most frequent diagnoses (accounting for 15.3%, 10.8%, 10.6%, 9.3% and 9.0% of all transplants, respectively). Median waiting time for non-urgent liver transplantation during the last 10-year period was 39 days. Outcome has improved over time, and for patients transplanted during 2004–2013, overall one-, five- and 10-year survival rates were 91%, 80% and 71%, respectively. In an intention-to-treat analysis, corresponding numbers during the same time period were 87%, 75% and 66%, respectively. Conclusion. The liver transplant program in the Nordic countries provides comparable outcomes to programs with a MELD-based donor liver allocation system. Unique features comprise the diagnostic spectrum, waiting times and the availability of an integrated waiting list and transplant registry (NLTR). PMID:25959101

Method of making thermally removable adhesives

DOEpatents

Aubert, James H.

2004-11-30

A method of making a thermally-removable adhesive is provided where a bismaleimide compound, a monomeric furan compound, containing an oxirane group an amine curative are mixed together at an elevated temperature of greater than approximately 90.degree. C. to form a homogeneous solution, which, when cooled to less than approximately 70.degree. C., simultaneously initiates a Diels-Alder reaction between the furan and the bismaleimide and a epoxy curing reaction between the amine curative and the oxirane group to form a thermally-removable adhesive. Subsequent heating to a temperature greater than approximately 100.degree. C. causes the adhesive to melt and allows separation of adhered pieces.

[Early activation of heart-operated patients as a tool for optimization of cardio-surgery curation (review)].

PubMed

2014-04-01

During last years in foreign countries there was widely introduced tactic of early activation of cardio-surgery patients. Necessary components of this methodical approach are early finishing of post-operation artificial respiration and extubation of trachea, shortening of time spending in intensive therapy till 1 day and sign out from stationary after 5 days. As a result of reducing hospitalization period, the curation costs are reduced significantly. Goal of this research was the analysis of methods of anesthesia that allow early extubation and activation after cardio-surgery interventions. There were analyzed data of protocols of anesthesia and post-operation periods for 270 patients. It was concluded that applied methods of anesthesia ensure adequate protection from operation stress and allow reduce time of post-operation artificial respiration, early activation of patients without reducing level of their safety. It was also proved that application of any type of anesthesia medicines is not influencing the temp of post-operation activation. Conducted research is proving the advisability of using tactic of early activation of patients after heart operations and considers this as a tool for optimization of cardio-surgery curation.

Additive treatment improves survival in elderly patients after non-curative endoscopic resection for early gastric cancer.

PubMed

Jung, Da Hyun; Lee, Yong Chan; Kim, Jie-Hyun; Lee, Sang Kil; Shin, Sung Kwan; Park, Jun Chul; Chung, Hyunsoo; Park, Jae Jun; Youn, Young Hoon; Park, Hyojin

2017-03-01

Endoscopic resection (ER) is accepted as a curative treatment option for selected cases of early gastric cancer (EGC). Although additional surgery is often recommended for patients who have undergone non-curative ER, clinicians are cautious when managing elderly patients with GC because of comorbid conditions. The aim of the study was to investigate clinical outcomes in elderly patients following non-curative ER with and without additive treatment. Subjects included 365 patients (>75 years old) who were diagnosed with EGC and underwent ER between 2007 and 2015. Clinical outcomes of three patient groups [curative ER (n = 246), non-curative ER with additive treatment (n = 37), non-curative ER without additive treatment (n = 82)] were compared. Among the patients who underwent non-curative ER with additive treatment, 28 received surgery, three received a repeat ER, and six experienced argon plasma coagulation. Patients who underwent non-curative ER alone were significantly older than those who underwent additive treatment. Overall 5-year survival rates in the curative ER, non-curative ER with treatment, and non-curative ER without treatment groups were 84, 86, and 69 %, respectively. No significant difference in overall survival was found between patients in the curative ER and non-curative ER with additive treatment groups. The non-curative ER groups were categorized by lymph node metastasis risk factors to create a high-risk group that exhibited positive lymphovascular invasion or deep submucosal invasion greater than SM2 and a low-risk group without risk factors. Overall 5-year survival rate was lowest (60 %) in the high-risk group with non-curative ER and no additive treatment. Elderly patients who underwent non-curative ER with additive treatment showed better survival outcome than those without treatment. Therefore, especially with LVI or deep submucosal invasion, additive treatment is recommended in patients undergoing non-curative ER, even if they are older than 75 years.

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.

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

Quality Assurance Assessment of Diagnostic and Radiation Therapy–Simulation CT Image Registration for Head and Neck Radiation Therapy: Anatomic Region of Interest–based Comparison of Rigid and Deformable Algorithms

PubMed Central

Mohamed, Abdallah S. R.; Ruangskul, Manee-Naad; Awan, Musaddiq J.; Baron, Charles A.; Kalpathy-Cramer, Jayashree; Castillo, Richard; Castillo, Edward; Guerrero, Thomas M.; Kocak-Uzel, Esengul; Yang, Jinzhong; Court, Laurence E.; Kantor, Michael E.; Gunn, G. Brandon; Colen, Rivka R.; Frank, Steven J.; Garden, Adam S.; Rosenthal, David I.

2015-01-01

Purpose To develop a quality assurance (QA) workflow by using a robust, curated, manually segmented anatomic region-of-interest (ROI) library as a benchmark for quantitative assessment of different image registration techniques used for head and neck radiation therapy–simulation computed tomography (CT) with diagnostic CT coregistration. Materials and Methods Radiation therapy–simulation CT images and diagnostic CT images in 20 patients with head and neck squamous cell carcinoma treated with curative-intent intensity-modulated radiation therapy between August 2011 and May 2012 were retrospectively retrieved with institutional review board approval. Sixty-eight reference anatomic ROIs with gross tumor and nodal targets were then manually contoured on images from each examination. Diagnostic CT images were registered with simulation CT images rigidly and by using four deformable image registration (DIR) algorithms: atlas based, B-spline, demons, and optical flow. The resultant deformed ROIs were compared with manually contoured reference ROIs by using similarity coefficient metrics (ie, Dice similarity coefficient) and surface distance metrics (ie, 95% maximum Hausdorff distance). The nonparametric Steel test with control was used to compare different DIR algorithms with rigid image registration (RIR) by using the post hoc Wilcoxon signed-rank test for stratified metric comparison. Results A total of 2720 anatomic and 50 tumor and nodal ROIs were delineated. All DIR algorithms showed improved performance over RIR for anatomic and target ROI conformance, as shown for most comparison metrics (Steel test, P < .008 after Bonferroni correction). The performance of different algorithms varied substantially with stratification by specific anatomic structures or category and simulation CT section thickness. Conclusion Development of a formal ROI-based QA workflow for registration assessment demonstrated improved performance with DIR techniques over RIR. After QA, DIR implementation should be the standard for head and neck diagnostic CT and simulation CT allineation, especially for target delineation. © RSNA, 2014 Online supplemental material is available for this article. PMID:25380454

HIV Infection and Survival Among Women With Cervical Cancer

PubMed Central

Bvochora-Nsingo, Memory; Suneja, Gita; Efstathiou, Jason A.; Grover, Surbhi; Chiyapo, Sebathu; Ramogola-Masire, Doreen; Kebabonye-Pusoentsi, Malebogo; Clayman, Rebecca; Mapes, Abigail C.; Tapela, Neo; Asmelash, Aida; Medhin, Heluf; Viswanathan, Akila N.; Russell, Anthony H.; Lin, Lilie L.; Kayembe, Mukendi K.A.; Mmalane, Mompati; Randall, Thomas C.; Chabner, Bruce; Lockman, Shahin

2016-01-01

Purpose Cervical cancer is the leading cause of cancer death among the 20 million women with HIV worldwide. We sought to determine whether HIV infection affected survival in women with invasive cervical cancer. Patients and Methods We enrolled sequential patients with cervical cancer in Botswana from 2010 to 2015. Standard treatment included external beam radiation and brachytherapy with concurrent cisplatin chemotherapy. The effect of HIV on survival was estimated by using an inverse probability weighted marginal Cox model. Results A total of 348 women with cervical cancer were enrolled, including 231 (66.4%) with HIV and 96 (27.6%) without HIV. The majority (189 [81.8%]) of women with HIV received antiretroviral therapy before cancer diagnosis. The median CD4 cell count for women with HIV was 397 (interquartile range, 264 to 555). After a median follow-up of 19.7 months, 117 (50.7%) women with HIV and 40 (41.7%) without HIV died. One death was attributed to HIV and the remaining to cancer. Three-year survival for the women with HIV was 35% (95% CI, 27% to 44%) and 48% (95% CI, 35% to 60%) for those without HIV. In an adjusted analysis, HIV infection significantly increased the risk for death among all women (hazard ratio, 1.95; 95% CI, 1.20 to 3.17) and in the subset that received guideline-concordant curative treatment (hazard ratio, 2.63; 95% CI, 1.05 to 6.55). The adverse effect of HIV on survival was greater for women with a more-limited stage cancer (P = .035), those treated with curative intent (P = .003), and those with a lower CD4 cell count (P = .036). Advanced stage and poor treatment completion contributed to high mortality overall. Conclusion In the context of good access to and use of antiretroviral treatment in Botswana, HIV infection significantly decreases cervical cancer survival. PMID:27573661

Resource Utilization and Costs during the Initial Years of Lung Cancer Screening with Computed Tomography in Canada

PubMed Central

Lam, Stephen; Tammemagi, Martin C.; Evans, William K.; Leighl, Natasha B.; Regier, Dean A.; Bolbocean, Corneliu; Shepherd, Frances A.; Tsao, Ming-Sound; Manos, Daria; Liu, Geoffrey; Atkar-Khattra, Sukhinder; Cromwell, Ian; Johnston, Michael R.; Mayo, John R.; McWilliams, Annette; Couture, Christian; English, John C.; Goffin, John; Hwang, David M.; Puksa, Serge; Roberts, Heidi; Tremblay, Alain; MacEachern, Paul; Burrowes, Paul; Bhatia, Rick; Finley, Richard J.; Goss, Glenwood D.; Nicholas, Garth; Seely, Jean M.; Sekhon, Harmanjatinder S.; Yee, John; Amjadi, Kayvan; Cutz, Jean-Claude; Ionescu, Diana N.; Yasufuku, Kazuhiro; Martel, Simon; Soghrati, Kamyar; Sin, Don D.; Tan, Wan C.; Urbanski, Stefan; Xu, Zhaolin; Peacock, Stuart J.

2014-01-01

Background: It is estimated that millions of North Americans would qualify for lung cancer screening and that billions of dollars of national health expenditures would be required to support population-based computed tomography lung cancer screening programs. The decision to implement such programs should be informed by data on resource utilization and costs. Methods: Resource utilization data were collected prospectively from 2059 participants in the Pan-Canadian Early Detection of Lung Cancer Study using low-dose computed tomography (LDCT). Participants who had 2% or greater lung cancer risk over 3 years using a risk prediction tool were recruited from seven major cities across Canada. A cost analysis was conducted from the Canadian public payer’s perspective for resources that were used for the screening and treatment of lung cancer in the initial years of the study. Results: The average per-person cost for screening individuals with LDCT was $453 (95% confidence interval [CI], $400–$505) for the initial 18-months of screening following a baseline scan. The screening costs were highly dependent on the detected lung nodule size, presence of cancer, screening intervention, and the screening center. The mean per-person cost of treating lung cancer with curative surgery was $33,344 (95% CI, $31,553–$34,935) over 2 years. This was lower than the cost of treating advanced-stage lung cancer with chemotherapy, radiotherapy, or supportive care alone, ($47,792; 95% CI, $43,254–$52,200; p = 0.061). Conclusion: In the Pan-Canadian study, the average cost to screen individuals with a high risk for developing lung cancer using LDCT and the average initial cost of curative intent treatment were lower than the average per-person cost of treating advanced stage lung cancer which infrequently results in a cure. PMID:25105438

One-millimeter cancer-free margin is curative for colorectal liver metastases: a propensity score case-match approach.

PubMed

Hamady, Zaed Z R; Lodge, J Peter A; Welsh, Fenella K; Toogood, Giles J; White, Alan; John, Timothy; Rees, Myrddin

2014-03-01

To investigate the influence of clear surgical resection margin width on disease recurrence rate after intentionally curative resection of colorectal liver metastases. There is consensus that a histological positive resection margin is a predictor of disease recurrence after resection of colorectal liver metastases. The dispute, however, over the width of cancer-free resection margin required is ongoing. Analysis of observational prospectively collected data for 2715 patients who underwent primary resection of colorectal liver metastases from 2 major hepatobiliary units in the United Kingdom. Histological cancer-free resection margin was classified as positive (if cancer cells present at less than 1 mm from the resection margin) or negative (if the distance between the cancer and the margin is 1 mm or more). The negative margin was further classified according to the distance from the tumor in millimeters. Predictors of disease-free survival were analyzed in univariate and multivariate analyses. A case-match analysis by a propensity score method was undertaken to reduce bias. A 1-mm cancer-free resection margin was sufficient to achieve 33% 5-year overall disease-free survival. Extra margin width did not add disease-free survival advantage (P > 0.05). After the propensity case-match analysis, there is no statistical difference in disease-free survival between patients with negative narrow and wider margin clearance [hazard ratio (HR) 1.0; 95% (confidence interval) CI: 0.9-1.2; P = 0.579 at 5-mm cutoff and HR 1.1; 95% CI: 0.96-1.3; P = 0.149 at 10-mm cutoff]. Patients with extrahepatic disease and positive lymph node primary tumor did not have disease-free survival advantage despite surgical margin clearance (9 months for <1-mm vs 12 months for ≥1-mm margin clearance; P = 0.062). One-mm cancer-free resection margin achieved in patients with colorectal liver metastases should now be considered the standard of care.

Hypofractionated Intensity Modulated Radiation Therapy in Combined Modality Treatment for Bladder Preservation in Elderly Patients With Invasive Bladder Cancer

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

Turgeon, Guy-Anne; Souhami, Luis, E-mail: luis.souhami@muhc.mcgill.ca; Cury, Fabio L.

2014-02-01

Purpose/Objective(s): To review our experience with bladder-preserving trimodality treatment (TMT) using hypofractionated intensity modulated radiation therapy (IMRT) for the treatment of elderly patients with muscle-invasive bladder cancer. Methods and Materials: Retrospective study of elderly patients treated with TMT using hypofractionated IMRT (50 Gy in 20 fractions) with concomitant weekly radiosensitizing chemotherapy. Eligibility criteria were as follows: age ≥70 years, a proven diagnosis of muscle-invasive transitional cell bladder carcinoma, stage T2-T3N0M0 disease, and receipt of TMT with curative intent. Response rate was assessed by cystoscopic evaluation and bladder biopsy. Results: 24 patients with a median age of 79 years were eligible.more » A complete response was confirmed in 83% of the patients. Of the remaining patients, 1 of them underwent salvage cystectomy, and no disease was found in the bladder on histopathologic assessment. After a median follow-up time of 28 months, of the patients with a complete response, 2 patients had muscle-invasive recurrence, 1 experienced locoregional failure, and 3 experienced distant metastasis. The overall and cancer-specific survival rates at 3 years were 61% and 71%, respectively. Of the surviving patients, 75% have a disease-free and functioning bladder. All patients completed hypofractionated IMRT, and 19 patients tolerated all 4 cycles of chemotherapy. Acute grade 3 gastrointestinal or genitourinary toxicities occurred in only 4% of the patients, and acute grade 3 or 4 hematologic toxicities, liver toxicities, or both were experienced by 17% of the cohort. No patient experienced grade 4 gastrointestinal or genitourinary toxicity. Conclusions: Hypofractionated IMRT with concurrent radiosensitizing chemotherapy appears to be an effective and well-tolerated curative treatment strategy in the elderly population and should be considered for patients who are not candidates for cystectomy or who wish to avoid cystectomy.« less

Collaboration between Government and Non-Governmental Organizations (NGOs) in Delivering Curative Health Services in North Darfur State, Sudan- a National Report

PubMed Central

I A YAGUB, Abdallah

2014-01-01

Abstract Background North Darfur State has been affected by conflict since 2003 and the government has not been able to provide adequate curative health services to the people. The government has come to rely on Non-Governmental Organizations (NGOs) to provide curative health services. This study was conducted to examine the existing collaboration between government and NGOs in curative health service delivery in North Darfur State, and to identify the challenges that affect their collaboration. Methods Documentary data were collected from government offices and medical organizations. Primary data were obtained through interviews with government and NGOs representatives. The interviews were conducted with (1) expatriates working for international NGOs (N=15) and (2), health professionals and administrators working in the health sector (N= 45). Results The collaboration between the government and NGOs has been very weak because of security issues and lack of trust. The NGOs collaborate by providing human and financial resources, material and equipment, and communication facilities. The NGOs supply 70% of curative health services, and contribute 52.9% of the health budget in North Darfur State. The NGOs have employed 1 390 health personnel, established 44 health centres and manage and support 83 health facilities across the State. Conclusion The NGOs have played a positive role in collaborating with the government in North Darfur State in delivering curative health services, while government’s role has been negative. The problem that faces the government in future is how health facilities will be run should a peaceful settlement be reached and NGOs leave the region. PMID:26056656

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

Individualised mindfulness-based stress reduction for head and neck cancer patients undergoing radiotherapy of curative intent: a descriptive pilot study.

PubMed

Pollard, A; Burchell, J L; Castle, D; Neilson, K; Ftanou, M; Corry, J; Rischin, D; Kissane, D W; Krishnasamy, M; Carlson, L E; Couper, J

2017-03-01

People with head and neck cancer (HNC) experience elevated symptom toxicity and co-morbidity as a result of treatment, which is associated with poorer psychosocial and quality-of-life (QoL) outcomes. This Phase I study examined whether an individualised mindfulness-based stress reduction (IMBSR) programme could be successfully used with HNC patients undergoing curative treatment. Primary aims were to explore feasibility, compliance, acceptability and fidelity. Secondary aims were to determine whether (1) participation in the intervention was associated with changes in post-intervention mindfulness and (2) post-intervention mindfulness was associated with post-intervention distress and QoL. Nineteen HNC patients participated in a seven-session IMBSR programme with pre- and post-test outcome measures of psychological distress, depression, anxiety and QoL. Primary aims were assessed by therapists or participants. Mindfulness, distress and QoL were assessed using self-report questionnaires at pre- and post-intervention. Longer time spent meditating daily was associated with higher post-intervention mindfulness. After controlling for pre-intervention mindfulness, there was an association between higher post-intervention mindfulness and lower psychological distress and higher total, social and emotional QoL. This study offers important preliminary evidence than an IMBSR intervention can be administered to HNC patients during active cancer treatment. A randomised controlled trial is warranted to confirm these findings. © 2016 John Wiley & Sons Ltd.

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.

How and when I do allogeneic transplant in CLL.

PubMed

Gribben, John G

2018-05-11

Allogenic stem cell transplantation (allo-SCT) has been considered the treatment of choice for high-risk patients with chronic lymphocytic leukemia (CLL) and the only approach offered with curative intent in this disease. The availability novel agents including the B cell receptor inhibitors (BCRi) ibrutinib, acalabrutinib and idelalisib, as well as venetoclax which targets the BCL2 pathway and the success of these agents in treating high-risk disease patients has made it more difficult to assess who and when in their treatment course allo-SCT should be considered. In this review, I will discuss the different treatment options available for the treatment of high-risk CLL and how allo-SCT fits into the treatment algorithm in the era of novel agents. Copyright © 2018 American Society of Hematology.

Salvage of locally recurrent prostate cancer after definitive radiotherapy.

PubMed

Mendenhall, William M; Henderson, Randal H; Hoppe, Bradford S; Nichols, Romaine C; Mendenhall, Nancy P

2014-08-01

Although a significant proportion of patients with localized prostate cancer are cured after definitive radiotherapy, solitary local recurrence is observed in a subset of patients and poses a management challenge. Curative-intent treatment options include prostatectomy, reirradiation, cryotherapy, and high-intensity-focused ultrasound. Outcomes data after any of these options are relatively limited. The 5-year biochemical progression-free survival rate is approximately 50% after salvage prostatectomy. However, the morbidity rate of the procedure is significantly higher compared with that observed in previously untreated patients. The likelihood of cure after low dose rate brachytherapy is similar to that observed after salvage prostatectomy, and the morbidity, although significant is less. Although cryotherapy and high-intensity-focused ultrasound may be less morbid than a prostatectomy, the probability of cure is probably lower.

Combining Magnetic Resonance Imaging (MRI) and Medical Infrared Thermography (MIT) in the pre- and per-operating management of severe Hidradenitis Suppurativa (HS).

PubMed

Derruau, Stéphane; Renard, Yohann; Pron, Hervé; Taiar, Redha; Abdi, Ellie; Polidori, Guillaume; Lorimier, Sandrine

2018-05-12

Hidradenitis suppurativa (HS) is a chronic, inflammatory, and recurrent skin disease. Surgical excision of wounds appears to be the only curative treatment for the prevention of recurrence of moderate to severe stages. Magnetic resonance imaging (MRI) is a standard reference examination for the detection of HS peri-anal inflammatory fistula. In this case study, the use of real-time medical infrared thermography, in combination with MRI as appropriate imaging, is proposed. The aim is to assist surgeons in the pre- and peri-surgical management of severe perianal hidradenitis suppurativa with the intent to ensure that all diseased lesions were removed during surgery and therefore to limit recurrence. The results show that medical infrared thermography (MIT), coupled with MRI, could be highly effective strategy to address thermally distinguished health tissues and inflammatory sites during excision, as characterised by differential increases in temperature. Medical infrared thermography could be used to check the total excision of inflammatory lesions as a noninvasive method that is not painful, not radiant, and is easily transportable during surgery. Ultimately, this method could be complementary with MRI in providing clinicians with objective data on the status of tissues below the perianal skin surface in the pre- and per-operating management of severe hidradenitis suppurativa. Copyright © 2018 Elsevier B.V. All rights reserved.

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

Martin, Olga A.; Molecular Radiation Biology Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC

Purpose: To determine whether radiation therapy (RT) could mobilize viable tumor cells into the circulation of non-small cell lung cancer (NSCLC) patients. Methods and Materials: We enumerated circulating tumor cells (CTCs) by fluorescence microscopy of blood samples immunostained with conventional CTC markers. We measured their DNA damage levels using γ-H2AX, a biomarker for radiation-induced DNA double-strand breaks, either by fluorescence-activated cell sorting or by immunofluorescence microscopy. Results: Twenty-seven RT-treated NSCLC patients had blood samples analyzed by 1 or more methods. We identified increased CTC numbers after commencement of RT in 7 of 9 patients treated with palliative RT, and inmore » 4 of 8 patients treated with curative-intent RT. Circulating tumor cells were also identified, singly and in clumps in large numbers, during RT by cytopathologic examination (in all 5 cases studied). Elevated γ-H2AX signal in post-RT blood samples signified the presence of CTCs derived from irradiated tumors. Blood taken after the commencement of RT contained tumor cells that proliferated extensively in vitro (in all 6 cases studied). Circulating tumor cells formed γ-H2AX foci in response to ex vivo irradiation, providing further evidence of their viability. Conclusions: Our findings provide a rationale for the development of strategies to reduce the concentration of viable CTCs by modulating RT fractionation or by coadministering systemic therapies.« less

[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.

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

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.

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

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.

Orthology prediction methods: A quality assessment using curated protein families

PubMed Central

Trachana, Kalliopi; Larsson, Tomas A; Powell, Sean; Chen, Wei-Hua; Doerks, Tobias; Muller, Jean; Bork, Peer

2011-01-01

The increasing number of sequenced genomes has prompted the development of several automated orthology prediction methods. Tests to evaluate the accuracy of predictions and to explore biases caused by biological and technical factors are therefore required. We used 70 manually curated families to analyze the performance of five public methods in Metazoa. We analyzed the strengths and weaknesses of the methods and quantified the impact of biological and technical challenges. From the latter part of the analysis, genome annotation emerged as the largest single influencer, affecting up to 30% of the performance. Generally, most methods did well in assigning orthologous group but they failed to assign the exact number of genes for half of the groups. The publicly available benchmark set (http://eggnog.embl.de/orthobench/) should facilitate the improvement of current orthology assignment protocols, which is of utmost importance for many fields of biology and should be tackled by a broad scientific community. PMID:21853451

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

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.

Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information

PubMed Central

Wilbur, W. John

2012-01-01

The Comparative Toxicogenomics Database (CTD) contains manually curated literature that describes chemical–gene interactions, chemical–disease relationships and gene–disease relationships. Finding articles containing this information is the first and an important step to assist manual curation efficiency. However, the complex nature of named entities and their relationships make it challenging to choose relevant articles. In this article, we introduce a machine learning framework for prioritizing CTD-relevant articles based on our prior system for the protein–protein interaction article classification task in BioCreative III. To address new challenges in the CTD task, we explore a new entity identification method for genes, chemicals and diseases. In addition, latent topics are analyzed and used as a feature type to overcome the small size of the training set. Applied to the BioCreative 2012 Triage dataset, our method achieved 0.8030 mean average precision (MAP) in the official runs, resulting in the top MAP system among participants. Integrated with PubTator, a Web interface for annotating biomedical literature, the proposed system also received a positive review from the CTD curation team. PMID:23160415

Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information.

PubMed

Kim, Sun; Kim, Won; Wei, Chih-Hsuan; Lu, Zhiyong; Wilbur, W John

2012-01-01

The Comparative Toxicogenomics Database (CTD) contains manually curated literature that describes chemical-gene interactions, chemical-disease relationships and gene-disease relationships. Finding articles containing this information is the first and an important step to assist manual curation efficiency. However, the complex nature of named entities and their relationships make it challenging to choose relevant articles. In this article, we introduce a machine learning framework for prioritizing CTD-relevant articles based on our prior system for the protein-protein interaction article classification task in BioCreative III. To address new challenges in the CTD task, we explore a new entity identification method for genes, chemicals and diseases. In addition, latent topics are analyzed and used as a feature type to overcome the small size of the training set. Applied to the BioCreative 2012 Triage dataset, our method achieved 0.8030 mean average precision (MAP) in the official runs, resulting in the top MAP system among participants. Integrated with PubTator, a Web interface for annotating biomedical literature, the proposed system also received a positive review from the CTD curation team.

A curated gluten protein sequence database to support development of proteomics methods for determination of gluten in gluten-free foods.

PubMed

Bromilow, Sophie; Gethings, Lee A; Buckley, Mike; Bromley, Mike; Shewry, Peter R; Langridge, James I; Clare Mills, E N

2017-06-23

The unique physiochemical properties of wheat gluten enable a diverse range of food products to be manufactured. However, gluten triggers coeliac disease, a condition which is treated using a gluten-free diet. Analytical methods are required to confirm if foods are gluten-free, but current immunoassay-based methods can unreliable and proteomic methods offer an alternative but require comprehensive and well annotated sequence databases which are lacking for gluten. A manually a curated database (GluPro V1.0) of gluten proteins, comprising 630 discrete unique full length protein sequences has been compiled. It is representative of the different types of gliadin and glutenin components found in gluten. An in silico comparison of their coeliac toxicity was undertaken by analysing the distribution of coeliac toxic motifs. This demonstrated that whilst the α-gliadin proteins contained more toxic motifs, these were distributed across all gluten protein sub-types. Comparison of annotations observed using a discovery proteomics dataset acquired using ion mobility MS/MS showed that more reliable identifications were obtained using the GluPro V1.0 database compared to the complete reviewed Viridiplantae database. This highlights the value of a curated sequence database specifically designed to support the proteomic workflows and the development of methods to detect and quantify gluten. We have constructed the first manually curated open-source wheat gluten protein sequence database (GluPro V1.0) in a FASTA format to support the application of proteomic methods for gluten protein detection and quantification. We have also analysed the manually verified sequences to give the first comprehensive overview of the distribution of sequences able to elicit a reaction in coeliac disease, the prevalent form of gluten intolerance. Provision of this database will improve the reliability of gluten protein identification by proteomic analysis, and aid the development of targeted mass spectrometry methods in line with Codex Alimentarius Commission requirements for foods designed to meet the needs of gluten intolerant individuals. Copyright © 2017. Published by Elsevier B.V.

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.

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.

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.

CORAL: aligning conserved core regions across domain families.

PubMed

Fong, Jessica H; Marchler-Bauer, Aron

2009-08-01

Homologous protein families share highly conserved sequence and structure regions that are frequent targets for comparative analysis of related proteins and families. Many protein families, such as the curated domain families in the Conserved Domain Database (CDD), exhibit similar structural cores. To improve accuracy in aligning such protein families, we propose a profile-profile method CORAL that aligns individual core regions as gap-free units. CORAL computes optimal local alignment of two profiles with heuristics to preserve continuity within core regions. We benchmarked its performance on curated domains in CDD, which have pre-defined core regions, against COMPASS, HHalign and PSI-BLAST, using structure superpositions and comprehensive curator-optimized alignments as standards of truth. CORAL improves alignment accuracy on core regions over general profile methods, returning a balanced score of 0.57 for over 80% of all domain families in CDD, compared with the highest balanced score of 0.45 from other methods. Further, CORAL provides E-values to aid in detecting homologous protein families and, by respecting block boundaries, produces alignments with improved 'readability' that facilitate manual refinement. CORAL will be included in future versions of the NCBI Cn3D/CDTree software, which can be downloaded at http://www.ncbi.nlm.nih.gov/Structure/cdtree/cdtree.shtml. Supplementary data are available at Bioinformatics online.

Using support vector machines to improve elemental ion identification in macromolecular crystal structures

DOE PAGES

Morshed, Nader; Echols, Nathaniel; Adams, Paul D.

2015-04-25

In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalousmore » diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.« less

Automatic categorization of diverse experimental information in the bioscience literature

PubMed Central

2012-01-01

Background Curation of information from bioscience literature into biological knowledge databases is a crucial way of capturing experimental information in a computable form. During the biocuration process, a critical first step is to identify from all published literature the papers that contain results for a specific data type the curator is interested in annotating. This step normally requires curators to manually examine many papers to ascertain which few contain information of interest and thus, is usually time consuming. We developed an automatic method for identifying papers containing these curation data types among a large pool of published scientific papers based on the machine learning method Support Vector Machine (SVM). This classification system is completely automatic and can be readily applied to diverse experimental data types. It has been in use in production for automatic categorization of 10 different experimental datatypes in the biocuration process at WormBase for the past two years and it is in the process of being adopted in the biocuration process at FlyBase and the Saccharomyces Genome Database (SGD). We anticipate that this method can be readily adopted by various databases in the biocuration community and thereby greatly reducing time spent on an otherwise laborious and demanding task. We also developed a simple, readily automated procedure to utilize training papers of similar data types from different bodies of literature such as C. elegans and D. melanogaster to identify papers with any of these data types for a single database. This approach has great significance because for some data types, especially those of low occurrence, a single corpus often does not have enough training papers to achieve satisfactory performance. Results We successfully tested the method on ten data types from WormBase, fifteen data types from FlyBase and three data types from Mouse Genomics Informatics (MGI). It is being used in the curation work flow at WormBase for automatic association of newly published papers with ten data types including RNAi, antibody, phenotype, gene regulation, mutant allele sequence, gene expression, gene product interaction, overexpression phenotype, gene interaction, and gene structure correction. Conclusions Our methods are applicable to a variety of data types with training set containing several hundreds to a few thousand documents. It is completely automatic and, thus can be readily incorporated to different workflow at different literature-based databases. We believe that the work presented here can contribute greatly to the tremendous task of automating the important yet labor-intensive biocuration effort. PMID:22280404

Automatic categorization of diverse experimental information in the bioscience literature.

PubMed

Fang, Ruihua; Schindelman, Gary; Van Auken, Kimberly; Fernandes, Jolene; Chen, Wen; Wang, Xiaodong; Davis, Paul; Tuli, Mary Ann; Marygold, Steven J; Millburn, Gillian; Matthews, Beverley; Zhang, Haiyan; Brown, Nick; Gelbart, William M; Sternberg, Paul W

2012-01-26

Curation of information from bioscience literature into biological knowledge databases is a crucial way of capturing experimental information in a computable form. During the biocuration process, a critical first step is to identify from all published literature the papers that contain results for a specific data type the curator is interested in annotating. This step normally requires curators to manually examine many papers to ascertain which few contain information of interest and thus, is usually time consuming. We developed an automatic method for identifying papers containing these curation data types among a large pool of published scientific papers based on the machine learning method Support Vector Machine (SVM). This classification system is completely automatic and can be readily applied to diverse experimental data types. It has been in use in production for automatic categorization of 10 different experimental datatypes in the biocuration process at WormBase for the past two years and it is in the process of being adopted in the biocuration process at FlyBase and the Saccharomyces Genome Database (SGD). We anticipate that this method can be readily adopted by various databases in the biocuration community and thereby greatly reducing time spent on an otherwise laborious and demanding task. We also developed a simple, readily automated procedure to utilize training papers of similar data types from different bodies of literature such as C. elegans and D. melanogaster to identify papers with any of these data types for a single database. This approach has great significance because for some data types, especially those of low occurrence, a single corpus often does not have enough training papers to achieve satisfactory performance. We successfully tested the method on ten data types from WormBase, fifteen data types from FlyBase and three data types from Mouse Genomics Informatics (MGI). It is being used in the curation work flow at WormBase for automatic association of newly published papers with ten data types including RNAi, antibody, phenotype, gene regulation, mutant allele sequence, gene expression, gene product interaction, overexpression phenotype, gene interaction, and gene structure correction. Our methods are applicable to a variety of data types with training set containing several hundreds to a few thousand documents. It is completely automatic and, thus can be readily incorporated to different workflow at different literature-based databases. We believe that the work presented here can contribute greatly to the tremendous task of automating the important yet labor-intensive biocuration effort.

36 CFR 79.6 - Methods to secure curatorial services.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 36 Parks, Forests, and Public Property 1 2014-07-01 2014-07-01 false Methods to secure curatorial... INTERIOR CURATION OF FEDERALLY-OWNED AND ADMINISTERED ARCHAEOLOGICAL COLLECTIONS § 79.6 Methods to secure curatorial services. (a) Federal agencies may secure curatorial services using a variety of methods, subject...

36 CFR 79.6 - Methods to secure curatorial services.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 36 Parks, Forests, and Public Property 1 2010-07-01 2010-07-01 false Methods to secure curatorial... INTERIOR CURATION OF FEDERALLY-OWNED AND ADMINISTERED ARCHAEOLOGICAL COLLECTIONS § 79.6 Methods to secure curatorial services. (a) Federal agencies may secure curatorial services using a variety of methods, subject...

36 CFR 79.6 - Methods to secure curatorial services.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 36 Parks, Forests, and Public Property 1 2012-07-01 2012-07-01 false Methods to secure curatorial... INTERIOR CURATION OF FEDERALLY-OWNED AND ADMINISTERED ARCHAEOLOGICAL COLLECTIONS § 79.6 Methods to secure curatorial services. (a) Federal agencies may secure curatorial services using a variety of methods, subject...

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…

Data Curation Education in Research Centers (DCERC)

NASA Astrophysics Data System (ADS)

Marlino, M. R.; Mayernik, M. S.; Kelly, K.; Allard, S.; Tenopir, C.; Palmer, C.; Varvel, V. E., Jr.

2012-12-01

Digital data both enable and constrain scientific research. Scientists are enabled by digital data to develop new research methods, utilize new data sources, and investigate new topics, but they also face new data collection, management, and preservation burdens. The current data workforce consists primarily of scientists who receive little formal training in data management and data managers who are typically educated through on-the-job training. The Data Curation Education in Research Centers (DCERC) program is investigating a new model for educating data professionals to contribute to scientific research. DCERC is a collaboration between the University of Illinois at Urbana-Champaign Graduate School of Library and Information Science, the University of Tennessee School of Information Sciences, and the National Center for Atmospheric Research. The program is organized around a foundations course in data curation and provides field experiences in research and data centers for both master's and doctoral students. This presentation will outline the aims and the structure of the DCERC program and discuss results and lessons learned from the first set of summer internships in 2012. Four masters students participated and worked with both data mentors and science mentors, gaining first hand experiences in the issues, methods, and challenges of scientific data curation. They engaged in a diverse set of topics, including climate model metadata, observational data management workflows, and data cleaning, documentation, and ingest processes within a data archive. The students learned current data management practices and challenges while developing expertise and conducting research. They also made important contributions to NCAR data and science teams by evaluating data management workflows and processes, preparing data sets to be archived, and developing recommendations for particular data management activities. The master's student interns will return in summer of 2013, and two Ph.D. students will conduct data curation-related dissertation fieldwork during the 2013-2014 academic year.

Guidelines for the functional annotation of microRNAs using the Gene Ontology

PubMed Central

D'Eustachio, Peter; Smith, Jennifer R.; Zampetaki, Anna

2016-01-01

MicroRNA regulation of developmental and cellular processes is a relatively new field of study, and the available research data have not been organized to enable its inclusion in pathway and network analysis tools. The association of gene products with terms from the Gene Ontology is an effective method to analyze functional data, but until recently there has been no substantial effort dedicated to applying Gene Ontology terms to microRNAs. Consequently, when performing functional analysis of microRNA data sets, researchers have had to rely instead on the functional annotations associated with the genes encoding microRNA targets. In consultation with experts in the field of microRNA research, we have created comprehensive recommendations for the Gene Ontology curation of microRNAs. This curation manual will enable provision of a high-quality, reliable set of functional annotations for the advancement of microRNA research. Here we describe the key aspects of the work, including development of the Gene Ontology to represent this data, standards for describing the data, and guidelines to support curators making these annotations. The full microRNA curation guidelines are available on the GO Consortium wiki (http://wiki.geneontology.org/index.php/MicroRNA_GO_annotation_manual). PMID:26917558

A computational platform to maintain and migrate manual functional annotations for BioCyc databases.

PubMed

Walsh, Jesse R; Sen, Taner Z; Dickerson, Julie A

2014-10-12

BioCyc databases are an important resource for information on biological pathways and genomic data. Such databases represent the accumulation of biological data, some of which has been manually curated from literature. An essential feature of these databases is the continuing data integration as new knowledge is discovered. As functional annotations are improved, scalable methods are needed for curators to manage annotations without detailed knowledge of the specific design of the BioCyc database. We have developed CycTools, a software tool which allows curators to maintain functional annotations in a model organism database. This tool builds on existing software to improve and simplify annotation data imports of user provided data into BioCyc databases. Additionally, CycTools automatically resolves synonyms and alternate identifiers contained within the database into the appropriate internal identifiers. Automating steps in the manual data entry process can improve curation efforts for major biological databases. The functionality of CycTools is demonstrated by transferring GO term annotations from MaizeCyc to matching proteins in CornCyc, both maize metabolic pathway databases available at MaizeGDB, and by creating strain specific databases for metabolic engineering.

[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.

