WorldWideScience

Sample records for comprehensive cancer database

  1. [Establishment of a comprehensive database for laryngeal cancer related genes and the miRNAs].

    Science.gov (United States)

    Li, Mengjiao; E, Qimin; Liu, Jialin; Huang, Tingting; Liang, Chuanyu

    2015-09-01

    By collecting and analyzing the laryngeal cancer related genes and the miRNAs, to build a comprehensive laryngeal cancer-related gene database, which differs from the current biological information database with complex and clumsy structure and focuses on the theme of gene and miRNA, and it could make the research and teaching more convenient and efficient. Based on the B/S architecture, using Apache as a Web server, MySQL as coding language of database design and PHP as coding language of web design, a comprehensive database for laryngeal cancer-related genes was established, providing with the gene tables, protein tables, miRNA tables and clinical information tables of the patients with laryngeal cancer. The established database containsed 207 laryngeal cancer related genes, 243 proteins, 26 miRNAs, and their particular information such as mutations, methylations, diversified expressions, and the empirical references of laryngeal cancer relevant molecules. The database could be accessed and operated via the Internet, by which browsing and retrieval of the information were performed. The database were maintained and updated regularly. The database for laryngeal cancer related genes is resource-integrated and user-friendly, providing a genetic information query tool for the study of laryngeal cancer.

  2. The Mouse Tumor Biology Database: A Comprehensive Resource for Mouse Models of Human Cancer.

    Science.gov (United States)

    Krupke, Debra M; Begley, Dale A; Sundberg, John P; Richardson, Joel E; Neuhauser, Steven B; Bult, Carol J

    2017-11-01

    Research using laboratory mice has led to fundamental insights into the molecular genetic processes that govern cancer initiation, progression, and treatment response. Although thousands of scientific articles have been published about mouse models of human cancer, collating information and data for a specific model is hampered by the fact that many authors do not adhere to existing annotation standards when describing models. The interpretation of experimental results in mouse models can also be confounded when researchers do not factor in the effect of genetic background on tumor biology. The Mouse Tumor Biology (MTB) database is an expertly curated, comprehensive compendium of mouse models of human cancer. Through the enforcement of nomenclature and related annotation standards, MTB supports aggregation of data about a cancer model from diverse sources and assessment of how genetic background of a mouse strain influences the biological properties of a specific tumor type and model utility. Cancer Res; 77(21); e67-70. ©2017 AACR . ©2017 American Association for Cancer Research.

  3. HCSD: the human cancer secretome database

    DEFF Research Database (Denmark)

    Feizi, Amir; Banaei-Esfahani, Amir; Nielsen, Jens

    2015-01-01

    The human cancer secretome database (HCSD) is a comprehensive database for human cancer secretome data. The cancer secretome describes proteins secreted by cancer cells and structuring information about the cancer secretome will enable further analysis of how this is related with tumor biology...... database is limiting the ability to query the increasing community knowledge. We therefore developed the Human Cancer Secretome Database (HCSD) to fulfil this gap. HCSD contains >80 000 measurements for about 7000 nonredundant human proteins collected from up to 35 high-throughput studies on 17 cancer...

  4. The Danish Testicular Cancer database.

    Science.gov (United States)

    Daugaard, Gedske; Kier, Maria Gry Gundgaard; Bandak, Mikkel; Mortensen, Mette Saksø; Larsson, Heidi; Søgaard, Mette; Toft, Birgitte Groenkaer; Engvad, Birte; Agerbæk, Mads; Holm, Niels Vilstrup; Lauritsen, Jakob

    2016-01-01

    The nationwide Danish Testicular Cancer database consists of a retrospective research database (DaTeCa database) and a prospective clinical database (Danish Multidisciplinary Cancer Group [DMCG] DaTeCa database). The aim is to improve the quality of care for patients with testicular cancer (TC) in Denmark, that is, by identifying risk factors for relapse, toxicity related to treatment, and focusing on late effects. All Danish male patients with a histologically verified germ cell cancer diagnosis in the Danish Pathology Registry are included in the DaTeCa databases. Data collection has been performed from 1984 to 2007 and from 2013 onward, respectively. The retrospective DaTeCa database contains detailed information with more than 300 variables related to histology, stage, treatment, relapses, pathology, tumor markers, kidney function, lung function, etc. A questionnaire related to late effects has been conducted, which includes questions regarding social relationships, life situation, general health status, family background, diseases, symptoms, use of medication, marital status, psychosocial issues, fertility, and sexuality. TC survivors alive on October 2014 were invited to fill in this questionnaire including 160 validated questions. Collection of questionnaires is still ongoing. A biobank including blood/sputum samples for future genetic analyses has been established. Both samples related to DaTeCa and DMCG DaTeCa database are included. The prospective DMCG DaTeCa database includes variables regarding histology, stage, prognostic group, and treatment. The DMCG DaTeCa database has existed since 2013 and is a young clinical database. It is necessary to extend the data collection in the prospective database in order to answer quality-related questions. Data from the retrospective database will be added to the prospective data. This will result in a large and very comprehensive database for future studies on TC patients.

  5. DBGC: A Database of Human Gastric Cancer

    Science.gov (United States)

    Wang, Chao; Zhang, Jun; Cai, Mingdeng; Zhu, Zhenggang; Gu, Wenjie; Yu, Yingyan; Zhang, Xiaoyan

    2015-01-01

    The Database of Human Gastric Cancer (DBGC) is a comprehensive database that integrates various human gastric cancer-related data resources. Human gastric cancer-related transcriptomics projects, proteomics projects, mutations, biomarkers and drug-sensitive genes from different sources were collected and unified in this database. Moreover, epidemiological statistics of gastric cancer patients in China and clinicopathological information annotated with gastric cancer cases were also integrated into the DBGC. We believe that this database will greatly facilitate research regarding human gastric cancer in many fields. DBGC is freely available at http://bminfor.tongji.edu.cn/dbgc/index.do PMID:26566288

  6. The Danish Testicular Cancer database

    Directory of Open Access Journals (Sweden)

    Daugaard G

    2016-10-01

    . Collection of questionnaires is still ongoing. A biobank including blood/sputum samples for future genetic analyses has been established. Both samples related to DaTeCa and DMCG DaTeCa database are included. The prospective DMCG DaTeCa database includes variables regarding histology, stage, prognostic group, and treatment. Conclusion: The DMCG DaTeCa database has existed since 2013 and is a young clinical database. It is necessary to extend the data collection in the prospective database in order to answer quality-related questions. Data from the retrospective database will be added to the prospective data. This will result in a large and very comprehensive database for future studies on TC patients. Keywords: testis cancer, clinical indicators, database research, DaTeCa, DMCG DaTeCa database, hypogonadism

  7. Danish Gynecological Cancer Database

    DEFF Research Database (Denmark)

    Sørensen, Sarah Mejer; Bjørn, Signe Frahm; Jochumsen, Kirsten Marie

    2016-01-01

    AIM OF DATABASE: The Danish Gynecological Cancer Database (DGCD) is a nationwide clinical cancer database and its aim is to monitor the treatment quality of Danish gynecological cancer patients, and to generate data for scientific purposes. DGCD also records detailed data on the diagnostic measures...... data forms as follows: clinical data, surgery, pathology, pre- and postoperative care, complications, follow-up visits, and final quality check. DGCD is linked with additional data from the Danish "Pathology Registry", the "National Patient Registry", and the "Cause of Death Registry" using the unique...... Danish personal identification number (CPR number). DESCRIPTIVE DATA: Data from DGCD and registers are available online in the Statistical Analysis Software portal. The DGCD forms cover almost all possible clinical variables used to describe gynecological cancer courses. The only limitation...

  8. Danish Pancreatic Cancer Database

    DEFF Research Database (Denmark)

    Fristrup, Claus; Detlefsen, Sönke; Palnæs Hansen, Carsten

    2016-01-01

    : Death is monitored using data from the Danish Civil Registry. This registry monitors the survival status of the Danish population, and the registration is virtually complete. All data in the database are audited by all participating institutions, with respect to baseline characteristics, key indicators......AIM OF DATABASE: The Danish Pancreatic Cancer Database aims to prospectively register the epidemiology, diagnostic workup, diagnosis, treatment, and outcome of patients with pancreatic cancer in Denmark at an institutional and national level. STUDY POPULATION: Since May 1, 2011, all patients...... with microscopically verified ductal adenocarcinoma of the pancreas have been registered in the database. As of June 30, 2014, the total number of patients registered was 2,217. All data are cross-referenced with the Danish Pathology Registry and the Danish Patient Registry to ensure the completeness of registrations...

  9. Dansk kolorektal Cancer Database

    DEFF Research Database (Denmark)

    Harling, Henrik; Nickelsen, Thomas

    2005-01-01

    The Danish Colorectal Cancer Database was established in 1994 with the purpose of monitoring whether diagnostic and surgical principles specified in the evidence-based national guidelines of good clinical practice were followed. Twelve clinical indicators have been listed by the Danish Colorectal...... Cancer Group, and the performance of each hospital surgical department with respect to these indicators is reported annually. In addition, the register contains a large collection of data that provide valuable information on the influence of comorbidity and lifestyle factors on disease outcome...

  10. The Danish Testicular Cancer database

    DEFF Research Database (Denmark)

    Daugaard, Gedske; Kier, Maria Gry Gundgaard; Bandak, Mikkel

    2016-01-01

    AIM: The nationwide Danish Testicular Cancer database consists of a retrospective research database (DaTeCa database) and a prospective clinical database (Danish Multidisciplinary Cancer Group [DMCG] DaTeCa database). The aim is to improve the quality of care for patients with testicular cancer (TC......) in Denmark, that is, by identifying risk factors for relapse, toxicity related to treatment, and focusing on late effects. STUDY POPULATION: All Danish male patients with a histologically verified germ cell cancer diagnosis in the Danish Pathology Registry are included in the DaTeCa databases. Data...... collection has been performed from 1984 to 2007 and from 2013 onward, respectively. MAIN VARIABLES AND DESCRIPTIVE DATA: The retrospective DaTeCa database contains detailed information with more than 300 variables related to histology, stage, treatment, relapses, pathology, tumor markers, kidney function...

  11. The Danish Prostate Cancer Database

    DEFF Research Database (Denmark)

    Nguyen-Nielsen, Mary; Høyer, Søren; Friis, Søren

    2016-01-01

    variables include Gleason scores, cancer staging, prostate-specific antigen values, and therapeutic measures (active surveillance, surgery, radiotherapy, endocrine therapy, and chemotherapy). DESCRIPTIVE DATA: In total, 22,332 patients with prostate cancer were registered in DAPROCAdata as of April 2015......AIM OF DATABASE: The Danish Prostate Cancer Database (DAPROCAdata) is a nationwide clinical cancer database that has prospectively collected data on patients with incident prostate cancer in Denmark since February 2010. The overall aim of the DAPROCAdata is to improve the quality of prostate cancer...... care in Denmark by systematically collecting key clinical variables for the purposes of health care monitoring, quality improvement, and research. STUDY POPULATION: All Danish patients with histologically verified prostate cancer are included in the DAPROCAdata. MAIN VARIABLES: The DAPROCAdata...

  12. Danish Colorectal Cancer Group Database

    DEFF Research Database (Denmark)

    Ingeholm, Peter; Gögenur, Ismail; Iversen, Lene H

    2016-01-01

    AIM OF DATABASE: The aim of the database, which has existed for registration of all patients with colorectal cancer in Denmark since 2001, is to improve the prognosis for this patient group. STUDY POPULATION: All Danish patients with newly diagnosed colorectal cancer who are either diagnosed......, and other pathological risk factors. DESCRIPTIVE DATA: The database has had >95% completeness in including patients with colorectal adenocarcinoma with >54,000 patients registered so far with approximately one-third rectal cancers and two-third colon cancers and an overrepresentation of men among rectal...... diagnosis, surgical interventions, and short-term outcomes. The database does not have high-resolution oncological data and does not register recurrences after primary surgery. The Danish Colorectal Cancer Group provides high-quality data and has been documenting an increase in short- and long...

  13. Benchmarking comprehensive cancer care

    NARCIS (Netherlands)

    Wind, Anke

    2017-01-01

    The number of cancer patients and survivors is steadily increasing and despite or perhaps because of rapid improvements in diagnostics and therapeutics, important inequalities in cancer survival exist within and between different countries in Europe. Improving the quality of care is part of the

  14. Danish Colorectal Cancer Group Database.

    Science.gov (United States)

    Ingeholm, Peter; Gögenur, Ismail; Iversen, Lene H

    2016-01-01

    The aim of the database, which has existed for registration of all patients with colorectal cancer in Denmark since 2001, is to improve the prognosis for this patient group. All Danish patients with newly diagnosed colorectal cancer who are either diagnosed or treated in a surgical department of a public Danish hospital. The database comprises an array of surgical, radiological, oncological, and pathological variables. The surgeons record data such as diagnostics performed, including type and results of radiological examinations, lifestyle factors, comorbidity and performance, treatment including the surgical procedure, urgency of surgery, and intra- and postoperative complications within 30 days after surgery. The pathologists record data such as tumor type, number of lymph nodes and metastatic lymph nodes, surgical margin status, and other pathological risk factors. The database has had >95% completeness in including patients with colorectal adenocarcinoma with >54,000 patients registered so far with approximately one-third rectal cancers and two-third colon cancers and an overrepresentation of men among rectal cancer patients. The stage distribution has been more or less constant until 2014 with a tendency toward a lower rate of stage IV and higher rate of stage I after introduction of the national screening program in 2014. The 30-day mortality rate after elective surgery has been reduced from >7% in 2001-2003 to database is a national population-based clinical database with high patient and data completeness for the perioperative period. The resolution of data is high for description of the patient at the time of diagnosis, including comorbidities, and for characterizing diagnosis, surgical interventions, and short-term outcomes. The database does not have high-resolution oncological data and does not register recurrences after primary surgery. The Danish Colorectal Cancer Group provides high-quality data and has been documenting an increase in short- and long

  15. PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database.

    Science.gov (United States)

    Huang, Weiliang; Brewer, Luke K; Jones, Jace W; Nguyen, Angela T; Marcu, Ana; Wishart, David S; Oglesby-Sherrouse, Amanda G; Kane, Maureen A; Wilks, Angela

    2018-01-04

    The Pseudomonas aeruginosaMetabolome Database (PAMDB, http://pseudomonas.umaryland.edu) is a searchable, richly annotated metabolite database specific to P. aeruginosa. P. aeruginosa is a soil organism and significant opportunistic pathogen that adapts to its environment through a versatile energy metabolism network. Furthermore, P. aeruginosa is a model organism for the study of biofilm formation, quorum sensing, and bioremediation processes, each of which are dependent on unique pathways and metabolites. The PAMDB is modelled on the Escherichia coli (ECMDB), yeast (YMDB) and human (HMDB) metabolome databases and contains >4370 metabolites and 938 pathways with links to over 1260 genes and proteins. The database information was compiled from electronic databases, journal articles and mass spectrometry (MS) metabolomic data obtained in our laboratories. For each metabolite entered, we provide detailed compound descriptions, names and synonyms, structural and physiochemical information, nuclear magnetic resonance (NMR) and MS spectra, enzymes and pathway information, as well as gene and protein sequences. The database allows extensive searching via chemical names, structure and molecular weight, together with gene, protein and pathway relationships. The PAMBD and its future iterations will provide a valuable resource to biologists, natural product chemists and clinicians in identifying active compounds, potential biomarkers and clinical diagnostics. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. Computerized comprehensive data analysis of Lung Imaging Database Consortium (LIDC)

    International Nuclear Information System (INIS)

    Tan Jun; Pu Jiantao; Zheng Bin; Wang Xingwei; Leader, Joseph K.

    2010-01-01

    Purpose: Lung Image Database Consortium (LIDC) is the largest public CT image database of lung nodules. In this study, the authors present a comprehensive and the most updated analysis of this dynamically growing database under the help of a computerized tool, aiming to assist researchers to optimally use this database for lung cancer related investigations. Methods: The authors developed a computer scheme to automatically match the nodule outlines marked manually by radiologists on CT images. A large variety of characteristics regarding the annotated nodules in the database including volume, spiculation level, elongation, interobserver variability, as well as the intersection of delineated nodule voxels and overlapping ratio between the same nodules marked by different radiologists are automatically calculated and summarized. The scheme was applied to analyze all 157 examinations with complete annotation data currently available in LIDC dataset. Results: The scheme summarizes the statistical distributions of the abovementioned geometric and diagnosis features. Among the 391 nodules, (1) 365 (93.35%) have principal axis length ≤20 mm; (2) 120, 75, 76, and 120 were marked by one, two, three, and four radiologists, respectively; and (3) 122 (32.48%) have the maximum volume overlapping ratios ≥80% for the delineations of two radiologists, while 198 (50.64%) have the maximum volume overlapping ratios <60%. The results also showed that 72.89% of the nodules were assessed with malignancy score between 2 and 4, and only 7.93% of these nodules were considered as severely malignant (malignancy ≥4). Conclusions: This study demonstrates that LIDC contains examinations covering a diverse distribution of nodule characteristics and it can be a useful resource to assess the performance of the nodule detection and/or segmentation schemes.

  17. The Danish Gynecological Cancer Nursing Database

    DEFF Research Database (Denmark)

    Seibæk, Lene; Jakobsen, Dorthe Hjort; Høgdall, Claus

    2018-01-01

    Database (DGCD) established a nursing database in 2011. The aim of DGCD Nursing is to monitor the quality of preoperative and postoperative care and to generate data for research. MATERIAL AND METHODS: In accordance with the current data protection legislation, real-time data are entered by clinical nurses...... at all national cancer centers. The DGCD Nursing includes data of preoperative and postoperative care, and nurses are independently represented in the steering committee. The aim of the present article is to present the first results from DGCD Nursing and the national care improvements that have followed......, pain score, vital functions, and psychosocial support. CONCLUSIONS: At national level, DGCD offers a comprehensive overview of the total patient pathway within gynecological cancer surgery. The DGCD Nursing has added to the quality and implementation of evidence-based preoperative and postoperative...

  18. The Danish Bladder Cancer Database

    DEFF Research Database (Denmark)

    Hansen, Erik; Larsson, Heidi Jeanet; Nørgaard, Mette

    2016-01-01

    AIM OF DATABASE: The aim of the Danish Bladder Cancer Database (DaBlaCa-data) is to monitor the treatment of all patients diagnosed with invasive bladder cancer (BC) in Denmark. STUDY POPULATION: All patients diagnosed with BC in Denmark from 2012 onward were included in the study. Results......-intended radiation therapy. DESCRIPTIVE DATA: One-year mortality was 28% (95% confidence interval [CI]: 15-21). One-year cancer-specific mortality was 25% (95% CI: 22-27%). One-year mortality after cystectomy was 14% (95% CI: 10-18). Ninety-day mortality after cystectomy was 3% (95% CI: 1-5) in 2013. One......-year mortality following curative-intended radiation therapy was 32% (95% CI: 24-39) and 1-year cancer-specific mortality was 23% (95% CI: 16-31) in 2013. CONCLUSION: This preliminary DaBlaCa-data report showed that the treatment of MIBC in Denmark overall meet high international academic standards. The database...

  19. The Danish Bladder Cancer Database

    Directory of Open Access Journals (Sweden)

    Hansen E

    2016-10-01

    Full Text Available Erik Hansen,1–3 Heidi Larsson,4 Mette Nørgaard,4 Peter Thind,3,5 Jørgen Bjerggaard Jensen1–3 1Department of Urology, Hospital of West Jutland-Holstebro, Holstebro, 2Department of Urology, Aarhus University Hospital, Aarhus, 3The Danish Bladder Cancer Database Group, 4Department of Clinical Epidemiology, Aarhus University Hospital, Aarhus, 5Department of Urology, Copenhagen University Hospital, Copenhagen, Denmark Aim of database: The aim of the Danish Bladder Cancer Database (DaBlaCa-data is to monitor the treatment of all patients diagnosed with invasive bladder cancer (BC in Denmark. Study population: All patients diagnosed with BC in Denmark from 2012 onward were included in the study. Results presented in this paper are predominantly from the 2013 population. Main variables: In 2013, 970 patients were diagnosed with BC in Denmark and were included in a preliminary report from the database. A total of 458 (47% patients were diagnosed with non-muscle-invasive BC (non-MIBC and 512 (53% were diagnosed with muscle-invasive BC (MIBC. A total of 300 (31% patients underwent cystectomy. Among the 135 patients diagnosed with MIBC, who were 75 years of age or younger, 67 (50% received neoadjuvent chemotherapy prior to cystectomy. In 2013, a total of 147 patients were treated with curative-intended radiation therapy. Descriptive data: One-year mortality was 28% (95% confidence interval [CI]: 15–21. One-year cancer-specific mortality was 25% (95% CI: 22–27%. One-year mortality after cystectomy was 14% (95% CI: 10–18. Ninety-day mortality after cystectomy was 3% (95% CI: 1–5 in 2013. One-year mortality following curative-intended radiation therapy was 32% (95% CI: 24–39 and 1-year cancer-specific mortality was 23% (95% CI: 16–31 in 2013. Conclusion: This preliminary DaBlaCa-data report showed that the treatment of MIBC in Denmark overall meet high international academic standards. The database is able to identify Danish BC patients and

  20. Trends in intensity modulated radiation therapy use for locally advanced rectal cancer at National Comprehensive Cancer Network centers

    OpenAIRE

    Marsha Reyngold, MD, PhD; Joyce Niland, PhD; Anna ter Veer, MS; Tanios Bekaii-Saab, MD; Lily Lai, MD; Joshua E. Meyer, MD; Steven J. Nurkin, MD, MS; Deborah Schrag, MD, MPH; John M. Skibber, MD, FACS; Al B. Benson, MD; Martin R. Weiser, MD; Christopher H. Crane, MD; Karyn A. Goodman, MD, MS

    2018-01-01

    Purpose: Intensity modulated radiation therapy (IMRT) has been rapidly incorporated into clinical practice because of its technological advantages over 3-dimensional conformal radiation therapy (CRT). We characterized trends in IMRT utilization in trimodality treatment of locally advanced rectal cancer at National Comprehensive Cancer Network cancer centers between 2005 and 2011. Methods and materials: Using the prospective National Comprehensive Cancer Network Colorectal Cancer Database, ...

  1. The Danish Nonmelanoma Skin Cancer Dermatology Database

    DEFF Research Database (Denmark)

    Lamberg, Anna Lei; Sølvsten, Henrik; Lei, Ulrikke

    2016-01-01

    AIM OF DATABASE: The Danish Nonmelanoma Skin Cancer Dermatology Database was established in 2008. The aim of this database was to collect data on nonmelanoma skin cancer (NMSC) treatment and improve its treatment in Denmark. NMSC is the most common malignancy in the western countries and represents...... treatment. The database has revealed that overall, the quality of care of NMSC in Danish dermatological clinics is high, and the database provides the necessary data for continuous quality assurance....

  2. [A web-based integrated clinical database for laryngeal cancer].

    Science.gov (United States)

    E, Qimin; Liu, Jialin; Li, Yong; Liang, Chuanyu

    2014-08-01

    To establish an integrated database for laryngeal cancer, and to provide an information platform for laryngeal cancer in clinical and fundamental researches. This database also meet the needs of clinical and scientific use. Under the guidance of clinical expert, we have constructed a web-based integrated clinical database for laryngeal carcinoma on the basis of clinical data standards, Apache+PHP+MySQL technology, laryngeal cancer specialist characteristics and tumor genetic information. A Web-based integrated clinical database for laryngeal carcinoma had been developed. This database had a user-friendly interface and the data could be entered and queried conveniently. In addition, this system utilized the clinical data standards and exchanged information with existing electronic medical records system to avoid the Information Silo. Furthermore, the forms of database was integrated with laryngeal cancer specialist characteristics and tumor genetic information. The Web-based integrated clinical database for laryngeal carcinoma has comprehensive specialist information, strong expandability, high feasibility of technique and conforms to the clinical characteristics of laryngeal cancer specialties. Using the clinical data standards and structured handling clinical data, the database can be able to meet the needs of scientific research better and facilitate information exchange, and the information collected and input about the tumor sufferers are very informative. In addition, the user can utilize the Internet to realize the convenient, swift visit and manipulation on the database.

  3. CBD: a biomarker database for colorectal cancer.

    Science.gov (United States)

    Zhang, Xueli; Sun, Xiao-Feng; Cao, Yang; Ye, Benchen; Peng, Qiliang; Liu, Xingyun; Shen, Bairong; Zhang, Hong

    2018-01-01

    Colorectal cancer (CRC) biomarker database (CBD) was established based on 870 identified CRC biomarkers and their relevant information from 1115 original articles in PubMed published from 1986 to 2017. In this version of the CBD, CRC biomarker data were collected, sorted, displayed and analysed. The CBD with the credible contents as a powerful and time-saving tool provide more comprehensive and accurate information for further CRC biomarker research. The CBD was constructed under MySQL server. HTML, PHP and JavaScript languages have been used to implement the web interface. The Apache was selected as HTTP server. All of these web operations were implemented under the Windows system. The CBD could provide to users the multiple individual biomarker information and categorized into the biological category, source and application of biomarkers; the experiment methods, results, authors and publication resources; the research region, the average age of cohort, gender, race, the number of tumours, tumour location and stage. We only collect data from the articles with clear and credible results to prove the biomarkers are useful in the diagnosis, treatment or prognosis of CRC. The CBD can also provide a professional platform to researchers who are interested in CRC research to communicate, exchange their research ideas and further design high-quality research in CRC. They can submit their new findings to our database via the submission page and communicate with us in the CBD.Database URL: http://sysbio.suda.edu.cn/CBD/.

  4. Developing a comprehensive and accountable database after a radiological accident

    International Nuclear Information System (INIS)

    Berry, H.A.; Burson, Z.G.

    1986-09-01

    After a radiological accident occurs, it is highly desirable to promptly begin developing a comprehensive and accountable environmental database both for immediate health and safety needs and for long-term documentation. The need to assess and evaluate the impact of the accident as quickly as possible is always very urgent, the technical integrity of the data must also be assured and maintained. Care must therefore be taken to log, collate, and organize the environmental data into a complete and accountable database. The key components of the database development are summarized as well as the experience gained in organizing and handling environmental data acquired during: (1) TMI (1979); (2) the St. Lucie Reactor Accident Exercise (through the Federal Radiological Measurement and Assessment Center (FRMAC), March 1984); (3) the Sequoyah Fuels Inc., uranium hexafluoride accident near Gore, Oklahoma (January 1986); and (4) Chernobyl reactor accident in Russia (April 1986)

  5. CEBS: a comprehensive annotated database of toxicological data

    Science.gov (United States)

    Lea, Isabel A.; Gong, Hui; Paleja, Anand; Rashid, Asif; Fostel, Jennifer

    2017-01-01

    The Chemical Effects in Biological Systems database (CEBS) is a comprehensive and unique toxicology resource that compiles individual and summary animal data from the National Toxicology Program (NTP) testing program and other depositors into a single electronic repository. CEBS has undergone significant updates in recent years and currently contains over 11 000 test articles (exposure agents) and over 8000 studies including all available NTP carcinogenicity, short-term toxicity and genetic toxicity studies. Study data provided to CEBS are manually curated, accessioned and subject to quality assurance review prior to release to ensure high quality. The CEBS database has two main components: data collection and data delivery. To accommodate the breadth of data produced by NTP, the CEBS data collection component is an integrated relational design that allows the flexibility to capture any type of electronic data (to date). The data delivery component of the database comprises a series of dedicated user interface tables containing pre-processed data that support each component of the user interface. The user interface has been updated to include a series of nine Guided Search tools that allow access to NTP summary and conclusion data and larger non-NTP datasets. The CEBS database can be accessed online at http://www.niehs.nih.gov/research/resources/databases/cebs/. PMID:27899660

  6. Comprehensive T-Matrix Reference Database: A 2012 - 2013 Update

    Science.gov (United States)

    Mishchenko, Michael I.; Videen, Gorden; Khlebtsov, Nikolai G.; Wriedt, Thomas

    2013-01-01

    The T-matrix method is one of the most versatile, efficient, and accurate theoretical techniques widely used for numerically exact computer calculations of electromagnetic scattering by single and composite particles, discrete random media, and particles imbedded in complex environments. This paper presents the fifth update to the comprehensive database of peer-reviewed T-matrix publications initiated by us in 2004 and includes relevant publications that have appeared since 2012. It also lists several earlier publications not incorporated in the original database, including Peter Waterman's reports from the 1960s illustrating the history of the T-matrix approach and demonstrating that John Fikioris and Peter Waterman were the true pioneers of the multi-sphere method otherwise known as the generalized Lorenz - Mie theory.

  7. Respiratory cancer database: An open access database of respiratory cancer gene and miRNA

    Directory of Open Access Journals (Sweden)

    Jyotsna Choubey

    2017-01-01

    Results and Conclusions: RespCanDB is expected to contribute to the understanding of scientific community regarding respiratory cancer biology as well as developments of new way of diagnosing and treating respiratory cancer. Currently, the database consist the oncogenomic information of lung cancer, laryngeal cancer, and nasopharyngeal cancer. Data for other cancers, such as oral and tracheal cancers, will be added in the near future. The URL of RespCanDB is http://ridb.subdic-bioinformatics-nitrr.in/.

  8. Comprehensive Genetic Database of Expressed Sequence Tags for Coccolithophorids

    Science.gov (United States)

    Ranji, Mohammad; Hadaegh, Ahmad R.

    Coccolithophorids are unicellular, marine, golden-brown, single-celled algae (Haptophyta) commonly found in near-surface waters in patchy distributions. They belong to the Phytoplankton family that is known to be responsible for much of the earth reproduction. Phytoplankton, just like plants live based on the energy obtained by Photosynthesis which produces oxygen. Substantial amount of oxygen in the earth's atmosphere is produced by Phytoplankton through Photosynthesis. The single-celled Emiliana Huxleyi is the most commonly known specie of Coccolithophorids and is known for extracting bicarbonate (HCO3) from its environment and producing calcium carbonate to form Coccoliths. Coccolithophorids are one of the world's primary producers, contributing about 15% of the average oceanic phytoplankton biomass to the oceans. They produce elaborate, minute calcite platelets (Coccoliths), covering the cell to form a Coccosphere and supplying up to 60% of the bulk pelagic calcite deposited on the sea floors. In order to understand the genetics of Coccolithophorid and the complexities of their biochemical reactions, we decided to build a database to store a complete profile of these organisms' genomes. Although a variety of such databases currently exist, (http://www.geneservice.co.uk/home/) none have yet been developed to comprehensively address the sequencing efforts underway by the Coccolithophorid research community. This database is called CocooExpress and is available to public (http://bioinfo.csusm.edu) for both data queries and sequence contribution.

  9. Development of comprehensive material performance database for nuclear applications

    International Nuclear Information System (INIS)

    Tsuji, Hirokazu; Yokoyama, Norio; Tsukada, Takashi; Nakajima, Hajime

    1993-01-01

    This paper introduces the present status of the comprehensive material performance database for nuclear applications, which was named JAERI Material Performance Database (JMPD), and examples of its utilization. The JMPD has been developed since 1986 in JAERI with a view to utilizing various kinds of characteristics data of nuclear materials efficiently. Management system of relational database, PLANNER, was employed, and supporting systems for data retrieval and output were expanded. In order to improve user-friendliness of the retrieval system, the menu selection type procedures have been developed where knowledge of the system or the data structures are not required for end-users. As to utilization of the JMPD, two types of data analyses are mentioned as follows: (1) A series of statistical analyses was performed in order to estimate the design values both of the yield strength (Sy) and the tensile strength (Su) for aluminum alloys which are widely used as structural materials for research reactors. (2) Statistical analyses were accomplished by using the cyclic crack growth rate data for nuclear pressure vessel steels, and comparisons were made on variability and/or reproducibility of the data between obtained by ΔK-increasing and ΔK-constant type tests. (author)

  10. Respiratory cancer database: An open access database of respiratory cancer gene and miRNA.

    Science.gov (United States)

    Choubey, Jyotsna; Choudhari, Jyoti Kant; Patel, Ashish; Verma, Mukesh Kumar

    2017-01-01

    Respiratory cancer database (RespCanDB) is a genomic and proteomic database of cancer of respiratory organ. It also includes the information of medicinal plants used for the treatment of various respiratory cancers with structure of its active constituents as well as pharmacological and chemical information of drug associated with various respiratory cancers. Data in RespCanDB has been manually collected from published research article and from other databases. Data has been integrated using MySQL an object-relational database management system. MySQL manages all data in the back-end and provides commands to retrieve and store the data into the database. The web interface of database has been built in ASP. RespCanDB is expected to contribute to the understanding of scientific community regarding respiratory cancer biology as well as developments of new way of diagnosing and treating respiratory cancer. Currently, the database consist the oncogenomic information of lung cancer, laryngeal cancer, and nasopharyngeal cancer. Data for other cancers, such as oral and tracheal cancers, will be added in the near future. The URL of RespCanDB is http://ridb.subdic-bioinformatics-nitrr.in/.

  11. The Danish Nonmelanoma Skin Cancer Dermatology Database.

    Science.gov (United States)

    Lamberg, Anna Lei; Sølvsten, Henrik; Lei, Ulrikke; Vinding, Gabrielle Randskov; Stender, Ida Marie; Jemec, Gregor Borut Ernst; Vestergaard, Tine; Thormann, Henrik; Hædersdal, Merete; Dam, Tomas Norman; Olesen, Anne Braae

    2016-01-01

    The Danish Nonmelanoma Skin Cancer Dermatology Database was established in 2008. The aim of this database was to collect data on nonmelanoma skin cancer (NMSC) treatment and improve its treatment in Denmark. NMSC is the most common malignancy in the western countries and represents a significant challenge in terms of public health management and health care costs. However, high-quality epidemiological and treatment data on NMSC are sparse. The NMSC database includes patients with the following skin tumors: basal cell carcinoma (BCC), squamous cell carcinoma, Bowen's disease, and keratoacanthoma diagnosed by the participating office-based dermatologists in Denmark. Clinical and histological diagnoses, BCC subtype, localization, size, skin cancer history, skin phototype, and evidence of metastases and treatment modality are the main variables in the NMSC database. Information on recurrence, cosmetic results, and complications are registered at two follow-up visits at 3 months (between 0 and 6 months) and 12 months (between 6 and 15 months) after treatment. In 2014, 11,522 patients with 17,575 tumors were registered in the database. Of tumors with a histological diagnosis, 13,571 were BCCs, 840 squamous cell carcinomas, 504 Bowen's disease, and 173 keratoakanthomas. The NMSC database encompasses detailed information on the type of tumor, a variety of prognostic factors, treatment modalities, and outcomes after treatment. The database has revealed that overall, the quality of care of NMSC in Danish dermatological clinics is high, and the database provides the necessary data for continuous quality assurance.

  12. The Resistome: A Comprehensive Database of Escherichia coli Resistance Phenotypes.

    Science.gov (United States)

    Winkler, James D; Halweg-Edwards, Andrea L; Erickson, Keesha E; Choudhury, Alaksh; Pines, Gur; Gill, Ryan T

    2016-12-16

    The microbial ability to resist stressful environmental conditions and chemical inhibitors is of great industrial and medical interest. Much of the data related to mutation-based stress resistance, however, is scattered through the academic literature, making it difficult to apply systematic analyses to this wealth of information. To address this issue, we introduce the Resistome database: a literature-curated collection of Escherichia coli genotypes-phenotypes containing over 5,000 mutants that resist hundreds of compounds and environmental conditions. We use the Resistome to understand our current state of knowledge regarding resistance and to detect potential synergy or antagonism between resistance phenotypes. Our data set represents one of the most comprehensive collections of genomic data related to resistance currently available. Future development will focus on the construction of a combined genomic-transcriptomic-proteomic framework for understanding E. coli's resistance biology. The Resistome can be downloaded at https://bitbucket.org/jdwinkler/resistome_release/overview .

  13. DDEC: Dragon database of genes implicated in esophageal cancer

    KAUST Repository

    Essack, Magbubah

    2009-07-06

    Background: Esophageal cancer ranks eighth in order of cancer occurrence. Its lethality primarily stems from inability to detect the disease during the early organ-confined stage and the lack of effective therapies for advanced-stage disease. Moreover, the understanding of molecular processes involved in esophageal cancer is not complete, hampering the development of efficient diagnostics and therapy. Efforts made by the scientific community to improve the survival rate of esophageal cancer have resulted in a wealth of scattered information that is difficult to find and not easily amendable to data-mining. To reduce this gap and to complement available cancer related bioinformatic resources, we have developed a comprehensive database (Dragon Database of Genes Implicated in Esophageal Cancer) with esophageal cancer related information, as an integrated knowledge database aimed at representing a gateway to esophageal cancer related data. Description: Manually curated 529 genes differentially expressed in EC are contained in the database. We extracted and analyzed the promoter regions of these genes and complemented gene-related information with transcription factors that potentially control them. We further, precompiled text-mined and data-mined reports about each of these genes to allow for easy exploration of information about associations of EC-implicated genes with other human genes and proteins, metabolites and enzymes, toxins, chemicals with pharmacological effects, disease concepts and human anatomy. The resulting database, DDEC, has a useful feature to display potential associations that are rarely reported and thus difficult to identify. Moreover, DDEC enables inspection of potentially new \\'association hypotheses\\' generated based on the precompiled reports. Conclusion: We hope that this resource will serve as a useful complement to the existing public resources and as a good starting point for researchers and physicians interested in EC genetics. DDEC is

  14. DDEC: Dragon database of genes implicated in esophageal cancer

    International Nuclear Information System (INIS)

    Essack, Magbubah; Radovanovic, Aleksandar; Schaefer, Ulf; Schmeier, Sebastian; Seshadri, Sundararajan V; Christoffels, Alan; Kaur, Mandeep; Bajic, Vladimir B

    2009-01-01

    Esophageal cancer ranks eighth in order of cancer occurrence. Its lethality primarily stems from inability to detect the disease during the early organ-confined stage and the lack of effective therapies for advanced-stage disease. Moreover, the understanding of molecular processes involved in esophageal cancer is not complete, hampering the development of efficient diagnostics and therapy. Efforts made by the scientific community to improve the survival rate of esophageal cancer have resulted in a wealth of scattered information that is difficult to find and not easily amendable to data-mining. To reduce this gap and to complement available cancer related bioinformatic resources, we have developed a comprehensive database (Dragon Database of Genes Implicated in Esophageal Cancer) with esophageal cancer related information, as an integrated knowledge database aimed at representing a gateway to esophageal cancer related data. Manually curated 529 genes differentially expressed in EC are contained in the database. We extracted and analyzed the promoter regions of these genes and complemented gene-related information with transcription factors that potentially control them. We further, precompiled text-mined and data-mined reports about each of these genes to allow for easy exploration of information about associations of EC-implicated genes with other human genes and proteins, metabolites and enzymes, toxins, chemicals with pharmacological effects, disease concepts and human anatomy. The resulting database, DDEC, has a useful feature to display potential associations that are rarely reported and thus difficult to identify. Moreover, DDEC enables inspection of potentially new 'association hypotheses' generated based on the precompiled reports. We hope that this resource will serve as a useful complement to the existing public resources and as a good starting point for researchers and physicians interested in EC genetics. DDEC is freely accessible to academic

  15. The Danish Head and Neck Cancer database

    DEFF Research Database (Denmark)

    Overgaard, Jens; Jovanovic, Aleksandar; Godballe, Christian

    2016-01-01

    of continuous clinical trials and subsequent implementation in national guidelines. The database has furthermore been used to describe the effect of reduced waiting time, changed epidemiology, and influence of comorbidity and socioeconomic parameters. CONCLUSION: Half a century of registration of head and neck......AIM OF THE DATABASE: The Danish Head and Neck Cancer database is a nationwide clinical quality database that contains prospective data collected since the early 1960s. The overall aim of this study was to describe the outcome of the national strategy for multidisciplinary treatment of head and neck......) of cancer in the nasal sinuses, salivary glands, or thyroid gland (corresponding to the International Classification of Diseases, tenth revision, classifications C.01-C.11, C.30-C.32, C.73, and C.80). MAIN VARIABLES: The main variables used in the study were symptoms and the duration of the symptoms...

  16. Comprehensive update on cancer scenario of Bangladesh

    Directory of Open Access Journals (Sweden)

    Syed Md Akram Hussain

    2013-01-01

    Full Text Available Bangladesh, at 142 million people, is the ninth most populous country in the world. There are 13 to 15 lakh cancer patients in Bangladesh, with about two lakh patients newly diagnosed with cancer each year. As an overview, lung cancer and mouth-oropharynx cancer rank as the top two prevalent cancers in males. Other types of cancers are esophagus cancer and stomach cancer. In women, cancer cervix uteri and breast cancer are most prevalent. Other cancer types, which affect women, are mouth and oropharynx cancer, lung cancer, and esophagus cancer. There are around 150 qualified clinical oncologists and 16 pediatric oncologists working in the different parts of the country. Regular cancer treatment is available in 19 hospitals and 465 hospital beds are attached as indoor or day care facilities for chemotherapy in the oncology/radiotherapy departments. There are about 15 linear accelerators, 12 Co-60 teletherapy and 12 brachytherapy units currently available. Approximately, 56 cancer chemotherapeutic agents are obtainable in Bangladesh. Research facilities are available at tertiary care centers and a few multi country collaborative research activities are ongoing. Bangladesh has a unique National Cancer Control Strategy and Plan of Action 2009-2015 formulated with the assistance of WHO with an objective to develop and implement continuum of cancer care through a comprehensive cancer control programe. Preventive measures taken to reduce the incidence of cancer include reduced tobacco smoking, change of dietary habit and reduced food adulteration, ensuring reproductive hygiene, increased physical activity, and reduced occupational hazard. Awareness buildup and media campaign are going on by organizing the general people, opinion leaders of the society, and boy and girl scout. Training of general physicians on cancer warning signs and setup of early cancer detection centers at each medical college and district levels are ongoing. Beside these, some

  17. Feasibility of Creating a Comprehensive Real Property Database for Colombia

    National Research Council Canada - National Science Library

    Demarest, Geoffrey B

    2002-01-01

    The Defense Intelligence Agency asked the Foreign Military Studies Office (FMSO) to determine the feasibility of producing a digital database of Colombian real property, and to express the usefulness of such a database...

  18. Medicago truncatula transporter database: a comprehensive database resource for M. truncatula transporters

    Directory of Open Access Journals (Sweden)

    Miao Zhenyan

    2012-02-01

    Full Text Available Abstract Background Medicago truncatula has been chosen as a model species for genomic studies. It is closely related to an important legume, alfalfa. Transporters are a large group of membrane-spanning proteins. They deliver essential nutrients, eject waste products, and assist the cell in sensing environmental conditions by forming a complex system of pumps and channels. Although studies have effectively characterized individual M. truncatula transporters in several databases, until now there has been no available systematic database that includes all transporters in M. truncatula. Description The M. truncatula transporter database (MTDB contains comprehensive information on the transporters in M. truncatula. Based on the TransportTP method, we have presented a novel prediction pipeline. A total of 3,665 putative transporters have been annotated based on International Medicago Genome Annotated Group (IMGAG V3.5 V3 and the M. truncatula Gene Index (MTGI V10.0 releases and assigned to 162 families according to the transporter classification system. These families were further classified into seven types according to their transport mode and energy coupling mechanism. Extensive annotations referring to each protein were generated, including basic protein function, expressed sequence tag (EST mapping, genome locus, three-dimensional template prediction, transmembrane segment, and domain annotation. A chromosome distribution map and text-based Basic Local Alignment Search Tools were also created. In addition, we have provided a way to explore the expression of putative M. truncatula transporter genes under stress treatments. Conclusions In summary, the MTDB enables the exploration and comparative analysis of putative transporters in M. truncatula. A user-friendly web interface and regular updates make MTDB valuable to researchers in related fields. The MTDB is freely available now to all users at http://bioinformatics.cau.edu.cn/MtTransporter/.

  19. [A systematic evaluation of application of the web-based cancer database].

    Science.gov (United States)

    Huang, Tingting; Liu, Jialin; Li, Yong; Zhang, Rui

    2013-10-01

    In order to support the theory and practice of the web-based cancer database development in China, we applied a systematic evaluation to assess the development condition of the web-based cancer databases at home and abroad. We performed computer-based retrieval of the Ovid-MEDLINE, Springerlink, EBSCOhost, Wiley Online Library and CNKI databases, the papers of which were published between Jan. 1995 and Dec. 2011, and retrieved the references of these papers by hand. We selected qualified papers according to the pre-established inclusion and exclusion criteria, and carried out information extraction and analysis of the papers. Eventually, searching the online database, we obtained 1244 papers, and checking the reference lists, we found other 19 articles. Thirty-one articles met the inclusion and exclusion criteria and we extracted the proofs and assessed them. Analyzing these evidences showed that the U.S.A. counted for 26% in the first place. Thirty-nine percent of these web-based cancer databases are comprehensive cancer databases. As for single cancer databases, breast cancer and prostatic cancer are on the top, both counting for 10% respectively. Thirty-two percent of the cancer database are associated with cancer gene information. For the technical applications, MySQL and PHP applied most widely, nearly 23% each.

  20. MitBASE : a comprehensive and integrated mitochondrial DNA database. The present status

    NARCIS (Netherlands)

    Attimonelli, M.; Altamura, N.; Benne, R.; Brennicke, A.; Cooper, J. M.; D'Elia, D.; Montalvo, A.; Pinto, B.; de Robertis, M.; Golik, P.; Knoop, V.; Lanave, C.; Lazowska, J.; Licciulli, F.; Malladi, B. S.; Memeo, F.; Monnerot, M.; Pasimeni, R.; Pilbout, S.; Schapira, A. H.; Sloof, P.; Saccone, C.

    2000-01-01

    MitBASE is an integrated and comprehensive database of mitochondrial DNA data which collects, under a single interface, databases for Plant, Vertebrate, Invertebrate, Human, Protist and Fungal mtDNA and a Pilot database on nuclear genes involved in mitochondrial biogenesis in Saccharomyces

  1. MICA: desktop software for comprehensive searching of DNA databases

    Directory of Open Access Journals (Sweden)

    Glick Benjamin S

    2006-10-01

    Full Text Available Abstract Background Molecular biologists work with DNA databases that often include entire genomes. A common requirement is to search a DNA database to find exact matches for a nondegenerate or partially degenerate query. The software programs available for such purposes are normally designed to run on remote servers, but an appealing alternative is to work with DNA databases stored on local computers. We describe a desktop software program termed MICA (K-Mer Indexing with Compact Arrays that allows large DNA databases to be searched efficiently using very little memory. Results MICA rapidly indexes a DNA database. On a Macintosh G5 computer, the complete human genome could be indexed in about 5 minutes. The indexing algorithm recognizes all 15 characters of the DNA alphabet and fully captures the information in any DNA sequence, yet for a typical sequence of length L, the index occupies only about 2L bytes. The index can be searched to return a complete list of exact matches for a nondegenerate or partially degenerate query of any length. A typical search of a long DNA sequence involves reading only a small fraction of the index into memory. As a result, searches are fast even when the available RAM is limited. Conclusion MICA is suitable as a search engine for desktop DNA analysis software.

  2. MIPS: curated databases and comprehensive secondary data resources in 2010.

    Science.gov (United States)

    Mewes, H Werner; Ruepp, Andreas; Theis, Fabian; Rattei, Thomas; Walter, Mathias; Frishman, Dmitrij; Suhre, Karsten; Spannagl, Manuel; Mayer, Klaus F X; Stümpflen, Volker; Antonov, Alexey

    2011-01-01

    The Munich Information Center for Protein Sequences (MIPS at the Helmholtz Center for Environmental Health, Neuherberg, Germany) has many years of experience in providing annotated collections of biological data. Selected data sets of high relevance, such as model genomes, are subjected to careful manual curation, while the bulk of high-throughput data is annotated by automatic means. High-quality reference resources developed in the past and still actively maintained include Saccharomyces cerevisiae, Neurospora crassa and Arabidopsis thaliana genome databases as well as several protein interaction data sets (MPACT, MPPI and CORUM). More recent projects are PhenomiR, the database on microRNA-related phenotypes, and MIPS PlantsDB for integrative and comparative plant genome research. The interlinked resources SIMAP and PEDANT provide homology relationships as well as up-to-date and consistent annotation for 38,000,000 protein sequences. PPLIPS and CCancer are versatile tools for proteomics and functional genomics interfacing to a database of compilations from gene lists extracted from literature. A novel literature-mining tool, EXCERBT, gives access to structured information on classified relations between genes, proteins, phenotypes and diseases extracted from Medline abstracts by semantic analysis. All databases described here, as well as the detailed descriptions of our projects can be accessed through the MIPS WWW server (http://mips.helmholtz-muenchen.de).

  3. Surrogate for oropharyngeal cancer HPV status in cancer database studies.

    Science.gov (United States)

    Megwalu, Uchechukwu C; Chen, Michelle M; Ma, Yifei; Divi, Vasu

    2017-12-01

    The utility of cancer databases for oropharyngeal cancer studies is limited by lack of information on human papillomavirus (HPV) status. The purpose of this study was to develop a surrogate that can be used to adjust for the effect of HPV status on survival. The study cohort included 6419 patients diagnosed with oropharyngeal squamous cell carcinoma between 2004 and 2012, identified in the National Cancer Database (NCDB). The HPV surrogate score was developed using a logistic regression model predicting HPV-positive status. The HPV surrogate score was predictive of HPV status (area under the curve [AUC] 0.73; accuracy of 70.4%). Similar to HPV-positive tumors, HPV surrogate positive tumors were associated with improved overall survival (OS; hazard ratio [HR] 0.73; 95% confidence interval [CI] 0.59-0.91; P = .005), after adjusting for important covariates. The HPV surrogate score is useful for adjusting for the effect of HPV status on survival in studies utilizing cancer databases. © 2017 Wiley Periodicals, Inc.

  4. Cancer survivorship: a new challenge in comprehensive cancer control.

    Science.gov (United States)

    Pollack, Lori A; Greer, Greta E; Rowland, Julia H; Miller, Andy; Doneski, Donna; Coughlin, Steven S; Stovall, Ellen; Ulman, Doug

    2005-10-01

    Cancer survivors are a growing population in the United States because of earlier cancer diagnosis, the aging of society, and more effective risk reduction and treatment. Concerns about the long-term physical, psychosocial, and economic effects of cancer treatment on cancer survivors and their families are increasingly being recognized and addressed by public, private, and non-profit organizations. The purpose of this paper is to discuss how survivorship fits within the framework of comprehensive cancer control. We summarize three national reports on cancer survivorship and highlight how various organizations and programs are striving to address the needs of cancer survivors through public health planning, including the challenges these groups face and the gaps in knowledge and available services. As cancer survivorship issues are being recognized, many organizations have objectives and programs to address concerns of those diagnosed with cancer. However, better coordination and dissemination may decrease overlap and increase the reach of efforts and there is limited evidence for the effectiveness and impact of these efforts.

  5. MSDB: A Comprehensive Database of Simple Sequence Repeats.

    Science.gov (United States)

    Avvaru, Akshay Kumar; Saxena, Saketh; Sowpati, Divya Tej; Mishra, Rakesh Kumar

    2017-06-01

    Microsatellites, also known as Simple Sequence Repeats (SSRs), are short tandem repeats of 1-6 nt motifs present in all genomes, particularly eukaryotes. Besides their usefulness as genome markers, SSRs have been shown to perform important regulatory functions, and variations in their length at coding regions are linked to several disorders in humans. Microsatellites show a taxon-specific enrichment in eukaryotic genomes, and some may be functional. MSDB (Microsatellite Database) is a collection of >650 million SSRs from 6,893 species including Bacteria, Archaea, Fungi, Plants, and Animals. This database is by far the most exhaustive resource to access and analyze SSR data of multiple species. In addition to exploring data in a customizable tabular format, users can view and compare the data of multiple species simultaneously using our interactive plotting system. MSDB is developed using the Django framework and MySQL. It is freely available at http://tdb.ccmb.res.in/msdb. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  6. Comprehensive Thematic T-matrix Reference Database: a 2013-2014 Update

    Science.gov (United States)

    Mishchenko, Michael I.; Zakharova, Nadezhda T.; Khlebtsov, Nikolai G.; Wriedt, Thomas; Videen, Gorden

    2014-01-01

    This paper is the sixth update to the comprehensive thematic database of peer-reviewedT-matrix publications initiated by us in 2004 and includes relevant publications that have appeared since 2013. It also lists several earlier publications not incorporated in the original database and previous updates.

  7. Biodiversity of Antarctic echinoids: a comprehensive and interactive database

    Directory of Open Access Journals (Sweden)

    Bruno David

    2005-12-01

    Full Text Available Eighty-one echinoid species are present south of the Antarctic Convergence, and they represent an important component of the benthic fauna. “Antarctic echinoids” is an interactive database synthesising the results of more than 100 years of Antarctic expeditions, and comprising information about all echinoid species. It includes illustrated keys for determination of the species, and information about their morphology and ecology (text, illustrations and glossary and their distribution (maps and histograms of bathymetrical distribution; the sources of the information (bibliography, collections and expeditions are also provided. All these data (taxonomic, morphologic, geographic, bathymetric… can be interactively queried in two main ways: (1 display of listings that can be browsed, sorted according to various criteria, or printed; and (2 interactive requests crossing the different kinds of data. Many other possibilities are offered, and an on-line help file is also available.

  8. CHANT (CHinese ANcient Texts): a comprehensive database of all ancient Chinese texts up to 600 AD

    OpenAIRE

    Ho, Che Wah

    2006-01-01

    The CHinese ANcient Texts (CHANT) database is a long-term project which began in 1988 to build up a comprehensive database of all ancient Chinese texts up to the sixth century AD. The project is near completion and the entire database, which includes both traditional and excavated materials, will be released on the CHANT Web site (www.chant.org) in mid-2002. With more than a decade of experience in establishing an electronic Chinese literary database, we have gained much insight useful to the...

  9. DDPC: Dragon database of genes associated with prostate cancer

    KAUST Repository

    Maqungo, Monique; Kaur, Mandeep; Kwofie, Samuel K.; Radovanovic, Aleksandar; Schaefer, Ulf; Schmeier, Sebastian; Oppon, Ekow; Christoffels, Alan; Bajic, Vladimir B.

    2010-01-01

    associated with Prostate Cancer (DDPC) as an integrated knowledgebase of genes experimentally verified as implicated in PC. DDPC is distinctive from other databases in that (i) it provides pre-compiled biomedical text-mining information on PC, which otherwise

  10. Comprehensive T-matrix Reference Database: A 2009-2011 Update

    Science.gov (United States)

    Zakharova, Nadezhda T.; Videen, G.; Khlebtsov, Nikolai G.

    2012-01-01

    The T-matrix method is one of the most versatile and efficient theoretical techniques widely used for the computation of electromagnetic scattering by single and composite particles, discrete random media, and particles in the vicinity of an interface separating two half-spaces with different refractive indices. This paper presents an update to the comprehensive database of peer-reviewed T-matrix publications compiled by us previously and includes the publications that appeared since 2009. It also lists several earlier publications not included in the original database.

  11. Comprehensive T-Matrix Reference Database: A 2007-2009 Update

    Science.gov (United States)

    Mishchenko, Michael I.; Zakharova, Nadia T.; Videen, Gorden; Khlebtsov, Nikolai G.; Wriedt, Thomas

    2010-01-01

    The T-matrix method is among the most versatile, efficient, and widely used theoretical techniques for the numerically exact computation of electromagnetic scattering by homogeneous and composite particles, clusters of particles, discrete random media, and particles in the vicinity of an interface separating two half-spaces with different refractive indices. This paper presents an update to the comprehensive database of T-matrix publications compiled by us previously and includes the publications that appeared since 2007. It also lists several earlier publications not included in the original database.

  12. RaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites.

    Science.gov (United States)

    Zhang, Bofei; Hu, Senyang; Baskin, Elizabeth; Patt, Andrew; Siddiqui, Jalal K; Mathé, Ewy A

    2018-02-22

    The value of metabolomics in translational research is undeniable, and metabolomics data are increasingly generated in large cohorts. The functional interpretation of disease-associated metabolites though is difficult, and the biological mechanisms that underlie cell type or disease-specific metabolomics profiles are oftentimes unknown. To help fully exploit metabolomics data and to aid in its interpretation, analysis of metabolomics data with other complementary omics data, including transcriptomics, is helpful. To facilitate such analyses at a pathway level, we have developed RaMP (Relational database of Metabolomics Pathways), which combines biological pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, WikiPathways, and the Human Metabolome DataBase (HMDB). To the best of our knowledge, an off-the-shelf, public database that maps genes and metabolites to biochemical/disease pathways and can readily be integrated into other existing software is currently lacking. For consistent and comprehensive analysis, RaMP enables batch and complex queries (e.g., list all metabolites involved in glycolysis and lung cancer), can readily be integrated into pathway analysis tools, and supports pathway overrepresentation analysis given a list of genes and/or metabolites of interest. For usability, we have developed a RaMP R package (https://github.com/Mathelab/RaMP-DB), including a user-friendly RShiny web application, that supports basic simple and batch queries, pathway overrepresentation analysis given a list of genes or metabolites of interest, and network visualization of gene-metabolite relationships. The package also includes the raw database file (mysql dump), thereby providing a stand-alone downloadable framework for public use and integration with other tools. In addition, the Python code needed to recreate the database on another system is also publicly available (https://github.com/Mathelab/RaMP-BackEnd). Updates for databases in RaMP will be

  13. ChlamyCyc - a comprehensive database and web-portal centered on _Chlamydomonas reinhardtii_

    OpenAIRE

    Jan-Ole Christian; Patrick May; Stefan Kempa; Dirk Walther

    2009-01-01

    *Background* - The unicellular green alga _Chlamydomonas reinhardtii_ is an important eukaryotic model organism for the study of photosynthesis and growth, as well as flagella development and other cellular processes. In the era of high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the whole cellular system of a sin...

  14. Pepper EST database: comprehensive in silico tool for analyzing the chili pepper (Capsicum annuum transcriptome

    Directory of Open Access Journals (Sweden)

    Kim Woo Taek

    2008-10-01

    Full Text Available Abstract Background There is no dedicated database available for Expressed Sequence Tags (EST of the chili pepper (Capsicum annuum, although the interest in a chili pepper EST database is increasing internationally due to the nutritional, economic, and pharmaceutical value of the plant. Recent advances in high-throughput sequencing of the ESTs of chili pepper cv. Bukang have produced hundreds of thousands of complementary DNA (cDNA sequences. Therefore, a chili pepper EST database was designed and constructed to enable comprehensive analysis of chili pepper gene expression in response to biotic and abiotic stresses. Results We built the Pepper EST database to mine the complexity of chili pepper ESTs. The database was built on 122,582 sequenced ESTs and 116,412 refined ESTs from 21 pepper EST libraries. The ESTs were clustered and assembled into virtual consensus cDNAs and the cDNAs were assigned to metabolic pathway, Gene Ontology (GO, and MIPS Functional Catalogue (FunCat. The Pepper EST database is designed to provide a workbench for (i identifying unigenes in pepper plants, (ii analyzing expression patterns in different developmental tissues and under conditions of stress, and (iii comparing the ESTs with those of other members of the Solanaceae family. The Pepper EST database is freely available at http://genepool.kribb.re.kr/pepper/. Conclusion The Pepper EST database is expected to provide a high-quality resource, which will contribute to gaining a systemic understanding of plant diseases and facilitate genetics-based population studies. The database is also expected to contribute to analysis of gene synteny as part of the chili pepper sequencing project by mapping ESTs to the genome.

  15. The database of the Danish Renal Cancer Group

    DEFF Research Database (Denmark)

    Petersen, Astrid Christine; Søgaard, Mette; Mehnert, Frank

    2016-01-01

    AIM OF THE DATABASE: The main purpose of the database of the Danish Renal Cancer Group (DaRenCaData) is to improve the quality of renal cancer treatment in Denmark and secondarily to conduct observational research. STUDY POPULATION: DaRenCaData includes all Danish patients with a first......-time diagnosis of renal cancer in the Danish National Pathology Registry since August 1, 2010. MAIN VARIABLES: DaRenCaData holds data on demographic characteristics, treatments, and pathology collected through linkage to central registries and online registration of a few clinical key variables. Eight quality...... indicators have been selected for monitoring treatment quality and outcome after renal cancer. DESCRIPTIVE DATA: The incidence of renal cancer in Denmark has increased from 12.7 per 100,000 population-years in 2010-2011 to 15.9 per 100,000 population-years in 2014-2015. A total of 3,977 Danish patients...

  16. The Candidate Cancer Gene Database: a database of cancer driver genes from forward genetic screens in mice.

    Science.gov (United States)

    Abbott, Kenneth L; Nyre, Erik T; Abrahante, Juan; Ho, Yen-Yi; Isaksson Vogel, Rachel; Starr, Timothy K

    2015-01-01

    Identification of cancer driver gene mutations is crucial for advancing cancer therapeutics. Due to the overwhelming number of passenger mutations in the human tumor genome, it is difficult to pinpoint causative driver genes. Using transposon mutagenesis in mice many laboratories have conducted forward genetic screens and identified thousands of candidate driver genes that are highly relevant to human cancer. Unfortunately, this information is difficult to access and utilize because it is scattered across multiple publications using different mouse genome builds and strength metrics. To improve access to these findings and facilitate meta-analyses, we developed the Candidate Cancer Gene Database (CCGD, http://ccgd-starrlab.oit.umn.edu/). The CCGD is a manually curated database containing a unified description of all identified candidate driver genes and the genomic location of transposon common insertion sites (CISs) from all currently published transposon-based screens. To demonstrate relevance to human cancer, we performed a modified gene set enrichment analysis using KEGG pathways and show that human cancer pathways are highly enriched in the database. We also used hierarchical clustering to identify pathways enriched in blood cancers compared to solid cancers. The CCGD is a novel resource available to scientists interested in the identification of genetic drivers of cancer. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  17. Heterogeneous Biomedical Database Integration Using a Hybrid Strategy: A p53 Cancer Research Database

    Directory of Open Access Journals (Sweden)

    Vadim Y. Bichutskiy

    2006-01-01

    Full Text Available Complex problems in life science research give rise to multidisciplinary collaboration, and hence, to the need for heterogeneous database integration. The tumor suppressor p53 is mutated in close to 50% of human cancers, and a small drug-like molecule with the ability to restore native function to cancerous p53 mutants is a long-held medical goal of cancer treatment. The Cancer Research DataBase (CRDB was designed in support of a project to find such small molecules. As a cancer informatics project, the CRDB involved small molecule data, computational docking results, functional assays, and protein structure data. As an example of the hybrid strategy for data integration, it combined the mediation and data warehousing approaches. This paper uses the CRDB to illustrate the hybrid strategy as a viable approach to heterogeneous data integration in biomedicine, and provides a design method for those considering similar systems. More efficient data sharing implies increased productivity, and, hopefully, improved chances of success in cancer research. (Code and database schemas are freely downloadable, http://www.igb.uci.edu/research/research.html.

  18. CCDB: a curated database of genes involved in cervix cancer.

    Science.gov (United States)

    Agarwal, Subhash M; Raghav, Dhwani; Singh, Harinder; Raghava, G P S

    2011-01-01

    The Cervical Cancer gene DataBase (CCDB, http://crdd.osdd.net/raghava/ccdb) is a manually curated catalog of experimentally validated genes that are thought, or are known to be involved in the different stages of cervical carcinogenesis. In spite of the large women population that is presently affected from this malignancy still at present, no database exists that catalogs information on genes associated with cervical cancer. Therefore, we have compiled 537 genes in CCDB that are linked with cervical cancer causation processes such as methylation, gene amplification, mutation, polymorphism and change in expression level, as evident from published literature. Each record contains details related to gene like architecture (exon-intron structure), location, function, sequences (mRNA/CDS/protein), ontology, interacting partners, homology to other eukaryotic genomes, structure and links to other public databases, thus augmenting CCDB with external data. Also, manually curated literature references have been provided to support the inclusion of the gene in the database and establish its association with cervix cancer. In addition, CCDB provides information on microRNA altered in cervical cancer as well as search facility for querying, several browse options and an online tool for sequence similarity search, thereby providing researchers with easy access to the latest information on genes involved in cervix cancer.

  19. LCGbase: A Comprehensive Database for Lineage-Based Co-regulated Genes.

    Science.gov (United States)

    Wang, Dapeng; Zhang, Yubin; Fan, Zhonghua; Liu, Guiming; Yu, Jun

    2012-01-01

    Animal genes of different lineages, such as vertebrates and arthropods, are well-organized and blended into dynamic chromosomal structures that represent a primary regulatory mechanism for body development and cellular differentiation. The majority of genes in a genome are actually clustered, which are evolutionarily stable to different extents and biologically meaningful when evaluated among genomes within and across lineages. Until now, many questions concerning gene organization, such as what is the minimal number of genes in a cluster and what is the driving force leading to gene co-regulation, remain to be addressed. Here, we provide a user-friendly database-LCGbase (a comprehensive database for lineage-based co-regulated genes)-hosting information on evolutionary dynamics of gene clustering and ordering within animal kingdoms in two different lineages: vertebrates and arthropods. The database is constructed on a web-based Linux-Apache-MySQL-PHP framework and effective interactive user-inquiry service. Compared to other gene annotation databases with similar purposes, our database has three comprehensible advantages. First, our database is inclusive, including all high-quality genome assemblies of vertebrates and representative arthropod species. Second, it is human-centric since we map all gene clusters from other genomes in an order of lineage-ranks (such as primates, mammals, warm-blooded, and reptiles) onto human genome and start the database from well-defined gene pairs (a minimal cluster where the two adjacent genes are oriented as co-directional, convergent, and divergent pairs) to large gene clusters. Furthermore, users can search for any adjacent genes and their detailed annotations. Third, the database provides flexible parameter definitions, such as the distance of transcription start sites between two adjacent genes, which is extendable to genes that flanking the cluster across species. We also provide useful tools for sequence alignment, gene

  20. Completeness and validity in a national clinical thyroid cancer database

    DEFF Research Database (Denmark)

    Londero, Stefano Christian; Mathiesen, Jes Sloth; Krogdahl, Annelise

    2014-01-01

    cancer database: DATHYRCA. STUDY DESIGN AND SETTING: National prospective cohort. Denmark; population 5.5 million. Completeness of case ascertainment was estimated by the independent case ascertainment method using three governmental registries as a reference. The reabstracted record method was used...... to appraise the validity. For validity assessment 100 cases were randomly selected from the DATHYRCA database; medical records were used as a reference. RESULT: The database held 1934 cases of thyroid carcinoma and completeness of case ascertainment was estimated to 90.9%. Completeness of registration......BACKGROUND: Although a prospective national clinical thyroid cancer database (DATHYRCA) has been active in Denmark since January 1, 1996, no assessment of data quality has been performed. The purpose of the study was to evaluate completeness and data validity in the Danish national clinical thyroid...

  1. PlantNATsDB: a comprehensive database of plant natural antisense transcripts.

    Science.gov (United States)

    Chen, Dijun; Yuan, Chunhui; Zhang, Jian; Zhang, Zhao; Bai, Lin; Meng, Yijun; Chen, Ling-Ling; Chen, Ming

    2012-01-01

    Natural antisense transcripts (NATs), as one type of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and pathological processes. Although their important biological functions have been reported widely, a comprehensive database is lacking up to now. Consequently, we constructed a plant NAT database (PlantNATsDB) involving approximately 2 million NAT pairs in 69 plant species. GO annotation and high-throughput small RNA sequencing data currently available were integrated to investigate the biological function of NATs. PlantNATsDB provides various user-friendly web interfaces to facilitate the presentation of NATs and an integrated, graphical network browser to display the complex networks formed by different NATs. Moreover, a 'Gene Set Analysis' module based on GO annotation was designed to dig out the statistical significantly overrepresented GO categories from the specific NAT network. PlantNATsDB is currently the most comprehensive resource of NATs in the plant kingdom, which can serve as a reference database to investigate the regulatory function of NATs. The PlantNATsDB is freely available at http://bis.zju.edu.cn/pnatdb/.

  2. Computerized database management system for breast cancer patients.

    Science.gov (United States)

    Sim, Kok Swee; Chong, Sze Siang; Tso, Chih Ping; Nia, Mohsen Esmaeili; Chong, Aun Kee; Abbas, Siti Fathimah

    2014-01-01

    Data analysis based on breast cancer risk factors such as age, race, breastfeeding, hormone replacement therapy, family history, and obesity was conducted on breast cancer patients using a new enhanced computerized database management system. My Structural Query Language (MySQL) is selected as the application for database management system to store the patient data collected from hospitals in Malaysia. An automatic calculation tool is embedded in this system to assist the data analysis. The results are plotted automatically and a user-friendly graphical user interface is developed that can control the MySQL database. Case studies show breast cancer incidence rate is highest among Malay women, followed by Chinese and Indian. The peak age for breast cancer incidence is from 50 to 59 years old. Results suggest that the chance of developing breast cancer is increased in older women, and reduced with breastfeeding practice. The weight status might affect the breast cancer risk differently. Additional studies are needed to confirm these findings.

  3. Comprehensive Thematic T-Matrix Reference Database: A 2014-2015 Update

    Science.gov (United States)

    Mishchenko, Michael I.; Zakharova, Nadezhda; Khlebtsov, Nikolai G.; Videen, Gorden; Wriedt, Thomas

    2015-01-01

    The T-matrix method is one of the most versatile and efficient direct computer solvers of the macroscopic Maxwell equations and is widely used for the computation of electromagnetic scattering by single and composite particles, discrete random media, and particles in the vicinity of an interface separating two half-spaces with different refractive indices. This paper is the seventh update to the comprehensive thematic database of peer-reviewed T-matrix publications initiated by us in 2004 and includes relevant publications that have appeared since 2013. It also lists a number of earlier publications overlooked previously.

  4. Databases and web tools for cancer genomics study.

    Science.gov (United States)

    Yang, Yadong; Dong, Xunong; Xie, Bingbing; Ding, Nan; Chen, Juan; Li, Yongjun; Zhang, Qian; Qu, Hongzhu; Fang, Xiangdong

    2015-02-01

    Publicly-accessible resources have promoted the advance of scientific discovery. The era of genomics and big data has brought the need for collaboration and data sharing in order to make effective use of this new knowledge. Here, we describe the web resources for cancer genomics research and rate them on the basis of the diversity of cancer types, sample size, omics data comprehensiveness, and user experience. The resources reviewed include data repository and analysis tools; and we hope such introduction will promote the awareness and facilitate the usage of these resources in the cancer research community. Copyright © 2015 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

  5. TranslatomeDB: a comprehensive database and cloud-based analysis platform for translatome sequencing data.

    Science.gov (United States)

    Liu, Wanting; Xiang, Lunping; Zheng, Tingkai; Jin, Jingjie; Zhang, Gong

    2018-01-04

    Translation is a key regulatory step, linking transcriptome and proteome. Two major methods of translatome investigations are RNC-seq (sequencing of translating mRNA) and Ribo-seq (ribosome profiling). To facilitate the investigation of translation, we built a comprehensive database TranslatomeDB (http://www.translatomedb.net/) which provides collection and integrated analysis of published and user-generated translatome sequencing data. The current version includes 2453 Ribo-seq, 10 RNC-seq and their 1394 corresponding mRNA-seq datasets in 13 species. The database emphasizes the analysis functions in addition to the dataset collections. Differential gene expression (DGE) analysis can be performed between any two datasets of same species and type, both on transcriptome and translatome levels. The translation indices translation ratios, elongation velocity index and translational efficiency can be calculated to quantitatively evaluate translational initiation efficiency and elongation velocity, respectively. All datasets were analyzed using a unified, robust, accurate and experimentally-verifiable pipeline based on the FANSe3 mapping algorithm and edgeR for DGE analyzes. TranslatomeDB also allows users to upload their own datasets and utilize the identical unified pipeline to analyze their data. We believe that our TranslatomeDB is a comprehensive platform and knowledgebase on translatome and proteome research, releasing the biologists from complex searching, analyzing and comparing huge sequencing data without needing local computational power. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. CGPD: Cancer Genetics and Proteomics Database - A Dataset for Computational Analysis and Online Cancer Diagnostic Centre

    Directory of Open Access Journals (Sweden)

    Muhammad Rizwan Riaz

    2014-06-01

    Full Text Available Cancer Genetics and Proteomics Database (CGPD is a repository for genetics and proteomics data of those Homo sapiens genes which are involved in Cancer. These genes are categorized in the database on the basis of cancer type. 72 genes of 13 types of cancers are considered in this database yet. Primers, promoters and peptides of these genes are also made available. Primers provided for each gene, with their features and conditions given to facilitate the researchers, are useful in PCR amplification, especially in cloning experiments. CGPD also contains Online Cancer Diagnostic Center (OCDC. It also contains transcription and translation tools to assist research work in progressive manner. The database is publicly available at http://www.cgpd.comyr.com.

  7. A European Flood Database: facilitating comprehensive flood research beyond administrative boundaries

    Directory of Open Access Journals (Sweden)

    J. Hall

    2015-06-01

    Full Text Available The current work addresses one of the key building blocks towards an improved understanding of flood processes and associated changes in flood characteristics and regimes in Europe: the development of a comprehensive, extensive European flood database. The presented work results from ongoing cross-border research collaborations initiated with data collection and joint interpretation in mind. A detailed account of the current state, characteristics and spatial and temporal coverage of the European Flood Database, is presented. At this stage, the hydrological data collection is still growing and consists at this time of annual maximum and daily mean discharge series, from over 7000 hydrometric stations of various data series lengths. Moreover, the database currently comprises data from over 50 different data sources. The time series have been obtained from different national and regional data sources in a collaborative effort of a joint European flood research agreement based on the exchange of data, models and expertise, and from existing international data collections and open source websites. These ongoing efforts are contributing to advancing the understanding of regional flood processes beyond individual country boundaries and to a more coherent flood research in Europe.

  8. Spatial analyses identify the geographic source of patients at a National Cancer Institute Comprehensive Cancer Center.

    Science.gov (United States)

    Su, Shu-Chih; Kanarek, Norma; Fox, Michael G; Guseynova, Alla; Crow, Shirley; Piantadosi, Steven

    2010-02-01

    We examined the geographic distribution of patients to better understand the service area of the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, a designated National Cancer Institute (NCI) comprehensive cancer center located in an urban center. Like most NCI cancer centers, the Sidney Kimmel Comprehensive Cancer Center serves a population beyond city limits. Urban cancer centers are expected to serve their immediate neighborhoods and to address disparities in access to specialty care. Our purpose was to learn the extent and nature of the cancer center service area. Statistical clustering of patient residence in the continental United States was assessed for all patients and by gender, cancer site, and race using SaTScan. Primary clusters detected for all cases and demographically and tumor-defined subpopulations were centered at Baltimore City and consisted of adjacent counties in Delaware, Pennsylvania, Virginia, West Virginia, New Jersey and New York, and the District of Columbia. Primary clusters varied in size by race, gender, and cancer site. Spatial analysis can provide insights into the populations served by urban cancer centers, assess centers' performance relative to their communities, and aid in developing a cancer center business plan that recognizes strengths, regional utility, and referral patterns. Today, 62 NCI cancer centers serve a quarter of the U.S. population in their immediate communities. From the Baltimore experience, we might project that the population served by these centers is actually more extensive and varies by patient characteristics, cancer site, and probably cancer center services offered.

  9. Estimation of National Colorectal-Cancer Incidence Using Claims Databases

    International Nuclear Information System (INIS)

    Quantin, C.; Benzenine, E.; Hagi, M.; Auverlot, B.; Cottenet, J.; Binquet, M.; Compain, D.

    2012-01-01

    The aim of the study was to assess the accuracy of the colorectal-cancer incidence estimated from administrative data. Methods. We selected potential incident colorectal-cancer cases in 2004-2005 French administrative data, using two alternative algorithms. The first was based only on diagnostic and procedure codes, whereas the second considered the past history of the patient. Results of both methods were assessed against two corresponding local cancer registries, acting as “gold standards.” We then constructed a multivariable regression model to estimate the corrected total number of incident colorectal-cancer cases from the whole national administrative database. Results. The first algorithm provided an estimated local incidence very close to that given by the regional registries (646 versus 645 incident cases) and had good sensitivity and positive predictive values (about 75% for both). The second algorithm overestimated the incidence by about 50% and had a poor positive predictive value of about 60%. The estimation of national incidence obtained by the first algorithm differed from that observed in 14 registries by only 2.34%. Conclusion. This study shows the usefulness of administrative databases for countries with no national cancer registry and suggests a method for correcting the estimates provided by these data.

  10. A comprehensive database of Duchenne and Becker muscular dystrophy patients in Children's Hospital of Fudan University

    Directory of Open Access Journals (Sweden)

    Xi-hua LI

    2015-05-01

    Full Text Available Background China is one of the countries that have the largest number of patients suffering from Duchenne and Becker muscular dystrophy (DMD/BMD. Although the building of international DMD/BMD databases has laid a foundation for clinical drug development and clinical trials, it has not yet been carried out in China. In this study, a modified registry form of Remudy was applied to 229 DMD/BMD patients in order to establish a comprehensive database, which will lay the groundwork for international cooperation.  Methods A total of 229 DMD/BMD patients diagnosed by genetic testing or muscle biopsy admitted in Children's Hospital of Fudan University (CHFU during the period of August 2011 to December 2013 were enrolled in this study. The data included sex, age, age at diagnosis, geographic distribution of patients, DMD gene mutation types, family history, walking capability, cardiac and respiratory function, steroid treatment and rehabilitation intervention.  Results There were 194 DMD and 35 BMD male patients who were diagnosed at the age of 0-18 years, and among them, most patients were diagnosed at the age of > 3-4 (16.59%, 38/229 and > 7-8 (14.85%, 34/229 years. Exon deletion was the most frequent genetic mutations for DMD/BMD [65.46% (127/194 and 74.29% (26/35], respectively. Patients with a family history accounted for 23.14% (53/229. The rate of DMD registrants losing walking capability was 17.53% (34/194, and all the BMD registrants were able to walk. Cardiac functions were examined in 46.29% (106/229 DMD/BMD boys and respiratory functions were examined in 17.90% (41/229 DMD/BMD boys. The proportion of DMD patients receiving prednisone with dosage of 0.75 mg/(kg·d was 26.29% (51/194.  Conclusions This database describes in detail the genotype, clinical manifestation, diagnosis and treatment and rehabilitation status of 229 DMD/BMD patients in China. The database not only provides comprehensive information for DMD/BMD patient management

  11. SoyTEdb: a comprehensive database of transposable elements in the soybean genome

    Directory of Open Access Journals (Sweden)

    Zhu Liucun

    2010-02-01

    Full Text Available Abstract Background Transposable elements are the most abundant components of all characterized genomes of higher eukaryotes. It has been documented that these elements not only contribute to the shaping and reshaping of their host genomes, but also play significant roles in regulating gene expression, altering gene function, and creating new genes. Thus, complete identification of transposable elements in sequenced genomes and construction of comprehensive transposable element databases are essential for accurate annotation of genes and other genomic components, for investigation of potential functional interaction between transposable elements and genes, and for study of genome evolution. The recent availability of the soybean genome sequence has provided an unprecedented opportunity for discovery, and structural and functional characterization of transposable elements in this economically important legume crop. Description Using a combination of structure-based and homology-based approaches, a total of 32,552 retrotransposons (Class I and 6,029 DNA transposons (Class II with clear boundaries and insertion sites were structurally annotated and clearly categorized, and a soybean transposable element database, SoyTEdb, was established. These transposable elements have been anchored in and integrated with the soybean physical map and genetic map, and are browsable and visualizable at any scale along the 20 soybean chromosomes, along with predicted genes and other sequence annotations. BLAST search and other infrastracture tools were implemented to facilitate annotation of transposable elements or fragments from soybean and other related legume species. The majority (> 95% of these elements (particularly a few hundred low-copy-number families are first described in this study. Conclusion SoyTEdb provides resources and information related to transposable elements in the soybean genome, representing the most comprehensive and the largest manually

  12. Development of prostate cancer research database with the clinical data warehouse technology for direct linkage with electronic medical record system.

    Science.gov (United States)

    Choi, In Young; Park, Seungho; Park, Bumjoon; Chung, Byung Ha; Kim, Choung-Soo; Lee, Hyun Moo; Byun, Seok-Soo; Lee, Ji Youl

    2013-01-01

    In spite of increased prostate cancer patients, little is known about the impact of treatments for prostate cancer patients and outcome of different treatments based on nationwide data. In order to obtain more comprehensive information for Korean prostate cancer patients, many professionals urged to have national system to monitor the quality of prostate cancer care. To gain its objective, the prostate cancer database system was planned and cautiously accommodated different views from various professions. This prostate cancer research database system incorporates information about a prostate cancer research including demographics, medical history, operation information, laboratory, and quality of life surveys. And, this system includes three different ways of clinical data collection to produce a comprehensive data base; direct data extraction from electronic medical record (EMR) system, manual data entry after linking EMR documents like magnetic resonance imaging findings and paper-based data collection for survey from patients. We implemented clinical data warehouse technology to test direct EMR link method with St. Mary's Hospital system. Using this method, total number of eligible patients were 2,300 from 1997 until 2012. Among them, 538 patients conducted surgery and others have different treatments. Our database system could provide the infrastructure for collecting error free data to support various retrospective and prospective studies.

  13. Validity of data in the Danish colorectal cancer screening database

    DEFF Research Database (Denmark)

    Thomsen, Mette Kielsholm; Njor, Sisse Helle; Rasmussen, Morten

    2017-01-01

    Background: In Denmark, a nationwide screening program for colorectal cancer was implemented in March 2014. Along with this, a clinical database for program monitoring and research purposes was established. Objective: The aim of this study was to estimate the agreement and validity of diagnosis...... and procedure codes in the Danish Colorectal Cancer Screening Database (DCCSD). Methods: All individuals with a positive immunochemical fecal occult blood test (iFOBT) result who were invited to screening in the first 3 months since program initiation were identified. From these, a sample of 150 individuals...... was selected using stratified random sampling by age, gender and region of residence. Data from the DCCSD were compared with data from hospital records, which were used as the reference. Agreement, sensitivity, specificity and positive and negative predictive values were estimated for categories of codes...

  14. Saudi anti-human cancer plants database (SACPD): A collection of plants with anti-human cancer activities.

    Science.gov (United States)

    Al-Zahrani, Ateeq Ahmed

    2018-01-30

    Several anticancer drugs have been developed from natural products such as plants. Successful experiments in inhibiting the growth of human cancer cell lines using Saudi plants were published over the last three decades. Up to date, there is no Saudi anticancer plants database as a comprehensive source for the interesting data generated from these experiments. Therefore, there was a need for creating a database to collect, organize, search and retrieve such data. As a result, the current paper describes the generation of the Saudi anti-human cancer plants database (SACPD). The database contains most of the reported information about the naturally growing Saudi anticancer plants. SACPD comprises the scientific and local names of 91 plant species that grow naturally in Saudi Arabia. These species belong to 38 different taxonomic families. In Addition, 18 species that represent16 family of medicinal plants and are intensively sold in the local markets in Saudi Arabia were added to the database. The website provides interesting details, including plant part containing the anticancer bioactive compounds, plants locations and cancer/cell type against which they exhibit their anticancer activity. Our survey revealed that breast, liver and leukemia were the most studied cancer cell lines in Saudi Arabia with percentages of 27%, 19% and 15%, respectively. The current SACPD represents a nucleus around which more development efforts can expand to accommodate all future submissions about new Saudi plant species with anticancer activities. SACPD will provide an excellent starting point for researchers and pharmaceutical companies who are interested in developing new anticancer drugs. SACPD is available online at https://teeqrani1.wixsite.com/sapd.

  15. Alphabetical co-authorship in the social sciences and humanities: evidence from a comprehensive local database

    Energy Technology Data Exchange (ETDEWEB)

    Guns, R

    2016-07-01

    We present an analysis of alphabetical co-authorship in the social sciences and humanities (SSH), based on data from the VABB-SHW, a comprehensive database of SSH research output in Flanders (2000-2013). Using an unbiased estimator of the share of intentional alphabetical co-authorship (IAC), we find that alphabetical co-authorship is more engrained in SSH than in science as a whole. Within the SSH, large differences exist between disciplines. The highest proportions of IAC are found for Literature, Economics & business, and History. Furthermore, alphabetical co-authorship varies with publication type: it occurs most often in books, is less common in articles in journals or in books, and is rare in proceedings papers. The use of alphabetical co-authorship appears to be slowly declining. (Author)

  16. WATCHDOG: A COMPREHENSIVE ALL-SKY DATABASE OF GALACTIC BLACK HOLE X-RAY BINARIES

    International Nuclear Information System (INIS)

    Tetarenko, B. E.; Sivakoff, G. R.; Heinke, C. O.; Gladstone, J. C.

    2016-01-01

    With the advent of more sensitive all-sky instruments, the transient universe is being probed in greater depth than ever before. Taking advantage of available resources, we have established a comprehensive database of black hole (and black hole candidate) X-ray binary (BHXB) activity between 1996 and 2015 as revealed by all-sky instruments, scanning surveys, and select narrow-field X-ray instruments on board the INTErnational Gamma-Ray Astrophysics Laboratory, Monitor of All-Sky X-ray Image, Rossi X-ray Timing Explorer, and Swift telescopes; the Whole-sky Alberta Time-resolved Comprehensive black-Hole Database Of the Galaxy or WATCHDOG. Over the past two decades, we have detected 132 transient outbursts, tracked and classified behavior occurring in 47 transient and 10 persistently accreting BHs, and performed a statistical study on a number of outburst properties across the Galactic population. We find that outbursts undergone by BHXBs that do not reach the thermally dominant accretion state make up a substantial fraction (∼40%) of the Galactic transient BHXB outburst sample over the past ∼20 years. Our findings suggest that this “hard-only” behavior, observed in transient and persistently accreting BHXBs, is neither a rare nor recent phenomenon and may be indicative of an underlying physical process, relatively common among binary BHs, involving the mass-transfer rate onto the BH remaining at a low level rather than increasing as the outburst evolves. We discuss how the larger number of these “hard-only” outbursts and detected outbursts in general have significant implications for both the luminosity function and mass-transfer history of the Galactic BHXB population

  17. Development of a comprehensive database of scattering environmental conditions and simulation constraints for offshore wind turbines

    Directory of Open Access Journals (Sweden)

    C. Hübler

    2017-10-01

    Full Text Available For the design and optimisation of offshore wind turbines, the knowledge of realistic environmental conditions and utilisation of well-founded simulation constraints is very important, as both influence the structural behaviour and power output in numerical simulations. However, real high-quality data, especially for research purposes, are scarcely available. This is why, in this work, a comprehensive database of 13 environmental conditions at wind turbine locations in the North and Baltic Sea is derived using data of the FINO research platforms. For simulation constraints, like the simulation length and the time of initial simulation transients, well-founded recommendations in the literature are also rare. Nevertheless, it is known that the choice of simulation lengths and times of initial transients fundamentally affects the quality and computing time of simulations. For this reason, studies of convergence for both parameters are conducted to determine adequate values depending on the type of substructure, the wind speed, and the considered loading (fatigue or ultimate. As the main purpose of both the database and the simulation constraints is to compromise realistic data for probabilistic design approaches and to serve as a guidance for further studies in order to enable more realistic and accurate simulations, all results are freely available and easy to apply.

  18. [Role and management of cancer clinical database in the application of gastric cancer precision medicine].

    Science.gov (United States)

    Li, Yuanfang; Zhou, Zhiwei

    2016-02-01

    Precision medicine is a new medical concept and medical model, which is based on personalized medicine, rapid progress of genome sequencing technology and cross application of biological information and big data science. Precision medicine improves the diagnosis and treatment of gastric cancer to provide more convenience through more profound analyses of characteristics, pathogenesis and other core issues in gastric cancer. Cancer clinical database is important to promote the development of precision medicine. Therefore, it is necessary to pay close attention to the construction and management of the database. The clinical database of Sun Yat-sen University Cancer Center is composed of medical record database, blood specimen bank, tissue bank and medical imaging database. In order to ensure the good quality of the database, the design and management of the database should follow the strict standard operation procedure(SOP) model. Data sharing is an important way to improve medical research in the era of medical big data. The construction and management of clinical database must also be strengthened and innovated.

  19. Comprehensive geriatric assessment for older women with early breast cancer – a systematic review of literature

    Directory of Open Access Journals (Sweden)

    Parks Ruth M

    2012-05-01

    Full Text Available Abstract Background The Comprehensive Geriatric Assessment (CGA is an analytical tool increasingly implemented in clinical practice. Breast cancer is primarily a disease of older people; however, most evidence-based research is aimed at younger patients. Methods A systematic review of literature was carried out to assess the use of CGA in older breast cancer patients for clinical decision making. The PubMed, Embase and Cochrane databases were searched. Results A total of nine useful full text article results were found. Only five of these were exclusively concerned with early breast cancer; thus, studies involving a variety of cancer types, stages and treatments were accepted, as long as they included early breast cancer.The results comprised a series of low sources of evidence. However, all results shared a common theme: the CGA has a use in determining patient suitability for different types of cancer treatment and subsequently maximizing the patient’s quality of life. Conclusions There is not yet sufficient high level evidence to instate CGA guidelines as a mandatory practice in the management of breast cancer, due to the heterogeneity of available studies. More studies need to be conducted to cement current work on the benefits of the CGA. An area of particular interest is with regard to treatment options, especially surgery and chemotherapy, and identifying patients who may be suitable for these treatments.

  20. DDPC: Dragon database of genes associated with prostate cancer

    KAUST Repository

    Maqungo, Monique

    2010-09-29

    Prostate cancer (PC) is one of the most commonly diagnosed cancers in men. PC is relatively difficult to diagnose due to a lack of clear early symptoms. Extensive research of PC has led to the availability of a large amount of data on PC. Several hundred genes are implicated in different stages of PC, which may help in developing diagnostic methods or even cures. In spite of this accumulated information, effective diagnostics and treatments remain evasive. We have developed Dragon Database of Genes associated with Prostate Cancer (DDPC) as an integrated knowledgebase of genes experimentally verified as implicated in PC. DDPC is distinctive from other databases in that (i) it provides pre-compiled biomedical text-mining information on PC, which otherwise require tedious computational analyses, (ii) it integrates data on molecular interactions, pathways, gene ontologies, gene regulation at molecular level, predicted transcription factor binding sites on promoters of PC implicated genes and transcription factors that correspond to these binding sites and (iii) it contains DrugBank data on drugs associated with PC. We believe this resource will serve as a source of useful information for research on PC. DDPC is freely accessible for academic and non-profit users via http://apps.sanbi.ac.za/ddpc/ and http://cbrc .kaust.edu.sa/ddpc/. The Author(s) 2010.

  1. Comprehensive database of Manufactured Gas Plant tars. Part C. Heterocyclic and hydroxylated polycyclic aromatic hydrocarbons.

    Science.gov (United States)

    Gallacher, Christopher; Thomas, Russell; Lord, Richard; Kalin, Robert M; Taylor, Chris

    2017-08-15

    Coal tars are a mixture of organic and inorganic compounds that were by-products from the manufactured gas and coke making industries. The tar compositions varied depending on many factors such as the temperature of production and the type of retort used. For this reason a comprehensive database of the compounds found in different tar types is of value to understand both how their compositions differ and what potential chemical hazards are present. This study focuses on the heterocyclic and hydroxylated compounds present in a database produced from 16 different tars from five different production processes. Samples of coal tar were extracted using accelerated solvent extraction (ASE) and derivatized post-extraction using N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA) with 1% trimethylchlorosilane (TMCS). The derivatized samples were analysed using two-dimensional gas chromatography combined with time-of-flight mass spectrometry (GCxGC/TOFMS). A total of 865 heterocyclic compounds and 359 hydroxylated polycyclic aromatic hydrocarbons (PAHs) were detected in 16 tar samples produced by five different processes. The contents of both heterocyclic and hydroxylated PAHs varied greatly with the production process used, with the heterocyclic compounds giving information about the feedstock used. Of the 359 hydroxylated PAHs detected the majority would not have been be detected without the use of derivatization. Coal tars produced using different production processes and feedstocks yielded tars with significantly different heterocyclic and hydroxylated contents. The concentrations of the individual heterocyclic compounds varied greatly even within the different production processes and provided information about the feedstock used to produce the tars. The hydroxylated PAH content of the samples provided important analytical information that would otherwise not have been obtained without the use of derivatization and GCxGC/TOFMS. Copyright © 2017 John Wiley & Sons, Ltd.

  2. Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks.

    Science.gov (United States)

    Balaur, Irina; Mazein, Alexander; Saqi, Mansoor; Lysenko, Artem; Rawlings, Christopher J; Auffray, Charles

    2017-04-01

    The goal of this work is to offer a computational framework for exploring data from the Recon2 human metabolic reconstruction model. Advanced user access features have been developed using the Neo4j graph database technology and this paper describes key features such as efficient management of the network data, examples of the network querying for addressing particular tasks, and how query results are converted back to the Systems Biology Markup Language (SBML) standard format. The Neo4j-based metabolic framework facilitates exploration of highly connected and comprehensive human metabolic data and identification of metabolic subnetworks of interest. A Java-based parser component has been developed to convert query results (available in the JSON format) into SBML and SIF formats in order to facilitate further results exploration, enhancement or network sharing. The Neo4j-based metabolic framework is freely available from: https://diseaseknowledgebase.etriks.org/metabolic/browser/ . The java code files developed for this work are available from the following url: https://github.com/ibalaur/MetabolicFramework . ibalaur@eisbm.org. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  3. GPCR-SSFE: A comprehensive database of G-protein-coupled receptor template predictions and homology models

    Directory of Open Access Journals (Sweden)

    Kreuchwig Annika

    2011-05-01

    Full Text Available Abstract Background G protein-coupled receptors (GPCRs transduce a wide variety of extracellular signals to within the cell and therefore have a key role in regulating cell activity and physiological function. GPCR malfunction is responsible for a wide range of diseases including cancer, diabetes and hyperthyroidism and a large proportion of drugs on the market target these receptors. The three dimensional structure of GPCRs is important for elucidating the molecular mechanisms underlying these diseases and for performing structure-based drug design. Although structural data are restricted to only a handful of GPCRs, homology models can be used as a proxy for those receptors not having crystal structures. However, many researchers working on GPCRs are not experienced homology modellers and are therefore unable to benefit from the information that can be gleaned from such three-dimensional models. Here, we present a comprehensive database called the GPCR-SSFE, which provides initial homology models of the transmembrane helices for a large variety of family A GPCRs. Description Extending on our previous theoretical work, we have developed an automated pipeline for GPCR homology modelling and applied it to a large set of family A GPCR sequences. Our pipeline is a fragment-based approach that exploits available family A crystal structures. The GPCR-SSFE database stores the template predictions, sequence alignments, identified sequence and structure motifs and homology models for 5025 family A GPCRs. Users are able to browse the GPCR dataset according to their pharmacological classification or search for results using a UniProt entry name. It is also possible for a user to submit a GPCR sequence that is not contained in the database for analysis and homology model building. The models can be viewed using a Jmol applet and are also available for download along with the alignments. Conclusions The data provided by GPCR-SSFE are useful for investigating

  4. GPCR-SSFE: a comprehensive database of G-protein-coupled receptor template predictions and homology models.

    Science.gov (United States)

    Worth, Catherine L; Kreuchwig, Annika; Kleinau, Gunnar; Krause, Gerd

    2011-05-23

    G protein-coupled receptors (GPCRs) transduce a wide variety of extracellular signals to within the cell and therefore have a key role in regulating cell activity and physiological function. GPCR malfunction is responsible for a wide range of diseases including cancer, diabetes and hyperthyroidism and a large proportion of drugs on the market target these receptors. The three dimensional structure of GPCRs is important for elucidating the molecular mechanisms underlying these diseases and for performing structure-based drug design. Although structural data are restricted to only a handful of GPCRs, homology models can be used as a proxy for those receptors not having crystal structures. However, many researchers working on GPCRs are not experienced homology modellers and are therefore unable to benefit from the information that can be gleaned from such three-dimensional models. Here, we present a comprehensive database called the GPCR-SSFE, which provides initial homology models of the transmembrane helices for a large variety of family A GPCRs. Extending on our previous theoretical work, we have developed an automated pipeline for GPCR homology modelling and applied it to a large set of family A GPCR sequences. Our pipeline is a fragment-based approach that exploits available family A crystal structures. The GPCR-SSFE database stores the template predictions, sequence alignments, identified sequence and structure motifs and homology models for 5025 family A GPCRs. Users are able to browse the GPCR dataset according to their pharmacological classification or search for results using a UniProt entry name. It is also possible for a user to submit a GPCR sequence that is not contained in the database for analysis and homology model building. The models can be viewed using a Jmol applet and are also available for download along with the alignments. The data provided by GPCR-SSFE are useful for investigating general and detailed sequence-structure-function relationships

  5. Databases

    Digital Repository Service at National Institute of Oceanography (India)

    Kunte, P.D.

    Information on bibliographic as well as numeric/textual databases relevant to coastal geomorphology has been included in a tabular form. Databases cover a broad spectrum of related subjects like coastal environment and population aspects, coastline...

  6. XML Storage for Magnetotelluric Transfer Functions: Towards a Comprehensive Online Reference Database

    Science.gov (United States)

    Kelbert, A.; Blum, C.

    2015-12-01

    Magnetotelluric Transfer Functions (MT TFs) represent most of the information about Earth electrical conductivity found in the raw electromagnetic data, providing inputs for further inversion and interpretation. To be useful for scientific interpretation, they must also contain carefully recorded metadata. Making these data available in a discoverable and citable fashion would provide the most benefit to the scientific community, but such a development requires that the metadata is not only present in the file but is also searchable. The most commonly used MT TF format to date, the historical Society of Exploration Geophysicists Electromagnetic Data Interchange Standard 1987 (EDI), no longer supports some of the needs of modern magnetotellurics, most notably accurate error bars recording. Moreover, the inherent heterogeneity of EDI's and other historic MT TF formats has mostly kept the community away from healthy data sharing practices. Recently, the MT team at Oregon State University in collaboration with IRIS Data Management Center developed a new, XML-based format for MT transfer functions, and an online system for long-term storage, discovery and sharing of MT TF data worldwide (IRIS SPUD; www.iris.edu/spud/emtf). The system provides a query page where all of the MT transfer functions collected within the USArray MT experiment and other field campaigns can be searched for and downloaded; an automatic on-the-fly conversion to the historic EDI format is also included. To facilitate conversion to the new, more comprehensive and sustainable, XML format for MT TFs, and to streamline inclusion of historic data into the online database, we developed a set of open source format conversion tools, which can be used for rotation of MT TFs as well as a general XML EDI converter (https://seiscode.iris.washington.edu/projects/emtf-fcu). Here, we report on the newly established collaboration between the USGS Geomagnetism Program and the Oregon State University to gather and

  7. Are twins at risk of cancer: results from the Swedish family-cancer database.

    Science.gov (United States)

    Hemminki, Kari; Chen, Bowang

    2005-10-01

    A few twin studies on cancer have addressed questions on the possible carcinogenic or protective effects of twining by comparing the occurrence of cancer in twins and singletons. The nationwide Swedish Family-Cancer Database of 10.2 million individuals and 69,654 0- to 70-year-old twin pairs were used to calculate standardized incidence ratios (SIRs) and 95% confidence intervals (CIs) for all main cancers compared to singletons. The overall risk of cancer in same- or different-sex twins was at the same level as the risk for singletons. Testicular cancer, particularly seminoma, was increased among same-sex twins (1.54) and all twins to an SIR of 1.38. Among other tumors, neurinomas and non-thyroid endocrine gland tumors were increased. Colorectal cancers and leukemia were decreased among all twins. Melanoma and squamous cell skin cancer were decreased in male same-sex twins. The data on this unselected population of twins suggest that twinning per se is not a risk factor of cancer. In utero hormonal exposures or postnatal growth stimulation may be related to the risk of testicular cancer and pituitary tumors. Protective effects against colorectal cancer may be related to a beneficial diet, and in melanoma and skin cancer, to socioeconomic factors. The study involved multiple comparisons, and internal consistency between the results was one of the main factors considered for their plausibility. The results should encourage others working on twin and singleton populations to examine the specific associations and emerging hypotheses.

  8. Comprehensive research synopsis and systematic meta-analyses in Parkinson's disease genetics: The PDGene database.

    Directory of Open Access Journals (Sweden)

    Christina M Lill

    Full Text Available More than 800 published genetic association studies have implicated dozens of potential risk loci in Parkinson's disease (PD. To facilitate the interpretation of these findings, we have created a dedicated online resource, PDGene, that comprehensively collects and meta-analyzes all published studies in the field. A systematic literature screen of -27,000 articles yielded 828 eligible articles from which relevant data were extracted. In addition, individual-level data from three publicly available genome-wide association studies (GWAS were obtained and subjected to genotype imputation and analysis. Overall, we performed meta-analyses on more than seven million polymorphisms originating either from GWAS datasets and/or from smaller scale PD association studies. Meta-analyses on 147 SNPs were supplemented by unpublished GWAS data from up to 16,452 PD cases and 48,810 controls. Eleven loci showed genome-wide significant (P < 5 × 10(-8 association with disease risk: BST1, CCDC62/HIP1R, DGKQ/GAK, GBA, LRRK2, MAPT, MCCC1/LAMP3, PARK16, SNCA, STK39, and SYT11/RAB25. In addition, we identified novel evidence for genome-wide significant association with a polymorphism in ITGA8 (rs7077361, OR 0.88, P  =  1.3 × 10(-8. All meta-analysis results are freely available on a dedicated online database (www.pdgene.org, which is cross-linked with a customized track on the UCSC Genome Browser. Our study provides an exhaustive and up-to-date summary of the status of PD genetics research that can be readily scaled to include the results of future large-scale genetics projects, including next-generation sequencing studies.

  9. The clinical database and implementation of treatment guidelines by the Danish Breast Cancer Cooperative Group in 2007-2016

    DEFF Research Database (Denmark)

    Jensen, Maj-Britt; Laenkholm, Anne-Vibeke; Offersen, Birgitte V

    2018-01-01

    BACKGROUND: Since 40 years, Danish Breast Cancer Cooperative Group (DBCG) has provided comprehensive guidelines for diagnosis and treatment of breast cancer. This population-based analysis aimed to describe the plurality of modifications introduced over the past 10 years in the national Danish...... guidelines for the management of early breast cancer. By use of the clinical DBCG database we analyze the effectiveness of the implementation of guideline revisions in Denmark. METHODS: From the DBCG guidelines we extracted modifications introduced in 2007-2016 and selected examples regarding surgery......, radiotherapy (RT) and systemic treatment. We assessed introduction of modifications from release on the DBCG webpage to change in clinical practice using the DBCG clinical database. RESULTS: Over a 10-year period data from 48,772 patients newly diagnosed with malignant breast tumors were entered into DBCG...

  10. The Swedish Family-Cancer Database: Update, Application to Colorectal Cancer and Clinical Relevance

    Directory of Open Access Journals (Sweden)

    Hemminki Kari

    2005-01-01

    Full Text Available Abstract The Swedish Family-Cancer Database has been used for almost 10 years in the study of familial risks at all common sites. In the present paper we describe some main features of version VI of this Database, assembled in 2004. This update included all Swedes born in 1932 and later (offspring with their biological parents, a total of 10.5 million individuals. Cancer cases were retrieved from the Swedish Cancer Registry from 1958-2002, including over 1.2 million first and multiple primary cancers and in situ tumours. Compared to previous versions, only 6.0% of deceased offspring with a cancer diagnosis lack any parental information. We show one application of the Database in the study of familial risks in colorectal adenocarcinoma, with defined age-group and anatomic site specific analyses. Familial standardized incidence ratios (SIRs were determined for offspring when parents or sibling were diagnosed with colon or rectal cancer. As a novel finding it was shown that risks for siblings were higher than those for offspring of affected parents. The excess risk was limited to colon cancer and particularly to right-sided colon cancer. The SIRs for colon cancer in age matched populations were 2.58 when parents were probands and 3.81 when siblings were probands; for right-sided colon cancer the SIRs were 3.66 and 7.53, respectively. Thus the familial excess (SIR-1.00 was more than two fold higher for right-sided colon cancer. Colon and rectal cancers appeared to be distinguished between high-penetrant and recessive conditions that only affect the colon, whereas low-penetrant familial effects are shared by the two sites. Epidemiological studies can be used to generate clinical estimates for familial risk, conditioned on numbers of affected family members and their ages of onset. Useful risk estimates have been developed for familial breast and prostate cancers. Reliable risk estimates for other cancers should also be seriously considered for

  11. N-glycans released from glycoproteins using a commercial kit and comprehensively analyzed with a hypothetical database

    Directory of Open Access Journals (Sweden)

    Xue Sun

    2017-04-01

    Full Text Available The glycosylation of proteins is responsible for their structural and functional roles in many cellular activities. This work describes a strategy that combines an efficient release, labeling and liquid chromatography-mass spectral analysis with the use of a comprehensive database to analyze N-glycans. The analytical method described relies on a recently commercialized kit in which quick deglycosylation is followed by rapid labeling and cleanup of labeled glycans. This greatly improves the separation, mass spectrometry (MS analysis and fluorescence detection of N-glycans. A hypothetical database, constructed using GlycResoft, provides all compositional possibilities of N-glycans based on the common sugar residues found in N-glycans. In the initial version this database contains >8,700 N-glycans, and is compatible with MS instrument software and expandable. N-glycans from four different well-studied glycoproteins were analyzed by this strategy. The results provided much more accurate and comprehensive data than had been previously reported. This strategy was then used to analyze the N-glycans present on the membrane glycoproteins of gastric carcinoma cells with different degrees of differentiation. Accurate and comprehensive N-glycan data from those cells was obtained efficiently and their differences compared corresponding to their differentiation states. Thus, the novel strategy developed greatly improves accuracy, efficiency and comprehensiveness of N-glycan analysis.