Research-Grade 3D Virtual Astromaterials Samples: Novel Visualization of NASA's Apollo Lunar Samples and Antarctic Meteorite Samples to Benefit Curation, Research, and Education

NASA Technical Reports Server (NTRS)

Blumenfeld, E. H.; Evans, C. A.; Oshel, E. R.; Liddle, D. A.; Beaulieu, K. R.; Zeigler, R. A.; Righter, K.; Hanna, R. D.; Ketcham, R. A.

2017-01-01

NASA's vast and growing collections of astromaterials are both scientifically and culturally significant, requiring unique preservation strategies that need to be recurrently updated to contemporary technological capabilities and increasing accessibility demands. New technologies have made it possible to advance documentation and visualization practices that can enhance conservation and curation protocols for NASA's Astromaterials Collections. Our interdisciplinary team has developed a method to create 3D Virtual Astromaterials Samples (VAS) of the existing collections of Apollo Lunar Samples and Antarctic Meteorites. Research-grade 3D VAS will virtually put these samples in the hands of researchers and educators worldwide, increasing accessibility and visibility of these significant collections. With new sample return missions on the horizon, it is of primary importance to develop advanced curation standards for documentation and visualization methodologies.

Comparison of closed-chest drainage with rib resection closed drainage for treatment of chronic tuberculous empyema

PubMed Central

Fang, Yong; Xiao, Heping; Hu, Haili

2018-01-01

Background This study aimed to compare the efficacy of closed-chest drainage with rib resection closed drainage of chronic tuberculous empyema. Methods This retrospective study reviewed 86 patients with tuberculous empyema in Shanghai Pulmonary Hospital from August 2010 to November 2015. Among these included patients, 22 patients received closed-chest drainage, and 64 patients received rib resection closed drainage. Results The results showed that after intercostal chest closed drain treatment, 2 (9.09%) patients were recovery, 13 (59.09%) patients had significantly curative effect, 6 (27.27%) patients had partly curative effect, and 1 (4.55%) patient had negative effect. After treatment of rib resection closed drainage, 9 (14.06%) patients were successfully recovery, 31 (48.44%) patients had significantly curative effect, 19 (29.69%) patients had partly curative effect, and 5 (7.81%) patients had negative effect. There was no significant difference in the curative effect (P>0.05), while the average catheterization time of rib resection closed drainage (130.05±13.12 days) was significant longer than that (126.14±36.84 days) in course of intercostal chest closed drain (P<0.05). Conclusions This study had demonstrated that closed-chest drainage was an effective procedure for treating empyema in young patients. It was less invasive than rib resection closed drainage and was associated with less severe pain. We advocated closed-chest drainage for the majority of young patients with empyema, except for those with other diseases. PMID:29600066

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.

DNA-based immunotherapy for HPV-associated head and neck cancer.

PubMed

Aggarwal, Charu

2016-10-01

Squamous cell carcinoma of the head and neck (SCCHN) accounts for 3% of all cancers. Most patients present with locally advanced disease, where multimodality therapies are used with curative intent. Despite favorable early local treatment results, about one third of the patients will eventually develop metastatic disease. Immunotherapy offers a novel therapeutic strategy beyond cytotoxic chemotherapy, with initial approvals in melanoma and non-small-cell lung cancer. HPV-associated SCCHN is a distinct subset, with unique epidemiology and treatment outcomes. Both subsets of SCCHN (HPV-related or not) are particularly favorable for immunotherapy, as immune evasion and dysregulation have been shown to play a key role in the initiation and progression of disease. This review focuses on the latest developments in immunotherapy in SCCHN, with a particular focus on DNA-based approaches including vaccine and adoptive cellular therapies.

Microwave Ablation (MWA) for the Treatment of a Solitary, Chemorefractory Testicular Cancer Liver Metastasis

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

Violari, Elena G., E-mail: eviolari@live.com; Petre, Elena N., E-mail: petree@mskcc.org; Feldman, Darren R., E-mail: feldmand@mskcc.org

2015-04-15

We present a case of a patient with stage IIIC metastatic seminoma with a persistent chemorefractory liver lesion. The patient was deemed a poor surgical candidate due to the tumor’s aggressive biology with numerous other liver lesions treated with chemotherapy and a relatively high probability for additional recurrences. Further chemotherapy with curative intent was not a feasible option due to the fact that the patient had already received second-line high-dose chemotherapy and four cycles of third-line treatment complicated by renal failure, refractory thrombocytopenia, and debilitating neuropathy. After initial failure of laser, microwave ablation of the chemorefractory liver metastasis resulted inmore » prolonged local tumor control and rendered the patient disease-free for more than 35 months, allowing him to regain an improved quality of life.« less

Treatment of peritoneal carcinomatosis with hyperthermic intraperitoneal chemotherapy in colorectal cancer.

PubMed

Behrenbruch, Corina; Hollande, Frédéric; Thomson, Benjamin; Michael, Michael; Warrier, Satish K; Lynch, Craig; Heriot, Alexander

2017-09-01

The peritoneum is the second most common site of metastasis after the liver and the only site of metastatic disease in approximately 25% of patients with colorectal cancer (CRC). In the past, peritoneal carcinomatosis in CRC was thought to be equivalent to distant metastasis; however, the transcoelomic spread of malignant cells is an acknowledged alternative pathway. Metastasectomy with curative intent is well accepted in patients with liver metastasis in CRC despite the paucity of randomized trials. Therefore, there is rationale for local treatment with peritonectomy to eliminate macroscopic disease, followed by hyperthermic intraperitoneal chemotherapy to destroy any residual free tumour cells within the peritoneal cavity. The aim of this paper is to summarize the current evidence for cytoreduction and hyperthermic intraperitoneal chemotherapy in the treatment of peritoneal carcinomatosis in CRC. © 2017 Royal Australasian College of Surgeons.

Intention stability assessed using residual change scores moderates the intention-behaviour association: a prospective cohort study.

PubMed

Rowan, Alicia A; McDermott, Máirtín S; Allen, Mark S

2017-12-01

Intention stability is considered to be one of the key pre-requisites for a strong association between intention and behaviour. It has been claimed, however, that studies examining the moderating impact of intention stability may be invalid, as they have relied on statistically inferior methods. Residual change scores have been suggested as a more appropriate method of measuring change (or lack thereof) in constructs. The aim of the current study, therefore, is to test whether intention stability, calculated using residual change scores, moderates the intention-physical activity behaviour association. A total of 163 participants (124 women, 39 men) completed questionnaires online at three time points separated by 14 day intervals. The moderating impact of intention stability was assessed using multiple linear regression followed up using simple slope analyses to identify the direction of any effect. The interaction of intention and intention stability was found to significantly improve the overall model fit. Intentions had a stronger positive association with behaviour when intentions were more stable than when they were more unstable. However, sensitivity analyses revealed that the association was not robust and reduced to non-significant with the removal of potential multivariate outliers. Future research should use residual change scores as the preferred method of assessing intention stability.

Advancing the application of systems thinking in health: why cure crowds out prevention

PubMed Central

2014-01-01

Introduction This paper presents a system dynamics computer simulation model to illustrate unintended consequences of apparently rational allocations to curative and preventive services. Methods 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. Results 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. Conclusions 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. PMID:24935344

Severity of suicidal intent, method and behaviour antecedent to an act of self-harm: a cross sectional study of survivors of self-harm referred to a tertiary hospital in Mysore, south India.

PubMed

Krishna, Murali; Rajendra, Rajagopal; Majgi, Sumanth M; Heggere, Narendra; Parimoo, Shruti; Robinson, Catherine; Poole, Rob

2014-12-01

Rates of self harm are high in south India, but little is known about the relationship between antecedent behaviour, suicidal intent and method. Aims: To identify clinical, social and behavioural antecedents preceding an act of self-harm. 200 participants, consecutively presenting with deliberate self harm to a hospital in south India,were interviewed. Socio-demographic and clinical characteristics were recorded, together with behaviours preceding self-harm. The Pierce Suicidal Intent Scale and Mini International Neuropsychiatric Inventory were administered. Pesticide poisoning was the most common method, especially amongst men, in rural areas, and amongst professionals. No particular antecedent behaviour or activity appears to be associated with higher levels of suicidal intent. Absenteeism from work was the most commonly reported change of behaviour in the month preceding an act of self-harm. Unskilled labourers and professionals had significantly greater suicidal intent (adjusted for age, gender and method) than skilled labourers and the unemployed. There were no differences in suicidal intent between different methods. Rural dwellers had significantly greater suicidal intent compared to urban dwellers, irrespective of the method. Major Depressive Disorder was associated with significantly greater suicidal intent compared with other diagnoses and no diagnosis. Amongst people who harm themselves in south India, professionals and unskilled labourers, rural residents, and people with current major depressive disorder have higher levels of suicidal intent. Severity of suicidal intent does not appear to influence choice of method of self-harm. Behaviours predictive of self-harm in the west may not be relevant in south India.

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.

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.;

Gauchers disease--a reappraisal of hematopoietic stem cell transplantation.

PubMed

Ito, Sawa; Barrett, A John

2013-03-01

Hematopoietic stem cell transplantation (HSCT), first performed in 1984, was the first treatment approach for Gaucher's disease (GD) which had curative intent. The early successes in HSCT were soon eclipsed by the introduction of a highly effective enzyme replacement therapy (ERT), which has remained the single most widely used treatment. Experience with HSCT is limited to about 50 reported cases, mainly performed in the last century, with an overall survival around 85%. HSCT typically achieves complete correction of visceral and bony changes and can fully stabilize neurological features in otherwise progressive type II and III GD. ERT, in contrast, is completely safe and effective, but is limited by cost, incomplete resolution of visceral, hematological, and bony features in some patients, and lack of neurological correction in type II and III disease. In this review, we summarize and compare HSCT and ERT. With 20 years of experience of ERT, its limitations as well as its advantages are now well delineated. Meanwhile progress in HSCT over the last decade suggests that transplantation would today represent a very safe curative approach for GD offering one time complete correction of the disease, contrasting with the lifelong need for ERT with its associated expense and dependence on sophisticated drug manufacture. Additionally, unlike ERT, HSCT can be beneficial for neurological forms of GD. We conclude that the time has come to re-evaluate HSCT in selected patients with GD where ERT is less likely to fully eradicate symptoms of the disease.

Actual 5-Year Nutritional Outcomes of Patients with Gastric Cancer.

PubMed

Kim, Ki Hyun; Park, Dong Jin; Park, Young Suk; Ahn, Sang Hoon; Park, Do Joong; Kim, Hyung Ho

2017-06-01

In this study, we aimed to evaluate the rarely reported long-term nutritional results of patients with gastric cancer after curative gastrectomy. We retrospectively reviewed the prospectively collected medical records of 658 patients who underwent radical gastrectomy with curative intent for gastric cancer from January 2008 to December 2009 and had no recurrences. All patients were followed for 5 years. Nutritional statuses were assessed using measurements of body weight, serum hemoglobin, total lymphocyte count (TLC), protein, albumin, cholesterol, and nutritional risk index (NRI). Patients who underwent total gastrectomy had lower body weights, hemoglobin, protein, albumin, and cholesterol levels. TLC and NRI valued after the first postoperative year (P<0.05), and lower hemoglobin and NRI valued during the fifth postoperative year than patients who underwent distal gastrectomy (P<0.05). Patients who received adjuvant chemotherapy after gastrectomy had lower hemoglobin, protein, albumin, and cholesterol levels. TLC and NRI valued during the first postoperative year, than those who underwent gastrectomy only (P<0.05). Regarding post-distal gastrectomy reconstruction, those who underwent Roux-en-Y had lower cholesterol levels than did those who underwent Billroth-I and Billroth-II reconstruction at the first and fifth years after gastrectomy, respectively (P<0.05). Patients undergoing total or distal gastrectomy with Roux-en-Y anastomosis or adjuvant chemotherapy after surgery should be monitored carefully for malnutrition during the first postoperative year, and patients undergoing total gastrectomy should be monitored for malnutrition and anemia for 5 years.

Value of radiofrequency ablation in the treatment of hepatocellular carcinoma

PubMed Central

Feng, Kai; Ma, Kuan-Sheng

2014-01-01

Hepatocellular carcinoma (HCC) is a malignant disease that substantially affects public health worldwide. It is especially prevalent in east Asia and sub-Saharan Africa, where the main etiology is the endemic status of chronic hepatitis B. Effective treatments with curative intent for early HCC include liver transplantation, liver resection (LR), and radiofrequency ablation (RFA). RFA has become the most widely used local thermal ablation method in recent years because of its technical ease, safety, satisfactory local tumor control, and minimally invasive nature. This technique has also emerged as an important treatment strategy for HCC in recent years. RFA, liver transplantation, and hepatectomy can be complementary to one another in the treatment of HCC, and the outcome benefits have been demonstrated by numerous clinical studies. As a pretransplantation bridge therapy, RFA extends the average waiting time without increasing the risk of dropout or death. In contrast to LR, RFA causes almost no intra-abdominal adhesion, thus producing favorable conditions for subsequent liver transplantation. Many studies have demonstrated mutual interactions between RFA and hepatectomy, effectively expanding the operative indications for patients with HCC and enhancing the efficacy of these approaches. However, treated tumor tissue remains within the body after RFA, and residual tumors or satellite nodules can limit the effectiveness of this treatment. Therefore, future research should focus on this issue. PMID:24876721

Skin-Tissue-sparing Excision with Electrosurgical Peeling (STEEP): a surgical treatment option for severe hidradenitis suppurativa Hurley stage II/III.

PubMed

Blok, J L; Spoo, J R; Leeman, F W J; Jonkman, M F; Horváth, B

2015-02-01

Surgery is the only curative treatment for removal of the persistent sinus tracts in the skin that are characteristic of severe hidradenitis suppurativa (HS). Complete resection of the affected tissue by wide excision is currently regarded as the preferred surgical technique in these cases. However, relatively large amounts of healthy tissue are removed with this method and suitable skin-tissue-saving techniques aiming at creating less-extensive surgical defects are therefore needed in severe HS. We describe a skin-tissue-saving surgical technique for HS Hurley stage II-III disease: the Skin-Tissue-sparing Excision with Electrosurgical Peeling (STEEP) procedure. In contrast to wide excisions that generally reach into the deep subcutaneous fat, the fat is maximally spared with the STEEP procedure by performing successive tangential excisions of lesional tissue until the epithelialized bottom of the sinus tracts has been reached. From here, secondary intention healing can occur. In addition, fibrotic tissue is completely removed in the same manner as this also serves as a source of recurrence. This tissue-sparing technique results in low recurrence rates, high patient satisfaction with relatively short healing times and favourable cosmetic outcomes without contractures. © 2014 European Academy of Dermatology and Venereology.

Predictors of Radiation Therapy Noncompliance in an Urban Academic Cancer Center

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

Ohri, Nitin; Rapkin, Bruce D.; Guha, Debayan

Purpose: To quantify the frequency of patient noncompliance in an urban radiation oncology department and identify predictors of noncompliance. Methods and Materials: We identified patients treated with external beam radiation therapy (RT) with curative intent in our department from 2007 to 2012 for 1 of 7 commonly treated malignancies. Patients who missed 2 or more scheduled RT appointments were deemed “noncompliant.” An institutional database was referenced to obtain clinical and demographic information for each patient, as well as a quantitative estimate of each patient's socioeconomic status. Logistic regression was used to identify factors associated with RT noncompliance. Results: A total ofmore » 2184 patients met eligibility criteria. Of these, 442 (20.2%) were deemed “noncompliant.” On multivariate analysis, statistically significant predictors of noncompliance included diagnosis of head-and-neck, cervical, or uterine cancer, treatment during winter months, low socioeconomic status, and use of a long treatment course (all P<.05). Conclusion: This is the first large effort examining patient noncompliance with daily RT. We have identified demographic, clinical, and treatment-related factors that can be used to identify patients at high risk for noncompliance. These findings may inform future strategies to improve adherence to prescribed therapy.« less

Primary radiotherapy for carcinoma of the endometrium using external beam radiotherapy and single line source brachytherapy.

PubMed

Churn, M; Jones, B

1999-01-01

A small proportion of patients with adenocarcinoma of the endometrium are inoperable by virtue of severe concurrent medical conditions, gross obesity or advanced stage disease. They can be treated with primary radiotherapy with either curative or palliative intent. We report 37 such patients treated mainly with a combination of external beam radiotherapy and intracavitary brachytherapy using a single line source technique. The 5-year disease-specific survival for nonsurgically staged patients was 68.4% for FIGO Stages I and II and 33.3% for Stages III and IV. The incidence of late morbidity was acceptably low. Using the Franco-Italian Glossary, there was 27.0% grade 1 but no grade 2-4 bladder toxicity. For the rectum the rates were 18.9% grade 1, 5.4% grade 2, 2.7% grade 3, and no grade 4 toxicity. Methods of optimizing the dose distribution of the brachytherapy by means of variation of treatment length, radioactive source positions, and prescription point according to tumour bulk and individual anatomy are discussed. The biologically equivalent doses (BED) for combined external beam radiotherapy and brachytherapy were calculated to be in the range of 78-107 Gy(3) or 57-75 Gy(10) at point 'A' and appear adequate for the control of Stage I cancers.

Does altered fractionation influence the risk of radiation-induced optic neuropathy?

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

Bhandare, Niranjan; Monroe, Alan T.; Morris, Christopher G.

2005-07-15

Purpose: To analyze the parameters that influence the risk of radiation-induced optic neuropathy (RION) after radiotherapy for head-and-neck tumors. Methods and Materials: Between 1964 and 2000, 273 patients with tumors of the nasopharynx, paranasal sinuses, nasal cavity, and hard palate adenoid cystic carcinomas were treated with curative intent and had radiation fields that included the optic nerves and/or chiasm. Patients were followed for at least 1 year after radiotherapy. Results: Radiation-induced optic neuropathy developed in 32 eyes of 24 patients (9%). The 5-year rates of freedom from RION according to the total dose and once- vs. twice-daily fractionation were asmore » follows: {<=}63 Gy once daily, 95%; {<=}63 Gy twice daily, 98%; >63 Gy once daily, 78%; and >63 Gy twice daily, 91%. Multivariate analysis revealed that the total dose affected the risk of RION (p = 0.0047), with patient age (p = 0.0909), once-daily vs. twice-daily fractionation (p = 0.0684), and overall treatment time (p = 0.0972) were marginally significant. The use of adjuvant chemotherapy did not significantly influence the likelihood of developing RION. Conclusion: The likelihood of developing RION is primarily influenced by the total dose. Hyperfractionation may reduce the risk of experiencing this complication.« less

Orthology prediction methods: a quality assessment using curated protein families.

PubMed

Trachana, Kalliopi; Larsson, Tomas A; Powell, Sean; Chen, Wei-Hua; Doerks, Tobias; Muller, Jean; Bork, Peer

2011-10-01

The increasing number of sequenced genomes has prompted the development of several automated orthology prediction methods. Tests to evaluate the accuracy of predictions and to explore biases caused by biological and technical factors are therefore required. We used 70 manually curated families to analyze the performance of five public methods in Metazoa. We analyzed the strengths and weaknesses of the methods and quantified the impact of biological and technical challenges. From the latter part of the analysis, genome annotation emerged as the largest single influencer, affecting up to 30% of the performance. Generally, most methods did well in assigning orthologous group but they failed to assign the exact number of genes for half of the groups. The publicly available benchmark set (http://eggnog.embl.de/orthobench/) should facilitate the improvement of current orthology assignment protocols, which is of utmost importance for many fields of biology and should be tackled by a broad scientific community. Copyright © 2011 WILEY Periodicals, Inc.

Curating and sharing structures and spectra for the environmental community

EPA Science Inventory

The increasing popularity of high mass accuracy non-target mass spectrometry methods has yielded extensive identification efforts based on spectral and chemical compound databases in the environmental community and beyond. Increasingly, new methods are relying on open data resour...

ITEP: an integrated toolkit for exploration of microbial pan-genomes.

PubMed

Benedict, Matthew N; Henriksen, James R; Metcalf, William W; Whitaker, Rachel J; Price, Nathan D

2014-01-03

Comparative genomics is a powerful approach for studying variation in physiological traits as well as the evolution and ecology of microorganisms. Recent technological advances have enabled sequencing large numbers of related genomes in a single project, requiring computational tools for their integrated analysis. In particular, accurate annotations and identification of gene presence and absence are critical for understanding and modeling the cellular physiology of newly sequenced genomes. Although many tools are available to compare the gene contents of related genomes, new tools are necessary to enable close examination and curation of protein families from large numbers of closely related organisms, to integrate curation with the analysis of gain and loss, and to generate metabolic networks linking the annotations to observed phenotypes. We have developed ITEP, an Integrated Toolkit for Exploration of microbial Pan-genomes, to curate protein families, compute similarities to externally-defined domains, analyze gene gain and loss, and generate draft metabolic networks from one or more curated reference network reconstructions in groups of related microbial species among which the combination of core and variable genes constitute the their "pan-genomes". The ITEP toolkit consists of: (1) a series of modular command-line scripts for identification, comparison, curation, and analysis of protein families and their distribution across many genomes; (2) a set of Python libraries for programmatic access to the same data; and (3) pre-packaged scripts to perform common analysis workflows on a collection of genomes. ITEP's capabilities include de novo protein family prediction, ortholog detection, analysis of functional domains, identification of core and variable genes and gene regions, sequence alignments and tree generation, annotation curation, and the integration of cross-genome analysis and metabolic networks for study of metabolic network evolution. ITEP is a powerful, flexible toolkit for generation and curation of protein families. ITEP's modular design allows for straightforward extension as analysis methods and tools evolve. By integrating comparative genomics with the development of draft metabolic networks, ITEP harnesses the power of comparative genomics to build confidence in links between genotype and phenotype and helps disambiguate gene annotations when they are evaluated in both evolutionary and metabolic network contexts.

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.

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.

[Gerontodietology].

PubMed

Baranovskiĭ, A Iu; Protopopova, O B

2012-01-01

Gerontodietology is one of the most important parts of dietetics studying problems of nutrition of elderly and old persons and persons with high risk of early and pathological aging, developing principles of rational nutrition, prophylactic and curative nutrition and methods of its organization. Functional structure of modern gerontodietology, its scientific-methodical bases, terminological features are presented. Composition and features of healthy nutrition of elderly people is described in details, methods of its optimization and individualization are given. Notions of geriatric dietotherapy, its principal difference from curative nutrition of patients of other ages are described. Large section of the article is devoted to the modern problems of prophylactic gerontodietology, intended more for persons with high risk of early aging than for elderly persons. Theoretic basis and methodological contents of prophylactic gerontodietology are presented; practical recommendations on dietetic means to prevent intensive development of involution processes and organic pathology in the body are described.

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.

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.

Alcea rosea root extract as a preventive and curative agent in ethylene glycol-induced urolithiasis in rats

PubMed Central

Ahmadi, Marzieh; Rad, Abolfazl Khajavi; Rajaei, Ziba; Hadjzadeh, Mousa-Al-Reza; Mohammadian, Nema; Tabasi, Nafiseh Sadat

2012-01-01

Introduction: Alcea rosea L. is used in Asian folk medicine as a remedy for a wide range of ailments. The aim of the present study was to investigate the effect of hydroalcoholic extract of Alcea rosea roots on ethylene glycol-induced kidney calculi in rats. Materials and Methods: Male Wistar rats were randomly divided into control, ethylene glycol (EG), curative and preventive groups. Control group received tap drinking water for 28 days. Ethylene glycol (EG), curative and preventive groups received 1% ethylene glycol for induction of calcium oxalate (CaOx) calculus formation; preventive and curative subjects also received the hydroalcoholic extract of Alcea rosea roots in drinking water at dose of 170 mg/kg, since day 0 or day 14, respectively. Urinary oxalate concentration was measured by spectrophotometer on days 0, 14 and 28. On day 28, the kidneys were removed and examined histopathologically under light microscopy for counting the calcium oxalate deposits in 50 microscopic fields. Results: In both preventive and curative protocols, treatment of rats with hydroalcoholic extract of Alcea rosea roots significantly reduced the number of kidney calcium oxalate deposits compared to ethylene glycol group. Administration of Alcea rosea extract also reduced the elevated urinary oxalate due to ethylene glycol. Conclusion: Alcea rosea showed a beneficial effect in preventing and eliminating calcium oxalate deposition in the rat kidney. This effect is possibly due to diuretic and anti-inflammatory effects or presence of mucilaginous polysaccharides in the plant. It may also be related to lowering of urinary concentration of stone-forming constituents. PMID:22701236

Sharing Responsibility for Data Stewardship Between Scientists and Curators

NASA Astrophysics Data System (ADS)

Hedstrom, M. L.

2012-12-01

Data stewardship is becoming increasingly important to support accurate conclusions from new forms of data, integration of and computation across heterogeneous data types, interactions between models and data, replication of results, data governance and long-term archiving. In addition to increasing recognition of the importance of data management, data science, and data curation by US and international scientific agencies, the National Academies of Science Board on Research Data and Information is sponsoring a study on Data Curation Education and Workforce Issues. Effective data stewardship requires a distributed effort among scientists who produce data, IT staff and/or vendors who provide data storage and computational facilities and services, and curators who enhance data quality, manage data governance, provide access to third parties, and assume responsibility for long-term archiving of data. The expertise necessary for scientific data management includes a mix of knowledge of the scientific domain; an understanding of domain data requirements, standards, ontologies and analytical methods; facility with leading edge information technology; and knowledge of data governance, standards, and best practices for long-term preservation and access that rarely are found in a single individual. Rather than developing data science and data curation as new and distinct occupations, this paper examines the set of tasks required for data stewardship. The paper proposes an alternative model that embeds data stewardship in scientific workflows and coordinates hand-offs between instruments, repositories, analytical processing, publishers, distributors, and archives. This model forms the basis for defining knowledge and skill requirements for specific actors in the processes required for data stewardship and the corresponding educational and training needs.

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.

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.

Hepatic iron overload in the portal tract predicts poor survival in hepatocellular carcinoma after curative resection.

PubMed

Chung, Jung Wha; Shin, Eun; Kim, Haeryoung; Han, Ho-Seong; Cho, Jai Young; Choi, Young Rok; Hong, Sukho; Jang, Eun Sun; Kim, Jin-Wook; Jeong, Sook-Hyang

2018-05-01

Hepatic iron overload is associated with liver injury and hepatocarcinogenesis; however, it has not been evaluated in patients with hepatocellular carcinoma (HCC) in Asia. The aim of this study was to clarify the degree and distribution of intrahepatic iron deposition, and their effects on the survival of HCC patients. Intrahepatic iron deposition was examined using non-tumorous liver tissues from 204 HCC patients after curative resection, and they were scored by 2 semi-quantitative methods: simplified Scheuer's and modified Deugnier's methods. For the Scheuer's method, iron deposition in hepatocytes and Kupffer cells was separately evaluated, while for the modified Deugnier's method, hepatocyte iron score (HIS), sinusoidal iron score (SIS) and portal iron score (PIS) were systematically evaluated, and the corrected total iron score (cTIS) was calculated by multiplying the sum (TIS) of the HIS, SIS, and PIS by the coefficient. The overall prevalence of hepatic iron was 40.7% with the simplified Scheuer's method and 45.1% with the modified Deugnier's method with a mean cTIS score of 2.46. During a median follow-up of 67 months, the cTIS was not associated with overall survival. However, a positive PIS was significantly associated with a lower 5-year overall survival rate (50.0%) compared with a negative PIS (73.7%, P = .006). In the multivariate analysis, a positive PIS was an independent factor for overall mortality (hazard ratio, 2.310; 95% confidence interval, 1.181-4.517). Intrahepatic iron deposition was common, and iron overload in the portal tract indicated poor survival in curatively resected HCC patients. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Measuring the Value of Research Data: A Citation Analysis of Oceanographic Data Sets

PubMed Central

Belter, Christopher W.

2014-01-01

Evaluation of scientific research is becoming increasingly reliant on publication-based bibliometric indicators, which may result in the devaluation of other scientific activities - such as data curation – that do not necessarily result in the production of scientific publications. This issue may undermine the movement to openly share and cite data sets in scientific publications because researchers are unlikely to devote the effort necessary to curate their research data if they are unlikely to receive credit for doing so. This analysis attempts to demonstrate the bibliometric impact of properly curated and openly accessible data sets by attempting to generate citation counts for three data sets archived at the National Oceanographic Data Center. My findings suggest that all three data sets are highly cited, with estimated citation counts in most cases higher than 99% of all the journal articles published in Oceanography during the same years. I also find that methods of citing and referring to these data sets in scientific publications are highly inconsistent, despite the fact that a formal citation format is suggested for each data set. These findings have important implications for developing a data citation format, encouraging researchers to properly curate their research data, and evaluating the bibliometric impact of individuals and institutions. PMID:24671177

Measuring the value of research data: a citation analysis of oceanographic data sets.

PubMed

Belter, Christopher W

2014-01-01

Evaluation of scientific research is becoming increasingly reliant on publication-based bibliometric indicators, which may result in the devaluation of other scientific activities--such as data curation--that do not necessarily result in the production of scientific publications. This issue may undermine the movement to openly share and cite data sets in scientific publications because researchers are unlikely to devote the effort necessary to curate their research data if they are unlikely to receive credit for doing so. This analysis attempts to demonstrate the bibliometric impact of properly curated and openly accessible data sets by attempting to generate citation counts for three data sets archived at the National Oceanographic Data Center. My findings suggest that all three data sets are highly cited, with estimated citation counts in most cases higher than 99% of all the journal articles published in Oceanography during the same years. I also find that methods of citing and referring to these data sets in scientific publications are highly inconsistent, despite the fact that a formal citation format is suggested for each data set. These findings have important implications for developing a data citation format, encouraging researchers to properly curate their research data, and evaluating the bibliometric impact of individuals and institutions.

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."

20180318 - Curating and sharing structures and spectra for the environmental community (ACS Spring)

EPA Science Inventory

The increasing popularity of high mass accuracy non-target mass spectrometry methods has yielded extensive identification efforts based on spectral and chemical compound databases in the environmental community and beyond. Increasingly, new methods are relying on open data resour...

Clinical Characterization of Canine Acanthomatous Ameloblastoma (CAA) in 263 dogs and the Influence of Postsurgical Histopathological Margin on Local Recurrence.

PubMed

Goldschmidt, Stephanie L; Bell, Cindy M; Hetzel, Scott; Soukup, Jason

2017-12-01

Canine acanthomatous ameloblastoma (CAA) has been reported to be the most common odontogenic tumor in dogs. This retrospective study evaluated 263 dogs with histopathologically confirmed CAA. Within this data set, CAA presents most commonly in the rostral mandible in adult large breed dogs, with golden retriever dogs being overrepresented. Patients with appropriate follow-up after curative intent surgery were evaluated to assess the effect of histopathological margin on local tumor recurrence. No local recurrence was noted in any patient. This study raises questions about what the recommended surgical margin should be for treatment of CAA. It also serves as a stimulus for discussion as to whether further treatment for CAA is required when inadequate surgical margins are obtained, or if medical surveillance would be an appropriate management recommendation. Prospective studies are necessary to answer these questions.

Reirradiation of head and neck cancer using modern highly conformal techniques.

PubMed

Ho, Jennifer C; Phan, Jack

2018-04-23

Locoregional disease recurrence or development of a second primary cancer after definitive radiotherapy for head and neck cancers remains a treatment challenge. Reirradiation utilizing traditional techniques has been limited by concern for serious toxicity. With the advent of newer, more precise radiotherapy techniques, such as intensity-modulated radiotherapy (IMRT), proton radiotherapy, and stereotactic body radiotherapy (SBRT), there has been renewed interest in curative-intent head and neck reirradiation. However, as most studies were retrospective, single-institutional experiences, the optimal modality is not clear. We provide a comprehensive review of the outcomes of relevant studies using these 3 head and neck reirradiation techniques, followed by an analysis and comparison of the toxicity, tumor control, concurrent systemic therapy, and prognostic factors. Overall, there is evidence that IMRT, proton therapy, and SBRT reirradiation are feasible treatment options that offer a chance for durable local control and survival. Prospective studies, particularly randomized trials, are needed. © 2018 Wiley Periodicals, Inc.

[Immune checkpoint inhibitors (antibodies to PD1 and PD-L1), a new therapeutic weapon against non-small cell bronchial carcinoma].

PubMed

Berghmans, T; Grigoriu, B; Sculier, J P; Meert, A P

2018-02-01

Classical therapeutic strategy for advanced and metastatic non-small cell lung cancer, without activable oncogenic driver mutation, has been based mainly on cytotoxic chemotherapy with modest benefits in terms of increased survival. A better understanding of the mechanisms involved in the regulation of the immune system led to the development of antibodies directed against immune checkpoints such as PD-L1. The first encouraging clinical data from phase I studies assessing anti-PD1 and anti-PD-L1 antibodies have been confirmed in randomised phase III trials. These new drugs now constitute a standard second-line treatment for metastatic tumours and in the future, at least for pembrolizumab, in the first line. Their adjuvant role after locoregional treatment with curative intent is currently under investigation. Copyright © 2017 SPLF. Published by Elsevier Masson SAS. All rights reserved.

Radiofrequency thermo-ablation of PVNS in the knee: initial results.

PubMed

Lalam, Radhesh K; Cribb, Gillian L; Cassar-Pullicino, Victor N; Cool, Wim P; Singh, Jaspreet; Tyrrell, Prudencia N M; Tins, Bernhard J; Winn, Naomi

2015-12-01

Pigmented villonodular synovitis (PVNS) is normally treated by arthroscopic or open surgical excision. We present our initial experience with radiofrequency thermo-ablation (RF ablation) of PVNS located in an inaccessible location in the knee. Review of all patients with histologically proven PVNS treated with RF ablation and with at least 2-year follow-up. Three patients met inclusion criteria and were treated with RF ablation. Two of the patients were treated successfully by one ablation procedure. One of the three patients had a recurrence which was also treated successfully by repeat RF ablation. There were no complications and all patients returned to their previous occupations following RF ablation. In this study we demonstrated the feasibility of performing RF ablation to treat PVNS in relatively inaccessible locations with curative intent. We have also discussed various post-ablation imaging appearances which can confound the assessment for residual/recurrent disease.

Strategies for optimizing the response of cancer and normal tissues to radiation

PubMed Central

Moding, Everett J.; Kastan, Michael B.; Kirsch, David G.

2014-01-01

Approximately 50% of all patients with cancer receive radiation therapy at some point during the course of their treatment, and the majority of these patients are treated with curative intent. Despite recent advances in the planning of radiation treatment and the delivery of image-guided radiation therapy, acute toxicity and potential long-term side effects often limit the ability to deliver a sufficient dose of radiation to control tumours locally. In the past two decades, a better understanding of the hallmarks of cancer and the discovery of specific signalling pathways by which cells respond to radiation have provided new opportunities to design molecularly targeted therapies to increase the therapeutic window of radiation therapy. Here, we review efforts to develop approaches that could improve outcomes with radiation therapy by increasing the probability of tumour cure or by decreasing normal tissue toxicity. PMID:23812271

Prognostic and predictive biomarkers post curative intent therapy

PubMed Central

Feldman, Rebecca

2017-01-01

Large-scale screening trials have demonstrated that early diagnosis of lung cancer results in a significant reduction in lung cancer mortality. Despite improvements in detecting more lung cancers at early stages, the 5-year survival rates of lung cancers diagnosed before widespread disease is only 30–50%. High rates of recurrence, despite early diagnosis, suggest the need to improve treatment strategies based on the likelihood of recurrence in patient subsets, as well as explore the role of predictive markers for therapy selection in the adjuvant setting. In the era of personalized medicine, there have been a wide array of molecular alterations and signatures studied for their potential prognostic and predictive utility, however most have failed to translate into clinical tools. This review will discuss progress made in clinical management of lung cancer, and recent progress in the development of patient selection tools for the refinement of early stage lung cancers. PMID:29057234

Do the benefits outweigh the side effects of colorectal cancer surveillance? A systematic review.

PubMed

Augestad, Knut Magne; Rose, Johnie; Crawshaw, Benjamin; Cooper, Gregory; Delaney, Conor

2014-05-15

Most patients treated with curative intent for colorectal cancer (CRC) are included in a follow-up program involving periodic evaluations. The survival benefits of a follow-up program are well delineated, and previous meta-analyses have suggested an overall survival improvement of 5%-10% by intensive follow-up. However, in a recent randomized trial, there was no survival benefit when a minimal vs an intensive follow-up program was compared. Less is known about the potential side effects of follow-up. Well-known side effects of preventive programs are those of somatic complications caused by testing, negative psychological consequences of follow-up itself, and the downstream impact of false positive or false negative tests. Accordingly, the potential survival benefits of CRC follow-up must be weighed against these potential negatives. The present review compares the benefits and side effects of CRC follow-up, and we propose future areas for research.

An analysis of the therapeutic benefits of genotyping in pediatric hematopoietic stem cell transplantation.

PubMed

Wright, Felicity A; Bebawy, Mary; O'Brien, Tracey A

2015-01-01

Hematopoietic stem cell transplantation is a high-risk procedure that is offered, with curative intent, to patients with malignant and nonmalignant disease. The clinical benefits of personalization of therapy by genotyping have been demonstrated by the reduction in transplant related mortality from donor-recipient HLA matching. However, defining the relationship between genotype and transplant conditioning agents is yet to be translated into clinical practice. A number of the therapeutic agents used in stem cell transplant preparative regimens have pharmacokinetic parameters that predict benefit of incorporating pharmacogenomic data into dosing strategies. Busulfan, cyclophosphamide, thio-TEPA and etoposide have well-described drug metabolism pathways, however candidate gene studies have identified there is a gap in the identification of pharmacogenomic data that can be used to improve transplant outcomes. Incorporating pharmacogenomics into pharmacokinetic modeling may demonstrate the therapeutic benefits of genotyping in transplant preparative regimen agents.

Circulating tumor cells: silent predictors of metastasis

PubMed Central

Zhou, LanLan; Dicker, David T.; Matthew, Elizabeth; El-Deiry, Wafik S.; Alpaugh, R. Katherine

2017-01-01

Circulating tumor cells (CTCs) were added to the arsenal of clinical testing in 2004 for three cancer types: metastatic breast, prostate, and colorectal cancer. CTCs were found to be an independent prognostic indicator of survival for these three diseases. Multiple enrichment/isolation strategies have been developed and numerous assay applications have been performed using both single and pooled captured/enriched CTCs. We have reviewed the isolation techniques and touched on many analyses. The true utility of a CTC is that it acts as a “silent” predictor of metastatic disease. The mere presence of a single CTC is an indication that disease has spread from the primary site. Comments and suggestions have been set forth for CTCs and cell-free DNA to be used as a screening panel for the early detection of disease recurrence and metastatic spread, providing the opportunity for early intervention with curative intent to treat metastatic disease. PMID:28868131

Indigenous cosmology, art forms and past medicinal practices: towards an interpretation of ancient Koma Land sites in northern Ghana.