  12. Databases

    Directory of Open Access Journals (Sweden)

    Nick Ryan

    2004-01-01

    Full Text Available Databases are deeply embedded in archaeology, underpinning and supporting many aspects of the subject. However, as well as providing a means for storing, retrieving and modifying data, databases themselves must be a result of a detailed analysis and design process. This article looks at this process, and shows how the characteristics of data models affect the process of database design and implementation. The impact of the Internet on the development of databases is examined, and the article concludes with a discussion of a range of issues associated with the recording and management of archaeological data.

  13. The dark side of SOX2: cancer - a comprehensive overview.

    Science.gov (United States)

    Wuebben, Erin L; Rizzino, Angie

    2017-07-04

    The pluripotency-associated transcription factor SOX2 is essential during mammalian embryogenesis and later in life, but SOX2 expression can also be highly detrimental. Over the past 10 years, SOX2 has been shown to be expressed in at least 25 different cancers. This review provides a comprehensive overview of the roles of SOX2 in cancer and focuses on two broad topics. The first delves into the expression and function of SOX2 in cancer focusing on the connection between SOX2 levels and tumor grade as well as patient survival. As part of this discussion, we address the developing connection between SOX2 expression and tumor drug resistance. We also call attention to an under-appreciated property of SOX2, its levels in actively proliferating tumor cells appear to be optimized to maximize tumor growth - too little or too much SOX2 dramatically alters tumor growth. The second topic of this review focuses on the exquisite array of molecular mechanisms that control the expression and transcriptional activity of SOX2. In addition to its complex regulation at the transcriptional level, SOX2 expression and activity are controlled carefully by microRNAs, long non-coding RNAs, and post-translational modifications. In the Conclusion and Future Perspectives section, we point out that there are still important unanswered questions. Addressing these questions is expected to lead to new insights into the functions of SOX2 in cancer, which will help design novels strategies for more effectively treating some of the most deadly cancers.

  14. Autism genetic database (AGD: a comprehensive database including autism susceptibility gene-CNVs integrated with known noncoding RNAs and fragile sites

    Directory of Open Access Journals (Sweden)

    Talebizadeh Zohreh

    2009-09-01

    Full Text Available Abstract Background Autism is a highly heritable complex neurodevelopmental disorder, therefore identifying its genetic basis has been challenging. To date, numerous susceptibility genes and chromosomal abnormalities have been reported in association with autism, but most discoveries either fail to be replicated or account for a small effect. Thus, in most cases the underlying causative genetic mechanisms are not fully understood. In the present work, the Autism Genetic Database (AGD was developed as a literature-driven, web-based, and easy to access database designed with the aim of creating a comprehensive repository for all the currently reported genes and genomic copy number variations (CNVs associated with autism in order to further facilitate the assessment of these autism susceptibility genetic factors. Description AGD is a relational database that organizes data resulting from exhaustive literature searches for reported susceptibility genes and CNVs associated with autism. Furthermore, genomic information about human fragile sites and noncoding RNAs was also downloaded and parsed from miRBase, snoRNA-LBME-db, piRNABank, and the MIT/ICBP siRNA database. A web client genome browser enables viewing of the features while a web client query tool provides access to more specific information for the features. When applicable, links to external databases including GenBank, PubMed, miRBase, snoRNA-LBME-db, piRNABank, and the MIT siRNA database are provided. Conclusion AGD comprises a comprehensive list of susceptibility genes and copy number variations reported to-date in association with autism, as well as all known human noncoding RNA genes and fragile sites. Such a unique and inclusive autism genetic database will facilitate the evaluation of autism susceptibility factors in relation to known human noncoding RNAs and fragile sites, impacting on human diseases. As a result, this new autism database offers a valuable tool for the research

  15. Sustainability in a state comprehensive cancer control coalition: lessons learned.

    Science.gov (United States)

    Desmond, Renee A; Chapman, Kathryn; Graf, Gavin; Stanfield, Bret; Waterbor, John W

    2014-03-01

    The Alabama Comprehensive Cancer Control Coalition (ACCCC) has developed an integrated and coordinated approach to reducing cancer incidence, morbidity, and mortality, and to improving the quality of life for cancer survivors, their families, and their caregivers. The ACCCC is currently in a maintenance phase and a formal plan for sustainability of the coalition was needed to keep the members engaged and productive. A training session in coalition sustainability conducted in 2013 identified the following elements as essential to success: (1) increased marketing of the coalition by simplifying its mission; (2) improved networking including flexibility in coalition meeting location and attendance; (3) increased membership satisfaction through transformational leadership; (4) revision of the working structure of committees and improved accountability; and (5) enhancement of partner satisfaction with coalition activities designed to recruit and retain new partners. A self-administered membership satisfaction survey was given to assess coalition mission, meeting logistics, organization, capacity building, and coalition goals. Results indicated that the subcategories of communication, mission, and meeting logistics were rated satisfied to very satisfied on a five-point scale. Although the ACCCC had clearly written goals, improvement could be made in leadership participation and new member orientation could be improved. Most members rated their parent organization as highly involved with the ACCCC and many offered suggestions on capacity building. Results of the sustainability training have clarified the ACCCC's plans to ensure coalition viability and improve strategies to inform stakeholders of the benefits of participation in the coalition.

  16. Validation of the Provincial Transfer Authorization Centre database: a comprehensive database containing records of all inter-facility patient transfers in the province of Ontario

    Directory of Open Access Journals (Sweden)

    MacDonald Russell D

    2006-10-01

    Full Text Available Abstract Background The Provincial Transfer Authorization Centre (PTAC was established as a part of the emergency response in Ontario, Canada to the Severe Acute Respiratory Syndrome (SARS outbreak in 2003. Prior to 2003, data relating to inter-facility patient transfers were not collected in a systematic manner. Then, in an emergency setting, a comprehensive database with a complex data collection process was established. For the first time in Ontario, population-based data for patient movement between healthcare facilities for a population of twelve million are available. The PTAC database stores all patient transfer data in a large database. There are few population-based patient transfer databases and the PTAC database is believed to be the largest example to house this novel dataset. A patient transfer database has also never been validated. This paper presents the validation of the PTAC database. Methods A random sample of 100 patient inter-facility transfer records was compared to the corresponding institutional patient records from the sending healthcare facilities. Measures of agreement, including sensitivity, were calculated for the 12 common data variables. Results Of the 100 randomly selected patient transfer records, 95 (95% of the corresponding institutional patient records were located. Data variables in the categories patient demographics, facility identification and timing of transfer and reason and urgency of transfer had strong agreement levels. The 10 most commonly used data variables had accuracy rates that ranged from 85.3% to 100% and error rates ranging from 0 to 12.6%. These same variables had sensitivity values ranging from 0.87 to 1.0. Conclusion The very high level of agreement between institutional patient records and the PTAC data for fields compared in this study supports the validity of the PTAC database. For the first time, a population-based patient transfer database has been established. Although it was created

  17. Acquire: an open-source comprehensive cancer biobanking system.

    Science.gov (United States)

    Dowst, Heidi; Pew, Benjamin; Watkins, Chris; McOwiti, Apollo; Barney, Jonathan; Qu, Shijing; Becnel, Lauren B

    2015-05-15

    The probability of effective treatment of cancer with a targeted therapeutic can be improved for patients with defined genotypes containing actionable mutations. To this end, many human cancer biobanks are integrating more tightly with genomic sequencing facilities and with those creating and maintaining patient-derived xenografts (PDX) and cell lines to provide renewable resources for translational research. To support the complex data management needs and workflows of several such biobanks, we developed Acquire. It is a robust, secure, web-based, database-backed open-source system that supports all major needs of a modern cancer biobank. Its modules allow for i) up-to-the-minute 'scoreboard' and graphical reporting of collections; ii) end user roles and permissions; iii) specimen inventory through caTissue Suite; iv) shipping forms for distribution of specimens to pathology, genomic analysis and PDX/cell line creation facilities; v) robust ad hoc querying; vi) molecular and cellular quality control metrics to track specimens' progress and quality; vii) public researcher request; viii) resource allocation committee distribution request review and oversight and ix) linkage to available derivatives of specimen. © The Author 2015. Published by Oxford University Press.

  18. A comprehensive change detection method for updating the National Land Cover Database to circa 2011

    Science.gov (United States)

    Jin, Suming; Yang, Limin; Danielson, Patrick; Homer, Collin G.; Fry, Joyce; Xian, George

    2013-01-01

    The importance of characterizing, quantifying, and monitoring land cover, land use, and their changes has been widely recognized by global and environmental change studies. Since the early 1990s, three U.S. National Land Cover Database (NLCD) products (circa 1992, 2001, and 2006) have been released as free downloads for users. The NLCD 2006 also provides land cover change products between 2001 and 2006. To continue providing updated national land cover and change datasets, a new initiative in developing NLCD 2011 is currently underway. We present a new Comprehensive Change Detection Method (CCDM) designed as a key component for the development of NLCD 2011 and the research results from two exemplar studies. The CCDM integrates spectral-based change detection algorithms including a Multi-Index Integrated Change Analysis (MIICA) model and a novel change model called Zone, which extracts change information from two Landsat image pairs. The MIICA model is the core module of the change detection strategy and uses four spectral indices (CV, RCVMAX, dNBR, and dNDVI) to obtain the changes that occurred between two image dates. The CCDM also includes a knowledge-based system, which uses critical information on historical and current land cover conditions and trends and the likelihood of land cover change, to combine the changes from MIICA and Zone. For NLCD 2011, the improved and enhanced change products obtained from the CCDM provide critical information on location, magnitude, and direction of potential change areas and serve as a basis for further characterizing land cover changes for the nation. An accuracy assessment from the two study areas show 100% agreement between CCDM mapped no-change class with reference dataset, and 18% and 82% disagreement for the change class for WRS path/row p22r39 and p33r33, respectively. The strength of the CCDM is that the method is simple, easy to operate, widely applicable, and capable of capturing a variety of natural and

  19. Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer. | Office of Cancer Genomics

    Science.gov (United States)

    We report a comprehensive analysis of 412 muscle-invasive bladder cancers characterized by multiple TCGA analytical platforms. Fifty-eight genes were significantly mutated, and the overall mutational load was associated with APOBEC-signature mutagenesis. Clustering by mutation signature identified a high-mutation subset with 75% 5-year survival.

  20. University of Michigan Comprehensive Cancer Center opportunities for improvement project.

    Science.gov (United States)

    Breslin, Tara M; Waldinger, Marcy; Silver, Samuel M

    2014-02-01

    The University of Michigan Comprehensive Cancer Center (UMCCC) Opportunities for Improvement project involved a detailed patient-level medical record review, feedback to medical providers and clinical leadership, and discussion of potential predictors of discordant or delayed care. The medical record review revealed that reasons for discordant or delayed care were well documented by clinical providers, and medical comorbidity was the most common predisposing factor. Another common theme was the difficulty in obtaining treatment records for patients who received a portion of their care outside UMCCC. The project provided a valuable opportunity to examine established processes of care and data collection and consider how the newly implemented electronic health record might support future efforts aimed at improving efficiency and communication among providers.

  1. Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer.

    Science.gov (United States)

    Robertson, A Gordon; Kim, Jaegil; Al-Ahmadie, Hikmat; Bellmunt, Joaquim; Guo, Guangwu; Cherniack, Andrew D; Hinoue, Toshinori; Laird, Peter W; Hoadley, Katherine A; Akbani, Rehan; Castro, Mauro A A; Gibb, Ewan A; Kanchi, Rupa S; Gordenin, Dmitry A; Shukla, Sachet A; Sanchez-Vega, Francisco; Hansel, Donna E; Czerniak, Bogdan A; Reuter, Victor E; Su, Xiaoping; de Sa Carvalho, Benilton; Chagas, Vinicius S; Mungall, Karen L; Sadeghi, Sara; Pedamallu, Chandra Sekhar; Lu, Yiling; Klimczak, Leszek J; Zhang, Jiexin; Choo, Caleb; Ojesina, Akinyemi I; Bullman, Susan; Leraas, Kristen M; Lichtenberg, Tara M; Wu, Catherine J; Schultz, Nicholaus; Getz, Gad; Meyerson, Matthew; Mills, Gordon B; McConkey, David J; Weinstein, John N; Kwiatkowski, David J; Lerner, Seth P

    2017-10-19

    We report a comprehensive analysis of 412 muscle-invasive bladder cancers characterized by multiple TCGA analytical platforms. Fifty-eight genes were significantly mutated, and the overall mutational load was associated with APOBEC-signature mutagenesis. Clustering by mutation signature identified a high-mutation subset with 75% 5-year survival. mRNA expression clustering refined prior clustering analyses and identified a poor-survival "neuronal" subtype in which the majority of tumors lacked small cell or neuroendocrine histology. Clustering by mRNA, long non-coding RNA (lncRNA), and miRNA expression converged to identify subsets with differential epithelial-mesenchymal transition status, carcinoma in situ scores, histologic features, and survival. Our analyses identified 5 expression subtypes that may stratify response to different treatments. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Gynecologic Cancer Prevention and Control in the National Comprehensive Cancer Control Program: Progress, Current Activities, and Future Directions

    OpenAIRE

    Stewart, Sherri L.; Lakhani, Naheed; Brown, Phaeydra M.; Larkin, O. Ann; Moore, Angela R.; Hayes, Nikki S.

    2013-01-01

    Gynecologic cancer confers a large burden among women in the United States. Several evidence-based interventions are available to reduce the incidence, morbidity, and mortality from these cancers. The National Comprehensive Cancer Control Program (NCCCP) is uniquely positioned to implement these interventions in the US population. This review discusses progress and future directions for the NCCCP in preventing and controlling gynecologic cancer.

  3. Gynecologic cancer prevention and control in the National Comprehensive Cancer Control Program: progress, current activities, and future directions.

    Science.gov (United States)

    Stewart, Sherri L; Lakhani, Naheed; Brown, Phaeydra M; Larkin, O Ann; Moore, Angela R; Hayes, Nikki S

    2013-08-01

    Gynecologic cancer confers a large burden among women in the United States. Several evidence-based interventions are available to reduce the incidence, morbidity, and mortality from these cancers. The National Comprehensive Cancer Control Program (NCCCP) is uniquely positioned to implement these interventions in the US population. This review discusses progress and future directions for the NCCCP in preventing and controlling gynecologic cancer.

  4. ARCPHdb: A comprehensive protein database for SF1 and SF2 helicase from archaea.

    Science.gov (United States)

    Moukhtar, Mirna; Chaar, Wafi; Abdel-Razzak, Ziad; Khalil, Mohamad; Taha, Samir; Chamieh, Hala

    2017-01-01

    Superfamily 1 and Superfamily 2 helicases, two of the largest helicase protein families, play vital roles in many biological processes including replication, transcription and translation. Study of helicase proteins in the model microorganisms of archaea have largely contributed to the understanding of their function, architecture and assembly. Based on a large phylogenomics approach, we have identified and classified all SF1 and SF2 protein families in ninety five sequenced archaea genomes. Here we developed an online webserver linked to a specialized protein database named ARCPHdb to provide access for SF1 and SF2 helicase families from archaea. ARCPHdb was implemented using MySQL relational database. Web interfaces were developed using Netbeans. Data were stored according to UniProt accession numbers, NCBI Ref Seq ID, PDB IDs and Entrez Databases. A user-friendly interactive web interface has been developed to browse, search and download archaeal helicase protein sequences, their available 3D structure models, and related documentation available in the literature provided by ARCPHdb. The database provides direct links to matching external databases. The ARCPHdb is the first online database to compile all protein information on SF1 and SF2 helicase from archaea in one platform. This database provides essential resource information for all researchers interested in the field. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer.

    Science.gov (United States)

    Ciriello, Giovanni; Gatza, Michael L; Beck, Andrew H; Wilkerson, Matthew D; Rhie, Suhn K; Pastore, Alessandro; Zhang, Hailei; McLellan, Michael; Yau, Christina; Kandoth, Cyriac; Bowlby, Reanne; Shen, Hui; Hayat, Sikander; Fieldhouse, Robert; Lester, Susan C; Tse, Gary M K; Factor, Rachel E; Collins, Laura C; Allison, Kimberly H; Chen, Yunn-Yi; Jensen, Kristin; Johnson, Nicole B; Oesterreich, Steffi; Mills, Gordon B; Cherniack, Andrew D; Robertson, Gordon; Benz, Christopher; Sander, Chris; Laird, Peter W; Hoadley, Katherine A; King, Tari A; Perou, Charles M

    2015-10-08

    Invasive lobular carcinoma (ILC) is the second most prevalent histologic subtype of invasive breast cancer. Here, we comprehensively profiled 817 breast tumors, including 127 ILC, 490 ductal (IDC), and 88 mixed IDC/ILC. Besides E-cadherin loss, the best known ILC genetic hallmark, we identified mutations targeting PTEN, TBX3, and FOXA1 as ILC enriched features. PTEN loss associated with increased AKT phosphorylation, which was highest in ILC among all breast cancer subtypes. Spatially clustered FOXA1 mutations correlated with increased FOXA1 expression and activity. Conversely, GATA3 mutations and high expression characterized luminal A IDC, suggesting differential modulation of ER activity in ILC and IDC. Proliferation and immune-related signatures determined three ILC transcriptional subtypes associated with survival differences. Mixed IDC/ILC cases were molecularly classified as ILC-like and IDC-like revealing no true hybrid features. This multidimensional molecular atlas sheds new light on the genetic bases of ILC and provides potential clinical options. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. Traditional Chinese medical comprehensive therapy for cancer-related fatigue.

    Science.gov (United States)

    Yang, Lu; Li, Tian-Tian; Chu, Yu-Ting; Chen, Ke; Tian, Shao-Dan; Chen, Xin-Yi; Yang, Guo-Wang

    2016-01-01

    Cancer-related fatigue (CRF) is a common and one of the most severe symptom in the period of onset, diagnosis, treatment and rehabilitation process of cancer. But there are no confirmed measures to relieve this problem at present. Traditional Chinese medical comprehensive therapy has its advantages in dealing with this condition. Based on the research status of CRF, the following problems have been analyzed and solved: the term of CRF has been defined and recommended, and the definition has been made clear; the disease mechanism is proposed, i.e. healthy qi has been impaired in the long-term disease duration, in the process of surgery, chemotherapy, radiotherapy and biology disturbing; it is clear that the clinical manifestations are related to six Chinese medicine patterns: decreased functioning of the Pi (Spleen) and Wei (Stomach), deficiency of the Pi with dampness retention, deficiency of the Xin (Heart) and Pi, disharmony between the Gan (Liver) and Pi, deficiency of the Pi and Shen (Kidney), and deficiency of the Fei (Lung) and Shen. Based on its severity, the mild patients are advised to have non-drug psychological intervention and sleep treatment in cooperation with appropriate exercise; diet therapy are recommended to moderate patients together with sleep treatment and acupuncture, severe patients are recommended to have herbal treatment based on pattern differentiation together with physiological sleep therapy.

  7. Comprehensible knowledge model creation for cancer treatment decision making.

    Science.gov (United States)

    Afzal, Muhammad; Hussain, Maqbool; Ali Khan, Wajahat; Ali, Taqdir; Lee, Sungyoung; Huh, Eui-Nam; Farooq Ahmad, Hafiz; Jamshed, Arif; Iqbal, Hassan; Irfan, Muhammad; Abbas Hydari, Manzar

    2017-03-01

    A wealth of clinical data exists in clinical documents in the form of electronic health records (EHRs). This data can be used for developing knowledge-based recommendation systems that can assist clinicians in clinical decision making and education. One of the big hurdles in developing such systems is the lack of automated mechanisms for knowledge acquisition to enable and educate clinicians in informed decision making. An automated knowledge acquisition methodology with a comprehensible knowledge model for cancer treatment (CKM-CT) is proposed. With the CKM-CT, clinical data are acquired automatically from documents. Quality of data is ensured by correcting errors and transforming various formats into a standard data format. Data preprocessing involves dimensionality reduction and missing value imputation. Predictive algorithm selection is performed on the basis of the ranking score of the weighted sum model. The knowledge builder prepares knowledge for knowledge-based services: clinical decisions and education support. Data is acquired from 13,788 head and neck cancer (HNC) documents for 3447 patients, including 1526 patients of the oral cavity site. In the data quality task, 160 staging values are corrected. In the preprocessing task, 20 attributes and 106 records are eliminated from the dataset. The Classification and Regression Trees (CRT) algorithm is selected and provides 69.0% classification accuracy in predicting HNC treatment plans, consisting of 11 decision paths that yield 11 decision rules. Our proposed methodology, CKM-CT, is helpful to find hidden knowledge in clinical documents. In CKM-CT, the prediction models are developed to assist and educate clinicians for informed decision making. The proposed methodology is generalizable to apply to data of other domains such as breast cancer with a similar objective to assist clinicians in decision making and education. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. CancerLectinDB: a database of lectins relevant to cancer.

    Science.gov (United States)

    Damodaran, Deepa; Jeyakani, Justin; Chauhan, Alok; Kumar, Nirmal; Chandra, Nagasuma R; Surolia, Avadhesha

    2008-04-01

    The role of lectins in mediating cancer metastasis, apoptosis as well as various other signaling events has been well established in the past few years. Data on various aspects of the role of lectins in cancer is being accumulated at a rapid pace. The data on lectins available in the literature is so diverse, that it becomes difficult and time-consuming, if not impossible to comprehend the advances in various areas and obtain the maximum benefit. Not only do the lectins vary significantly in their individual functional roles, but they are also diverse in their sequences, structures, binding site architectures, quaternary structures, carbohydrate affinities and specificities as well as their potential applications. An organization of these seemingly independent data into a common framework is essential in order to achieve effective use of all the data towards understanding the roles of different lectins in different aspects of cancer and any resulting applications. An integrated knowledge base (CancerLectinDB) together with appropriate analytical tools has therefore been developed for lectins relevant for any aspect of cancer, by collating and integrating diverse data. This database is unique in terms of providing sequence, structural, and functional annotations for lectins from all known sources in cancer and is expected to be a useful addition to the number of glycan related resources now available to the community. The database has been implemented using MySQL on a Linux platform and web-enabled using Perl-CGI and Java tools. Data for individual lectins pertain to taxonomic, biochemical, domain architecture, molecular sequence and structural details as well as carbohydrate specificities. Extensive links have also been provided for relevant bioinformatics resources and analytical tools. Availability of diverse data integrated into a common framework is expected to be of high value for various studies on lectin cancer biology. CancerLectinDB can be accessed through

  9. Novel LOVD databases for hereditary breast cancer and colorectal cancer genes in the Chinese population.

    Science.gov (United States)

    Pan, Min; Cong, Peikuan; Wang, Yue; Lin, Changsong; Yuan, Ying; Dong, Jian; Banerjee, Santasree; Zhang, Tao; Chen, Yanling; Zhang, Ting; Chen, Mingqing; Hu, Peter; Zheng, Shu; Zhang, Jin; Qi, Ming

    2011-12-01

    The Human Variome Project (HVP) is an international consortium of clinicians, geneticists, and researchers from over 30 countries, aiming to facilitate the establishment and maintenance of standards, systems, and infrastructure for the worldwide collection and sharing of all genetic variations effecting human disease. The HVP-China Node will build new and supplement existing databases of genetic diseases. As the first effort, we have created a novel variant database of BRCA1 and BRCA2, mismatch repair genes (MMR), and APC genes for breast cancer, Lynch syndrome, and familial adenomatous polyposis (FAP), respectively, in the Chinese population using the Leiden Open Variation Database (LOVD) format. We searched PubMed and some Chinese search engines to collect all the variants of these genes in the Chinese population that have already been detected and reported. There are some differences in the gene variants between the Chinese population and that of other ethnicities. The database is available online at http://www.genomed.org/LOVD/. Our database will appear to users who survey other LOVD databases (e.g., by Google search, or by NCBI GeneTests search). Remote submissions are accepted, and the information is updated monthly. © 2011 Wiley Periodicals, Inc.

  10. Development of a Publicly Available, Comprehensive Database of Fiber and Health Outcomes: Rationale and Methods.

    Directory of Open Access Journals (Sweden)

    Kara A Livingston

    Full Text Available Dietary fiber is a broad category of compounds historically defined as partially or completely indigestible plant-based carbohydrates and lignin with, more recently, the additional criteria that fibers incorporated into foods as additives should demonstrate functional human health outcomes to receive a fiber classification. Thousands of research studies have been published examining fibers and health outcomes.(1 Develop a database listing studies testing fiber and physiological health outcomes identified by experts at the Ninth Vahouny Conference; (2 Use evidence mapping methodology to summarize this body of literature. This paper summarizes the rationale, methodology, and resulting database. The database will help both scientists and policy-makers to evaluate evidence linking specific fibers with physiological health outcomes, and identify missing information.To build this database, we conducted a systematic literature search for human intervention studies published in English from 1946 to May 2015. Our search strategy included a broad definition of fiber search terms, as well as search terms for nine physiological health outcomes identified at the Ninth Vahouny Fiber Symposium. Abstracts were screened using a priori defined eligibility criteria and a low threshold for inclusion to minimize the likelihood of rejecting articles of interest. Publications then were reviewed in full text, applying additional a priori defined exclusion criteria. The database was built and published on the Systematic Review Data Repository (SRDR™, a web-based, publicly available application.A fiber database was created. This resource will reduce the unnecessary replication of effort in conducting systematic reviews by serving as both a central database archiving PICO (population, intervention, comparator, outcome data on published studies and as a searchable tool through which this data can be extracted and updated.

  11. BtoxDB: a comprehensive database of protein structural data on toxin-antitoxin systems.

    Science.gov (United States)

    Barbosa, Luiz Carlos Bertucci; Garrido, Saulo Santesso; Marchetto, Reinaldo

    2015-03-01

    Toxin-antitoxin (TA) systems are diverse and abundant genetic modules in prokaryotic cells that are typically formed by two genes encoding a stable toxin and a labile antitoxin. Because TA systems are able to repress growth or kill cells and are considered to be important actors in cell persistence (multidrug resistance without genetic change), these modules are considered potential targets for alternative drug design. In this scenario, structural information for the proteins in these systems is highly valuable. In this report, we describe the development of a web-based system, named BtoxDB, that stores all protein structural data on TA systems. The BtoxDB database was implemented as a MySQL relational database using PHP scripting language. Web interfaces were developed using HTML, CSS and JavaScript. The data were collected from the PDB, UniProt and Entrez databases. These data were appropriately filtered using specialized literature and our previous knowledge about toxin-antitoxin systems. The database provides three modules ("Search", "Browse" and "Statistics") that enable searches, acquisition of contents and access to statistical data. Direct links to matching external databases are also available. The compilation of all protein structural data on TA systems in one platform is highly useful for researchers interested in this content. BtoxDB is publicly available at http://www.gurupi.uft.edu.br/btoxdb. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. dEMBF: A Comprehensive Database of Enzymes of Microalgal Biofuel Feedstock.

    Science.gov (United States)

    Misra, Namrata; Panda, Prasanna Kumar; Parida, Bikram Kumar; Mishra, Barada Kanta

    2016-01-01

    Microalgae have attracted wide attention as one of the most versatile renewable feedstocks for production of biofuel. To develop genetically engineered high lipid yielding algal strains, a thorough understanding of the lipid biosynthetic pathway and the underpinning enzymes is essential. In this work, we have systematically mined the genomes of fifteen diverse algal species belonging to Chlorophyta, Heterokontophyta, Rhodophyta, and Haptophyta, to identify and annotate the putative enzymes of lipid metabolic pathway. Consequently, we have also developed a database, dEMBF (Database of Enzymes of Microalgal Biofuel Feedstock), which catalogues the complete list of identified enzymes along with their computed annotation details including length, hydrophobicity, amino acid composition, subcellular location, gene ontology, KEGG pathway, orthologous group, Pfam domain, intron-exon organization, transmembrane topology, and secondary/tertiary structural data. Furthermore, to facilitate functional and evolutionary study of these enzymes, a collection of built-in applications for BLAST search, motif identification, sequence and phylogenetic analysis have been seamlessly integrated into the database. dEMBF is the first database that brings together all enzymes responsible for lipid synthesis from available algal genomes, and provides an integrative platform for enzyme inquiry and analysis. This database will be extremely useful for algal biofuel research. It can be accessed at http://bbprof.immt.res.in/embf.

  13. Toward a comprehensive and systematic methylome signature in colorectal cancers.

    Science.gov (United States)

    Ashktorab, Hassan; Rahi, Hamed; Wansley, Daniel; Varma, Sudhir; Shokrani, Babak; Lee, Edward; Daremipouran, Mohammad; Laiyemo, Adeyinka; Goel, Ajay; Carethers, John M; Brim, Hassan

    2013-08-01

    CpG Island Methylator Phenotype (CIMP) is one of the underlying mechanisms in colorectal cancer (CRC). This study aimed to define a methylome signature in CRC through a methylation microarray analysis and a compilation of promising CIMP markers from the literature. Illumina HumanMethylation27 (IHM27) array data was generated and analyzed based on statistical differences in methylation data (1st approach) or based on overall differences in methylation percentages using lower 95% CI (2nd approach). Pyrosequencing was performed for the validation of nine genes. A meta-analysis was used to identify CIMP and non-CIMP markers that were hypermethylated in CRC but did not yet make it to the CIMP genes' list. Our 1st approach for array data analysis demonstrated the limitations in selecting genes for further validation, highlighting the need for the 2nd bioinformatics approach to adequately select genes with differential aberrant methylation. A more comprehensive list, which included non-CIMP genes, such as APC, EVL, CD109, PTEN, TWIST1, DCC, PTPRD, SFRP1, ICAM5, RASSF1A, EYA4, 30ST2, LAMA1, KCNQ5, ADHEF1, and TFPI2, was established. Array data are useful to categorize and cluster colonic lesions based on their global methylation profiles; however, its usefulness in identifying robust methylation markers is limited and rely on the data analysis method. We have identified 16 non-CIMP-panel genes for which we provide rationale for inclusion in a more comprehensive characterization of CIMP+ CRCs. The identification of a definitive list for methylome specific genes in CRC will contribute to better clinical management of CRC patients.

  14. DOG-SPOT database for comprehensive management of dog genetic research data

    Directory of Open Access Journals (Sweden)

    Sutter Nathan B

    2010-12-01

    Full Text Available Abstract Research laboratories studying the genetics of companion animals have no database tools specifically designed to aid in the management of the many kinds of data that are generated, stored and analyzed. We have developed a relational database, "DOG-SPOT," to provide such a tool. Implemented in MS-Access, the database is easy to extend or customize to suit a lab's particular needs. With DOG-SPOT a lab can manage data relating to dogs, breeds, samples, biomaterials, phenotypes, owners, communications, amplicons, sequences, markers, genotypes and personnel. Such an integrated data structure helps ensure high quality data entry and makes it easy to track physical stocks of biomaterials and oligonucleotides.

  15. Variation in Definitive Therapy for Localized Non-Small Cell Lung Cancer Among National Comprehensive Cancer Network Institutions

    Energy Technology Data Exchange (ETDEWEB)

    Valle, Luca F. [Geisel School of Medicine at Dartmouth College, Dartmouth College, Hanover, New Hampshire (United States); Jagsi, Reshma [Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, Ann Arbor, Michigan (United States); Bobiak, Sarah N.; Zornosa, Carrie [National Comprehensive Cancer Network, Fort Washington, Pennsylvania (United States); D' Amico, Thomas A. [Department of Surgery, Division of Thoracic Surgery, Duke Cancer Institute, Durham, North Carolina (United States); Pisters, Katherine M. [Department of Thoracic/Head and Neck Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Dexter, Elisabeth U. [Department of Thoracic Surgery, Roswell Park Cancer Institute, Buffalo, New York (United States); Niland, Joyce C. [Department of Information Sciences, City of Hope Comprehensive Cancer Center, Duarte, California (United States); Hayman, James A. [Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, Ann Arbor, Michigan (United States); Kapadia, Nirav S., E-mail: Nirav.S.Kapadia@hitchcock.org [Department of Radiation Oncology, Dartmouth-Hitchcock Norris Cotton Cancer Center, Lebanon, New Hampshire (United States); Dartmouth Institute for Health Policy and Clinical Practice, Lebanon, New Hampshire (United States)

    2016-02-01

    Purpose: This study determined practice patterns in the staging and treatment of patients with stage I non-small cell lung cancer (NSCLC) among National Comprehensive Cancer Network (NCCN) member institutions. Secondary aims were to determine trends in the use of definitive therapy, predictors of treatment type, and acute adverse events associated with primary modalities of treatment. Methods and Materials: Data from the National Comprehensive Cancer Network Oncology Outcomes Database from 2007 to 2011 for US patients with stage I NSCLC were used. Main outcome measures included patterns of care, predictors of treatment, acute morbidity, and acute mortality. Results: Seventy-nine percent of patients received surgery, 16% received definitive radiation therapy (RT), and 3% were not treated. Seventy-four percent of the RT patients received stereotactic body RT (SBRT), and the remainder received nonstereotactic RT (NSRT). Among participating NCCN member institutions, the number of surgeries-to-RT course ratios varied between 1.6 and 34.7 (P<.01), and the SBRT-to-NSRT ratio varied between 0 and 13 (P=.01). Significant variations were also observed in staging practices, with brain imaging 0.33 (0.25-0.43) times as likely and mediastinoscopy 31.26 (21.84-44.76) times more likely for surgical patients than for RT patients. Toxicity rates for surgical and for SBRT patients were similar, although the rates were double for NSRT patients. Conclusions: The variations in treatment observed among NCCN institutions reflects the lack of level I evidence directing the use of surgery or SBRT for stage I NSCLC. In this setting, research of patient and physician preferences may help to guide future decision making.

  16. Variation in Definitive Therapy for Localized Non-Small Cell Lung Cancer Among National Comprehensive Cancer Network Institutions

    International Nuclear Information System (INIS)

    Valle, Luca F.; Jagsi, Reshma; Bobiak, Sarah N.; Zornosa, Carrie; D'Amico, Thomas A.; Pisters, Katherine M.; Dexter, Elisabeth U.; Niland, Joyce C.; Hayman, James A.; Kapadia, Nirav S.

    2016-01-01

    Purpose: This study determined practice patterns in the staging and treatment of patients with stage I non-small cell lung cancer (NSCLC) among National Comprehensive Cancer Network (NCCN) member institutions. Secondary aims were to determine trends in the use of definitive therapy, predictors of treatment type, and acute adverse events associated with primary modalities of treatment. Methods and Materials: Data from the National Comprehensive Cancer Network Oncology Outcomes Database from 2007 to 2011 for US patients with stage I NSCLC were used. Main outcome measures included patterns of care, predictors of treatment, acute morbidity, and acute mortality. Results: Seventy-nine percent of patients received surgery, 16% received definitive radiation therapy (RT), and 3% were not treated. Seventy-four percent of the RT patients received stereotactic body RT (SBRT), and the remainder received nonstereotactic RT (NSRT). Among participating NCCN member institutions, the number of surgeries-to-RT course ratios varied between 1.6 and 34.7 (P<.01), and the SBRT-to-NSRT ratio varied between 0 and 13 (P=.01). Significant variations were also observed in staging practices, with brain imaging 0.33 (0.25-0.43) times as likely and mediastinoscopy 31.26 (21.84-44.76) times more likely for surgical patients than for RT patients. Toxicity rates for surgical and for SBRT patients were similar, although the rates were double for NSRT patients. Conclusions: The variations in treatment observed among NCCN institutions reflects the lack of level I evidence directing the use of surgery or SBRT for stage I NSCLC. In this setting, research of patient and physician preferences may help to guide future decision making.

  17. Building-Up a comprehensive database of flavonoids based on nuclear magnetic resonance data.

    NARCIS (Netherlands)

    Moco, S.I.A.; Tseng, L.; Spraul, M.; Chen, Z.; Vervoort, J.J.M.

    2006-01-01

    The improvements in separation and analysis of complex mixtures by LC-NMR during the last decade have shifted its emphasis from data acquisition to data analysis. For correct data analysis, not only high quality datasets are necessary, but adequate software and adequate databases for semi (or

  18. Comprehensive database of diameter-based biomass regressions for North American tree species

    Science.gov (United States)

    Jennifer C. Jenkins; David C. Chojnacky; Linda S. Heath; Richard A. Birdsey

    2004-01-01

    A database consisting of 2,640 equations compiled from the literature for predicting the biomass of trees and tree components from diameter measurements of species found in North America. Bibliographic information, geographic locations, diameter limits, diameter and biomass units, equation forms, statistical errors, and coefficients are provided for each equation,...

  19. CycleBase.org - a comprehensive multi-organism online database of cell-cycle experiments

    DEFF Research Database (Denmark)

    Gauthier, Nicholas Paul; Larsen, Malene Erup; Wernersson, Rasmus

    2007-01-01

    The past decade has seen the publication of a large number of cell-cycle microarray studies and many more are in the pipeline. However, data from these experiments are not easy to access, combine and evaluate. We have developed a centralized database with an easy-to-use interface, Cyclebase...

  20. Valid and complete data on endometrial cancer in the Danish Gynaecological Cancer Database

    DEFF Research Database (Denmark)

    Juhl, Caroline S; Hansen, Estrid S; Høgdall, Claus K

    2014-01-01

    INTRODUCTION: It is a comparative register study designed for data validation of surgery, pathology and recurrence for endometrial cancer in the Danish Gynaecological Cancer Database (DGCD) in the 2005-2009 period. The main outcomes were completeness of the data registered in the DGCD, agreement...... concerning data reported and comparability between the DGCD and a definite reference. MATERIAL AND METHODS: DGCD data on women with endometrial cancer or adenomatous hyperplasia supplemented with patient charts for data on recurrence were retrieved and compared with a definite reference (the pathology report...... and clinical journals). RESULTS: The completeness of data on pathology and surgery reported to the DGCD was 97.3%. The comparability between the DGCG and the definite reference was 94.4%. The agreement for the reported data in the DGCD was 88.3%. For recurrence, the comparability was 94.5% and the agreement...

  1. Prevalence and Predictors of Neoadjuvant Therapy for Stage IIIA Non-Small Cell Lung Cancer in the National Cancer Database: Importance of Socioeconomic Status and Treating Institution

    Energy Technology Data Exchange (ETDEWEB)

    Sher, David J., E-mail: david_sher@rush.edu [Department of Radiation Oncology, Rush University Medical Center, Chicago, Illinois (United States); Liptay, Michael J. [Department of Cardiothoracic Surgery, Rush University Medical Center, Chicago, Illinois (United States); Fidler, Mary Jo [Section of Medical Oncology, Rush University Medical Center, Chicago, Illinois (United States)

    2014-06-01

    Purpose: The optimal locoregional therapy for stage IIIA non-small cell lung cancer (NSCLC) is controversial, with definitive chemoradiation therapy (CRT) and neoadjuvant therapy followed by surgery (NT-S) serving as competing strategies. In this study, we used the National Cancer Database to determine the prevalence and predictors of NT in a large, modern cohort of patients. Methods and Materials: Patients with stage IIIA NSCLC treated with CRT or NT-S between 2003 and 2010 at programs accredited by the Commission on Cancer were included. Predictors were categorized as clinical, time/geographic, socioeconomic, and institutional. In accord with the National Cancer Database, institutions were classified as academic/research program and as comprehensive and noncomprehensive community cancer centers. Logistic regression and random effects multilevel logistic regression were performed for univariable and multivariable analyses, respectively. Results: The cohort consisted of 18,581 patients, 3,087 (16.6%) of whom underwent NT-S (10.6% induction CRT, 6% induction chemotherapy). The prevalence of NT-S was constant over time, but there were significant relative 31% and 30% decreases in pneumonectomy and right-sided pneumonectomy, respectively, over time (P trend <.02). In addition to younger age, lower T stage, and favorable comorbidity score, indicators of higher socioeconomic status were strong independent predictors of NT-S, including white race, higher income, and private/managed insurance. The type of institution (academic/research program vs comprehensive or noncomprehensive community cancer centers, odds ratio 1.54 and 2.08, respectively) strongly predicted NT-S, but treatment volume did not. Conclusions: Neoadjuvant therapy followed by surgery was an uncommon treatment approach in Commission on Cancer programs, and the prevalence of postinduction pneumonectomy decreased over time. Higher socioeconomic status and treatment at academic institutions were significant

  2. Prevalence and Predictors of Neoadjuvant Therapy for Stage IIIA Non-Small Cell Lung Cancer in the National Cancer Database: Importance of Socioeconomic Status and Treating Institution

    International Nuclear Information System (INIS)

    Sher, David J.; Liptay, Michael J.; Fidler, Mary Jo

    2014-01-01

    Purpose: The optimal locoregional therapy for stage IIIA non-small cell lung cancer (NSCLC) is controversial, with definitive chemoradiation therapy (CRT) and neoadjuvant therapy followed by surgery (NT-S) serving as competing strategies. In this study, we used the National Cancer Database to determine the prevalence and predictors of NT in a large, modern cohort of patients. Methods and Materials: Patients with stage IIIA NSCLC treated with CRT or NT-S between 2003 and 2010 at programs accredited by the Commission on Cancer were included. Predictors were categorized as clinical, time/geographic, socioeconomic, and institutional. In accord with the National Cancer Database, institutions were classified as academic/research program and as comprehensive and noncomprehensive community cancer centers. Logistic regression and random effects multilevel logistic regression were performed for univariable and multivariable analyses, respectively. Results: The cohort consisted of 18,581 patients, 3,087 (16.6%) of whom underwent NT-S (10.6% induction CRT, 6% induction chemotherapy). The prevalence of NT-S was constant over time, but there were significant relative 31% and 30% decreases in pneumonectomy and right-sided pneumonectomy, respectively, over time (P trend <.02). In addition to younger age, lower T stage, and favorable comorbidity score, indicators of higher socioeconomic status were strong independent predictors of NT-S, including white race, higher income, and private/managed insurance. The type of institution (academic/research program vs comprehensive or noncomprehensive community cancer centers, odds ratio 1.54 and 2.08, respectively) strongly predicted NT-S, but treatment volume did not. Conclusions: Neoadjuvant therapy followed by surgery was an uncommon treatment approach in Commission on Cancer programs, and the prevalence of postinduction pneumonectomy decreased over time. Higher socioeconomic status and treatment at academic institutions were significant

  3. Toxic Substances Control Act test submissions database (TSCATS) - comprehensive update. Data file

    International Nuclear Information System (INIS)

    1993-01-01

    The Toxic Substances Control Act Test Submissions Database (TSCATS) was developed to make unpublished test data available to the public. The test data is submitted to the U.S. Environmental Protection Agency by industry under the Toxic Substances Control Act. Test is broadly defined to include case reports, episodic incidents, such as spills, and formal test study presentations. The database allows searching of test submissions according to specific chemical identity or type of study when used with an appropriate search retrieval software program. Studies are indexed under three broad subject areas: health effects, environmental effects and environmental fate. Additional controlled vocabulary terms are assigned which describe the experimental protocol and test observations. Records identify reference information needed to locate the source document, as well as the submitting organization and reason for submission of the test data

  4. Development of a Comprehensive Blast-Related Auditory Injury Database (BRAID)

    Science.gov (United States)

    2016-05-01

    servicemembers included in the Blast-Related Auditory Injury Database. * Training injuries, accidents, and other noncombat injuries. †3,452 injuries...medications, exposures to ototoxic chemicals, recreational noise exposure, and other forms of temporary and persistent threshold shift. Combat marines...AC, Vecchiotti M, Kujawa SG, Lee DJ, Quesnel AM. Otologic outcomes after blast injury: The Boston Marathon experience. Otol Neurotol. 2014; 35(10

  5. Use of Lidocaine Patches for Neuropathic Pain in a Comprehensive Cancer Centre

    Directory of Open Access Journals (Sweden)

    Julia Ann Fleming

    2009-01-01

    Full Text Available BACKGROUND: There are few reports of the use of the lidocaine 5% patch (L5%P for neuropathic pain (NP in the cancer patient. Within a comprehensive cancer centre, L5%P has been prescribed by the Pain and Palliative Care Service (Peter McCallum Cancer Centre, East Melbourne, Victoria, Australia for selected patients with NP since 2001.

  6. CellMiner: a relational database and query tool for the NCI-60 cancer cell lines

    Directory of Open Access Journals (Sweden)

    Reinhold William C

    2009-06-01

    Full Text Available Abstract Background Advances in the high-throughput omic technologies have made it possible to profile cells in a large number of ways at the DNA, RNA, protein, chromosomal, functional, and pharmacological levels. A persistent problem is that some classes of molecular data are labeled with gene identifiers, others with transcript or protein identifiers, and still others with chromosomal locations. What has lagged behind is the ability to integrate the resulting data to uncover complex relationships and patterns. Those issues are reflected in full form by molecular profile data on the panel of 60 diverse human cancer cell lines (the NCI-60 used since 1990 by the U.S. National Cancer Institute to screen compounds for anticancer activity. To our knowledge, CellMiner is the first online database resource for integration of the diverse molecular types of NCI-60 and related meta data. Description CellMiner enables scientists to perform advanced querying of molecular information on NCI-60 (and additional types through a single web interface. CellMiner is a freely available tool that organizes and stores raw and normalized data that represent multiple types of molecular characterizations at the DNA, RNA, protein, and pharmacological levels. Annotations for each project, along with associated metadata on the samples and datasets, are stored in a MySQL database and linked to the molecular profile data. Data can be queried and downloaded along with comprehensive information on experimental and analytic methods for each data set. A Data Intersection tool allows selection of a list of genes (proteins in common between two or more data sets and outputs the data for those genes (proteins in the respective sets. In addition to its role as an integrative resource for the NCI-60, the CellMiner package also serves as a shell for incorporation of molecular profile data on other cell or tissue sample types. Conclusion CellMiner is a relational database tool for

  7. Organization and Running of the First Comprehensive Hereditary Cancer Clinic in India

    Directory of Open Access Journals (Sweden)

    Rajkumar T

    2005-11-01

    Full Text Available Abstract Hereditary cancers are thought to account for around 5% of cancers, particularly breast/ovarian and colorectal cancers. In India there is a paucity of data on hereditary cancers and the mutations in some of the common genes linked to hereditary cancers, such as BRCA1, BRCA2, hMSH2 and hMLH1. The country's first comprehensive hereditary cancer clinic was established in February 2002. The article describes the organization and running of the Clinic. It also discusses some of the social issues relevant to the given population in running the Hereditary Cancer Clinic.

  8. Copenhagen uPAR prostate cancer (CuPCa) database

    DEFF Research Database (Denmark)

    Lippert, Solvej; Berg, Kasper D; Høyer-Hansen, Gunilla

    2016-01-01

    AIM: Urokinase plasminogen activator receptor (uPAR) plays a central role during cancer invasion by facilitating pericellular proteolysis. We initiated the prospective 'Copenhagen uPAR Prostate Cancer' study to investigate the significance of uPAR levels in prostate cancer (PCa) patients. METHODS...

  9. Consumer attitudes towards the establishment of a national Australian familial cancer research database by the Inherited Cancer Connect (ICCon) Partnership.

    Science.gov (United States)

    Forrest, Laura; Mitchell, Gillian; Thrupp, Letitia; Petelin, Lara; Richardson, Kate; Mascarenhas, Lyon; Young, Mary-Anne

    2018-01-01

    Clinical genetics units hold large amounts of information which could be utilised to benefit patients and their families. In Australia, a national research database, the Inherited Cancer Connect (ICCon) database, is being established that comprises clinical genetic data held for all carriers of mutations in cancer predisposition genes. Consumer input was sought to establish the acceptability of the inclusion of clinical genetic data into a research database. A qualitative approach using a modified nominal group technique was used to collect data through consumer forums conducted in three Australian states. Individuals who had previously received care from Familial Cancer Centres were invited to participate. Twenty-four consumers participated in three forums. Participants expressed positive attitudes about the establishment of the ICCon database, which were informed by the perceived benefits of the database including improved health outcomes for individuals with inherited cancer syndromes. Most participants were comfortable to waive consent for their clinical information to be included in the research database in a de-identified format. As major stakeholders, consumers have an integral role in contributing to the development and conduct of the ICCon database. As an initial step in the development of the ICCon database, the forums demonstrated consumers' acceptance of important aspects of the database including waiver of consent.

  10. In silico identification of anti-cancer compounds and plants from traditional Chinese medicine database

    Science.gov (United States)

    Dai, Shao-Xing; Li, Wen-Xing; Han, Fei-Fei; Guo, Yi-Cheng; Zheng, Jun-Juan; Liu, Jia-Qian; Wang, Qian; Gao, Yue-Dong; Li, Gong-Hua; Huang, Jing-Fei

    2016-05-01

    There is a constant demand to develop new, effective, and affordable anti-cancer drugs. The traditional Chinese medicine (TCM) is a valuable and alternative resource for identifying novel anti-cancer agents. In this study, we aim to identify the anti-cancer compounds and plants from the TCM database by using cheminformatics. We first predicted 5278 anti-cancer compounds from TCM database. The top 346 compounds were highly potent active in the 60 cell lines test. Similarity analysis revealed that 75% of the 5278 compounds are highly similar to the approved anti-cancer drugs. Based on the predicted anti-cancer compounds, we identified 57 anti-cancer plants by activity enrichment. The identified plants are widely distributed in 46 genera and 28 families, which broadens the scope of the anti-cancer drug screening. Finally, we constructed a network of predicted anti-cancer plants and approved drugs based on the above results. The network highlighted the supportive role of the predicted plant in the development of anti-cancer drug and suggested different molecular anti-cancer mechanisms of the plants. Our study suggests that the predicted compounds and plants from TCM database offer an attractive starting point and a broader scope to mine for potential anti-cancer agents.

  11. GenoBase: comprehensive resource database of Escherichia coli K-12.

    Science.gov (United States)

    Otsuka, Yuta; Muto, Ai; Takeuchi, Rikiya; Okada, Chihiro; Ishikawa, Motokazu; Nakamura, Koichiro; Yamamoto, Natsuko; Dose, Hitomi; Nakahigashi, Kenji; Tanishima, Shigeki; Suharnan, Sivasundaram; Nomura, Wataru; Nakayashiki, Toru; Aref, Walid G; Bochner, Barry R; Conway, Tyrrell; Gribskov, Michael; Kihara, Daisuke; Rudd, Kenneth E; Tohsato, Yukako; Wanner, Barry L; Mori, Hirotada

    2015-01-01

    Comprehensive experimental resources, such as ORFeome clone libraries and deletion mutant collections, are fundamental tools for elucidation of gene function. Data sets by omics analysis using these resources provide key information for functional analysis, modeling and simulation both in individual and systematic approaches. With the long-term goal of complete understanding of a cell, we have over the past decade created a variety of clone and mutant sets for functional genomics studies of Escherichia coli K-12. We have made these experimental resources freely available to the academic community worldwide. Accordingly, these resources have now been used in numerous investigations of a multitude of cell processes. Quality control is extremely important for evaluating results generated by these resources. Because the annotation has been changed since 2005, which we originally used for the construction, we have updated these genomic resources accordingly. Here, we describe GenoBase (http://ecoli.naist.jp/GB/), which contains key information about comprehensive experimental resources of E. coli K-12, their quality control and several omics data sets generated using these resources. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Soybean Proteome Database 2012: Update on the comprehensive data repository for soybean proteomics

    Directory of Open Access Journals (Sweden)

    Hajime eOhyanagi

    2012-05-01

    Full Text Available The Soybean Proteome Database (SPD was created to provide a data repository for functional analyses of soybean responses to flooding stress, thought to be a major constraint for establishment and production of this plant. Since the last publication of the SPD, we thoroughly enhanced the contents of database, particularly protein samples and their annotations from several organelles. The current release contains 23 reference maps of soybean (Glycine max cv. Enrei proteins collected from several organs, tissues and organelles including the maps for plasma membrane, cell wall, chloroplast and mitochondrion, which were electrophoresed on two-dimensional polyacrylamide gels. Furthermore, the proteins analyzed with gel-free proteomics technique have been added and available online. In addition to protein fluctuations under flooding, those of salt and drought stress have been included in the current release. An omics table also has been provided to reveal relationships among mRNAs, proteins and metabolites with a unified temporal-profile tag in order to facilitate retrieval of the data based on the temporal profiles. An intuitive user interface based on dynamic HTML enables users to browse the network as well as the profiles of multiple omes in an integrated fashion. The SPD is available at: http://proteome.dc.affrc.go.jp/Soybean/.

  13. DenHunt - A Comprehensive Database of the Intricate Network of Dengue-Human Interactions.

    Directory of Open Access Journals (Sweden)

    Prashanthi Karyala

    2016-09-01

    Full Text Available Dengue virus (DENV is a human pathogen and its etiology has been widely established. There are many interactions between DENV and human proteins that have been reported in literature. However, no publicly accessible resource for efficiently retrieving the information is yet available. In this study, we mined all publicly available dengue-human interactions that have been reported in the literature into a database called DenHunt. We retrieved 682 direct interactions of human proteins with dengue viral components, 382 indirect interactions and 4120 differentially expressed human genes in dengue infected cell lines and patients. We have illustrated the importance of DenHunt by mapping the dengue-human interactions on to the host interactome and observed that the virus targets multiple host functional complexes of important cellular processes such as metabolism, immune system and signaling pathways suggesting a potential role of these interactions in viral pathogenesis. We also observed that 7 percent of the dengue virus interacting human proteins are also associated with other infectious and non-infectious diseases. Finally, the understanding that comes from such analyses could be used to design better strategies to counteract the diseases caused by dengue virus. The whole dataset has been catalogued in a searchable database, called DenHunt (http://proline.biochem.iisc.ernet.in/DenHunt/.