PubMed

Kankpeyeng, Benjamin W; Nkumbaan, Samuel N; Insoll, Timothy

2011-08-01

The ancient cultural tradition in the middle belt region of northern Ghana, with its stone circle and house mounds, contains varied material culture. The unique contextual arrangements of the material culture within the stone circle mounds and the diverse ceramic art forms, as well as their ethnographic analogues in West Africa, indicate the mounds' association with past shrines that have multiple functions, including curative purposes. The archaeology of the mounds and ethnographic associations related to past indigenous medical practices is reviewed and discussed. This paper will also consider how some of the figurines through which the Koma tradition has achieved 'fame' possibly functioned as physical representations of disease, perhaps underpinned by intentions of transference from afflicted to image. The notions of protection and healing are also examined with reference to the resorted and disarticulated human remains sometimes recovered from the sites.

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

Long-term control of olfactory neuroblastoma in a dog treated with surgery and radiation therapy.

PubMed

Gumpel, E; Moore, A S; Simpson, D J; Hoffmann, K L; Taylor, D P

2017-07-01

Olfactory neuroblastoma is a rare malignancy of the nasal cavity in dogs that is thought to arise from specialised sensory neuroendocrine olfactory cells derived from the neural crest. An 8-year-old dog was presented for reclusiveness and pacing. On CT and MRI, a contract-enhancing mass was disclosed within the rostral fossa, extending caudally from the cribriform plate into the left nasal sinus. Surgical excision was performed and the diagnosis was histological grade III (Hyams grading scheme) olfactory neuroblastoma. Based on human CT criteria this was high stage (modified Kadish stage C). Surgical excision was incomplete and was followed by curative-intent radiation therapy using a linear accelerator to a total dose of 48 Gy. The dog survived 20 months after diagnosis. Although olfactory neuroblastoma is a rare tumour in dogs, aggressive local therapy may allow for prolonged survival, even when the tumour is advanced. © 2017 Australian Veterinary Association.

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

Triage by ranking to support the curation of protein interactions

PubMed Central

Pasche, Emilie; Gobeill, Julien; Rech de Laval, Valentine; Gleizes, Anne; Michel, Pierre-André; Bairoch, Amos

2017-01-01

Abstract Today, molecular biology databases are the cornerstone of knowledge sharing for life and health sciences. The curation and maintenance of these resources are labour intensive. Although text mining is gaining impetus among curators, its integration in curation workflow has not yet been widely adopted. The Swiss Institute of Bioinformatics Text Mining and CALIPHO groups joined forces to design a new curation support system named nextA5. In this report, we explore the integration of novel triage services to support the curation of two types of biological data: protein–protein interactions (PPIs) and post-translational modifications (PTMs). The recognition of PPIs and PTMs poses a special challenge, as it not only requires the identification of biological entities (proteins or residues), but also that of particular relationships (e.g. binding or position). These relationships cannot be described with onto-terminological descriptors such as the Gene Ontology for molecular functions, which makes the triage task more challenging. Prioritizing papers for these tasks thus requires the development of different approaches. In this report, we propose a new method to prioritize articles containing information specific to PPIs and PTMs. The new resources (RESTful APIs, semantically annotated MEDLINE library) enrich the neXtA5 platform. We tuned the article prioritization model on a set of 100 proteins previously annotated by the CALIPHO group. The effectiveness of the triage service was tested with a dataset of 200 annotated proteins. We defined two sets of descriptors to support automatic triage: the first set to enrich for papers with PPI data, and the second for PTMs. All occurrences of these descriptors were marked-up in MEDLINE and indexed, thus constituting a semantically annotated version of MEDLINE. These annotations were then used to estimate the relevance of a particular article with respect to the chosen annotation type. This relevance score was combined with a local vector-space search engine to generate a ranked list of PMIDs. We also evaluated a query refinement strategy, which adds specific keywords (such as ‘binds’ or ‘interacts’) to the original query. Compared to PubMed, the search effectiveness of the nextA5 triage service is improved by 190% for the prioritization of papers with PPIs information and by 260% for papers with PTMs information. Combining advanced retrieval and query refinement strategies with automatically enriched MEDLINE contents is effective to improve triage in complex curation tasks such as the curation of protein PPIs and PTMs. Database URL: http://candy.hesge.ch/nextA5 PMID:29220432

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

New insights into protein-protein interaction data lead to increased estimates of the S. cerevisiae interactome size.

PubMed

Sambourg, Laure; Thierry-Mieg, Nicolas

2010-12-21

As protein interactions mediate most cellular mechanisms, protein-protein interaction networks are essential in the study of cellular processes. Consequently, several large-scale interactome mapping projects have been undertaken, and protein-protein interactions are being distilled into databases through literature curation; yet protein-protein interaction data are still far from comprehensive, even in the model organism Saccharomyces cerevisiae. Estimating the interactome size is important for evaluating the completeness of current datasets, in order to measure the remaining efforts that are required. We examined the yeast interactome from a new perspective, by taking into account how thoroughly proteins have been studied. We discovered that the set of literature-curated protein-protein interactions is qualitatively different when restricted to proteins that have received extensive attention from the scientific community. In particular, these interactions are less often supported by yeast two-hybrid, and more often by more complex experiments such as biochemical activity assays. Our analysis showed that high-throughput and literature-curated interactome datasets are more correlated than commonly assumed, but that this bias can be corrected for by focusing on well-studied proteins. We thus propose a simple and reliable method to estimate the size of an interactome, combining literature-curated data involving well-studied proteins with high-throughput data. It yields an estimate of at least 37, 600 direct physical protein-protein interactions in S. cerevisiae. Our method leads to higher and more accurate estimates of the interactome size, as it accounts for interactions that are genuine yet difficult to detect with commonly-used experimental assays. This shows that we are even further from completing the yeast interactome map than previously expected.

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

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

EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation.

PubMed

Pafilis, Evangelos; Buttigieg, Pier Luigi; Ferrell, Barbra; Pereira, Emiliano; Schnetzer, Julia; Arvanitidis, Christos; Jensen, Lars Juhl

2016-01-01

The microbial and molecular ecology research communities have made substantial progress on developing standards for annotating samples with environment metadata. However, sample manual annotation is a highly labor intensive process and requires familiarity with the terminologies used. We have therefore developed an interactive annotation tool, EXTRACT, which helps curators identify and extract standard-compliant terms for annotation of metagenomic records and other samples. Behind its web-based user interface, the system combines published methods for named entity recognition of environment, organism, tissue and disease terms. The evaluators in the BioCreative V Interactive Annotation Task found the system to be intuitive, useful, well documented and sufficiently accurate to be helpful in spotting relevant text passages and extracting organism and environment terms. Comparison of fully manual and text-mining-assisted curation revealed that EXTRACT speeds up annotation by 15-25% and helps curators to detect terms that would otherwise have been missed. Database URL: https://extract.hcmr.gr/. © The Author(s) 2016. Published by Oxford University Press.

EXTRACT: Interactive extraction of environment metadata and term suggestion for metagenomic sample annotation

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

Pafilis, Evangelos; Buttigieg, Pier Luigi; Ferrell, Barbra

The microbial and molecular ecology research communities have made substantial progress on developing standards for annotating samples with environment metadata. However, sample manual annotation is a highly labor intensive process and requires familiarity with the terminologies used. We have therefore developed an interactive annotation tool, EXTRACT, which helps curators identify and extract standard-compliant terms for annotation of metagenomic records and other samples. Behind its web-based user interface, the system combines published methods for named entity recognition of environment, organism, tissue and disease terms. The evaluators in the BioCreative V Interactive Annotation Task found the system to be intuitive, useful, wellmore » documented and sufficiently accurate to be helpful in spotting relevant text passages and extracting organism and environment terms. Here the comparison of fully manual and text-mining-assisted curation revealed that EXTRACT speeds up annotation by 15–25% and helps curators to detect terms that would otherwise have been missed.« less

EXTRACT: Interactive extraction of environment metadata and term suggestion for metagenomic sample annotation

DOE PAGES

Pafilis, Evangelos; Buttigieg, Pier Luigi; Ferrell, Barbra; ...

2016-01-01

The microbial and molecular ecology research communities have made substantial progress on developing standards for annotating samples with environment metadata. However, sample manual annotation is a highly labor intensive process and requires familiarity with the terminologies used. We have therefore developed an interactive annotation tool, EXTRACT, which helps curators identify and extract standard-compliant terms for annotation of metagenomic records and other samples. Behind its web-based user interface, the system combines published methods for named entity recognition of environment, organism, tissue and disease terms. The evaluators in the BioCreative V Interactive Annotation Task found the system to be intuitive, useful, wellmore » documented and sufficiently accurate to be helpful in spotting relevant text passages and extracting organism and environment terms. Here the comparison of fully manual and text-mining-assisted curation revealed that EXTRACT speeds up annotation by 15–25% and helps curators to detect terms that would otherwise have been missed.« less

ADAGE signature analysis: differential expression analysis with data-defined gene sets.

PubMed

Tan, Jie; Huyck, Matthew; Hu, Dongbo; Zelaya, René A; Hogan, Deborah A; Greene, Casey S

2017-11-22

Gene set enrichment analysis and overrepresentation analyses are commonly used methods to determine the biological processes affected by a differential expression experiment. This approach requires biologically relevant gene sets, which are currently curated manually, limiting their availability and accuracy in many organisms without extensively curated resources. New feature learning approaches can now be paired with existing data collections to directly extract functional gene sets from big data. Here we introduce a method to identify perturbed processes. In contrast with methods that use curated gene sets, this approach uses signatures extracted from public expression data. We first extract expression signatures from public data using ADAGE, a neural network-based feature extraction approach. We next identify signatures that are differentially active under a given treatment. Our results demonstrate that these signatures represent biological processes that are perturbed by the experiment. Because these signatures are directly learned from data without supervision, they can identify uncurated or novel biological processes. We implemented ADAGE signature analysis for the bacterial pathogen Pseudomonas aeruginosa. For the convenience of different user groups, we implemented both an R package (ADAGEpath) and a web server ( http://adage.greenelab.com ) to run these analyses. Both are open-source to allow easy expansion to other organisms or signature generation methods. We applied ADAGE signature analysis to an example dataset in which wild-type and ∆anr mutant cells were grown as biofilms on the Cystic Fibrosis genotype bronchial epithelial cells. We mapped active signatures in the dataset to KEGG pathways and compared with pathways identified using GSEA. The two approaches generally return consistent results; however, ADAGE signature analysis also identified a signature that revealed the molecularly supported link between the MexT regulon and Anr. We designed ADAGE signature analysis to perform gene set analysis using data-defined functional gene signatures. This approach addresses an important gap for biologists studying non-traditional model organisms and those without extensive curated resources available. We built both an R package and web server to provide ADAGE signature analysis to the community.

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.

Treatment using oxaliplatin and S-1 adjuvant chemotherapy for pathological stage III gastric cancer: a multicenter phase II study (TOSA trial) protocol.

PubMed

Namikawa, Tsutomu; Maeda, Hiromichi; Kitagawa, Hiroyuki; Oba, Koji; Tsuji, Akihito; Yoshikawa, Takaki; Kobayashi, Michiya; Hanazaki, Kazuhiro

2018-02-13

Recent studies demonstrated the efficacy of S-1-based adjuvant chemotherapy administered for six months after curative surgery for stage III gastric cancer; however, it is unproven whether this type of combination chemotherapy is more effective than the standard adjuvant chemotherapy of S-1 for one year. This multicenter phase II study evaluate the efficacy and safety of adjuvant chemotherapy using S-1 plus oxaliplatin followed by S-1 for up to one year for curatively resected stage III gastric cancer in patients aged over 20 years. Treatment initially comprises oral fluoropyrimidine S-1 (80 mg/m 2 ) administered twice daily for the first 2 weeks of a 3-week cycle. On day 1 of a second 3-week cycle, patients will receive 100 mg/m 2 of intravenous oxaliplatin followed by 80 mg/m 2 of S-1 (maximum 8 cycles). Then, the patients will receive 80 mg/m 2 of S-1 daily for 4 weeks, followed by 2 weeks of no chemotherapy. This 6-week cycle will be repeated during the first year after surgery. The primary endpoint is relapse-free survival for 3 years and secondary endpoints are safety, including the incidence of adverse events, and grading of neuropathy with each treatment cycle. The planned sample size of 75 patients is appropriate for this trial. The data will be analyzed on an intention-to-treat basis, assuming a two-sided test with a 5% level of significance. In contrast to previous trials, the current study involves administration of S-1 until one year after surgery in addition to prior S-1 plus oxaliplatin, and is the first study to evaluate the safety and efficacy of S-1 plus oxaliplatin followed by S-1 for up to one year in patients with curatively resected stage III gastric cancer. This trial is registered in the University Hospital Medical Information Network's Clinical Trials Registry (UMIN-CTR) registration number, R000029656  ( https://upload.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000029656 ). Registered January 24, 2017.

Prognostic factors for head and neck cancer of unknown primary including the impact of human papilloma virus infection.

PubMed

Axelsson, Lars; Nyman, Jan; Haugen-Cange, Hedda; Bove, Mogens; Johansson, Leif; De Lara, Shahin; Kovács, Anikó; Hammerlid, Eva

2017-06-10

Head and neck cancer of unknown primary (HNCUP) is rare and prospective studies are lacking. The impact of different prognostic factors such as age and N stage is not completely known, the optimal treatment is not yet established, and the reported survival rates vary. In the last decade, human papilloma virus (HPV) has been identified as a common cause of and important prognostic factor in oropharyngeal cancer, and there is now growing interest in the importance of HPV for HNCUP. The aim of the present study on curatively treated HNCUP was to investigate the prognostic importance of different factors, including HPV status, treatment, and overall survival. A search for HNCUP was performed in the Swedish Cancer Registry, Western health district, between the years 1992-2009. The medical records were reviewed, and only patients with squamous cell carcinoma or undifferentiated carcinoma treated with curative intent were included. The tumor specimens were retrospectively analyzed for HPV with p16 immunostaining. Sixty-eight patients were included. The mean age was 59 years. The majority were males, and had N2 tumors. Sixty-nine percent of the tumors were HPV positive using p16 staining. Patients who were older than 70 years, patients with N3-stage tumors, and patients with tumors that were p16 negative had a significantly worse prognosis. The overall 5-year survival rate for patients with p16-positive tumors was 88% vs 61% for p16-negative tumors. Treatment with neck dissection and postoperative radiation or (chemo) radiation had 81 and 88% 5-year survival rates, respectively. The overall and disease-free 5-year survival rates for all patients in the study were 82 and 74%. Curatively treated HNCUP had good survival. HPV infection was common. Independent prognostic factors for survival were age over 70 years, HPV status and N3 stage. We recommend that HPV analysis should be performed routinely for HNCUP. Treatment with neck dissection and postoperative radiation or (chemo) radiation showed similar survival rates.

Definitive chemoradiation for locoregional recurrences of esophageal cancer after primary curative treatment.

PubMed

Jeene, P M; Versteijne, E; van Berge Henegouwen, M I; Bergmann, J J G H M; Geijsen, E D; Muller, K; van Laarhoven, H W M; Hulshof, M C C M

2017-02-01

The aim of this study was to determine the outcome of salvage definitive chemoradiation (dCRT) for a locoregional recurrence after any prior curative treatment outside previously irradiated areas. Thirty-nine patients treated between January 2005 and December 2014 were reviewed for locoregional recurrent esophageal cancer outside previously irradiated areas. All patients received salvage treatment with external beam radiotherapy (50.4 Gy in 28 fractions) combined with weekly concurrent paclitaxel and carboplatin. The median follow-up period was 15 months (range 1.7-120). The median overall survival (OS) for all patients after salvage dCRT was 22 months (95% CI 6.2-37.6). The 1-, 3-, and 5-year OS was 72%, 31%, and 28%, respectively. Median survival after salvage dCRT for a regional lymph node recurrence was 33 months (95% CI 5.8-60.3) versus 14 months (95% CI 6.8-21.6) for a recurrence at the anastomosis (P = 0.022, logrank). Median OS was 35 months for the squamous cell carcinoma group and 19 months for the adenocarcinoma group (P = 0.67). Sixteen of 39 patients developed a locoregional recurrence after salvaged dCRT. The median locoregional recurrence-free survival (LRFS) was 24 months. The 1-, 3-, and 5-year LRFS was 79%, 36%, and 36%, respectively. Median disease-free survival (DFS) was 15 months. The 1-, 3-, and 5-year DFS was 66%, 27%, and 27%, respectively. Of 16 patients, 8 (50%) with a primary failure at the site of the anastomosis developed a local recurrence after salvaged dCRT compared to 7 of 22 patients (32%) with a primary recurrence in a lymph node. Definitive chemoradiation is a feasible and effective treatment for locoregional recurrent esophageal cancer outside a previously irradiated area, and should be given with a curative intent. This holds true for recurrence of both squamous cell carcinoma and adenocarcinoma. Lymph node recurrences have a markedly better prognosis than recurrences at the site of the anastomosis. © 2016 International Society for Diseases of the Esophagus.

Subtotal gastrectomy for gastric cancer

PubMed Central

Santoro, Roberto; Ettorre, Giuseppe Maria; Santoro, Eugenio

2014-01-01

Although a steady decline in the incidence and mortality rates of gastric carcinoma has been observed in the last century worldwide, the absolute number of new cases/year is increasing because of the aging of the population. So far, surgical resection with curative intent has been the only treatment providing hope for cure; therefore, gastric cancer surgery has become a specialized field in digestive surgery. Gastrectomy with lymph node (LN) dissection for cancer patients remains a challenging procedure which requires skilled, well-trained surgeons who are very familiar with the fast-evolving oncological principles of gastric cancer surgery. As a matter of fact, the extent of gastric resection and LN dissection depends on the size of the disease and gastric cancer surgery has become a patient and “disease-tailored” surgery, ranging from endoscopic resection to laparoscopic assisted gastrectomy and conventional extended multivisceral resections. LN metastases are the most important prognostic factor in patients that undergo curative resection. LN dissection remains the most challenging part of the operation due to the location of LN stations around major retroperitoneal vessels and adjacent organs, which are not routinely included in the resected specimen and need to be preserved in order to avoid dangerous intra- and postoperative complications. Hence, the surgeon is the most important non-TMN prognostic factor in gastric cancer. Subtotal gastrectomy is the treatment of choice for middle and distal-third gastric cancer as it provides similar survival rates and better functional outcome compared to total gastrectomy, especially in early-stage disease with favorable prognosis. Nonetheless, the resection range for middle-third gastric cancer cases and the extent of LN dissection at early stages remains controversial. Due to the necessity of a more extended procedure at advanced stages and the trend for more conservative treatments in early gastric cancer, the indication for conventional subtotal gastrectomy depends on multiple variables. This review aims to clarify and define the actual landmarks of this procedure and the role it plays compared to the whole range of new and old treatment methods. PMID:25320505

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.

Using support vector machines to improve elemental ion identification in macromolecular crystal structures

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

Morshed, Nader; Lawrence Berkeley National Laboratory, Berkeley, CA 94720; Echols, Nathaniel, E-mail: nechols@lbl.gov

2015-05-01

A method to automatically identify possible elemental ions in X-ray crystal structures has been extended to use support vector machine (SVM) classifiers trained on selected structures in the PDB, with significantly improved sensitivity over manually encoded heuristics. In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here,more » the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalous diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.« less

Reirradiation of Head and Neck Cancers With Intensity Modulated Radiation Therapy: Outcomes and Analyses

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

Takiar, Vinita; Garden, Adam S.; Ma, Dominic

Purpose: To review our 15-year institutional experience using intensity modulated radiation therapy (IMRT) to reirradiate patients with head and neck squamous cell carcinomas (HNSCC) and identify predictors of outcomes and toxicity. Methods and Materials: We retrospectively reviewed the records of 227 patients who received head and neck reirradiation using IMRT from 1999 to 2014. Patients treated with noncurative intent were excluded. Radiation-related acute and late toxicities were recorded. Prognostic variables included performance status, disease site, disease-free interval, chemotherapy, and RT dose and volume. Correlative analyses were performed separately for surgery and nonsurgery patients. Results: Two hundred six patients (91%) were retreatedmore » with curative intent, and 173 had HNSCC histology; 104 (50%) underwent salvage resection, and 135 (66%) received chemotherapy. Median follow-up after reirradiation was 24.7 months. Clinical outcomes were worse for HNSCC patients, with 5-year locoregional control, progression-free survival, and overall survival rates of 53%, 22%, and 32%, respectively, compared with 74%, 59%, and 79%, respectively, for non-HNSCC patients. On multivariate analysis, concurrent chemotherapy and retreatment site were associated with tumor control, whereas performance status was associated with survival. Favorable prognostic factors specific to surgery patients were neck retreatment and lack of extracapsular extension, whereas for nonsurgery patients, these were a nasopharynx subsite and complete response to induction chemotherapy. Actuarial rates of grade ≥3 toxicity were 32% at 2 years and 48% at 5 years, with dysphagia or odynophagia being most common. Increased grade ≥3 toxicity was associated with retreatment volume >50 cm{sup 3} and concurrent chemotherapy. Conclusions: Reirradiation with IMRT either definitively or after salvage surgery can produce promising local control and survival in selected patients with head and neck cancers. Treatment-related toxicity remains significant. Prognostic factors are emerging to guide multidisciplinary treatment approaches and clinical trial design.« less

Patient education-level affects treatment allocation and prognosis in esophageal- and gastroesophageal junctional cancer in Sweden.

PubMed

Linder, Gustav; Sandin, Fredrik; Johansson, Jan; Lindblad, Mats; Lundell, Lars; Hedberg, Jakob

2018-02-01

Low socioeconomic status and poor education elevate the risk of developing esophageal- and junctional cancer. High education level also increases survival after curative surgery. The present study aimed to investigate associations, if any, between patient education-level and treatment allocation after diagnosis of esophageal- and junctional cancer and its subsequent impact on survival. A nation-wide cohort study was undertaken. Data from a Swedish national quality register for esophageal cancer (NREV) was linked to the National Cancer Register, National Patient Register, Prescribed Drug Register, Cause of Death Register and educational data from Statistics Sweden. The effect of education level (low; ≤9 years, intermediate; 10-12 years and high >12 years) on the probability of allocation to curative treatment was analyzed with logistic regression. The Kaplan-Meier-method and Cox proportional hazard models were used to assess the effect of education on survival. A total of 4112 patients were included. In a multivariate logistic regression model, high education level was associated with greater probability of allocation to curative treatment (adjusted OR: 1.48, 95% CI: 1.08-2.03, p = 0,014) as was adherence to a multidisciplinary treatment-conference (adjusted OR: 3.13, 95% CI: 2.40-4.08, p < 0,001). High education level was associated with improved survival in the patients allocated to curative treatment (HR: 0.82, 95% CI: 0.69-0.99, p = 0,036). In this nation-wide cohort of esophageal- and junctional cancer patients, including data regarding many confounders, high education level was associated with greater probability of being offered curative treatment and improved survival. Copyright © 2017 Elsevier Ltd. All rights reserved.

Portal vein embolization improves rate of resection of extensive colorectal liver metastases without worsening survival outcomes

PubMed Central

Shindoh, Junichi; Tzeng, Ching-Wei D.; Aloia, Thomas A.; Curley, Steven A.; Zimmitti, Giuseppe; Wei, Steven H.; Huang, Steven Y.; Gupta, Sanjay; Wallace, Michael J.; Vauthey, Jean-Nicolas

2017-01-01

Background Most patients requiring an extended right hepatectomy (ERH) have an inadequate standardized future liver remnant (sFLR) and need preoperative portal vein embolization (PVE). However, the clinical and oncologic impact of PVE in such patients remains unclear. Methods All consecutive patients from MD Anderson Cancer Center with colorectal liver metastases (CLM) requiring ERH at presentation from 1995 through 2012. The surgical and oncologic outcomes were compared between patients with adequate and inadequate sFLRs at presentation. Results Of the 265 patients requiring ERH, 126 (47.5%) had an adequate sFLR at presentation, and 123 of them underwent curative resection. Of the 139 patients (52.5%) who had an inadequate sFLR and underwent PVE, 87 (62.6% PVE) underwent curative resection. Thus, PVE increased the curative resection rate from 123/265 (46.4%) at baseline to 210/265 (79.2%). Among patients who underwent ERH, rates of major complications and 90-day mortality were similar in the non-PVE and PVE groups (22.0% and 4.1% vs. 31% and 7%, respectively); overall survival (OS) and disease-free survival (DFS) were also similar in these 2 groups. Among patients with an inadequate sFLR at presentation, patients who underwent ERH had significantly better median OS (50.2 months) than patients who underwent noncurative surgery (21.3 months) or did not undergo surgery (24.7 months) (p=0.002). Conclusions PVE enables curative resection in two-thirds of patients with CLM who have an inadequate sFLR to tolerate ERH at presentation. Patients who undergo curative resection after PVE have OS and DFS equivalent to that of patients who never needed PVE. PMID:24227364

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.

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.

76 FR 38122 - Notice of Availability for Exclusive, Non-Exclusive, or Partially-Exclusive Licensing of an...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-29

... compounds have radical curative antimalarial activity. Brenda S. Bowen, Army Federal Register Liaison... Guanidylimidazoline Derivatives as Antimalarial Agents, Synthesis of and Methods of Use Thereof AGENCY: Department of... ``Guanidylimidazole and Guanidylimidazoline Derivatives as Antimalarial Agents, Synthesis of and Methods of Use...

Cost-effectiveness and clinical efficacy of biliary stents in patients undergoing neoadjuvant therapy for pancreatic adenocarcinoma in a randomized controlled trial.

PubMed

Gardner, Timothy B; Spangler, Chad C; Byanova, Katerina L; Ripple, Gregory H; Rockacy, Matthew J; Levenick, John M; Smith, Kerrington D; Colacchio, Thomas A; Barth, Richard J; Zaki, Bassem I; Tsapakos, Michael J; Gordon, Stuart R

2016-09-01

The optimal type of stent for the palliation of malignant biliary obstruction in patients with pancreatic adenocarcinoma undergoing neoadjuvant chemoradiotherapy with curative intent is unknown. We performed a prospective trial comparing 3 types of biliary stents-fully covered self-expandable metal (fcSEMS), uncovered self-expandable metal (uSEMS), and plastic-to determine which best optimized cost-effectiveness and important clinical outcomes. In this prospective randomized trial, consecutive patients with malignant biliary obstruction from newly diagnosed pancreatic adenocarcinoma who were to start neoadjuvant chemoradiotherapy were randomized to receive fcSEMSs, uSEMSs, or plastic stents during the index ERCP. The primary outcomes were time to stent occlusion, attempted surgical resection, or death after the initiation of neoadjuvant therapy, and the secondary outcomes were total patient costs associated with the stent, including the index ERCP cost, downstream hospitalization cost due to stent occlusion, and the cost associated with procedural adverse event. Fifty-four patients were randomized and reached the primary end point: 16 in the fcSEMS group, 17 in the uSEMS group, and 21 in the plastic stent group. No baseline demographic or tumor characteristic differences were noted among the groups. The fcSEMSs had a longer time to stent occlusion compared with uSEMSs and plastic stents (220 vs 74 and 76 days, P < .01), although the groups had equivalent rates of stent occlusion, attempted surgical resection, and death. Although SEMS placement cost more during the index ERCP (uSEMS = $24,874 and fcSEMS = $22,729 vs plastic = $18,701; P < .01), they resulted in higher procedural AE costs per patient (uSEMS = $5522 and fcSEMS = $12,701 vs plastic = $0; P < .01). Conversely, plastic stents resulted in an $11,458 hospitalization cost per patient due to stent occlusion compared with $2301 for uSEMSs and $0 for fcSEMSs (P < .01). In a prospective trial comparing fcSEMSs, uSEMSs, and plastic stents for malignant biliary obstruction in patients undergoing neoadjuvant therapy with curative intent for pancreatic adenocarcinoma, no stent type was superior in optimizing cost-effectiveness, although fcSEMSs resulted in fewer days of neoadjuvant treatment delay and a longer time to stent occlusion. (Clincial trial registration number: NCT01038713.). Copyright © 2016 American Society for Gastrointestinal Endoscopy. Published by Elsevier Inc. All rights reserved.

Diagnosis before treatment: Identifying dairy farmers' determinants for the adoption of sustainable practices in gastrointestinal nematode control.

PubMed

Vande Velde, F; Claerebout, E; Cauberghe, V; Hudders, L; Van Loo, H; Vercruysse, J; Charlier, J

2015-09-15

Anthelmintic resistance is emerging in dairy cattle and this can result in a lack of effective control and production losses. Therefore, sustainable control strategies, such as targeted treatments (TT) and targeted selected treatments (TST), should be adopted by the industry. TT and TST approaches require the use of diagnostic methods to take informed treatment decisions. To understand the factors affecting the farmers' intention to adopt diagnostic methods before implementing anthelmintic drugs ('adoption intention'), a cross-sectional survey was carried out in dairy farms in Belgium (Flanders). A framework was constructed to predict adoption intentions based on two fundamental theories in the field of behavioural psychology and health psychology: the Theory of Planned Behaviour and the Health Belief Model. In the tested model, adoption intentions were predicted based on attitudes towards anthelminthics, attitudes towards diagnostic methods, subjective norms, behavioural control and perceived risk. Structural equation modelling was used for analyses. The model fitted the data well and explained 46% of the variance in adoption intention of diagnostics. The factors 'attitude towards diagnostic methods' and 'subjective norm'; i.e. the influence of significant others, had the strongest, positive influence on adoption intention of diagnostic methods. 'Perceived behavioural control' had a weak, positive effect on intention. Further, 'attitude towards the use of anthelmintic drugs' had a negative effect on adoption intention of the diagnostic methods. This implicates an effect of current behaviour on future adoption, which should be considered in future research. Factors measuring risk perception of anthelmintic resistance; perceived severity and perceived susceptibility, had no effect on the adoption intention of diagnostic methods. The threat of anthelmintic resistance is perceived to be low for dairy herds. The study further did not find any differences in the effects of the predictors for young stock and adult dairy cows. The results of this study can be used to develop communication strategies to advertise sustainable nematode control on dairy farms. Copyright © 2015 Elsevier B.V. All rights reserved.

Success of salvage treatment: a critical appraisal of salvage rates for different subsites of HNSCC.

PubMed

Matoscevic, Katja; Graf, Nicole; Pezier, Thomas F; Huber, Gerhard F

2014-09-01

Despite advances in interdisciplinary treatment protocols, the chance of cure for recurrent head and neck squamous cell carcinoma (HNSCC) following failed primary therapy is poor and often entails a high morbidity. Recurrence rates vary widely in the literature depending on tumor localization, primary tumor stage, and treatment modality, and only a minority of patients can be salvaged. Historical cohort study. This study valuates the outcomes of patients treated for recurrent squamous cell carcinoma of the larynx, pharynx, and oral cavity in the largest tertiary referral center of Switzerland to find predictors for survival in salvage surgery with curative intent. Included were 176 consecutive patients with recurrent disease after primary curative treatment of HNSCC, in locations mentioned previously. Kaplan-Meier survival analyses with log-rank testing were performed depending on T and N stage, gender, treatment, and location of first relapse to evaluate the impact on overall survival, disease specific survival, and recurrence free survival. Overall successful salvage rates were 49.2% for laryngeal recurrence, 35.1% for oral cavity, 32.7% for oropharyngeal, and a mere 17.4% for hypopharyngeal recurrences. Predictive factors for better outcome were location of recurrence, female gender, lymph node status, and extent of salvage treatment. In case of recurrent disease, laryngeal cancers showed the best salvage rates, whereas in hypopharyngeal relapses, very few patients could be successfully salvaged. Patients therefore should be carefully selected and counseled for salvage treatment according to patient motivation, age, type of previous treatment, surgical resectability, and exclusion of distant recurrence. © American Academy of Otolaryngology—Head and Neck Surgery Foundation 2014.

Evaluation of prognostic factors on recurrence after curative resections for hepatocellular carcinoma.

PubMed

Han, Jae Hyun; Kim, Dong Goo; Na, Gun Hyung; Kim, Eun Young; Lee, Soo Ho; Hong, Tae Ho; You, Young Kyoung

2014-12-07

To select appropriate patients before surgical resection for hepatocellular carcinoma (HCC), especially those with advanced tumors. From January 2000 to December 2012, we retrospectively analyzed the medical records of 298 patients who had undergone surgical resections for HCC with curative intent at our hospital. We evaluated preoperative prognostic factors associated with histologic grade of tumor, recurrence and survival, especially the findings of pre-operative imaging studies such as positron emission tomography-computed tomography (PET-CT) and magnetic resonance imaging (MRI). And then, we established a scoring system to predict recurrence and survival after surgery dividing the patients into two groups based on a tumor size of 5 cm. Of the 298 patients, 129 (43.3%) developed recurrence during the follow-up period. The 5 year disease free survival and overall survival were 47.0% and 58.7% respectively. In multivariate analysis, a serum alpha-fetoprotein (AFP) level of > 100 ng/mL and a standardized uptake value (SUV) of PET-CT of > 3.5 were predictive factors for histologic grade of tumor, recurrence, and survival. Tumor size of > 5 cm and a relative enhancement ratio (RER) calculated from preoperative MRI were also significantly associated with prognosis in univariate analysis. We established a scoring system to predict prognosis using AFP, SUV, and RER. In those with tumors of > 5 cm, it showed predicted both recurrence (P = 0.005) and survival (P = 0.001). The AFP, tumor size, SUV and RER are useful for prognosis preoperatively. An accurate prediction of prognosis is possible using our scoring system in large size tumors.

Cholangiocarcinoma in Italy: A national survey on clinical characteristics, diagnostic modalities and treatment. Results from the "Cholangiocarcinoma" committee of the Italian Association for the Study of Liver disease.

PubMed

Alvaro, Domenico; Bragazzi, Maria Consiglia; Benedetti, Antonio; Fabris, Luca; Fava, Giammarco; Invernizzi, Pietro; Marzioni, Marco; Nuzzo, Gennaro; Strazzabosco, Mario; Stroffolini, Tommaso

2011-01-01

Very few studies assessed cholangiocarcinoma clinical characteristics. To evaluate the clinical characteristics of intra-hepatic (IH) and extra-hepatic (EH)-CCA. We performed a national survey based on a questionnaire. 218 cholangiocarcinomas were observed (47% EH-CCA, 53% IH-CCA) with an age at the diagnosis higher for EH-CCA. Coexistence of cirrhosis or viral cirrhosis was more frequent in IH-CCA than EH-CCA. An incidental asymptomatic presentation occurred in 28% of IH-CCA vs 4% EH-CCA whilst, 74% EH-CCA vs 28% IH-CCA presented with jaundice. 91% of IH-CCA presented as a single intra-hepatic mass, whilst 50% of EH-CCA was peri-hilar. In the diagnostic work-up, 70% of all cholangiocarcinoma cases received at least 3 different imaging procedures. Tissue-proven diagnosis was obtained in 80% cholangiocarcinoma. Open surgery with curative intent was performed in 45% of IH-CCA and 29% EH-CCA. 18% IH-CCA vs 4% EH-CCA did not received treatment. In Italy IH-CCA is managed as frequently as EH-CCA. In comparison to EH-CCA, IH-CCA occurs at younger age and is more frequently associated with cirrhosis and with an incidental asymptomatic presentation. In contrast, most EH-CCAs are jaundiced at the diagnosis. Cholangiocarcinoma diagnostic management is cost- and time-consuming with curative surgical treatment applicable more frequently in IH-CCA. Copyright © 2010 Editrice Gastroenterologica Italiana S.r.l. Published by Elsevier Ltd. All rights reserved.

Lesion guided stereotactic radiofrequency thermocoagulation for palliative, in selected cases curative epilepsy surgery.

PubMed

Wellmer, Jörg; Parpaley, Yaroslav; Rampp, Stefan; Popkirov, Stoyan; Kugel, Harald; Aydin, Ümit; Wolters, Carsten H; von Lehe, Marec; Voges, Jürgen

2016-03-01

Resective epilepsy surgery is an established treatment option in patients with pharmacoresistant, lesion related epilepsy. Yet, if the presurgical work-up proves multi-focal organization of the epileptogenic zone, or the area of intended resection is close to eloquent brain areas, patients may decide against resections because of an unfavorable risk-benefit-ratio. We assess if lesion guided cortical stereotactic radiofrequency thermocoagulation (L-RFTC) is a potential surgical alternative in these patients. We performed seven procedures of L-RFTC. Three patients had monofocal epilepsy arising close to eloquent structures; in four, invasive pre-surgical workup documented monofocal seizure onset but strong interictal epileptic activity also independent and distant from the seizure onset zone. L-RFTC was restricted to the lesional area (=seizure onset site). 12 to 37 months after RFTC worthwhile seizure improvement was achieved in 6 patients. One patient became seizure free following complete coagulation of a focal cortical dysplasia, two had had 1-2 auras under tapered but not under continued medication. In one patient only subclinical seizures persisted. In one patient hypermotor seizures were transformed into milder short tonic seizures and another one had a seizure reduction by 50%. Only one patient did not profit at all. One patient developed a persisting neurological deficit. In patients with complex epileptogenic zones L-RFTC can lead to worthwhile seizure reduction. This qualifies this procedure as a palliative surgical technique with potential good risk-benefit ratio. In patients with small focal cortical dysplasias L-RFTC may even allow minimal-invasive surgery with curative intention. Copyright © 2016 Elsevier B.V. All rights reserved.

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.

Definitive intensity-modulated radiotherapy concurrent with systemic therapy for oropharyngeal squamous cell carcinoma: Outcomes from an integrated regional Australian cancer centre.

PubMed

Masoud Rahbari, Reza; Winkley, Lauren; Hill, Jacques; Tahir, Abdul Rahim Mohammed; McKay, Michael; Last, Andrew; Shakespeare, Thomas P; Dwyer, Patrick

2016-06-01

Oropharyngeal squamous cell carcinoma (OPSCC) incidence has increased over the past two decades largely because of an increase in human papilloma virus (HPV)-related OPSCC. We report here outcomes of definitive radiation therapy for OPSCC with simultaneous integrated boost intensity-modulated radiotherapy (IMRT) in a regional Australian cancer centre. We retrospectively reviewed electronic medical records (EMR) of all patients treated with IMRT for head and neck cancer. We included patients who received a curative intent IMRT for OPSCC (2010-2014). Of 61 patients, 80% were men, and the median age was 57 years. Ninety percent of our patients received concurrent systemic therapy, and 68% were p16 positive. The median radiotherapy dose received was 70 Gy in 35 fractions. The median follow up for surviving patients was 22 months. Twenty-four month actuarial data show that the loco-regional recurrence free, metastasis-free MFS, cancer-specific (CaSS) and overall survival percentages were 98.3%, 92.6%, 91% and 90.3%, respectively. We did not observe grades 4 or 5 acute or late toxicities, and 10 patients (16.2%) exhibited persistent grade 3 toxicity 6 months after completing the treatment. The results from curative IMRTs for OPSCC delivered in a regional cancer centre are comparable with results published by tertiary referral centres. A long-term follow up of this patient cohort will continue for further analyses and comparisons with tertiary centres. © 2016 The Royal Australian and New Zealand College of Radiologists.

Genome-wide analysis of esophageal adenocarcinoma yields specific copy number aberrations that correlate with prognosis.

PubMed

Frankel, Adam; Armour, Nicola; Nancarrow, Derek; Krause, Lutz; Hayward, Nicholas; Lampe, Guy; Smithers, B Mark; Barbour, Andrew

2014-04-01

The incidence of esophageal adenocarcinoma (EAC) has been increasing rapidly for the past 3 decades in Western (Caucasian) populations. Curative treatment is based around esophagectomy, which has a major impact on quality of life. For those suitable for treatment with curative intent, 5-year survival is ∼30%. More accurate prognostic tools are therefore needed, and copy number aberrations (CNAs) may offer the ability to act as prospective biomarkers in this regard. We performed a genome-wide examination of CNAs in 54 samples of EAC using single-nucleotide polymorphism (SNP) arrays. Our aims were to describe frequent regions of CNA, to define driver CNAs, and to identify CNAs that correlated with survival. Regions of frequent amplification included oncogenes such as EGFR, MYC, KLF12, and ERBB2, while frequently deleted regions included tumor suppressor genes such as CDKN2A/B, PTPRD, FHIT, and SMAD4. The genomic identification of significant targets in cancer (GISTIC) algorithm identified 24 regions of gain and 28 regions of loss that were likely to contain driver changes. We discovered 61 genes in five regions that, when stratified by CNA type (gain or loss), correlated with a statistically significant difference in survival. Pathway analysis of the genes residing in both the GISTIC and prognostic regions showed they were significantly enriched for cancer-related networks. Finally, we discovered that copy-neutral loss of heterozygosity is a frequent mechanism of CNA in genes currently targetable by chemotherapy, potentially leading to under-reporting of cases suitable for such treatment. Copyright © 2014 Wiley Periodicals, Inc.

Neuroendocrine tumours of the ampulla of Vater: clinico-pathological features, surgical approach and assessment of prognosis.

PubMed

Dumitrascu, Traian; Dima, Simona; Herlea, Vlad; Tomulescu, Victor; Ionescu, Mihnea; Popescu, Irinel

2012-08-01

Neuroendocrine tumours occur very rarely in the ampulla of Vater and their clinical behaviour is unknown. The aim of this study is to assess the clinico-pathological features, surgical approach and prognosis of these patients. Six patients with neuroendocrine tumours of the ampulla of Vater treated with curative intent surgery at a single centre were retrospectively analysed. A univariate analysis of potential prognostic factors was also performed (data provided from the present study and literature review). Pancreaticoduodenectomy was curative in all the patients. Overall and disease-free survival rates were significantly better for G1/G2 tumours (p = 0.006 and p = 0.004, respectively). Although frequent, lymph node metastases did not influenced both overall (p = 0.760) and disease-free survival rates (p = 0.745). No significant differences of survival were observed in patients with ENETS stage I/II disease, as compared to ENETS stage III disease (p = 0.169 and p = 0.137, respectively). No differences were observed according to UICC staging system (p = 0.073 and p = 0.177, respectively). Tumours that are less than 2 cm or limited to the ampulla appear to have a better prognosis. The WHO 2010 classification appear to accurately predict patient prognosis, while the ENETS or UICC staging systems have a limited value (especially in regard to lymph node metastases). Radical surgery (i.e. pancreaticoduodenectomy with lymphadenectomy) should be the standard approach in most patients with NET of the ampulla of Vater because this procedure removes all the potential tumour-bearing tissue.

Managing Data and Facilitating Science: A spectrum of activities in the Centre for Environmental Data Archival. (Invited)

NASA Astrophysics Data System (ADS)

Lawrence, B.; Bennett, V.; Callaghan, S.; Juckes, M. N.; Pepler, S.

2013-12-01

The UK Centre for Environmental Data Archival (CEDA) hosts a number of formal data centres, including the British Atmospheric Data Centre (BADC), and is a partner in a range of national and international data federations, including the InfraStructure for the European Network for Earth system Simulation, the Earth System Grid Federation, and the distributed IPCC Data Distribution Centres. The mission of CEDA is to formally curate data from, and facilitate the doing of, environmental science. The twin aims are symbiotic: data curation helps facilitate science, and facilitating science helps with data curation. Here we cover how CEDA delivers this strategy by established internal processes supplemented by short-term projects, supported by staff with a range of roles. We show how CEDA adds value to data in the curated archive, and how it supports science, and show examples of the aforementioned symbiosis. We begin by discussing curation: CEDA has the formal responsibility for curating the data products of atmospheric science and earth observation research funded by the UK Natural Environment Research Council (NERC). However, curation is not just about the provider community, the consumer communities matter too, and the consumers of these data cross the boundaries of science, including engineers, medics, as well as the gamut of the environmental sciences. There is a small, and growing cohort of non-science users. For both producers and consumers of data, information about data is crucial, and a range of CEDA staff have long worked on tools and techniques for creating, managing, and delivering metadata (as well as data). CEDA "science support" staff work with scientists to help them prepare and document data for curation. As one of a spectrum of activities, CEDA has worked on data Publication as a method of both adding value to some data, and rewarding the effort put into the production of quality datasets. As such, we see this activity as both a curation and a facilitation activity. A range of more focused facilitation activities are carried out, from providing a computing platform suitable for big-data analytics (the Joint Analysis System, JASMIN), to working on distributed data analysis (EXARCH), and the acquisition of third party data to support science and impact (e.g. in the context of the facility for Climate and Environmental Monitoring from Space, CEMS). We conclude by confronting the view of Parsons and Fox (2013) that metaphors such as Data Publication, Big Iron, Science Support etc are limiting, and suggest the CEDA experience is that these sorts of activities can and do co-exist, much as they conclude they should. However, we also believe that within co-existing metaphors, production systems need to be limited in their scope, even if they are on a road to a more joined up infrastructure. We shouldn't confuse what we can do now with what we might want to do in the future.

Changing the Curation Equation: A Data Lifecycle Approach to Lowering Costs and Increasing Value

NASA Astrophysics Data System (ADS)

Myers, J.; Hedstrom, M.; Plale, B. A.; Kumar, P.; McDonald, R.; Kooper, R.; Marini, L.; Kouper, I.; Chandrasekar, K.

2013-12-01

What if everything that researchers know about their data, and everything their applications know, were directly available to curators? What if all the information that data consumers discover and infer about data were also available? What if curation and preservation activities occurred incrementally, during research projects instead of after they end, and could be leveraged to make it easier to manage research data from the moment of its creation? These are questions that the Sustainable Environments - Actionable Data (SEAD) project, funded as part of the National Science Foundation's DataNet partnership, was designed to answer. Data curation is challenging, but it is made more difficult by the historical separation of data production, data use, and formal curation activities across organizations, locations, and applications, and across time. Modern computing and networking technologies allow a much different approach in which data and metadata can easily flow between these activities throughout the data lifecycle, and in which heterogeneous and evolving data and metadata can be managed. Sustainability research, SEAD's initial focus area, is a clear example of an area where the nature of the research (cross-disciplinary, integrating heterogeneous data from independent sources, small teams, rapid evolution of sensing and analysis techniques) and the barriers and costs inherent in traditional methods have limited adoption of existing curation tools and techniques, to the detriment of overall scientific progress. To explore these ideas and create a sustainable curation capability for communities such as sustainability research, the SEAD team has developed and is now deploying an interacting set of open source data services that demonstrate this approach. These services provide end-to-end support for management of data during research projects; publication of that data into long-term archives; and integration of it into community networks of publications, research center activities, and synthesis efforts. They build on a flexible ';semantic content management' architecture and incorporate notions of ';active' and ';social' curation - continuous, incremental curation activities performed by the data producers (active) and the community (social) that are motivated by a range of direct benefits. Examples include the use of metadata (tags) to allow generation of custom geospatial maps, automated metadata extraction to generate rich data pages for known formats, and the use of information about data authorship to allow automatic updates of personal and project research profiles when data is published. In this presentation, we describe the core capabilities of SEAD's services and their application in sustainability research. We also outline the key features of the SEAD architecture - the use of global semantic identifiers, extensible data and metadata models, web services to manage context shifts, scalable cloud storage - and highlight how this approach is particularly well suited to extension by independent third parties. We conclude with thoughts on how this approach can be applied to challenging issues such as exposing ';dark' data and reducing duplicate creation of derived data products, and can provide a new level of analytics for community analysis and coordination.

Study protocol of the TIRED study: a randomised controlled trial comparing either graded exercise therapy for severe fatigue or cognitive behaviour therapy with usual care in patients with incurable cancer.

PubMed

Poort, Hanneke; Verhagen, Constans A H H V M; Peters, Marlies E W J; Goedendorp, Martine M; Donders, A Rogier T; Hopman, Maria T E; Nijhuis-van der Sanden, Maria W G; Berends, Thea; Bleijenberg, Gijs; Knoop, Hans

2017-01-28

Fatigue is a common and debilitating symptom for patients with incurable cancer receiving systemic treatment with palliative intent. There is evidence that non-pharmacological interventions such as graded exercise therapy (GET) or cognitive behaviour therapy (CBT) reduce cancer-related fatigue in disease-free cancer patients and in patients receiving treatment with curative intent. These interventions may also result in a reduction of fatigue in patients receiving treatment with palliative intent, by improving physical fitness (GET) or changing fatigue-related cognitions and behaviour (CBT). The primary aim of our study is to assess the efficacy of GET or CBT compared to usual care (UC) in reducing fatigue in patients with incurable cancer. The TIRED study is a multicentre three-armed randomised controlled trial (RCT) for incurable cancer patients receiving systemic treatment with palliative intent. Participants will be randomised to GET, CBT, or UC. In addition to UC, the GET group will participate in a 12-week supervised exercise programme. The CBT group will receive a 12-week CBT intervention in addition to UC. Primary and secondary outcome measures will be assessed at baseline, post-intervention (14 weeks), and at follow-up assessments (18 and 26 weeks post-randomisation). The primary outcome measure is fatigue severity (Checklist Individual Strength subscale fatigue severity). Secondary outcome measures are fatigue (EORTC-QLQ-C30 subscale fatigue), functional impairments (Sickness Impact Profile total score, EORTC-QLQ-C30 subscale emotional functioning, subscale physical functioning) and quality of life (EORTC-QLQ-C30 subscale QoL). Outcomes at 14 weeks (primary endpoint) of either treatment arm will be compared to those of UC participants. In addition, outcomes at 18 and 26 weeks (follow-up assessments) of either treatment arm will be compared to those of UC participants. To our knowledge, the TIRED study is the first RCT investigating the efficacy of GET and CBT on reducing fatigue during treatment with palliative intent in incurable cancer patients. The results of this study will provide information about the possibility and efficacy of GET and CBT for severely fatigued incurable cancer patients. NTR3812 ; date of registration: 23/01/2013.

Diagnostic laparoscopy should be performed before definitive resection for pancreatic cancer: a financial argument

PubMed Central

Jayakrishnan, Thejus T; Nadeem, Hasan; Groeschl, Ryan T; George, Ben; Thomas, James P; Ritch, Paul S; Christians, Kathleen K; Tsai, Susan; Evans, Douglas B; Pappas, Sam G; Gamblin, T Clark; Turaga, Kiran K

2015-01-01

Objectives Laparoscopy is recommended to detect radiographically occult metastases in patients with pancreatic cancer before curative resection. This study was conducted to test the hypothesis that diagnostic laparoscopy (DL) is cost-effective in patients undergoing curative resection with or without neoadjuvant therapy (NAT). Methods Decision tree modelling compared routine DL with exploratory laparotomy (ExLap) at the time of curative resection in resectable cancer treated with surgery first, (SF) and borderline resectable cancer treated with NAT. Costs (US$) from the payer's perspective, quality-adjusted life months (QALMs) and incremental cost-effectiveness ratios (ICERs) were calculated. Base case estimates and multi-way sensitivity analyses were performed. Willingness to pay (WtP) was US$4166/QALM (or US$50 000/quality-adjusted life year). Results Base case costs were US$34 921 for ExLap and US$33 442 for DL in SF patients, and US$39 633 for ExLap and US$39 713 for DL in NAT patients. Routine DL is the dominant (preferred) strategy in both treatment types: it allows for cost reductions of US$10 695/QALM in SF and US$4158/QALM in NAT patients. Conclusions The present analysis supports the cost-effectiveness of routine DL before curative resection in pancreatic cancer patients treated with either SF or NAT. PMID:25123702

Intentions to use contraceptives in Pakistan: implications for behavior change campaigns

PubMed Central

2010-01-01

Background Since 1990-91, traditional method use has increased at a faster rate in Pakistan than modern method use. The importance of hormonal methods or the IUD has diminished and that of traditional methods has increased in the method mix. There is a need to identify factors motivating and deterring the adoption of specific family planning methods among married men and women in Pakistan. Methods In addition to social and demographic characteristics of respondents, a representative household survey collected information on psychological correlates of family planning behavior from 1,788 non-pregnant wives and 1,805 husbands with not-pregnant wives. Males and females were from separate households. Principal components analysis was conducted to identify the underlying constructs that were important for each gender. Multinomial logistic regression analysis was conducted to determine the correlates of male and female intentions to use contraceptive methods. Results Amongst women, the perception that her in-laws support family planning use was the strongest determinant of her intentions to use contraceptive methods. A woman's belief in the importance of spacing children and her perception that a choice of methods and facilities with competent staff were available were also powerful drivers of her intentions to use contraceptive methods. The strongest obstacle to a woman's forming an intention to use contraceptive methods was her belief that family planning decisions were made by the husband and fertility was determined by God's will. Fears that family planning would harm a woman's womb lowered a woman's intentions to use methods requiring procedures, such as the IUD and female sterilization. The perception that a responsible, caring, husband uses family planning to improve the standard of living of his family and to protect his wife's health was the most important determinant of a man's intention to use condoms. A husband's lack of self-efficacy in being able to discuss family planning with his wife was the strongest driver of the intention to use withdrawal. A man's fear that contraceptives would make a woman sterile and harm her womb lowered his intention to use modern contraceptive methods. Conclusions These findings highlight the importance of having secondary target audiences such as mothers-in-law and husbands in family planning behavior change campaigns implemented in Pakistan. Campaigns that stress the importance of child spacing are likely to have an impact. Client perceptions of the quality of care are important determinants of intentions to use contraceptive methods in Pakistan. Client concerns that the IUD and sterilization procedures might harm a woman's womb and cause sterility should be addressed. The findings suggest that there is a need to assess the actual quality of service delivery in Pakistan. PMID:20673374

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.

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.

Chronological changes in lung cancer surgery in a single Japanese institution

PubMed Central

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

2017-01-01

Background The aim of this study was to evaluate the chronological changes in epidemiological factors and surgical outcomes in patients with lung cancer who underwent surgery in a single Japanese institution. Patients and methods A clinicopathological database of patients with lung cancer who underwent surgery with curative intent from January 1974 to December 2014 was reviewed. The chronological changes in various factors, including patient’s age, sex, histological type, tumor size, pathological stage (p-stage), surgical method, operative time, intraoperative blood loss, 30-day mortality, and postoperative overall survival (OS), were evaluated. Results A total of 1,616 patients were included. The numbers of resected patients, females, adenocarcinomas, p-stage IA patients, and age at the time of surgery increased with time, but tumor size decreased (all P<0.0001). Concerning surgical methods, the number of sublobar resections increased, but that of pneumonectomies decreased (P<0.0001). The mean operative time, intraoperative blood loss, and the postoperative 30-day mortality rate decreased (all P<0.0001). When the patients were divided into two groups (1974–2004 and 2005–2014), the 5-year OS rates for all patients and for p-stage IA patients improved from 44% to 79% and from 73% to 89%, respectively (all P<0.0001). The best 5-year OS rate was obtained for sublobar resection (73%), followed by lobectomy (60%), combined resection (22%), and pneumonectomy (21%; P<0.0001). Conclusion Changes in epidemiological factors, a trend toward less invasive surgery, and a remarkably improved postoperative OS were confirmed, which demonstrated the increasingly important role of surgery in therapeutic strategies for lung cancer. PMID:28331339

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

Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature.

PubMed

Dahdul, Wasila M; Balhoff, James P; Engeman, Jeffrey; Grande, Terry; Hilton, Eric J; Kothari, Cartik; Lapp, Hilmar; Lundberg, John G; Midford, Peter E; Vision, Todd J; Westerfield, Monte; Mabee, Paula M

2010-05-20

The wealth of phenotypic descriptions documented in the published articles, monographs, and dissertations of phylogenetic systematics is traditionally reported in a free-text format, and it is therefore largely inaccessible for linkage to biological databases for genetics, development, and phenotypes, and difficult to manage for large-scale integrative work. The Phenoscape project aims to represent these complex and detailed descriptions with rich and formal semantics that are amenable to computation and integration with phenotype data from other fields of biology. This entails reconceptualizing the traditional free-text characters into the computable Entity-Quality (EQ) formalism using ontologies. We used ontologies and the EQ formalism to curate a collection of 47 phylogenetic studies on ostariophysan fishes (including catfishes, characins, minnows, knifefishes) and their relatives with the goal of integrating these complex phenotype descriptions with information from an existing model organism database (zebrafish, http://zfin.org). We developed a curation workflow for the collection of character, taxonomic and specimen data from these publications. A total of 4,617 phenotypic characters (10,512 states) for 3,449 taxa, primarily species, were curated into EQ formalism (for a total of 12,861 EQ statements) using anatomical and taxonomic terms from teleost-specific ontologies (Teleost Anatomy Ontology and Teleost Taxonomy Ontology) in combination with terms from a quality ontology (Phenotype and Trait Ontology). Standards and guidelines for consistently and accurately representing phenotypes were developed in response to the challenges that were evident from two annotation experiments and from feedback from curators. The challenges we encountered and many of the curation standards and methods for improving consistency that we developed are generally applicable to any effort to represent phenotypes using ontologies. This is because an ontological representation of the detailed variations in phenotype, whether between mutant or wildtype, among individual humans, or across the diversity of species, requires a process by which a precise combination of terms from domain ontologies are selected and organized according to logical relations. The efficiencies that we have developed in this process will be useful for any attempt to annotate complex phenotypic descriptions using ontologies. We also discuss some ramifications of EQ representation for the domain of systematics.

Descriptive Analysis of Oligometastatic Lesions Treated With Curative-Intent Stereotactic Body Radiotherapy

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

Milano, Michael T.; Katz, Alan W.; Schell, Michael C.

Purpose: To characterize oligometastases in patients enrolled on two prospective pilot studies, treating oligometastases with hypofractionated stereotactic body radiotherapy and stereotactic radiosurgery to cranial lesions. Methods and Materials: We describe the characteristics and local control (LC) of 293 lesions in 121 patients with five or fewer metastases treated with stereotactic body radiation and/or cranial stereotactic radiosurgery. For each lesion, the primary cancer site, tumor histology, site of metastasis, gross tumor volume, and prescribed dose were ascertained. The prescribed dose is expressed by the biologically effective dose in 2-Gy fractions (BED2), calculated using the linear quadratic model, assuming an {alpha}/{beta} ratiomore » of 10. Results: Lung lesions were significantly smaller than other lesions in our cohort, whereas liver lesions were significantly larger, possibly reflecting a detection and/or referral bias. The 2-year and 4-year tumor LC rates were 77% and 73% respectively. A larger gross tumor volume was significantly (p < 0.0001) correlated with worse lesion LC. Lesions originating from primary pancreatic, biliary or liver cancer exhibited significantly poorer LC, as did lesions from colorectal cancer. Lesions from breast cancer were better controlled. A higher BED2 did not correlate with improved tumor control. Conclusions: Stereotactic body radiation to aggressively treat oligometastatic lesions results in good local tumor control. Bulkier lesions are more difficult to control and may benefit from dose escalation.« less

CDK4 Amplification Predicts Recurrence of Well-Differentiated Liposarcoma of the Abdomen

PubMed Central

Ha, Sang Yun; Paik, Kwang Yeol; Lee, Seung Eun; Kim, Jong Man; Park, Jae Berm; Kwon, Choon Hyuck David; Joh, Jae-Won; Choi, Yoon-La; Kim, Sung Joo

2014-01-01

Background The absence of CDK4 amplification in liposarcomas is associated with favorable prognosis. We aimed to identify the factors associated with tumor recurrence in patients with well-differentiated (WD) and dedifferentiated (DD) liposarcomas. Methods From 2000 to 2010, surgical resections for 101 WD and DD liposarcomas were performed. Cases in which complete surgical resections with curative intent were carried out were selected. MDM2 and CDK4 gene amplification were analyzed by quantitative real-time polymerase chain reaction (Q-PCR). Results There were 31 WD and 17 DD liposarcomas. Locoregional recurrence was observed in 11 WD and 3 DD liposarcomas. WD liposarcomas showed better patient survival compared to DD liposarcomas (P<0.05). Q-PCR analysis of the liposarcomas revealed the presence of CDK4 amplification in 44 cases (91.7%) and MDM2 amplification in 46 cases (95.8%). WD liposarcomas with recurrence after surgical resection had significantly higher levels of CDK4 amplification compared to those without recurrence (P = 0.041). High level of CDK4 amplification (cases with CDK4 amplification higher than the median 7.54) was associated with poor recurrence-free survival compared to low CDK4 amplification in both univariate (P = 0.012) and multivariate analyses (P = 0.020). Conclusions Level of CDK4 amplification determined by Q-PCR was associated with the recurrence of WD liposarcomas after surgical resection. PMID:25121597

Prognostic significance of Fas and Fas ligand system-associated apoptosis in gastric cancer.

PubMed

Ohno, S; Tachibana, M; Shibakita, M; Dhar, D K; Yoshimura, H; Kinugasa, S; Kubota, H; Masunaga, R; Nagasue, N

2000-12-01

Previous studies indicate that gastric carcinomas express Fas ligand and down-regulate Fas to escape from the host immune attack; however, the prognostic importance of Fas/FasL expression in this tumor is yet to be evaluated. Specimens from 87 gastric carcinoma patients of different stages treated in a defined period with curative intent were evaluated for apoptosis, Fas, FasL, and CD8 expression using an immunohistochemical method. The percentage of terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL)-positive apoptotic cells expressed as apoptotic index (AI) was higher in 43 patients when the cut-off value was set at the median value. There were no significant correlations between AI and clinicopathologic parameters. Thirty-nine patients showed a high number of CD8+ cells within cancer nests. Positive FasL and Fas expression was seen in 53 and 72 patients, respectively. CD8 and FasL expressions were related only to patients' age. Fas expression had significant correlations with tumor invasion and Lauren classification. There were significant direct correlations between AI and number of nest CD8+ cells and between AI and grade of Fas expression. Apoptotic index, pT stage, CD8 expression, and Fas expression were identified as independent prognostic factors. Spontaneous apoptosis in gastric carcinoma may be an independent prognosticator for survival and is significantly influenced by tumor Fas expression and number of nest CD8 + cells.

76 FR 38122 - Notice of Availability for Exclusive, Non-Exclusive, or Partially-Exclusive Licensing of an...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-29

... curative antimalarial activity. Brenda S. Bowen, Army Federal Register Liaison Officer. [FR Doc. 2011-16258... Derivatives as Antimalarial Agents, Synthesis of and Methods of Use Thereof AGENCY: Department of the Army, Do...-Imidazoline Derivatives as Antimalarial Agents, Synthesis and Methods of Use Thereof,'' filed on April 26...

[Cost variation in care groups?

PubMed

Mohnen, S M; Molema, C C M; Steenbeek, W; van den Berg, M J; de Bruin, S R; Baan, C A; Struijs, J N

2017-01-01

Is the simple mean of the costs per diabetes patient a suitable tool with which to compare care groups? Do the total costs of care per diabetes patient really give the best insight into care group performance? Cross-sectional, multi-level study. The 2009 insurance claims of 104,544 diabetes patients managed by care groups in the Netherlands were analysed. The data were obtained from Vektis care information centre. For each care group we determined the mean costs per patient of all the curative care and diabetes-specific hospital care using the simple mean method, then repeated it using the 'generalized linear mixed model'. We also calculated for which proportion the differences found could be attributed to the care groups themselves. The mean costs of the total curative care per patient were €3,092 - €6,546; there were no significant differences between care groups. The mixed model method resulted in less variation (€2,884 - €3,511), and there were a few significant differences. We found a similar result for diabetes-specific hospital care and the ranking position of the care groups proved to be dependent on the method used. The care group effect was limited, although it was greater in the diabetes-specific hospital costs than in the total costs of curative care (6.7% vs. 0.4%). The method used to benchmark care groups carries considerable weight. Simply stated, determining the mean costs of care (still often done) leads to an overestimation of the differences between care groups. The generalized linear mixed model is more accurate and yields better comparisons. However, the fact remains that 'total costs of care' is a faulty indicator since care groups have little impact on them. A more informative indicator is 'costs of diabetes-specific hospital care' as these costs are more influenced by care groups.

Benchmark analysis of native and artificial NAD+-dependent enzymes generated by a sequence based design method with or without phylogenetic data.

PubMed

Nakano, Shogo; Motoyama, Tomoharu; Miyashita, Yurina; Ishizuka, Yuki; Matsuo, Naoya; Tokiwa, Hiroaki; Shinoda, Suguru; Asano, Yasuhisa; Ito, Sohei

2018-05-22

The expansion of protein sequence databases has enabled us to design artificial proteins by sequence-based design methods, such as full consensus design (FCD) and ancestral sequence reconstruction (ASR). Artificial proteins with enhanced activity levels compared with native ones can potentially be generated by such methods, but successful design is rare because preparing a sequence library by curating the database and selecting a method is difficult. Utilizing a curated library prepared by reducing conservation energies, we successfully designed two artificial L-threonine 3-dehydrogenase (SDR-TDH) with higher activity levels than native SDR-TDH, FcTDH-N1 and AncTDH, using FCD and ASR, respectively. The artificial SDR-TDHs had excellent thermal stability and NAD+ recognition compared to native SDR-TDH from Cupriavidus necator (CnTDH): the melting temperatures of FcTDH-N1 and AncTDH were about 10 and 5°C higher than CnTDH, respectively, and the dissociation constants toward NAD+ of FcTDH-N1 and AncTDH were two- and seven-fold lower than that of CnTDH, respectively. Enzymatic efficiency of the artificial SDR-TDHs were comparable to that of CnTDH. Crystal structures of FcTDH-N1 and AncTDH were determined at 2.8 and 2.1 Å resolution, respectively. Structural and MD simulation analysis of the SDR-TDHs indicated that only the flexibility at specific regions was changed, suggesting that multiple mutations introduced in the artificial SDR-TDHs altered their flexibility and thereby affected their enzymatic properties. Benchmark analysis of the SDR-TDHs indicated that both FCD and ASR can generate highly functional proteins if a curated library is prepared appropriately.

Twenty-year follow-up study of long-term survival of limited-stage small-cell lung cancer and overview of prognostic and treatment factors.

PubMed

Tai, Patricia; Tonita, Jon; Yu, Edward; Skarsgard, David

2003-07-01

To predict the long-term survival results of clinical trials earlier than using actuarial methods and to assess the factors predictive of long-term cure in patients with limited-stage small-cell lung cancer. Between 1981 and 1998, 1417 new cases of small-cell lung cancer were diagnosed in Saskatchewan, Canada, of which 244 were limited stage and treated with curative intent. They were followed to the end of February 2002. A parametric lognormal statistical model was retrospectively validated to determine whether long-term survival rates could be estimated several years earlier than is possible using the standard life-table actuarial method. The survival time of the uncured group followed a lognormal distribution. Four 2-year periods of diagnosis were combined, and patients were followed as a cohort for an additional 2 years. The estimated 10-year cause-specific survival rate was 13% by the lognormal model. The Kaplan-Meier calculation for 10-year cause-specific survival rate was 15% +/- 3%. The data also showed that the absence of mediastinal lymphadenopathy and higher chest radiotherapy dose were significant prognostic factors on multivariate analysis (p < 0.05). Among the 163 patients given prophylactic cranial irradiation, a higher biologically effective dose to the brain did not improve survival or decrease the incidence of brain metastases. The lognormal model has been validated for the estimation of survival in patients with limited-stage small-cell lung cancer. A higher biologically effective dose to the brain did not improve survival or decrease the incidence of brain metastases.

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

Mass Spectral Library Quality Assurance by Inter-Library Comparison

NASA Astrophysics Data System (ADS)

Wallace, William E.; Ji, Weihua; Tchekhovskoi, Dmitrii V.; Phinney, Karen W.; Stein, Stephen E.

2017-04-01

A method to discover and correct errors in mass spectral libraries is described. Comparing across a set of highly curated reference libraries compounds that have the same chemical structure quickly identifies entries that are outliers. In cases where three or more entries for the same compound are compared, the outlier as determined by visual inspection was almost always found to contain the error. These errors were either in the spectrum itself or in the chemical descriptors that accompanied it. The method is demonstrated on finding errors in compounds of forensic interest in the NIST/EPA/NIH Mass Spectral Library. The target list of compounds checked was the Scientific Working Group for the Analysis of Seized Drugs (SWGDRUG) mass spectral library. Some examples of errors found are described. A checklist of errors that curators should look for when performing inter-library comparisons is provided.

Mass Spectral Library Quality Assurance by Inter-Library Comparison

PubMed Central

Wallace, W.E.; Ji, W.; Tchekhovskoi, D.V.; Phinney, K.W.; Stein, S.E.

2017-01-01

A method to discover and correct errors in mass spectral libraries is described. Comparing across a set of highly curated reference libraries compounds that have the same chemical structure quickly identifies entries that are outliers. In cases where three or more entries for the same compound are compared the outlier as determined by visual inspection was almost always found to contain the error. These errors were either in the spectrum itself or in the chemical descriptors that accompanied it. The method is demonstrated on finding errors in compounds of forensic interest in the NIST/EPA/NIH Mass Spectral Library. The target list of compounds checked was the Scientific Working Group for the Analysis of Seized Drugs (SWGDRUG) mass spectral library. Some examples of errors found are described. A checklist of errors that curators should look for when performing inter-library comparisons is provided. PMID:28127680

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

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.

Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments.

PubMed

Van Valen, David A; Kudo, Takamasa; Lane, Keara M; Macklin, Derek N; Quach, Nicolas T; DeFelice, Mialy M; Maayan, Inbal; Tanouchi, Yu; Ashley, Euan A; Covert, Markus W

2016-11-01

Live-cell imaging has opened an exciting window into the role cellular heterogeneity plays in dynamic, living systems. A major critical challenge for this class of experiments is the problem of image segmentation, or determining which parts of a microscope image correspond to which individual cells. Current approaches require many hours of manual curation and depend on approaches that are difficult to share between labs. They are also unable to robustly segment the cytoplasms of mammalian cells. Here, we show that deep convolutional neural networks, a supervised machine learning method, can solve this challenge for multiple cell types across the domains of life. We demonstrate that this approach can robustly segment fluorescent images of cell nuclei as well as phase images of the cytoplasms of individual bacterial and mammalian cells from phase contrast images without the need for a fluorescent cytoplasmic marker. These networks also enable the simultaneous segmentation and identification of different mammalian cell types grown in co-culture. A quantitative comparison with prior methods demonstrates that convolutional neural networks have improved accuracy and lead to a significant reduction in curation time. We relay our experience in designing and optimizing deep convolutional neural networks for this task and outline several design rules that we found led to robust performance. We conclude that deep convolutional neural networks are an accurate method that require less curation time, are generalizable to a multiplicity of cell types, from bacteria to mammalian cells, and expand live-cell imaging capabilities to include multi-cell type systems.

Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013

PubMed Central

2015-01-01

Background Since their introduction in 2009, the BioNLP Shared Task events have been instrumental in advancing the development of methods and resources for the automatic extraction of information from the biomedical literature. In this paper, we present the Cancer Genetics (CG) and Pathway Curation (PC) tasks, two event extraction tasks introduced in the BioNLP Shared Task 2013. The CG task focuses on cancer, emphasizing the extraction of physiological and pathological processes at various levels of biological organization, and the PC task targets reactions relevant to the development of biomolecular pathway models, defining its extraction targets on the basis of established pathway representations and ontologies. Results Six groups participated in the CG task and two groups in the PC task, together applying a wide range of extraction approaches including both established state-of-the-art systems and newly introduced extraction methods. The best-performing systems achieved F-scores of 55% on the CG task and 53% on the PC task, demonstrating a level of performance comparable to the best results achieved in similar previously proposed tasks. Conclusions The results indicate that existing event extraction technology can generalize to meet the novel challenges represented by the CG and PC task settings, suggesting that extraction methods are capable of supporting the construction of knowledge bases on the molecular mechanisms of cancer and the curation of biomolecular pathway models. The CG and PC tasks continue as open challenges for all interested parties, with data, tools and resources available from the shared task homepage. PMID:26202570

Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments

DOE PAGES

Van Valen, David A.; Kudo, Takamasa; Lane, Keara M.; ...

2016-11-04

Live-cell imaging has opened an exciting window into the role cellular heterogeneity plays in dynamic, living systems. A major critical challenge for this class of experiments is the problem of image segmentation, or determining which parts of a microscope image correspond to which individual cells. Current approaches require many hours of manual curation and depend on approaches that are difficult to share between labs. They are also unable to robustly segment the cytoplasms of mammalian cells. Here, we show that deep convolutional neural networks, a supervised machine learning method, can solve this challenge for multiple cell types across the domainsmore » of life. We demonstrate that this approach can robustly segment fluorescent images of cell nuclei as well as phase images of the cytoplasms of individual bacterial and mammalian cells from phase contrast images without the need for a fluorescent cytoplasmic marker. These networks also enable the simultaneous segmentation and identification of different mammalian cell types grown in co-culture. A quantitative comparison with prior methods demonstrates that convolutional neural networks have improved accuracy and lead to a significant reduction in curation time. We relay our experience in designing and optimizing deep convolutional neural networks for this task and outline several design rules that we found led to robust performance. We conclude that deep convolutional neural networks are an accurate method that require less curation time, are generalizable to a multiplicity of cell types, from bacteria to mammalian cells, and expand live-cell imaging capabilities to include multi-cell type systems.« less

Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments

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

Van Valen, David A.; Kudo, Takamasa; Lane, Keara M.

Live-cell imaging has opened an exciting window into the role cellular heterogeneity plays in dynamic, living systems. A major critical challenge for this class of experiments is the problem of image segmentation, or determining which parts of a microscope image correspond to which individual cells. Current approaches require many hours of manual curation and depend on approaches that are difficult to share between labs. They are also unable to robustly segment the cytoplasms of mammalian cells. Here, we show that deep convolutional neural networks, a supervised machine learning method, can solve this challenge for multiple cell types across the domainsmore » of life. We demonstrate that this approach can robustly segment fluorescent images of cell nuclei as well as phase images of the cytoplasms of individual bacterial and mammalian cells from phase contrast images without the need for a fluorescent cytoplasmic marker. These networks also enable the simultaneous segmentation and identification of different mammalian cell types grown in co-culture. A quantitative comparison with prior methods demonstrates that convolutional neural networks have improved accuracy and lead to a significant reduction in curation time. We relay our experience in designing and optimizing deep convolutional neural networks for this task and outline several design rules that we found led to robust performance. We conclude that deep convolutional neural networks are an accurate method that require less curation time, are generalizable to a multiplicity of cell types, from bacteria to mammalian cells, and expand live-cell imaging capabilities to include multi-cell type systems.« less

Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments

PubMed Central

Van Valen, David A.; Lane, Keara M.; Quach, Nicolas T.; Maayan, Inbal

2016-01-01

Live-cell imaging has opened an exciting window into the role cellular heterogeneity plays in dynamic, living systems. A major critical challenge for this class of experiments is the problem of image segmentation, or determining which parts of a microscope image correspond to which individual cells. Current approaches require many hours of manual curation and depend on approaches that are difficult to share between labs. They are also unable to robustly segment the cytoplasms of mammalian cells. Here, we show that deep convolutional neural networks, a supervised machine learning method, can solve this challenge for multiple cell types across the domains of life. We demonstrate that this approach can robustly segment fluorescent images of cell nuclei as well as phase images of the cytoplasms of individual bacterial and mammalian cells from phase contrast images without the need for a fluorescent cytoplasmic marker. These networks also enable the simultaneous segmentation and identification of different mammalian cell types grown in co-culture. A quantitative comparison with prior methods demonstrates that convolutional neural networks have improved accuracy and lead to a significant reduction in curation time. We relay our experience in designing and optimizing deep convolutional neural networks for this task and outline several design rules that we found led to robust performance. We conclude that deep convolutional neural networks are an accurate method that require less curation time, are generalizable to a multiplicity of cell types, from bacteria to mammalian cells, and expand live-cell imaging capabilities to include multi-cell type systems. PMID:27814364

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.

Intentional Forgetting, Anxiety, and EFL Listening Comprehension among Chinese College Students

ERIC Educational Resources Information Center

Yang, Xiaohu

2010-01-01

Intentional forgetting refers to impaired memory arising from an instruction to forget unwanted material. Intentional forgetting yielded with a list-method task is often interpreted as evidence for retrieval inhibition. This paper presents a study on the relationships among intentional forgetting, anxiety, and EFL listening comprehension among…

Perceptions of health stakeholders on task shifting and motivation of community health workers in different socio demographic contexts in Kenya (nomadic, peri-urban and rural agrarian)

PubMed Central

2014-01-01

Background The shortage of health professionals in low income countries is recognized as a crisis. Community health workers are part of a “task-shift” strategy to address this crisis. Task shifting in this paper refers to the delegation of tasks from health professionals to lay, trained volunteers. In Kenya, there is a debate as to whether these volunteers should be compensated, and what motivation strategies would be effective in different socio-demographic contexts, based type of tasks shifted. The purpose of this study was to find out, from stakeholders’ perspectives, the type of tasks to be shifted to community health workers and the appropriate strategies to motivate and retain them. Methods This was an analytical comparative study employing qualitative methods: key informant interviews with health policy makers, managers, and service providers, and focus group discussions with community health workers and service consumers, to explore their perspectives on tasks to be shifted and appropriate motivation strategies. Results The study found that there were tasks to be shifted and motivation strategies that were common to all three contexts. Common tasks were promotive, preventive, and simple curative services. Common motivation strategies were supportive supervision, means of identification, equitable allocation of resources, training, compensation, recognition, and evidence based community dialogue. Further, in the nomadic and peri-urban sites, community health workers had assumed curative services beyond the range provided for in the Kenyan task shifting policy. This was explained to be influenced by lack of access to care due to distance to health facilities, population movement, and scarcity of health providers in the nomadic setting and the harsh economic realities in peri-urban set up. Therefore, their motivation strategies included training on curative skills, technical support, and resources for curative care. Data collection was viewed as an important task in the rural site, but was not recognized as priority in nomadic and peri-urban sites, where they sought monetary compensation for data collection. Conclusions The study concluded that inclusion of curative tasks for community health workers, particularly in nomadic contexts, is inevitable but raises the need for accreditation of their training and regulation of their tasks. PMID:25079588

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.