  14. DenHunt - A Comprehensive Database of the Intricate Network of Dengue-Human Interactions.

    Science.gov (United States)

    Karyala, Prashanthi; Metri, Rahul; Bathula, Christopher; Yelamanchi, Syam K; Sahoo, Lipika; Arjunan, Selvam; Sastri, Narayan P; Chandra, Nagasuma

    2016-09-01

    Dengue virus (DENV) is a human pathogen and its etiology has been widely established. There are many interactions between DENV and human proteins that have been reported in literature. However, no publicly accessible resource for efficiently retrieving the information is yet available. In this study, we mined all publicly available dengue-human interactions that have been reported in the literature into a database called DenHunt. We retrieved 682 direct interactions of human proteins with dengue viral components, 382 indirect interactions and 4120 differentially expressed human genes in dengue infected cell lines and patients. We have illustrated the importance of DenHunt by mapping the dengue-human interactions on to the host interactome and observed that the virus targets multiple host functional complexes of important cellular processes such as metabolism, immune system and signaling pathways suggesting a potential role of these interactions in viral pathogenesis. We also observed that 7 percent of the dengue virus interacting human proteins are also associated with other infectious and non-infectious diseases. Finally, the understanding that comes from such analyses could be used to design better strategies to counteract the diseases caused by dengue virus. The whole dataset has been catalogued in a searchable database, called DenHunt (http://proline.biochem.iisc.ernet.in/DenHunt/).

  15. Incidental pulmonary embolism in cancer patients: clinical characteristics and outcome – a comprehensive cancer center experience

    Directory of Open Access Journals (Sweden)

    Abdel-Razeq H

    2011-03-01

    Full Text Available Hikmat N Abdel-Razeq1, Asem H Mansour2, Yousef M Ismael11Department of Internal Medicine, 2Department of Radiology, King Hussein Cancer Center, Amman, JordanBackground and objectives: Cancer patients undergo routine imaging studies much more than others. The widespread use of the recently introduced multi-detector CT scanners has resulted in an increasing number of incidentally diagnosed pulmonary embolism (PE in asymptomatic cancer patients. The significance and clinical outcome of such incidental PE is described.Methods: Both radiology department and hospital databases were searched for all cancer patients with a diagnosis of incidental PE. CT scans were performed using a 64-slice scanner with a 5.0 mm slice thickness.Results: During the study period, 34 patients with incidental PE were identified. The mean age (±SD was 57.7 (±12.4 years. All patients had active cancer, gastric, lung, colorectal, and lymphomas being the most frequent. Most patients had advanced-stage disease at the time of PE diagnosis; 26 (77% patients had stage IV, whereas only 3 patients had stages I or II disease. Twenty-seven (79% patients had their PE while undergoing active treatment with chemotherapy (68% or radiotherapy (12%; none, however, were on hormonal therapy. Most (74% patients had their PE diagnosed without history of recent hospital admission. Except for 5 (15%, all other patients were anticoagulated. With follow-up, 2 patients developed recurrent PE, 2 others had clinical and echocardiographic evidence of pulmonary hypertension, and 9 (26% died suddenly within 30 days of the diagnosis of incidental PE; 2 of these where among the 5 patients who were not anticoagulated.Conclusion: Incidental PE in cancer patients is increasingly encountered. Similar to symptomatic PE, many were diagnosed in patients with advanced stage disease and while undergoing active anti-cancer therapy. A significant percentage of patients had recurrent emboli, pulmonary hypertension

  16. A Comprehensive Database and Analysis Framework To Incorporate Multiscale Data Types and Enable Integrated Analysis of Bioactive Polyphenols.

    Science.gov (United States)

    Ho, Lap; Cheng, Haoxiang; Wang, Jun; Simon, James E; Wu, Qingli; Zhao, Danyue; Carry, Eileen; Ferruzzi, Mario G; Faith, Jeremiah; Valcarcel, Breanna; Hao, Ke; Pasinetti, Giulio M

    2018-03-05

    The development of a given botanical preparation for eventual clinical application requires extensive, detailed characterizations of the chemical composition, as well as the biological availability, biological activity, and safety profiles of the botanical. These issues are typically addressed using diverse experimental protocols and model systems. Based on this consideration, in this study we established a comprehensive database and analysis framework for the collection, collation, and integrative analysis of diverse, multiscale data sets. Using this framework, we conducted an integrative analysis of heterogeneous data from in vivo and in vitro investigation of a complex bioactive dietary polyphenol-rich preparation (BDPP) and built an integrated network linking data sets generated from this multitude of diverse experimental paradigms. We established a comprehensive database and analysis framework as well as a systematic and logical means to catalogue and collate the diverse array of information gathered, which is securely stored and added to in a standardized manner to enable fast query. We demonstrated the utility of the database in (1) a statistical ranking scheme to prioritize response to treatments and (2) in depth reconstruction of functionality studies. By examination of these data sets, the system allows analytical querying of heterogeneous data and the access of information related to interactions, mechanism of actions, functions, etc., which ultimately provide a global overview of complex biological responses. Collectively, we present an integrative analysis framework that leads to novel insights on the biological activities of a complex botanical such as BDPP that is based on data-driven characterizations of interactions between BDPP-derived phenolic metabolites and their mechanisms of action, as well as synergism and/or potential cancellation of biological functions. Out integrative analytical approach provides novel means for a systematic integrative

  17. Citrus sinensis annotation project (CAP): a comprehensive database for sweet orange genome.

    Science.gov (United States)

    Wang, Jia; Chen, Dijun; Lei, Yang; Chang, Ji-Wei; Hao, Bao-Hai; Xing, Feng; Li, Sen; Xu, Qiang; Deng, Xiu-Xin; Chen, Ling-Ling

    2014-01-01

    Citrus is one of the most important and widely grown fruit crop with global production ranking firstly among all the fruit crops in the world. Sweet orange accounts for more than half of the Citrus production both in fresh fruit and processed juice. We have sequenced the draft genome of a double-haploid sweet orange (C. sinensis cv. Valencia), and constructed the Citrus sinensis annotation project (CAP) to store and visualize the sequenced genomic and transcriptome data. CAP provides GBrowse-based organization of sweet orange genomic data, which integrates ab initio gene prediction, EST, RNA-seq and RNA-paired end tag (RNA-PET) evidence-based gene annotation. Furthermore, we provide a user-friendly web interface to show the predicted protein-protein interactions (PPIs) and metabolic pathways in sweet orange. CAP provides comprehensive information beneficial to the researchers of sweet orange and other woody plants, which is freely available at http://citrus.hzau.edu.cn/.

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

    Science.gov (United States)

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

    2016-01-04

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

  19. AT_CHLORO, a comprehensive chloroplast proteome database with subplastidial localization and curated information on envelope proteins.

    Science.gov (United States)

    Ferro, Myriam; Brugière, Sabine; Salvi, Daniel; Seigneurin-Berny, Daphné; Court, Magali; Moyet, Lucas; Ramus, Claire; Miras, Stéphane; Mellal, Mourad; Le Gall, Sophie; Kieffer-Jaquinod, Sylvie; Bruley, Christophe; Garin, Jérôme; Joyard, Jacques; Masselon, Christophe; Rolland, Norbert

    2010-06-01

    Recent advances in the proteomics field have allowed a series of high throughput experiments to be conducted on chloroplast samples, and the data are available in several public databases. However, the accurate localization of many chloroplast proteins often remains hypothetical. This is especially true for envelope proteins. We went a step further into the knowledge of the chloroplast proteome by focusing, in the same set of experiments, on the localization of proteins in the stroma, the thylakoids, and envelope membranes. LC-MS/MS-based analyses first allowed building the AT_CHLORO database (http://www.grenoble.prabi.fr/protehome/grenoble-plant-proteomics/), a comprehensive repertoire of the 1323 proteins, identified by 10,654 unique peptide sequences, present in highly purified chloroplasts and their subfractions prepared from Arabidopsis thaliana leaves. This database also provides extensive proteomics information (peptide sequences and molecular weight, chromatographic retention times, MS/MS spectra, and spectral count) for a unique chloroplast protein accurate mass and time tag database gathering identified peptides with their respective and precise analytical coordinates, molecular weight, and retention time. We assessed the partitioning of each protein in the three chloroplast compartments by using a semiquantitative proteomics approach (spectral count). These data together with an in-depth investigation of the literature were compiled to provide accurate subplastidial localization of previously known and newly identified proteins. A unique knowledge base containing extensive information on the proteins identified in envelope fractions was thus obtained, allowing new insights into this membrane system to be revealed. Altogether, the data we obtained provide unexpected information about plastidial or subplastidial localization of some proteins that were not suspected to be associated to this membrane system. The spectral counting-based strategy was further

  20. Comprehensive target populations for current active safety systems using national crash databases.

    Science.gov (United States)

    Kusano, Kristofer D; Gabler, Hampton C

    2014-01-01

    The objective of active safety systems is to prevent or mitigate collisions. A critical component in the design of active safety systems is the identification of the target population for a proposed system. The target population for an active safety system is that set of crashes that a proposed system could prevent or mitigate. Target crashes have scenarios in which the sensors and algorithms would likely activate. For example, the rear-end crash scenario, where the front of one vehicle contacts another vehicle traveling in the same direction and in the same lane as the striking vehicle, is one scenario for which forward collision warning (FCW) would be most effective in mitigating or preventing. This article presents a novel set of precrash scenarios based on coded variables from NHTSA's nationally representative crash databases in the United States. Using 4 databases (National Automotive Sampling System-General Estimates System [NASS-GES], NASS Crashworthiness Data System [NASS-CDS], Fatality Analysis Reporting System [FARS], and National Motor Vehicle Crash Causation Survey [NMVCCS]) the scenarios developed in this study can be used to quantify the number of police-reported crashes, seriously injured occupants, and fatalities that are applicable to proposed active safety systems. In this article, we use the precrash scenarios to identify the target populations for FCW, pedestrian crash avoidance systems (PCAS), lane departure warning (LDW), and vehicle-to-vehicle (V2V) or vehicle-to-infrastructure (V2I) systems. Crash scenarios were derived using precrash variables (critical event, accident type, precrash movement) present in all 4 data sources. This study found that these active safety systems could potentially mitigate approximately 1 in 5 of all severity and serious injury crashes in the United States and 26 percent of fatal crashes. Annually, this corresponds to 1.2 million all severity, 14,353 serious injury (MAIS 3+), and 7412 fatal crashes. In addition

  1. Discerning molecular interactions: A comprehensive review on biomolecular interaction databases and network analysis tools.

    Science.gov (United States)

    Miryala, Sravan Kumar; Anbarasu, Anand; Ramaiah, Sudha

    2018-02-05

    Computational analysis of biomolecular interaction networks is now gaining a lot of importance to understand the functions of novel genes/proteins. Gene interaction (GI) network analysis and protein-protein interaction (PPI) network analysis play a major role in predicting the functionality of interacting genes or proteins and gives an insight into the functional relationships and evolutionary conservation of interactions among the genes. An interaction network is a graphical representation of gene/protein interactome, where each gene/protein is a node, and interaction between gene/protein is an edge. In this review, we discuss the popular open source databases that serve as data repositories to search and collect protein/gene interaction data, and also tools available for the generation of interaction network, visualization and network analysis. Also, various network analysis approaches like topological approach and clustering approach to study the network properties and functional enrichment server which illustrates the functions and pathway of the genes and proteins has been discussed. Hence the distinctive attribute mentioned in this review is not only to provide an overview of tools and web servers for gene and protein-protein interaction (PPI) network analysis but also to extract useful and meaningful information from the interaction networks. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. A comprehensive database of the geographic spread of past human Ebola outbreaks

    Science.gov (United States)

    Mylne, Adrian; Brady, Oliver J.; Huang, Zhi; Pigott, David M.; Golding, Nick; Kraemer, Moritz U.G.; Hay, Simon I.

    2014-01-01

    Ebola is a zoonotic filovirus that has the potential to cause outbreaks of variable magnitude in human populations. This database collates our existing knowledge of all known human outbreaks of Ebola for the first time by extracting details of their suspected zoonotic origin and subsequent human-to-human spread from a range of published and non-published sources. In total, 22 unique Ebola outbreaks were identified, composed of 117 unique geographic transmission clusters. Details of the index case and geographic spread of secondary and imported cases were recorded as well as summaries of patient numbers and case fatality rates. A brief text summary describing suspected routes and means of spread for each outbreak was also included. While we cannot yet include the ongoing Guinea and DRC outbreaks until they are over, these data and compiled maps can be used to gain an improved understanding of the initial spread of past Ebola outbreaks and help evaluate surveillance and control guidelines for limiting the spread of future epidemics. PMID:25984346

  3. Human transporter database: comprehensive knowledge and discovery tools in the human transporter genes.

    Directory of Open Access Journals (Sweden)

    Adam Y Ye

    Full Text Available Transporters are essential in homeostatic exchange of endogenous and exogenous substances at the systematic, organic, cellular, and subcellular levels. Gene mutations of transporters are often related to pharmacogenetics traits. Recent developments in high throughput technologies on genomics, transcriptomics and proteomics allow in depth studies of transporter genes in normal cellular processes and diverse disease conditions. The flood of high throughput data have resulted in urgent need for an updated knowledgebase with curated, organized, and annotated human transporters in an easily accessible way. Using a pipeline with the combination of automated keywords query, sequence similarity search and manual curation on transporters, we collected 1,555 human non-redundant transporter genes to develop the Human Transporter Database (HTD (http://htd.cbi.pku.edu.cn. Based on the extensive annotations, global properties of the transporter genes were illustrated, such as expression patterns and polymorphisms in relationships with their ligands. We noted that the human transporters were enriched in many fundamental biological processes such as oxidative phosphorylation and cardiac muscle contraction, and significantly associated with Mendelian and complex diseases such as epilepsy and sudden infant death syndrome. Overall, HTD provides a well-organized interface to facilitate research communities to search detailed molecular and genetic information of transporters for development of personalized medicine.

  4. A comprehensive database of the geographic spread of past human Ebola outbreaks.

    Science.gov (United States)

    Mylne, Adrian; Brady, Oliver J; Huang, Zhi; Pigott, David M; Golding, Nick; Kraemer, Moritz U G; Hay, Simon I

    2014-01-01

    Ebola is a zoonotic filovirus that has the potential to cause outbreaks of variable magnitude in human populations. This database collates our existing knowledge of all known human outbreaks of Ebola for the first time by extracting details of their suspected zoonotic origin and subsequent human-to-human spread from a range of published and non-published sources. In total, 22 unique Ebola outbreaks were identified, composed of 117 unique geographic transmission clusters. Details of the index case and geographic spread of secondary and imported cases were recorded as well as summaries of patient numbers and case fatality rates. A brief text summary describing suspected routes and means of spread for each outbreak was also included. While we cannot yet include the ongoing Guinea and DRC outbreaks until they are over, these data and compiled maps can be used to gain an improved understanding of the initial spread of past Ebola outbreaks and help evaluate surveillance and control guidelines for limiting the spread of future epidemics.

  5. Clinical and mutational characteristics of Duchenne muscular dystrophy patients based on a comprehensive database in South China.

    Science.gov (United States)

    Wang, Dan-Ni; Wang, Zhi-Qiang; Yan, Lei; He, Jin; Lin, Min-Ting; Chen, Wan-Jin; Wang, Ning

    2017-08-01

    The development of clinical trials for Duchenne muscular dystrophy (DMD) in China faces many challenges due to limited information about epidemiological data, natural history and clinical management. To provide these detailed data, we developed a comprehensive database based on registered DMD patients from South China and analysed their clinical and mutational characteristics. The database included DMD registrants confirmed by clinical presentation, family history, genetic detection, prognostic outcome, and/or muscle biopsy. Clinical data were collected by a registry form. Mutations of dystrophin were detected by multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing. Currently, 132 DMD patients from 128 families in South China have been registered, and 91.7% of them were below 10 years old. In mutational detection, large deletions were the most frequent type (57.8%), followed by small deletion/insertion mutations (14.1%), nonsense mutations (13.3%), large duplications (10.9%), and splice site mutations (3.1%). Clinical analysis revealed that most patients reported initial symptoms between 1 and 3 years of age, but the diagnostic age was more frequently between 6 and 8 years. 81.4% of patients were ambulatory. Baseline cardiac assessments at diagnosis were conducted in 39.4% and 29.5% of patients by echocardiograms and electrocardiograms, respectively. Only 22.7% of registrants performed baseline respiratory assessments. A small numbers of patients (20.5%) were treated with glucocorticoids. 13.3% of patients were eligible for stop codon read-through therapy, and 48.4% of patients would potentially benefit from exon skipping. The top five exon skips applicable to the largest group of registrants were skipping of exons 51 (14.8% of total mutations), 53 (12.5%), 45 (7.0%), 55 (4.7%), and 44 (3.9%). In conclusion, our database provided information on the natural history, diagnosis and management status of DMD in South China, as well as potential

  6. The identification of incident cancers in UK primary care databases : a systematic review

    NARCIS (Netherlands)

    Rañopa, Michael; Douglas, Ian; van Staa, Tjeerd; Smeeth, Liam; Klungel, Olaf; Reynolds, Robert; Bhaskaran, Krishnan

    2015-01-01

    PURPOSE: UK primary care databases are frequently used in observational studies with cancer outcomes. We aimed to systematically review methods used by such studies to identify and validate incident cancers of the breast, colorectum, and prostate. METHODS: Medline and Embase (1980-2013) were

  7. Melanoma of the Skin in the Danish Cancer Registry and the Danish Melanoma Database: A Validation Study.

    Science.gov (United States)

    Pedersen, Sidsel Arnspang; Schmidt, Sigrun Alba Johannesdottir; Klausen, Siri; Pottegård, Anton; Friis, Søren; Hölmich, Lisbet Rosenkrantz; Gaist, David

    2018-05-01

    The nationwide Danish Cancer Registry and the Danish Melanoma Database both record data on melanoma for purposes of monitoring, quality assurance, and research. However, the data quality of the Cancer Registry and the Melanoma Database has not been formally evaluated. We estimated the positive predictive value (PPV) of melanoma diagnosis for random samples of 200 patients from the Cancer Registry (n = 200) and the Melanoma Database (n = 200) during 2004-2014, using the Danish Pathology Registry as "gold standard" reference. We further validated tumor characteristics in the Cancer Registry and the Melanoma Database. Additionally, we estimated the PPV of in situ melanoma diagnoses in the Melanoma Database, and the sensitivity of melanoma diagnoses in 2004-2014. The PPVs of melanoma in the Cancer Registry and the Melanoma Database were 97% (95% CI = 94, 99) and 100%. The sensitivity was 90% in the Cancer Registry and 77% in the Melanoma Database. The PPV of in situ melanomas in the Melanoma Database was 97% and the sensitivity was 56%. In the Melanoma Database, we observed PPVs of ulceration of 75% and Breslow thickness of 96%. The PPV of histologic subtypes varied between 87% and 100% in the Cancer Registry and 93% and 100% in the Melanoma Database. The PPVs for anatomical localization were 83%-95% in the Cancer Registry and 93%-100% in the Melanoma Database. The data quality in both the Cancer Registry and the Melanoma Database is high, supporting their use in epidemiologic studies.

  8. Evaluation of algorithms to identify incident cancer cases by using French health administrative databases.

    Science.gov (United States)

    Ajrouche, Aya; Estellat, Candice; De Rycke, Yann; Tubach, Florence

    2017-08-01

    Administrative databases are increasingly being used in cancer observational studies. Identifying incident cancer in these databases is crucial. This study aimed to develop algorithms to estimate cancer incidence by using health administrative databases and to examine the accuracy of the algorithms in terms of national cancer incidence rates estimated from registries. We identified a cohort of 463 033 participants on 1 January 2012 in the Echantillon Généraliste des Bénéficiaires (EGB; a representative sample of the French healthcare insurance system). The EGB contains data on long-term chronic disease (LTD) status, reimbursed outpatient treatments and procedures, and hospitalizations (including discharge diagnoses, and costly medical procedures and drugs). After excluding cases of prevalent cancer, we applied 15 algorithms to estimate the cancer incidence rates separately for men and women in 2012 and compared them to the national cancer incidence rates estimated from French registries by indirect age and sex standardization. The most accurate algorithm for men combined information from LTD status, outpatient anticancer drugs, radiotherapy sessions and primary or related discharge diagnosis of cancer, although it underestimated the cancer incidence (standardized incidence ratio (SIR) 0.85 [0.80-0.90]). For women, the best algorithm used the same definition of the algorithm for men but restricted hospital discharge to only primary or related diagnosis with an additional inpatient procedure or drug reimbursement related to cancer and gave comparable estimates to those from registries (SIR 1.00 [0.94-1.06]). The algorithms proposed could be used for cancer incidence monitoring and for future etiological cancer studies involving French healthcare databases. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  9. Cancer, Fertility Preservation, and Future Pregnancy: A Comprehensive Review

    OpenAIRE

    Matthews, Michelle L.; Hurst, Bradley S.; Marshburn, Paul B.; Usadi, Rebecca S.; Papadakis, Margaret A.; Sarantou, Terry

    2012-01-01

    Given the increases in 5-year cancer survival and recent advances in fertility preserving technologies, an increasing number of women with cancer are presenting for discussion of fertility preserving options. This review will summarize the risk of infertility secondary to cancer treatment, available treatment options for fertility preservation, and techniques to reduce future risks for patients. Concerns that will be addressed include the risk of the medications and procedures, the potential ...

  10. Comprehensive Molecular Profiling of African-American Prostate Cancer to Inform on Prognosis and Disease Biology

    Science.gov (United States)

    2017-10-01

    including suggestions for reducing this burden to Department of Defense, Washington Headquarters Services, Directorate for Information Operations...2% Movember-Prostate Cancer Foundation $250,000/yr Challenge Award Interrogating DNA Repair Defects to Improve Management...Improve Treatment for Advanced Prostate Cancer Goal(s): Comprehensively interrogate DNA repair alterations in both AR-positive and AR-negative CRPC

  11. Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems.

    Science.gov (United States)

    Boué, Stéphanie; Talikka, Marja; Westra, Jurjen Willem; Hayes, William; Di Fabio, Anselmo; Park, Jennifer; Schlage, Walter K; Sewer, Alain; Fields, Brett; Ansari, Sam; Martin, Florian; Veljkovic, Emilija; Kenney, Renee; Peitsch, Manuel C; Hoeng, Julia

    2015-01-01

    With the wealth of publications and data available, powerful and transparent computational approaches are required to represent measured data and scientific knowledge in a computable and searchable format. We developed a set of biological network models, scripted in the Biological Expression Language, that reflect causal signaling pathways across a wide range of biological processes, including cell fate, cell stress, cell proliferation, inflammation, tissue repair and angiogenesis in the pulmonary and cardiovascular context. This comprehensive collection of networks is now freely available to the scientific community in a centralized web-based repository, the Causal Biological Network database, which is composed of over 120 manually curated and well annotated biological network models and can be accessed at http://causalbionet.com. The website accesses a MongoDB, which stores all versions of the networks as JSON objects and allows users to search for genes, proteins, biological processes, small molecules and keywords in the network descriptions to retrieve biological networks of interest. The content of the networks can be visualized and browsed. Nodes and edges can be filtered and all supporting evidence for the edges can be browsed and is linked to the original articles in PubMed. Moreover, networks may be downloaded for further visualization and evaluation. Database URL: http://causalbionet.com © The Author(s) 2015. Published by Oxford University Press.

  12. KoVariome: Korean National Standard Reference Variome database of whole genomes with comprehensive SNV, indel, CNV, and SV analyses.

    Science.gov (United States)

    Kim, Jungeun; Weber, Jessica A; Jho, Sungwoong; Jang, Jinho; Jun, JeHoon; Cho, Yun Sung; Kim, Hak-Min; Kim, Hyunho; Kim, Yumi; Chung, OkSung; Kim, Chang Geun; Lee, HyeJin; Kim, Byung Chul; Han, Kyudong; Koh, InSong; Chae, Kyun Shik; Lee, Semin; Edwards, Jeremy S; Bhak, Jong

    2018-04-04

    High-coverage whole-genome sequencing data of a single ethnicity can provide a useful catalogue of population-specific genetic variations, and provides a critical resource that can be used to more accurately identify pathogenic genetic variants. We report a comprehensive analysis of the Korean population, and present the Korean National Standard Reference Variome (KoVariome). As a part of the Korean Personal Genome Project (KPGP), we constructed the KoVariome database using 5.5 terabases of whole genome sequence data from 50 healthy Korean individuals in order to characterize the benign ethnicity-relevant genetic variation present in the Korean population. In total, KoVariome includes 12.7M single-nucleotide variants (SNVs), 1.7M short insertions and deletions (indels), 4K structural variations (SVs), and 3.6K copy number variations (CNVs). Among them, 2.4M (19%) SNVs and 0.4M (24%) indels were identified as novel. We also discovered selective enrichment of 3.8M SNVs and 0.5M indels in Korean individuals, which were used to filter out 1,271 coding-SNVs not originally removed from the 1,000 Genomes Project when prioritizing disease-causing variants. KoVariome health records were used to identify novel disease-causing variants in the Korean population, demonstrating the value of high-quality ethnic variation databases for the accurate interpretation of individual genomes and the precise characterization of genetic variations.

  13. Comprehensive analysis of NuMA variation in breast cancer

    Directory of Open Access Journals (Sweden)

    Aittomäki Kristiina

    2008-03-01

    Full Text Available Abstract Background A recent genome wide case-control association study identified NuMA region on 11q13 as a candidate locus for breast cancer susceptibility. Specifically, the variant Ala794Gly was suggested to be associated with increased risk of breast cancer. Methods In order to evaluate the NuMa gene for breast cancer susceptibility, we have here screened the entire coding region and exon-intron boundaries of NuMa in 92 familial breast cancer patients and constructed haplotypes of the identified variants. Five missense variants were further screened in 341 breast cancer cases with a positive family history and 368 controls. We examined the frequency of Ala794Gly in an extensive series of familial (n = 910 and unselected (n = 884 breast cancer cases and controls (n = 906, with a high power to detect the suggested breast cancer risk. We also tested if the variant is associated with histopathologic features of breast tumors. Results Screening of NuMA resulted in identification of 11 exonic variants and 12 variants in introns or untranslated regions. Five missense variants that were further screened in breast cancer cases with a positive family history and controls, were each carried on a unique haplotype. None of the variants, or the haplotypes represented by them, was associated with breast cancer risk although due to low power in this analysis, very low risk alleles may go unrecognized. The NuMA Ala794Gly showed no difference in frequency in the unselected breast cancer case series or familial case series compared to control cases. Furthermore, Ala794Gly did not show any significant association with histopathologic characteristics of the tumors, though Ala794Gly was slightly more frequent among unselected cases with lymph node involvement. Conclusion Our results do not support the role of NuMA variants as breast cancer susceptibility alleles.

  14. Comprehensive analysis of NuMA variation in breast cancer

    International Nuclear Information System (INIS)

    Kilpivaara, Outi; Rantanen, Matias; Tamminen, Anitta; Aittomäki, Kristiina; Blomqvist, Carl; Nevanlinna, Heli

    2008-01-01

    A recent genome wide case-control association study identified NuMA region on 11q13 as a candidate locus for breast cancer susceptibility. Specifically, the variant Ala794Gly was suggested to be associated with increased risk of breast cancer. In order to evaluate the NuMa gene for breast cancer susceptibility, we have here screened the entire coding region and exon-intron boundaries of NuMa in 92 familial breast cancer patients and constructed haplotypes of the identified variants. Five missense variants were further screened in 341 breast cancer cases with a positive family history and 368 controls. We examined the frequency of Ala794Gly in an extensive series of familial (n = 910) and unselected (n = 884) breast cancer cases and controls (n = 906), with a high power to detect the suggested breast cancer risk. We also tested if the variant is associated with histopathologic features of breast tumors. Screening of NuMA resulted in identification of 11 exonic variants and 12 variants in introns or untranslated regions. Five missense variants that were further screened in breast cancer cases with a positive family history and controls, were each carried on a unique haplotype. None of the variants, or the haplotypes represented by them, was associated with breast cancer risk although due to low power in this analysis, very low risk alleles may go unrecognized. The NuMA Ala794Gly showed no difference in frequency in the unselected breast cancer case series or familial case series compared to control cases. Furthermore, Ala794Gly did not show any significant association with histopathologic characteristics of the tumors, though Ala794Gly was slightly more frequent among unselected cases with lymph node involvement. Our results do not support the role of NuMA variants as breast cancer susceptibility alleles

  15. DDEC: Dragon database of genes implicated in esophageal cancer

    KAUST Repository

    Essack, Magbubah; Radovanovic, Aleksandar; Schaefer, Ulf; Schmeier, Sebastian; Seshadri, Sundararajan V; Christoffels, Alan; Kaur, Mandeep; Bajic, Vladimir B.

    2009-01-01

    expressed in EC are contained in the database. We extracted and analyzed the promoter regions of these genes and complemented gene-related information with transcription factors that potentially control them. We further, precompiled text-mined and data-mined

  16. dbEM: A database of epigenetic modifiers curated from cancerous and normal genomes

    Science.gov (United States)

    Singh Nanda, Jagpreet; Kumar, Rahul; Raghava, Gajendra P. S.

    2016-01-01

    We have developed a database called dbEM (database of Epigenetic Modifiers) to maintain the genomic information of about 167 epigenetic modifiers/proteins, which are considered as potential cancer targets. In dbEM, modifiers are classified on functional basis and comprise of 48 histone methyl transferases, 33 chromatin remodelers and 31 histone demethylases. dbEM maintains the genomic information like mutations, copy number variation and gene expression in thousands of tumor samples, cancer cell lines and healthy samples. This information is obtained from public resources viz. COSMIC, CCLE and 1000-genome project. Gene essentiality data retrieved from COLT database further highlights the importance of various epigenetic proteins for cancer survival. We have also reported the sequence profiles, tertiary structures and post-translational modifications of these epigenetic proteins in cancer. It also contains information of 54 drug molecules against different epigenetic proteins. A wide range of tools have been integrated in dbEM e.g. Search, BLAST, Alignment and Profile based prediction. In our analysis, we found that epigenetic proteins DNMT3A, HDAC2, KDM6A, and TET2 are highly mutated in variety of cancers. We are confident that dbEM will be very useful in cancer research particularly in the field of epigenetic proteins based cancer therapeutics. This database is available for public at URL: http://crdd.osdd.net/raghava/dbem.

  17. ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining.

    Science.gov (United States)

    Lee, Myunggyo; Lee, Kyubum; Yu, Namhee; Jang, Insu; Choi, Ikjung; Kim, Pora; Jang, Ye Eun; Kim, Byounggun; Kim, Sunkyu; Lee, Byungwook; Kang, Jaewoo; Lee, Sanghyuk

    2017-01-04

    Fusion gene is an important class of therapeutic targets and prognostic markers in cancer. ChimerDB is a comprehensive database of fusion genes encompassing analysis of deep sequencing data and manual curations. In this update, the database coverage was enhanced considerably by adding two new modules of The Cancer Genome Atlas (TCGA) RNA-Seq analysis and PubMed abstract mining. ChimerDB 3.0 is composed of three modules of ChimerKB, ChimerPub and ChimerSeq. ChimerKB represents a knowledgebase including 1066 fusion genes with manual curation that were compiled from public resources of fusion genes with experimental evidences. ChimerPub includes 2767 fusion genes obtained from text mining of PubMed abstracts. ChimerSeq module is designed to archive the fusion candidates from deep sequencing data. Importantly, we have analyzed RNA-Seq data of the TCGA project covering 4569 patients in 23 cancer types using two reliable programs of FusionScan and TopHat-Fusion. The new user interface supports diverse search options and graphic representation of fusion gene structure. ChimerDB 3.0 is available at http://ercsb.ewha.ac.kr/fusiongene/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Comprehensive Characterization of Cancer Driver Genes and Mutations

    NARCIS (Netherlands)

    Bailey, Matthew H.; Tokheim, Collin; Porta-Pardo, Eduard; Sengupta, Sohini; Bertrand, Denis; Weerasinghe, Amila; Colaprico, Antonio; Wendl, Michael C.; Kim, Jaegil; Reardon, Brendan; Ng, Patrick Kwok Shing; Jeong, Kang Jin; Cao, Song; Wang, Zixing; Gao, Jianjiong; Gao, Qingsong; Wang, Fang; Liu, Eric Minwei; Mularoni, Loris; Rubio-Perez, Carlota; Nagarajan, Niranjan; Cortés-Ciriano, Isidro; Zhou, Daniel Cui; Liang, Wen Wei; Hess, Julian M.; Yellapantula, Venkata D.; Tamborero, David; Gonzalez-Perez, Abel; Suphavilai, Chayaporn; Ko, Jia Yu; Khurana, Ekta; Park, Peter J.; Van Allen, Eliezer M.; Liang, Han; Caesar-Johnson, Samantha J.; Demchok, John A.; Felau, Ina; Kasapi, Melpomeni; Ferguson, Martin L.; Hutter, Carolyn M.; Sofia, Heidi J.; Tarnuzzer, Roy; Wang, Zhining; Yang, Liming; Zenklusen, Jean C.; Zhang, Jiashan (Julia); Chudamani, Sudha; Liu, Jia; Lolla, Laxmi; Naresh, Rashi; Pihl, Todd; Sun, Qiang; Wan, Yunhu; Wu, Ye; Cho, Juok; DeFreitas, Timothy; Frazer, Scott; Gehlenborg, Nils; Getz, Gad; Heiman, David I.; Kim, Jaegil; Lawrence, Michael S.; Lin, Pei; Meier, Sam; Noble, Michael S.; Saksena, Gordon; Voet, Doug; Zhang, Hailei; Bernard, Brady; Chambwe, Nyasha; Dhankani, Varsha; Knijnenburg, Theo; Kramer, Roger; Leinonen, Kalle; Liu, Yuexin; Miller, Michael; Reynolds, Sheila; Shmulevich, Ilya; Thorsson, Vesteinn; Zhang, Wei; Akbani, Rehan; Broom, Bradley M.; Hegde, Apurva M.; Ju, Zhenlin; Kanchi, Rupa S.; Korkut, Anil; Li, Jun; Liang, Han; Ling, Shiyun; Liu, Wenbin; Lu, Yiling; Mills, Gordon B.; Ng, Kwok Shing; Rao, Arvind; Ryan, Michael; Wang, Jing; Weinstein, John N.; Zhang, Jiexin; Abeshouse, Adam; Armenia, Joshua; Chakravarty, Debyani; Chatila, Walid K.; de Bruijn, Ino; Gao, Jianjiong; Gross, Benjamin E.; Heins, Zachary J.; Kundra, Ritika; La, Konnor; Ladanyi, Marc; Luna, Augustin; Nissan, Moriah G.; Ochoa, Angelica; Phillips, Sarah M.; Reznik, Ed; Sanchez-Vega, Francisco; Sander, Chris; Schultz, Nikolaus; Sheridan, Robert; Sumer, S. Onur; Sun, Yichao; Taylor, Barry S.; Wang, Jioajiao; Zhang, Hongxin; Anur, Pavana; Peto, Myron; Spellman, Paul; Benz, Christopher; Stuart, Joshua M.; Wong, Christopher K.; Yau, Christina; Hayes, D. Neil; Parker, Joel S.; Wilkerson, Matthew D.; Ally, Adrian; Balasundaram, Miruna; Bowlby, Reanne; Brooks, Denise; Carlsen, Rebecca; Chuah, Eric; Dhalla, Noreen; Holt, Robert; Jones, Steven J.M.; Kasaian, Katayoon; Lee, Darlene; Ma, Yussanne; Marra, Marco A.; Mayo, Michael; Moore, Richard A.; Mungall, Andrew J.; Mungall, Karen; Robertson, A. Gordon; Sadeghi, Sara; Schein, Jacqueline E.; Sipahimalani, Payal; Tam, Angela; Thiessen, Nina; Tse, Kane; Wong, Tina; Berger, Ashton C.; Beroukhim, Rameen; Cherniack, Andrew D.; Cibulskis, Carrie; Gabriel, Stacey B.; Gao, Galen F.; Ha, Gavin; Meyerson, Matthew; Schumacher, Steven E.; Shih, Juliann; Kucherlapati, Melanie H.; Kucherlapati, Raju S.; Baylin, Stephen; Cope, Leslie; Danilova, Ludmila; Bootwalla, Moiz S.; Lai, Phillip H.; Maglinte, Dennis T.; Van Den Berg, David J.; Weisenberger, Daniel J.; Auman, J. Todd; Balu, Saianand; Bodenheimer, Tom; Fan, Cheng; Hoadley, Katherine A.; Hoyle, Alan P.; Jefferys, Stuart R.; Jones, Corbin D.; Meng, Shaowu; Mieczkowski, Piotr A.; Mose, Lisle E.; Perou, Amy H.; Perou, Charles M.; Roach, Jeffrey; Shi, Yan; Simons, Janae V.; Skelly, Tara; Soloway, Matthew G.; Tan, Donghui; Veluvolu, Umadevi; Fan, Huihui; Hinoue, Toshinori; Laird, Peter W.; Shen, Hui; Zhou, Wanding; Bellair, Michelle; Chang, Kyle; Covington, Kyle; Creighton, Chad J.; Dinh, Huyen; Doddapaneni, Harsha Vardhan; Donehower, Lawrence A.; Drummond, Jennifer; Gibbs, Richard A.; Glenn, Robert; Hale, Walker; Han, Yi; Hu, Jianhong; Korchina, Viktoriya; Lee, Sandra; Lewis, Lora; Li, Wei; Liu, Xiuping; Morgan, Margaret; Morton, Donna; Muzny, Donna; Santibanez, Jireh; Sheth, Margi; Shinbrot, Eve; Wang, Linghua; Wang, Min; Wheeler, David; Xi, Liu; Zhao, Fengmei; Hess, Julian; Appelbaum, Elizabeth L.; Bailey, Matthew; Cordes, Matthew G.; Ding, Li; Fronick, Catrina C.; Fulton, Lucinda A.; Fulton, Robert S.; Kandoth, Cyriac; Mardis, Elaine R.; McLellan, Michael D.; Miller, Christopher A.; Schmidt, Heather K.; Wilson, Richard K.; Crain, Daniel; Curley, Erin; Gardner, Johanna; Lau, Kevin; Mallery, David; Morris, Scott; Paulauskis, Joseph; Penny, Robert; Shelton, Candace; Shelton, Troy; Sherman, Mark; Thompson, Eric; Yena, Peggy; Bowen, Jay; Gastier-Foster, Julie M.; Gerken, Mark; Leraas, Kristen M.; Lichtenberg, Tara M.; Ramirez, Nilsa C.; Wise, Lisa; Zmuda, Erik; Corcoran, Niall; Costello, Tony; Hovens, Christopher; Carvalho, Andre L.; de Carvalho, Ana C.; Fregnani, José H.; Longatto-Filho, Adhemar; Reis, Rui M.; Scapulatempo-Neto, Cristovam; Silveira, Henrique C.S.; Vidal, Daniel O.; Burnette, Andrew; Eschbacher, Jennifer; Hermes, Beth; Noss, Ardene; Singh, Rosy; Anderson, Matthew L.; Castro, Patricia D.; Ittmann, Michael; Huntsman, David; Kohl, Bernard; Le, Xuan; Thorp, Richard; Andry, Chris; Duffy, Elizabeth R.; Lyadov, Vladimir; Paklina, Oxana; Setdikova, Galiya; Shabunin, Alexey; Tavobilov, Mikhail; McPherson, Christopher; Warnick, Ronald; Berkowitz, Ross; Cramer, Daniel; Feltmate, Colleen; Horowitz, Neil; Kibel, Adam; Muto, Michael; Raut, Chandrajit P.; Malykh, Andrei; Barnholtz-Sloan, Jill S.; Barrett, Wendi; Devine, Karen; Fulop, Jordonna; Ostrom, Quinn T.; Shimmel, Kristen; Wolinsky, Yingli; Sloan, Andrew E.; De Rose, Agostino; Giuliante, Felice; Goodman, Marc; Karlan, Beth Y.; Hagedorn, Curt H.; Eckman, John; Harr, Jodi; Myers, Jerome; Tucker, Kelinda; Zach, Leigh Anne; Deyarmin, Brenda; Hu, Hai; Kvecher, Leonid; Larson, Caroline; Mural, Richard J.; Somiari, Stella; Vicha, Ales; Zelinka, Tomas; Bennett, Joseph; Iacocca, Mary; Rabeno, Brenda; Swanson, Patricia; Latour, Mathieu; Lacombe, Louis; Têtu, Bernard; Bergeron, Alain; McGraw, Mary; Staugaitis, Susan M.; Chabot, John; Hibshoosh, Hanina; Sepulveda, Antonia; Su, Tao; Wang, Timothy; Potapova, Olga; Voronina, Olga; Desjardins, Laurence; Mariani, Odette; Roman-Roman, Sergio; Sastre, Xavier; Stern, Marc Henri; Cheng, Feixiong; Signoretti, Sabina; Berchuck, Andrew; Bigner, Darell; Lipp, Eric; Marks, Jeffrey; McCall, Shannon; McLendon, Roger; Secord, Angeles; Sharp, Alexis; Behera, Madhusmita; Brat, Daniel J.; Chen, Amy; Delman, Keith; Force, Seth; Khuri, Fadlo; Magliocca, Kelly; Maithel, Shishir; Olson, Jeffrey J.; Owonikoko, Taofeek; Pickens, Alan; Ramalingam, Suresh; Shin, Dong M.; Sica, Gabriel; Van Meir, Erwin G.; Zhang, Hongzheng; Eijckenboom, Wil; Gillis, Ad; Korpershoek, Esther; Looijenga, Leendert; Oosterhuis, Wolter; Stoop, Hans; van Kessel, Kim E.; Zwarthoff, Ellen C.; Calatozzolo, Chiara; Cuppini, Lucia; Cuzzubbo, Stefania; DiMeco, Francesco; Finocchiaro, Gaetano; Mattei, Luca; Perin, Alessandro; Pollo, Bianca; Chen, Chu; Houck, John; Lohavanichbutr, Pawadee; Hartmann, Arndt; Stoehr, Christine; Stoehr, Robert; Taubert, Helge; Wach, Sven; Wullich, Bernd; Kycler, Witold; Murawa, Dawid; Wiznerowicz, Maciej; Chung, Ki; Edenfield, W. Jeffrey; Martin, Julie; Baudin, Eric; Bubley, Glenn; Bueno, Raphael; De Rienzo, Assunta; Richards, William G.; Kalkanis, Steven; Mikkelsen, Tom; Noushmehr, Houtan; Scarpace, Lisa; Girard, Nicolas; Aymerich, Marta; Campo, Elias; Giné, Eva; Guillermo, Armando López; Van Bang, Nguyen; Hanh, Phan Thi; Phu, Bui Duc; Tang, Yufang; Colman, Howard; Evason, Kimberley; Dottino, Peter R.; Martignetti, John A.; Gabra, Hani; Juhl, Hartmut; Akeredolu, Teniola; Stepa, Serghei; Hoon, Dave; Ahn, Keunsoo; Kang, Koo Jeong; Beuschlein, Felix; Breggia, Anne; Birrer, Michael; Bell, Debra; Borad, Mitesh; Bryce, Alan H.; Castle, Erik; Chandan, Vishal; Cheville, John; Copland, John A.; Farnell, Michael; Flotte, Thomas; Giama, Nasra; Ho, Thai; Kendrick, Michael; Kocher, Jean Pierre; Kopp, Karla; Moser, Catherine; Nagorney, David; O'Brien, Daniel; O'Neill, Brian Patrick; Patel, Tushar; Petersen, Gloria; Que, Florencia; Rivera, Michael; Roberts, Lewis; Smallridge, Robert; Smyrk, Thomas; Stanton, Melissa; Thompson, R. Houston; Torbenson, Michael; Yang, Ju Dong; Zhang, Lizhi; Brimo, Fadi; Ajani, Jaffer A.; Gonzalez, Ana Maria Angulo; Behrens, Carmen; Bondaruk, Jolanta; Broaddus, Russell; Czerniak, Bogdan; Esmaeli, Bita; Fujimoto, Junya; Gershenwald, Jeffrey; Guo, Charles; Lazar, Alexander J.; Logothetis, Christopher; Meric-Bernstam, Funda; Moran, Cesar; Ramondetta, Lois; Rice, David; Sood, Anil; Tamboli, Pheroze; Thompson, Timothy; Troncoso, Patricia; Tsao, Anne; Wistuba, Ignacio; Carter, Candace; Haydu, Lauren; Hersey, Peter; Jakrot, Valerie; Kakavand, Hojabr; Kefford, Richard; Lee, Kenneth; Long, Georgina; Mann, Graham; Quinn, Michael; Saw, Robyn; Scolyer, Richard; Shannon, Kerwin; Spillane, Andrew; Stretch, Jonathan; Synott, Maria; Thompson, John; Wilmott, James; Al-Ahmadie, Hikmat; Chan, Timothy A.; Ghossein, Ronald; Gopalan, Anuradha; Levine, Douglas A.; Reuter, Victor; Singer, Samuel; Singh, Bhuvanesh; Tien, Nguyen Viet; Broudy, Thomas; Mirsaidi, Cyrus; Nair, Praveen; Drwiega, Paul; Miller, Judy; Smith, Jennifer; Zaren, Howard; Park, Joong Won; Hung, Nguyen Phi; Kebebew, Electron; Linehan, W. Marston; Metwalli, Adam R.; Pacak, Karel; Pinto, Peter A.; Schiffman, Mark; Schmidt, Laura S.; Vocke, Cathy D.; Wentzensen, Nicolas; Worrell, Robert; Yang, Hannah; Moncrieff, Marc; Goparaju, Chandra; Melamed, Jonathan; Pass, Harvey; Botnariuc, Natalia; Caraman, Irina; Cernat, Mircea; Chemencedji, Inga; Clipca, Adrian; Doruc, Serghei; Gorincioi, Ghenadie; Mura, Sergiu; Pirtac, Maria; Stancul, Irina; Tcaciuc, Diana; Albert, Monique; Alexopoulou, Iakovina; Arnaout, Angel; Bartlett, John; Engel, Jay; Gilbert, Sebastien; Parfitt, Jeremy; Sekhon, Harman; Thomas, George; Rassl, Doris M.; Rintoul, Robert C.; Bifulco, Carlo; Tamakawa, Raina; Urba, Walter; Hayward, Nicholas; Timmers, Henri; Antenucci, Anna; Facciolo, Francesco; Grazi, Gianluca; Marino, Mirella; Merola, Roberta; de Krijger, Ronald; Gimenez-Roqueplo, Anne Paule; Piché, Alain; Chevalier, Simone; McKercher, Ginette; Birsoy, Kivanc; Barnett, Gene; Brewer, Cathy; Farver, Carol; Naska, Theresa; Pennell, Nathan A.; Raymond, Daniel; Schilero, Cathy; Smolenski, Kathy; Williams, Felicia; Morrison, Carl; Borgia, Jeffrey A.; Liptay, Michael J.; Pool, Mark; Seder, Christopher W.; Junker, Kerstin; Omberg, Larsson; Dinkin, Mikhail; Manikhas, George; Alvaro, Domenico; Bragazzi, Maria Consiglia; Cardinale, Vincenzo; Carpino, Guido; Gaudio, Eugenio; Chesla, David; Cottingham, Sandra; Dubina, Michael; Moiseenko, Fedor; Dhanasekaran, Renumathy; Becker, Karl Friedrich; Janssen, Klaus Peter; Slotta-Huspenina, Julia; Abdel-Rahman, Mohamed H.; Aziz, Dina; Bell, Sue; Cebulla, Colleen M.; Davis, Amy; Duell, Rebecca; Elder, J. Bradley; Hilty, Joe; Kumar, Bahavna; Lang, James; Lehman, Norman L.; Mandt, Randy; Nguyen, Phuong; Pilarski, Robert; Rai, Karan; Schoenfield, Lynn; Senecal, Kelly; Wakely, Paul; Hansen, Paul; Lechan, Ronald; Powers, James; Tischler, Arthur; Grizzle, William E.; Sexton, Katherine C.; Kastl, Alison; Henderson, Joel; Porten, Sima; Waldmann, Jens; Fassnacht, Martin; Asa, Sylvia L.; Schadendorf, Dirk; Couce, Marta; Graefen, Markus; Huland, Hartwig; Sauter, Guido; Schlomm, Thorsten; Simon, Ronald; Tennstedt, Pierre; Olabode, Oluwole; Nelson, Mark; Bathe, Oliver; Carroll, Peter R.; Chan, June M.; Disaia, Philip; Glenn, Pat; Kelley, Robin K.; Landen, Charles N.; Phillips, Joanna; Prados, Michael; Simko, Jeffry; Smith-McCune, Karen; VandenBerg, Scott; Roggin, Kevin; Fehrenbach, Ashley; Kendler, Ady; Sifri, Suzanne; Steele, Ruth; Jimeno, Antonio; Carey, Francis; Forgie, Ian; Mannelli, Massimo; Carney, Michael; Hernandez, Brenda; Campos, Benito; Herold-Mende, Christel; Jungk, Christin; Unterberg, Andreas; von Deimling, Andreas; Bossler, Aaron; Galbraith, Joseph; Jacobus, Laura; Knudson, Michael; Knutson, Tina; Ma, Deqin; Milhem, Mohammed; Sigmund, Rita; Godwin, Andrew K.; Madan, Rashna; Rosenthal, Howard G.; Adebamowo, Clement; Adebamowo, Sally N.; Boussioutas, Alex; Beer, David; Giordano, Thomas; Mes-Masson, Anne Marie; Saad, Fred; Bocklage, Therese; Landrum, Lisa; Mannel, Robert; Moore, Kathleen; Moxley, Katherine; Postier, Russel; Walker, Joan; Zuna, Rosemary; Feldman, Michael; Valdivieso, Federico; Dhir, Rajiv; Luketich, James; Pinero, Edna M.Mora; Quintero-Aguilo, Mario; Carlotti, Carlos Gilberto; Dos Santos, Jose Sebastião; Kemp, Rafael; Sankarankuty, Ajith; Tirapelli, Daniela; Catto, James; Agnew, Kathy; Swisher, Elizabeth; Creaney, Jenette; Robinson, Bruce; Shelley, Carl Simon; Godwin, Eryn M.; Kendall, Sara; Shipman, Cassaundra; Bradford, Carol; Carey, Thomas; Haddad, Andrea; Moyer, Jeffey; Peterson, Lisa; Prince, Mark; Rozek, Laura; Wolf, Gregory; Bowman, Rayleen; Fong, Kwun M.; Yang, Ian; Korst, Robert; Rathmell, W. Kimryn; Fantacone-Campbell, J. Leigh; Hooke, Jeffrey A.; Kovatich, Albert J.; Shriver, Craig D.; DiPersio, John; Drake, Bettina; Govindan, Ramaswamy; Heath, Sharon; Ley, Timothy; Van Tine, Brian; Westervelt, Peter; Rubin, Mark A.; Lee, Jung Il; Aredes, Natália D.; Mariamidze, Armaz; Lawrence, Michael S.; Godzik, Adam; Lopez-Bigas, Nuria; Stuart, Josh; Wheeler, David; Getz, Gad; Chen, Ken; Lazar, Alexander J.; Mills, Gordon B.; Karchin, Rachel; Ding, Li

    2018-01-01

    Identifying molecular cancer drivers is critical for precision oncology. Multiple advanced algorithms to identify drivers now exist, but systematic attempts to combine and optimize them on large datasets are few. We report a PanCancer and PanSoftware analysis spanning 9,423 tumor exomes (comprising

  19. A Comprehensive Nuclear Receptor Network for Breast Cancer Cells

    Directory of Open Access Journals (Sweden)

    Ralf Kittler

    2013-02-01

    Full Text Available In breast cancer, nuclear receptors (NRs play a prominent role in governing gene expression, have prognostic utility, and are therapeutic targets. We built a regulatory map for 24 NRs, six chromatin state markers, and 14 breast-cancer-associated transcription factors (TFs that are expressed in the breast cancer cell line MCF-7. The resulting network reveals a highly interconnected regulatory matrix where extensive crosstalk occurs among NRs and other breast -cancer-associated TFs. We show that large numbers of factors are coordinately bound to highly occupied target regions throughout the genome, and these regions are associated with active chromatin state and hormone-responsive gene expression. This network also provides a framework for stratifying and predicting patient outcomes, and we use it to show that the peroxisome proliferator-activated receptor delta binds to a set of genes also regulated by the retinoic acid receptors and whose expression is associated with poor prognosis in breast cancer.