Toxicological and biochemical studies on Schinus terebinthifolius concerning its curative and hepatoprotective effects against carbon tetrachloride-induced liver injury

PubMed Central

Abdou, Rania H.; Saleh, Sherif Y.; Khalil, Waleed F.

2015-01-01

Background: Recently, many efforts have been made to discover new products of natural origin which can limit the xenobiotic-induced hepatic injury. Carbon tetrachloride (CCl4) is a highly toxic chemical that is widely used to study hepatotoxicity in animal models. Objective: The present study was conducted to investigate the curative and protective effects of Schinus terbenthifolius ethanolic extract against CCl4 -induced acute hepatotoxicity in rats. Materials and Methods: S. terbenthifolius extract was orally administered in a dose of 350 mg dried extract/kg b.wt. before and after intoxication with CCl4 for curative and protective experiments, respectively. A group of hepatotoxicity indicative enzymes, oxidant-antioxidant capacity, DNA oxidation, and apoptosis markers were measured. Results: CCl4 increased liver enzyme leakage, oxidative stress, hepatic apoptosis, DNA oxidation, and inflammatory markers. Administration of S. terebinthifolius, either before or after CCl4 intoxication, significantly decreased elevated serum liver enzymes and reinstated the antioxidant capacity. Interestingly, S. terebinthifolius extract inhibited hepatocyte apoptosis as revealed by approximately 20 times down-regulation in caspase-3 expression when compared to CCl4 untreated group. On the other hand, there was neither protective nor curative effect of S. terebinthifolius against DNA damage caused by CCl4. Conclusion: The present study suggests that S. terebinthifolius extract could be a substantially promising hepatoprotective agent against CCl4 toxic effects and may be against other hepatotoxic chemical or drugs. PMID:26109780

Effects of a 24-week course of interferon-α therapy after curative treatment of hepatitis C virus-associated hepatocellular carcinoma

PubMed Central

Jeong, Soo Cheol; Aikata, Hiroshi; Katamura, Yoshio; Azakami, Takahiro; Kawaoka, Tomokazu; Saneto, Hiromi; Uka, Kiminori; Mori, Nami; Takaki, Shintaro; Kodama, Hideaki; Waki, Koji; Imamura, Michio; Shirakawa, Hiroo; Kawakami, Yoshiiku; Takahashi, Shoichi; Chayama, Kazuaki

2007-01-01

AIM: To assess whether a 24-wk course of interferon (IFN) could prevent hepatocellular carcinoma (HCC) recurrence and worsening of liver function in patients with hepatitis C virus (HCV)-infected patients after receiving curative treatment for primary HCC. METHODS: Outcomes in 42 patients with HCV infection treated with IFN-α, after curative treatment for primary HCC (IFN group), were compared with 42 matched curatively treated historical controls not given IFN (non-IFN group). RESULTS: Although the rate of initial recurrence did not differ significantly between IFN group and non-IFN group (0%, 44%, 61%, and 67% vs 4.8%, 53%, 81%, and 87% at 1, 3, 5, and 7 years, P = 0.153, respectively), IFN group showed a lower rate than the non-IFN group for second recurrence (0%, 10.4%, 28%, and 35% vs 0%, 30%, 59%, and 66% at 1, 3, 5 and 7 years, P = 0.022, respectively). Among the IFN group, patients with sustained virologic response (SVR) were less likely to have a second HCC recurrence than IFN patients without an SVR, or non-IFN patients. Multivariate analysis identified the lack of SVR as the only independent risk factor for a second recurrence, while SVR and Child-Pugh class A independently favored overall survival. CONCLUSION: Most intrahepatic recurrences of HCV-related HCC occurred during persistent viral infection. Eradication of HCV is essential for the prevention of HCC recurrence and improvement of survival. PMID:17879404

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.

A practical method of predicting client revisit intention in a hospital setting.

PubMed

Lee, Kyun Jick

2005-01-01

Data mining (DM) models are an alternative to traditional statistical methods for examining whether higher customer satisfaction leads to higher revisit intention. This study used a total of 906 outpatients' satisfaction data collected from a nationwide survey interviews conducted by professional interviewers on a face-to-face basis in South Korea, 1998. Analyses showed that the relationship between overall satisfaction with hospital services and outpatients' revisit intention, along with word-of-mouth recommendation as intermediate variables, developed into a nonlinear relationship. The five strongest predictors of revisit intention were overall satisfaction, intention to recommend to others, awareness of hospital promotion, satisfaction with physician's kindness, and satisfaction with treatment level.

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

What factors explain pregnant women’s feeding intentions in Bradford, England: A multi-methods, multi-ethnic study

PubMed Central

2014-01-01

Background Using a multi-methods approach we aimed to explore the relative prediction of demographic, socioeconomic and modifiable predictors from the Theory of Planned behaviour (TPB) in explaining feeding intentions amongst a multi-ethnic sample. Methods 476 women completed a questionnaire at 28 weeks gestation. They were grouped into breastfeeding (N = 258), mixed-feeding (N = 50), bottle-feeding (N = 88) intenders, or a no clear intention (N = 88). Multinomial adjusted regressions explored the influence of modifiable TPB factors, along with ethnicity and socioeconomic status in predicting group membership. Free-text responses allowed women to elaborate on reasons behind their intention. Results TPB factors were significant predictors of feeding intention. Women with high intention to breastfeed were less likely to report high attitudes in any other feeding alternative. Bottle-feeding intenders reported poorer self-efficacy regarding breastfeeding compared to breastfeeding intenders (prevalence rate ratio, PRR = 0.10). Mixed and bottle-feeding intenders reported greater self-efficacy for mixed-feeding (PRR = 1.80, 5.50 respectively). Descriptive norms for mixed (PRR = 13.77) and bottle-feeding (PRR = 10.68) were predictive of mixed-feeding intention. Reasons for breastfeeding intentions related to health considerations, whilst bottle-feeding reasons related to convenience. Mixed-feeding intenders reported both breast and bottle-related factors. Conclusions Understanding modifiable predictors related to feeding intentions like TPB factors can help professionals target appropriate interventions to encourage breastfeeding. PMID:24472414

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.

Preservice Teachers' Attitudes and Beliefs about Democratic Classroom Practice: Influences on Intentions for Pedagogical Integration

ERIC Educational Resources Information Center

Pryor, Caroline R.; Pryor, Brandt W.

2005-01-01

This study investigated preservice teachers' intentions to integrate democratic practice into their teaching and the influence of attitudes and beliefs on intentions. Participants were 76 undergraduates from 3 social studies methods classes. A theory of reasoned action (Fishbein & Ajzen, 1975) guided instrument development. Intention was…

Comprehensive Non-Destructive Conservation Documentation of Lunar Samples Using High-Resolution Image-Based 3D Reconstructions and X-Ray CT Data

NASA Technical Reports Server (NTRS)

Blumenfeld, E. H.; Evans, C. A.; Oshel, E. R.; Liddle, D. A.; Beaulieu, K.; Zeigler, R. A.; Hanna, R. D.; Ketcham, R. A.

2015-01-01

Established contemporary conservation methods within the fields of Natural and Cultural Heritage encourage an interdisciplinary approach to preservation of heritage material (both tangible and intangible) that holds "Outstanding Universal Value" for our global community. NASA's lunar samples were acquired from the moon for the primary purpose of intensive scientific investigation. These samples, however, also invoke cultural significance, as evidenced by the millions of people per year that visit lunar displays in museums and heritage centers around the world. Being both scientifically and culturally significant, the lunar samples require a unique conservation approach. Government mandate dictates that NASA's Astromaterials Acquisition and Curation Office develop and maintain protocols for "documentation, preservation, preparation and distribution of samples for research, education and public outreach" for both current and future collections of astromaterials. Documentation, considered the first stage within the conservation methodology, has evolved many new techniques since curation protocols for the lunar samples were first implemented, and the development of new documentation strategies for current and future astromaterials is beneficial to keeping curation protocols up to date. We have developed and tested a comprehensive non-destructive documentation technique using high-resolution image-based 3D reconstruction and X-ray CT (XCT) data in order to create interactive 3D models of lunar samples that would ultimately be served to both researchers and the public. These data enhance preliminary scientific investigations including targeted sample requests, and also provide a new visual platform for the public to experience and interact with the lunar samples. We intend to serve these data as they are acquired on NASA's Astromaterials Acquisistion and Curation website at http://curator.jsc.nasa.gov/. Providing 3D interior and exterior documentation of astromaterial samples addresses the increasing demands for accessability to data and contemporary techniques for documentation, which can be realized for both current collections as well as future sample return missions.

Follow-up of patients with localized breast cancer and first indicators of advanced breast cancer recurrence: A retrospective study.

PubMed

Viot, Julien; Bachour, Martin; Meurisse, Aurélia; Pivot, Xavier; Fiteni, Frédéric

2017-08-01

We conducted a retrospective study to assess the follow-up of patients with localized breast cancer and the first indicators of advanced breast cancer recurrence. All patients with advanced breast cancer recurrence treated between January 2010 and June 2016 in our institution were registered. Among these patients, 303 patients initially treated for early breast cancer with curative intent were identified. After initial curative treatment, follow-up involved the oncologist, the general practitioner and the gynecologist in 68.0%, 48.9% and 19.1% of cases, respectively. The median DFI was 4 years for luminal A, 3.8 years for luminal B, 3.7 years for HER2-positive and 1.5 years for TNBC (p = 0.07). Breast cancer tumor marker was prescribed for 164 patients (54.1%). No difference in terms of follow-up was observed according to the molecular subtype. Symptoms were the primary indicator of relapse for 143 patients (47.2%). Breast cancer recurrence was discovered by CA 15.3 elevation in 57 patients (18.8%) and by CAE elevation in 3 patients (1%). The rate of relapse diagnosed by elevation of CA 15.3 or CAE was not statistically associated with the molecular subtype (p = 0.65). Luminal A cases showed a significantly higher rate of bone metastases (p = 0.0003). TNBC cases showed a significantly higher rate of local recurrence (p = 0.002) and a borderline statistical significant higher rate of lung/pleural metastases (p = 0.07). Follow-up recommendations could be adapted in clinical practice according to the molecular subtype. General practitioners should be more involved by the specialists in breast cancer follow-up. Copyright © 2017 Elsevier Ltd. All rights reserved.

Treatment cost and life expectancy of diffuse large B-cell lymphoma (DLBCL): a discrete event simulation model on a UK population-based observational cohort.

PubMed

Wang, Han-I; Smith, Alexandra; Aas, Eline; Roman, Eve; Crouch, Simon; Burton, Cathy; Patmore, Russell

2017-03-01

Diffuse large B-cell lymphoma (DLBCL) is the commonest non-Hodgkin lymphoma. Previous studies examining the cost of treating DLBCL have generally focused on a specific first-line therapy alone; meaning that their findings can neither be extrapolated to the general patient population nor to other points along the treatment pathway. Based on empirical data from a representative population-based patient cohort, the objective of this study was to develop a simulation model that could predict costs and life expectancy of treating DLBCL. All patients newly diagnosed with DLBCL in the UK's population-based Haematological Malignancy Research Network ( www.hmrn.org ) in 2007 were followed until 2013 (n = 271). Mapped treatment pathways, alongside cost information derived from the National Tariff 2013/14, were incorporated into a patient-level simulation model in order to reflect the heterogeneities of patient characteristics and treatment options. The NHS and social services perspective was adopted, and all outcomes were discounted at 3.5 % per annum. Overall, the expected total medical costs were £22,122 for those treated with curative intent, and £2930 for those managed palliatively. For curative chemotherapy, the predicted medical costs were £14,966, £23,449 and £7376 for first-, second- and third-line treatments, respectively. The estimated annual cost for treating DLBCL across the UK was around £88-92 million. This is the first cost modelling study using empirical data to provide 'real world' evidence throughout the DLBCL treatment pathway. Future application of the model could include evaluation of new technologies/treatments to support healthcare decision makers, especially in the era of personalised medicine.

Quality of care and variability in lung cancer management across Belgian hospitals: a population-based study using routinely available data.

PubMed

Vrijens, France; De Gendt, Cindy; Verleye, Leen; Robays, Jo; Schillemans, Viki; Camberlin, Cécile; Stordeur, Sabine; Dubois, Cécile; Van Eycken, Elisabeth; Wauters, Isabelle; Van Meerbeeck, Jan P

2018-05-01

To evaluate the quality of care for all patients diagnosed with lung cancer in Belgium based on a set of evidence-based quality indicators and to study the variability of care between hospitals. A retrospective study based on linked data from the cancer registry, insurance claims and vital status for all patients diagnosed with lung cancer between 2010 and 2011. Evidence-based quality indicators were identified from a systematic literature search. A specific algorithm to attribute patients to a centre was developed, and funnel plots were used to assess variability of care between centres. None. The proportion of patients who received appropriate care as defined by the indicator. Secondary outcome included the variability of care between centres. Twenty indicators were measured for a total of 12 839 patients. Good results were achieved for 60-day post-surgical mortality (3.9%), histopathological confirmation of diagnosis (93%) and for the use of PET-CT before treatment with curative intent (94%). Areas to be improved include the reporting of staging information to the Belgian Cancer Registry (80%), the use of brain imaging for clinical stage III patients eligible for curative treatment (79%), and the time between diagnosis and start of first active treatment (median 20 days). High variability between centres was observed for several indicators. Twenty-three indicators were found relevant but could not be measured. This study highlights the feasibility to develop a multidisciplinary set of quality indicators using population-based data. The main advantage of this approach is that not additional registration is required, but the non-measurability of many relevant indicators is a hamper. It allows however to easily point to areas of large variability in care.

Resource utilization and costs during the initial years of lung cancer screening with computed tomography in Canada.

PubMed

Cressman, Sonya; Lam, Stephen; Tammemagi, Martin C; Evans, William K; Leighl, Natasha B; Regier, Dean A; Bolbocean, Corneliu; Shepherd, Frances A; Tsao, Ming-Sound; Manos, Daria; Liu, Geoffrey; Atkar-Khattra, Sukhinder; Cromwell, Ian; Johnston, Michael R; Mayo, John R; McWilliams, Annette; Couture, Christian; English, John C; Goffin, John; Hwang, David M; Puksa, Serge; Roberts, Heidi; Tremblay, Alain; MacEachern, Paul; Burrowes, Paul; Bhatia, Rick; Finley, Richard J; Goss, Glenwood D; Nicholas, Garth; Seely, Jean M; Sekhon, Harmanjatinder S; Yee, John; Amjadi, Kayvan; Cutz, Jean-Claude; Ionescu, Diana N; Yasufuku, Kazuhiro; Martel, Simon; Soghrati, Kamyar; Sin, Don D; Tan, Wan C; Urbanski, Stefan; Xu, Zhaolin; Peacock, Stuart J

2014-10-01

It is estimated that millions of North Americans would qualify for lung cancer screening and that billions of dollars of national health expenditures would be required to support population-based computed tomography lung cancer screening programs. The decision to implement such programs should be informed by data on resource utilization and costs. Resource utilization data were collected prospectively from 2059 participants in the Pan-Canadian Early Detection of Lung Cancer Study using low-dose computed tomography (LDCT). Participants who had 2% or greater lung cancer risk over 3 years using a risk prediction tool were recruited from seven major cities across Canada. A cost analysis was conducted from the Canadian public payer's perspective for resources that were used for the screening and treatment of lung cancer in the initial years of the study. The average per-person cost for screening individuals with LDCT was $453 (95% confidence interval [CI], $400-$505) for the initial 18-months of screening following a baseline scan. The screening costs were highly dependent on the detected lung nodule size, presence of cancer, screening intervention, and the screening center. The mean per-person cost of treating lung cancer with curative surgery was $33,344 (95% CI, $31,553-$34,935) over 2 years. This was lower than the cost of treating advanced-stage lung cancer with chemotherapy, radiotherapy, or supportive care alone, ($47,792; 95% CI, $43,254-$52,200; p = 0.061). In the Pan-Canadian study, the average cost to screen individuals with a high risk for developing lung cancer using LDCT and the average initial cost of curative intent treatment were lower than the average per-person cost of treating advanced stage lung cancer which infrequently results in a cure.

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.

Role of curative radiotherapy in the treatment of lung cancer. [Clinical factors effecting efficacy and incidence of complications

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

Coy, P.; Kennelly, G.M.

1980-02-15

From 1963 to 1974, 141 patients with lung cancer were treated with curative intent in the A. Maxwell Evans Clinic in Vancouver. The clinical presentation, age and sex distribution, histology, and reasons for surgery not being carried out are examined. The results of this treatment are presented. An attempt has been made to isolate a group of patients who have a better prognosis so that treatment selection can be improved. Hemoptysis, cough, dyspnea, and incidental finding on routine chest x-ray were the most common manner of presentation. Thirty-four percent of the patients were over 70 years of age and 13%more » were women. The crude overall three- and five-year survival rates were 18 and 10% (19 and 9% in the men, 17 and 14% in the women). Patients presenting with dyspnea had a better survival than those presenting with cough and hemoptysis. Patients with lesions less than 3 cm in diameter had a 28% three-year survival, compared with 14% for lesions greater than 5 cm in diameter. The three- and five-year survival rates in patients over 70 years of age were 23 and 17% respectively. The response to treatment and the survival were better in the patients with squamous cell carcinoma. Twenty-two percent were alive at three years and 12% at five years as compared with 9 and 5% for other histologies. Fifty-four percent of the 35 patients with a complete response and with squamous cell carcinoma were alive at three years, compared with only 8% of the 12 patients with other histologies who showed a complete response.« less

Porphyrin lipid nanoparticles for enhanced photothermal therapy in a patient-derived orthotopic pancreas xenograft cancer model

NASA Astrophysics Data System (ADS)

MacLaughlin, Christina M.; Ding, Lili; Jin, Cheng; Cao, Pingjiang; Siddiqui, Iram; Hwang, David M.; Chen, Juan; Wilson, Brian C.; Zheng, Gang; Hedley, David W.

2016-03-01

Local disease control is a major problem in the treatment of pancreatic cancer, because curative-intent surgery is only possible in a minority of patients, and radiotherapy cannot be delivered in curative doses. Despite the promise of photothermal therapy (PTT) for ablation of pancreatic tumors, this approach remains under investigated. Using photothermal sensitizers in combination with laser light for PTT can result in more efficient conversion of light energy to heat, and confinement of thermal destruction to the tumor, thus sparing adjacent organs and vasculature. Porphyrins have been previously employed as photosensitizers for PDT and PTT, however their incorporation in to "porphysomes", lipid-based nanoparticles each containing ~80,000 porphyrins through conjugation of pyropheophorbide to phospholipids, carries two distinct advantages: 1) high-density porphyrin packing imparts the nanoparticles with enhanced photonic properties for imaging and phototherapy; 2) the enhanced permeability and retention effect may be exploited for optimal delivery of porphysomes to the tumor region thus high payload porphyrin delivery. The feasibility of porphysome-enhanced PTT for pancreatic cancer treatment was investigated using a patient-derived orthotopic pancreas xenograft tumor model. Uptake of porphysomes at the orthotopic tumor site was validated using ex vivo fluorescence imaging of intact organs of interest. The accumulation of porphysomes in orthotopic tumor microstructure was also confirmed by fluorescence imaging of excised tissue slices. PTT progress was monitored as changes in tumor surface temperature using IR optical imaging. Histological analyses were conducted to examine microstructure changes in tissue morphology, and the viability of remaining tumor tissues following exposure to heat. These studies may also provide insight as to the contribution of heat sink in application of thermal therapies to highly vascularized pancreatic tumors.

To analyze the impact of intracavitary brachytherapy as boost radiation after external beam radiotherapy in carcinoma of the external auditory canal and middle ear: a retrospective analysis.

PubMed

Badakh, Dinesh K; Grover, Amit H

2014-01-01

The purpose of this study was to analyze the impact of intra-cavitary brachytherapy (ICBT) as boost radiation after external beam radiotherapy (EBRT) in carcinoma of the external auditory canal and middle ear (EACMA): A retrospective analysis. A retrospective study of 18 patients with carcinoma of the EACMA who were treated with a curative intent from the year 1998 to 2010 was carried out. The age of the patients ranged from 25 years to 67 years. There were 11 male patients (61.1%) and 7 female patients (38.9%). A total of 15 (88.2%) patients were treated with curative radiation alone after a biopsy and two patients received post-operative radiation therapy. The patients were initially treated with EBRT with cobalt 60 machine up to 60-64 Gy. In our department, all the patients who were technically suitable for ICBT received an ICBT boost. The overall survival (OS) in these patients ranged from 7 months to 151 months (9 out of 17 patients, no evidence of disease 53%). The OS in patients treated with a combination of EBRT with ICBT was (8 out of 11) 72.7%, P value statistically significant (P value: 0.0024). The multivariate analysis shows statistically significant difference only for patients who got an ICBT boost (P Value: 0.020). ICBT as a boost after EBRT has got a positive impact on the OS. In conclusion, our results demonstrate that radical radiation therapy (EBRT and ICBT) is the treatment of choice for stage T2, carcinoma of EACMA.

The impact of prostate cancer diagnosis and treatment decision-making on health-related quality of life before treatment onset.

PubMed

Cuypers, Maarten; Lamers, Romy E D; Cornel, Erik B; van de Poll-Franse, Lonneke V; de Vries, Marieke; Kil, Paul J M

2018-04-01

The objective of this study is to test if patients' health-related quality of life (HRQoL) declines after prostate biopsy to detect Pca, and after subsequent treatment decision-making in case Pca is confirmed, and to test whether personality state and traits are associated with these potential changes in HRQoL. Patients who were scheduled for prostate biopsy to detect Pca (N = 377) filled out a baseline questionnaire about HRQoL (EORTC QLQ-C30 and PR25), "big five" personality traits (BFI-10), optimism (LOT-r), and self-efficacy (Decision Self-efficacy Scale) (t0). Patients with confirmed Pca (N = 126) filled out a follow-up questionnaire on HRQoL within 2 weeks after treatment was chosen but had not yet started (t1). HRQoL declined between t0 and t1, reflected in impaired role and cognitive functioning, and elevated fatigue, constipation, and prostate-specific symptoms. Sexual activity and functioning improved. Baseline HRQoL scores were unrelated to the selection of a particular treatment, but for patients who chose a curative treatment, post-decision HRQoL showed a greater decline compared to patients who chose active surveillance. Optimism was associated with HRQoL at baseline; decisional self-efficacy was positively associated with HRQoL at follow-up. No associations between HRQoL and the "big five" personality traits were found. Patients who have undergone prostate biopsy and treatment decision-making for Pca experience a decline in HRQoL. Choosing treatment with a curative intent was associated with greater decline in HRQoL. Interventions aimed at optimism and decision self-efficacy could be helpful to reduce HRQoL impairment around the time of prostate biopsy and treatment decision-making.

Automated detection of discourse segment and experimental types from the text of cancer pathway results sections.

PubMed

Burns, Gully A P C; Dasigi, Pradeep; de Waard, Anita; Hovy, Eduard H

2016-01-01

Automated machine-reading biocuration systems typically use sentence-by-sentence information extraction to construct meaning representations for use by curators. This does not directly reflect the typical discourse structure used by scientists to construct an argument from the experimental data available within a article, and is therefore less likely to correspond to representations typically used in biomedical informatics systems (let alone to the mental models that scientists have). In this study, we develop Natural Language Processing methods to locate, extract, and classify the individual passages of text from articles' Results sections that refer to experimental data. In our domain of interest (molecular biology studies of cancer signal transduction pathways), individual articles may contain as many as 30 small-scale individual experiments describing a variety of findings, upon which authors base their overall research conclusions. Our system automatically classifies discourse segments in these texts into seven categories (fact, hypothesis, problem, goal, method, result, implication) with an F-score of 0.68. These segments describe the essential building blocks of scientific discourse to (i) provide context for each experiment, (ii) report experimental details and (iii) explain the data's meaning in context. We evaluate our system on text passages from articles that were curated in molecular biology databases (the Pathway Logic Datum repository, the Molecular Interaction MINT and INTACT databases) linking individual experiments in articles to the type of assay used (coprecipitation, phosphorylation, translocation etc.). We use supervised machine learning techniques on text passages containing unambiguous references to experiments to obtain baseline F1 scores of 0.59 for MINT, 0.71 for INTACT and 0.63 for Pathway Logic. Although preliminary, these results support the notion that targeting information extraction methods to experimental results could provide accurate, automated methods for biocuration. We also suggest the need for finer-grained curation of experimental methods used when constructing molecular biology databases. © The Author(s) 2016. Published by Oxford University Press.

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.

Current treatment options for recurrent/metastatic head and neck cancer: a post-ASCO 2011 update and review of last year's literature.

PubMed

Kurzweg, T; Möckelmann, N; Laban, S; Knecht, R

2012-10-01

The majority of patients with a squamous cell carcinoma of the head and neck present with locally advanced tumors. The first-line treatment of locally advanced tumor stages consists of a combined modality management. Despite these aggressive protocols, many patients develop locoregional recurrences or metastasis and place particularly high demands on the interdisciplinary treatment team. Treatment with a curative intent must be differentiated from a palliative one. In addition to prior treatment, resectability, age and performance status, patient wishes must be taken into consideration in treatment planning, especially considering that most therapies offer little to no overall survival benefit. Salvage surgery, chemo- and target therapies, and reirradiation are head and neck surgeon's and radiooncologist's weapons in the fight against these strong opponents. This review focuses on publications and meeting news from last year and reviews the current status of the clinical application of each treatment modality in recurrent or metastatic head and neck cancer.

A Case of Recurrent Pneumothorax Associated with Birt-Hogg-Dubé Syndrome Treated with Bilateral Simultaneous Surgery and Total Pleural Covering.

PubMed

Takegahara, Kyoshiro; Yoshino, Naoyuki; Usuda, Jitsuo

2017-12-20

Birt-Hogg-Dubé syndrome is an autosomal dominant genetic disorder characterized by a triad of skin tumors, renal tumors, and multiple pulmonary cysts. Our patient was a 40-year-old man with a history of recurrent bilateral pneumothorax and a family history of pneumothorax. The patient visited our department with chest pain and was diagnosed with left pneumothorax based on a chest X-ray. Thoracic computed tomography (CT) showed multiple cysts in both lungs. We performed thoracoscopic bilateral bullectomy with curative intent. Intraoperative observation showed numerous cysts in the lung apex, interlobular region, and mediastinum. We resected the cysts that we suspected to be responsible for the symptoms and ligated the lesions, and then performed total pleural covering. After surgery, genetic testing was performed. The result enabled us to diagnose Birt-Hogg-Dubé syndrome in this patient. Although the patient has developed neither recurrent pneumothorax nor any renal tumors, to date, long-term monitoring is necessary.

From the Cover: A Howiesons Poort tradition of engraving ostrich eggshell containers dated to 60,000 years ago at Diepkloof Rock Shelter, South Africa.

PubMed

Texier, Pierre-Jean; Porraz, Guillaume; Parkington, John; Rigaud, Jean-Philippe; Poggenpoel, Cedric; Miller, Christopher; Tribolo, Chantal; Cartwright, Caroline; Coudenneau, Aude; Klein, Richard; Steele, Teresa; Verna, Christine

2010-04-06

Ongoing debates about the emergence of modern human behavior, however defined, regularly incorporate observations from the later part of the southern African Middle Stone Age and emphasize the early appearance of artifacts thought to reflect symbolic practice. Here we report a large sample of 270 fragments of intentionally marked ostrich eggshell from the Howiesons Poort at Diepkloof Rock Shelter, Western Cape, South Africa. Dating from approximately 60,000 years ago, these pieces attest to an engraving tradition that is the earliest reliable evidence of what is a widespread modern practice. These abstract linear depictions were made on functional items (eggshell containers), which were curated and involved in daily hunter-gatherer life. The standardized production of repetitive patterns, including a hatched band motif, suggests a system of symbolic representation in which collective identities and individual expressions are clearly communicated, suggesting social, cultural, and cognitive underpinnings that overlap with those of modern people.

[11C]choline-PET-guided helical tomotherapy and estramustine in a patient with pelvic-recurrent prostate cancer: local control and toxicity profile after 24 months.

PubMed

Alongi, Filippo; Schipani, Stefano; Samanes Gajate, Ana Maria; Rosso, Alberto; Cozzarini, Cesare; Fiorino, Claudio; Alongi, Pierpaolo; Picchio, Maria; Gianolli, Luigi; Messa, Cristina; Di Muzio, Nadia

2010-01-01

[11C]choline positron emission tomograhy can be useful to detect metastatic disease and to localize isolated lymph node relapse after primary treatment in case of prostate-specific antigen failure. In case of lymph node failure in prostate cancer patients, surgery or radiotherapy can be proposed with a curative intent. Some reports have suggested that radiotherapy could have a role in local control of oligometastatic lymph node disease. This is the first reported case of [11C]choline positron emission tomography-guided helical tomotherapy concomitant with estramustine for the treatment of pelvic-recurrent prostate cancer. At 24 months after the end of helical tomotherapy, prostate-specific antigen was undetectable and no late toxicities were recorded. A disease-free survival of 24 months, in the absence of any type of systemic therapy, is uncommon in metastatic prostate cancer. The therapeutic approach of the case report is discussed and a literature review on the issue is presented.

New Perspectives Regarding Anaplastic Thyroid Carcinoma Approach Improvement.

PubMed

Figueiredo, Ana Sofia; Andrea-Ferreira, Patricia

2018-06-10

Anaplastic thyroid carcinoma is rare, but represents the deadliest type of thyroid cancer that is characterised by a rapid course. Diagnosis is usually made at a late stage, when more than half of the patients have distant metastasis. Our main purpose is to review the current information on anaplastic thyroid aetiology and risk factors that might contribute to an earlier diagnosis as well as to give new perspectives regarding the most recent treatment options and future directions. The treatment options are mainly palliative and lack efficacy. In particular, the multikinase inhibitors, BRAF inhibitors and other directed agents aim to stabilize the tumour growth and might enable a radical surgery with curative intent. With the mutational landscape investigation and the discovery of new targets, new directed treatments are being tried. Considering the current tendency to be more conservative regarding the multinodular goitre approach and some differentiated thyroid carcinomas treatment, it is vital to understand that it might evolve to anaplastic cancers. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

A comparison of oncological outcomes between transoral surgical and non-surgical treatment protocols in the management of oropharyngeal squamous cell carcinoma.

PubMed

Kao, S S; Micklem, J; Ofo, E; Edwards, S; Dhatrak, D; Foreman, A; Krishnan, S; Hodge, J-C

2018-04-01

The incidence of oropharyngeal squamous cell carcinoma in the Western world is increasing, with the human papillomavirus epidemic implicated in this observed trend. The optimal treatment modality is yet undetermined regarding oncological outcomes. This study comprised 98 patients with oropharyngeal squamous cell carcinoma, treated with either primary transoral surgery with adjuvant therapy or primary chemoradiotherapy with curative intent, between 2008 and 2012. Clinicopathological characteristics including tumour-node-metastasis stage, human papillomavirus status, treatment modality, recurrence and overall survival were collated. Five per cent of primary surgical patients had locoregional recurrences compared with 25 per cent of primary chemoradiotherapy patients. A lower rate of locoregional recurrence was observed in the human papillomavirus positive group. This paper reports higher rates of overall survival and local control for oropharyngeal squamous cell carcinoma treated with primary surgery compared with primary chemoradiotherapy. This reflects overall lower tumour stage and higher human papillomavirus status in this group.

Anaplastic thyroid cancer: Clinical outcomes with conformal radiotherapy.

PubMed

Bhatia, Aarti; Rao, Archana; Ang, Kie-Kian; Garden, Adam S; Morrison, William H; Rosenthal, David I; Evans, Douglas B; Clayman, Gary; Sherman, Steven I; Schwartz, David L

2010-07-01

The aim of this study was to review institutional outcomes for anaplastic thyroid cancer treated with conformal 3-dimensional radiotherapy (3DRT) or intensity-modulated radiotherapy (IMRT). In all, 53 consecutive patients were analyzed. Thirty-one (58%) patients were irradiated with curative intent. Median radiation dose was 55 Gray (Gy; range, 4-70 Gy). Thirteen (25%) patients received IMRT to a median 60 Gy (range, 39.9-69.0 Gy). Thirty-nine (74%) patients received chemotherapy with radiation. The Kaplan-Meier estimate of overall survival (OS) at 1 year for definitively irradiated patients was 29%. Patients without distant metastases receiving >or=50 Gy had superior survival outcomes; 5 such patients had no evidence of disease at last follow-up. Use of IMRT versus 3DRT did not influence toxicity. Outcomes for anaplastic thyroid cancer treated with 3DRT or IMRT remain equivalent to historical results. Healthy patients with localized disease who tolerate full dose irradiation can potentially enjoy prolonged survival. Biologically targeted radiosensitization merits prioritized investigation. (c) 2009 Wiley Periodicals, Inc.

Psychoneuroimmunology and cancer: A decade of discovery, paradigm shifts, and methodological innovations

PubMed Central

McDonald, Paige Green; O’Connell, Mary; Lutgendorf, Susan K.

2013-01-01

This article introduces the supplemental issue of “Cancer, Brain, Behavior, and Immunity” and outlines important discoveries, paradigm shifts, and methodological innovations that have emerged in the past decade to advance mechanistic and translational understanding of biobehavioral influences on tumor biology, cancer treatment-related sequelae, and cancer outcomes. We offer a heuristic framework for research on biobehavioral pathways in cancer. The shifting survivorship landscape is highlighted and we propose that the changing demographics suggest prudent adoption of a life course perspective of cancer and cancer survivorship. We note opportunities for psychoneuroimmunology (PNI) research to ameliorate the long-term, unintended consequences of aggressive curative intent and call attention to the critical role of reciprocal translational pathways between animal and human studies. Lastly, we briefly summarize the articles included in this compilation and offer our perspectives on future research directions. HighlightsThis article introduces the National Cancer Institute sponsored special issue Cancer, Brain, Behavior, and Immunity and highlights the last decade of PNI-cancer research. PMID:23333846

Primary health care, community participation and community-financing: experiences of two middle hill villages in Nepal.

PubMed

Sepehri, A; Pettigrew, J

1996-03-01

Although community involvement in health related activities is generally acknowledged by international and national health planners to be the key to the successful organization of primary health care, comparatively little is known about its potential and limitations. Drawing on the experiences of two middle hill villages in Nepal, this paper reports on research undertaken to compare and contrast the scope and extent of community participation in the delivery of primary health care in a community run and financed health post and a state run and financed health post. Unlike many other health posts in Nepal these facilities do provide effective curative services, and neither of them suffer from chronic shortage of drugs. However, community-financing did not appear to widen the scope and the extent of participation. Villagers in both communities relied on the health post for the treatment of less than one-third of symptoms, and despite the planners' intentions, community involvement outside participation in benefits was found to be very limited.

Revisiting the potential signs of colorectal cancer on contrast-enhanced computed tomography without bowel preparation.

PubMed

Naqvi, Jawad; Hosmane, Sharath; Lapsia, Snehal

2015-10-01

Colorectal cancer (CRC) is the second most common cause of cancer death in the US. Earlier detection can allow treatment with curative intent and improve prognosis. Optical and virtual colonoscopy are widely used in screening for colonic polyps and in the investigation of suspected CRC. However, contrast-enhanced computed tomography (CT) is still performed to investigate various non-specific abdominal complaints. Hence, a significant number of CRC are identified on contrast-enhanced CT without bowel preparation. We describe several signs, which when present in tandem, raise suspicion of CRC, and may warrant further investigation with optical colonoscopy. These include an intraluminal mass, eccentric or circumferential wall thickening >3 mm, focal wall enhancement, pericolic fat stranding, a cluster of >3 local lymph nodes, and enlarged lymph nodes >10 mm in short axis. Multiplanar evaluation of the bowel should be performed on all CT abdominal studies, including those without bowel preparation, to identify subtle features of CRC.

Adverse effect of splenectomy on recurrence in total gastrectomy cancer patients with perioperative transfusion.

PubMed

Shen, Jian Guo; Cheong, Jae Ho; Hyung, Woo Jin; Kim, Junuk; Choi, Seung Ho; Noh, Sung Hoon

2006-09-01

To investigate the interactions between splenectomy and perioperative transfusion in gastric cancer patients. Medical records of 449 gastric cancer patients who had undergone total gastrectomies for curative intent between 1991 and 1995 were reviewed. The influence of splenectomy on tumor recurrence and survival both in the transfused and nontransfused patients were evaluated by univariate and multivariate analysis. The recurrence rate in the splenectomy group was 48.1% as compared with 22.6% in the spleen-preserved group among transfused patients (P=.001); it was 40.7% compared with 26.5% among nontransfused patients (P=.086). There was no significant difference in the mean survival between the splenectomy group and the spleen-preserved group in a subgroup analysis by stage. Multivariate analysis identified splenectomy as an independent risk factor for recurrence but not as a predictor for survival among transfused patients. Splenectomy does not appear to abrogate the adverse effect of perioperative transfusion on prognosis in gastric cancer patients. Moreover, it may increase postoperative recurrence in transfused patients.

Digital curation and online resources: digital scanning of surgical tools at the royal college of physicians and surgeons of Glasgow for an open university learning resource.

PubMed

Earley, Kirsty; Livingstone, Daniel; Rea, Paul M

2017-01-01

Collection preservation is essential for the cultural status of any city. However, presenting a collection publicly risks damage. Recently this drawback has been overcome by digital curation. Described here is a method of digitisation using photogrammetry and virtual reality software. Items were selected from the Royal College of Physicians and Surgeons of Glasgow archives, and implemented into an online learning module for the Open University. Images were processed via Agisoft Photoscan, Autodesk Memento, and Garden Gnome Object 2VR. Although problems arose due to specularity, 2VR digital models were developed for online viewing. Future research must minimise the difficulty of digitising specular objects.

[Effect of jian-gan-le on advanced schistosomiasis].

PubMed

He, Zheng-Wen; Wang, You-Bin; Huang, Wen-Jun

2011-06-01

A total of 80 cases of advanced schistosomiasis were selected and divided into an experiment group and a control group, 40 cases each group, by the random sampling method. The patients in the experiment group were administered with Jian-gan-le, and the patients in the control group received compound purple granules. In the experiment group, the curative rate was 25.0%, the improving rate was 70.0%, the inefficacy rate was 5%, and the efficiency rate was 95.0%. In the control group, the curative rate was 12.5%, the improving rate was 75%, the inefficacy rate was 12.5%. There was no statistic difference between the 2 groups (P all > 0.05). The expense was cheaper in the experiment group than in the control group.

Review of a series of proctosigmoidoscopies done at Wallops Station, Virginia

NASA Technical Reports Server (NTRS)

White, E.

1969-01-01

Routine proctosigmoidoscopic examinations for incidence of polyps in NASA installation asymptomatic personnel establish the value of this method in detecting cancer without invasion beyond the stalk and resulting in curative operation at greater survival rates than in later detections.