  20. Impact of database quality in knowledge-based treatment planning for prostate cancer.

    Science.gov (United States)

    Wall, Phillip D H; Carver, Robert L; Fontenot, Jonas D

    2018-03-13

    This article investigates dose-volume prediction improvements in a common knowledge-based planning (KBP) method using a Pareto plan database compared with using a conventional, clinical plan database. Two plan databases were created using retrospective, anonymized data of 124 volumetric modulated arc therapy (VMAT) prostate cancer patients. The clinical plan database (CPD) contained planning data from each patient's clinically treated VMAT plan, which were manually optimized by various planners. The multicriteria optimization database (MCOD) contained Pareto-optimal plan data from VMAT plans created using a standardized multicriteria optimization protocol. Overlap volume histograms, incorporating fractional organ at risk volumes only within the treatment fields, were computed for each patient and used to match new patient anatomy to similar database patients. For each database patient, CPD and MCOD KBP predictions were generated for D 10 , D 30 , D 50 , D 65 , and D 80 of the bladder and rectum in a leave-one-out manner. Prediction achievability was evaluated through a replanning study on a subset of 31 randomly selected database patients using the best KBP predictions, regardless of plan database origin, as planning goals. MCOD predictions were significantly lower than CPD predictions for all 5 bladder dose-volumes and rectum D 50 (P = .004) and D 65 (P databases affects the performance and achievability of dose-volume predictions from a common knowledge-based planning approach for prostate cancer. Bladder and rectum dose-volume predictions derived from a database of standardized Pareto-optimal plans were compared with those derived from clinical plans manually designed by various planners. Dose-volume predictions from the Pareto plan database were significantly lower overall than those from the clinical plan database, without compromising achievability. Copyright © 2018 Elsevier Inc. All rights reserved.

  1. Comprehensive Genetic Characterization of Intraprostatic Chronic Inflammation and Prostate Cancer in African American Men

    Science.gov (United States)

    2017-09-01

    Response and Eradication of Androgen Receptor Amplification with High-dose Testosterone in Prostate Cancer ." Eur Urol 71(6): 997-998. Case Report...34 Prostate -specific Antigen Response and Eradication of Androgen Receptor Amplification with High-dose Testosterone in Prostate Cancer ." Eur Urol 71...AWARD NUMBER: W81XWH-15-1-0379 TITLE: Comprehensive genetic characterization of intraprostatic chronic inflammation and prostate cancer in

  2. Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets

    Directory of Open Access Journals (Sweden)

    Lemoine Nicholas R

    2007-11-01

    Full Text Available Abstract Background Pancreatic cancer is the 5th leading cause of cancer death in both males and females. In recent years, a wealth of gene and protein expression studies have been published broadening our understanding of pancreatic cancer biology. Due to the explosive growth in publicly available data from multiple different sources it is becoming increasingly difficult for individual researchers to integrate these into their current research programmes. The Pancreatic Expression database, a generic web-based system, is aiming to close this gap by providing the research community with an open access tool, not only to mine currently available pancreatic cancer data sets but also to include their own data in the database. Description Currently, the database holds 32 datasets comprising 7636 gene expression measurements extracted from 20 different published gene or protein expression studies from various pancreatic cancer types, pancreatic precursor lesions (PanINs and chronic pancreatitis. The pancreatic data are stored in a data management system based on the BioMart technology alongside the human genome gene and protein annotations, sequence, homologue, SNP and antibody data. Interrogation of the database can be achieved through both a web-based query interface and through web services using combined criteria from pancreatic (disease stages, regulation, differential expression, expression, platform technology, publication and/or public data (antibodies, genomic region, gene-related accessions, ontology, expression patterns, multi-species comparisons, protein data, SNPs. Thus, our database enables connections between otherwise disparate data sources and allows relatively simple navigation between all data types and annotations. Conclusion The database structure and content provides a powerful and high-speed data-mining tool for cancer research. It can be used for target discovery i.e. of biomarkers from body fluids, identification and analysis

  3. Comprehensive Evaluation of Altered Systemic Metabolism and Pancreatic Cancer Risk

    Science.gov (United States)

    2015-10-01

    09/08/15-08/31/19 0.96 cal. mo. NIH/NCI $168,300 A prospective investigation of the oral microbiome and pancreatic cancer 1.To perform a...and BWHS. 2.To evaluate racial differences in the oral microbiome using 165 AA and 165 EA controls (from the SCCS only), and to identify any racial...risk factors for pancreatic cancer (cigarette smoking, obesity, red meat and processed meat consumption, alcohol consumption, type 2 diabetes) and oral

  4. Targeted Therapy Database (TTD): a model to match patient's molecular profile with current knowledge on cancer biology.

    Science.gov (United States)

    Mocellin, Simone; Shrager, Jeff; Scolyer, Richard; Pasquali, Sandro; Verdi, Daunia; Marincola, Francesco M; Briarava, Marta; Gobbel, Randy; Rossi, Carlo; Nitti, Donato

    2010-08-10

    The efficacy of current anticancer treatments is far from satisfactory and many patients still die of their disease. A general agreement exists on the urgency of developing molecularly targeted therapies, although their implementation in the clinical setting is in its infancy. In fact, despite the wealth of preclinical studies addressing these issues, the difficulty of testing each targeted therapy hypothesis in the clinical arena represents an intrinsic obstacle. As a consequence, we are witnessing a paradoxical situation where most hypotheses about the molecular and cellular biology of cancer remain clinically untested and therefore do not translate into a therapeutic benefit for patients. To present a computational method aimed to comprehensively exploit the scientific knowledge in order to foster the development of personalized cancer treatment by matching the patient's molecular profile with the available evidence on targeted therapy. To this aim we focused on melanoma, an increasingly diagnosed malignancy for which the need for novel therapeutic approaches is paradigmatic since no effective treatment is available in the advanced setting. Relevant data were manually extracted from peer-reviewed full-text original articles describing any type of anti-melanoma targeted therapy tested in any type of experimental or clinical model. To this purpose, Medline, Embase, Cancerlit and the Cochrane databases were searched. We created a manually annotated database (Targeted Therapy Database, TTD) where the relevant data are gathered in a formal representation that can be computationally analyzed. Dedicated algorithms were set up for the identification of the prevalent therapeutic hypotheses based on the available evidence and for ranking treatments based on the molecular profile of individual patients. In this essay we describe the principles and computational algorithms of an original method developed to fully exploit the available knowledge on cancer biology with the

  5. Cancer, immunodeficiency and antiretroviral treatment: results from the Australian HIV Observational Database (AHOD).

    Science.gov (United States)

    Petoumenos, K; van Leuwen, M T; Vajdic, C M; Woolley, I; Chuah, J; Templeton, D J; Grulich, A E; Law, M G

    2013-02-01

    The objective of the study was to conduct a within-cohort assessment of risk factors for incident AIDS-defining cancers (ADCs) and non-ADCs (NADCs) within the Australian HIV Observational Database (AHOD). A total of 2181 AHOD registrants were linked to the National AIDS Registry/National HIV Database (NAR/NHD) and the Australian Cancer Registry to identify those with a notified cancer diagnosis. Included in the current analyses were cancers diagnosed after HIV infection. Risk factors for cancers were also assessed using logistic regression methods. One hundred and thirty-nine cancer cases were diagnosed after HIV infection among 129 patients. More than half the diagnoses (n = 68; 60%) were ADCs, of which 69% were Kaposi's sarcoma and 31% non-Hodgkin's lymphoma. Among the NADCs, the most common cancers were melanoma (n = 10), lung cancer (n = 6), Hodgkin's lymphoma (n = 5) and anal cancer (n = 5). Over a total of 21021 person-years (PY) of follow-up since HIV diagnosis, the overall crude cancer incidence rate for any cancer was 5.09/1000 PY. The overall rate of cancers decreased from 15.9/1000 PY [95% confidence interval (CI) 9.25-25.40/1000 PY] for CD4 counts 350 cells/μL. Lower CD4 cell count and prior AIDS diagnoses were significant predictors for both ADCs and NADCs. ADCs remain the predominant cancers in this population, although NADC rates have increased in the more recent time period. Immune deficiency is a risk factor for both ADCs and NADCs. © 2012 British HIV Association.

  6. Comprehensive Evaluation of Altered Systemic Metabolism and Pancreatic Cancer Risk

    Science.gov (United States)

    2016-10-01

    information. Send comments regarding this burden estimate or any other aspect of this collection of information, including suggestions for reducing...individuals provide extensive data on metabolic phenotypes, such as obesity and diabetes, and banked plasma samples for interrogation . The potential...banked plasma samples for interrogation . The potential impact of understanding the mechanisms underlying early pancreatic cancer growth is

  7. New procedures. Comprehensive staging of lung cancer by MRI

    International Nuclear Information System (INIS)

    Hintze, C.; Dinkel, J.; Biederer, J.; Heussel, C.P.; Puderbach, M.

    2010-01-01

    Lung cancer staging according to the TNM system is based on morphological assessment of the primary cancer, lymph nodes and metastases. All aspects of this important oncological classification are measurable with MRI. Pulmonary nodules can be detected at the clinically relevant size of 4-5 mm in diameter. The extent of mediastinal, hilar and supraclavicular lymph node affection can be assessed at the same time. The predominant metastatic spread to the adrenal glands and spine can be detected in coronal orientation during dedicated MRI of the lungs. Search focused whole body MRI completes the staging. Various additional MR imaging techniques provide further functional and clinically relevant information during a single examination. In the oncological context the most important techniques are imaging of perfusion and tumor motion. Functional MRI of the lungs complements the pure staging and improves surgical approaches and radiotherapy planning. (orig.) [de

  8. Toward a comprehensive and systematic methylome signature in colorectal cancers

    OpenAIRE

    Ashktorab, Hassan; Rahi, Hamed; Wansley, Daniel; Varma, Sudhir; Shokrani, Babak; Lee, Edward; Daremipouran, Mohammad; Laiyemo, Adeyinka; Goel, Ajay; Carethers, John M; Brim, Hassan

    2013-01-01

    CpG Island Methylator Phenotype (CIMP) is one of the underlying mechanisms in colorectal cancer (CRC). This study aimed to define a methylome signature in CRC through a methylation microarray analysis and a compilation of promising CIMP markers from the literature. Illumina HumanMethylation27 (IHM27) array data was generated and analyzed based on statistical differences in methylation data (1st approach) or based on overall differences in methylation percentages using lower 95% CI (2nd approa...

  9. Comprehensive visualization of paresthesia in breast cancer survivors.

    Science.gov (United States)

    Jud, Sebastian M; Hatko, Reinhard; Maihöfner, Christian; Bani, Mayada R; Schrauder, Michael G; Lux, Michael P; Beckmann, Matthias W; Bani, Gassan; Eder, Irina; Fasching, Peter A; Loehberg, Christian R; Rauh, Claudia; Hein, Alexander

    2014-07-01

    As breast cancer survivors are benefiting increasingly from advanced forms of therapy, the side effects of locoregional treatment in the adjuvant setting are becoming more and more important. This article presents a new method of assessing the spatial distribution of paresthesia in breast cancer survivors after different locoregional treatments. A structured questionnaire assessing paresthesia, with body pictograms for marking paresthesia areas, was completed by 343 breast cancer survivors. The image information was digitized, generating gray-scale summation images with numbers from 0, indicating black (100 % of the patients had paresthesia), to 255, indicating white (none had paresthesia). The resulting map visualization showed the locations of paresthesia on body pictograms. The group included patients who had undergone breast-conserving surgery (BCS) and mastectomy, and also patients who had received percutaneous and interstitial radiation. A total of 56.5 % of the patients stated that they had paresthesia. The paresthesia areas were distributed within the range suggested by clinical experience. Most patients stated that they had paresthesia in the upper outer quadrant and axilla. Patients who had undergone mastectomy or percutaneous radiotherapy appeared to have more paresthesia on some areas of the body surface. Patients who had undergone mastectomy indicated larger areas of paresthesia than those with BCS-4,066 pixels (px) vs. 2,275 px. Radiotherapy did not appear to influence the spatial distribution of paresthesia. Paresthesia is a common symptom after breast cancer treatment. This paper describes a new method of assessing this side effect to improve and individualize treatment for it in the future.

  10. From the endometrium physiology to a comprehensive strategy for the discovery of ovarian cancer biomarkers

    OpenAIRE

    Janos L. Tanyi; Nathalie Scholler

    2011-01-01

    The development of comprehensive strategies for biomarker discovery of gynecological cancers is needed. The unique physiology of the female genital track revolves around ovulatory cycles ending by the proteolysis of the endometrium triggered by progesterone decline during the last part of the luteal phase. Building on the known link between incessant ovulation and ovarian cancer, we hypothesize that life-long menstruations could damage neighboring organs such as fallopian tubes, ovaries and p...

  11. Melanoma of the skin in the Danish Cancer Registry and the Danish Melanoma Database

    DEFF Research Database (Denmark)

    Pedersen, Sidsel Arnspang; Schmidt, Sigrun Alba Johannesdottir; Klausen, Siri

    2018-01-01

    estimated the positive predictive value (PPV) of melanoma diagnosis for random samples of 200 patients from the Cancer Registry (n=200) and the Melanoma Database (n=200) during 2004-2014, using the Danish Pathology Registry as 'gold-standard' reference. We further validated tumor characteristics...

  12. Subject and authorship of records related to the Organization for Tropical Studies (OTS) in BINABITROP, a comprehensive database about Costa Rican biology.

    Science.gov (United States)

    Monge-Nájera, Julián; Nielsen-Muñoz, Vanessa; Azofeifa-Mora, Ana Beatriz

    2013-06-01

    BINABITROP is a bibliographical database of more than 38000 records about the ecosystems and organisms of Costa Rica. In contrast with commercial databases, such as Web of Knowledge and Scopus, which exclude most of the scientific journals published in tropical countries, BINABITROP is a comprehensive record of knowledge on the tropical ecosystems and organisms of Costa Rica. We analyzed its contents in three sites (La Selva, Palo Verde and Las Cruces) and recorded scientific field, taxonomic group and authorship. We found that most records dealt with ecology and systematics, and that most authors published only one article in the study period (1963-2011). Most research was published in four journals: Biotropica, Revista de Biología Tropical/ International Journal of Tropical Biology and Conservation, Zootaxa and Brenesia. This may be the first study of a such a comprehensive database for any case of tropical biology literature.

  13. Subject and authorship of records related to the Organization for Tropical Studies (OTS in BINABITROP, a comprehensive database about Costa Rican biology

    Directory of Open Access Journals (Sweden)

    Julián Monge-Nájera

    2013-06-01

    Full Text Available BINABITROP is a bibliographical database of more than 38 000 records about the ecosystems and organisms of Costa Rica. In contrast with commercial databases, such as Web of Knowledge and Scopus, which exclude most of the scientific journals published in tropical countries, BINABITROP is a comprehensive record of knowledge on the tropical ecosystems and organisms of Costa Rica. We analyzed its contents in three sites (La Selva, Palo Verde and Las Cruces and recorded scientific field, taxonomic group and authorship. We found that most records dealt with ecology and systematics, and that most authors published only one article in the study period (1963-2011. Most research was published in four journals: Biotropica, Revista de Biología Tropical/ International Journal of Tropical Biology and Conservation, Zootaxa and Brenesia. This may be the first study of a such a comprehensive database for any case of tropical biology literature.

  14. Comprehensive assessment of cancer patients' concerns and the association with quality of life.

    Science.gov (United States)

    Yokoo, Minori; Akechi, Tatsuo; Takayama, Tomoko; Karato, Atsuya; Kikuuchi, Yuki; Okamoto, Naoyuki; Katayama, Kayoko; Nakanotani, Takako; Ogawa, Asao

    2014-07-01

    Comprehensive assessment of perceived concerns can be used to guide supportive care appropriate to individual cancer patients. This study sought to determine the prevalence of cancer patients' concerns and the degree to which these concerns contribute to patients' quality of life. Participants were patients with all types of cancer, who completed an Internet survey questionnaire regarding comprehensive concerns about physical, psychological, psychosocial and economic aspects of having cancer. The questionnaire was based on the newly developed Comprehensive Concerns Assessment Tool and the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire. We obtained complete data from 807 patients. Factors related to 'self-management' concerns were the most common (61.2%), followed by concerns about 'psychological symptoms' (48.5%), 'medical information' (46.2%), 'daily living' (29.9%), 'pain' (17.6%), 'constipation' (15.6%) and other 'physical symptoms' (15.2%). Multiple regression analysis revealed that all concerns except those about 'medical information' significantly contributed to quality of life. Cancer patients' concerns were shown to be multidimensional and significantly associated with quality of life. Thus, assessment of patients' concerns should be multidimensional in nature, and a multidisciplinary care team should help patients improve their quality of life. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  15. The IARC TP53 mutation database: a resource for studying the significance of TP53 mutations in human cancers

    Directory of Open Access Journals (Sweden)

    Magali Olivier

    2007-02-01

    Full Text Available

    The tumor suppressor gene TP53 is frequently inactivated by gene mutations in many types of human sporadic cancers, and inherited TP53 mutations predispose to a wide spectrum of early-onset tumors (Li-Fraumeni et Li-Fraumenilike Syndromes. All TP53 gene variations (somatic and germline mutations, as well as polymorphisms that are reported in the scientific literature or in SNP databases are compiled in the IARC TP53 Database. This database provides structured data and analysis tools to study mutation patterns in human cancers and cell-lines and to investigate the clinical impact of mutations. It contains annotations related to the clinical and pathological characteristics of tumors, as well as the demographics and carcinogen exposure of patients. The IARC TP53 web site (http://www-p53.iarc.fr/ provides a search interface for the core database and includes a comprehensive user guide, a slideshow on TP53 mutations in human cancer, protocols and references for sequencing TP53 gene, and links to relevant publications and bioinformatics databases. The database interface allows download of entire data sets and propose various tools for the selection, analysis and downloads of specific sets of data according to user's query.

    Recently, new annotations on the functional properties of mutant p53 proteins have been integrated in this database. Indeed, the most frequent TP53 alterations observed in cancers (75% are missense mutations that result in the production of a mutant protein that differ from the wildtype by one single amino-acid. The characterization of the biological activities of these mutant proteins is thus very important. Over the last ten years, a great amount of systematic data has been generated from experimental assays performed in

  16. Psychosocial predictors of health outcomes in colorectal cancer: a comprehensive review.

    Science.gov (United States)

    Sales, Paulo M G; Carvalho, André F; McIntyre, Roger S; Pavlidis, Nicholas; Hyphantis, Thomas N

    2014-07-01

    A diagnosis of colorectal cancer (CRC) and its long-term treatment may lead to significant psychological distress and impaired health-related quality of life (HRQoL) for a significant proportion of patients. We searched the PubMed/MEDLINE electronic database for available literature on the associations between personality characteristics, depression, psychological distress and HRQoL in CRC. Additional references were identified through the citation tracking of the included articles. Recent evidence indicates that Type-D (distressed) personality may predict distress among CRC patients. Additionally, other personality traits, such as specific ego defense mechanisms, influence the coping responses and HRQoL. Although the presence of a stoma has been linked to the development of depressive symptoms and impairment in HRQoL in CRC patients, more prospective studies are necessary to confirm these associations. Sense of coherence (SOC) has both a moderating and mediating effect on health (especially mental health and HRQoL), and preliminary data indicate that SOC may be an independent predictor of CRC survival. The interplay between personality variables during the elaboration of "the impaired role" is complex, and the assessment of personality traits may be incorporated into a comprehensive psychosomatic evaluation of CRC patients. More well-designed prospective investigations are necessary to establish the contributory role of personality dimensions for the development of and protection from distress and impairment in the HRQoL of CRC patients, which could eventually lead to the development of psychosocial interventions that are personalized to this patient population (for example, manual-based psychotherapies). Copyright © 2014 Elsevier Ltd. All rights reserved.

  17. Comprehension of a Colon Cancer Pamphlet among American Adults at Least 50 Years of Age

    Science.gov (United States)

    Liu, Chiung-ju

    2010-01-01

    Objective: The purpose of this study was to identify determinants of comprehension of an educational pamphlet on colon cancer, by adults at least 50 years of age living in the United States. Design: Data were analysed from the "2003 National Assessment of Adult Literacy" survey. The survey was designed to assess functional English…

  18. The effect of nurse navigation on timeliness of breast cancer care at an academic comprehensive cancer center.

    Science.gov (United States)

    Basu, Mohua; Linebarger, Jared; Gabram, Sheryl G A; Patterson, Sharla Gayle; Amin, Miral; Ward, Kevin C

    2013-07-15

    A patient navigation process is required for accreditation by the National Accreditation Program for Breast Centers (NAPBC). Patient navigation has previously been shown to improve timely diagnosis in patients with breast cancer. This study sought to assess the effect of nurse navigation on timeliness of care following the diagnosis of breast cancer by comparing patients who were treated in a comprehensive cancer center with and without the assistance of nurse navigation. Navigation services were initiated at an NAPBC-accredited comprehensive breast center in July 2010. Two 9-month study intervals were chosen for comparison of timeliness of care: October 2009 through June 2010 and October 2010 through June 2011. All patients with breast cancer diagnosed in the cancer center with stage 0 to III disease during the 2 study periods were identified by retrospective cancer registry review. Time from diagnosis to initial oncology consultation was measured in business days, excluding holidays and weekends. Overall, 176 patients met inclusion criteria: 100 patients prior to and 76 patients following nurse navigation implementation. Nurse navigation was found to significantly shorten time to consultation for patients older than 60 years (B = -4.90, P = .0002). There was no change in timeliness for patients 31 to 60 years of age. Short-term analysis following navigation implementation showed decreased time to consultation for older patients, but not younger patients. Further studies are indicated to assess the long-term effects and durability of this quality improvement initiative. © 2013 American Cancer Society.

  19. A comprehensive review of prostate cancer brachytherapy: defining an optimal technique

    International Nuclear Information System (INIS)

    Vicini, Frank A.; Kini, Vijay R.; Edmundson, Gregory B.S.; Gustafson, Gary S.; Stromberg, Jannifer; Martinez, Alvaro

    1999-01-01

    Purpose: A comprehensive review of prostate cancer brachytherapy literature was performed to determine if an optimal method of implantation could be identified, and to compare and contrast techniques currently in use. Methods and Materials: A MEDLINE search was conducted to obtain all articles in the English language on prostate cancer brachytherapy from 1985 through 1998. Articles were reviewed and grouped to determine the primary technique of implantation, the method or philosophy of source placement and/or dose specification, the technique to evaluate implant quality, overall treatment results (based upon pretreatment prostate specific antigen, (PSA), and biochemical control) and clinical, pathological or biochemical outcome based upon implant quality. Results: A total of 178 articles were identified in the MEDLINE database. Of these, 53 studies discussed evaluable techniques of implantation and were used for this analysis. Of these studies, 52% used preoperative ultrasound to determine the target volume to be implanted, 16% used preoperative computerized tomography (CT) scans, and 18% placed seeds with an open surgical technique. An additional 11% of studies placed seeds or needles under ultrasound guidance using interactive real-time dosimetry. The number and distribution of radioactive sources to be implanted or the method used to prescribe dose was determined using nomograms in 27% of studies, a least squares optimization technique in 11%, or not stated in 35%. In the remaining 26%, sources were described as either uniformly, differentially, or peripherally placed in the gland. To evaluate implant quality, 28% of studies calculated some type of dose-volume histogram, 21% calculated the matched peripheral dose, 19% the minimum peripheral dose, 14% used some type of CT-based qualitative review and, in 18% of studies, no implant quality evaluation was mentioned. Six studies correlated outcome with implant dose. One study showed an association of implant dose

  20. Factors Affecting Adjuvant Therapy in Stage III Pancreatic Cancer—Analysis of the National Cancer Database

    Directory of Open Access Journals (Sweden)

    Mridula Krishnan

    2017-08-01

    Full Text Available Background: Adjuvant therapy after curative resection is associated with survival benefit in stage III pancreatic cancer. We analyzed the factors affecting the outcome of adjuvant therapy in stage III pancreatic cancer and compared overall survival with different modalities of adjuvant treatment. Methods: This is a retrospective study of patients with stage III pancreatic cancer listed in the National Cancer Database (NCDB who were diagnosed between 2004 and 2012. Patients were stratified based on adjuvant therapy they received. Unadjusted Kaplan-Meier and multivariable Cox regression analysis were performed. Results: We analyzed a cohort included 1731 patients who were recipients of adjuvant therapy for stage III pancreatic cancer within the limits of our database. Patients who received adjuvant chemoradiation had the longest postdiagnosis survival time, followed by patients who received adjuvant chemotherapy, and finally patients who received no adjuvant therapy. On multivariate analysis, advancing age and patients with Medicaid had worse survival, whereas Spanish origin and lower Charlson comorbidity score had better survival. Conclusions: Our study is the largest trial using the NCDB addressing the effects of adjuvant therapy specifically in stage III pancreatic cancer. Within the limits of our study, survival benefit with adjuvant therapy was more apparent with longer duration from date of diagnosis.

  1. Histologic heterogeneity of triple negative breast cancer: A National Cancer Centre Database analysis.

    Science.gov (United States)

    Mills, Matthew N; Yang, George Q; Oliver, Daniel E; Liveringhouse, Casey L; Ahmed, Kamran A; Orman, Amber G; Laronga, Christine; Hoover, Susan J; Khakpour, Nazanin; Costa, Ricardo L B; Diaz, Roberto

    2018-06-02

    Triple negative breast cancer (TNBC) is an aggressive disease, but recent studies have identified heterogeneity in patient outcomes. However, the utility of histologic subtyping in TNBC has not yet been well-characterised. This study utilises data from the National Cancer Center Database (NCDB) to complete the largest series to date investigating the prognostic importance of histology within TNBC. A total of 729,920 patients (pts) with invasive ductal carcinoma (IDC), metaplastic breast carcinoma (MBC), medullary breast carcinoma (MedBC), adenoid cystic carcinoma (ACC), invasive lobular carcinoma (ILC) or apocrine breast carcinoma (ABC) treated between 2004 and 2012 were identified in the NCDB. Of these, 89,222 pts with TNBC that received surgery were analysed. Kaplan-Meier analysis, log-rank testing and multivariate Cox proportional hazards regression were utilised with overall survival (OS) as the primary outcome. MBC (74.1%), MedBC (60.6%), ACC (75.7%), ABC (50.1%) and ILC (1.8%) had significantly different proportions of triple negativity when compared to IDC (14.0%, p < 0.001). TNBC predicted an inferior OS in IDC (p < 0.001) and ILC (p < 0.001). Lumpectomy and radiation (RT) were more common in MedBC (51.7%) and ACC (51.5%) and less common in MBC (33.1%) and ILC (25.4%), when compared to IDC (42.5%, p < 0.001). TNBC patients with MBC (HR 1.39, p < 0.001), MedBC (HR 0.42, p < 0.001) and ACC (HR 0.32, p = 0.003) differed significantly in OS when compared to IDC. Our results indicate that histologic heterogeneity in TNBC significantly informs patient outcomes and thus, has the potential to aid in the development of optimum personalised treatments. Copyright © 2018 Elsevier Ltd. All rights reserved.

  2. Online Cancer Information Seeking: Applying and Extending the Comprehensive Model of Information Seeking.

    Science.gov (United States)

    Van Stee, Stephanie K; Yang, Qinghua

    2017-10-30

    This study applied the comprehensive model of information seeking (CMIS) to online cancer information and extended the model by incorporating an exogenous variable: interest in online health information exchange with health providers. A nationally representative sample from the Health Information National Trends Survey 4 Cycle 4 was analyzed to examine the extended CMIS in predicting online cancer information seeking. Findings from a structural equation model supported most of the hypotheses derived from the CMIS, as well as the extension of the model related to interest in online health information exchange. In particular, socioeconomic status, beliefs, and interest in online health information exchange predicted utility. Utility, in turn, predicted online cancer information seeking, as did information-carrier characteristics. An unexpected but important finding from the study was the significant, direct relationship between cancer worry and online cancer information seeking. Theoretical and practical implications are discussed.

  3. NPACT: Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database.

    Science.gov (United States)

    Mangal, Manu; Sagar, Parul; Singh, Harinder; Raghava, Gajendra P S; Agarwal, Subhash M

    2013-01-01

    Plant-derived molecules have been highly valued by biomedical researchers and pharmaceutical companies for developing drugs, as they are thought to be optimized during evolution. Therefore, we have collected and compiled a central resource Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database (NPACT, http://crdd.osdd.net/raghava/npact/) that gathers the information related to experimentally validated plant-derived natural compounds exhibiting anti-cancerous activity (in vitro and in vivo), to complement the other databases. It currently contains 1574 compound entries, and each record provides information on their structure, manually curated published data on in vitro and in vivo experiments along with reference for users referral, inhibitory values (IC(50)/ED(50)/EC(50)/GI(50)), properties (physical, elemental and topological), cancer types, cell lines, protein targets, commercial suppliers and drug likeness of compounds. NPACT can easily be browsed or queried using various options, and an online similarity tool has also been made available. Further, to facilitate retrieval of existing data, each record is hyperlinked to similar databases like SuperNatural, Herbal Ingredients' Targets, Comparative Toxicogenomics Database, PubChem and NCI-60 GI(50) data.

  4. NPACT: Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database

    Science.gov (United States)

    Mangal, Manu; Sagar, Parul; Singh, Harinder; Raghava, Gajendra P. S.; Agarwal, Subhash M.

    2013-01-01

    Plant-derived molecules have been highly valued by biomedical researchers and pharmaceutical companies for developing drugs, as they are thought to be optimized during evolution. Therefore, we have collected and compiled a central resource Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database (NPACT, http://crdd.osdd.net/raghava/npact/) that gathers the information related to experimentally validated plant-derived natural compounds exhibiting anti-cancerous activity (in vitro and in vivo), to complement the other databases. It currently contains 1574 compound entries, and each record provides information on their structure, manually curated published data on in vitro and in vivo experiments along with reference for users referral, inhibitory values (IC50/ED50/EC50/GI50), properties (physical, elemental and topological), cancer types, cell lines, protein targets, commercial suppliers and drug likeness of compounds. NPACT can easily be browsed or queried using various options, and an online similarity tool has also been made available. Further, to facilitate retrieval of existing data, each record is hyperlinked to similar databases like SuperNatural, Herbal Ingredients’ Targets, Comparative Toxicogenomics Database, PubChem and NCI-60 GI50 data. PMID:23203877

  5. Development of a comprehensive list of criteria for evaluating consumer education materials on colorectal cancer screening.

    Science.gov (United States)

    Dreier, Maren; Borutta, Birgit; Seidel, Gabriele; Kreusel, Inga; Töppich, Jürgen; Bitzer, Eva M; Dierks, Marie-Luise; Walter, Ulla

    2013-09-13

    Appropriate patient information materials may support the consumer's decision to attend or not to attend colorectal cancer (CRC) screening tests (fecal occult blood test and screening colonoscopy). The aim of this study was to develop a list of criteria to assess whether written health information materials on CRC screening provide balanced, unbiased, quantified, understandable, and evidence-based health information (EBHI) about CRC and CRC screening. The list of criteria was developed based on recommendations and assessment tools for health information in the following steps: (1) Systematic literature search in 13 electronic databases (search period: 2000-2010) and completed by an Internet search (2) Extraction of identified criteria (3) Grouping of criteria into categories and domains (4) Compilation of a manual of adequate answers derived from systematic reviews and S3 guidelines (5) Review by external experts (6) Modification (7) Final discussion with external experts. Thirty-one publications on health information tools and recommendations were identified. The final list of criteria includes a total of 230 single criteria in three generic domains (formal issues, presentation and understandability, and neutrality and balance) and one CRC-specific domain. A multi-dimensional rating approach was used whenever appropriate (e.g., rating for the presence, correctness, presentation and level of evidence of information). Free text input was allowed to ensure the transparency of assessment. The answer manual proved to be essential to the rating process. Quantitative analyses can be made depending on the level and dimensions of criteria. This comprehensive list of criteria clearly has a wider range of evaluation than previous assessment tools. It is not intended as a final quality assessment tool, but as a first step toward thorough evaluation of specific information materials for their adherence to EBHI requirements. This criteria list may also be used to revise

  6. FARE-CAFE: a database of functional and regulatory elements of cancer-associated fusion events.

    Science.gov (United States)

    Korla, Praveen Kumar; Cheng, Jack; Huang, Chien-Hung; Tsai, Jeffrey J P; Liu, Yu-Hsuan; Kurubanjerdjit, Nilubon; Hsieh, Wen-Tsong; Chen, Huey-Yi; Ng, Ka-Lok

    2015-01-01

    Chromosomal translocation (CT) is of enormous clinical interest because this disorder is associated with various major solid tumors and leukemia. A tumor-specific fusion gene event may occur when a translocation joins two separate genes. Currently, various CT databases provide information about fusion genes and their genomic elements. However, no database of the roles of fusion genes, in terms of essential functional and regulatory elements in oncogenesis, is available. FARE-CAFE is a unique combination of CTs, fusion proteins, protein domains, domain-domain interactions, protein-protein interactions, transcription factors and microRNAs, with subsequent experimental information, which cannot be found in any other CT database. Genomic DNA information including, for example, manually collected exact locations of the first and second break points, sequences and karyotypes of fusion genes are included. FARE-CAFE will substantially facilitate the cancer biologist's mission of elucidating the pathogenesis of various types of cancer. This database will ultimately help to develop 'novel' therapeutic approaches. Database URL: http://ppi.bioinfo.asia.edu.tw/FARE-CAFE. © The Author(s) 2015. Published by Oxford University Press.

  7. Automated prostate cancer detection via comprehensive multi-parametric magnetic resonance imaging texture feature models

    International Nuclear Information System (INIS)

    Khalvati, Farzad; Wong, Alexander; Haider, Masoom A.

    2015-01-01

    Prostate cancer is the most common form of cancer and the second leading cause of cancer death in North America. Auto-detection of prostate cancer can play a major role in early detection of prostate cancer, which has a significant impact on patient survival rates. While multi-parametric magnetic resonance imaging (MP-MRI) has shown promise in diagnosis of prostate cancer, the existing auto-detection algorithms do not take advantage of abundance of data available in MP-MRI to improve detection accuracy. The goal of this research was to design a radiomics-based auto-detection method for prostate cancer via utilizing MP-MRI data. In this work, we present new MP-MRI texture feature models for radiomics-driven detection of prostate cancer. In addition to commonly used non-invasive imaging sequences in conventional MP-MRI, namely T2-weighted MRI (T2w) and diffusion-weighted imaging (DWI), our proposed MP-MRI texture feature models incorporate computed high-b DWI (CHB-DWI) and a new diffusion imaging modality called correlated diffusion imaging (CDI). Moreover, the proposed texture feature models incorporate features from individual b-value images. A comprehensive set of texture features was calculated for both the conventional MP-MRI and new MP-MRI texture feature models. We performed feature selection analysis for each individual modality and then combined best features from each modality to construct the optimized texture feature models. The performance of the proposed MP-MRI texture feature models was evaluated via leave-one-patient-out cross-validation using a support vector machine (SVM) classifier trained on 40,975 cancerous and healthy tissue samples obtained from real clinical MP-MRI datasets. The proposed MP-MRI texture feature models outperformed the conventional model (i.e., T2w+DWI) with regard to cancer detection accuracy. Comprehensive texture feature models were developed for improved radiomics-driven detection of prostate cancer using MP-MRI. Using a

  8. Unplanned 30-Day Readmissions in a General Internal Medicine Hospitalist Service at a Comprehensive Cancer Center.

    Science.gov (United States)

    Manzano, Joanna-Grace M; Gadiraju, Sahitya; Hiremath, Adarsh; Lin, Heather Yan; Farroni, Jeff; Halm, Josiah

    2015-09-01

    Hospital readmissions are considered by the Centers for Medicare and Medicaid as a metric for quality of health care delivery. Robust data on the readmission profile of patients with cancer are currently insufficient to determine whether this measure is applicable to cancer hospitals as well. To address this knowledge gap, we estimated the unplanned readmission rate and identified factors influencing unplanned readmissions in a hospitalist service at a comprehensive cancer center. We retrospectively analyzed unplanned 30-day readmission of patients discharged from the General Internal Medicine Hospitalist Service at a comprehensive cancer center between April 1, 2012, and September 30, 2012. Multiple independent variables were studied using univariable and multivariable logistic regression models, with generalized estimating equations to identify risk factors associated with readmissions. We observed a readmission rate of 22.6% in our cohort. The median time to unplanned readmission was 10 days. Unplanned readmission was more likely in patients with metastatic cancer and those with three or more comorbidities. Patients discharged to hospice were less likely to be readmitted (all P values quality measures in cancer hospitals. Copyright © 2015 by American Society of Clinical Oncology.

  9. Causes of death in long-term lung cancer survivors: a SEER database analysis.

    Science.gov (United States)

    Abdel-Rahman, Omar

    2017-07-01

    Long-term (>5 years) lung cancer survivors represent a small but distinct subgroup of lung cancer patients and information about the causes of death of this subgroup is scarce. The Surveillance, Epidemiology and End Results (SEER) database (1988-2008) was utilized to determine the causes of death of long-term survivors of lung cancer. Survival analysis was conducted using Kaplan-Meier analysis and multivariate analysis was conducted using a Cox proportional hazard model. Clinicopathological characteristics and survival outcomes were assessed for the whole cohort. A total of 78,701 lung cancer patients with >5 years survival were identified. This cohort included 54,488 patients surviving 5-10 years and 24,213 patients surviving >10 years. Among patients surviving 5-10 years, 21.8% were dead because of primary lung cancer, 10.2% were dead because of other cancers, 6.8% were dead because of cardiac disease and 5.3% were dead because of non-malignant pulmonary disease. Among patients surviving >10 years, 12% were dead because of primary lung cancer, 6% were dead because of other cancers, 6.9% were dead because of cardiac disease and 5.6% were dead because of non-malignant pulmonary disease. On multivariate analysis, factors associated with longer cardiac-disease-specific survival in multivariate analysis include younger age at diagnosis (p death from primary lung cancer is still significant among other causes of death even 20 years after diagnosis of lung cancer. Moreover, cardiac as well as non-malignant pulmonary causes contribute a considerable proportion of deaths in long-term lung cancer survivors.

  10. Improving quality of breast cancer surgery through development of a national breast cancer surgical outcomes (BRCASO research database

    Directory of Open Access Journals (Sweden)

    Aiello Bowles Erin J

    2012-04-01

    Full Text Available Abstract Background Common measures of surgical quality are 30-day morbidity and mortality, which poorly describe breast cancer surgical quality with extremely low morbidity and mortality rates. Several national quality programs have collected additional surgical quality measures; however, program participation is voluntary and results may not be generalizable to all surgeons. We developed the Breast Cancer Surgical Outcomes (BRCASO database to capture meaningful breast cancer surgical quality measures among a non-voluntary sample, and study variation in these measures across providers, facilities, and health plans. This paper describes our study protocol, data collection methods, and summarizes the strengths and limitations of these data. Methods We included 4524 women ≥18 years diagnosed with breast cancer between 2003-2008. All women with initial breast cancer surgery performed by a surgeon employed at the University of Vermont or three Cancer Research Network (CRN health plans were eligible for inclusion. From the CRN institutions, we collected electronic administrative data including tumor registry information, Current Procedure Terminology codes for breast cancer surgeries, surgeons, surgical facilities, and patient demographics. We supplemented electronic data with medical record abstraction to collect additional pathology and surgery detail. All data were manually abstracted at the University of Vermont. Results The CRN institutions pre-filled 30% (22 out of 72 of elements using electronic data. The remaining elements, including detailed pathology margin status and breast and lymph node surgeries, required chart abstraction. The mean age was 61 years (range 20-98 years; 70% of women were diagnosed with invasive ductal carcinoma, 20% with ductal carcinoma in situ, and 10% with invasive lobular carcinoma. Conclusions The BRCASO database is one of the largest, multi-site research resources of meaningful breast cancer surgical quality data

  11. The FREGAT biobank: a clinico-biological database dedicated to esophageal and gastric cancers.

    Science.gov (United States)

    Mariette, Christophe; Renaud, Florence; Piessen, Guillaume; Gele, Patrick; Copin, Marie-Christine; Leteurtre, Emmanuelle; Delaeter, Christine; Dib, Malek; Clisant, Stéphanie; Harter, Valentin; Bonnetain, Franck; Duhamel, Alain; Christophe, Véronique; Adenis, Antoine

    2018-02-06

    While the incidence of esophageal and gastric cancers is increasing, the prognosis of these cancers remains bleak. Endoscopy and surgery are the standard treatments for localized tumors, but multimodal treatments, associated chemotherapy, targeted therapies, immunotherapy, radiotherapy, and surgery are needed for the vast majority of patients who present with locally advanced or metastatic disease at diagnosis. Although survival has improved, most patients still present with advanced disease at diagnosis. In addition, most patients exhibit a poor or incomplete response to treatment, experience early recurrence and have an impaired quality of life. Compared with several other cancers, the therapeutic approach is not personalized, and research is much less developed. It is, therefore, urgent to hasten the development of research protocols, and consequently, develop a large, ambitious and innovative tool through which future scientific questions may be answered. This research must be patient-related so that rapid feedback to the bedside is achieved and should aim to identify clinical-, biological- and tumor-related factors that are associated with treatment resistance. Finally, this research should also seek to explain epidemiological and social facets of disease behavior. The prospective FREGAT database, established by the French National Cancer Institute, is focused on adult patients with carcinomas of the esophagus and stomach and on whatever might be the tumor stage or therapeutic strategy. The database includes epidemiological, clinical, and tumor characteristics data as well as follow-up, human and social sciences quality of life data, along with a tumor and serum bank. This innovative method of research will allow for the banking of millions of data for the development of excellent basic, translational and clinical research programs for esophageal and gastric cancer. This will ultimately improve general knowledge of these diseases, therapeutic strategies and

  12. A User's Guide to the Comprehensive Water Quality Database for Groundwater in the Vicinity of the Nevada Test Site, Rev. No.: 1

    International Nuclear Information System (INIS)

    Farnham, Irene

    2006-01-01

    This water quality database (viz.GeochemXX.mdb) has been developed as part of the Underground Test Area (UGTA) Program with the cooperation of several agencies actively participating in ongoing evaluation and characterization activities under contract to the U.S. Department of Energy (DOE), National Nuclear Security Administration Nevada Site Office (NNSA/NSO). The database has been constructed to provide up-to-date, comprehensive, and quality controlled data in a uniform format for the support of current and future projects. This database provides a valuable tool for geochemical and hydrogeologic evaluations of the Nevada Test Site (NTS) and surrounding region. Chemistry data have been compiled for groundwater within the NTS and the surrounding region. These data include major ions, organic compounds, trace elements, radionuclides, various field parameters, and environmental isotopes. Colloid data are also included in the database. The GeochemXX.mdb database is distributed on an annual basis. The extension ''XX'' within the database title is replaced by the last two digits of the release year (e.g., Geochem06 for the version released during the 2006 fiscal year). The database is distributed via compact disc (CD) and is also uploaded to the Common Data Repository (CDR) in order to make it available to all agencies with DOE intranet access. This report provides an explanation of the database configuration and summarizes the general content and utility of the individual data tables. In addition to describing the data, subsequent sections of this report provide the data user with an explanation of the quality assurance/quality control (QA/QC) protocols for this database

  13. Classification of a palliative care population in a comprehensive cancer centre

    DEFF Research Database (Denmark)

    Benthien, K.S; Nordly, M.; Videbæk, K.

    2016-01-01

    PURPOSE: The purposes of the present study were to classify the palliative care population (PCP) in a comprehensive cancer centre by using information on antineoplastic treatment options and to analyse associations between socio-demographic factors, cancer diagnoses, treatment characteristics...... and receiving specialist palliative care (SPC). METHODS: This is a cross-sectional screening study of patients with cancer in the Department of Oncology, Rigshospitalet, Copenhagen University Hospital for 6 months. Patients were assessed to be included in the DOMUS study: a randomised controlled trial...... of accelerated transition to SPC at home (NCT01885637). The PCP was classified as patients with incurable cancer and limited or no antineoplastic treatment options. Patients with performance status 2-4 were further classified as the essential palliative care population (EPCP). RESULTS: During the study period...

  14. Breast cancer screening with mammography as part of our comprehensive medical check-up

    International Nuclear Information System (INIS)

    Ishii, Kaname; Kaburaki, Tomonori; Iwata, Keiko; Tsuneda, Atsushi; Mori, Kazuhiro; Takeyama, Shigeru; Tsuji, Hiroshi

    2012-01-01

    In the breast cancer screening program adopted by our hospital's Health Care Center as part of a comprehensive medical check-up, mammography (MMG) is performed in addition to a clinical breast examination to provide better screening quality. The clinical breast examination is performed by our surgeons. Two-view MMG is performed for women in their 40's and one-view MMG for the others. If any abnormality is detected in the clinical breast examination, or if MMG reveals abnormalities of category 3 or over, a more thorough diagnostic work-up is recommended. Each year, 1,400 or more women undergo breast cancer screening at the center, with an average recall rate of 12% and an average breast cancer detection rate of 0.14%. The high recall rate indicates the need for improvement of screening accuracy. Although the breast cancer detection rate and positive predictive value are somewhat low, the majority of the detected cases are early-stage breast cancer, thus demonstrating the efficacy of the screening. Herein, we describe the current state of MMG screening in our comprehensive medical check-up, along with a discussion of the screening procedure. However, further efforts are needed to improve screening accuracy. (author)

  15. From the endometrium physiology to a comprehensive strategy for the discovery of ovarian cancer biomarkers

    Directory of Open Access Journals (Sweden)

    Janos L. Tanyi

    2011-12-01

    Full Text Available The development of comprehensive strategies for biomarker discovery of gynecological cancers is needed. The unique physiology of the female genital track revolves around ovulatory cycles ending by the proteolysis of the endometrium triggered by progesterone decline during the last part of the luteal phase. Building on the known link between incessant ovulation and ovarian cancer, we hypothesize that life-long menstruations could damage neighboring organs such as fallopian tubes, ovaries and peritoneum via endometrial secretions, and thus endometrium neighboring structures may have developed highly efficient protective strategies that could, in turn, be hijacked by cancer cells for survival and invasion. After literature review, we could classify the molecules involved in ovulation and menstruation pathways in three main categories: proteases, proteases inhibitors and cell-surface protectors. Strikingly, all validated biomarkers for ovarian cancers belong to at least one of these categories. We thus propose the development of comprehensive methods for identification of early diagnostic markers for gynecological cancers using systematical mapping and characterization of surface or soluble molecules belonging to physiological pathways linked to menstruation and differently expressed during luteal cycles.

  16. Service of Remembrance: a comprehensive cancer center's response to bereaved family members.

    Science.gov (United States)

    Knight, Louise; Cooper, Rhonda S; Hypki, Cinder

    2012-01-01

    Comprehensive cancer centers that offer an array of clinical trials and treatment options often experience significant patient mortality rates. Bereavement resources may not be routinely incorporated into the service delivery model in these specialty hospitals. In response, an interdisciplinary team at one cancer center proposed, planned, and implemented an annual Service of Remembrance. The incorporation of music, poetry, and visual arts was important in designing a program that would provide a meaningful, spiritual experience. A community artist who designed an interactive memorial art piece played a pivotal role. This article outlines the process of institutional culture change and describes future challenges in the implementation of this type of bereavement service.

  17. Targeted Therapy Database (TTD: a model to match patient's molecular profile with current knowledge on cancer biology.

    Directory of Open Access Journals (Sweden)

    Simone Mocellin

    Full Text Available BACKGROUND: The efficacy of current anticancer treatments is far from satisfactory and many patients still die of their disease. A general agreement exists on the urgency of developing molecularly targeted therapies, although their implementation in the clinical setting is in its infancy. In fact, despite the wealth of preclinical studies addressing these issues, the difficulty of testing each targeted therapy hypothesis in the clinical arena represents an intrinsic obstacle. As a consequence, we are witnessing a paradoxical situation where most hypotheses about the molecular and cellular biology of cancer remain clinically untested and therefore do not translate into a therapeutic benefit for patients. OBJECTIVE: To present a computational method aimed to comprehensively exploit the scientific knowledge in order to foster the development of personalized cancer treatment by matching the patient's molecular profile with the available evidence on targeted therapy. METHODS: To this aim we focused on melanoma, an increasingly diagnosed malignancy for which the need for novel therapeutic approaches is paradigmatic since no effective treatment is available in the advanced setting. Relevant data were manually extracted from peer-reviewed full-text original articles describing any type of anti-melanoma targeted therapy tested in any type of experimental or clinical model. To this purpose, Medline, Embase, Cancerlit and the Cochrane databases were searched. RESULTS AND CONCLUSIONS: We created a manually annotated database (Targeted Therapy Database, TTD where the relevant data are gathered in a formal representation that can be computationally analyzed. Dedicated algorithms were set up for the identification of the prevalent therapeutic hypotheses based on the available evidence and for ranking treatments based on the molecular profile of individual patients. In this essay we describe the principles and computational algorithms of an original method

  18. [Fibromyalgia syndrome after comprehensive treatment of breast cancer: a case report].

    Science.gov (United States)

    Ding, Xia; Li, Yan; Cui, Yiyi; Shen, Yingying; Gu, Jianzhong; Guo, Yong

    2016-05-25

    Fibromyalgia syndrome after comprehensive treatment of breast cancer is rare and seldom reported. Here we present a case of a 50-year-old female patient,who was admitted to the hospital because of generalized fibromyalgia for 3 months and brain metastasis after the right breast carcinoma surgery for 1 month, and the clinical diagnosis was brain metastasis from breast carcinoma combined with fibromyalgia syndrome. The fibromyalgia were relieved with proper symptomatic treatment but the patient eventually died of tumor progression.

  19. The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

    OpenAIRE

    Christopher J. Ricketts; Aguirre A. De Cubas; Huihui Fan; Christof C. Smith; Martin Lang; Ed Reznik; Reanne Bowlby; Ewan A. Gibb; Rehan Akbani; Rameen Beroukhim; Donald P. Bottaro; Toni K. Choueiri; Richard A. Gibbs; Andrew K. Godwin; Scott Haake

    2018-01-01

    Summary: Renal cell carcinoma (RCC) is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and therapeutic responses. The current study evaluated 843 RCC from the three major histologic subtypes, including 488 clear cell RCC, 274 papillary RCC, and 81 chromophobe RCC. Comprehensive genomic and phenotypic analysis of the RCC subtypes reveals distinctive features of each subtype that provide the foundation for the development of sub...

  20. Comprehensive analysis of the transcriptional profile of the Mediator complex across human cancer types.

    Science.gov (United States)

    Syring, Isabella; Klümper, Niklas; Offermann, Anne; Braun, Martin; Deng, Mario; Boehm, Diana; Queisser, Angela; von Mässenhausen, Anne; Brägelmann, Johannes; Vogel, Wenzel; Schmidt, Doris; Majores, Michael; Schindler, Anne; Kristiansen, Glen; Müller, Stefan C; Ellinger, Jörg; Shaikhibrahim, Zaki; Perner, Sven

    2016-04-26

    The Mediator complex is a key regulator of gene transcription and several studies demonstrated altered expressions of particular subunits in diverse human diseases, especially cancer. However a systematic study deciphering the transcriptional expression of the Mediator across different cancer entities is still lacking.We therefore performed a comprehensive in silico cancer vs. benign analysis of the Mediator complex subunits (MEDs) for 20 tumor entities using Oncomine datasets. The transcriptional expression profiles across almost all cancer entities showed differentially expressed MEDs as compared to benign tissue. Differential expression of MED8 in renal cell carcinoma (RCC) and MED12 in lung cancer (LCa) were validated and further investigated by immunohistochemical staining on tissue microarrays containing large numbers of specimen. MED8 in clear cell RCC (ccRCC) associated with shorter survival and advanced TNM stage and showed higher expression in metastatic than primary tumors. In vitro, siRNA mediated MED8 knockdown significantly impaired proliferation and motility in ccRCC cell lines, hinting at a role for MED8 to serve as a novel therapeutic target in ccRCC. Taken together, our Mediator complex transcriptome proved to be a valid tool for identifying cancer-related shifts in Mediator complex composition, revealing that MEDs do exhibit cancer specific transcriptional expression profiles.

  1. The National Deep-Sea Coral and Sponge Database: A Comprehensive Resource for United States Deep-Sea Coral and Sponge Records

    Science.gov (United States)

    Dornback, M.; Hourigan, T.; Etnoyer, P.; McGuinn, R.; Cross, S. L.

    2014-12-01

    Research on deep-sea corals has expanded rapidly over the last two decades, as scientists began to realize their value as long-lived structural components of high biodiversity habitats and archives of environmental information. The NOAA Deep Sea Coral Research and Technology Program's National Database for Deep-Sea Corals and Sponges is a comprehensive resource for georeferenced data on these organisms in U.S. waters. The National Database currently includes more than 220,000 deep-sea coral records representing approximately 880 unique species. Database records from museum archives, commercial and scientific bycatch, and from journal publications provide baseline information with relatively coarse spatial resolution dating back as far as 1842. These data are complemented by modern, in-situ submersible observations with high spatial resolution, from surveys conducted by NOAA and NOAA partners. Management of high volumes of modern high-resolution observational data can be challenging. NOAA is working with our data partners to incorporate this occurrence data into the National Database, along with images and associated information related to geoposition, time, biology, taxonomy, environment, provenance, and accuracy. NOAA is also working to link associated datasets collected by our program's research, to properly archive them to the NOAA National Data Centers, to build a robust metadata record, and to establish a standard protocol to simplify the process. Access to the National Database is provided through an online mapping portal. The map displays point based records from the database. Records can be refined by taxon, region, time, and depth. The queries and extent used to view the map can also be used to download subsets of the database. The database, map, and website is already in use by NOAA, regional fishery management councils, and regional ocean planning bodies, but we envision it as a model that can expand to accommodate data on a global scale.