Mining dark information resources to develop new informatics capabilities to support science

NASA Astrophysics Data System (ADS)

Ramachandran, Rahul; Maskey, Manil; Bugbee, Kaylin

2016-04-01

Dark information resources are digital resources that organizations collect, process, and store for regular business or operational activities but fail to realize their potential for other purposes. The challenge for any organization is to recognize, identify and effectively exploit these dark information stores. Metadata catalogs at different data centers store dark information resources consisting of structured information, free form descriptions of data and browse images. These information resources are never fully exploited beyond a few fields used for search and discovery. For example, the NASA Earth science catalog holds greater than 6000 data collections, 127 million records for individual files and 67 million browse images. We believe that the information contained in the metadata catalogs and the browse images can be utilized beyond their original design intent to provide new data discovery and exploration pathways to support science and education communities. In this paper we present two research applications using information stored in the metadata catalog in a completely novel way. The first application is designing a data curation service. The objective of the data curation service is to augment the existing data search capabilities. Given a specific atmospheric phenomenon, the data curation service returns the user a ranked list of relevant data sets. Different fields in the metadata records including textual descriptions are mined. A specialized relevancy ranking algorithm has been developed that uses a "bag of words" to define phenomena along with an ensemble of known approaches such as the Jaccard Coefficient, Cosine Similarity and Zone ranking to rank the data sets. This approach is also extended to map from the data set level to data file variable level. The second application is focused on providing a service where a user can search and discover browse images containing specific phenomena from the vast catalog. This service will aid researchers in uncovering interesting event in the data for case study analysis. The challenge of this second application is to bridge the semantic gap between the low level image pixel values and the semantic concept perceived by a user when he or she sees an image. A deep learning algorithm, specifically the Convolution Neural Network (CNN), has been trained and tested to identify three types of Earth science phenomena - Hurricanes, Dust, and Smoke/Haze in MODIS imagery. Latest results from both the applications will be presented in this paper.

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

Estimating individual influences of behavioral intentions: an application of random-effects modeling to the theory of reasoned action.

PubMed

Hedeker, D; Flay, B R; Petraitis, J

1996-02-01

Methods are proposed and described for estimating the degree to which relations among variables vary at the individual level. As an example of the methods, M. Fishbein and I. Ajzen's (1975; I. Ajzen & M. Fishbein, 1980) theory of reasoned action is examined, which posits first that an individual's behavioral intentions are a function of 2 components: the individual's attitudes toward the behavior and the subjective norms as perceived by the individual. A second component of their theory is that individuals may weight these 2 components differently in assessing their behavioral intentions. This article illustrates the use of empirical Bayes methods based on a random-effects regression model to estimate these individual influences, estimating an individual's weighting of both of these components (attitudes toward the behavior and subjective norms) in relation to their behavioral intentions. This method can be used when an individual's behavioral intentions, subjective norms, and attitudes toward the behavior are all repeatedly measured. In this case, the empirical Bayes estimates are derived as a function of the data from the individual, strengthened by the overall sample data.

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.

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

Radical curative efficacy of tafenoquine combination regimens in Plasmodium cynomolgi-infected Rhesus monkeys (Macaca mulatta)

PubMed Central

2011-01-01

Background Tafenoquine is an 8-aminoquinoline being developed for radical cure (blood and liver stage elimination) of Plasmodium vivax. During monotherapy treatment, the compound exhibits slow parasite and fever clearance times, and toxicity in glucose-6-phosphate dehydrogenase (G6PD) deficiency is a concern. Combination with other antimalarials may mitigate these concerns. Methods In 2005, the radical curative efficacy of tafenoquine combinations was investigated in Plasmodium cynomolgi-infected naïve Indian-origin Rhesus monkeys. In the first cohort, groups of two monkeys were treated with a three-day regimen of tafenoquine at different doses alone and in combination with a three-day chloroquine regimen to determine the minimum curative dose (MCD). In the second cohort, the radical curative efficacy of a single-day regimen of tafenoquine-mefloquine was compared to that of two three-day regimens comprising tafenoquine at its MCD with chloroquine or artemether-lumefantrine in groups of six monkeys. In a final cohort, the efficacy of the MCD of tafenoquine against hypnozoites alone and in combination with chloroquine was investigated in groups of six monkeys after quinine pre-treatment to eliminate asexual parasites. Plasma tafenoquine, chloroquine and desethylchloroquine concentrations were determined by LC-MS in order to compare doses of the drugs to those used clinically in humans. Results The total MCD of tafenoquine required in combination regimens for radical cure was ten-fold lower (1.8 mg/kg versus 18 mg/kg) than for monotherapy. This regimen (1.8 mg/kg) was equally efficacious as monotherapy or in combination with chloroquine after quinine pre-treatment to eliminate asexual stages. The same dose of (1.8 mg/kg) was radically curative in combination with artemether-lumefantrine. Tafenoquine was also radically curative when combined with mefloquine. The MCD of tafenoquine monotherapy for radical cure (18 mg/kg) appears to be biologically equivalent to a 600-1200 mg dose in humans. At its MCD in combination with blood schizonticidal drugs (1.8 mg/kg), the maximum observed plasma concentrations were substantially lower than (20-84 versus 550-1,100 ng/ml) after administration of 1, 200 mg in clinical studies. Conclusions Ten-fold lower clinical doses of tafenoquine than used in prior studies may be effective against P. vivax hypnozoites if the drug is deployed in combination with effective blood-schizonticidal drugs. PMID:21801400

SU-E-T-119: Analysis the Efficacy of Different Radiotherapy Methods and Failure Mode in No-Metastasis Esophageal Squamous Cell Carcinoma

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

Yankun, C; Zhihui, T; Runxiao, L

2015-06-15

Purpose: To evaluate the curative effect of radio (chemo) therapy and mode of treatment failure in no-metastasis and lesion length ≤ 5.0cm esophageal squamous cell carcinoma (ESCC). Methods: There were 158 eligible patients were retrospectively analyzed, to analysis the curative effect of radio (chemo) therapy, prognosis factors, toxicity and prognostic index model. Results: To all patients the 1, 3, 5 overall survival rate were 83.54%, 52.53%, 32.58%, the local recurrence rate were 15.08%, 33.60% and 38.14%; distant metastasis rate were 10.64%, 25.21% and 36.06%; tumor specific survival rate were 76.64%, 54.07% and 44.51%. Multivariate analysis showed that patients with ECOGmore » grade (χ2=13.945, P=0.000), short-term effect (χ2=19.360, P=0.000) and different radiotherapy methods (χ2=9.866, P=0.002) as the independent prognostic factors. Prognostic index model showed that the survival rate was significantly higher in the lower value of PI group than in the larger value of PI group (χ2=49.19, P=0.0000). In our whole group, there were simple locoregional recurrence (LR) 40 cases (25.3%), simple Distant metastasis (DM) 31 cases (19.6%), LR and DM in 14 cases (8.9%) after treatment. The chi-square test showed that there were no significant difference in the incidence of Elective Nodal Irradiation (ENI )and Involved Field Irradiation (IFI) patients with LR and DM ( χ2=2.363, 2.950, P=0.124, 0.085). Conclusion: Radio (chemo) therapy has a good curative effect in no-metastasis and lesion length ≤ 5.0cm ESCC patients.« less

Toward high-throughput phenotyping: unbiased automated feature extraction and selection from knowledge sources.

PubMed

Yu, Sheng; Liao, Katherine P; Shaw, Stanley Y; Gainer, Vivian S; Churchill, Susanne E; Szolovits, Peter; Murphy, Shawn N; Kohane, Isaac S; Cai, Tianxi

2015-09-01

Analysis of narrative (text) data from electronic health records (EHRs) can improve population-scale phenotyping for clinical and genetic research. Currently, selection of text features for phenotyping algorithms is slow and laborious, requiring extensive and iterative involvement by domain experts. This paper introduces a method to develop phenotyping algorithms in an unbiased manner by automatically extracting and selecting informative features, which can be comparable to expert-curated ones in classification accuracy. Comprehensive medical concepts were collected from publicly available knowledge sources in an automated, unbiased fashion. Natural language processing (NLP) revealed the occurrence patterns of these concepts in EHR narrative notes, which enabled selection of informative features for phenotype classification. When combined with additional codified features, a penalized logistic regression model was trained to classify the target phenotype. The authors applied our method to develop algorithms to identify patients with rheumatoid arthritis and coronary artery disease cases among those with rheumatoid arthritis from a large multi-institutional EHR. The area under the receiver operating characteristic curves (AUC) for classifying RA and CAD using models trained with automated features were 0.951 and 0.929, respectively, compared to the AUCs of 0.938 and 0.929 by models trained with expert-curated features. Models trained with NLP text features selected through an unbiased, automated procedure achieved comparable or slightly higher accuracy than those trained with expert-curated features. The majority of the selected model features were interpretable. The proposed automated feature extraction method, generating highly accurate phenotyping algorithms with improved efficiency, is a significant step toward high-throughput phenotyping. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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

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.

EVALUATING THE PREDICTIVE VALIDITY OF SUICIDAL INTENT AND MEDICAL LETHALITY IN YOUTH

PubMed Central

Sapyta, Jeffrey; Goldston, David B.; Erkanli, Alaattin; Daniel, Stephanie S.; Heilbron, Nicole; Mayfield, Andrew; Treadway, S. Lyn

2012-01-01

Objectives To examine whether suicidal intent and medical lethality of past suicide attempts are predictive of future attempts, the association between intent and lethality, and the consistency of these characteristics across repeated attempts among youth. Method Suicide attempts in a 15-year prospective study of 180 formerly psychiatrically hospitalized adolescents (Mage at hospitalization = 14.83; 51% female; 80% Caucasian) were characterized using the Subjective Intent Rating Scale and Lethality of Attempt Rating Scale. Anderson-Gill recurrent events survival models and generalized estimating equations were used to assess predictive validity. Generalized linear models were used to examine stability of characteristics across attempts. Results Neither intent nor lethality from the most recent attempt predicted future attempts. The highest level of intent and most severe lethality of attempts during the follow-up predicted subsequent attempts, but the degree to which highest intent and most severe lethality contributed to prediction after considering methods of suicide attempts, past number of attempts, or psychiatric diagnoses was mixed. Across successive attempts, there was little consistency in reported characteristics. Intent and lethality were related to each other only for attempts occurring in early adulthood. Conclusions Highest intent and lethality were better predictors of future attempts than intent and lethality of the most recent attempt. However, these characteristics should only be considered as predictors within the context of other factors. For youth, clinicians should not infer true intent from the lethality of attempts, nor assume that characteristics of future suicide attempts will be similar to previous attempts. PMID:22250854

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

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

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.

On deception detection in multi-agent systems and deception intent

NASA Astrophysics Data System (ADS)

Santos, Eugene, Jr.; Li, Deqing; Yuan, Xiuqing

2008-04-01

Deception detection plays an important role in the military decision-making process, but detecting deception is a challenging task. The deception planning process involves a number of human factors. It is intent-driven where intentions are usually hidden or not easily observable. As a result, in order to detect deception, any adversary model must have the capability to capture the adversary's intent. This paper discusses deception detection in multi-agent systems and in adversary modeling. We examined psychological and cognitive science research on deception and implemented various theories of deception within our approach. First, in multi-agent expert systems, one detection method uses correlations between agents to predict reasonable opinions/responses of other agents (Santos & Johnson, 2004). We further explore this idea and present studies that show the impact of different factors on detection success rate. Second, from adversary modeling, our detection method focuses on inferring adversary intent. By combining deception "branches" with intent inference models, we can estimate an adversary's deceptive activities and at the same time enhance intent inference. Two major kinds of deceptions are developed in this approach in different fashions. Simulative deception attempts to find inconsistency in observables, while dissimulative deception emphasizes the inference of enemy intentions.

Advancing Models and Data for Characterizing Exposures to Chemicals in Consumer Products

EPA Science Inventory

EPA’s Office of Research and Development (ORD) is leading several efforts to develop data and methods for estimating population chemical exposures related to the use of consumer products. New curated chemical, ingredient, and product use information are being collected fro...

Scrubchem: Building Bioactivity Datasets from Pubchem Bioassay Data (SOT)

EPA Science Inventory

The PubChem Bioassay database is a non-curated public repository with data from 64 sources, including: ChEMBL, BindingDb, DrugBank, EPA Tox21, NIH Molecular Libraries Screening Program, and various other academic, government, and industrial contributors. Methods for extracting th...

Rapid construction of a whole-genome transposon insertion collection for Shewanella oneidensis by Knockout Sudoku.

PubMed

Baym, Michael; Shaket, Lev; Anzai, Isao A; Adesina, Oluwakemi; Barstow, Buz

2016-11-10

Whole-genome knockout collections are invaluable for connecting gene sequence to function, yet traditionally, their construction has required an extraordinary technical effort. Here we report a method for the construction and purification of a curated whole-genome collection of single-gene transposon disruption mutants termed Knockout Sudoku. Using simple combinatorial pooling, a highly oversampled collection of mutants is condensed into a next-generation sequencing library in a single day, a 30- to 100-fold improvement over prior methods. The identities of the mutants in the collection are then solved by a probabilistic algorithm that uses internal self-consistency within the sequencing data set, followed by rapid algorithmically guided condensation to a minimal representative set of mutants, validation, and curation. Starting from a progenitor collection of 39,918 mutants, we compile a quality-controlled knockout collection of the electroactive microbe Shewanella oneidensis MR-1 containing representatives for 3,667 genes that is functionally validated by high-throughput kinetic measurements of quinone reduction.

The Biomolecular Interaction Network Database and related tools 2005 update

PubMed Central

Alfarano, C.; Andrade, C. E.; Anthony, K.; Bahroos, N.; Bajec, M.; Bantoft, K.; Betel, D.; Bobechko, B.; Boutilier, K.; Burgess, E.; Buzadzija, K.; Cavero, R.; D'Abreo, C.; Donaldson, I.; Dorairajoo, D.; Dumontier, M. J.; Dumontier, M. R.; Earles, V.; Farrall, R.; Feldman, H.; Garderman, E.; Gong, Y.; Gonzaga, R.; Grytsan, V.; Gryz, E.; Gu, V.; Haldorsen, E.; Halupa, A.; Haw, R.; Hrvojic, A.; Hurrell, L.; Isserlin, R.; Jack, F.; Juma, F.; Khan, A.; Kon, T.; Konopinsky, S.; Le, V.; Lee, E.; Ling, S.; Magidin, M.; Moniakis, J.; Montojo, J.; Moore, S.; Muskat, B.; Ng, I.; Paraiso, J. P.; Parker, B.; Pintilie, G.; Pirone, R.; Salama, J. J.; Sgro, S.; Shan, T.; Shu, Y.; Siew, J.; Skinner, D.; Snyder, K.; Stasiuk, R.; Strumpf, D.; Tuekam, B.; Tao, S.; Wang, Z.; White, M.; Willis, R.; Wolting, C.; Wong, S.; Wrong, A.; Xin, C.; Yao, R.; Yates, B.; Zhang, S.; Zheng, K.; Pawson, T.; Ouellette, B. F. F.; Hogue, C. W. V.

2005-01-01

The Biomolecular Interaction Network Database (BIND) (http://bind.ca) archives biomolecular interaction, reaction, complex and pathway information. Our aim is to curate the details about molecular interactions that arise from published experimental research and to provide this information, as well as tools to enable data analysis, freely to researchers worldwide. BIND data are curated into a comprehensive machine-readable archive of computable information and provides users with methods to discover interactions and molecular mechanisms. BIND has worked to develop new methods for visualization that amplify the underlying annotation of genes and proteins to facilitate the study of molecular interaction networks. BIND has maintained an open database policy since its inception in 1999. Data growth has proceeded at a tremendous rate, approaching over 100 000 records. New services provided include a new BIND Query and Submission interface, a Standard Object Access Protocol service and the Small Molecule Interaction Database (http://smid.blueprint.org) that allows users to determine probable small molecule binding sites of new sequences and examine conserved binding residues. PMID:15608229

Predicting Physical Interactions between Protein Complexes*

PubMed Central

Clancy, Trevor; Rødland, Einar Andreas; Nygard, Ståle; Hovig, Eivind

2013-01-01

Protein complexes enact most biochemical functions in the cell. Dynamic interactions between protein complexes are frequent in many cellular processes. As they are often of a transient nature, they may be difficult to detect using current genome-wide screens. Here, we describe a method to computationally predict physical interactions between protein complexes, applied to both humans and yeast. We integrated manually curated protein complexes and physical protein interaction networks, and we designed a statistical method to identify pairs of protein complexes where the number of protein interactions between a complex pair is due to an actual physical interaction between the complexes. An evaluation against manually curated physical complex-complex interactions in yeast revealed that 50% of these interactions could be predicted in this manner. A community network analysis of the highest scoring pairs revealed a biologically sensible organization of physical complex-complex interactions in the cell. Such analyses of proteomes may serve as a guide to the discovery of novel functional cellular relationships. PMID:23438732

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

Effect of More vs Less Frequent Follow-up Testing on Overall and Colorectal Cancer-Specific Mortality in Patients With Stage II or III Colorectal Cancer: The COLOFOL Randomized Clinical Trial.

PubMed

Wille-Jørgensen, Peer; Syk, Ingvar; Smedh, Kenneth; Laurberg, Søren; Nielsen, Dennis T; Petersen, Sune H; Renehan, Andrew G; Horváth-Puhó, Erzsébet; Påhlman, Lars; Sørensen, Henrik T

2018-05-22

Intensive follow-up of patients after curative surgery for colorectal cancer is common in clinical practice, but evidence of a survival benefit is limited. To examine overall mortality, colorectal cancer-specific mortality, and colorectal cancer-specific recurrence rates among patients with stage II or III colorectal cancer who were randomized after curative surgery to 2 alternative schedules for follow-up testing with computed tomography and carcinoembryonic antigen. Unblinded randomized trial including 2509 patients with stage II or III colorectal cancer treated at 24 centers in Sweden, Denmark, and Uruguay from January 2006 through December 2010 and followed up for 5 years; follow-up ended on December 31, 2015. Patients were randomized either to follow-up testing with computed tomography of the thorax and abdomen and serum carcinoembryonic antigen at 6, 12, 18, 24, and 36 months after surgery (high-frequency group; n = 1253 patients) or at 12 and 36 months after surgery (low-frequency group; n = 1256 patients). The primary outcomes were 5-year overall mortality and colorectal cancer-specific mortality rates. The secondary outcome was the colorectal cancer-specific recurrence rate. Both intention-to-treat and per-protocol analyses were performed. Among 2555 patients who were randomized, 2509 were included in the intention-to-treat analysis (mean age, 63.5 years; 1128 women [45%]) and 2365 (94.3%) completed the trial. The 5-year overall patient mortality rate in the high-frequency group was 13.0% (161/1253) compared with 14.1% (174/1256) in the low-frequency group (risk difference, 1.1% [95% CI, -1.6% to 3.8%]; P = .43). The 5-year colorectal cancer-specific mortality rate in the high-frequency group was 10.6% (128/1248) compared with 11.4% (137/1250) in the low-frequency group (risk difference, 0.8% [95% CI, -1.7% to 3.3%]; P = .52). The colorectal cancer-specific recurrence rate was 21.6% (265/1248) in the high-frequency group compared with 19.4% (238/1250) in the low-frequency group (risk difference, 2.2% [95% CI, -1.0% to 5.4%]; P = .15). Among patients with stage II or III colorectal cancer, follow-up testing with computed tomography and carcinoembryonic antigen more frequently compared with less frequently did not result in a significant rate reduction in 5-year overall mortality or colorectal cancer-specific mortality. clinicaltrials.gov Identifier: NCT00225641.

Adjuvant treatment of resectable biliary tract cancer with cisplatin plus gemcitabine: A prospective single center phase II study.

PubMed

Siebenhüner, Alexander R; Seifert, Heike; Bachmann, Helga; Seifert, Burkhardt; Winder, Thomas; Feilchenfeldt, Jonas; Breitenstein, Stefan; Clavien, Pierre-Alain; Stupp, Roger; Knuth, Alexander; Pestalozzi, Bernhard; Samaras, Panagiotis

2018-01-11

Biliary tract cancer (BTC) is a dismal disease, even after curative intent surgery. We conducted this prospective, non-randomized phase II study to evaluate the feasibility and efficacy of cisplatin and gemcitabine as adjuvant treatment in patients with resected BTC. Patients initially received gemcitabine 1000 mg/m 2 alone on days 1, 8 and 15 every 28-days for a total of six cycles (single agent cohort), and after protocol amendment a combination therapy with gemcitabine 1000 mg/m 2 and cisplatin 25 mg/m 2 on days 1 and 8 was administered every 21 days for a total of eight cycles (combined regimen cohort). Treatment was planned to start within eight weeks after curative intent resection. Adverse events, disease-free survival and overall survival were assessed. Overall 30 patients were enrolled in the study from August 2008 and last patient was enrolled at 2nd December 2014. The follow-up of the patients ended at 31st December 2016. The first 9 patients received single-agent gemcitabine. The interim analysis met the predefined feasibility criteria and, from September 2010 on, the second group of 21 patients received the combination of cisplatin plus gemcitabine. In the single-agent cohort with gemcitabine the median relative dose intensity (RDI) was 100% (IQR 88.3-100). Patients treated with the combination cisplatin-gemcitabine received an overall median RDI of 100% (IQR 50-100) for cisplatin and 100% (IQR 75-100) for gemcitabine respectively. The most significant non-hematological adverse events (grade 3 or 4) were fatigue (20%), infections during neutropenia (10%), and two cases of biliary sepsis (7%). Abnormal liver function was seen in 10% of the patients. One patient died due to infectious complications during treatment with cisplatin and gemcitabine. The median disease-free survival (DFS) was 14.9 months (95% CI 0-33.8) with a corresponding 3-year DFS of 43.1 ± 9.1%. The median overall survival (OS) was 40.6 months (95% CI 18.8-62.3) with a 3-year OS of 55.7 ± 9.2%. No statistically significant differences in survival were seen between the two treatment cohorts. Adjuvant chemotherapy with gemcitabine with or without cisplatin was well tolerated and resulted in promising survival of the patients. The study was retrospectively registered on 25th June 2009 at clinicaltrials.gov ( NCT01073839 ).

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.

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…

Management of Mediastinal Relapse after Treatment with Stereotactic Body Radiotherapy or Accelerated Hypofractionated Radiotherapy for Stage I/II Non–Small-Cell Lung Cancer

PubMed Central

Kilburn, Jeremy M.; Lester, Scott C.; Lucas, John T.; Soike, Michael H.; Blackstock, A. William; Kearns, William T.; Hinson, William H.; Miller, Antonius A.; Petty, William J.; Munley, Michael T.; Urbanic, James J.

2014-01-01

Purpose/Objective(s) Regional failures occur in up to 15% of patients treated with stereotactic body radiotherapy (SBRT) for stage I/II lung cancer. This report focuses on the management of the unique scenario of isolated regional failures. Methods Patients treated initially with SBRT or accelerated hypo-fractionated radiotherapy were screened for curative intent treatment of isolated mediastinal failures (IMFs). Local control, regional control, progression-free survival, and distant control were estimated from the date of salvage treatment using the Kaplan–Meier method. Results Among 160 patients treated from 2002 to 2012, 12 suffered IMF and were amenable to salvage treatment. The median interval between treatments was 16 months (2–57 mo). Median salvage dose was 66 Gy (60–70 Gy). With a median follow-up of 10 months, the median overall survival was 15 months (95% confidence interval, 5.8–37 mo). When estimated from original treatment, the median overall survival was 38 months (95% confidence interval, 17–71 mo). No subsequent regional failures occurred. Distant failure was the predominant mode of relapse following salvage for IMF with a 2-year distant control rate of 38%. At the time of this analysis, three patients have died without recurrence while four are alive and no evidence of disease. High-grade toxicity was uncommon. Conclusions To our knowledge, this is first analysis of salvage mediastinal radiation after SBRT or accelerated hypofractionated radiotherapy in lung cancer. Outcomes appear similar to stage III disease at presentation. Distant failures were common, suggesting a role for concurrent or sequential chemotherapy. A standard full course of external beam radiotherapy is advisable in this unique clinical scenario. PMID:24736084

Unusual Application Of Ion Beam Analysis For The Study Of Surface Layers On Materials Relevant To Cultural Heritage

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

Mathis, F.; Service de Recherche en Metallurgie Physique CEA Saclay 91191 Gif sur Yvette Cedex; Centre Europeen d'Archeometrie Universite de Liege Sart Tilman B15 4000 Liege

2006-12-01

Recently a new thematic of research -- intentional patinas on antic copper-base objects -- lead the AGLAE (Accelerateur Grand Louvre pour l'Analyse Elementaire) team of the C2RMF (Centre de Recherche et de Restauration des Musees de France) to improve its methods of analyzing thin surface layers both in their elemental composition and in-depth elemental distribution. A new beam extraction set-up containing a particle detector has been developed in order to use a 6 MeV alpha beam both in PIXE and RBS mode and to monitor precisely the ion dose received by the sample. Both RBS and ionization cross sections weremore » assessed in order to make sure that the analysis can be quantitative. This set up allows great progresses in the understanding of both nature and structure of this very particular oxide layer obtained in the antiquity by chemical treatment on copper alloys, containing gold and/or silver and presenting very interesting properties of color and stability.Besides the non destructive properties of the IBA in external beam mode, this method of analyzing allows the study of samples in interaction with its environment. This was used to study the high temperature oxidation of Cu-Sn alloys using a furnace developed in order to heat a sample and analyze it in RBS mode at the same time. This new way of studying the growth of oxide layers permits to understand the oxidation mechanism of this system and to propose an experimental model for the identification of oxide layers due to an exposition to a high temperature, model needed for a long time by curators in charge of the study and the conservation of archaeological bronzes.« less

Early results of prostate cancer radiation therapy: an analysis with emphasis on research strategies to improve treatment delivery and outcomes

PubMed Central

2013-01-01

Background There is scant data regarding disease presentation and treatment response among black men living in Africa. In this study we evaluate disease presentation and early clinical outcomes among Ghanaian men with prostate cancer treated with external beam radiotherapy (EBRT). Methods A total of 379 men with prostate cancer were referred to the National Center for Radiotherapy, Ghana from 2003 to 2009. Data were collected regarding patient-and tumor-related factors such as age, prostate specific antigen (PSA), Gleason score (GS), clinical stage (T), and use of androgen deprivation therapy (ADT). For patients who received EBRT, freedom from biochemical failure (FFbF) was evaluated using the Kaplan-Meier method. Results Of 379 patients referred for treatment 69.6% had initial PSA (iPSA) > 20 ng/ml, and median iPSA was 39.0 ng/ml. A total of 128 men, representing 33.8% of the overall cohort, were diagnosed with metastatic disease at time of referral. Among patients with at least 2 years of follow-up after EBRT treatment (n=52; median follow-up time: 38.9 months), 3- and 5-year actuarial FFbF was 73.8% and 65.1% respectively. There was significant association between higher iPSA and GS (8–10 vs. ≤7, p < 0.001), and T stage (T3/4 vs. T1/2, p < 0.001). Conclusions This is the largest series reporting on outcomes after prostate cancer treatment in West Africa. That one-third of patients presented with metastatic disease suggests potential need for earlier detection to permit curative-intent therapy. Data from this study will aid in the strategic development of prostate cancer research roadmap in Ghana. PMID:23324165

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

Impact of Pretreatment Body Mass Index on Patients With Head-and-Neck Cancer Treated With Radiation

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

Pai, Ping-Ching; Chuang, Chi-Cheng; Tseng, Chen-Kan

2012-05-01

Purpose: To investigate the association of pretreatment body mass index (preT BMI) with outcomes of head-and-neck cancer in patients treated with radiotherapy (RT). Methods and Materials: All 1,562 patients diagnosed with head-and-neck cancer and treated with curative-intent RT to a dose of 60 Gy or higher were retrospectively studied. Body weight was measured both at entry and at the end of RT. Cancer-specific survival (CSS), overall survival (OS), locoregional control (LRC), and distant metastasis (DM) were analyzed by preT BMI (<25 kg/m{sup 2} vs. {>=}25 kg/m{sup 2}). The median follow-up was 8.6 years. Results: Patients with lower preT BMI weremore » statistically significantly associated with poorer CSS and OS than those with higher preT BMI. There was no significant difference between preT BMI groups in terms of LRC and DM. Body weight loss (BWL) during radiation did not influence survival outcomes. However, in the group with higher preT BMI, CSS, OS, and DM-free survival of patients with less BWL during radiation were statistically longer when compared with greater BWL. Conclusion: This study demonstrates that higher preT BMI positively influenced survival outcomes for patients with head-and-neck cancer. Patients with higher preT BMI who were able to maintain their weight during radiation had significantly better survival than patients with greater BWL.« less

Impact of HPV Status on the Prognostic Potential of the AJCC Staging System for Larynx Cancer.

PubMed

Davidson, Stacey M; Ko, Huasing C; Harari, Paul M; Wieland, Aaron M; Chen, Shuai; Baschnagel, Andrew M; Kimple, Randall J; Witek, And Matthew E

2018-04-01

Objective We evaluated the ability of the American Joint Committee on Cancer (AJCC) seventh edition staging system to prognosticate the overall survival of patients with human papillomavirus (HPV)-positive laryngeal squamous cell carcinoma. Study Design Retrospective analysis. Setting National Cancer Database. Subjects and Methods Patients diagnosed with laryngeal squamous cell carcinoma who were treated with curative intent were identified in the National Cancer Database. Multivariate analysis was utilized to determine factors correlated with overall survival in the HPV-negative and HPV-positive cohorts. Unadjusted and propensity score-weighted Kaplan-Meier estimation was used to determine overall survival of HPV-negative and HPV-positive patients across AJCC stage groupings. Results We identified 3238 patients with laryngeal squamous cell carcinoma, of which 2812 were HPV negative and 426 were HPV positive. Overall survival adjusted for age, sex, and comorbidity status confirmed significant differences among all consecutive stage groupings (I vs II, P < .001; II vs III, P < .05; III vs IVA, P < .001; IVA vs IVB, P < .05) in the HPV-negative cohort, whereas only stages IVAs and IVB ( P < .01) exhibited a significant difference in overall survival for HPV-positive patients. Conclusion The current AJCC staging system does not accurately distinguish risk of mortality for patients with HPV-positive disease. These data support the consideration of HPV status in estimating prognosis as well as clinical trial design and clinical decision making for patients with laryngeal squamous cell carcinoma.

[Integrated therapeutic strategy in large bowel neoplastic occlusion. An innovative therapeutic protocol].

PubMed

Gattai, Riccardo; Mascitelli, Erminia Macera; Bechi, Paolo; Pace, Marcello

2007-01-01

Occlusive complication is a common event in the colo-rectal cancer (20-30% of cases). Operative mortality and 5 yrs survival of not occlusive cancer vs occlusive cancer is 11% vs 23% and 45% vs 25% rispectively. In occlusive cancer the level of parietal infiltration affects considerably the local and peritoneal recurrence. 50% of all patients underwent a surgical re-operation for colo-rectal cancer have peritoneal neoplastic implant. The resolution of occlusive complication in immediate or delayed urgency with decompressive derivation, it allows to perform an integrated treatment of choice that it could guarantee the oncological radical procedure. RATIONALE-METHODS: The intraperitoneal hyperthermic chemotherapy (IPHC) combined with radical or cytoriductive surgery performs its action through sinergistic effects of high dosage and concentration of drugs and hyperthermia. These agents perform a cell killing with a direct contact against micro and/or macroscopic neoplastic residue. In radical surgery with curative intent, the association with IPHC ("preventive" adjuvant) has got as objective the distruction of microscopic local or peritoneal metastasis. In occlusive cancer with synchronous or metachronous peritoneal carcinomatosis, the performance of the cytoreductive surgery with IPHC ("therapeutic" adjuvant) is the only treatment that improves the survival and the quality of remainig life. The clinical results reported by many Istitutions indicates that the 2-5 yrs survivals are 45-60% and 20-30% rispectively. These data lead us to believe that an optimal eradication of micro and/or macroscopic peritoneal spreading could be optained also in occlusive colo-rectal cancer.

A prospective evaluation of the impact of 18-F-fluoro-deoxy-D-glucose positron emission tomography staging on survival for patients with locally advanced esophageal cancer

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

Blackstock, A. William; Farmer, Michael R.; Lovato, James

2006-02-01

Purpose: To determine the impact of 18-F-fluoro-deoxy-D-glucose positron emission tomography (FDG-PET) in the staging and prognosis of patients with locally advanced esophageal cancer (LAEC). Methods and Materials: Between January 2000 and October 2004, all patients with LAEC evaluated in the Department of Radiation Oncology were considered for enrollment into a Phase II trial of preoperative chemoradiation. Entry required a staging whole-body FDG-PET scan. Results: One hundred ten consecutive patients were evaluated; 38 were ineligible for reasons including treatment elsewhere, prior malignancy, or refusal of treatment. After conventional staging (clinical examination, endoscopic ultrasound, and chest/abdominal computerized tomography), 33 patients were ineligiblemore » because of metastatic disease or poor performance status. Of the remaining 39 patients, 23 were confirmed to have LAEC after FDG-PET staging and were treated in the Phase II trial (Cohort I). Sixteen patients, however, had FDG-PET findings consistent with occult metastatic disease and were deemed ineligible for the trial but were treated with curative intent (Cohort II). The 2-year survival rate for the 23 patients in Cohort I was 64%, compared with 17% (p = 0.003) for patients in Cohort II (FDG-PET positive). Conclusions: More than one-third of patients determined to have LAEC with conventional staging were upstaged with the use of FDG-PET. Despite comparable therapy, upstaging with FDG-PET predicts poor 2-year survival.« less

Perineural Infiltration of Cutaneous Squamous Cell Carcinoma and Basal Cell Carcinoma Without Clinical Features

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

Lin, Charles, E-mail: Charles_Lin@health.qld.gov.au; Tripcony, Lee; Keller, Jacqui

2012-01-01

Purpose: To review the factors that influence outcome and patterns of relapse in patients with cutaneous squamous cell carcinoma (SCC) and basal cell carcinoma (BCC) with perineural infiltration (PNI) without clinical or radiologic features, treated with surgery and radiotherapy. Methods and Materials: Between 1991 and 2004, 222 patients with SCC or BCC with PNI on pathologic examination but without clinical or radiologic PNI features were identified. Charts were reviewed retrospectively and relevant data collected. All patients were treated with curative intent; all had radiotherapy, and most had surgery. The primary endpoint was 5-year relapse-free survival from the time of diagnosis.more » Results: Patients with SCC did significantly worse than those with BCC (5-year relapse-free survival, 78% vs. 91%; p < 0.01). Squamous cell carcinoma with PNI at recurrence did significantly worse than de novo in terms of 5-year local failure (40% vs. 19%; p < 0.01) and regional relapse (29% vs. 5%; p < 0.01). Depth of invasion was also a significant factor. Of the PNI-specific factors for SCC, focal PNI did significantly better than more-extensive PNI, but involved nerve diameter or presence of PNI at the periphery of the tumor were not significant factors. Conclusions: Radiotherapy in conjunction with surgery offers an acceptable outcome for cutaneous SCC and BCC with PNI. This study suggests that focal PNI is not an adverse feature.« less

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

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

Barral, M., E-mail: matthias-barral@yahoo.fr; Auperin, A., E-mail: anne.auperin@gustaveroussy.fr; Hakime, A., E-mail: thakime@yahoo.com

ObjectiveTo evaluate prognostic factors associated with local control and disease-free-survival (DFS) of oligometastatic breast cancer patients treated by percutaneous thermal ablation (PTA).Materials and MethodsSeventy-nine consecutive patients (54.5 ± 11.2 years old) with 114 breast cancer metastases (28.9 ± 16.1 mm in diameter), involving the lungs, the liver, and/or the bone, were treated using PTA with a curative intent. The goal was to achieve a complete remission in association with systemic chemotherapy and hormonal therapy. We retrospectively evaluated the prognostic factors associated with 1- and 2-year local control and the 1- and 2-year DFS rates.ResultsThe 1- and 2-year local control rates were 83.0 and 76.1 %, respectively. Tumormore » burden was associated with a poorer outcome for local control after PTA (HR 1.027 by additional millimeter, p = 0.026; >4 cm HR 3.90). The 1- and 2-year DFS rates were 54.2 and 30.4 %, respectively. In multivariate analysis, triple-negative histological subtype and increased size of treated metastases were associated with a poorer DFS (HR 2.22; 95 % CI [1.13–4.36]; p = 0.02 and HR 2.43; 95 % CI [1.22–4.82]; p = 0.011, respectively).ConclusionPTA is effective for local control of breast cancer oligometastases. Tumor burden >4 cm and triple-negative histological subtype are associated with a poorer outcome.« less

Margin to tumor thickness ratio - A predictor of local recurrence and survival in oral squamous cell carcinoma.

PubMed

Heiduschka, Gregor; Virk, Sohaib A; Palme, Carsten E; Ch'ng, Sydney; Elliot, Michael; Gupta, Ruta; Clark, Jonathan

2016-04-01

To assess whether small oral squamous cell carcinomas (OSCC) require the same margin clearance as large tumors. We evaluated the association between the ratio of the closest margin to tumor size (MSR) and tumor thickness (MTR) with local control and survival. The clinicopathologic and follow up data were obtained for 501 OSCC patients who had surgical resection with curative intent at our institution. MTR and MSR were computed and their associations with local control and survival were assessed using multivariable Cox-regression model. Survival curves were generated using the Kaplan-Meier method. MTR was a better predictor of disease control than MSR. MTR was a predictor of local failure (p=0.033) and disease specific death (p=0.038) after adjusting for perineural invasion, lymphovascular involvement, nodal status, and radiotherapy. A threshold MTR value of 0.3 was identified, above which the risk of local recurrence was low. The ratio of margin to tumor thickness was an independent predictor for local recurrence and disease specific death in this cohort. A MTR>0.3 can serve as a useful tool for adjuvant therapy planning as it combines tumor thickness and margin clearance, two well established prognostic factors. The minimum safe margin can be calculated by multiplying the tumor thickness by 0.3. Further prospective studies in other institutions are warranted to confirm the prognostic utility of MTR and assess the generalizability of our threshold values. Copyright © 2016 Elsevier Ltd. All rights reserved.

Decision-making by surgeons about referral for adjuvant therapy for patients with non-small-cell lung, breast or colorectal cancer: a qualitative study

PubMed Central

Urquhart, Robin; Kendell, Cynthia; Buduhan, Gordon; Rayson, Daniel; Sargeant, Joan; Johnson, Paul; Grunfeld, Eva; Porter, Geoffrey A.