  2. GreekLex 2: A comprehensive lexical database with part-of-speech, syllabic, phonological, and stress information.

    Science.gov (United States)

    Kyparissiadis, Antonios; van Heuven, Walter J B; Pitchford, Nicola J; Ledgeway, Timothy

    2017-01-01

    Databases containing lexical properties on any given orthography are crucial for psycholinguistic research. In the last ten years, a number of lexical databases have been developed for Greek. However, these lack important part-of-speech information. Furthermore, the need for alternative procedures for calculating syllabic measurements and stress information, as well as combination of several metrics to investigate linguistic properties of the Greek language are highlighted. To address these issues, we present a new extensive lexical database of Modern Greek (GreekLex 2) with part-of-speech information for each word and accurate syllabification and orthographic information predictive of stress, as well as several measurements of word similarity and phonetic information. The addition of detailed statistical information about Greek part-of-speech, syllabification, and stress neighbourhood allowed novel analyses of stress distribution within different grammatical categories and syllabic lengths to be carried out. Results showed that the statistical preponderance of stress position on the pre-final syllable that is reported for Greek language is dependent upon grammatical category. Additionally, analyses showed that a proportion higher than 90% of the tokens in the database would be stressed correctly solely by relying on stress neighbourhood information. The database and the scripts for orthographic and phonological syllabification as well as phonetic transcription are available at http://www.psychology.nottingham.ac.uk/greeklex/.

  3. A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen-fixing bacteria.

    Science.gov (United States)

    Gaby, John Christian; Buckley, Daniel H

    2014-01-01

    We describe a nitrogenase gene sequence database that facilitates analysis of the evolution and ecology of nitrogen-fixing organisms. The database contains 32 954 aligned nitrogenase nifH sequences linked to phylogenetic trees and associated sequence metadata. The database includes 185 linked multigene entries including full-length nifH, nifD, nifK and 16S ribosomal RNA (rRNA) gene sequences. Evolutionary analyses enabled by the multigene entries support an ancient horizontal transfer of nitrogenase genes between Archaea and Bacteria and provide evidence that nifH has a different history of horizontal gene transfer from the nifDK enzyme core. Further analyses show that lineages in nitrogenase cluster I and cluster III have different rates of substitution within nifD, suggesting that nifD is under different selection pressure in these two lineages. Finally, we find that that the genetic divergence of nifH and 16S rRNA genes does not correlate well at sequence dissimilarity values used commonly to define microbial species, as stains having <3% sequence dissimilarity in their 16S rRNA genes can have up to 23% dissimilarity in nifH. The nifH database has a number of uses including phylogenetic and evolutionary analyses, the design and assessment of primers/probes and the evaluation of nitrogenase sequence diversity. Database URL: http://www.css.cornell.edu/faculty/buckley/nifh.htm.

  4. Quality of life and symptoms in patients with malignant diseases admitted to a comprehensive cancer centre

    DEFF Research Database (Denmark)

    Strömgren, Lene Annette Sand; Niemann, Carsten Utoft; Tange, Ulla Brix

    2014-01-01

    PURPOSE: Quality of life and symptomatology in patients with malignancies admitted to comprehensive cancer centres are rarely investigated. Thus, this study aimed to investigate symptomatology and health-related quality of life of inpatients with cancer. METHODS: A prospective, cross......-sample test, rank tests and Fisher's exact test. RESULTS: One hundred twenty-four patients were analysed, mean age = 59 years (SD = 13.7), 42 % admitted to haematological department; lung cancer was the most frequent diagnosis (15 %). Low health-related quality of life and severe symptom burden, especially...... in oncology patients (P = 0.0194 and 0.0064, respectively). CONCLUSIONS: Patients in the wards of haematology and oncology had pronounced symptomatology and low quality of life. A more systematic focus on the amelioration of problems with functioning and symptoms among inpatients with malignant diseases...

  5. CracidMex1: a comprehensive database of global occurrences of cracids (Aves, Galliformes with distribution in Mexico

    Directory of Open Access Journals (Sweden)

    Gonzalo Pinilla-Buitrago

    2014-06-01

    Full Text Available Cracids are among the most vulnerable groups of Neotropical birds. Almost half of the species of this family are included in a conservation risk category. Twelve taxa occur in Mexico, six of which are considered at risk at national level and two are globally endangered. Therefore, it is imperative that high quality, comprehensive, and high-resolution spatial data on the occurrence of these taxa are made available as a valuable tool in the process of defining appropriate management strategies for conservation at a local and global level. We constructed the CracidMex1 database by collating global records of all cracid taxa that occur in Mexico from available electronic databases, museum specimens, publications, “grey literature”, and unpublished records. We generated a database with 23,896 clean, validated, and standardized geographic records. Database quality control was an iterative process that commenced with the consolidation and elimination of duplicate records, followed by the geo-referencing of records when necessary, and their taxonomic and geographic validation using GIS tools and expert knowledge. We followed the geo-referencing protocol proposed by the Mexican National Commission for the Use and Conservation of Biodiversity. We could not estimate the geographic coordinates of 981 records due to inconsistencies or lack of sufficient information in the description of the locality.Given that current records for most of the taxa have some degree of distributional bias, with redundancies at different spatial scales, the CracidMex1 database has allowed us to detect areas where more sampling effort is required to have a better representation of the global spatial occurrence of these cracids. We also found that particular attention needs to be given to taxa identification in those areas where congeners or conspecifics co-occur in order to avoid taxonomic uncertainty. The construction of the CracidMex1 database represents the first

  6. Knowledge production status of Iranian researchers in the gastric cancer area: based on the medline database.

    Science.gov (United States)

    Ghojazadeh, Morteza; Naghavi-Behzad, Mohammad; Nasrolah-Zadeh, Raheleh; Bayat-Khajeh, Parvaneh; Piri, Reza; Mirnia, Keyvan; Azami-Aghdash, Saber

    2014-01-01

    Scientometrics is a useful method for management of financial and human resources and has been applied many times in medical sciences during recent years. The aim of this study was to investigate the status of science production by Iranian scientists in the gastric cancer field based on the Medline database. In this descriptive-cross sectional study Iranian science production concerning gastric cancer during 2000-2011 was investigated based on Medline. After two stages of searching, 121 articles were found, then we reviewed publication date, authors names, journal title, impact factor (IF), and cooperation coefficient between researchers. SPSS.19 was used for statistical analysis. There was a significant increase in published articles about gastric cancer by Iranian researchers in Medline database during 2006-2011. Mean cooperation coefficient between researchers was 6.14±3.29 person per article. Articles of this field were published in 19 countries and 56 journals. Those basex in Thailand, England, and America had the most published Iranian articles. Tehran University of Medical Sciences and Mohammadreza Zali had the most outstanding role in publishing scientific articles. According to results of this study, improving cooperation of researchers in conducting research and scientometric studies about other fields may have an important role in increasing both quality and quantity of published studies.

  7. Prioritizing strategies for comprehensive liver cancer control in Asia: a conjoint analysis

    Directory of Open Access Journals (Sweden)

    Bridges John FP

    2012-10-01

    Full Text Available Abstract Background Liver cancer is a complex and burdensome disease, with Asia accounting for 75% of known cases. Comprehensive cancer control requires the use of multiple strategies, but various stakeholders may have different views as to which strategies should have the highest priority. This study identified priorities across multiple strategies for comprehensive liver cancer control (CLCC from the perspective of liver cancer clinical, policy, and advocacy stakeholders in China, Japan, South Korea and Taiwan. Concordance of priorities was assessed across the region and across respondent roles. Methods Priorities for CLCC were examined as part of a cross-sectional survey of liver cancer experts. Respondents completed several conjoint-analysis choice tasks to prioritize 11 strategies. In each task, respondents judged which of two competing CLCC plans, consisting of mutually exclusive and exhaustive subsets of the strategies, would have the greatest impact. The dependent variable was the chosen plan, which was then regressed on the strategies of different plans. The restricted least squares (RLS method was utilized to compare aggregate and stratified models, and t-tests and Wald tests were used to test for significance and concordance, respectively. Results Eighty respondents (69.6% were eligible and completed the survey. Their primary interests were hepatitis (26%, hepatocellular carcinoma (HCC (58%, metastatic liver cancer (10% and transplantation (6%. The most preferred strategies were monitoring at-risk populations (pclinician education (pnational guidelines (ptransplantation infrastructure (p=0.009 was valued lower in China, measuring social burden (p=0.037 was valued higher in Taiwan, and national guidelines (p=0.025 was valued higher in China. Priorities did not differ across stakeholder groups (p=0.438. Conclusions Priorities for CLCC in Asia include monitoring at-risk populations, clinician education, national guidelines

  8. Prioritizing strategies for comprehensive liver cancer control in Asia: a conjoint analysis.

    Science.gov (United States)

    Bridges, John F P; Dong, Liming; Gallego, Gisselle; Blauvelt, Barri M; Joy, Susan M; Pawlik, Timothy M

    2012-10-30

    Liver cancer is a complex and burdensome disease, with Asia accounting for 75% of known cases. Comprehensive cancer control requires the use of multiple strategies, but various stakeholders may have different views as to which strategies should have the highest priority. This study identified priorities across multiple strategies for comprehensive liver cancer control (CLCC) from the perspective of liver cancer clinical, policy, and advocacy stakeholders in China, Japan, South Korea and Taiwan. Concordance of priorities was assessed across the region and across respondent roles. Priorities for CLCC were examined as part of a cross-sectional survey of liver cancer experts. Respondents completed several conjoint-analysis choice tasks to prioritize 11 strategies. In each task, respondents judged which of two competing CLCC plans, consisting of mutually exclusive and exhaustive subsets of the strategies, would have the greatest impact. The dependent variable was the chosen plan, which was then regressed on the strategies of different plans. The restricted least squares (RLS) method was utilized to compare aggregate and stratified models, and t-tests and Wald tests were used to test for significance and concordance, respectively. Eighty respondents (69.6%) were eligible and completed the survey. Their primary interests were hepatitis (26%), hepatocellular carcinoma (HCC) (58%), metastatic liver cancer (10%) and transplantation (6%). The most preferred strategies were monitoring at-risk populations (p<0.001), clinician education (p<0.001), and national guidelines (p<0.001). Most priorities were concordant across sites except for three strategies: transplantation infrastructure (p=0.009) was valued lower in China, measuring social burden (p=0.037) was valued higher in Taiwan, and national guidelines (p=0.025) was valued higher in China. Priorities did not differ across stakeholder groups (p=0.438). Priorities for CLCC in Asia include monitoring at-risk populations

  9. Epigenomic diversity of colorectal cancer indicated by LINE-1 methylation in a database of 869 tumors

    Directory of Open Access Journals (Sweden)

    Schernhammer Eva S

    2010-05-01

    Full Text Available Abstract Background Genome-wide DNA hypomethylation plays a role in genomic instability and carcinogenesis. LINE-1 (L1 retrotransposon constitutes a substantial portion of the human genome, and LINE-1 methylation correlates with global DNA methylation status. LINE-1 hypomethylation in colon cancer has been strongly associated with poor prognosis. However, whether LINE-1 hypomethylators constitute a distinct cancer subtype remains uncertain. Recent evidence for concordant LINE-1 hypomethylation within synchronous colorectal cancer pairs suggests the presence of a non-stochastic mechanism influencing tumor LINE-1 methylation level. Thus, it is of particular interest to examine whether its wide variation can be attributed to clinical, pathologic or molecular features. Design Utilizing a database of 869 colorectal cancers in two prospective cohort studies, we constructed multivariate linear and logistic regression models for LINE-1 methylation (quantified by Pyrosequencing. Variables included age, sex, body mass index, family history of colorectal cancer, smoking status, tumor location, stage, grade, mucinous component, signet ring cells, tumor infiltrating lymphocytes, CpG island methylator phenotype (CIMP, microsatellite instability, expression of TP53 (p53, CDKN1A (p21, CTNNB1 (β-catenin, PTGS2 (cyclooxygenase-2, and FASN, and mutations in KRAS, BRAF, and PIK3CA. Results Tumoral LINE-1 methylation ranged from 23.1 to 90.3 of 0-100 scale (mean 61.4; median 62.3; standard deviation 9.6, and distributed approximately normally except for extreme hypomethylators [LINE-1 methylation Conclusions LINE-1 extreme hypomethylators appear to constitute a previously-unrecognized, distinct subtype of colorectal cancers, which needs to be confirmed by additional studies. Our tumor LINE-1 methylation data indicate enormous epigenomic diversity of individual colorectal cancers.

  10. Breast Cancer Survivorship: A Comprehensive Review of Long-Term Medical Issues and Lifestyle Recommendations

    Science.gov (United States)

    Bodai, Balazs I; Tuso, Phillip

    2015-01-01

    Long-term survival rates after a diagnosis of breast cancer are steadily rising. This is good news, but clinicians must also recognize that this brings new challenges to the medical community. As breast cancer becomes a chronic condition rather than a life-threatening illness owing to advances in early diagnosis and more effective treatments, health care practitioners must recognize and manage the long-term sequelae of the constellation of therapeutic modalities. Survivors of breast cancer represent a unique and extremely complex group of patients; not only do they have the challenge of dealing with multiple long-term side effects of treatment protocols, but many are also forced to address the preexisting comorbidities of their therapies, which often include multiple other issues. Therapies have additional and/or additive side effects that may interfere with treatments directed toward the new primary diagnosis of breast cancer. Our mandate is to establish a smooth transition from patient with breast cancer to survivor of breast cancer while providing ongoing and future guidance. Certainly, the information and resources to accomplish this transition are readily available; however, they are scattered throughout the literature and therefore are not easily accessible or available to the primary care physician. It is imperative that the information available regarding survivorship issues be accessible in an organized and useful format. This article is a modest attempt to provide a comprehensive review of the long-term medical issues relevant to survivorship after the diagnosis and treatment of breast cancer. A predicted shortage of oncologists by 2020 is well-recognized. Therefore, the bulk of long-term care will become dependent on the primary care physician. This shift of care means that these physicians will need to be well educated in the long-term medical issues related to breast cancer treatment. PMID:25902343

  11. Locus-Specific Databases and Recommendations to Strengthen Their Contribution to the Classification of Variants in Cancer Susceptibility Genes

    NARCIS (Netherlands)

    Greenblatt, Marc S.; Brody, Lawrence C.; Foulkes, William D.; Genuardi, Maurizio; Hofstra, Robert M. W.; Olivier, Magali; Plon, Sharon E.; Sijmons, Rolf H.; Sinilnikova, Olga; Spurdle, Amanda B.

    2008-01-01

    Locus-specific databases (LSDBs) are curated collections of sequence variants in genes associated with disease. LSDBs of cancer-related genes often serve as a critical resource to researchers, diagnostic laboratories, clinicians, and others in the cancer genetics community. LSDBs are poised to play

  12. Tissue Molecular Anatomy Project (TMAP): an expression database for comparative cancer proteomics.

    Science.gov (United States)

    Medjahed, Djamel; Luke, Brian T; Tontesh, Tawady S; Smythers, Gary W; Munroe, David J; Lemkin, Peter F

    2003-08-01

    By mining publicly accessible databases, we have developed a collection of tissue-specific predictive protein expression maps as a function of cancer histological state. Data analysis is applied to the differential expression of gene products in pooled libraries from the normal to the altered state(s). We wish to report the initial results of our survey across different tissues and explore the extent to which this comparative approach may help uncover panels of potential biomarkers of tumorigenesis which would warrant further examination in the laboratory.

  13. The NIH genetic testing registry: a new, centralized database of genetic tests to enable access to comprehensive information and improve transparency.

    Science.gov (United States)

    Rubinstein, Wendy S; Maglott, Donna R; Lee, Jennifer M; Kattman, Brandi L; Malheiro, Adriana J; Ovetsky, Michael; Hem, Vichet; Gorelenkov, Viatcheslav; Song, Guangfeng; Wallin, Craig; Husain, Nora; Chitipiralla, Shanmuga; Katz, Kenneth S; Hoffman, Douglas; Jang, Wonhee; Johnson, Mark; Karmanov, Fedor; Ukrainchik, Alexander; Denisenko, Mikhail; Fomous, Cathy; Hudson, Kathy; Ostell, James M

    2013-01-01

    The National Institutes of Health Genetic Testing Registry (GTR; available online at http://www.ncbi.nlm.nih.gov/gtr/) maintains comprehensive information about testing offered worldwide for disorders with a genetic basis. Information is voluntarily submitted by test providers. The database provides details of each test (e.g. its purpose, target populations, methods, what it measures, analytical validity, clinical validity, clinical utility, ordering information) and laboratory (e.g. location, contact information, certifications and licenses). Each test is assigned a stable identifier of the format GTR000000000, which is versioned when the submitter updates information. Data submitted by test providers are integrated with basic information maintained in National Center for Biotechnology Information's databases and presented on the web and through FTP (ftp.ncbi.nih.gov/pub/GTR/_README.html).

  14. The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine.

    Science.gov (United States)

    Stenson, Peter D; Mort, Matthew; Ball, Edward V; Shaw, Katy; Phillips, Andrew; Cooper, David N

    2014-01-01

    The Human Gene Mutation Database (HGMD®) is a comprehensive collection of germline mutations in nuclear genes that underlie, or are associated with, human inherited disease. By June 2013, the database contained over 141,000 different lesions detected in over 5,700 different genes, with new mutation entries currently accumulating at a rate exceeding 10,000 per annum. HGMD was originally established in 1996 for the scientific study of mutational mechanisms in human genes. However, it has since acquired a much broader utility as a central unified disease-oriented mutation repository utilized by human molecular geneticists, genome scientists, molecular biologists, clinicians and genetic counsellors as well as by those specializing in biopharmaceuticals, bioinformatics and personalized genomics. The public version of HGMD (http://www.hgmd.org) is freely available to registered users from academic institutions/non-profit organizations whilst the subscription version (HGMD Professional) is available to academic, clinical and commercial users under license via BIOBASE GmbH.

  15. Implementing a Death with Dignity program at a comprehensive cancer center.

    Science.gov (United States)

    Loggers, Elizabeth Trice; Starks, Helene; Shannon-Dudley, Moreen; Back, Anthony L; Appelbaum, Frederick R; Stewart, F Marc

    2013-04-11

    The majority of Death with Dignity participants in Washington State and Oregon have received a diagnosis of terminal cancer. As more states consider legislation regarding physician-assisted death, the experience of a comprehensive cancer center may be informative. We describe the implementation of a Death with Dignity program at Seattle Cancer Care Alliance, the site of care for the Fred Hutchinson-University of Washington Cancer Consortium, a comprehensive cancer center in Seattle that serves the Pacific Northwest. Institution-level data were compared with publicly available statewide data from Oregon and Washington. A total of 114 patients inquired about our Death with Dignity program between March 5, 2009, and December 31, 2011. Of these, 44 (38.6%) did not pursue the program, and 30 (26.3%) initiated the process but either elected not to continue or died before completion. Of the 40 participants who, after counseling and upon request, received a prescription for a lethal dose of secobarbital (35.1% of the 114 patients who inquired about the program), all died, 24 after medication ingestion (60% of those obtaining prescriptions). The participants at our center accounted for 15.7% of all participants in the Death with Dignity program in Washington (255 persons) and were typically white, male, and well educated. The most common reasons for participation were loss of autonomy (97.2%), inability to engage in enjoyable activities (88.9%), and loss of dignity (75.0%). Eleven participants lived for more than 6 months after prescription receipt. Qualitatively, patients and families were grateful to receive the lethal prescription, whether it was used or not. Overall, our Death with Dignity program has been well accepted by patients and clinicians.

  16. Exosomes in Cancer Development, Metastasis and Drug Resistance: A Comprehensive Review

    Science.gov (United States)

    Azmi, Asfar S.; Bao, Bin; Sarkar, Fazlul H.

    2013-01-01

    Trafficking of biological material across membranes is an evolutionary conserved mechanism and is part of any normal cell homeostasis. Such transport is comprised of active, passive, export through microparticles and vesicular transport (exosomes) that collectively maintain proper compartmentalization of important micro and macromolecules. In pathological states, such as cancer, aberrant activity of export machinery results in expulsion of a number of key proteins and microRNAs resulting in their misexpression. Exosome mediated expulsion of intracellular drugs could be another barrier in the proper action of most of the commonly used therapeutics, targeted agents and their intracellular metabolites. Over the last decade, a number of studies have revealed that exosomes cross-talk and/or influence major tumor related pathways such as hypoxia driven EMT, cancer stemness, angiogenesis and metastasis involving many cell types within the tumor microenvironment. Emerging evidence suggest that exosome secreted proteins can also propel fibroblast growth, resulting in Desmoplastic reaction (DR); a major barrier in effective cancer drug delivery. This comprehensive review highlights the advancements in the understanding of the biology of exosomes secretions and the consequence on cancer drug resistance. We propose that the successful combination of cancer treatments to tackle exosome mediated drug resistance requires an interdisciplinary understanding of these cellular exclusion mechanisms, and how secreted biomolecules are involved in cellular cross-talk within the tumor microenvironment. PMID:23709120

  17. Demographic and medication characteristics of traditional Chinese medicine users among colorectal cancer survivors: A nationwide database study in Taiwan

    OpenAIRE

    Wu, Chien-Tung; Tsai, Yueh-Ting; Lai, Jung-Nien

    2016-01-01

    Chinese herbal product (CHP) is the major type of traditional Chinese medicine (TCM) and widely used to relief the symptom of colorectal cancer. The aim of the study was to analyze the utilization of CHP for treating patients with colorectal cancer in Taiwan. The usage of CHP, frequency of services, and prescription pattern for colorectal cancer were analyzed from a randomly sampled cohort of 1 million beneficiaries from the National Health Insurance Research Database. The odds ratios for uti...

  18. Evaluation of the TRPM2 channel as a biomarker in breast cancer using public databases analysis.

    Science.gov (United States)

    Sumoza-Toledo, Adriana; Espinoza-Gabriel, Mario Iván; Montiel-Condado, Dvorak

    Breast cancer is one of the most common malignancies affecting women. Recent investigations have revealed a major role of ion channels in cancer. The transient receptor potential melastatin-2 (TRPM2) is a plasma membrane and lysosomal channel with important roles in cell migration and cell death in immune cells and tumor cells. In this study, we investigated the prognostic value of TRPM2 channel in breast cancer, analyzing public databases compiled in Oncomine™ (Thermo Fisher, Ann Arbor, MI) and online Kaplan-Meier Plotter platforms. The results revealed that TRPM2 mRNA overexpression is significant in situ and invasive breast carcinoma compared to normal breast tissue. Furthermore, multi-gene validation using Oncomine™ showed that this channel is coexpressed with proteins related to cellular migration, transformation, and apoptosis. On the other hand, Kaplan-Meier analysis exhibited that low expression of TRPM2 could be used to predict poor outcome in ER- and HER2+ breast carcinoma patients. TRPM2 is a promising biomarker for aggressiveness of breast cancer, and a potential target for the development of new therapies. Copyright © 2016 Hospital Infantil de México Federico Gómez. Publicado por Masson Doyma México S.A. All rights reserved.

  19. Risk of secondary malignancies after radiation therapy for breast cancer: Comprehensive results.

    Science.gov (United States)

    Burt, Lindsay M; Ying, Jian; Poppe, Matthew M; Suneja, Gita; Gaffney, David K

    2017-10-01

    To assess risks of secondary malignancies in breast cancer patients who received radiation therapy compared to patients who did not. The SEER database was used to identify females with a primary diagnosis of breast cancer as their first malignancy, during 1973-2008. We excluded patients with metastatic disease, age breast cancer recurrence, or who developed a secondary malignancy within 1 year of diagnosis. Standardized incidence ratios and absolute excess risk were calculated using SEER*Stat, version 8.2.1 and SAS, version 9.4. There were 374,993 patients meeting the inclusion criteria, with 154,697 who received radiation therapy. With a median follow-up of 8.9 years, 13% of patients (49,867) developed a secondary malignancy. The rate of secondary malignancies was significantly greater than the endemic rate in breast cancer patients treated without radiation therapy, (O/E 1.2, 95% CI 1.19-1.22) and with radiation therapy (O/E 1.33, 95% CI 1.31-1.35). Approximately 3.4% of secondary malignancies were attributable to radiation therapy. The increased risk of secondary malignancies in breast cancer patients treated with radiation therapy compared to those without was significant regardless of age at breast cancer diagnosis (p breast cancer patients both with and without radiation therapy compared to the general population. There was an increased risk in specific sites for patients treated with radiation therapy. This risk was most evident in young patients and who had longer latency periods. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Risk Evaluation of Postoperative Delirium Using Comprehensive Geriatric Assessment in Elderly Patients with Esophageal Cancer.

    Science.gov (United States)

    Yamamoto, Masaaki; Yamasaki, Makoto; Sugimoto, Ken; Maekawa, Yoshihiro; Miyazaki, Yasuhiro; Makino, Tomoki; Takahashi, Tsuyoshi; Kurokawa, Yukinori; Nakajima, Kiyokazu; Takiguchi, Shuji; Rakugi, Hiromi; Mori, Masaki; Doki, Yuichiro

    2016-11-01

    The number of geriatric patients with esophageal cancer is increasing in step with the aging of the population. Geriatric patients have a higher risk of postoperative complications, including delirium that can cause a fall or impact survival. Therefore, it is very important that we evaluate risks of postoperative complications before surgery. The aim of this study was to predict postoperative delirium in elderly patients. We retrospectively reviewed the medical records of 91 patients aged 75 years and over who underwent esophagectomy between January 2006 and December 2014. We investigated the association between postoperative delirium and clinicopathological factors, including comprehensive geriatric assessment (CGA). Postoperative delirium developed in 24 (26 %) patients. Postoperative delirium was significantly associated with low mini-mental state examination (MMSE) and high Geriatric Depression Scale 15 (GDS15), which are components of CGA, and psychiatric disorder (P patients undergoing esophagectomy for esophageal cancer. Intervention by a multidisciplinary team using CGA might help prevent postoperative delirium.

  1. Time trends in prostate cancer surgery: data from an Internet-based multicentre database.

    Science.gov (United States)

    Schostak, Martin; Baumunk, Daniel; Jagota, Anita; Klopf, Christian; Winter, Alexander; Schäfers, Sebastian; Kössler, Robert; Brennecke, Volker; Fischer, Tom; Hagel, Susanne; Höchel, Steffen; Jäkel, Dierk; Lehsnau, Mike; Krege, Susanne; Rüffert, Bernd; Pretzer, Jana; Becht, Eduard; Zegenhagen, Thomas; Miller, Kurt; Weikert, Steffen

    2012-02-01

    To report our experience with an Internet-based multicentre database that enables tumour documentation, as well as the collection of quality-related parameters and follow-up data, in surgically treated patients with prostate cancer. The system was used to assess the quality of prostate cancer surgery and to analyze possible time-dependent trends in the quality of care. An Internet-based database system enabled a standardized collection of treatment data and clinical findings from the participating urological centres for the years 2005-2009. An analysis was performed aiming to evaluate relevant patient characteristics (age, pathological tumour stage, preoperative International Index of Erectile Function-5 score), intra-operative parameters (operating time, percentage of nerve-sparing operations, complication rate, transfusion rate, number of resected lymph nodes) and postoperative parameters (hospitalization time, re-operation rate, catheter indwelling time). Mean values were calculated and compared for each annual cohort from 2005 to 2008. The overall survival rate was also calculated for a subgroup of the Berlin patients. A total of 914, 1120, 1434 and 1750 patients submitted to radical prostatectomy in 2005, 2006, 2007 and 2008 were documented in the database. The mean age at the time of surgery remained constant (66 years) during the study period. More than half the patients already had erectile dysfunction before surgery (median International Index of Erectile Function-5 score of 19-20). During the observation period, there was a decrease in the percentage of pT2 tumours (1% in 2005; 64% in 2008) and a slight increase in the percentage of patients with lymph node metastases (8% in 2005; 10% in 2008). No time trend was found for the operating time (142-155 min) or the percentage of nerve-sparing operations (72-78% in patients without erectile dysfunction). A decreasing frequency was observed for the parameters: blood transfusions (1.9% in 2005; 0.5% in 2008

  2. Providing inbuilt economic resilience options : an obligation of comprehensive cancer care.

    Science.gov (United States)

    Cross, Eva Reitschuler; Emanuel, Linda

    2008-12-15

    For many, a cancer death in the family is the immediately obvious part of what is actually a double devastation. Overwhelming financial damage also results for many families, from the cost of medical care and from the loss of earning power by the patient and family. For some families, the consequences may be multigenerational and can affect the health of the survivors. Although this situation is not limited to cancer, the authors argue that oncology can take a lead in attending to these consequences of cancer as an integral part of its commitment to comprehensive cancer care. They make this case for both the national and the international settings. They also articulate and illustrate the notion of inbuilt options for economic resilience (IERs), which the authors suggest the medical industry, and its cancer care sectors in particular, should be providing to all patients and their families if they are at risk for damaging financial losses. After describing key features to IER, the authors illustrate it with 1 type of approach for households of the terminally ill: hospice care with provision of supplementary training and certification to the family caregiver. Such programming could generate a low-technology, semiskilled healthcare service economy as trained family caregivers provide support to other households in need, thereby both providing a recovery option for themselves and reduced economic devastation to the households which, by receiving the services, can stay in the workforce. Finally, the authors call for invigorated research on the economic impact of cancer on families and for the modeling, demonstration, and study of options for economic resilience, including IER programs.

  3. PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database.

    Science.gov (United States)

    Wang, Xia; Shen, Yihang; Wang, Shiwei; Li, Shiliang; Zhang, Weilin; Liu, Xiaofeng; Lai, Luhua; Pei, Jianfeng; Li, Honglin

    2017-07-03

    The PharmMapper online tool is a web server for potential drug target identification by reversed pharmacophore matching the query compound against an in-house pharmacophore model database. The original version of PharmMapper includes more than 7000 target pharmacophores derived from complex crystal structures with corresponding protein target annotations. In this article, we present a new version of the PharmMapper web server, of which the backend pharmacophore database is six times larger than the earlier one, with a total of 23 236 proteins covering 16 159 druggable pharmacophore models and 51 431 ligandable pharmacophore models. The expanded target data cover 450 indications and 4800 molecular functions compared to 110 indications and 349 molecular functions in our last update. In addition, the new web server is united with the statistically meaningful ranking of the identified drug targets, which is achieved through the use of standard scores. It also features an improved user interface. The proposed web server is freely available at http://lilab.ecust.edu.cn/pharmmapper/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. Marital status independently predicts testis cancer survival--an analysis of the SEER database.

    Science.gov (United States)

    Abern, Michael R; Dude, Annie M; Coogan, Christopher L

    2012-01-01

    Previous reports have shown that married men with malignancies have improved 10-year survival over unmarried men. We sought to investigate the effect of marital status on 10-year survival in a U.S. population-based cohort of men with testis cancer. We examined 30,789 cases of testis cancer reported to the Surveillance, Epidemiology, and End Results (SEER 17) database between 1973 and 2005. All staging were converted to the 1997 AJCC TNM system. Patients less than 18 years of age at time of diagnosis were excluded. A subgroup analysis of patients with stages I or II non-seminomatous germ cell tumors (NSGCT) was performed. Univariate analysis using t-tests and χ(2) tests compared characteristics of patients separated by marital status. Multivariate analysis was performed using a Cox proportional hazard model to generate Kaplan-Meier survival curves, with all-cause and cancer-specific mortality as the primary endpoints. 20,245 cases met the inclusion criteria. Married men were more likely to be older (38.9 vs. 31.4 years), Caucasian (94.4% vs. 92.1%), stage I (73.1% vs. 61.4%), and have seminoma as the tumor histology (57.3% vs. 43.4%). On multivariate analysis, married status (HR 0.58, P married status (HR 0.60, P married and unmarried men (44.8% vs. 43.4%, P = 0.33). Marital status is an independent predictor of improved overall and cancer-specific survival in men with testis cancer. In men with stages I or II NSGCT, RPLND is an additional predictor of improved overall survival. Marital status does not appear to influence whether men undergo RPLND. Copyright © 2012 Elsevier Inc. All rights reserved.

  5. A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers

    NARCIS (Netherlands)

    Berger, Ashton C.; Korkut, Anil; Kanchi, Rupa S.; Hegde, Apurva M.; Lenoir, Walter; Liu, Wenbin; Liu, Yuexin; Fan, Huihui; Shen, Hui; Ravikumar, Visweswaran; Rao, Arvind; Schultz, Andre; Li, Xubin; Sumazin, Pavel; Williams, Cecilia; Mestdagh, Pieter; Gunaratne, Preethi H.; Yau, Christina; Bowlby, Reanne; Robertson, A. Gordon; Tiezzi, Daniel G.; Wang, Chen; Cherniack, Andrew D.; Godwin, Andrew K.; Kuderer, Nicole M.; Rader, Janet S.; Zuna, Rosemary E.; Sood, Anil K.; Lazar, Alexander J.; Ojesina, Akinyemi I.; Adebamowo, Clement; Adebamowo, Sally N.; Baggerly, Keith A.; Chen, Ting Wen; Chiu, Hua Sheng; Lefever, Steve; Liu, Liang; MacKenzie, Karen; Orsulic, Sandra; Roszik, Jason; Shelley, Carl Simon; Song, Qianqian; Vellano, Christopher P.; Wentzensen, Nicolas; Caesar-Johnson, Samantha J.; Demchok, John A.; Felau, Ina; Kasapi, Melpomeni; Ferguson, Martin L.; Hutter, Carolyn M.; Sofia, Heidi J.; Tarnuzzer, Roy; Wang, Zhining; Yang, Liming; Zenklusen, Jean C.; Zhang, Jiashan (Julia); Chudamani, Sudha; Liu, Jia; Lolla, Laxmi; Naresh, Rashi; Pihl, Todd; Sun, Qiang; Wan, Yunhu; Wu, Ye; Cho, Juok; DeFreitas, Timothy; Frazer, Scott; Gehlenborg, Nils; Getz, Gad; Heiman, David I.; Kim, Jaegil; Lawrence, Michael S.; Lin, Pei; Meier, Sam; Noble, Michael S.; Saksena, Gordon; Voet, Doug; Zhang, Hailei; Bernard, Brady; Chambwe, Nyasha; Dhankani, Varsha; Knijnenburg, Theo; Kramer, Roger; Leinonen, Kalle; Liu, Yuexin; Miller, Michael; Reynolds, Sheila; Shmulevich, Ilya; Thorsson, Vesteinn; Zhang, Wei; Akbani, Rehan; Broom, Bradley M.; Hegde, Apurva M.; Ju, Zhenlin; Kanchi, Rupa S.; Korkut, Anil; Li, Jun; Liang, Han; Ling, Shiyun; Liu, Wenbin; Lu, Yiling; Mills, Gordon B.; Ng, Kwok Shing; Rao, Arvind; Ryan, Michael; Wang, Jing; Weinstein, John N.; Zhang, Jiexin; Abeshouse, Adam; Armenia, Joshua; Chakravarty, Debyani; Chatila, Walid K.; de Bruijn, Ino; Gao, Jianjiong; Gross, Benjamin E.; Heins, Zachary J.; Kundra, Ritika; La, Konnor; Ladanyi, Marc; Luna, Augustin; Nissan, Moriah G.; Ochoa, Angelica; Phillips, Sarah M.; Reznik, Ed; Sanchez-Vega, Francisco; Sander, Chris; Schultz, Nikolaus; Sheridan, Robert; Sumer, S. Onur; Sun, Yichao; Taylor, Barry S.; Wang, Jioajiao; Zhang, Hongxin; Anur, Pavana; Peto, Myron; Spellman, Paul; Benz, Christopher; Stuart, Joshua M.; Wong, Christopher K.; Yau, Christina; Hayes, D. Neil; Parker, Joel S.; Wilkerson, Matthew D.; Ally, Adrian; Balasundaram, Miruna; Bowlby, Reanne; Brooks, Denise; Carlsen, Rebecca; Chuah, Eric; Dhalla, Noreen; Holt, Robert; Jones, Steven J.M.; Kasaian, Katayoon; Lee, Darlene; Ma, Yussanne; Marra, Marco A.; Mayo, Michael; Moore, Richard A.; Mungall, Andrew J.; Mungall, Karen; Robertson, A. Gordon; Sadeghi, Sara; Schein, Jacqueline E.; Sipahimalani, Payal; Tam, Angela; Thiessen, Nina; Tse, Kane; Wong, Tina; Berger, Ashton C.; Beroukhim, Rameen; Cherniack, Andrew D.; Cibulskis, Carrie; Gabriel, Stacey B.; Gao, Galen F.; Ha, Gavin; Meyerson, Matthew; Schumacher, Steven E.; Shih, Juliann; Kucherlapati, Melanie H.; Kucherlapati, Raju S.; Baylin, Stephen; Cope, Leslie; Danilova, Ludmila; Bootwalla, Moiz S.; Lai, Phillip H.; Maglinte, Dennis T.; Van Den Berg, David J.; Weisenberger, Daniel J.; Auman, J. Todd; Balu, Saianand; Bodenheimer, Tom; Fan, Cheng; Hoadley, Katherine A.; Hoyle, Alan P.; Jefferys, Stuart R.; Jones, Corbin D.; Meng, Shaowu; Mieczkowski, Piotr A.; Mose, Lisle E.; Perou, Amy H.; Perou, Charles M.; Roach, Jeffrey; Shi, Yan; Simons, Janae V.; Skelly, Tara; Soloway, Matthew G.; Tan, Donghui; Veluvolu, Umadevi; Fan, Huihui; Hinoue, Toshinori; Laird, Peter W.; Shen, Hui; Zhou, Wanding; Bellair, Michelle; Chang, Kyle; Covington, Kyle; Creighton, Chad J.; Dinh, Huyen; Doddapaneni, Harsha Vardhan; Donehower, Lawrence A.; Drummond, Jennifer; Gibbs, Richard A.; Glenn, Robert; Hale, Walker; Han, Yi; Hu, Jianhong; Korchina, Viktoriya; Lee, Sandra; Lewis, Lora; Li, Wei; Liu, Xiuping; Morgan, Margaret; Morton, Donna; Muzny, Donna; Santibanez, Jireh; Sheth, Margi; Shinbrot, Eve; Wang, Linghua; Wang, Min; Wheeler, David A.; Xi, Liu; Zhao, Fengmei; Hess, Julian; Appelbaum, Elizabeth L.; Bailey, Matthew; Cordes, Matthew G.; Ding, Li; Fronick, Catrina C.; Fulton, Lucinda A.; Fulton, Robert S.; Kandoth, Cyriac; Mardis, Elaine R.; McLellan, Michael D.; Miller, Christopher A.; Schmidt, Heather K.; Wilson, Richard K.; Crain, Daniel; Curley, Erin; Gardner, Johanna; Lau, Kevin; Mallery, David; Morris, Scott; Paulauskis, Joseph; Penny, Robert; Shelton, Candace; Shelton, Troy; Sherman, Mark; Thompson, Eric; Yena, Peggy; Bowen, Jay; Gastier-Foster, Julie M.; Gerken, Mark; Leraas, Kristen M.; Lichtenberg, Tara M.; Ramirez, Nilsa C.; Wise, Lisa; Zmuda, Erik; Corcoran, Niall; Costello, Tony; Hovens, Christopher; Carvalho, Andre L.; de Carvalho, Ana C.; Fregnani, José H.; Longatto-Filho, Adhemar; Reis, Rui M.; Scapulatempo-Neto, Cristovam; Silveira, Henrique C.S.; Vidal, Daniel O.; Burnette, Andrew; Eschbacher, Jennifer; Hermes, Beth; Noss, Ardene; Singh, Rosy; Anderson, Matthew L.; Castro, Patricia D.; Ittmann, Michael; Huntsman, David; Kohl, Bernard; Le, Xuan; Thorp, Richard; Andry, Chris; Duffy, Elizabeth R.; Lyadov, Vladimir; Paklina, Oxana; Setdikova, Galiya; Shabunin, Alexey; Tavobilov, Mikhail; McPherson, Christopher; Warnick, Ronald; Berkowitz, Ross; Cramer, Daniel; Feltmate, Colleen; Horowitz, Neil; Kibel, Adam; Muto, Michael; Raut, Chandrajit P.; Malykh, Andrei; Barnholtz-Sloan, Jill S.; Barrett, Wendi; Devine, Karen; Fulop, Jordonna; Ostrom, Quinn T.; Shimmel, Kristen; Wolinsky, Yingli; Sloan, Andrew E.; De Rose, Agostino; Giuliante, Felice; Goodman, Marc; Karlan, Beth Y.; Hagedorn, Curt H.; Eckman, John; Harr, Jodi; Myers, Jerome; Tucker, Kelinda; Zach, Leigh Anne; Deyarmin, Brenda; Hu, Hai; Kvecher, Leonid; Larson, Caroline; Mural, Richard J.; Somiari, Stella; Vicha, Ales; Zelinka, Tomas; Bennett, Joseph; Iacocca, Mary; Rabeno, Brenda; Swanson, Patricia; Latour, Mathieu; Lacombe, Louis; Têtu, Bernard; Bergeron, Alain; McGraw, Mary; Staugaitis, Susan M.; Chabot, John; Hibshoosh, Hanina; Sepulveda, Antonia; Su, Tao; Wang, Timothy; Potapova, Olga; Voronina, Olga; Desjardins, Laurence; Mariani, Odette; Roman-Roman, Sergio; Sastre, Xavier; Stern, Marc Henri; Cheng, Feixiong; Signoretti, Sabina; Berchuck, Andrew; Bigner, Darell; Lipp, Eric; Marks, Jeffrey; McCall, Shannon; McLendon, Roger; Secord, Angeles; Sharp, Alexis; Behera, Madhusmita; Brat, Daniel J.; Chen, Amy; Delman, Keith; Force, Seth; Khuri, Fadlo; Magliocca, Kelly; Maithel, Shishir; Olson, Jeffrey J.; Owonikoko, Taofeek; Pickens, Alan; Ramalingam, Suresh; Shin, Dong M.; Sica, Gabriel; Van Meir, Erwin G.; Zhang, Hongzheng; Eijckenboom, Wil; Gillis, Ad; Korpershoek, Esther; Looijenga, Leendert; Oosterhuis, Wolter; Stoop, Hans; van Kessel, Kim E.; Zwarthoff, Ellen C.; Calatozzolo, Chiara; Cuppini, Lucia; Cuzzubbo, Stefania; DiMeco, Francesco; Finocchiaro, Gaetano; Mattei, Luca; Perin, Alessandro; Pollo, Bianca; Chen, Chu; Houck, John; Lohavanichbutr, Pawadee; Hartmann, Arndt; Stoehr, Christine; Stoehr, Robert; Taubert, Helge; Wach, Sven; Wullich, Bernd; Kycler, Witold; Murawa, Dawid; Wiznerowicz, Maciej; Chung, Ki; Edenfield, W. Jeffrey; Martin, Julie; Baudin, Eric; Bubley, Glenn; Bueno, Raphael; De Rienzo, Assunta; Richards, William G.; Kalkanis, Steven; Mikkelsen, Tom; Noushmehr, Houtan; Scarpace, Lisa; Girard, Nicolas; Aymerich, Marta; Campo, Elias; Giné, Eva; Guillermo, Armando López; Van Bang, Nguyen; Hanh, Phan Thi; Phu, Bui Duc; Tang, Yufang; Colman, Howard; Evason, Kimberley; Dottino, Peter R.; Martignetti, John A.; Gabra, Hani; Juhl, Hartmut; Akeredolu, Teniola; Stepa, Serghei; Hoon, Dave; Ahn, Keunsoo; Kang, Koo Jeong; Beuschlein, Felix; Breggia, Anne; Birrer, Michael; Bell, Debra; Borad, Mitesh; Bryce, Alan H.; Castle, Erik; Chandan, Vishal; Cheville, John; Copland, John A.; Farnell, Michael; Flotte, Thomas; Giama, Nasra; Ho, Thai; Kendrick, Michael; Kocher, Jean Pierre; Kopp, Karla; Moser, Catherine; Nagorney, David; O'Brien, Daniel; O'Neill, Brian Patrick; Patel, Tushar; Petersen, Gloria; Que, Florencia; Rivera, Michael; Roberts, Lewis; Smallridge, Robert; Smyrk, Thomas; Stanton, Melissa; Thompson, R. Houston; Torbenson, Michael; Yang, Ju Dong; Zhang, Lizhi; Brimo, Fadi; Ajani, Jaffer A.; Angulo Gonzalez, Ana Maria; Behrens, Carmen; Bondaruk, Jolanta; Broaddus, Russell; Czerniak, Bogdan; Esmaeli, Bita; Fujimoto, Junya; Gershenwald, Jeffrey; Guo, Charles; Lazar, Alexander J.; Logothetis, Christopher; Meric-Bernstam, Funda; Moran, Cesar; Ramondetta, Lois; Rice, David; Sood, Anil; Tamboli, Pheroze; Thompson, Timothy; Troncoso, Patricia; Tsao, Anne; Wistuba, Ignacio; Carter, Candace; Haydu, Lauren; Hersey, Peter; Jakrot, Valerie; Kakavand, Hojabr; Kefford, Richard; Lee, Kenneth; Long, Georgina; Mann, Graham; Quinn, Michael; Saw, Robyn; Scolyer, Richard; Shannon, Kerwin; Spillane, Andrew; Stretch, Jonathan; Synott, Maria; Thompson, John; Wilmott, James; Al-Ahmadie, Hikmat; Chan, Timothy A.; Ghossein, Ronald; Gopalan, Anuradha; Levine, Douglas A.; Reuter, Victor; Singer, Samuel; Singh, Bhuvanesh; Tien, Nguyen Viet; Broudy, Thomas; Mirsaidi, Cyrus; Nair, Praveen; Drwiega, Paul; Miller, Judy; Smith, Jennifer; Zaren, Howard; Park, Joong Won; Hung, Nguyen Phi; Kebebew, Electron; Linehan, W. Marston; Metwalli, Adam R.; Pacak, Karel; Pinto, Peter A.; Schiffman, Mark; Schmidt, Laura S.; Vocke, Cathy D.; Wentzensen, Nicolas; Worrell, Robert; Yang, Hannah; Moncrieff, Marc; Goparaju, Chandra; Melamed, Jonathan; Pass, Harvey; Botnariuc, Natalia; Caraman, Irina; Cernat, Mircea; Chemencedji, Inga; Clipca, Adrian; Doruc, Serghei; Gorincioi, Ghenadie; Mura, Sergiu; Pirtac, Maria; Stancul, Irina; Tcaciuc, Diana; Albert, Monique; Alexopoulou, Iakovina; Arnaout, Angel; Bartlett, John; Engel, Jay; Gilbert, Sebastien; Parfitt, Jeremy; Sekhon, Harman; Thomas, George; Rassl, Doris M.; Rintoul, Robert C.; Bifulco, Carlo; Tamakawa, Raina; Urba, Walter; Hayward, Nicholas; Timmers, Henri; Antenucci, Anna; Facciolo, Francesco; Grazi, Gianluca; Marino, Mirella; Merola, Roberta; de Krijger, Ronald; Gimenez-Roqueplo, Anne Paule; Piché, Alain; Chevalier, Simone; McKercher, Ginette; Birsoy, Kivanc; Barnett, Gene; Brewer, Cathy; Farver, Carol; Naska, Theresa; Pennell, Nathan A.; Raymond, Daniel; Schilero, Cathy; Smolenski, Kathy; Williams, Felicia; Morrison, Carl; Borgia, Jeffrey A.; Liptay, Michael J.; Pool, Mark; Seder, Christopher W.; Junker, Kerstin; Omberg, Larsson; Dinkin, Mikhail; Manikhas, George; Alvaro, Domenico; Bragazzi, Maria Consiglia; Cardinale, Vincenzo; Carpino, Guido; Gaudio, Eugenio; Chesla, David; Cottingham, Sandra; Dubina, Michael; Moiseenko, Fedor; Dhanasekaran, Renumathy; Becker, Karl Friedrich; Janssen, Klaus Peter; Slotta-Huspenina, Julia; Abdel-Rahman, Mohamed H.; Aziz, Dina; Bell, Sue; Cebulla, Colleen M.; Davis, Amy; Duell, Rebecca; Elder, J. Bradley; Hilty, Joe; Kumar, Bahavna; Lang, James; Lehman, Norman L.; Mandt, Randy; Nguyen, Phuong; Pilarski, Robert; Rai, Karan; Schoenfield, Lynn; Senecal, Kelly; Wakely, Paul; Hansen, Paul; Lechan, Ronald; Powers, James; Tischler, Arthur; Grizzle, William E.; Sexton, Katherine C.; Kastl, Alison; Henderson, Joel; Porten, Sima; Waldmann, Jens; Fassnacht, Martin; Asa, Sylvia L.; Schadendorf, Dirk; Couce, Marta; Graefen, Markus; Huland, Hartwig; Sauter, Guido; Schlomm, Thorsten; Simon, Ronald; Tennstedt, Pierre; Olabode, Oluwole; Nelson, Mark; Bathe, Oliver; Carroll, Peter R.; Chan, June M.; Disaia, Philip; Glenn, Pat; Kelley, Robin K.; Landen, Charles N.; Phillips, Joanna; Prados, Michael; Simko, Jeffry; Smith-McCune, Karen; VandenBerg, Scott; Roggin, Kevin; Fehrenbach, Ashley; Kendler, Ady; Sifri, Suzanne; Steele, Ruth; Jimeno, Antonio; Carey, Francis; Forgie, Ian; Mannelli, Massimo; Carney, Michael; Hernandez, Brenda; Campos, Benito; Herold-Mende, Christel; Jungk, Christin; Unterberg, Andreas; von Deimling, Andreas; Bossler, Aaron; Galbraith, Joseph; Jacobus, Laura; Knudson, Michael; Knutson, Tina; Ma, Deqin; Milhem, Mohammed; Sigmund, Rita; Godwin, Andrew K.; Madan, Rashna; Rosenthal, Howard G.; Adebamowo, Clement; Adebamowo, Sally N.; Boussioutas, Alex; Beer, David; Giordano, Thomas; Mes-Masson, Anne Marie; Saad, Fred; Bocklage, Therese; Landrum, Lisa; Mannel, Robert; Moore, Kathleen; Moxley, Katherine; Postier, Russel; Walker, Joan; Zuna, Rosemary; Feldman, Michael; Valdivieso, Federico; Dhir, Rajiv; Luketich, James; Mora Pinero, Edna M.; Quintero-Aguilo, Mario; Carlotti, Carlos Gilberto; Dos Santos, Jose Sebastião; Kemp, Rafael; Sankarankuty, Ajith; Tirapelli, Daniela; Catto, James; Agnew, Kathy; Swisher, Elizabeth; Creaney, Jenette; Robinson, Bruce; Shelley, Carl Simon; Godwin, Eryn M.; Kendall, Sara; Shipman, Cassaundra; Bradford, Carol; Carey, Thomas; Haddad, Andrea; Moyer, Jeffey; Peterson, Lisa; Prince, Mark; Rozek, Laura; Wolf, Gregory; Bowman, Rayleen; Fong, Kwun M.; Yang, Ian; Korst, Robert; Rathmell, W. Kimryn; Fantacone-Campbell, J. Leigh; Hooke, Jeffrey A.; Kovatich, Albert J.; Shriver, Craig D.; DiPersio, John; Drake, Bettina; Govindan, Ramaswamy; Heath, Sharon; Ley, Timothy; Van Tine, Brian; Westervelt, Peter; Rubin, Mark A.; Lee, Jung Il; Aredes, Natália D.; Mariamidze, Armaz; Weinstein, John N.; Mills, Gordon B.; Levine, Douglas A.; Akbani, Rehan

    2018-01-01

    We analyzed molecular data on 2,579 tumors from The Cancer Genome Atlas (TCGA) of four gynecological types plus breast. Our aims were to identify shared and unique molecular features, clinically significant subtypes, and potential therapeutic targets. We found 61 somatic copy-number alterations

  6. Probiotic Survey in Cancer Patients Treated in the Outpatient Department in a Comprehensive Cancer Center.

    Science.gov (United States)

    Ciernikova, Sona; Mego, Michal; Semanova, Maria; Wachsmannova, Lenka; Adamcikova, Zuzana; Stevurkova, Viola; Drgona, Lubos; Zajac, Vladimir

    2017-06-01

    Availability without prescription restriction, low cost, and simple oral administration allow cancer patients to use probiotics without knowledge of potential risks. We present a survey of probiotic use and the association with patient tumor characteristics in cancer patients treated at the outpatient department of the National Cancer Institute in Slovakia. Between March and December 2014, 499 patients were asked to evaluate their overall experience with probiotics by questionnaire form, including the length and method of use relative to anticancer therapy, expectations, side-effect experiences, understanding of the possible risks, dietary supplement use, and others. The relevant data were statistically evaluated. The cohort consisted of 323 women (64.7%) and 176 men (35.3%); 91.6% were undergoing chemotherapy (2.6% together with radiotherapy) and 8.4% had no anticancer therapy. The prevalence of probiotic use was 28.5% and only 12 patients using probiotics (8.5%) described negative side effects. Most patients declared consideration of probiotic use based on recommendation from a physician (37.3%) or a pharmacist (14.8%). Nevertheless, up to 86.6% of patients declared no knowledge of possible risks. Statistically significant correlation was found between probiotic use and age of patients (P probiotic use in cancer patients. Minimal knowledge of risks underlines the importance of an active approach by oncologists to inform patients about probiotic safety.

  7. National Cancer Database Analysis of Proton Versus Photon Radiation Therapy in Non-Small Cell Lung Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Higgins, Kristin A., E-mail: kristin.higgins@emory.edu [Department of Radiation Oncology, Emory University, Atlanta, Georgia (United States); Winship Cancer Institute, Emory University, Atlanta, Georgia (United States); O' Connell, Kelli [Rollins School of Public Health, Emory University, Atlanta, Georgia (United States); Liu, Yuan [Winship Cancer Institute, Emory University, Atlanta, Georgia (United States); Rollins School of Public Health, Emory University, Atlanta, Georgia (United States); Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia (United States); Gillespie, Theresa W. [Winship Cancer Institute, Emory University, Atlanta, Georgia (United States); Department of Surgery, Emory University, Atlanta, Georgia (United States); McDonald, Mark W. [Department of Radiation Oncology, Emory University, Atlanta, Georgia (United States); Winship Cancer Institute, Emory University, Atlanta, Georgia (United States); Pillai, Rathi N. [Winship Cancer Institute, Emory University, Atlanta, Georgia (United States); Department of Hematology and Medical Oncology, Emory University, Atlanta, Georgia (United States); Patel, Kirtesh R.; Patel, Pretesh R. [Department of Radiation Oncology, Emory University, Atlanta, Georgia (United States); Winship Cancer Institute, Emory University, Atlanta, Georgia (United States); Robinson, Clifford G. [Department of Radiation Oncology, Washington University, St. Louis, Missouri (United States); Simone, Charles B. [Department of Radiation Oncology, University of Pennsylvania, Philadelphia, Pennsylvania (United States); Owonikoko, Taofeek K. [Winship Cancer Institute, Emory University, Atlanta, Georgia (United States); Department of Hematology and Medical Oncology, Emory University, Atlanta, Georgia (United States); Belani, Chandra P. [Penn State Hershey Cancer Institute, Pennsylvania University, Hershey, Pennsylvania (United States); and others

    2017-01-01

    Purpose: To analyze outcomes and predictors associated with proton radiation therapy for non-small cell lung cancer (NSCLC) in the National Cancer Database. Methods and Materials: The National Cancer Database was queried to capture patients with stage I-IV NSCLC treated with thoracic radiation from 2004 to 2012. A logistic regression model was used to determine the predictors for utilization of proton radiation therapy. The univariate and multivariable association with overall survival were assessed by Cox proportional hazards models along with log–rank tests. A propensity score matching method was implemented to balance baseline covariates and eliminate selection bias. Results: A total of 243,822 patients (photon radiation therapy: 243,474; proton radiation therapy: 348) were included in the analysis. Patients in a ZIP code with a median income of <$46,000 per year were less likely to receive proton treatment, with the income cohort of $30,000 to $35,999 least likely to receive proton therapy (odds ratio 0.63 [95% confidence interval (CI) 0.44-0.90]; P=.011). On multivariate analysis of all patients, non-proton therapy was associated with significantly worse survival compared with proton therapy (hazard ratio 1.21 [95% CI 1.06-1.39]; P<.01). On propensity matched analysis, proton radiation therapy (n=309) was associated with better 5-year overall survival compared with non-proton radiation therapy (n=1549), 22% versus 16% (P=.025). For stage II and III patients, non-proton radiation therapy was associated with worse survival compared with proton radiation therapy (hazard ratio 1.35 [95% CI 1.10-1.64], P<.01). Conclusions: Thoracic radiation with protons is associated with better survival in this retrospective analysis; further validation in the randomized setting is needed to account for any imbalances in patient characteristics, including positron emission tomography–computed tomography staging.

  8. Proton beam radiotherapy as part of comprehensive regional nodal irradiation for locally advanced breast cancer.

    Science.gov (United States)

    Verma, Vivek; Iftekaruddin, Zaid; Badar, Nida; Hartsell, William; Han-Chih Chang, John; Gondi, Vinai; Pankuch, Mark; Gao, Ming; Schmidt, Stacey; Kaplan, Darren; McGee, Lisa

    2017-05-01

    This study evaluates acute toxicity outcomes in breast cancer patients treated with adjuvant proton beam therapy (PBT). From 2011 to 2016, 91 patients (93 cancers) were treated with adjuvant PBT targeting the intact breast/chest wall and comprehensive regional nodes including the axilla, supraclavicular fossa, and internal mammary lymph nodes. Toxicity was recorded weekly during treatment, one month following treatment, and then every 6months according to the Common Terminology Criteria for Adverse Events (CTCAE) v4.0. Charts were retrospectively reviewed to verify toxicities, patient parameters, disease and treatment characteristics, and disease-related outcomes. Median follow-up was 15.5months. Median PBT dose was 50.4 Gray relative biological effectiveness (GyRBE), with subsequent boost as clinically indicated (N=61, median 10 GyRBE). Chemotherapy, when administered, was given adjuvantly (N=42) or neoadjuvantly (N=46). Grades 1, 2, and 3 dermatitis occurred in 23%, 72%, and 5%, respectively. Eight percent required treatment breaks owing to dermatitis. Median time to resolution of dermatitis was 32days. Grades 1, 2, and 3 esophagitis developed in 31%, 33%, and 0%, respectively. PBT displays acceptable toxicity in the setting of comprehensive regional nodal irradiation. Copyright © 2017. Published by Elsevier B.V.

  9. Algorithm for comprehensive care for patients with non melanoma skin cancer

    International Nuclear Information System (INIS)

    Victoria Bárzaga, Hector Oscar

    2011-01-01

    Sequence of actions, roles of doctors and paramedical staff, preventive and therapeutic methods, diagnostic and clinical monitoring mode: an algorithm for the comprehensive care of patients with non-melanoma skin cancer including presents. Consensus on the theoretical and practical basis of the algorithm was established by the Delphi expert method variant and health personnel involved were trained in its implementation. Algorithm for making national and international specialized literature on the subject was reviewed; a critical analysis of the methods specified in Cuba for the prevention, diagnosis and treatment of disease was made, and weaknesses were determined in the process of medical care for these patients in the Clinical Surgical Teaching Military Hospital D r. Octavio de la Concepción and Pedraja a nd health areas. The results obtained with the implementation of the algorithm demonstrated its effectiveness in comprehensive care for patients with non-melanoma skin cancer, because the prevention, early diagnosis, appropriate physical examination, the correct treatment ensured notification, monitoring periodic clinical and referral of complicated patients, the occurrence of rare complications. (author)

  10. The validation and clinical implementation of BRCAplus: a comprehensive high-risk breast cancer diagnostic assay.

    Directory of Open Access Journals (Sweden)

    Hansook Kim Chong

    Full Text Available Breast cancer is the most commonly diagnosed cancer in women, with 10% of disease attributed to hereditary factors. Although BRCA1 and BRCA2 account for a high percentage of hereditary cases, there are more than 25 susceptibility genes that differentially impact the risk for breast cancer. Traditionally, germline testing for breast cancer was performed by Sanger dideoxy terminator sequencing in a reflexive manner, beginning with BRCA1 and BRCA2. The introduction of next-generation sequencing (NGS has enabled the simultaneous testing of all genes implicated in breast cancer resulting in diagnostic labs offering large, comprehensive gene panels. However, some physicians prefer to only test for those genes in which established surveillance and treatment protocol exists. The NGS based BRCAplus test utilizes a custom tiled PCR based target enrichment design and bioinformatics pipeline coupled with array comparative genomic hybridization (aCGH to identify mutations in the six high-risk genes: BRCA1, BRCA2, PTEN, TP53, CDH1, and STK11. Validation of the assay with 250 previously characterized samples resulted in 100% detection of 3,025 known variants and analytical specificity of 99.99%. Analysis of the clinical performance of the first 3,000 BRCAplus samples referred for testing revealed an average coverage greater than 9,000X per target base pair resulting in excellent specificity and the sensitivity to detect low level mosaicism and allele-drop out. The unique design of the assay enabled the detection of pathogenic mutations missed by previous testing. With the abundance of NGS diagnostic tests being released, it is essential that clinicians understand the advantages and limitations of different test designs.

  11. Work Experiences of Patients Receiving Palliative Care at a Comprehensive Cancer Center: Exploratory Analysis.

    Science.gov (United States)

    Glare, Paul A; Nikolova, Tanya; Alickaj, Alberta; Patil, Sujata; Blinder, Victoria

    2017-07-01

    Employment-related issues have been largely overlooked in cancer patients needing palliative care. These issues may become more relevant as cancer evolves into more of a chronic illness and palliative care is provided independent of stage or prognosis. To characterize the employment situations of working-age palliative care patients. Cross-sectional survey setting/subjects: Consecutive sample of 112 patients followed in palliative care outpatient clinics at a comprehensive cancer center. Thirty-seven-item self-report questionnaire covering demographics, clinical status, and work experiences since diagnosis. The commonest cancer diagnoses were breast, colorectal, gynecological, and lung. Eighty-one percent had active disease. Seventy-four percent were on treatment. Eighty percent recalled being employed at the time of diagnosis, with 65% working full time. At the time of the survey, 44% were employed and 26% were working full time. Most participants said work was important, made them feel normal, and helped them feel they were "beating the cancer". Factors associated with being employed included male gender, self-employed, and taking less than three months off work. Respondents with pain and/or other symptoms were significantly less likely to be working. On multivariate analysis, only pain (odds ratio [OR] 8.16, p gender (OR 2.07), self-employed (OR 3.07), and current chemotherapy (OR 1.81) were included in the model, but were not statistically significant in this small sample. Work may be an important issue for some palliative care patients. Additional research is needed to facilitate ongoing employment for those who wish or need to continue working.

  12. A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability

    Directory of Open Access Journals (Sweden)

    Reinders Marcel JT

    2009-11-01

    Full Text Available Abstract Background Large discrepancies in signature composition and outcome concordance have been observed between different microarray breast cancer expression profiling studies. This is often ascribed to differences in array platform as well as biological variability. We conjecture that other reasons for the observed discrepancies are the measurement error associated with each feature and the choice of preprocessing method. Microarray data are known to be subject to technical variation and the confidence intervals around individual point estimates of expression levels can be wide. Furthermore, the estimated expression values also vary depending on the selected preprocessing scheme. In microarray breast cancer classification studies, however, these two forms of feature variability are almost always ignored and hence their exact role is unclear. Results We have performed a comprehensive sensitivity analysis of microarray breast cancer classification under the two types of feature variability mentioned above. We used data from six state of the art preprocessing methods, using a compendium consisting of eight diferent datasets, involving 1131 hybridizations, containing data from both one and two-color array technology. For a wide range of classifiers, we performed a joint study on performance, concordance and stability. In the stability analysis we explicitly tested classifiers for their noise tolerance by using perturbed expression profiles that are based on uncertainty information directly related to the preprocessing methods. Our results indicate that signature composition is strongly influenced by feature variability, even if the array platform and the stratification of patient samples are identical. In addition, we show that there is often a high level of discordance between individual class assignments for signatures constructed on data coming from different preprocessing schemes, even if the actual signature composition is identical

  13. Bibliographic survey on methodologies for development of health database of the population in case of cancer occurrences

    International Nuclear Information System (INIS)

    Cavinato, Christianne C.; Andrade, Delvonei A. de; Sabundjian, Gaiane; Diz, Maria Del Pilar E.

    2014-01-01

    The objective is to make a survey of existing methodologies and for the development of public health database, focusing on health (fatal and nonfatal cancer) of the population surrounding a nuclear facility, for purposes of calculating the environmental cost of the same. From methodologies found to develop this type of database, a methodology will be developed to be applied to the internal public of IPEN/CNEN-SP, Brazil, as a pre-test for the acquisition of health information desired

  14. Primary treatments for clinically localised prostate cancer: a comprehensive lifetime cost-utility analysis.

    Science.gov (United States)

    Cooperberg, Matthew R; Ramakrishna, Naren R; Duff, Steven B; Hughes, Kathleen E; Sadownik, Sara; Smith, Joseph A; Tewari, Ashutosh K

    2013-03-01

    WHAT'S KNOWN ON THE SUBJECT? AND WHAT DOES THE STUDY ADD?: Multiple treatment alternatives exist for localised prostate cancer, with few high-quality studies directly comparing their comparative effectiveness and costs. The present study is the most comprehensive cost-effectiveness analysis to date for localised prostate cancer, conducted with a lifetime horizon and accounting for survival, health-related quality-of-life, and cost impact of secondary treatments and other downstream events, as well as primary treatment choices. The analysis found minor differences, generally slightly favouring surgical methods, in quality-adjusted life years across treatment options. However, radiation therapy (RT) was consistently more expensive than surgery, and some alternatives, e.g. intensity-modulated RT for low-risk disease, were dominated - that is, both more expensive and less effective than competing alternatives. To characterise the costs and outcomes associated with radical prostatectomy (open, laparoscopic, or robot-assisted) and radiation therapy (RT: dose-escalated three-dimensional conformal RT, intensity-modulated RT, brachytherapy, or combination), using a comprehensive, lifetime decision analytical model. A Markov model was constructed to follow hypothetical men with low-, intermediate-, and high-risk prostate cancer over their lifetimes after primary treatment; probabilities of outcomes were based on an exhaustive literature search yielding 232 unique publications. In each Markov cycle, patients could have remission, recurrence, salvage treatment, metastasis, death from prostate cancer, and death from other causes. Utilities for each health state were determined, and disutilities were applied for complications and toxicities of treatment. Costs were determined from the USA payer perspective, with incorporation of patient costs in a sensitivity analysis. Differences across treatments in quality-adjusted life years across methods were modest, ranging from 10.3 to

  15. A Comprehensive Software and Database Management System for Glomerular Filtration Rate Estimation by Radionuclide Plasma Sampling and Serum Creatinine Methods.

    Science.gov (United States)

    Jha, Ashish Kumar

    2015-01-01

    Glomerular filtration rate (GFR) estimation by plasma sampling method is considered as the gold standard. However, this method is not widely used because the complex technique and cumbersome calculations coupled with the lack of availability of user-friendly software. The routinely used Serum Creatinine method (SrCrM) of GFR estimation also requires the use of online calculators which cannot be used without internet access. We have developed user-friendly software "GFR estimation software" which gives the options to estimate GFR by plasma sampling method as well as SrCrM. We have used Microsoft Windows(®) as operating system and Visual Basic 6.0 as the front end and Microsoft Access(®) as database tool to develop this software. We have used Russell's formula for GFR calculation by plasma sampling method. GFR calculations using serum creatinine have been done using MIRD, Cockcroft-Gault method, Schwartz method, and Counahan-Barratt methods. The developed software is performing mathematical calculations correctly and is user-friendly. This software also enables storage and easy retrieval of the raw data, patient's information and calculated GFR for further processing and comparison. This is user-friendly software to calculate the GFR by various plasma sampling method and blood parameter. This software is also a good system for storing the raw and processed data for future analysis.

  16. Patients with advanced and metastatic renal cell carcinoma treated with targeted therapy in the Czech Republic: twenty cancer centres, six agents, one database.

    Science.gov (United States)

    Poprach, Alexandr; Bortlíček, Zbyněk; Büchler, Tomáš; Melichar, Bohuslav; Lakomý, Radek; Vyzula, Rostislav; Brabec, Petr; Svoboda, Marek; Dušek, Ladislav; Gregor, Jakub

    2012-12-01

    The incidence and mortality of renal cell carcinoma (RCC) in the Czech Republic are among the highest in the world. Several targeted agents have been recently approved for the treatment of advanced/metastatic RCC. Presentation of a national clinical database for monitoring and assessment of patients with advanced/metastatic RCC treated with targeted therapy. The RenIS (RENal Information System, http://renis.registry.cz ) registry is a non-interventional post-registration database of epidemiological and clinical data of patients with RCC treated with targeted therapies in the Czech Republic. Twenty cancer centres eligible for targeted therapy administration participate in the project. As of November 2011, six agents were approved and reimbursed from public health insurance, including bevacizumab, everolimus, pazopanib, sorafenib, sunitinib, and temsirolimus. As of 10 October 2011, 1,541 patients with valid records were entered into the database. Comparison with population-based data from the Czech National Cancer Registry revealed that RCC patients treated with targeted therapy are significantly younger (median age at diagnosis 59 vs. 66 years). Most RenIS registry patients were treated with sorafenib and sunitinib, many patients sequentially with both agents. Over 10 % of patients were also treated with everolimus in the second or third line. Progression-free survival times achieved were comparable to phase III clinical trials. The RenIS registry has become an important tool and source of information for the management of cancer care and clinical practice, providing comprehensive data on monitoring and assessment of RCC targeted therapy on a national level.

  17. [Using cancer case identification algorithms in medico-administrative databases: Literature review and first results from the REDSIAM Tumors group based on breast, colon, and lung cancer].

    Science.gov (United States)

    Bousquet, P-J; Caillet, P; Coeuret-Pellicer, M; Goulard, H; Kudjawu, Y C; Le Bihan, C; Lecuyer, A I; Séguret, F

    2017-10-01

    The development and use of healthcare databases accentuates the need for dedicated tools, including validated selection algorithms of cancer diseased patients. As part of the development of the French National Health Insurance System data network REDSIAM, the tumor taskforce established an inventory of national and internal published algorithms in the field of cancer. This work aims to facilitate the choice of a best-suited algorithm. A non-systematic literature search was conducted for various cancers. Results are presented for lung, breast, colon, and rectum. Medline, Scopus, the French Database in Public Health, Google Scholar, and the summaries of the main French journals in oncology and public health were searched for publications until August 2016. An extraction grid adapted to oncology was constructed and used for the extraction process. A total of 18 publications were selected for lung cancer, 18 for breast cancer, and 12 for colorectal cancer. Validation studies of algorithms are scarce. When information is available, the performance and choice of an algorithm are dependent on the context, purpose, and location of the planned study. Accounting for cancer disease specificity, the proposed extraction chart is more detailed than the generic chart developed for other REDSIAM taskforces, but remains easily usable in practice. This study illustrates the complexity of cancer detection through sole reliance on healthcare databases and the lack of validated algorithms specifically designed for this purpose. Studies that standardize and facilitate validation of these algorithms should be developed and promoted. Copyright © 2017. Published by Elsevier Masson SAS.

  18. Report on comprehensive surveys of nationwide geothermal resources in fiscal 1979. Conceptual design of a database system; 1979 nendo zenkoku chinetsu shigen sogo chosa hokokusho. Database system gainen sekkei

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1980-03-31

    Conceptual design was made on a database system as part of the comprehensive surveys of nationwide geothermal resources. Underground hot water in depths of several kilometers close to the ground surface is a utilizable geothermal energy. Exploration using the ground surface survey is much less expensive than the test drilling survey, but has greater error in estimation because of being an indirect method. However, integrating data by freely using a number of exploration methods can improve the accuracy of estimation on the whole. In performing the conceptual design of a geothermal resource information system, the functions of this large scale database were used as the framework. Further data collection, distribution and interactive type man-machine communication, modeling, and environment surveillance functions were incorporated. Considerations were also given on further diversified utilization patterns and on support to users in remote areas and end users. What is important in designing the system is that constituting elements of hardware and software should function while being combined organically as one system, rather than the elements work independently. In addition, sufficient expandability and flexibility are indispensable. (NEDO)

  19. CIG-DB: the database for human or mouse immunoglobulin and T cell receptor genes available for cancer studies

    Directory of Open Access Journals (Sweden)

    Furue Motoki

    2010-07-01

    Full Text Available Abstract Background Immunoglobulin (IG or antibody and the T-cell receptor (TR are pivotal proteins in the immune system of higher organisms. In cancer immunotherapy, the immune responses mediated by tumor-epitope-binding IG or TR play important roles in anticancer effects. Although there are public databases specific for immunological genes, their contents have not been associated with clinical studies. Therefore, we developed an integrated database of IG/TR data reported in cancer studies (the Cancer-related Immunological Gene Database [CIG-DB]. Description This database is designed as a platform to explore public human and murine IG/TR genes sequenced in cancer studies. A total of 38,308 annotation entries for IG/TR proteins were collected from GenBank/DDBJ/EMBL and the Protein Data Bank, and 2,740 non-redundant corresponding MEDLINE references were appended. Next, we filtered the MEDLINE texts by MeSH terms, titles, and abstracts containing keywords related to cancer. After we performed a manual check, we classified the protein entries into two groups: 611 on cancer therapy (Group I and 1,470 on hematological tumors (Group II. Thus, a total of 2,081 cancer-related IG and TR entries were tabularized. To effectively classify future entries, we developed a computational method based on text mining and canonical discriminant analysis by parsing MeSH/title/abstract words. We performed a leave-one-out cross validation for the method, which showed high accuracy rates: 94.6% for IG references and 94.7% for TR references. We also collected 920 epitope sequences bound with IG/TR. The CIG-DB is equipped with search engines for amino acid sequences and MEDLINE references, sequence analysis tools, and a 3D viewer. This database is accessible without charge or registration at http://www.scchr-cigdb.jp/, and the search results are freely downloadable. Conclusions The CIG-DB serves as a bridge between immunological gene data and cancer studies, presenting

  20. Marital status independently predicts gastric cancer survival after surgical resection--an analysis of the SEER database

    OpenAIRE

    Shi, Rong-liang; Chen, Qian; Yang, Zhen; Pan, Gaofeng; Zhang, Ziping; Wang, WeiHua; Liu, Shaoqun; Zhang, Dongbin; Jiang, Daowen; Liu, Weiyan

    2016-01-01

    Marital status was found to be an independent prognostic factor for survival in various cancer types, but it hasn't been studied in gastric cancer. The Surveillance, Epidemiology and End Results database was used to compare survival outcomes with marital status. A total of 16,106 eligible patients were identified. Patients in the widowed group had the highest proportion of women, more common site of stomach, more prevalence of elderly patients, higher percentage of adenocarcinoma, and more tu...

  1. Comprehensive evaluation of one-carbon metabolism pathway gene variants and renal cell cancer risk.

    Directory of Open Access Journals (Sweden)

    Todd M Gibson

    Full Text Available Folate and one-carbon metabolism are linked to cancer risk through their integral role in DNA synthesis and methylation. Variation in one-carbon metabolism genes, particularly MTHFR, has been associated with risk of a number of cancers in epidemiologic studies, but little is known regarding renal cancer.Tag single nucleotide polymorphisms (SNPs selected to produce high genomic coverage of 13 gene regions of one-carbon metabolism (ALDH1L1, BHMT, CBS, FOLR1, MTHFR, MTR, MTRR, SHMT1, SLC19A1, TYMS and the closely associated glutathione synthesis pathway (CTH, GGH, GSS were genotyped for 777 renal cell carcinoma (RCC cases and 1,035 controls in the Central and Eastern European Renal Cancer case-control study. Associations of individual SNPs (n = 163 with RCC risk were calculated using unconditional logistic regression adjusted for age, sex and study center. Minimum p-value permutation (Min-P tests were used to identify gene regions associated with risk, and haplotypes were evaluated within these genes.The strongest associations with RCC risk were observed for SLC19A1 (P(min-P = 0.03 and MTHFR (P(min-P = 0.13. A haplotype consisting of four SNPs in SLC19A1 (rs12483553, rs2838950, rs2838951, and rs17004785 was associated with a 37% increased risk (p = 0.02, and exploratory stratified analysis suggested the association was only significant among those in the lowest tertile of vegetable intake.To our knowledge, this is the first study to comprehensively examine variation in one-carbon metabolism genes in relation to RCC risk. We identified a novel association with SLC19A1, which is important for transport of folate into cells. Replication in other populations is required to confirm these findings.

  2. Prevalence, risk factors and clinical implications of malnutrition in French Comprehensive Cancer Centres

    Science.gov (United States)

    Pressoir, M; Desné, S; Berchery, D; Rossignol, G; Poiree, B; Meslier, M; Traversier, S; Vittot, M; Simon, M; Gekiere, J P; Meuric, J; Serot, F; Falewee, M N; Rodrigues, I; Senesse, P; Vasson, M P; Chelle, F; Maget, B; Antoun, S; Bachmann, P

    2010-01-01

    Background: This epidemiological observational study aimed at determining the prevalence of malnutrition in non-selected adults with cancer, to identify risk factors of malnutrition and correlate the results with length of stay and 2-month mortality. Methods: This prospective multicentre 1-day study conducted in 17 French Comprehensive Cancer Centres included 1545 patients. Body mass index (BMI), weight loss (WL) in the past 6 months and age were routinely recorded according to the French national recommendations for hospitalised patients; malnutrition was rated as absent, moderate or severe according to the level of WL and BMI. Age, sex, tumour site, type of hospitalisation and treatment, disease stage, World Health Organisation performance status (PS) and antibiotic therapy were the potential malnutrition risk factors tested. Follow-up at 2 months allowed to determine the correlation with length of stay and mortality. Results: Malnutrition was reported in 30.9% of patients, and was rated as severe in 12.2%. In multivariate analysis, only pre-existing obesity (BMI⩾30), PS ⩾2 and head-and-neck or upper digestive cancers were associated with increased risk of malnutrition. Antibiotics use was significantly higher in malnourished patients (35.5 vs 22.8% Pmalnutrition was independently associated with mortality. The median length of stay was 19.3±19.4 days for malnourished patients vs 13.3±19.4 days for others (Pmalnutrition in our cancer patient population perhaps because of a misidentification or a delay in nutrition support in this category of patients. PMID:20160725

  3. Differences in esophageal cancer characteristics and survival between Chinese and Caucasian patients in the SEER database

    Directory of Open Access Journals (Sweden)

    Lin MQ

    2016-10-01

    Full Text Available Min-Qiang Lin,1,* Yue-Ping Li,2,* San-Gang Wu,3 Jia-Yuan Sun,4 Huan-Xin Lin,4 Shi-Yang Zhang,5 Zhen-Yu He4 1Department of Scientific Management, The First Affiliated Hospital of Xiamen University, Xiamen, 2Public Health School of Fujian Medical University, Fuzhou, 3Department of Radiation Oncology, The First Affiliated Hospital of Xiamen University, Xiamen, 4Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 5Department of Hospital Infection Management, The First Affiliated Hospital of Xiamen University, Xiamen, People’s Republic of China *These authors contributed equally to this work Background: To compare the clinicopathologic characteristics and survival of Chinese and Caucasian esophageal cancer (EC patients residing in the US, using a population-based national registry (Surveillance Epidemiology and End Results [SEER] database. Methods: Patients with EC were identified from the SEER program from 1988 to 2012. Kaplan–Meier survival methods and Cox proportional hazards regression were performed.Results: A total of 479 Chinese and 35,748 Caucasian EC patients were identified. Compared with Caucasian patients, the Chinese patients had a later year of diagnosis, remained married after EC was diagnosed, had esophageal squamous cell carcinomas (ESCCs more frequently, had tumors located in the upper-third and middle-third of the esophagus more frequently, and fewer patients presented with poorly/undifferentiated EC and underwent cancer-directed surgery. In Chinese patients, the incidence of esophageal adenocarcinomas (EACs increased from 1988 to 2012 (P=0.054, and the majority of EAC patients had tumors located in the lower thoracic esophagus. The overall survival (OS was not significantly different between Chinese and Caucasian patients (P=0.767. However, Chinese patients with ESCC had a significantly better

  4. Oncological Outcomes After Robotic Proctectomy for Rectal Cancer: Analysis of a Prospective Database.

    Science.gov (United States)

    Sammour, Tarik; Malakorn, Songphol; Bednarski, Brian K; Kaur, Harmeet; Shin, Ui Sup; Messick, Craig; You, Yi-Qian Nancy; Chang, George J

    2018-03-01

    The aim of this study is to evaluate the oncological outcomes of robotic total mesorectal excision (TME) at an NCI designated cancer center. The effectiveness of laparoscopic TME could not be established, but the robotic-assisted approach may hold some promise, with improved visualization and ergonomics for pelvic dissection. Oncological outcome data is presently lacking. Patients who underwent total mesorectal excision or tumor-specific mesorectal excision for rectal cancer between April 2009 and April 2016 via a robotic approach were identified from a prospective single-institution database. The circumferential resection margin (CRM), distal resection margin, and TME completeness rates were determined. Kaplan-Meier analysis of disease-free survival and overall survival was performed for all patients treated with curative intent. A total of 276 patients underwent robotic proctectomy during the study period. Robotic surgery was performed initially by 1 surgeon with 3 additional surgeons progressively transitioning from open to robotic during the study period with annual increase in the total number of cases performed robotically. Seven patients had involved circumferential resection margins (2.5%), and there were no positive distal or proximal resection margins. One hundred eighty-six patients had TME quality assessed, and only 1 patient (0.5%) had an incomplete TME. Eighty-three patients were followed up for a minimum of 3 years, with a local recurrence rate of 2.4%, and a distant recurrence rate of 16.9%. Five-year disease-free survival on Kaplan-Meier analysis was 82%, and 5-year overall survival was 87%. Robotic proctectomy for rectal cancer can be performed with good short and medium term oncological outcomes in selected patients.

  5. Comprehensive evaluation of cervical cancer screening programs: the case of Colombia

    Directory of Open Access Journals (Sweden)

    Raúl Murillo

    2011-12-01

    Full Text Available OBJECTIVE: To identify critical screening program factors for reducing cervical cancer mortality in Colombia. MATERIAL AND METHODS: Coverage, quality, and screening follow-up were evaluated in four Colombian states with different mortality rates. A case-control study (invasive cancer and healthy controls evaluating screening history was performed. RESULTS: 3-year cytology coverage was 72.7%, false negative rate 49%, positive cytology follow-up 64.2%. There was no association between screening history and invasive cancer in two states having high cytology coverage but high false negative rates. Two states revealed association between deficient screening history and invasive cancer as well as lower positive-cytology follow-up. CONCLUSIONS: Reduced number of visits between screening and treatment is more relevant when low access to health care is present. Improved quality is a priority if access to screening is available. Suitable interventions for specific scenarios and proper appraisal of new technologies are compulsory to improve cervical cancer screening. Comprehensive process-failure audits among invasive cancer cases could improve program evaluation since mortality is a late outcome.OBJETIVO: Identificar factores críticos para reducir la mortalidad por cáncer cervical en Colombia. MATERIAL Y MÉTODOS: Se evaluó cobertura, calidad y seguimiento del tamizaje en cuatro departamentos con tasas de mortalidad diferenciales. Un estudio de casos (cáncer invasor y controles (sanos evaluó historia de tamizaje. RESULTADOS: Cobertura 72,7%; falsos negativos 49%; acceso a diagnóstico-tratamiento de HSIL 64,2%. La historia de tamizaje no se asoció con cáncer invasor en dos departamentos con elevada cobertura pero elevada proporción de falsos negativos. Dos departamentos con asociación entre historia de tamizaje deficiente y cáncer invasor tuvieron cobertura aceptable pero bajo acceso a diagnóstico-tratamiento. No hubo relación entre mortalidad

  6. LoopX: A Graphical User Interface-Based Database for Comprehensive Analysis and Comparative Evaluation of Loops from Protein Structures.

    Science.gov (United States)

    Kadumuri, Rajashekar Varma; Vadrevu, Ramakrishna

    2017-10-01

    Due to their crucial role in function, folding, and stability, protein loops are being targeted for grafting/designing to create novel or alter existing functionality and improve stability and foldability. With a view to facilitate a thorough analysis and effectual search options for extracting and comparing loops for sequence and structural compatibility, we developed, LoopX a comprehensively compiled library of sequence and conformational features of ∼700,000 loops from protein structures. The database equipped with a graphical user interface is empowered with diverse query tools and search algorithms, with various rendering options to visualize the sequence- and structural-level information along with hydrogen bonding patterns, backbone φ, ψ dihedral angles of both the target and candidate loops. Two new features (i) conservation of the polar/nonpolar environment and (ii) conservation of sequence and conformation of specific residues within the loops have also been incorporated in the search and retrieval of compatible loops for a chosen target loop. Thus, the LoopX server not only serves as a database and visualization tool for sequence and structural analysis of protein loops but also aids in extracting and comparing candidate loops for a given target loop based on user-defined search options.

  7. Comprehensive profiling of DNA methylation in colorectal cancer reveals subgroups with distinct clinicopathological and molecular features

    International Nuclear Information System (INIS)

    Ang, Pei Woon; Soong, Richie; Loh, Marie; Liem, Natalia; Lim, Pei Li; Grieu, Fabienne; Vaithilingam, Aparna; Platell, Cameron; Yong, Wei Peng; Iacopetta, Barry

    2010-01-01

    Most previous studies of the CpG island methylator phenotype (CIMP) in colorectal cancer (CRC) have been conducted on a relatively small numbers of CpG sites. In the present study we performed comprehensive DNA methylation profiling of CRC with the aim of characterizing CIMP subgroups. DNA methylation at 1,505 CpG sites in 807 cancer-related genes was evaluated using the Illumina GoldenGate ® methylation array in 28 normal colonic mucosa and 91 consecutive CRC samples. Methylation data was analyzed using unsupervised hierarchical clustering. CIMP subgroups were compared for various clinicopathological and molecular features including patient age, tumor site, microsatellite instability (MSI), methylation at a consensus panel of CpG islands and mutations in BRAF and KRAS. A total of 202 CpG sites were differentially methylated between tumor and normal tissue. Unsupervised hierarchical clustering of methylation data from these sites revealed the existence of three CRC subgroups referred to as CIMP-low (CIMP-L, 21% of cases), CIMP-mid (CIMP-M, 14%) and CIMP-high (CIMP-H, 65%). In comparison to CIMP-L tumors, CIMP-H tumors were more often located in the proximal colon and showed more frequent mutation of KRAS and BRAF (P < 0.001). Comprehensive DNA methylation profiling identified three CRC subgroups with distinctive clinicopathological and molecular features. This study suggests that both KRAS and BRAF mutations are involved with the CIMP-H pathway of CRC rather than with distinct CIMP subgroups

  8. Comprehensive profiling of DNA methylation in colorectal cancer reveals subgroups with distinct clinicopathological and molecular features

    Directory of Open Access Journals (Sweden)

    Vaithilingam Aparna

    2010-05-01

    Full Text Available Abstract Background Most previous studies of the CpG island methylator phenotype (CIMP in colorectal cancer (CRC have been conducted on a relatively small numbers of CpG sites. In the present study we performed comprehensive DNA methylation profiling of CRC with the aim of characterizing CIMP subgroups. Methods DNA methylation at 1,505 CpG sites in 807 cancer-related genes was evaluated using the Illumina GoldenGate® methylation array in 28 normal colonic mucosa and 91 consecutive CRC samples. Methylation data was analyzed using unsupervised hierarchical clustering. CIMP subgroups were compared for various clinicopathological and molecular features including patient age, tumor site, microsatellite instability (MSI, methylation at a consensus panel of CpG islands and mutations in BRAF and KRAS. Results A total of 202 CpG sites were differentially methylated between tumor and normal tissue. Unsupervised hierarchical clustering of methylation data from these sites revealed the existence of three CRC subgroups referred to as CIMP-low (CIMP-L, 21% of cases, CIMP-mid (CIMP-M, 14% and CIMP-high (CIMP-H, 65%. In comparison to CIMP-L tumors, CIMP-H tumors were more often located in the proximal colon and showed more frequent mutation of KRAS and BRAF (P Conclusions Comprehensive DNA methylation profiling identified three CRC subgroups with distinctive clinicopathological and molecular features. This study suggests that both KRAS and BRAF mutations are involved with the CIMP-H pathway of CRC rather than with distinct CIMP subgroups.

  9. Incorporating person centred care principles into an ongoing comprehensive cancer management program: An experiential account

    Directory of Open Access Journals (Sweden)

    Vallath Nandini

    2011-01-01

    Full Text Available Recent research indicates a definite positive impact on treatment outcomes when an integrative approach that focuses on symptom control and quality of life is provided along with the standard therapeutic regimens. However implementation or practice of this approach is not seen widely due to the culture of medical training and practice. This article presents the initial development of a program for incorporating integrative care principles into an ongoing comprehensive cancer care program at a tertiary centre. The key purpose of the program being to develop, facilitate, and establish comprehensive and holistic processes including palliative care principles, that would positively enhance the quantity and quality of life of the person with disease, as well as create an environment that reflects and sustains this approach. The vision, objectives, goals, strategies, activities and results within the 7 months of implementation are documented. The new learnings gained during the process have also been noted in the hope that the model described may be used to conceptualize similar care giving facilities in other centres.

  10. Subject and authorship of records related to the Organization for Tropical Studies (OTS in BINABITROP, a comprehensive database about Costa Rican biology

    Directory of Open Access Journals (Sweden)

    Julián Monge-Nájera

    2013-06-01

    Full Text Available BINABITROP is a bibliographical database of more than 38 000 records about the ecosystems and organisms of Costa Rica. In contrast with commercial databases, such as Web of Knowledge and Scopus, which exclude most of the scientific journals published in tropical countries, BINABITROP is a comprehensive record of knowledge on the tropical ecosystems and organisms of Costa Rica. We analyzed its contents in three sites (La Selva, Palo Verde and Las Cruces and recorded scientific field, taxonomic group and authorship. We found that most records dealt with ecology and systematics, and that most authors published only one article in the study period (1963-2011. Most research was published in four journals: Biotropica, Revista de Biología Tropical/ International Journal of Tropical Biology and Conservation, Zootaxa and Brenesia. This may be the first study of a such a comprehensive database for any case of tropical biology literature.BINABITROP es una base de datos bibliográfica con más de 38 000 registros sobre los ecosistemas y organismos de Costa Rica. En contraste con bases de datos comerciales como Web of Knowledge y Scopus, que excluyen a la mayoría de las revistas científicas publicadas en los países tropicales, BINABITROP registra casi por completo la literatura biológica sobre Costa Rica. Analizamos los registros de La Selva, Palo Verde y Las Cruces. Hallamos que la mayoría de los registros corresponden a estudios sobre ecología y sistemática; que la mayoría de los autores sólo registraron un artículo en el período de estudio (1963-2011 y que la mayoría de la investigación formalmente publicada apareció en cuatro revistas: Biotropica, Revista de Biología Tropical/International Journal of Tropical Biology, Zootaxa y Brenesia. Este parece ser el primer estudio de una base de datos integral sobre literatura de biología tropical.

  11. Recent Advances in the Surgical Treatment of Differentiated Thyroid Cancer: A Comprehensive Review

    Directory of Open Access Journals (Sweden)

    Raghunandan Venkat

    2013-01-01

    Full Text Available Differentiated thyroid cancers have become one of the fastest growing malignancies in the world. While surgery has remained the cornerstone of management of these tumors, the surgical approach has seen numerous innovations over the past few decades. The use of video-assistance and robotics has revolutionized thyroid surgery. This paper provides a comprehensive evaluation of the different approaches to thyroid surgery, the utility of prophylactic and therapeutic lymph node dissection, and evidence-based guidelines in the treatment of differentiated thyroid cancers. Minimally invasive video-ssisted thyroidectomy is both safe and effective in the hands of the trained surgeon and, in selected patient populations, has comparative perioperative morbidity and better cosmesis as compared to conventional open thyroidectomy. It is universally accepted that therapeutic central lymph node dissection should be performed when metastatic lymph nodes are identified on physical exam, ultrasound, or intraoperatively. In the absence of overt nodal metastasis, the role of elective prophylactic central lymph node dissection remains a matter of debate and prospective, randomized studies are warranted to evaluate the utility of this procedure.

  12. Disparities in Adherence to National Comprehensive Cancer Network Treatment Guidelines and Survival for Stage IB-IIA Cervical Cancer in California.

    Science.gov (United States)

    Pfaendler, Krista S; Chang, Jenny; Ziogas, Argyrios; Bristow, Robert E; Penner, Kristine R

    2018-05-01

    To evaluate the association of sociodemographic and hospital characteristics with adherence to National Comprehensive Cancer Network treatment guidelines for stage IB-IIA cervical cancer and to analyze the relationship between adherent care and survival. This is a retrospective population-based cohort study of patients with stage IB-IIA invasive cervical cancer reported to the California Cancer Registry from January 1, 1995, through December 31, 2009. Adherence to National Comprehensive Cancer Network guideline care was defined by year- and stage-appropriate surgical procedures, radiation, and chemotherapy. Multivariate logistic regression, Kaplan-Meier estimate, and Cox proportional hazard models were used to examine associations between patient, tumor, and treatment characteristics and National Comprehensive Cancer Network guideline adherence and cervical cancer-specific 5-year survival. A total of 6,063 patients were identified. Forty-seven percent received National Comprehensive Cancer Network guideline-adherent care, and 18.8% were treated in high-volume centers (20 or more patients/year). On multivariate analysis, lowest socioeconomic status (adjusted odds ratio [OR] 0.69, 95% CI 0.57-0.84), low-middle socioeconomic status (adjusted OR 0.76, 95% CI 0.64-0.92), and Charlson-Deyo comorbidity score 1 or higher (adjusted OR 0.78, 95% CI 0.69-0.89) were patient characteristics associated with receipt of nonguideline care. Receiving adherent care was less common in low-volume centers (45.9%) than in high-volume centers (50.9%) (effect size 0.90, 95% CI 0.84-0.96). Death from cervical cancer was more common in the nonadherent group (13.3%) than in the adherent group (8.6%) (effect size 1.55, 95% CI 1.34-1.80). Black race (adjusted hazard ratio 1.56, 95% CI 1.08-2.27), Medicaid payer status (adjusted hazard ratio 1.47, 95% CI 1.15-1.87), and Charlson-Deyo comorbidity score 1 or higher (adjusted hazard ratio 2.07, 95% CI 1.68-2.56) were all associated with increased

  13. A Comprehensive Comparison of IMRT and VMAT Plan Quality for Prostate Cancer Treatment

    International Nuclear Information System (INIS)

    Quan, Enzhuo M.; Li Xiaoqiang; Li Yupeng; Wang Xiaochun; Kudchadker, Rajat J.; Johnson, Jennifer L.; Kuban, Deborah A.; Lee, Andrew K.; Zhang Xiaodong

    2012-01-01

    Purpose: We performed a comprehensive comparative study of the plan quality between volumetric-modulated arc therapy (VMAT) and intensity-modulated radiation therapy (IMRT) for the treatment of prostate cancer. Methods and Materials: Eleven patients with prostate cancer treated at our institution were randomly selected for this study. For each patient, a VMAT plan and a series of IMRT plans using an increasing number of beams (8, 12, 16, 20, and 24 beams) were examined. All plans were generated using our in-house–developed automatic inverse planning (AIP) algorithm. An existing eight-beam clinical IMRT plan, which was used to treat the patient, was used as the reference plan. For each patient, all AIP-generated plans were optimized to achieve the same level of planning target volume (PTV) coverage as the reference plan. Plan quality was evaluated by measuring mean dose to and dose–volume statistics of the organs at risk, especially the rectum, from each type of plan. Results: For the same PTV coverage, the AIP-generated VMAT plans had significantly better plan quality in terms of rectum sparing than the eight-beam clinical and AIP-generated IMRT plans (p < 0.0001). However, the differences between the IMRT and VMAT plans in all the dosimetric indices decreased as the number of beams used in IMRT increased. IMRT plan quality was similar or superior to that of VMAT when the number of beams in IMRT was increased to a certain number, which ranged from 12 to 24 for the set of patients studied. The superior VMAT plan quality resulted in approximately 30% more monitor units than the eight-beam IMRT plans, but the delivery time was still less than 3 min. Conclusions: Considering the superior plan quality as well as the delivery efficiency of VMAT compared with that of IMRT, VMAT may be the preferred modality for treating prostate cancer.

  14. International benchmarking of specialty hospitals. A series of case studies on comprehensive cancer centres

    Science.gov (United States)

    2010-01-01

    Background Benchmarking is one of the methods used in business that is applied to hospitals to improve the management of their operations. International comparison between hospitals can explain performance differences. As there is a trend towards specialization of hospitals, this study examines the benchmarking process and the success factors of benchmarking in international specialized cancer centres. Methods Three independent international benchmarking studies on operations management in cancer centres were conducted. The first study included three comprehensive cancer centres (CCC), three chemotherapy day units (CDU) were involved in the second study and four radiotherapy departments were included in the final study. Per multiple case study a research protocol was used to structure the benchmarking process. After reviewing the multiple case studies, the resulting description was used to study the research objectives. Results We adapted and evaluated existing benchmarking processes through formalizing stakeholder involvement and verifying the comparability of the partners. We also devised a framework to structure the indicators to produce a coherent indicator set and better improvement suggestions. Evaluating the feasibility of benchmarking as a tool to improve hospital processes led to mixed results. Case study 1 resulted in general recommendations for the organizations involved. In case study 2, the combination of benchmarking and lean management led in one CDU to a 24% increase in bed utilization and a 12% increase in productivity. Three radiotherapy departments of case study 3, were considering implementing the recommendations. Additionally, success factors, such as a well-defined and small project scope, partner selection based on clear criteria, stakeholder involvement, simple and well-structured indicators, analysis of both the process and its results and, adapt the identified better working methods to the own setting, were found. Conclusions The improved

  15. Advances in Parallel Computing and Databases for Digital Pathology in Cancer Research

    Science.gov (United States)

    2016-11-13

    databases. The advent of NewSQL and NoSQL (Not Only SQL) databases has led to the development of new technologies that are well suited for applications... NoSQL graph databases are tuned to support graph operations and NoSQL key-value databases excel at rapid ingest of unstructured data. Recent NewSQL

  16. A Ten-Year Assessment of a Biomedical Engineering Summer Research Internship within a Comprehensive Cancer Center

    Science.gov (United States)

    Wright, A. S.; Wu, X.; Frye, C. A.; Mathur, A. B.; Patrick, C. W., Jr.

    2007-01-01

    A Biomedical Engineering Internship Program conducted within a Comprehensive Cancer Center over a 10 year period was assessed and evaluated. Although this is a non-traditional location for an internship, it is an ideal site for a multidisciplinary training program for science, technology, engineering, and mathematics (STEM) students. We made a…

  17. Verbal versus Numerical Probabilities: Does Format Presentation of Probabilistic Information regarding Breast Cancer Screening Affect Women's Comprehension?

    Science.gov (United States)

    Vahabi, Mandana

    2010-01-01

    Objective: To test whether the format in which women receive probabilistic information about breast cancer and mammography affects their comprehension. Methods: A convenience sample of 180 women received pre-assembled randomized packages containing a breast health information brochure, with probabilities presented in either verbal or numeric…

  18. Differences in esophageal cancer characteristics and survival between Chinese and Caucasian patients in the SEER database

    Science.gov (United States)

    Lin, Min-Qiang; Li, Yue-Ping; Wu, San-Gang; Sun, Jia-Yuan; Lin, Huan-Xin; Zhang, Shi-Yang; He, Zhen-Yu

    2016-01-01

    Background To compare the clinicopathologic characteristics and survival of Chinese and Caucasian esophageal cancer (EC) patients residing in the US, using a population-based national registry (Surveillance Epidemiology and End Results [SEER]) database. Methods Patients with EC were identified from the SEER program from 1988 to 2012. Kaplan–Meier survival methods and Cox proportional hazards regression were performed. Results A total of 479 Chinese and 35,748 Caucasian EC patients were identified. Compared with Caucasian patients, the Chinese patients had a later year of diagnosis, remained married after EC was diagnosed, had esophageal squamous cell carcinomas (ESCCs) more frequently, had tumors located in the upper-third and middle-third of the esophagus more frequently, and fewer patients presented with poorly/undifferentiated EC and underwent cancer-directed surgery. In Chinese patients, the incidence of esophageal adenocarcinomas (EACs) increased from 1988 to 2012 (P=0.054), and the majority of EAC patients had tumors located in the lower thoracic esophagus. The overall survival (OS) was not significantly different between Chinese and Caucasian patients (P=0.767). However, Chinese patients with ESCC had a significantly better OS when compared to their Caucasian counterparts, whereas there was no significant difference in the OS between Chinese and Caucasian patients with EAC. Conclusion The presenting demographic features, tumor characteristics, and outcomes of EC patients differed between Chinese and Caucasian patients residing in the US. Chinese patients diagnosed with EAC tended to share similar clinical features with their Caucasian counterparts, and the Chinese patients with ESCC had better OS than their Caucasian counterparts. PMID:27799791

  19. Registration in the Danish Regional Nonmelanoma Skin Cancer Dermatology Database: completeness of registration and accuracy of key variables

    Directory of Open Access Journals (Sweden)

    Anna L Lamberg

    2010-05-01

    Full Text Available Anna L Lamberg1, Deirdre Cronin-Fenton2, Anne B Olesen11Department of Dermatology, 2Department of Clinical Epidemiology, Aarhus University Hospital, Aarhus, C, DenmarkObjective: To validate a clinical database for nonmelanoma skin cancer (NMSC with the aim of monitoring and predicting the prognosis of NMSC treated by dermatologists in clinics in the central and north Denmark regions.Methods: We assessed the completeness of registration of patients and follow-up visits, and positive predictive value (PPV, negative predictive value (NPV, sensitivity, and specificity of registrations in the database. We used the Danish Pathology Registry (DPR (n = 288 and a review of randomly selected medical records (n = 67 from two clinics as gold standards.Results: The completeness of registration of patients was 62% and 76% with DPR and medical record review as gold standards, respectively. The completeness of registration of 1st and 2nd follow up visits was 85% and 69%, respectively. The PPV and NPV ranged from 85% to 99%, and the sensitivity and specificity from 67% to 100%.Conclusion: Overall, the accuracy of variables registered in the NMSC database was satisfactory but completeness of patient registration and follow-up visits were modest. The NMSC database is a potentially valuable tool for monitoring and facilitating improvement of NMSC treatment in dermatology clinics. However, there is still room for improvement of registration of both patients and their follow-up visits.Keywords: nonmelanoma skin cancer, validation, database, positive predictive value, completeness

  20. The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

    Directory of Open Access Journals (Sweden)

    Christopher J. Ricketts

    2018-04-01

    Full Text Available Summary: Renal cell carcinoma (RCC is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and therapeutic responses. The current study evaluated 843 RCC from the three major histologic subtypes, including 488 clear cell RCC, 274 papillary RCC, and 81 chromophobe RCC. Comprehensive genomic and phenotypic analysis of the RCC subtypes reveals distinctive features of each subtype that provide the foundation for the development of subtype-specific therapeutic and management strategies for patients affected with these cancers. Somatic alteration of BAP1, PBRM1, and PTEN and altered metabolic pathways correlated with subtype-specific decreased survival, while CDKN2A alteration, increased DNA hypermethylation, and increases in the immune-related Th2 gene expression signature correlated with decreased survival within all major histologic subtypes. CIMP-RCC demonstrated an increased immune signature, and a uniform and distinct metabolic expression pattern identified a subset of metabolically divergent (MD ChRCC that associated with extremely poor survival. : Ricketts et al. find distinctive features of each RCC subtype, providing the foundation for development of subtype-specific therapeutic and management strategies. Somatic alteration of BAP1, PBRM1, and metabolic pathways correlates with subtype-specific decreased survival, while CDKN2A alteration, DNA hypermethylation, and Th2 immune signature correlate with decreased survival within all subtypes. Keywords: clear cell renal cell carcinoma, papillary renal cell carcinoma, chromophobe renal cell carcinoma, CDKN2A, DNA hypermethylation, immune signature, chromatin remodeling, TCGA, PanCanAtlas

  1. National Cancer Patient Registry--a patient registry/clinical database to evaluate the health outcomes of patients undergoing treatment for cancers in Malaysia.

    Science.gov (United States)

    Lim, G C C; Azura, D

    2008-09-01

    Cancer burden in Malaysia is increasing. Although there have been improvements in cancer treatment, these new therapies may potentially cause an exponential increase in the cost of cancer treatment. Therefore, justification for the use of these treatments is mandated. Availability of local data will enable us to evaluate and compare the outcome of our patients. This will help to support our clinical decision making and local policy, improve access to treatment and improve the provision and delivery of oncology services in Malaysia. The National Cancer Patient Registry was proposed as a database for cancer patients who seek treatment in Malaysia. It will be a valuable tool to provide timely and robust data on the actual setting in oncology practice, safety and cost effectiveness of treatment and most importantly the outcome of these patients.