2016-01-01

Background: Because surgeons are the main gatekeepers to oncology services, understanding how they make decisions related to referral for adjuvant therapies is important to optimize referral rates and use of oncology services for patients with potentially curable disease. We examined decision-making by surgeons related to referral to oncology services for patients having undergone curative-intent surgery for non-small-cell lung, breast or colorectal cancer. Methods: We conducted a qualitative study, whose design was guided by the principles of grounded theory. Semi-structured interviews were held with 29 surgeons who performed non-small-cell lung, breast or colorectal cancer surgery in the province of Nova Scotia. Data were collected and analyzed concurrently. Analysis involved an inductive, grounded approach using constant comparative analysis. Data collection and analysis continued until theoretical saturation was reached. Results: Seven factors influenced the surgeons' decision-making related to referral to oncology services: indications and contraindications for therapy; patients' beliefs and preferences; a belief that oncologists are the experts; knowledge of local standards of care; consultation with oncology colleagues; navigating patient logistics (e.g., lodging, caregiving responsibilities, insurance coverage); and system resources and capacity. Interpretation: Our study's findings provide a novel understanding of how surgeons make decisions about oncology referral and point to potential areas for intervention to promote referral to oncology services for patients for whom adjuvant therapy is recommended. PMID:27570760

High dose hypofractionated frameless volumetric modulated arc radiotherapy is a feasible method for treating canine trigeminal nerve sheath tumors.

PubMed

Dolera, Mario; Malfassi, Luca; Marcarini, Silvia; Mazza, Giovanni; Carrara, Nancy; Pavesi, Simone; Sala, Massimo; Finesso, Sara; Urso, Gaetano

2018-06-08

The aim of this prospective pilot study was to evaluate the feasibility and effectiveness of curative intent high dose hypofractionated frameless volumetric modulated arc radiotherapy for treatment of canine trigeminal peripheral nerve sheath tumors. Client-owned dogs with a presumptive imaging-based diagnosis of trigeminal peripheral nerve sheath tumor were recruited for the study during the period of February 2010 to December 2013. Seven dogs were enrolled and treated with high dose hypofractionated volumetric modulated arc radiotherapy delivered by a 6 MV linear accelerator equipped with a micro-multileaf beam collimator. The plans were computed using a Monte Carlo algorithm with a prescription dose of 37 Gy delivered in five fractions on alternate days. Overall survival was estimated using a Kaplan-Meier curve analysis. Magnetic resonance imaging (MRI) follow-up examinations revealed complete response in one dog, partial response in four dogs, and stable disease in two dogs. Median overall survival was 952 days with a 95% confidence interval of 543-1361 days. Volumetric modulated arc radiotherapy was demonstrated to be feasible and effective for trigeminal peripheral nerve sheath tumor treatment in this sample of dogs. The technique required few sedations and spared organs at risk. Even though larger studies are required, these preliminary results supported the use of high dose hypofractionated volumetric modulated arc radiotherapy as an alternative to other treatment modalities. © 2018 American College of Veterinary Radiology.

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

Huang, Eugene H.; Strom, Eric A.; Valero, Vicente

Purpose: To evaluate the locoregional efficacy of multimodality treatment for breast cancer patients who present with ipsilateral supraclavicular (SCV) disease without systemic metastases. Methods: We retrospectively reviewed the data from 71 patients with ipsilateral SCV involvement at presentation. SCV involvement in 16 patients (23%) was diagnosed by ultrasound examination only, without palpable disease. All patients were treated with curative intent using neoadjuvant chemotherapy, mastectomy or breast-conserving surgery (BCT), and radiotherapy. Results: The 5-year SCV control, locoregional control (LRC), disease-free survival, and overall survival rate was 90%, 77%, 30%, and 47%, respectively. Patients with persistent SCV disease after neoadjuvant chemotherapy bymore » physical examination had a lower rate of LRC (64% vs. 86%, p = 0.026), as did those with persistent SCV disease by ultrasound examination (66% vs. 96%, p = 0.007). Of those with a complete response of SCV disease by physical examination after neoadjuvant chemotherapy, those with persistently abnormal ultrasound findings had significantly worse disease-free survival (0% vs. 55%, p = 0.03). BCT was not associated with lower rates of LRC (82% for BCT vs. 76% for mastectomy, p = 0.80). Conclusion: Radiotherapy achieved excellent LRC after surgery for patients with ipsilateral SCV metastases who achieved a complete response of the SCV disease after neoadjuvant chemotherapy. For patients who achieved a complete response of the SCV disease by physical examination, ultrasonography of the SCV fossa may help assess the risk of disease recurrence. SCV involvement should not be considered a contraindication for BCT.« less

CA 19-9 as a Marker of Survival and a Predictor of Metastization in Cholangiocarcinoma

PubMed Central

Coelho, Rosa; Silva, Marco; Rodrigues-Pinto, Eduardo; Cardoso, Hélder; Lopes, Susana; Pereira, Pedro; Vilas-Boas, Filipe; Santos-Antunes, João; Costa-Maia, José; Macedo, Guilherme

2017-01-01

Background Cholangiocarcinoma is the second most frequent primitive liver malignancy and is responsible for 3% of the malignant gastrointestinal neoplasms. The aims of this study were to determine the association of serum levels of CA 19-9 at diagnosis with other clinical data and serum liver function tests and to identify possible factors that influence the survival rates during follow-up. Methods Retrospective observational study of 89 patients with a diagnosis of cholangiocarcinoma followed at the Department of Gastroenterology during 5 years. Statistical analyses were performed using SPSS version 20.0. Results Patients were followed up for a median time of 127 days (IQR: 48–564), and the median age at diagnosis was 71.0 years (IQR: 62.0–77.5). The median survival rate was 14.0 months (IQR: 4.3–23.7), and the mortality rate was 79%. Patients with CA 19-9 levels ≥103 U/L had lower albumin levels and higher levels of alanine aminotransferase and γ-glutamyltransferase. CA 19-9 levels ≥103 U/L were associated with a higher probability of metastization (p = 0.001) and lower rates of treatment with curative intent (p = 0.024). In a multivariate analysis, CA 19-9 levels <103 U/L and surgery were independent predictors of survival. Conclusion Predictive factors for overall survival were identified, namely presence of metastasis, surgery, and chemotherapy. CA 19-9 levels ≥103 U/L were predictive factors for survival and metastization. PMID:28848795

Retroperitoneal liposarcomas: the experience of a tertiary Asian center

PubMed Central

2011-01-01

Background Liposarcoma is the single most common soft tissue sarcoma in the retroperitoneum. Materials and methods A retrospective review of patients with primary retroperitoneal liposarcoma treated between June 1990 and June 2005 were conducted to evaluate the clinical results of resection for retroperitoneal liposarcomas (RPLS) and the prognostic factors for disease recurrence and patient survival in an Asian population. Results Twenty-one patients operated on for curative intent (12 Males, 9 Females; mean age: 52.4 years) were evaluated. Of these, 13 presented with tumors that were well differentiated (61.9%), 4 (19.0%) with myxoid/round cell, 3 (14.3%) with dedifferentiated and 1(4.8%) with pleomorphic morphology. The median tumor burden was 36 cm (9-83). Median follow-up time was 62 months. There was no peri-operative mortality and morbidity occurred in 6(28.6%) patients. Surgical margins were involved in 10(47.6%) patients. Resection of contiguous organs was required in 15(71.4%) to achieve gross surgical margins. Eleven out of the 21(52%) of the patients had recurrence of the tumor. Median disease-free survival was 19 months and the overall 3- and 5-year survival rate was 87% and 49% respectively. Conclusion An aggressive surgical approach in both primary and recurrent RPLS in our institution is associated with 3- and 5-year survival rate of 87% and 49% respectively. Contiguous organ resection is often required to achieve local control. PMID:21284868

Undergraduate Health Students' Intention to Use Evidence-Based Practice After Graduation: A Systematic Review of Predictive Modeling Studies.

PubMed

Ramis, Mary-Anne; Chang, Anne; Nissen, Lisa

2018-04-01

Incorporating evidence-based practice (EBP) into clinical decision making and professional practice is a requirement for many health disciplines, yet research across health disciplines on factors that influence and predict student intention to use EBP following graduation has not been previously synthesized. To synthesize research on factors that influence development of EBP behaviors and subsequently predict undergraduate students' intention toward EBP uptake. A systematic review of prediction modeling studies was conducted according to a protocol previously published on the Prospero database: https://www.crd.york.ac.uk/PROSPERO/. The outcome variable was undergraduate students' future use or intention to use EBP. Evidence synthesis methods were guided by resources from the Cochrane Methods Prognosis Group Web site (https://prognosismethods.cochrane.org). Only three studies were found to meet inclusion criteria for the review. Factors relating to EBP capability, EBP attitudes, as well as clinical and academic support were identified as influential toward students' intention to use evidence in practice. Heterogeneity limited data pooling, consequently, results are presented in narrative and tabular form. Although using a developing method, this review presents a unique contribution to further discussions regarding students' intention to use EBP following graduation. Despite limitations, consideration of identified factors for undergraduate curriculum could support student's intention to use EBP in their respective clinical environments. © 2017 Sigma Theta Tau International.

Reducing data friction through site-based data curation

NASA Astrophysics Data System (ADS)

Thomer, A.; Palmer, C. L.

2017-12-01

Much of geoscience research takes place at "scientifically significant sites": localities which have attracted a critical mass of scientific interest, and thereby merit protection by government bodies, as well as the preservation of specimen and data collections and the development of site-specific permitting requirements for access to the site and its associated collections. However, many data standards and knowledge organization schemas do not adequately describe key characteristics of the sites, despite their centrality to research projects. Through work conducted as part of the IMLS-funded Site-Based Data Curation (SBDC) project, we developed a Minimum Information Framework (MIF) for site-based science, in which "information about a site's structure" is considered a core class of information. Here we present our empirically-derived information framework, as well as the methods used to create it. We believe these approaches will lead to the development of more effective data repositories and tools, and thereby will reduce "data friction" in interdisciplinary, yet site-based, geoscience workflows. The Minimum Information Framework for Site-based Research was developed through work at two scientifically significant sites: the hot springs at Yellowstone National Park, which are key to geobiology research; and the La Brea Tar Pits, an important paleontology locality in Southern California. We employed diverse methods of participatory engagement, in which key stakeholders at our sites (e.g. curators, collections managers, researchers, permit officers) were consulted through workshops, focus groups, interviews, action research methods, and collaborative information modeling and systems analysis. These participatory approaches were highly effective in fostering on-going partnership among a diverse team of domain scientists, information scientists, and software developers. The MIF developed in this work may be viewed as a "proto-standard" that can inform future repository development and data standards. Further, the approaches used to develop the MIF represent an important step toward systematic methods of developing geoscience data standards. Finally, we argue that organizing data around aspects of a site makes data collections more accessible to a range of scientific communities.

Women and postfertilization effects of birth control: consistency of beliefs, intentions and reported use.

PubMed

Dye, Huong M; Stanford, Joseph B; Alder, Stephen C; Kim, Han S; Murphy, Patricia A

2005-11-28

This study assesses the consistency of responses among women regarding their beliefs about the mechanisms of actions of birth control methods, beliefs about when human life begins, the intention to use or not use birth control methods that they believe may act after fertilization or implantation, and their reported use of specific methods. A questionnaire was administered in family practice and obstetrics and gynecology clinics in Salt Lake City, Utah, and Tulsa, Oklahoma. Participants included women ages 18-50 presenting for any reason and women under age 18 presenting for family planning or pregnancy care. Analyses were based on key questions addressing beliefs about whether specific birth control methods may act after fertilization, beliefs about when human life begins, intention to use a method that may act after fertilization, and reported use of specific methods. The questionnaire contained no information about the mechanism of action of any method of birth control. Responses were considered inconsistent if actual use contradicted intentions, if one intention contradicted another, or if intentions contradicted beliefs. Of all respondents, 38% gave consistent responses about intention to not use or to stop use of any birth control method that acted after fertilization, while 4% gave inconsistent responses. The corresponding percentages for birth control methods that work after implantation were 64% consistent and 2% inconsistent. Of all respondents, 34% reported they believed that life begins at fertilization and would not use any birth control method that acts after fertilization (a consistent response), while 3% reported they believed that life begins at fertilization but would use a birth control method that acts after fertilization (inconsistent). For specific methods of birth control, less than 1% of women gave inconsistent responses. A majority of women (68% or greater) responded accurately about the mechanism of action of condoms, abstinence, sterilization, and abortion, but a substantial percentage of women (between 19% and 57%) were uncertain about the mechanisms of action of oral contraceptives, intrauterine devices (IUDs), Depo-Provera, or natural family planning. Women who believe that life begins at fertilization may not intend to use a birth control method that could have postfertilization effects. More research is needed to understand the relative importance of postfertilization effects for women in other populations, and in relation to other properties of and priorities for birth control methods. However, many women were uncertain about the mechanisms of action of specific methods. To respect the principles of informed consent, some women may need more education about what is known and not known about the mechanisms of action of birth control methods.

Brain imaging before primary lung cancer resection: a controversial topic.

PubMed

Hudson, Zoe; Internullo, Eveline; Edey, Anthony; Laurence, Isabel; Bianchi, Davide; Addeo, Alfredo

2017-01-01

International and national recommendations for brain imaging in patients planned to undergo potentially curative resection of non-small-cell lung cancer (NSCLC) are variably implemented throughout the United Kingdom [Hudson BJ, Crawford MB, and Curtin J et al (2015) Brain imaging in lung cancer patients without symptoms of brain metastases: a national survey of current practice in England Clin Radiol https://doi.org/10.1016/j.crad.2015.02.007]. However, the recommendations are not based on high-quality evidence and do not take into account cost implications and local resources. Our aim was to determine local practice based on historic outcomes in this patient cohort. This retrospective study took place in a regional thoracic surgical centre in the United Kingdom. Pathology records for all patients who had undergone lung resection with curative intent during the time period January 2012-December 2014 were analysed in October 2015. Electronic pathology and radiology reports were accessed for each patient and data collected about their histological findings, TNM stage, resection margins, and the presence of brain metastases on either pre-operative or post-operative imaging. From the dates given on imaging, we calculated the number of days post-resection that the brain metastases were detected. 585 patients were identified who had undergone resection of their lung cancer. Of these, 471 had accessible electronic radiology records to assess for the radiological evidence of brain metastases. When their electronic records were evaluated, 25/471 (5.3%) patients had radiological evidence of brain metastasis. Of these, five patients had been diagnosed with a brain metastasis at initial presentation and had undergone primary resection of the brain metastasis followed by resection of the lung primary. One patient had been diagnosed with both a primary lung and a primary bowel adenocarcinoma; on review of the case, it was felt that the brain metastasis was more likely to have originated from the bowel cancer. One had been clinically diagnosed with a cerebral abscess while the radiology had been reported as showing a metastatic deposit. Of the remaining 18/471 (3.8%) patients who presented with brain metastases after their surgical resection, 12 patients had adenocarcinoma, four patients had squamous cell carcinoma, one had basaloid, and one had large-cell neuroendocrine. The mean number of days post-resection that the brain metastases were identified was 371 days, range 14-1032 days, median 295 days (date of metastases not available for two patients). The rate of brain metastases identified in this study was similar to previous studies. This would suggest that preoperative staging of the central nervous system may change the management pathway in a small group of patients. However, for this group of patients, the change would be significant either sparing them non-curative surgery or allowing aggressive management of oligometastatic disease. Therefore, we would recommend pre-operative brain imaging with MRI for all patients undergoing potentially curative lung resection.

Phase 1 Trial of Bevacizumab With Concurrent Chemoradiation Therapy for Squamous Cell Carcinoma of the Head and Neck With Exploratory Functional Imaging of Tumor Hypoxia, Proliferation, and Perfusion

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

Nyflot, Matthew J., E-mail: nyflot@uw.edu; Kruser, Tim J.; Traynor, Anne M.

2015-04-01

Purpose: A phase 1 trial was completed to examine the safety and feasibility of combining bevacizumab with radiation and cisplatin in patients with locoregionally advanced squamous cell carcinoma of the head and neck (HNSCC) treated with curative intent. Additionally, we assessed the capacity of bevacizumab to induce an early tumor response as measured by a series of biological imaging studies. Methods and Materials: All patients received a single induction dose of bevacizumab (15 mg/kg) delivered 3 weeks (±3 days) before the initiation of chemoradiation therapy. After the initial dose of bevacizumab, comprehensive head and neck chemoradiation therapy was delivered with curativemore » intent to 70 Gy in 33 fractions with concurrent weekly cisplatin at 30 mg/m{sup 2} and bevacizumab every 3 weeks (weeks 1, 4, 7) with dose escalation from 5 to 10 to 15 mg/kg. All patients underwent experimental imaging with [{sup 18}F]fluorothymidine positron emission tomography (FLT-PET) (proliferation), [{sup 61}Cu]Cu-diacetyl-bis(N4-methylthiosemicarbazone) PET (Cu-ATSM-PET) (hypoxia), and dynamic contrast-enhanced computed tomography (DCE-CT) (perfusion) at 3 time points: before bevacizumab monotherapy, after bevacizumab monotherapy, and during the combined therapy course. Results: Ten patients were enrolled. All had stage IV HNSCC, all achieved a complete response to treatment, and 9 of 10 remain alive, with a mean survival time of 61.3 months. All patients experienced grade 3 toxicity, but no dose-limiting toxicities or significant bleeding episodes were observed. Significant reductions were noted in tumor proliferation (FLT-PET), tumor hypoxia (Cu-ATSM-PET), and DCE-CT contrast enhancement after bevacizumab monotherapy, with further decreases in FLT-PET and Cu-ATSM-PET during the combined therapy course. Conclusions: The incorporation of bevacizumab into comprehensive chemoradiation therapy regimens for patients with HNSCC appears safe and feasible. Experimental imaging demonstrates measureable changes in tumor proliferation, hypoxia, and perfusion after bevacizumab monotherapy and during chemoradiation therapy. These findings suggest opportunities to preview the clinical outcomes for individual patients and thereby design personalized therapy approaches in future trials.« less

[Clinical observation of using composite resin to fill dental attrition on occlusal surface].

PubMed

Guo, Li-juan; Xu, Yan; Chen, Guang-quan

2005-10-01

The purpose of this study was to evaluate the clinical effect of using composite resin to fill dental attrition on occlusal surface. Whether the dental attrition had enough space to the material was determined first. Sometimes grinding the sharp and steep cusps or ridges of the opposite teeth was needed. Then the dental attrition was cleaned thoroughly, and finally filled with CLEARFIL bond and composite resin without preparing cavity. The follow-up period was 1 year. Out of 70 teeth from 25 patients, 52 were successful, 16 were curative, and 2 were failed. The curative rate was 97.14%. The method avoids endangering the dental pulp. It was easily accepted by the patients and operated by dentists, and can be widely applied in clinical cases.

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…

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.

Who meets their intentions to stop childbearing? Results of a longitudinal study in rural eastern Bali, Indonesia.

PubMed

Withers, Mellissa; Tavrow, Paula; Abe, Denise

2012-01-01

In this longitudinal study from rural Bali, Indonesia, we sought to identify the predictors of birth avoidance among 665 married women of reproductive age who reported the intention to stop childbearing. We found that almost 30% of women who wanted no more children had a subsequent birth during the 4-year study period. Women at highest risk for an unwanted birth were younger, had fewer children, and did not use a long-term contraceptive method. The ability to meet intentions to stop childbearing depended on women's motivation (family size), fecundity (proxied by age), and their use of long-term contraceptive methods. Our results suggest that to reduce unwanted births among rural women, family planning providers should recommend long-term methods to younger women with smaller family sizes who express clear intentions to stop childbearing.

Pregnancy Intentions and Safer Pregnancy Knowledge Among Female Sex Workers in Port Elizabeth, South Africa.

PubMed

Rao, Amrita; Baral, Stefan; Phaswana-Mafuya, Nancy; Lambert, Andrew; Kose, Zamakayise; Mcingana, Mfezi; Holland, Claire; Ketende, Sosthenes; Schwartz, Sheree

2016-07-01

To assess the association between human immunodeficiency virus (HIV) and pregnancy intentions and safer conception knowledge among female sex workers in Port Elizabeth, South Africa. This cross-sectional study recruited female sex workers in Port Elizabeth using respondent-driven sampling and completed an interviewer-administered questionnaire alongside HIV testing and counseling. In this secondary analysis, robust Poisson regression was used to model prevalence ratios for positive fertility intentions in this cross-sectional study. Knowledge of safer conception methods by HIV status was compared using Fisher exact tests. Overall 391 women were represented in the analyses. More than 50% had a prior HIV diagnosis, and an additional 12% were diagnosed with HIV during the study. Approximately half (n=185) of the women reported future pregnancy intentions. In univariate analysis, a prior HIV diagnosis was negatively associated with pregnancy intentions as compared with HIV-negative women (prevalence ratio 0.68, 95% confidence interval 0.55-0.85). Only parity remained independently associated with future pregnancy intentions in multivariate regression after controlling for HIV status, age, race, relationship status, and years selling sex. Knowledge of safer conception methods such as timed sex without a condom, preexposure prophylaxis, or self-insemination was low and similar between those with and without future pregnancy plans. Pregnancy intentions did not significantly vary according to HIV status. Fertility intentions were high, however, and knowledge of safer conception methods low, suggesting a need to provide female sex workers with advice around options to conceive safely in the context of high HIV prevalence.

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.

Principle-based concept analysis: intentionality in holistic nursing theories.

PubMed

Aghebati, Nahid; Mohammadi, Eesa; Ahmadi, Fazlollah; Noaparast, Khosrow Bagheri

2015-03-01

This is a report of a principle-based concept analysis of intentionality in holistic nursing theories. A principle-based concept analysis method was used to analyze seven holistic theories. The data included eight books and 31 articles (1998-2011), which were retrieved through MEDLINE and CINAHL. Erickson, Kriger, Parse, Watson, and Zahourek define intentionality as a capacity, a focused consciousness, and a pattern of human being. Rogers and Newman do not explicitly mention intentionality; however, they do explain pattern and consciousness (epistemology). Intentionality has been operationalized as a core concept of nurse-client relationships (pragmatic). The theories are consistent on intentionality as a noun and as an attribute of the person-intentionality is different from intent and intention (linguistic). There is ambiguity concerning the boundaries between intentionality and consciousness (logic). Theoretically, intentionality is an evolutionary capacity to integrate human awareness and experience. Because intentionality is an individualized concept, we introduced it as "a matrix of continuous known changes" that emerges in two forms: as a capacity of human being and as a capacity of transpersonal caring. This study has produced a theoretical definition of intentionality and provides a foundation for future research to further investigate intentionality to better delineate its boundaries. © The Author(s) 2014.

Intention to use long acting and permanent contraceptive methods and factors affecting it among married women in Adigrat town, Tigray, Northern Ethiopia

PubMed Central

2014-01-01

Background Despite the increase in contraceptive use worldwide over the last decade, there is still discrepancy in the need to limit birth and utilization of modern contraceptives specifically long acting and permanent contraceptive methods in sub-Saharan Africa including Ethiopia. Intention to use long acting and permanent methods of contraception is an important indicator of the potential demand for family planning services. Objective To assess intention to use long acting and permanent contraceptive methods (LAPMs) and identifying associated factors among currently married women in Adigrat town. Methods A community based cross sectional study design complemented with a qualitative method was conducted in three selected Kebeles of Adigrat town. A total of 594 study subjects were interviewed. Systematic random sampling method was used to select study subjects. Quantitative data were analyzed using SPSS version 16. Open code software version 3.6.2.0 was used to facilitate coding of the qualitative data. Factors associated with intention were identified using logistic regression model and content analysis was done on the qualitative data. Results Intention to use LAPMs was 48.4%. Intention to use LAPMs was higher among women who knew at least one of LAPMs (AOR = 4.7, 95% CI = 1.58, 14.01) and women who do not want to have birth within the next 2 years (AOR = 1.9, 95% CI = 1.22, 3.13). Intention to use LAMPs was less among women who perceive poor support from their husbands (AOR = 0.2, 95% CI = 0.09, 0.45) and those who perceive LAPMs are harmful for the womb (AOR = 0.24, 95% CI = 0.14, 0.41). Similarly, participants in the focus group discussion have expressed their concern on the return of fertility after using implants or IUCD as well as insertion and removal procedures. Conclusions The magnitude of intention to use LAPMs in the study area was low. The main limiting factors were fear of side effect, infertility after LAPMs use, knowledge on LAPMs and perception on partner’s support of LAPMs use. To further promote the use of LAPMs addressing associated misconceptions through effective communication strategies and involving spouses in family planning programs is essential. PMID:24628764

Intentionality: evolutionary development in healing: a grounded theory study for holistic nursing.

PubMed

Zahourek, Rothlyn P

2005-03-01

Although intentionality has been implicated as a causal variable in healing research, its definition has been inconsistent and vague. The objective of this grounded theory study is to develop a substantive theory of intentionality in a naturalistic encounter between nurse-healers and their healee-clients, and to consider the implications for practice and research. Six expert nurse-healers and six healee-clients were interviewed as individuals and in dyads before and after treatments. Interviews and observational data were analyzed using the constant comparative method and synthesized analysis. Participants described their experience of intentionality in healing as an evolutionary process characterized by distinctive shifts. The theory of intentionality: the matrix for healing (IMH) includes definitions of intentionality and a conceptual framework of three developmental phases of intentionality (generic, healing, and transforming intentionalities). The predominant attribute, development, is described. The theory contributes to knowledge about healing and intentionality and has implications for practice and future research.

A multilocus sequence typing method and curated database for Mycoplasma bovis

USDA-ARS?s Scientific Manuscript database

Mycoplasma bovis is a primary agent of mastitis, pneumonia and arthritis in cattle and is the bacterium isolated most frequently from the polymicrobial syndrome known as bovine respiratory disease complex (BRDC). Recently, M. bovis has emerged as a significant problem in bison, causing necrotic pha...

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.

Original Intent, Judicial Subjectivism, and the Establishment Clause: Implications for Educational Leaders

ERIC Educational Resources Information Center

Seigler, Timothy John

2005-01-01

The purpose of this article is to 1) examine the interpretive method applied to the United States Constitution referred of as"Original Intent" and the degree, if any, to which it is superior in objectivity than other methods, 2) discuss whether the application of the interpretive method would have an effect preferred by conservative or…

Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae

PubMed Central

Reguly, Teresa; Breitkreutz, Ashton; Boucher, Lorrie; Breitkreutz, Bobby-Joe; Hon, Gary C; Myers, Chad L; Parsons, Ainslie; Friesen, Helena; Oughtred, Rose; Tong, Amy; Stark, Chris; Ho, Yuen; Botstein, David; Andrews, Brenda; Boone, Charles; Troyanskya, Olga G; Ideker, Trey; Dolinski, Kara; Batada, Nizar N; Tyers, Mike

2006-01-01

Background The study of complex biological networks and prediction of gene function has been enabled by high-throughput (HTP) methods for detection of genetic and protein interactions. Sparse coverage in HTP datasets may, however, distort network properties and confound predictions. Although a vast number of well substantiated interactions are recorded in the scientific literature, these data have not yet been distilled into networks that enable system-level inference. Results We describe here a comprehensive database of genetic and protein interactions, and associated experimental evidence, for the budding yeast Saccharomyces cerevisiae, as manually curated from over 31,793 abstracts and online publications. This literature-curated (LC) dataset contains 33,311 interactions, on the order of all extant HTP datasets combined. Surprisingly, HTP protein-interaction datasets currently achieve only around 14% coverage of the interactions in the literature. The LC network nevertheless shares attributes with HTP networks, including scale-free connectivity and correlations between interactions, abundance, localization, and expression. We find that essential genes or proteins are enriched for interactions with other essential genes or proteins, suggesting that the global network may be functionally unified. This interconnectivity is supported by a substantial overlap of protein and genetic interactions in the LC dataset. We show that the LC dataset considerably improves the predictive power of network-analysis approaches. The full LC dataset is available at the BioGRID () and SGD () databases. Conclusion Comprehensive datasets of biological interactions derived from the primary literature provide critical benchmarks for HTP methods, augment functional prediction, and reveal system-level attributes of biological networks. PMID:16762047

Machine learning classifier for identification of damaging missense mutations exclusive to human mitochondrial DNA-encoded polypeptides.

PubMed

Martín-Navarro, Antonio; Gaudioso-Simón, Andrés; Álvarez-Jarreta, Jorge; Montoya, Julio; Mayordomo, Elvira; Ruiz-Pesini, Eduardo

2017-03-07

Several methods have been developed to predict the pathogenicity of missense mutations but none has been specifically designed for classification of variants in mtDNA-encoded polypeptides. Moreover, there is not available curated dataset of neutral and damaging mtDNA missense variants to test the accuracy of predictors. Because mtDNA sequencing of patients suffering mitochondrial diseases is revealing many missense mutations, it is needed to prioritize candidate substitutions for further confirmation. Predictors can be useful as screening tools but their performance must be improved. We have developed a SVM classifier (Mitoclass.1) specific for mtDNA missense variants. Training and validation of the model was executed with 2,835 mtDNA damaging and neutral amino acid substitutions, previously curated by a set of rigorous pathogenicity criteria with high specificity. Each instance is described by a set of three attributes based on evolutionary conservation in Eukaryota of wildtype and mutant amino acids as well as coevolution and a novel evolutionary analysis of specific substitutions belonging to the same domain of mitochondrial polypeptides. Our classifier has performed better than other web-available tested predictors. We checked performance of three broadly used predictors with the total mutations of our curated dataset. PolyPhen-2 showed the best results for a screening proposal with a good sensitivity. Nevertheless, the number of false positive predictions was too high. Our method has an improved sensitivity and better specificity in relation to PolyPhen-2. We also publish predictions for the complete set of 24,201 possible missense variants in the 13 human mtDNA-encoded polypeptides. Mitoclass.1 allows a better selection of candidate damaging missense variants from mtDNA. A careful search of discriminatory attributes and a training step based on a curated dataset of amino acid substitutions belonging exclusively to human mtDNA genes allows an improved performance. Mitoclass.1 accuracy could be improved in the future when more mtDNA missense substitutions will be available for updating the attributes and retraining the model.

Using random forests for assistance in the curation of G-protein coupled receptor databases.

PubMed

Shkurin, Aleksei; Vellido, Alfredo

2017-08-18

Biology is experiencing a gradual but fast transformation from a laboratory-centred science towards a data-centred one. As such, it requires robust data engineering and the use of quantitative data analysis methods as part of database curation. This paper focuses on G protein-coupled receptors, a large and heterogeneous super-family of cell membrane proteins of interest to biology in general. One of its families, Class C, is of particular interest to pharmacology and drug design. This family is quite heterogeneous on its own, and the discrimination of its several sub-families is a challenging problem. In the absence of known crystal structure, such discrimination must rely on their primary amino acid sequences. We are interested not as much in achieving maximum sub-family discrimination accuracy using quantitative methods, but in exploring sequence misclassification behavior. Specifically, we are interested in isolating those sequences showing consistent misclassification, that is, sequences that are very often misclassified and almost always to the same wrong sub-family. Random forests are used for this analysis due to their ensemble nature, which makes them naturally suited to gauge the consistency of misclassification. This consistency is here defined through the voting scheme of their base tree classifiers. Detailed consistency results for the random forest ensemble classification were obtained for all receptors and for all data transformations of their unaligned primary sequences. Shortlists of the most consistently misclassified receptors for each subfamily and transformation, as well as an overall shortlist including those cases that were consistently misclassified across transformations, were obtained. The latter should be referred to experts for further investigation as a data curation task. The automatic discrimination of the Class C sub-families of G protein-coupled receptors from their unaligned primary sequences shows clear limits. This study has investigated in some detail the consistency of their misclassification using random forest ensemble classifiers. Different sub-families have been shown to display very different discrimination consistency behaviors. The individual identification of consistently misclassified sequences should provide a tool for quality control to GPCR database curators.

Improving transcriptome construction in non-model organisms: integrating manual and automated gene definition in Emiliania huxleyi.

PubMed

Feldmesser, Ester; Rosenwasser, Shilo; Vardi, Assaf; Ben-Dor, Shifra

2014-02-22

The advent of Next Generation Sequencing technologies and corresponding bioinformatics tools allows the definition of transcriptomes in non-model organisms. Non-model organisms are of great ecological and biotechnological significance, and consequently the understanding of their unique metabolic pathways is essential. Several methods that integrate de novo assembly with genome-based assembly have been proposed. Yet, there are many open challenges in defining genes, particularly where genomes are not available or incomplete. Despite the large numbers of transcriptome assemblies that have been performed, quality control of the transcript building process, particularly on the protein level, is rarely performed if ever. To test and improve the quality of the automated transcriptome reconstruction, we used manually defined and curated genes, several of them experimentally validated. Several approaches to transcript construction were utilized, based on the available data: a draft genome, high quality RNAseq reads, and ESTs. In order to maximize the contribution of the various data, we integrated methods including de novo and genome based assembly, as well as EST clustering. After each step a set of manually curated genes was used for quality assessment of the transcripts. The interplay between the automated pipeline and the quality control indicated which additional processes were required to improve the transcriptome reconstruction. We discovered that E. huxleyi has a very high percentage of non-canonical splice junctions, and relatively high rates of intron retention, which caused unique issues with the currently available tools. While individual tools missed genes and artificially joined overlapping transcripts, combining the results of several tools improved the completeness and quality considerably. The final collection, created from the integration of several quality control and improvement rounds, was compared to the manually defined set both on the DNA and protein levels, and resulted in an improvement of 20% versus any of the read-based approaches alone. To the best of our knowledge, this is the first time that an automated transcript definition is subjected to quality control using manually defined and curated genes and thereafter the process is improved. We recommend using a set of manually curated genes to troubleshoot transcriptome reconstruction.

Methods of Estimating Strategic Intentions

DTIC Science & Technology

1982-05-01

34mental Images of future events" which might be brought to reality. To assess this step In the intention process the analyst may have to consler the...li. DESCRIPTION OF THE INTENTION EST!MATION PROCESS AND RELATED ANALYTICAL AIDS ........ ....... ................ A...OF AIDS AND PROCESS SUMMARY ............................... 115 v . BIBLIOGRAPHY ....................... .. . . . ............... . ...... 138 3on

Beliefs and Intentions for Skin Protection and UV Exposure in Young Adults

ERIC Educational Resources Information Center

Heckman, Carolyn J.; Manne, Sharon L.; Kloss, Jacqueline D.; Bass, Sarah Bauerle; Collins, Bradley; Lessin, Stuart R.

2011-01-01

Objective: To evaluate Fishbein's integrative model in predicting young adults' skin protection, sun exposure, and indoor tanning intentions. Methods: Two hundred twelve participants completed an online survey. Results: Damage distress, self-efficacy, and perceived control accounted for 34% of the variance in skin protection intentions. Outcome…

Intention for Healthy Eating among Southern Appalachian Teens

ERIC Educational Resources Information Center

Wu, Tiejian; Snider, Jeromy Blake; Floyd, Michael R.; Florence, James E.; Stoots, James Michael; Makamey, Michael I.

2009-01-01

Objective: To describe the intention for healthy eating and its correlates among southern Appalachian teens. Methods: Four hundred sixteen adolescents 14 to 16 years old were surveyed with self-administered questionnaires. Results: About 30% of the adolescents surveyed had definite intentions to eat healthfully during the next 2 weeks. The scales…

MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

PubMed Central

Vallenet, David; Belda, Eugeni; Calteau, Alexandra; Cruveiller, Stéphane; Engelen, Stefan; Lajus, Aurélie; Le Fèvre, François; Longin, Cyrille; Mornico, Damien; Roche, David; Rouy, Zoé; Salvignol, Gregory; Scarpelli, Claude; Thil Smith, Adam Alexander; Weiman, Marion; Médigue, Claudine

2013-01-01

MicroScope is an integrated platform dedicated to both the methodical updating of microbial genome annotation and to comparative analysis. The resource provides data from completed and ongoing genome projects (automatic and expert annotations), together with data sources from post-genomic experiments (i.e. transcriptomics, mutant collections) allowing users to perfect and improve the understanding of gene functions. MicroScope (http://www.genoscope.cns.fr/agc/microscope) combines tools and graphical interfaces to analyse genomes and to perform the manual curation of gene annotations in a comparative context. Since its first publication in January 2006, the system (previously named MaGe for Magnifying Genomes) has been continuously extended both in terms of data content and analysis tools. The last update of MicroScope was published in 2009 in the Database journal. Today, the resource contains data for >1600 microbial genomes, of which ∼300 are manually curated and maintained by biologists (1200 personal accounts today). Expert annotations are continuously gathered in the MicroScope database (∼50 000 a year), contributing to the improvement of the quality of microbial genomes annotations. Improved data browsing and searching tools have been added, original tools useful in the context of expert annotation have been developed and integrated and the website has been significantly redesigned to be more user-friendly. Furthermore, in the context of the European project Microme (Framework Program 7 Collaborative Project), MicroScope is becoming a resource providing for the curation and analysis of both genomic and metabolic data. An increasing number of projects are related to the study of environmental bacterial (meta)genomes that are able to metabolize a large variety of chemical compounds that may be of high industrial interest. PMID:23193269

Trustworthy Digital Repositories: Building Trust the Old Fashion Way, EARNING IT.

NASA Astrophysics Data System (ADS)

Kinkade, D.; Chandler, C. L.; Shepherd, A.; Rauch, S.; Groman, R. C.; Wiebe, P. H.; Glover, D. M.; Allison, M. D.; Copley, N. J.; Ake, H.; York, A.

2016-12-01

There are several drivers increasing the importance of high quality data management and curation in today's research process (e.g., OSTP PARR memo, journal publishers, funders, academic and private institutions), and proper management is necessary throughout the data lifecycle to enable reuse and reproducibility of results. Many digital data repositories are capable of satisfying the basic management needs of an investigator looking to share their data (i.e., publish data in the public domain), but repository services vary greatly and not all provide mature services that facilitate discovery, access, and reuse of research data. Domain-specific repositories play a vital role in the data curation process by working closely with investigators to create robust metadata, perform first order QC, and assemble and publish research data. In addition, they may employ technologies and services that enable increased discovery, access, and long-term archive. However, smaller domain facilities operate in varying states of capacity and curation ability. Within this repository environment, individual investigators (driven by publishers, funders, or institutions) need to find trustworthy repositories for their data; and funders need to direct investigators to quality repositories to ensure return on their investment. So, how can one determine the best home for valuable research data? Metrics can be applied to varying aspects of data curation, and many credentialing organizations offer services that assess and certify the trustworthiness of a given data management facility. Unfortunately, many of these certifications can be inaccessible to a small repository in cost, time, or scope. Are there alternatives? This presentation will discuss methods and approaches used by the Biological and Chemical Oceanography Data Management Office (BCO-DMO; a domain-specific, intermediate digital data repository) to demonstrate trustworthiness in the face of a daunting accreditation landscape.

Folliculitis Induced by EGFR Inhibitors, Preventive and Curative Efficacy of Tetracyclines in the Management and Incidence Rates According to the Type of EGFR Inhibitor Administered: A Systematic Literature Review

PubMed Central

Bachet, Jean-Baptiste; Peuvrel, Lucie; Bachmeyer, Claude; Reguiai, Ziad; Gourraud, Pierre A.; Bouché, Olivier; Ychou, Marc; Bensadoun, Rene J.; Dreno, Brigitte

2012-01-01

Introduction. Folliculitis is the most common side effect of epidermal growth factor receptor (EGFR) inhibitors (EGFRIs). It is often apparent, altering patients' quality of life and possibly impacting compliance. Variations in terms of the treatment-related incidence and intensity have not been fully elucidated. Tetracyclines have been recommended for the prophylaxis and treatment of folliculitis but their efficacy is yet to be established. Materials and Methods. We carried out two systematic literature reviews. The first assessed the preventive and curative efficacy of tetracyclines. The second assessed the incidence of grade 3–4 folliculitis in the main clinical studies published. Results. In four randomized studies, preventive tetracycline treatment was associated with a significantly lower incidence of grade 2–3 folliculitis and a better quality of life in three of the four studies. In curative terms, tetracycline efficacy was not evaluated in any randomized study, but an improvement in grade ≥2 folliculitis was reported in case series. The frequency and severity of folliculitis seem to be greater with the antibodies than with the tyrosine kinase inhibitors. Analysis restricted to lung cancer studies showed a statistically greater incidence in terms of grade 3–4 folliculitis with cetuximab (9%) and erlotinib (8%) than with gefitinib (2%) (p < .0001). Conclusion. Unless contraindicated, a tetracycline should be routinely prescribed prophylactically for patients treated with an EGFRI (level of evidence, B2). In curative therapy, the level of evidence for tetracycline efficacy is low (level of evidence, D). The incidence of grade 3–4 folliculitis induced by EGFRIs appears to be lower with gefitinib. PMID:22426526

Talking Cure Models: A Framework of Analysis

PubMed Central

Marx, Christopher; Benecke, Cord; Gumz, Antje

2017-01-01

Psychotherapy is commonly described as a “talking cure,” a treatment method that operates through linguistic action and interaction. The operative specifics of therapeutic language use, however, are insufficiently understood, mainly due to a multitude of disparate approaches that advance different notions of what “talking” means and what “cure” implies in the respective context. Accordingly, a clarification of the basic theoretical structure of “talking cure models,” i.e., models that describe therapeutic processes with a focus on language use, is a desideratum of language-oriented psychotherapy research. Against this background the present paper suggests a theoretical framework of analysis which distinguishes four basic components of “talking cure models”: (1) a foundational theory (which suggests how linguistic activity can affect and transform human experience), (2) an experiential problem state (which defines the problem or pathology of the patient), (3) a curative linguistic activity (which defines linguistic activities that are supposed to effectuate a curative transformation of the experiential problem state), and (4) a change mechanism (which defines the processes and effects involved in such transformations). The purpose of the framework is to establish a terminological foundation that allows for systematically reconstructing basic properties and operative mechanisms of “talking cure models.” To demonstrate the applicability and utility of the framework, five distinct “talking cure models” which spell out the details of curative “talking” processes in terms of (1) catharsis, (2) symbolization, (3) narrative, (4) metaphor, and (5) neurocognitive inhibition are introduced and discussed in terms of the framework components. In summary, we hope that our framework will prove useful for the objective of clarifying the theoretical underpinnings of language-oriented psychotherapy research and help to establish a more comprehensive understanding of how curative language use contributes to the process of therapeutic change. PMID:28955286

Curative embolization of pediatric intracranial arteriovenous malformations using Onyx: the role of new embolization techniques on patient outcomes.

PubMed

de Castro-Afonso, L H; Nakiri, G S; Oliveira, R S; Santos, M V; Santos, A C Dos; Machado, H R; Abud, D G

2016-06-01

Intracranial arteriovenous malformations (AVMs) are the most frequent cause of hemorrhagic strokes in the pediatric population. The study aim was to retrospectively assess the safety and efficacy of Onyx embolization with the intention to cure AVMs in a pediatric population. A retrospective analysis of all patients (<18 years) who underwent endovascular embolization using Onyx at our institution was conducted. The primary endpoint was the composite complete angiographic occlusion of AVM immediately after the last embolization session that had no procedure-related complication requiring emergency surgery. Secondary endpoints were angiographic occlusion rates, procedure-related complications, and clinical outcomes after treatment and at the 6-month follow-up Twenty-three patients (mean age, 11.7 years) underwent a total of 45 embolization sessions. The median Spetzler-Martin grade was 3 (range 1 to 4). The primary endpoint was achieved in 19 patients (82.6 %). Complete angiographic occlusion of the AVM was obtained in 21 patients (91.3 %) immediately after embolization and at the 6-month follow-up. Embolization-related complications were observed in three patients (13 %). None of the complications resulted in permanent functional disability or death. In two patients (8.7 %), the AVM could not be completely occluded by embolization alone and the patients were referred to radiosurgery and microsurgery, respectively. Onyx embolization of AVM in pediatric patients with the intention to cure resulted in high occlusion rates without increasing neurological disability or death. The development of new embolization techniques and devices seems to improve the safety of Onyx embolization.

Considering Value in Rectal Cancer Surgery: An Analysis of Costs and Outcomes Based on the Open, Laparoscopic, and Robotic Approach for Proctectomy.

PubMed

Silva-Velazco, Jorge; Dietz, David W; Stocchi, Luca; Costedio, Meagan; Gorgun, Emre; Kalady, Matthew F; Kessler, Hermann; Lavery, Ian C; Remzi, Feza H

2017-05-01

The aim of the study was to compare value (outcomes/costs) of proctectomy in patients with rectal cancer by 3 approaches: open, laparoscopic, and robotic. The role of minimally invasive proctectomy in rectal cancer is controversial. In the era of value-based medicine, costs must be considered along with outcomes. Primary rectal cancer patients undergoing curative intent proctectomy at our institution between 2010 and 2014 were included. Patients were grouped by approach [open surgery, laparoscopic surgery, and robotic surgery (RS)] on an intent-to-treat basis. Groups were compared by direct costs of hospitalization for the primary resection, 30-day readmissions, and ileostomy closure and for short-term outcomes. A total of 488 patients were evaluated; 327 were men (67%), median age was 59 (27-93) years, and restorative procedures were performed in 333 (68.2%). Groups were similar in demographics, tumor characteristics, and treatment details. Significant outcome differences between groups were found in operative and anesthesia times (longer in the RS group), and in estimated blood loss, intraoperative transfusion, length of stay, and postoperative complications (all higher in the open surgery group). No significant differences were found in short-term oncologic outcomes. Direct cost of the hospitalization for primary resection and total direct cost (including readmission/ileostomy closure hospitalizations) were significantly greater in the RS group. The laparoscopic and open approaches to proctectomy in patients with rectal cancer provide similar value. If robotic proctectomy is to be widely applied in the future, the costs of the procedure must be reduced.

Decoding intentions from movement kinematics

PubMed Central

Cavallo, Andrea; Koul, Atesh; Ansuini, Caterina; Capozzi, Francesca; Becchio, Cristina

2016-01-01

How do we understand the intentions of other people? There has been a longstanding controversy over whether it is possible to understand others’ intentions by simply observing their movements. Here, we show that indeed movement kinematics can form the basis for intention detection. By combining kinematics and psychophysical methods with classification and regression tree (CART) modeling, we found that observers utilized a subset of discriminant kinematic features over the total kinematic pattern in order to detect intention from observation of simple motor acts. Intention discriminability covaried with movement kinematics on a trial-by-trial basis, and was directly related to the expression of discriminative features in the observed movements. These findings demonstrate a definable and measurable relationship between the specific features of observed movements and the ability to discriminate intention, providing quantitative evidence of the significance of movement kinematics for anticipating others’ intentional actions. PMID:27845434

An Interdisciplinary Method for the Visualization of Novel High-Resolution Precision Photography and Micro-XCT Data Sets of NASA's Apollo Lunar Samples and Antarctic Meteorite Samples to Create Combined Research-Grade 3D Virtual Samples for the Benefit of Astromaterials Collections Conservation, Curation, Scientific Research and Education

NASA Technical Reports Server (NTRS)

Blumenfeld, E. H.; Evans, C. A.; Oshel, E. R.; Liddle, D. A.; Beaulieu, K.; Zeigler, R. A.; Hanna, R. D.; Ketcham, R. A.

2016-01-01

New technologies make possible the advancement of documentation and visualization practices that can enhance conservation and curation protocols for NASA's Astromaterials Collections. With increasing demands for accessibility to updated comprehensive data, and with new sample return missions on the horizon, it is of primary importance to develop new standards for contemporary documentation and visualization methodologies. Our interdisciplinary team has expertise in the fields of heritage conservation practices, professional photography, photogrammetry, imaging science, application engineering, data curation, geoscience, and astromaterials curation. Our objective is to create virtual 3D reconstructions of Apollo Lunar and Antarctic Meteorite samples that are a fusion of two state-of-the-art data sets: the interior view of the sample by collecting Micro-XCT data and the exterior view of the sample by collecting high-resolution precision photography data. These new data provide researchers an information-rich visualization of both compositional and textural information prior to any physical sub-sampling. Since January 2013 we have developed a process that resulted in the successful creation of the first image-based 3D reconstruction of an Apollo Lunar Sample correlated to a 3D reconstruction of the same sample's Micro- XCT data, illustrating that this technique is both operationally possible and functionally beneficial. In May of 2016 we began a 3-year research period during which we aim to produce Virtual Astromaterials Samples for 60 high-priority Apollo Lunar and Antarctic Meteorite samples and serve them on NASA's Astromaterials Acquisition and Curation website. Our research demonstrates that research-grade Virtual Astromaterials Samples are beneficial in preserving for posterity a precise 3D reconstruction of the sample prior to sub-sampling, which greatly improves documentation practices, provides unique and novel visualization of the sample's interior and exterior features, offers scientists a preliminary research tool for targeted sub-sample requests, and additionally is a visually engaging interactive tool for bringing astromaterials science to the public.

An Interdisciplinary Method for the Visualization of Novel High-Resolution Precision Photography and Micro-XCT Data Sets of NASA's Apollo Lunar Samples and Antarctic Meteorite Samples to Create Combined Research-Grade 3D Virtual Samples for the Benefit of Astromaterials Collections Conservation, Curation, Scientific Research and Education

NASA Astrophysics Data System (ADS)

Blumenfeld, E. H.; Evans, C. A.; Zeigler, R. A.; Righter, K.; Beaulieu, K. R.; Oshel, E. R.; Liddle, D. A.; Hanna, R.; Ketcham, R. A.; Todd, N. S.

2016-12-01

New technologies make possible the advancement of documentation and visualization practices that can enhance conservation and curation protocols for NASA's Astromaterials Collections. With increasing demands for accessibility to updated comprehensive data, and with new sample return missions on the horizon, it is of primary importance to develop new standards for contemporary documentation and visualization methodologies. Our interdisciplinary team has expertise in the fields of heritage conservation practices, professional photography, photogrammetry, imaging science, application engineering, data curation, geoscience, and astromaterials curation. Our objective is to create virtual 3D reconstructions of Apollo Lunar and Antarctic Meteorite samples that are a fusion of two state-of-the-art data sets: the interior view of the sample by collecting Micro-XCT data and the exterior view of the sample by collecting high-resolution precision photography data. These new data provide researchers an information-rich visualization of both compositional and textural information prior to any physical sub-sampling. Since January 2013 we have developed a process that resulted in the successful creation of the first image-based 3D reconstruction of an Apollo Lunar Sample correlated to a 3D reconstruction of the same sample's Micro-XCT data, illustrating that this technique is both operationally possible and functionally beneficial. In May of 2016 we began a 3-year research period during which we aim to produce Virtual Astromaterials Samples for 60 high-priority Apollo Lunar and Antarctic Meteorite samples and serve them on NASA's Astromaterials Acquisition and Curation website. Our research demonstrates that research-grade Virtual Astromaterials Samples are beneficial in preserving for posterity a precise 3D reconstruction of the sample prior to sub-sampling, which greatly improves documentation practices, provides unique and novel visualization of the sample's interior and exterior features, offers scientists a preliminary research tool for targeted sub-sample requests, and additionally is a visually engaging interactive tool for bringing astromaterials science to the public.

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.

[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.

Curative effect of chemotherapy, KTP lasers, and CO2 lasers combined with chemotherapy in the treatment of adult laryngeal hemangioma.

PubMed

Wu, Xiufa; Mao, Wenjing; He, Peijie; Wei, Chunsheng

2018-06-01

To evaluate three methods for treating adult laryngeal hemangiomas: conventional chemotherapy, CO 2 laser combined with chemotherapy, and KTP laser. And to identify risk factors that affected the prognosis of the lesions. A retrospective analysis was performed on the data from patients with adult laryngeal hemangiomas treated by one of three aforementioned methods, the curative efficacy, and safety of those methods was compared. All cases were confirmed by suspension micro-laryngoscope examination. Pre- and post-treatment clinical photographs were taken and the outcomes were graded. Thirty-eight patients in 48 different cases were enrolled in the study between June 2010 and June 2016, and some patients were treated more than once. The treatment efficacy of the KTP laser was higher than that of chemotherapy according to the Kruskal-Wallis ANOVA test; however, the ordinal logistic regression showed that the choice of surgical procedure did not affect the treatment results; only the size of the bases of the lesions affected the prognosis of adult laryngeal hemangiomas. Pingyangmycin injection, KTP laser, and CO 2 laser combined with chemotherapy are safe and effective methods for the treatment of adult laryngeal hemangiomas. The size of base of the lesion affects the prognosis of the hemangiomas.

Women and postfertilization effects of birth control: consistency of beliefs, intentions and reported use

PubMed Central

Dye, Huong M; Stanford, Joseph B; Alder, Stephen C; Kim, Han S; Murphy, Patricia A

2005-01-01

Background This study assesses the consistency of responses among women regarding their beliefs about the mechanisms of actions of birth control methods, beliefs about when human life begins, the intention to use or not use birth control methods that they believe may act after fertilization or implantation, and their reported use of specific methods. Methods A questionnaire was administered in family practice and obstetrics and gynecology clinics in Salt Lake City, Utah, and Tulsa, Oklahoma. Participants included women ages 18–50 presenting for any reason and women under age 18 presenting for family planning or pregnancy care. Analyses were based on key questions addressing beliefs about whether specific birth control methods may act after fertilization, beliefs about when human life begins, intention to use a method that may act after fertilization, and reported use of specific methods. The questionnaire contained no information about the mechanism of action of any method of birth control. Responses were considered inconsistent if actual use contradicted intentions, if one intention contradicted another, or if intentions contradicted beliefs. Results Of all respondents, 38% gave consistent responses about intention to not use or to stop use of any birth control method that acted after fertilization, while 4% gave inconsistent responses. The corresponding percentages for birth control methods that work after implantation were 64% consistent and 2% inconsistent. Of all respondents, 34% reported they believed that life begins at fertilization and would not use any birth control method that acts after fertilization (a consistent response), while 3% reported they believed that life begins at fertilization but would use a birth control method that acts after fertilization (inconsistent). For specific methods of birth control, less than 1% of women gave inconsistent responses. A majority of women (68% or greater) responded accurately about the mechanism of action of condoms, abstinence, sterilization, and abortion, but a substantial percentage of women (between 19% and 57%) were uncertain about the mechanisms of action of oral contraceptives, intrauterine devices (IUDs), Depo-Provera, or natural family planning. Conclusion Women who believe that life begins at fertilization may not intend to use a birth control method that could have postfertilization effects. More research is needed to understand the relative importance of postfertilization effects for women in other populations, and in relation to other properties of and priorities for birth control methods. However, many women were uncertain about the mechanisms of action of specific methods. To respect the principles of informed consent, some women may need more education about what is known and not known about the mechanisms of action of birth control methods. PMID:16313677

[Application and prospect of scale measurement and appraisal in the assessment in TCM therapeutic efficacy evaluation].

PubMed

Liu, Feng-Bin

2007-12-01

The assessing contents of the health related quality of life (HRQOL) and the patient reported outcomes (PRO) are identical with the inquiry of traditional Chinese medicine (TCM), which are uniformly soft indicators which could be evaluated with the scales for instruments. The assessing method for the soft indicator in the HRQOL and PRO was gradually accepted by TCM practitioners and applied in evaluating the curative effect of TCM. The applying scale in the assessment of curative effect of TCM and the developing scale with the TCM features just started in the TCM field. There was much inadequacy in the scale study, such as no penetrating understanding of the theory and connotation of the scale in the HRQOL and PRO, on scale system for TCM, no direction in selecting scale, not standardizing in the design of the study with scale in the practice. So, it is necessary that the international guideline of developing scale applied for worldwide should be carried out in the study for developing scale. Meanwhile, it must also be under the guidance of TCM theory in the whole course. It will promote the normalization development of applying scale in the assessment of curative effect in the TCM practice.

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

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

Awareness of Pap testing and factors associated with intent to undergo Pap testing by level of sexual experience in unmarried university students in Korea: results from an online survey

PubMed Central

2014-01-01

Background Young and unmarried women have not been a target group for cervical cancer prevention in Korea. No previous studies have investigated the awareness of Pap testing, the intention to undergo Pap testing, or the factors associated with that intention, in this group of women. This information would be useful for an expansion in the focus of primary cervical cancer prevention. This study aimed to compare the awareness of Pap testing between groups of unmarried university students in Korea, and to investigate the factors associated with the intention to undergo Pap testing, by level of sexual experience. Methods A total of 475 unmarried university students who had never undergone a Pap test completed a web-based survey. Differences in awareness of the importance of the Pap test, confidence in Pap testing, intention to undergo the test, attitudes, subjective norms, perceived control, stigma, and shame by level of sexual experience were analysed using independent t-tests. Associations between measurement variables and intention to undergo Pap testing were analysed using correlation analysis. Variables yielding significant associations (p < 0.05) were included in a stepwise multiple regression model of intention to undergo Pap testing. Results Most participants perceived that the need for regular Pap testing was less important (score, 77.76) than other methods of cervical cancer prevention. They were not confident that is was an effective method of cervical cancer prevention for themselves (score, 59.56). There were differences in confidence in Pap testing and in the factors associated with intention to undergo Pap testing between sexually experienced and sexually inexperienced students. Regardless of level of sexual experience, the subjective norm was the most important predictor of intention to undergo Pap testing. Conclusions There was a low level of Pap screening awareness among the students. The factors associated with intention to undergo Pap testing differed by level of sexual experience. Social influence was an important factor that could be used to increase the intention to receive a Pap test in the university student population. Strategies to increase the intention to undergo Pap screening should be introduced and should be adapted to the level of sexual experience. PMID:25163938

Attitudes, Norms, and the Effect of Social Connectedness on Adolescent Sexual Risk Intention

ERIC Educational Resources Information Center

Cederbaum, Julie A.; Rodriguez, Aubrey J.; Sullivan, Kathrine; Gray, Kandice

2017-01-01

Background: Risky sexual behaviors put adolescents at increased risk of adverse outcomes. Parents, school-based adults, and peers play important roles in influencing these sex intentions. Methods: This work explored the influence of parent-child sex communication on adolescent attitudes, perceived norms, and intentions to have sex, including the…

Evaluating the Predictive Validity of Suicidal Intent and Medical Lethality in Youth

ERIC Educational Resources Information Center

Sapyta, Jeffrey; Goldston, David B.; Erkanli, Alaattin; Daniel, Stephanie S.; Heilbron, Nicole; Mayfield, Andrew; Treadway, S. Lyn

2012-01-01

Objectives: To examine whether suicidal intent and medical lethality of past suicide attempts are predictive of future attempts, the association between intent and lethality, and the consistency of these characteristics across repeated attempts among youth. Method: Suicide attempts in a 15-year prospective study of 180 formerly psychiatrically…

Exploring migration intention of nursing students in Nepal: A mixed-methods study.

PubMed

Poudel, Chandra; Ramjan, Lucie; Everett, Bronwyn; Salamonson, Yenna

2018-03-01

The objective of this study was to assess the migration intention of students enrolled in pre-registration nursing programs in Nepal, and to explore factors influencing this intention. Using an embedded mixed methods design, 799 nursing students were surveyed, followed by 12 semi-structured face-to-face interviews. The result showed that the majority (92.5%) expressed some intention to migrate, with three quarters of these listed furthering their study abroad as the primary reason. In the multiple regression analysis, those with lower professional identity, and those who reported nursing was not their first choice were likely to express migration intention. Interview data identified low salaries, unemployment, poor working conditions, insufficient postgraduate education, and a lack of professional autonomy in Nepal as reasons for their intention to migrate. Increasing opportunities for nurses to undertake postgraduate education in Nepal, promoting a positive image of nursing, and facilitating a supportive learning environment during undergraduate nursing education could help address the potential loss of nurses from Nepal. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.;

Epistasis-list.org: A Curated Database of Gene-Gene and Gene-Environment Interactions in Human Epidemiology

EPA Science Inventory

The field of human genetics has experienced a paradigm shift in that common diseases are now thought to be due to the complex interactions among numerous genetic and environmental factors. This paradigm shift has prompted the development of myriad novel methods to detect such int...

Workplace violence, job satisfaction, burnout, perceived organisational support and their effects on turnover intention among Chinese nurses in tertiary hospitals: a cross-sectional study

PubMed Central

Zhang, Zhong; Liu, Xinyan; Li, Li; Duan, Xiaojian; Li, Guoqiang; Lou, Fengge; Jia, Xiaoli; Fan, Lihua; Sun, Tao; Ni, Xin

2018-01-01

Objectives Our aims were to assess the relationship between workplace violence, job satisfaction, burnout, organisational support and turnover intention, and to explore factors associated with turnover intention among nurses in Chinese tertiary hospitals. Methods The purposive sampling method was used to collect data from August 2016 through January 2017. A total of 1761 nurses from 9 public tertiary hospitals in 4 provinces (municipalities) located in eastern (Beijing), central (Heilongjiang, Anhui) and western (Shaanxi) regions of China completed the questionnaires (effective response rate=85.20%). A cross-sectional study was conducted using the Workplace Violence Scale, Chinese Maslach Burnout Inventory General Survey, Minnesota Job Satisfaction Questionnaire Revised Short Version, Perceived Organizational Support-Simplified Version Scale and Turnover Intention Scale. Results A total of 1216 of 1706 (69.1%) participants had high turnover intention. During the previous 12 months, the prevalence of physical violence and psychological violence towards nurses was 9.60% and 59.64%, respectively. As expected, the level of turnover intention was negatively correlated with participants’ scores on job satisfaction (r=−0.367, p<0.001) and perceived organisational support (r=−0.379, p<0.001), respectively. Burnout was positively associated with turnover intention (r=0.444, p<0.001). Workplace violence was positively associated with turnover intention (β=0.035, p<0.001) in linear regression analysis. The total effect (β=0.53) of workplace violence on turnover intention comprised its direct effect (β=0.36) and its indirect effect (β=0.17). Conclusions Perceived organisational support served as a mediator between workplace violence, job satisfaction, burnout and turnover intention, and it had a significantly negative impact on turnover intention. Therefore, nursing managers should understand the importance of the organisation’s support and establish a reasonable incentive system to decrease turnover intention. PMID:29886440

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.

Imagined Contact Improves Intentions towards a Hypothetical Peer with Asperger Syndrome but Not Attitudes towards Peers with Asperger Syndrome in General

ERIC Educational Resources Information Center

Fleva, Eleni

2015-01-01

The aim of this study is twofold. First, to investigate whether the imagined contact method (an indirect method of contact) can improve behavioural intentions towards a hypothetical peer with Asperger syndrome (AS). Second, to test whether the effect of the method can be generalised on attitudes towards young people with AS in general.…

Patterns of local recurrence after primary resection of cancers that arise in the sinonasal region and the maxillary alveolus.

PubMed

McMahon, Jeremy D; Wong, Ling Siew; Crowther, John; Taylor, William M; McManners, Joseph; Devine, John C; Wales, Craig; Maciver, Colin

2013-07-01

Local recurrence remains the most important sign of relapse of disease after treatment of advanced cancer of the maxilla and sinonasal region. In this retrospective study we describe patterns of recurrence in a group of patients who had had open resection for cancer of the sinonasal region and posterior maxillary alveolus with curative intent. Casenotes and imaging studies were reviewed to find out the pattern of any relapse, with particular reference to local recurrence. The minimum follow-up period was 12 months. Of 50 patients a total of 16 developed recurrences, 11 of which were local. Of those 11, a total of 8 were in posterior and superior locations (the orbit, the infratemporal and pterygopalatine fossas, the traversing neurovascular canals of the body of the sphenoid to the cavernous sinus, the Gasserian ganglion, and the dura of the middle cranial fossa). Advanced cancer of the midface often equates with disease at the skull base. Treatment, including surgical tactics, should reflect that. Copyright © 2012 The British Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

Shoulder and neck morbidity in quality of life after surgery for head and neck cancer.

PubMed

van Wilgen, C P; Dijkstra, P U; van der Laan, B F A M; Plukker, J Th; Roodenburg, J L N

2004-10-01

Quality of life has become a major issue in determining the outcome of treatment in head and neck surgery with curative intent. The aim of our study was to determine which factors in the postoperative care, especially shoulder and neck morbidity, are related to quality of life and how these outcomes compared between patients who had undergone surgery and a control group. We analyzed physical symptoms, psychological symptoms, and social and functional well-being at least 1 year after surgery and evaluated the differences in quality of life between patients who had undergone head and neck surgery and a control group. Depression scores contributed significantly to all domains of quality of life. Reduced shoulder abduction, shoulder pain, and neck pain are related to several domains of quality of life. The patient group scored significantly worse for social functioning and limitations from physical problems but scored significantly better for bodily pain and health changes. Depression and shoulder and neck morbidity are important factors in quality of life for patients who have undergone surgery for head and neck cancer. (c) 2004 Wiley Periodicals, Inc.

The Potential Role of Aerobic Exercise to Modulate Cardiotoxicity of Molecularly Targeted Cancer Therapeutics

PubMed Central

Lakoski, Susan; Mackey, John R.; Douglas, Pamela S.; Haykowsky, Mark J.; Jones, Lee W.

2013-01-01

Molecularly targeted therapeutics (MTT) are the future of cancer systemic therapy. They have already moved from palliative therapy for advanced solid malignancies into the setting of curative-intent treatment for early-stage disease. Cardiotoxicity is a frequent and potentially serious adverse complication of some targeted therapies, leading to a broad range of potentially life-threatening complications, therapy discontinuation, and poor quality of life. Low-cost pleiotropic interventions are therefore urgently required to effectively prevent and/or treat MTT-induced cardiotoxicity. Aerobic exercise therapy has the unique capacity to modulate, without toxicity, multiple gene expression pathways in several organ systems, including a plethora of cardiac-specific molecular and cell-signaling pathways implicated in MTT-induced cardiac toxicity. In this review, we examine the molecular signaling of antiangiogenic and HER2-directed therapies that may underpin cardiac toxicity and the hypothesized molecular mechanisms underlying the cardioprotective properties of aerobic exercise. It is hoped that this knowledge can be used to maximize the benefits of small molecule inhibitors, while minimizing cardiac damage in patients with solid malignancies. PMID:23335619

Lung Cancer in HIV Infection

PubMed Central

Mani, Deepthi; Haigentz, Missak; Aboulafia, David M

2011-01-01

Lung cancer is the most prevalent non-AIDS-defining malignancy in the HAART era. Smoking plays a significant role in the development of HIV-associated lung cancer, but the cancer risk is 2–4 times greater in HIV-infected persons than in the general population, even after adjusting for smoking intensity and duration. Lung cancer is typically diagnosed a decade or more earlier among HIV-infected persons (mean age, 46 years) compared to those without HIV infection. Adenocarcinoma is the commonest histological subtype, and the majority of patients are diagnosed with locally advanced or metastatic carcinoma. Since pulmonary infections are common among HIV-infected individuals, clinicians may not suspect lung cancer in this younger patient population. Surgery with curative intent remains the treatment of choice for early stage disease. Although there is increasing experience in using radiation and chemotherapy for HIV-infected patients who do not have surgical options, there is a need for prospective studies for this population frequently excluded from participating in cancer trials. Evidence-based treatments for smoking-cessation with demonstrated efficacy in the general population must be routinely incorporated into the care of HIV-positive smokers. PMID:21802373

Radiation-induced valvular heart disease.

PubMed

Gujral, Dorothy M; Lloyd, Guy; Bhattacharyya, Sanjeev

2016-02-15

Radiation to the mediastinum is a key component of treatment with curative intent for a range of cancers including Hodgkin's lymphoma and breast cancer. Exposure to radiation is associated with a risk of radiation-induced heart valve damage characterised by valve fibrosis and calcification. There is a latent interval of 10-20 years between radiation exposure and development of clinically significant heart valve disease. Risk is related to radiation dose received, interval from exposure and use of concomitant chemotherapy. Long-term outlook and the risk of valve surgery are related to the effects of radiation on mediastinal structures including pulmonary fibrosis and pericardial constriction. Dose prediction models to predict the risk of heart valve disease in the future and newer radiation techniques to reduce the radiation dose to the heart are being developed. Surveillance strategies for this cohort of cancer survivors at risk of developing significant heart valve complications are required. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Retrospective study and review of ocular radiation side effects following external-beam Cobalt-60 radiation therapy in 37 dogs and 12 cats

PubMed Central

Pinard, Chantale L.; Mutsaers, Anthony J.; Mayer, Monique N.; Woods, J. Paul

2012-01-01

This retrospective study evaluated the ocular side effects of cancer-bearing dogs and cats treated with external–beam Cobalt-60 (Co-60) radiation in which one or both orbit(s) were included in the radiation field. A total of 37 dogs and 12 cats presented to the Ontario Veterinary College during the 10-year study period (1999–2009) were evaluated. The radiation protocols ranged from a maximum of 60 Gray (Gy) in 24 fractions for curative intent to a minimum of 8 Gy in 1 fraction for palliative treatment. The main ocular side effect reported in both dogs and cats was conjunctivitis (79% and 55%, respectively). Other common ocular side effects included eyelid lesions in dogs (44%), ulcerative keratitis in cats (36%), and keratoconjunctivitis sicca in both dogs and cats (44% and 27%, respectively). The high incidence of ocular side effects in both patient populations indicates a need for regular ophthalmic examinations as a component of routine follow-up for radiation therapy involving the orbit. Radiation damage to ocular tissues is also reviewed. PMID:23729828

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.

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.

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.

Accident or Suicide? Single-Vehicle Car Accidents and the Intent Hypothesis.

ERIC Educational Resources Information Center

Peck, Dennis L.; Warner, Kenneth

1995-01-01

Brief case studies of single-vehicle car crashes are used to explore the relationship between this method of death and the intent to commit suicide. The author attempts to determine what criteria can be used to determine whether suicide was the intent, and how death by automobile crash can be determined a suicide. (JPS)

Investigating Predictors of Pre-Service Science Teachers' Behavioral Intention toward e-Resources for Teaching

ERIC Educational Resources Information Center

Shittu, Ahmed Tajudeen; Kareem, Bamidele Wahab; Obielodan, Omotayo Olabo; Fakomogbon, Michael Ayodele

2017-01-01

This study examined predictors of pre-service science teachers' behavioral intention toward e-resources use for teaching in Nigeria. The study used cross-sectional survey research method and a questionnaire with a set of items that measure technology preparedness, perceived usefulness, perceived ease of use and behavioral intention to gather the…

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

76 FR 52688 - Notice of Intent To Prepare an Environmental Impact Statement for the Sheep Mountain Uranium...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-23

... project employing open pit and underground mining methods and using heap leach methods for uranium...] Notice of Intent To Prepare an Environmental Impact Statement for the Sheep Mountain Uranium Project... comments regarding issues and resource information for the proposed Sheep Mountain Uranium Project (the...

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

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

Correlates of Intentional Tanning Among Adolescents in the United States: A Systematic Review of the Literature

PubMed Central

Holman, Dawn M.; Watson, Meg

2015-01-01

Purpose Exposure to ultraviolet radiation and a history of sunburn in childhood contribute to risk of skin cancer in adolescence and in adulthood, but many adolescents continue to seek a tan, either from the sun or from tanning beds (i.e., intentional tanning). To understand tanning behavior among adolescents, we conducted a systematic review of the literature to identify correlates of intentional tanning in the United States. Methods We included articles on original research published in English between January 1, 2001, and October 31, 2011, that used self-reported data on intentional tanning by U.S. adolescents aged 8 to 18 years and examined potential correlates of tanning behaviors. Thirteen articles met our criteria; all used cross-sectional survey data and quantitative methods to assess correlates of intentional tanning. Results Results indicate that multiple factors influence tanning among adolescents. Individual factors that correlated with intentional tanning include demographic factors (female sex, older age), attitudes (preferring tanned skin), and behaviors (participating in other risky or appearance-focused behaviors such as dieting). Social factors correlated with intentional tanning include parental influence (having a parent who tans or permits tanning) and peer influence (having friends who tan). Only four studies examined broad contextual factors such as indoor tanning laws and geographic characteristics; they found that proximity to tanning facilities and geographic characteristics (living in the Midwest or South, living in a low ultraviolet area, and attending a rural high school) are associated with intentional tanning. Conclusions These findings inform future public health research and intervention efforts to reduce intentional tanning. PMID:23601612

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.

A method of searching for related literature on protein structure analysis by considering a user's intention

PubMed Central

2015-01-01

Background In recent years, with advances in techniques for protein structure analysis, the knowledge about protein structure and function has been published in a vast number of articles. A method to search for specific publications from such a large pool of articles is needed. In this paper, we propose a method to search for related articles on protein structure analysis by using an article itself as a query. Results Each article is represented as a set of concepts in the proposed method. Then, by using similarities among concepts formulated from databases such as Gene Ontology, similarities between articles are evaluated. In this framework, the desired search results vary depending on the user's search intention because a variety of information is included in a single article. Therefore, the proposed method provides not only one input article (primary article) but also additional articles related to it as an input query to determine the search intention of the user, based on the relationship between two query articles. In other words, based on the concepts contained in the input article and additional articles, we actualize a relevant literature search that considers user intention by varying the degree of attention given to each concept and modifying the concept hierarchy graph. Conclusions We performed an experiment to retrieve relevant papers from articles on protein structure analysis registered in the Protein Data Bank by using three query datasets. The experimental results yielded search results with better accuracy than when user intention was not considered, confirming the effectiveness of the proposed method. PMID:25952498

Beliefs and Intentions for Skin Protection and Exposure

PubMed Central

Heckman, Carolyn J.; Manne, Sharon L.; Kloss, Jacqueline D.; Bass, Sarah Bauerle; Collins, Bradley; Lessin, Stuart R.

2010-01-01

Objectives To evaluate Fishbein’s Integrative Model in predicting young adults’ skin protection, sun exposure, and indoor tanning intentions. Methods 212 participants completed an online survey. Results Damage distress, self-efficacy, and perceived control accounted for 34% of the variance in skin protection intentions. Outcome beliefs and low self-efficacy for sun avoidance accounted for 25% of the variance in sun exposure intentions. Perceived damage, outcome evaluation, norms, and indoor tanning prototype accounted for 32% of the variance in indoor tanning intentions. Conclusions Future research should investigate whether these variables predict exposure and protection behaviors and whether intervening can reduce young adults’ skin cancer risk behaviors. PMID:22251761

EEG-based emergency braking intention prediction for brain-controlled driving considering one electrode falling-off.

PubMed

Huikang Wang; Luzheng Bi; Teng Teng

2017-07-01

This paper proposes a novel method of electroencephalography (EEG)-based driver emergency braking intention detection system for brain-controlled driving considering one electrode falling-off. First, whether one electrode falls off is discriminated based on EEG potentials. Then, the missing signals are estimated by using the signals collected from other channels based on multivariate linear regression. Finally, a linear decoder is applied to classify driver intentions. Experimental results show that the falling-off discrimination accuracy is 99.63% on average and the correlation coefficient and root mean squared error (RMSE) between the estimated and experimental data are 0.90 and 11.43 μV, respectively, on average. Given one electrode falls off, the system accuracy of the proposed intention prediction method is significantly higher than that of the original method (95.12% VS 79.11%) and is close to that (95.95%) of the original system under normal situations (i. e., no electrode falling-off).

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.

An Investigation of the Factors That Influence Preservice Teachers' Intentions and Actual Integration of Web 2.0 Technologies

ERIC Educational Resources Information Center

Sadaf, Ayesha

2013-01-01

The purpose of this two phase mixed methods sequential explanatory study was to investigate factors that predict preservice teachers' intentions to use Web 2.0 technologies in their future classrooms and their ability to carry out their intentions during student teaching. The first phase explored factors based on the Decomposed Theory of Planned…

Intent to Receive an HPV Vaccine among University Men and Women and Implications for Vaccine Administration

ERIC Educational Resources Information Center

Jones, Melissa; Cook, Robert

2008-01-01

Objective and Participants: In 2006, the authors examined intention to receive an HPV vaccine among 340 college students. Methods: A total of 138 men and 202 women completed questionnaires. The authors measured intention by asking participants how likely they would be to accept an HPV vaccine that prevented against (1) all HPV, (2) cervical cancer…

Semi-Automated Curation Allows Causal Network Model Building for the Quantification of Age-Dependent Plaque Progression in ApoE-/- Mouse.

PubMed

Szostak, Justyna; Martin, Florian; Talikka, Marja; Peitsch, Manuel C; Hoeng, Julia

2016-01-01

The cellular and molecular mechanisms behind the process of atherosclerotic plaque destabilization are complex, and molecular data from aortic plaques are difficult to interpret. Biological network models may overcome these difficulties and precisely quantify the molecular mechanisms impacted during disease progression. The atherosclerosis plaque destabilization biological network model was constructed with the semiautomated curation pipeline, BELIEF. Cellular and molecular mechanisms promoting plaque destabilization or rupture were captured in the network model. Public transcriptomic data sets were used to demonstrate the specificity of the network model and to capture the different mechanisms that were impacted in ApoE -/- mouse aorta at 6 and 32 weeks. We concluded that network models combined with the network perturbation amplitude algorithm provide a sensitive, quantitative method to follow disease progression at the molecular level. This approach can be used to investigate and quantify molecular mechanisms during plaque progression.

The public cancer radiology imaging collections of The Cancer Imaging Archive.

PubMed

Prior, Fred; Smith, Kirk; Sharma, Ashish; Kirby, Justin; Tarbox, Lawrence; Clark, Ken; Bennett, William; Nolan, Tracy; Freymann, John

2017-09-19

The Cancer Imaging Archive (TCIA) is the U.S. National Cancer Institute's repository for cancer imaging and related information. TCIA contains 30.9 million radiology images representing data collected from approximately 37,568 subjects. This data is organized into collections by tumor-type with many collections also including analytic results or clinical data. TCIA staff carefully de-identify and curate all incoming collections prior to making the information available via web browser or programmatic interfaces. Each published collection within TCIA is assigned a Digital Object Identifier that references the collection. Additionally, researchers who use TCIA data may publish the subset of information used in their analysis by requesting a TCIA generated Digital Object Identifier. This data descriptor is a review of a selected subset of existing publicly available TCIA collections. It outlines the curation and publication methods employed by TCIA and makes available 15 collections of cancer imaging data.