  2. Refactoring databases evolutionary database design

    CERN Document Server

    Ambler, Scott W

    2006-01-01

    Refactoring has proven its value in a wide range of development projects–helping software professionals improve system designs, maintainability, extensibility, and performance. Now, for the first time, leading agile methodologist Scott Ambler and renowned consultant Pramodkumar Sadalage introduce powerful refactoring techniques specifically designed for database systems. Ambler and Sadalage demonstrate how small changes to table structures, data, stored procedures, and triggers can significantly enhance virtually any database design–without changing semantics. You’ll learn how to evolve database schemas in step with source code–and become far more effective in projects relying on iterative, agile methodologies. This comprehensive guide and reference helps you overcome the practical obstacles to refactoring real-world databases by covering every fundamental concept underlying database refactoring. Using start-to-finish examples, the authors walk you through refactoring simple standalone databas...

  3. Optimal management of elderly cancer patients: usefulness of the Comprehensive Geriatric Assessment

    Directory of Open Access Journals (Sweden)

    Caillet P

    2014-09-01

    Full Text Available Philippe Caillet,1,2 Marie Laurent,1,2 Sylvie Bastuji-Garin,1,3,4 Evelyne Liuu,2 Stephane Culine,5 Jean-Leon Lagrange,6 Florence Canoui-Poitrine,1,2,3,* Elena Paillaud1,2,* 1Laboratoire d’Investigation Clinique (LIC, Faculté de Medecine, Université Paris Est Créteil (UPEC, Créteil, Paris, 2Unité de Coordination d’Onco-Gériatrie, Département de Médecine Interne et Gériatrie, Hôpital Henri-Mondor, Assistance Publique – Hopitaux de Paris (AP-HP, Créteil, 3Service de Santé Publique, Hôpital Henri-Mondor, AP-HP, Créteil, 4Unité de Recherche Clinique, Hôpital Henri-Mondor, AP-HP, Créteil, 5Service d’Oncologie Médicale, Hôpital Saint-Louis, AP-HP, Paris, 6Service de Radiotherapie, Hôpital Henri-Mondor, AP-HP, Créteil, France*These authors contributed equally to this workBackground: Cancer is common in older patients, who raise specific treatment challenges due to aging-related, organ-specific physiologic changes and the presence in most cases of comorbidities capable of affecting treatment tolerance and outcomes. Identifying comorbid conditions and physiologic changes due to aging allows oncologists to better assess the risk/benefit ratio and to adjust the treatment accordingly. Conducting a Comprehensive Geriatric Assessment (CGA is one approach developed for this purpose. We reviewed the evidence on the usefulness of CGA for assessing health problems and predicting cancer treatment outcomes, functional decline, morbidity, and mortality in older patients with solid malignancies. Methods: We searched Medline for articles published in English between January 1, 2000 and April 14, 2014, and reporting prospective observational or interventional studies of CGA feasibility or effectiveness in patients aged ≥65 years with solid malignancies. We identified studies with at least 100 patients, a multivariate analysis, and assessments of at least five of the following CGA domains: nutrition, cognition, mood, functional status

  4. Practice of geriatric oncology in the setting of a comprehensive cancer center

    International Nuclear Information System (INIS)

    Droz, J.

    2004-01-01

    Geriatric oncology is defined by the multidimensional and multidisciplinary approach of the elderly cancer patients. Autonomy, beneficence, non maleficence and justice are the four fundamental principles on which are based the treatment objectives and practical management of these patients. The Comprehensive Geriatric Assessment is the most used tool to detect the functional problems in these elderly patients. The standard oncologic managements of cancer is applies to these patients. However treatment plan and geriatric interventions must be adapted to each individual characteristics of the patients.Thus a strong interdependence between oncologic and geriatric teams is warranted. This implies specific teaching programs during initial medical studies and in the setting of continuous medical education. Furthermore, such wold wide teaching programs may help to the implementation of Geriatric Oncology. In the Geriatric Oncology Program in Lyon we have developed a specific miniassessement to be practiced in an oncologic setting. Geriatric data were obtained by the version of the geriatric multidimensional assessment tool, which we have called minimal comprehensive geriatric assessment” or mini-CGA. This procedure has been designed to collect information on several major domains including medical (co-morbidity), functional, cognitive, affective, social, and environmental aspects. It is essentially based on a very careful medical examination. We also used other evaluation tools previously validated in elderly people. Dependence was measured using three tools: Katz’s Activities of Daily Living (ADLs) scale that focuses on six basic activities of daily living (bathing, dressing, toile ting, transferring, continence, and feeding); Lawton’s Instrumental Activities of Daily Living (IADLs) scale that appraises more complex activities essential for independence in community residence; and the Karnofsky Performance scale (KPS) that is widely used in the oncology setting to

  5. Transporter Classification Database (TCDB)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Transporter Classification Database details a comprehensive classification system for membrane transport proteins known as the Transporter Classification (TC)...

  6. CTCAE v.3.0 in evaluation the radiation adverse events in cancer patients after pelvic irradiation (Contemporary mechanisms of radiation and comprehensive damage after cancer treatment)

    International Nuclear Information System (INIS)

    Encheva, E.; Zahariev, Z.; Sultanov, B.; Hadjieva, T.

    2010-01-01

    The authors present the first report of applying the NCI CTCAE v.3.0 for evaluation of radiation adverse events in Bulgaria. The adverse events are observed in early stage cervical and endometrial cancer patients receiving external beam radiotherapy after radical surgery during the radiotherapy and 3 months after it ended. The paper discusses the contemporary concepts of the normal tissue morbidity, the issue early-late adverse events, comprehensive factors and causes, except irradiation, involved in their occurrence. The possibility to define the single method contribution of the comprehensive cancer treatment for development of post-treatment adverse events in cancer survivors in effort to improve their quality of life is discussed. (authors)

  7. Comprehensive Genomic Profiling Facilitates Implementation of the National Comprehensive Cancer Network Guidelines for Lung Cancer Biomarker Testing and Identifies Patients Who May Benefit From Enrollment in Mechanism-Driven Clinical Trials.

    Science.gov (United States)

    Suh, James H; Johnson, Adrienne; Albacker, Lee; Wang, Kai; Chmielecki, Juliann; Frampton, Garrett; Gay, Laurie; Elvin, Julia A; Vergilio, Jo-Anne; Ali, Siraj; Miller, Vincent A; Stephens, Philip J; Ross, Jeffrey S

    2016-06-01

    The National Comprehensive Cancer Network (NCCN) guidelines for patients with metastatic non-small cell lung cancer (NSCLC) recommend testing for EGFR, BRAF, ERBB2, and MET mutations; ALK, ROS1, and RET rearrangements; and MET amplification. We investigated the feasibility and utility of comprehensive genomic profiling (CGP), a hybrid capture-based next-generation sequencing (NGS) test, in clinical practice. CGP was performed to a mean coverage depth of 576× on 6,832 consecutive cases of NSCLC (2012-2015). Genomic alterations (GAs) (point mutations, small indels, copy number changes, and rearrangements) involving EGFR, ALK, BRAF, ERBB2, MET, ROS1, RET, and KRAS were recorded. We also evaluated lung adenocarcinoma (AD) cases without GAs, involving these eight genes. The median age of the patients was 64 years (range: 13-88 years) and 53% were female. Among the patients studied, 4,876 (71%) harbored at least one GA involving EGFR (20%), ALK (4.1%), BRAF (5.7%), ERBB2 (6.0%), MET (5.6%), ROS1 (1.5%), RET (2.4%), or KRAS (32%). In the remaining cohort of lung AD without these known drivers, 273 cancer-related genes were altered in at least 0.1% of cases, including STK11 (21%), NF1 (13%), MYC (9.8%), RICTOR (6.4%), PIK3CA (5.4%), CDK4 (4.3%), CCND1 (4.0%), BRCA2 (2.5%), NRAS (2.3%), BRCA1 (1.7%), MAP2K1 (1.2%), HRAS (0.7%), NTRK1 (0.7%), and NTRK3 (0.2%). CGP is practical and facilitates implementation of the NCCN guidelines for NSCLC by enabling simultaneous detection of GAs involving all seven driver oncogenes and KRAS. Furthermore, without additional tissue use or cost, CGP identifies patients with "pan-negative" lung AD who may benefit from enrollment in mechanism-driven clinical trials. National Comprehensive Cancer Network guidelines for patients with metastatic non-small cell lung cancer (NSCLC) recommend testing for several genomic alterations (GAs). The feasibility and utility of comprehensive genomic profiling were studied in NSCLC and in lung adenocarcinoma

  8. Patterns of care, predictors and outcomes of chemotherapy for uterine carcinosarcoma: a National Cancer Database analysis.

    Science.gov (United States)

    Rauh-Hain, J Alejandro; Starbuck, Kristen D; Meyer, Larissa A; Clemmer, Joel; Schorge, John O; Lu, Karen H; Del Carmen, Marcela G

    2015-10-01

    Evaluate rates of chemotherapy and radiotherapy delivery in the treatment of uterine carcinosarcoma, and compare clinical outcomes of treated and untreated patients. The National Cancer Database was queried to identify patients diagnosed with uterine carcinosarcoma between 2003 and 2011. The impact of chemotherapy on survival was analyzed using the Kaplan-Meier method. Factors predictive of outcome were compared using the Cox proportional hazards model. A total of 10,609 patients met study eligibility criteria. Stages I, II, III, and IV disease accounted for 2997 (28.2%), 642 (6.1%), 2037 (19.2%), and 1316 (12.4%) of the study population, respectively. Most patients (91.0%) underwent definitive surgery, and lymphadenectomy was performed in 68.7% of the patients. Chemotherapy was administered in 2378 (22.4%) patients, radiotherapy to 2196 (20.7%), adjuvant chemo-radiation to 1804 (17.0%), and 4231 (39.9%) of women did not received adjuvant therapy. Utilization of chemotherapy became more frequent over time. Over the entire study period, after adjusting for race, period of diagnosis, facility location, facility type, insurance provider, stage, age, treatment modality, lymph node dissection, socioeconomic status, and comorbidity index, there was an association between treatment modality and survival. The lowest hazard ratio observed was in patients that received chemo-radiation. The strongest quantitative predictor of death was stage at the time of diagnosis. In addition, surgical treatment, lymph node dissection, most recent time-periods, lower comorbidity index, and higher socioeconomic status were associated with improved survival. The overall rates of chemotherapy use have increased over time. Adjuvant chemotherapy and chemo-radiation were associated with improved survival. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. An analysis of content in comprehensive cancer control plans that address chronic hepatitis B and C virus infections as major risk factors for liver cancer.

    Science.gov (United States)

    Momin, Behnoosh; Richardson, Lisa

    2012-08-01

    Chronic hepatitis B and hepatitis C virus (HBV and HCV) infections are among the leading causes of preventable death worldwide. Chronic viral hepatitis is the cause of most primary liver cancer, which is the third leading cause of cancer deaths globally and the ninth leading cause of cancer deaths in the United States. The extent to which comprehensive cancer control (CCC) programs in states, tribal governments and organizations, territories, and Pacific Island jurisdictions address chronic hepatitis B and/or hepatitis C infections as risk factors for liver cancer or recommend interventions for liver cancer prevention in their CCC plans remains unknown. We searched CCC plans for this information using the search tool at http://www.cdc.gov/cancer/ncccp/ to access the content of plans for this information. A combination of key search terms including "liver cancer", "hepatitis", "chronic alcohol", and "alcohol abuse" were used to identify potential content regarding liver cancer risk factors and prevention. Relevant content was abstracted for further review and classification. Of 66 (Although CDC funds 65 programs, one of the Pacific Island Jurisdiction grantees is the Federated States of Micronesia (FSM). This national program supports four FSM states, each of which submits a cancer plan to CDC for a total of 69 plans. During this time period, 66 plans were available on the website.) CCC plans, 27% (n = 18) addressed liver cancer using the above-mentioned search terms. In the 23 plans that addressed HBV and/or HCV, there were 25 goals, objectives, strategies, and outcomes aimed at reducing the incidence or prevalence of HBV and/or HCV infection. While nearly a third of CCC programs identify at least one goal, objective, strategy, outcome, or prevention program to reduce cancer burden in their CCC plans, few plans discuss specific actions needed to reduce the burden of liver cancer.

  10. Application of induced short-term hyperglycemia in comprehensive treatment of locally disseminated cancer of mammary gland

    International Nuclear Information System (INIS)

    Letyagin, V.P.; Poddubnyj, I.K.; Sokolova, I.G.; Ermilova, V.D.; Ajtakova, T.I.

    1984-01-01

    The paper deals with an analysis of the results of treatment of 12 patients with mammary gland cancer receiving preoperative radiation and chemotherapy and in whom short-term hyperglycemia was simultaneously induced. The peculiarities of the said modality and advantages offered by its application are discussed. The cases given the same treatment unaccompanied by hyperglycemia were in control. Since short-term hyperglycemia as a component of comprehensive treatment of mammary gland cancer resulted in a higher effectiveness of the latter, it merits attention and further studies

  11. Marital status independently predicts gastric cancer survival after surgical resection--an analysis of the SEER database.

    Science.gov (United States)

    Shi, Rong-Liang; Chen, Qian; Yang, Zhen; Pan, Gaofeng; Zhang, Ziping; Wang, WeiHua; Liu, Shaoqun; Zhang, Dongbin; Jiang, Daowen; Liu, Weiyan

    2016-03-15

    Marital status was found to be an independent prognostic factor for survival in various cancer types, but it hasn't been studied in gastric cancer. The Surveillance, Epidemiology and End Results database was used to compare survival outcomes with marital status. A total of 16,106 eligible patients were identified. Patients in the widowed group had the highest proportion of women, more common site of stomach, more prevalence of elderly patients, higher percentage of adenocarcinoma, and more tumors at localized stage (P married group had better 5year cause-specific survival (CSS) than those unmarried (P married patients at Localized stage (77.2% vs 70.1%, P vs 28.6%, P vs 8.6%, P unmarried patients were at greater risk of cancer specific mortality. Despite favorable clinicpathological characteristics, widowed patients were at highest risk of death compared with other groups.

  12. The effect of marital status on breast cancer-related outcomes in women under 65: A SEER database analysis.

    Science.gov (United States)

    Hinyard, Leslie; Wirth, Lorinette Saphire; Clancy, Jennifer M; Schwartz, Theresa

    2017-04-01

    Marital status is strongly associated with improved health and longevity. Being married has been shown to be positively associated with survival in patients with multiple different types of malignancy; however, little is known about the relationship between marital status and breast cancer in younger women. The purpose of this study is to investigate the effect of marital status on diagnosis, and survival of women under the age of 65 with breast cancer. The SEER 18 regions database was used to identify women between the ages of 25-64 diagnosed with invasive breast cancer in the years 2004-2009. Logistic regression was used to predict later stage diagnosis by marital status and Cox proportional hazards models were used to compare breast cancer-related and all-cause survival by marital status classification. Models were stratified by AJCC stage. After adjusting for age, race, and ER status, unmarried women were 1.18 times more likely to be diagnosed at a later stage than married women (95% CI 1.15, 1.20). In adjusted analysis unmarried women were more likely to die of breast cancer and more likely to die of all causes than married women across all AJCC stages. Younger unmarried women with breast cancer may benefit from additional counseling, psychosocial support and case management at the time of diagnosis to ensure their overall outcomes are optimized. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Utilization of retroperitoneal lymph node dissection for testicular cancer in the United States: Results from the National Cancer Database (1998-2011).

    Science.gov (United States)

    Hugen, Cory M; Hu, Brian; Jeldres, Claudio; Burton, Claire; Nichols, Craig R; Porter, Christopher R; Daneshmand, Siamak

    2016-11-01

    Retroperitoneal lymph node dissection (RPLND) for the treatment of testicular cancer is a relatively rare and complex operation that may contribute to differences in utilization. We sought to characterize the use of RPLND between different categories of cancer center facilities in the United States. The National Cancer Database was queried for patients with germ cell tumors treated at different types of cancer centers between 1998 and 2011. The proportion of patients who underwent RPLND was stratified by stage and histology and then compared between treatment facilities. RPLND utilization was then compared between facility types as a function of time. A total of 59,652 patients met inclusion criteria and 5,475 (9.2%) underwent RPLND. The proportion of patients treated with RPLND for non-seminomatous germ cell tumor (NSGCT) was significantly different between cancer center types for all stages (Pcancer centers. There was no difference in the proportion of RPLND utilization for stage II and III seminoma stratified by treatment facility. There was a significantly decreased trend in the utilization of RPLND for stage I (P = 0.032) NSGCT whereas utilization was increased for stage III NSGCT (P≤0.001) over the study period. The proportion of patients undergoing RPLND for NSGCT varies significantly by the type of cancer center and is used most often in academic cancer centers. Utilization of RPLND decreased for stage I NSGCT and increased for stage III NSGCTs during the study period. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. Trends in intensity modulated radiation therapy use for locally advanced rectal cancer at National Comprehensive Cancer Network centers

    Directory of Open Access Journals (Sweden)

    Marsha Reyngold, MD, PhD

    2018-01-01

    Conclusions: Although most patients with stage II-III rectal cancer at queried National Cancer Institute–designated cancer centers between 2005 and 2011 received 3-dimensional CRT, significant and increasing numbers received IMRT. IMRT utilization is highly variable among institutions and not uniform among sociodemographic groups but may be more consistently embraced in specific clinical settings. Given this trend, comparative-effectiveness research is needed to evaluate the benefits of IMRT for rectal cancer.

  15. EpiGeNet: A Graph Database of Interdependencies Between Genetic and Epigenetic Events in Colorectal Cancer.

    Science.gov (United States)

    Balaur, Irina; Saqi, Mansoor; Barat, Ana; Lysenko, Artem; Mazein, Alexander; Rawlings, Christopher J; Ruskin, Heather J; Auffray, Charles

    2017-10-01

    The development of colorectal cancer (CRC)-the third most common cancer type-has been associated with deregulations of cellular mechanisms stimulated by both genetic and epigenetic events. StatEpigen is a manually curated and annotated database, containing information on interdependencies between genetic and epigenetic signals, and specialized currently for CRC research. Although StatEpigen provides a well-developed graphical user interface for information retrieval, advanced queries involving associations between multiple concepts can benefit from more detailed graph representation of the integrated data. This can be achieved by using a graph database (NoSQL) approach. Data were extracted from StatEpigen and imported to our newly developed EpiGeNet, a graph database for storage and querying of conditional relationships between molecular (genetic and epigenetic) events observed at different stages of colorectal oncogenesis. We illustrate the enhanced capability of EpiGeNet for exploration of different queries related to colorectal tumor progression; specifically, we demonstrate the query process for (i) stage-specific molecular events, (ii) most frequently observed genetic and epigenetic interdependencies in colon adenoma, and (iii) paths connecting key genes reported in CRC and associated events. The EpiGeNet framework offers improved capability for management and visualization of data on molecular events specific to CRC initiation and progression.

  16. Molecular portrait of breast cancer in China reveals comprehensive transcriptomic likeness to Caucasian breast cancer and low prevalence of luminal A subtype

    International Nuclear Information System (INIS)

    Huang, Xiaoyan; Dugo, Matteo; Callari, Maurizio; Sandri, Marco; De Cecco, Loris; Valeri, Barbara; Carcangiu, Maria Luisa; Xue, Jingyan; Bi, Rui; Veneroni, Silvia; Daidone, Maria Grazia; Ménard, Sylvie; Tagliabue, Elda; Shao, Zhimin; Wu, Jiong; Orlandi, Rosaria

    2015-01-01

    The recent dramatic increase in breast cancer incidence across China with progressive urbanization and economic development has signaled the urgent need for molecular and clinical detailing of breast cancer in the Chinese population. Our analyses of a unique transethnic collection of breast cancer frozen specimens from Shanghai Fudan Cancer Center (Chinese Han) profiled simultaneously with an analogous Caucasian Italian series revealed consistent transcriptomic data lacking in batch effects. The prevalence of Luminal A subtype was significantly lower in Chinese series, impacting the overall prevalence of estrogen receptor (ER)-positive disease in a large cohort of Chinese/Caucasian patients. Unsupervised and supervised comparison of gene and microRNA (miRNA) profiles of Chinese and Caucasian samples revealed extensive similarity in the comprehensive taxonomy of transcriptional elements regulating breast cancer biology. Partition of gene expression data using gene lists relevant to breast cancer as “intrinsic” and “extracellular matrix” genes identified Chinese and Caucasian subgroups with equivalent global gene and miRNA profiles. These findings indicate that in the Chinese and Caucasian groups, breast neoplasia and the surrounding stromal characteristics undergo the same differentiation and molecular processes. Transcriptional similarity across transethnic cohorts may simplify translational medicine approaches and clinical management of breast cancer patients worldwide

  17. Management of Cancer Cachexia and Guidelines Implementation in a Comprehensive Cancer Center: A Physician-Led Cancer Nutrition Program Adapted to the Practices of a Country.

    Science.gov (United States)

    Senesse, Pierre; Isambert, Agnès; Janiszewski, Chloé; Fiore, Stéphanie; Flori, Nicolas; Poujol, Sylvain; Arroyo, Eric; Courraud, Julie; Guillaumon, Vanessa; Mathieu-Daudé, Hélène; Colasse, Sophie; Baracos, Vickie; de Forges, Hélène; Thezenas, Simon

    2017-09-01

    Cancer-associated cachexia is correlated with survival, side-effects, and alteration of the patients' well-being. We implemented an institution-wide multidisciplinary supportive care team, a Cancer Nutrition Program (CNP), to screen and manage cachexia in accordance with the guidelines and evaluated the impact of this new organization on nutritional care and funding. We estimated the workload associated with nutrition assessment and cachexia-related interventions and audited our clinical practice. We then planned, implemented, and evaluated the CNP, focusing on cachexia. The audit showed a 70% prevalence of unscreened cachexia. Parenteral nutrition was prescribed to patients who did not meet the guideline criteria in 65% cases. From January 2009 to December 2011, the CNP team screened 3078 inpatients. The screened/total inpatient visits ratio was 87%, 80%, and 77% in 2009, 2010, and 2011, respectively. Cachexia was reported in 74.5% (n = 2253) patients, of which 94.4% (n = 1891) required dietary counseling. Over three years, the number of patients with artificial nutrition significantly decreased by 57.3% (P < 0.001), and the qualitative inpatients enteral/parenteral ratio significantly increased: 0.41 in 2009, 0.74 in 2010, and 1.52 in 2011. Between 2009 and 2011, the CNP costs decreased significantly for inpatients nutritional care from 528,895€ to 242,272€, thus financing the nutritional team (182,520€ per year). Our results highlight the great benefits of implementing nutritional guidelines through a physician-led multidisciplinary team in charge of nutritional care in a comprehensive cancer center. Copyright © 2017 American Academy of Hospice and Palliative Medicine. Published by Elsevier Inc. All rights reserved.

  18. Isotopic reconstruction of ancient human migrations: A comprehensive Sr isotope reference database for France and the first case study at Tumulus de Sables, south-western France

    Science.gov (United States)

    Willmes, M.; Boel, C.; Grün, R.; Armstrong, R.; Chancerel, A.; Maureille, B.; Courtaud, P.

    2012-04-01

    Strontium isotope ratios (87Sr/86Sr) can be used for the reconstruction of human and animal migrations across geologically different terrains. Sr isotope ratios in rocks are a product of age and composition and thus vary between geologic units. From the eroding environment Sr is transported into the soils, plants and rivers of a region. Humans and animals incorporate Sr from their diet into their bones and teeth, where it substitutes for calcium. Tooth enamel contains Sr isotope signatures acquired during childhood and is most resistant to weathering and overprinting, while the dentine is often diagenetically altered towards the local Sr signature. For the reconstruction of human and animal migrations the tooth enamel 87Sr/86Sr ratio is compared to the Sr isotope signature in the vicinity of the burial site and the surrounding area. This study focuses on the establishment of a comprehensive reference map of bioavailable 87Sr/86Sr ratios for France. In a next step we will compare human and animal teeth from key archaeological sites to this reference map to investigate mobility. So far, we have analysed plant and soil samples from ~200 locations across France including the Aquitaine basin, the western and northern parts of the Paris basin, as well as three transects through the Pyrenees Mountains. The isotope data, geologic background information (BRGM 1:1M), field images, and detailed method descriptions are available through our online database iRhum (http://rses.anu.edu.au/research/ee). This database can also be used in forensic studies and food sciences. As an archaeological case study teeth from 16 adult and 8 juvenile individuals were investigated from an early Bell Beaker (2500-2000 BC) site at Le Tumulus des Sables, south-west France (Gironde). The teeth were analysed for Sr isotope ratios using laser ablation ICP-MS. Four teeth were also analysed using solution ICP-MS, which showed a significant offset to the laser ablation results. This requires further

  19. Comprehensive Analysis of Cancer-Proteogenome to Identify Biomarkers for the Early Diagnosis and Prognosis of Cancer.

    Science.gov (United States)

    Shukla, Hem D

    2017-10-25

    During the past century, our understanding of cancer diagnosis and treatment has been based on a monogenic approach, and as a consequence our knowledge of the clinical genetic underpinnings of cancer is incomplete. Since the completion of the human genome in 2003, it has steered us into therapeutic target discovery, enabling us to mine the genome using cutting edge proteogenomics tools. A number of novel and promising cancer targets have emerged from the genome project for diagnostics, therapeutics, and prognostic markers, which are being used to monitor response to cancer treatment. The heterogeneous nature of cancer has hindered progress in understanding the underlying mechanisms that lead to abnormal cellular growth. Since, the start of The Cancer Genome Atlas (TCGA), and the International Genome consortium projects, there has been tremendous progress in genome sequencing and immense numbers of cancer genomes have been completed, and this approach has transformed our understanding of the diagnosis and treatment of different types of cancers. By employing Genomics and proteomics technologies, an immense amount of genomic data is being generated on clinical tumors, which has transformed the cancer landscape and has the potential to transform cancer diagnosis and prognosis. A complete molecular view of the cancer landscape is necessary for understanding the underlying mechanisms of cancer initiation to improve diagnosis and prognosis, which ultimately will lead to personalized treatment. Interestingly, cancer proteome analysis has also allowed us to identify biomarkers to monitor drug and radiation resistance in patients undergoing cancer treatment. Further, TCGA-funded studies have allowed for the genomic and transcriptomic characterization of targeted cancers, this analysis aiding the development of targeted therapies for highly lethal malignancy. High-throughput technologies, such as complete proteome, epigenome, protein-protein interaction, and pharmacogenomics

  20. Comprehensive Analysis of Cancer-Proteogenome to Identify Biomarkers for the Early Diagnosis and Prognosis of Cancer

    Directory of Open Access Journals (Sweden)

    Hem D. Shukla

    2017-10-01

    Full Text Available During the past century, our understanding of cancer diagnosis and treatment has been based on a monogenic approach, and as a consequence our knowledge of the clinical genetic underpinnings of cancer is incomplete. Since the completion of the human genome in 2003, it has steered us into therapeutic target discovery, enabling us to mine the genome using cutting edge proteogenomics tools. A number of novel and promising cancer targets have emerged from the genome project for diagnostics, therapeutics, and prognostic markers, which are being used to monitor response to cancer treatment. The heterogeneous nature of cancer has hindered progress in understanding the underlying mechanisms that lead to abnormal cellular growth. Since, the start of The Cancer Genome Atlas (TCGA, and the International Genome consortium projects, there has been tremendous progress in genome sequencing and immense numbers of cancer genomes have been completed, and this approach has transformed our understanding of the diagnosis and treatment of different types of cancers. By employing Genomics and proteomics technologies, an immense amount of genomic data is being generated on clinical tumors, which has transformed the cancer landscape and has the potential to transform cancer diagnosis and prognosis. A complete molecular view of the cancer landscape is necessary for understanding the underlying mechanisms of cancer initiation to improve diagnosis and prognosis, which ultimately will lead to personalized treatment. Interestingly, cancer proteome analysis has also allowed us to identify biomarkers to monitor drug and radiation resistance in patients undergoing cancer treatment. Further, TCGA-funded studies have allowed for the genomic and transcriptomic characterization of targeted cancers, this analysis aiding the development of targeted therapies for highly lethal malignancy. High-throughput technologies, such as complete proteome, epigenome, protein–protein interaction

  1. Comprehensive analysis of the N-glycan biosynthetic pathway using bioinformatics to generate UniCorn: A theoretical N-glycan structure database.

    Science.gov (United States)

    Akune, Yukie; Lin, Chi-Hung; Abrahams, Jodie L; Zhang, Jingyu; Packer, Nicolle H; Aoki-Kinoshita, Kiyoko F; Campbell, Matthew P

    2016-08-05

    Glycan structures attached to proteins are comprised of diverse monosaccharide sequences and linkages that are produced from precursor nucleotide-sugars by a series of glycosyltransferases. Databases of these structures are an essential resource for the interpretation of analytical data and the development of bioinformatics tools. However, with no template to predict what structures are possible the human glycan structure databases are incomplete and rely heavily on the curation of published, experimentally determined, glycan structure data. In this work, a library of 45 human glycosyltransferases was used to generate a theoretical database of N-glycan structures comprised of 15 or less monosaccharide residues. Enzyme specificities were sourced from major online databases including Kyoto Encyclopedia of Genes and Genomes (KEGG) Glycan, Consortium for Functional Glycomics (CFG), Carbohydrate-Active enZymes (CAZy), GlycoGene DataBase (GGDB) and BRENDA. Based on the known activities, more than 1.1 million theoretical structures and 4.7 million synthetic reactions were generated and stored in our database called UniCorn. Furthermore, we analyzed the differences between the predicted glycan structures in UniCorn and those contained in UniCarbKB (www.unicarbkb.org), a database which stores experimentally described glycan structures reported in the literature, and demonstrate that UniCorn can be used to aid in the assignment of ambiguous structures whilst also serving as a discovery database. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. Common breast cancer risk variants in the post-COGS era: a comprehensive review

    OpenAIRE

    Maxwell, Kara N; Nathanson, Katherine L

    2013-01-01

    Breast cancer has a strong heritable component, with approximately 15% of cases exhibiting a family history of the disease. Mutations in genes such as BRCA1, BRCA2 and TP53 lead to autosomal dominant inherited cancer susceptibility and confer a high lifetime risk of breast cancers. Identification of mutations in these genes through clinical genetic testing enables patients to undergo screening and prevention strategies, some of which provide overall survival benefit. In addition, a number of ...

  3. Analyzing clinical outcomes in laparoscopic right vs. left colectomy in colon cancer patients using the NSQIP database.

    Science.gov (United States)

    Nfonsam, Valentine; Aziz, Hassan; Pandit, Viraj; Khalil, Mazhar; Jandova, Jana; Joseph, Bellal

    2016-01-01

    Optimization of surgical outcomes after colectomy continues to be actively studied, but most studies group right-sided and left-sided colectomies together. The aim of our study was to determine whether the complication rate differs between right-sided and left-sided colectomies for cancer. We identified patients who underwent laparoscopic colectomy for colon cancer between 2005 and 2010 in the American College of Surgeons National Surgical Quality Improvement Program database and stratified cases by right and left side. The two groups were matched using propensity score matching for demographics, previous abdominal surgery, pre-operative chemotherapy and radiotherapy, and preoperative laboratory data. Outcome measures were: 30-day mortality and morbidity. We identified 2512 patients who underwent elective laparoscopic colectomy for right-sided or left-sided colon cancer. The two groups were similar in demographics, and pre-operative characteristics. There was no difference in overall morbidity (15% vs. 17.7%; p value cancer. Further research on outcomes after colectomy should incorporate right vs. left side colon resection as a potential pre-operative risk factor.

  4. Common breast cancer risk variants in the post-COGS era: a comprehensive review.

    Science.gov (United States)

    Maxwell, Kara N; Nathanson, Katherine L

    2013-12-20

    Breast cancer has a strong heritable component, with approximately 15% of cases exhibiting a family history of the disease. Mutations in genes such as BRCA1, BRCA2 and TP53 lead to autosomal dominant inherited cancer susceptibility and confer a high lifetime risk of breast cancers. Identification of mutations in these genes through clinical genetic testing enables patients to undergo screening and prevention strategies, some of which provide overall survival benefit. In addition, a number of mutant alleles have been identified in genes such as CHEK2, PALB2, ATM and BRIP1, which often display incomplete penetrance and confer moderate lifetime risks of breast cancer. Studies are underway to determine how to use the identification of mutations in these genes to guide clinical practice. Altogether, however, mutations in high and moderate penetrance genes probably account for approximately 25% of familial breast cancer risk; the remainder may be due to mutations in as yet unidentified genes or lower penetrance variants. Common low penetrance alleles, which have been mainly identified through genome-wide association studies (GWAS), are generally present at 10 to 50% population frequencies and confer less than 1.5-fold increases in breast cancer risk. A number of single nucleotide polymorphisms (SNPs) have been identified and risk associations extensively replicated in populations of European ancestry, the number of which has substantially increased as a result of GWAS performed by the Collaborative Oncological Gene-environment Study consortium. It is now estimated that 28% of familial breast cancer risk is explained by common breast cancer susceptibility loci. In some cases, SNP associations may be specific to different subsets of women with breast cancer, as defined by ethnicity or estrogen receptor status. Although not yet clinically established, it is hoped that identification of common risk variants may eventually allow identification of women at higher risk of

  5. Neonates with cancer and causes of death; lessons from 615 cases in the SEER databases.

    Science.gov (United States)

    Alfaar, Ahmad S; Hassan, Waleed M; Bakry, Mohamed Sabry; Qaddoumi, Ibrahim

    2017-07-01

    Neonatal tumors are rare with no standard treatment approaches to these diseases, and the patients experience poor outcomes. Our aim was to determine the distribution of cancers affecting neonates and compare survival between these cancers and older children. We analyzed SEER data (1973-2007) from patients who were younger than 2 years at diagnosis of malignancy. Special permission was granted to access the detailed (i.e., age in months) data of those patients. The Chi-square Log-rank test was used to compare survival between neonates (aged 1 month to cancers (454 solid tumors, 93 leukemia/lymphoma, and 68 CNS neoplasms). Neuroblastoma was the most common neonatal tumor followed by Germ cell tumors. The 5-year overall survival (OS) for all neonates was 60.3% (95% CI, 56.2-64.4). Neonates with solid tumors had the highest 5-year OS (71.2%; 95% CI, 66.9-75.5), followed by those with leukemia (39.1%; 95% CI, 28.3-49.9) or CNS tumors (15%; 95% CI, 5.4-24.6). Except for neuroblastoma, all neonatal tumors showed inferior outcomes compared to that in the older group. The proportion of neonates who died from causes other than cancer was significantly higher than that of the older children (37.9% vs. 16.4%; P cancers has not improved over the last 34 years. The distribution of neonatal cancer is different than other pediatric age groups. Although the progress in neonatal and cancer care over the last 30 years, only death from noncancer causes showed improvement. Studying neonatal tumors as part of national studies is essential to understand their etiology, determine the best treatment approaches, and improve survival and quality of life for those patients. © 2017 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

  6. gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes.

    Science.gov (United States)

    Nakagawa, So; Takahashi, Mahoko Ueda

    2016-01-01

    In mammals, approximately 10% of genome sequences correspond to endogenous viral elements (EVEs), which are derived from ancient viral infections of germ cells. Although most EVEs have been inactivated, some open reading frames (ORFs) of EVEs obtained functions in the hosts. However, EVE ORFs usually remain unannotated in the genomes, and no databases are available for EVE ORFs. To investigate the function and evolution of EVEs in mammalian genomes, we developed EVE ORF databases for 20 genomes of 19 mammalian species. A total of 736,771 non-overlapping EVE ORFs were identified and archived in a database named gEVE (http://geve.med.u-tokai.ac.jp). The gEVE database provides nucleotide and amino acid sequences, genomic loci and functional annotations of EVE ORFs for all 20 genomes. In analyzing RNA-seq data with the gEVE database, we successfully identified the expressed EVE genes, suggesting that the gEVE database facilitates studies of the genomic analyses of various mammalian species.Database URL: http://geve.med.u-tokai.ac.jp. © The Author(s) 2016. Published by Oxford University Press.

  7. Comprehensive outreach, prevention education, and skin cancer screening for Utah ski resorts.

    Science.gov (United States)

    Varedi, Amir; Secrest, Aaron M; Harding, Garrett; Maness, Lori; Branson, Donna; Smith, Kristi; Hull, Christopher M

    2018-02-15

    Outdoor recreation can lead to substantial sun exposure. Employees of outdoor recreation establishments with extended time outdoors have amplified cumulative exposure to ultraviolet (UV) radiation and an increased risk of skin cancer. The "Sun Safe on the Slopes" program was created by Huntsman Cancer Institute at the University of Utah and the Utah Cancer Action Network to address increased UV exposure and skin cancer risk with free skin cancer screenings, outreach, and prevention education to local ski resorts. Herein, we describe the processes and barriers to implementation of a ski resort skin screening and education program and our 5-year report of the experience and screening data. Nine free skin cancer screenings were held at Utah ski resorts between 2011 and 2016, resulting in the presumptive diagnosis of 38 skin cancers (9.6%) in 394 participants. Behavioral data collected from participants indicates suboptimal sun safety practices, including underuse of sunscreen and protective clothing. Ski resort employees who experience sun exposure during peak hours at high altitudes and UV reflection from the snow are at an increased risk of skin cancer. These data indicate a need for emphasis on sun safety education and screening and can serve as a model for future endeavors.

  8. Characteristics and treatment of human epidermal growth factor receptor 2 positive breast cancer: 43,485 cases from the National Cancer Database treated in 2010 and 2011.

    Science.gov (United States)

    Killelea, Brigid K; Chagpar, Anees B; Horowitz, Nina R; Lannin, Donald R

    2017-02-01

    Although identification of human epidermal growth factor receptor 2 (Her2) positive breast cancer represents one of the greatest advances over the past 3 decades, it has not been studied extensively on a national level. The National Cancer Database is a joint project of the American Cancer Society and the American College of Surgeons and contains data on about 70% of the cancer cases in the United States. Data on Her2 have been collected since 2010 and was used for this study. Of 298,937 cases of invasive breast cancer with known Her2 status diagnosed in 2010 and 2011, 43,485 (14.5%) were Her2 positive. Her2 positivity was greatest in Asian/Pacific Islanders and least in non-Hispanic Whites and was markedly more common in younger women. The incidence of Her2 positive tumors ranged from a low of 13.9% in the Mountain West region to a high of 16.0% in the West South Central region (P breast preservation (odds ratio = .78, confidence interval = .76 to .80). Her2 positive tumors have distinct epidemiologic, clinical, and treatment characteristics. Copyright © 2016 Elsevier Inc. All rights reserved.

  9. A comprehensive examination of breast cancer risk loci in African American women.

    Science.gov (United States)

    Feng, Ye; Stram, Daniel O; Rhie, Suhn Kyong; Millikan, Robert C; Ambrosone, Christine B; John, Esther M; Bernstein, Leslie; Zheng, Wei; Olshan, Andrew F; Hu, Jennifer J; Ziegler, Regina G; Nyante, Sarah; Bandera, Elisa V; Ingles, Sue A; Press, Michael F; Deming, Sandra L; Rodriguez-Gil, Jorge L; Palmer, Julie R; Olopade, Olufunmilayo I; Huo, Dezheng; Adebamowo, Clement A; Ogundiran, Temidayo; Chen, Gary K; Stram, Alex; Park, Karen; Rand, Kristin A; Chanock, Stephen J; Le Marchand, Loic; Kolonel, Laurence N; Conti, David V; Easton, Douglas; Henderson, Brian E; Haiman, Christopher A

    2014-10-15

    Genome-wide association studies have identified 73 breast cancer risk variants mainly in European populations. Given considerable differences in linkage disequilibrium structure between populations of European and African ancestry, the known risk variants may not be informative for risk in African ancestry populations. In a previous fine-mapping investigation of 19 breast cancer loci, we were able to identify SNPs in four regions that better captured risk associations in African American women. In this study of breast cancer in African American women (3016 cases, 2745 controls), we tested an additional 54 novel breast cancer risk variants. Thirty-eight variants (70%) were found to have an association with breast cancer in the same direction as previously reported, with eight (15%) replicating at P University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  10. Assessment of training needs and preferences for geographic information systems (GIS) mapping in state comprehensive cancer-control programs.

    Science.gov (United States)

    Hopfer, Suellen; Chadwick, Amy E; Parrott, Roxanne L; Ghetian, Christie B; Lengerich, Eugene J

    2009-10-01

    Geographic information systems (GIS) mapping technologies have potential to advance public health promotion by mapping regional differences in attributes (e.g., disease burden, environmental exposures, access to health care services) to suggest priorities for public health interventions. Training in GIS for comprehensive cancer control (CCC) has been overlooked. State CCC programs' GIS training needs were assessed by interviewing 49 state CCC directors. A majority perceived a need for GIS training, slightly more than half of state CCC programs had access to geocoded data, and the majority of programs did not require continuing education credits of their staff. CCC directors perceived judging maps and realizing their limitations as important skills and identified epidemiologists, CCC staff, public health officials, policy makers, and cancer coalition members as training audiences. They preferred in-class training sessions that last a few hours to a day. Lessons learned are shared to develop training programs with translatable GIS skills for CCC.

  11. Securing a better future for all: Nuclear techniques for global development and environmental protection. NA factsheet on comprehensive cancer control: Fighting cancer in the developing world

    International Nuclear Information System (INIS)

    2012-01-01

    For over thirty years, the IAEA has worked in some 115 low and middle income (LMI) Member States to deploy robust radiotherapy and nuclear medicine programmes, expending over US $250 million on cancer related assistance under its Technical Cooperation Programme, with technical support provided by the Division of Human Health. This has enabled many Member States to establish safe and effective diagnostic imaging and radiation therapy capacity to provide treatment and higher quality care to many of their cancer patients. The IAEA also helps establish new nuclear medicine facilities and encourages their integration with diagnostic radiology procedures by facilitating appropriate human resources capacity building. This helps Member States to achieve and maintain high standards of professional practice. The IAEA addresses quality management though services such as the Quality Assurance in Nuclear Medicine (QUANUM), Quality Assurance Team in Radiation Oncology (QUATRO) and Quality Assurance in Diagnostic Radiology (QUADRIL), which allow the IAEA to provide tools for improving the practice of radiation medicine around the world. In 2004, the IAEA established the Programme of Action for Cancer Therapy (PACT) in support of the World Health Assembly's call to action against cancer. It stands as the IAEA's umbrella programme for combating cancer and builds upon the above experience in radiation medicine expertise and technology. PACT works closely with the World Health Organization (WHO), its regional offices and other key players through the WHO-IAEA Joint Programme on Cancer Control. The WHO-IAEA Joint Programme was established in 2009 to enable LMI Member States to introduce, expand and improve their cancer treatment capacities and therapeutic effectiveness by integrating radiotherapy into a comprehensive national cancer control programme.

  12. Comprehensive Geriatric Assessment (CGA) based risk factors for increased caregiver burden among elderly Asian patients with cancer.

    Science.gov (United States)

    Rajasekaran, Tanujaa; Tan, Tira; Ong, Whee Sze; Koo, Khai Nee; Chan, Lili; Poon, Donald; Roy Chowdhury, Anupama; Krishna, Lalit; Kanesvaran, Ravindran

    2016-05-01

    This study aims to identify Comprehensive Geriatric Assessment (CGA) based risk factors to help predict caregiver burden among elderly patients with cancer. The study evaluated 249 patients newly diagnosed with cancer, aged 70years and above, who attended the geriatric oncology clinic at the National Cancer Centre Singapore between 2007 and 2010. Out of 249 patients, 244 patients had information available on family caregiver burden and were analysed. On univariate analysis, ADL dependence, lower IADL scores, ECOG performance status of 3-4, higher fall risk, lower scores in dominant hand grip strength test and mini mental state examination, polypharmacy, higher nutritional risk, haemoglobin geriatric syndromes were significantly associated with mild to severe caregiver burden. On multivariate analysis, only ECOG performance status of 3-4 (odds ratio [OR], 4.47; 95% confidence interval [CI], 2.27-8.80) and haemoglobin patients were stratified into 3 risk groups with different proportion of patients with increased caregiver burden (low risk: 3.9% vs intermediate risk: 18.8% vs high risk: 39.6%; ppatients with cancer. Using these two factors in the clinic may help clinicians identify caregivers at risk and take preventive action to mitigate that. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. Validation of malayalam version of national comprehensive cancer network distress thermometer and its feasibility in oncology patients

    Directory of Open Access Journals (Sweden)

    M S Biji

    2018-01-01

    Full Text Available Context: This study was designed to translate and validate the National Comprehensive Cancer Network (NCCN distress thermometer (DT in regional language " Malayalam" and to see the feasibility of using it in our patients. Aims: (1 To translate and validate the NCCN DT. (2 To study the feasibility of using validated Malayalam translated DT in Malabar Cancer center. Settings and Design: This is a single-arm prospective observational study. The study was conducted at author's institution between December 8, 2015, and January 20, 2016 in the Department of Cancer Palliative Medicine. Materials and Methods: This was a prospective observational study carried out in two phases. In Phase 1, the linguistic validation of the NCCN DT was done. In Phase 2, the feasibility, face validity, and utility of the translated of NCCN DT in accordance with QQ-10 too was done. Statistical Analysis Used: SPSS version 16 (SPSS Inc. Released 2007. SPSS for Windows, Version 16.0. Chicago, SPSS Inc. was used for analysis. Results: Ten patients were enrolled in Phase 2. The median age was 51.5 years and 40% of patients were male. All patients had completed at least basic education up to the primary level. The primary site of cancer was heterogeneous. The NCCN DT completion rate was 100%. The face validity, utility, reliability, and feasibility were 100%, 100%, 100%, and 90%, respectively. Conclusion: It can be concluded that the Malayalam validated DT has high face validity, utility, and it is feasible for its use.

  14. Validation of Malayalam Version of National Comprehensive Cancer Network Distress Thermometer and its Feasibility in Oncology Patients.

    Science.gov (United States)

    Biji, M S; Dessai, Sampada; Sindhu, N; Aravind, Sithara; Satheesan, B

    2018-01-01

    This study was designed to translate and validate the National Comprehensive Cancer Network (NCCN) distress thermometer (DT) in regional language " Malayalam" and to see the feasibility of using it in our patients. (1) To translate and validate the NCCN DT. (2) To study the feasibility of using validated Malayalam translated DT in Malabar Cancer center. This is a single-arm prospective observational study. The study was conducted at author's institution between December 8, 2015, and January 20, 2016 in the Department of Cancer Palliative Medicine. This was a prospective observational study carried out in two phases. In Phase 1, the linguistic validation of the NCCN DT was done. In Phase 2, the feasibility, face validity, and utility of the translated of NCCN DT in accordance with QQ-10 too was done. SPSS version 16 (SPSS Inc. Released 2007. SPSS for Windows, Version 16.0. Chicago, SPSS Inc.) was used for analysis. Ten patients were enrolled in Phase 2. The median age was 51.5 years and 40% of patients were male. All patients had completed at least basic education up to the primary level. The primary site of cancer was heterogeneous. The NCCN DT completion rate was 100%. The face validity, utility, reliability, and feasibility were 100%, 100%, 100%, and 90%, respectively. It can be concluded that the Malayalam validated DT has high face validity, utility, and it is feasible for its use.

  15. Structure analysis of designated hospitals for cancer control in Japan from JASTRO census survey database 2005

    International Nuclear Information System (INIS)

    Ikeda, Hiroshi; Kagami, Yoshikazu; Nishio, Masamichi; Kataoka, Masaaki; Matsumoto, Yasuo; Hatano, Kazuo; Ogino, Takashi

    2008-01-01

    The structures of 288 hospitals designated for cancer control and approved by Ministry of Health, Labour and Welfare in February 2006 were analyzed from radiotherapy aspects according to the Japanese Society for Therapeutic Radiology and Oncology (JASTRO) 2005 census survey data. The data were compiled from 266 hospitals. Overall 78,086 new patients were treated at these designated hospitals, which accounts for just a half the total number of patients in Japan. The structure of radiotherapy (RT) must be essential for cancer management, and our study showed the designated hospitals are insufficient in the RT requirement. No RT equipment is installed in 14 hospitals. Of 266, 109 hospitals treated less than 200 new patients, and 25 hospitals less than 100 in 2005. The data analysis revealed that academic hospitals, JACC hospitals and others are reasonable in terms of structures and capacity of radiotherapy. Moreover, both academic and JACC hospitals play similar roles to designated prefectural hospitals in cancer management by radiotherapy. (author)

  16. Marital status is an independent prognostic factor for tracheal cancer patients: an analysis of the SEER database.

    Science.gov (United States)

    Li, Mu; Dai, Chen-Yang; Wang, Yu-Ning; Chen, Tao; Wang, Long; Yang, Ping; Xie, Dong; Mao, Rui; Chen, Chang

    2016-11-22

    Although marital status is an independent prognostic factor in many cancers, its prognostic impact on tracheal cancer has not yet been determined. The goal of this study was to examine the relationship between marital status and survival in patients with tracheal cancer. Compared with unmarried patients (42.67%), married patients (57.33%) had better 5-year OS (25.64% vs. 35.89%, p = 0.009) and 5-year TCSS (44.58% vs. 58.75%, p = 0.004). Results of multivariate analysis indicated that marital status is an independent prognostic factor, with married patients showing better OS (hazard ratio [HR] = 0.78, 95% confidence interval [CI] 0.64-0.95, p = 0.015) and TCSS (HR = 0.70, 95% CI 0.54-0.91, p = 0.008). In addition, subgroup analysis suggested that marital status plays a more important role in the TCSS of patients with non-low-grade malignant tumors (HR = 0.71, 95% CI 0.53-0.93, p = 0.015). We extracted 600 cases from the Surveillance, Epidemiology, and End Results (SEER) database. Variables were compared by Pearson chi-squared test, t-test, log-rank test, and multivariate Cox regression analysis. Overall survival (OS) and tracheal cancer-specific survival (TCSS) were compared between subgroups with different pathologic features and tumor stages. Marital status is an independent prognostic factor for survival in patients with tracheal cancer. For that reason, additional social support may be needed for unmarried patients, especially those with non-low-grade malignant tumors.

  17. A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability

    NARCIS (Netherlands)

    Sontrop, H.M.J.; Moerland, P.D.; Van den Ham, R.; Reinders, M.J.T.; Verhaegh, W.F.J.

    2009-01-01

    Background: Large discrepancies in signature composition and outcome concordance have been observed between different microarray breast cancer expression profiling studies. This is often ascribed to differences in array platform as well as biological variability. We conjecture that other reasons for

  18. A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability

    NARCIS (Netherlands)

    Sontrop, Herman M. J.; Moerland, Perry D.; van den Ham, René; Reinders, Marcel J. T.; Verhaegh, Wim F. J.

    2009-01-01

    Large discrepancies in signature composition and outcome concordance have been observed between different microarray breast cancer expression profiling studies. This is often ascribed to differences in array platform as well as biological variability. We conjecture that other reasons for the

  19. Disruptions in Liver Function among Cancer Patients and Patients Treated with Tyrosine Kinase Inhibiting Drugs: Comparisons of Two Population-Based Databases

    International Nuclear Information System (INIS)

    Landis, S. H.

    2013-01-01

    Liver toxicity is a recognized adverse event associated with small molecule tyrosine kinase inhibitors (TKIs). Electronic Medical Record (EMR) databases offer the most precise data to investigate the rate of liver function test (LFT) elevations; however, they can be limited in sample size and costly to access and analyze. Health insurance claims databases often contain larger samples sizes but may lack key health information. We evaluated the feasibility of utilizing a large claims database to calculate incidence rates (IRs) of LFT elevations among a general cohort of cancer patients and a cohort of patients treated with TKIs by comparing the results to a “gold standard” oncology-specific EMR database. IRs for the TKI cohorts were very similar between the two databases; however, IRs were higher in the EMR database for the cancer cohorts. Possible explanations for these differences include lack of specificity when defining a cancer case, poor capture of laboratory data, or inaccurate assessment of person-time in the insurance claims database. This study suggests that insurance claims data may provide reliable results when investigating liver toxicities associated with oncology drug exposure; however, there are limitations when assessing laboratory outcomes for cohorts defined solely by disease status.

  20. Aviation Safety Issues Database

    Science.gov (United States)

    Morello, Samuel A.; Ricks, Wendell R.

    2009-01-01

    The aviation safety issues database was instrumental in the refinement and substantiation of the National Aviation Safety Strategic Plan (NASSP). The issues database is a comprehensive set of issues from an extremely broad base of aviation functions, personnel, and vehicle categories, both nationally and internationally. Several aviation safety stakeholders such as the Commercial Aviation Safety Team (CAST) have already used the database. This broader interest was the genesis to making the database publically accessible and writing this report.

  1. A Comprehensive Model of Cancer-Related Information Seeking Applied to Magazines.

    Science.gov (United States)

    Johnson, J. David; Meischke, Hendrika

    1993-01-01

    Examines a comprehensive model of information seeking resulting from the synthesis of three theoretical research streams: the health belief model, uses and gratifications research, and a model of media exposure. Suggests that models of information seeking from mass media should focus on purely communicative factors. (RS)

  2. Comprehensive serum profiling for the discovery of epithelial ovarian cancer biomarkers.

    Directory of Open Access Journals (Sweden)

    Ping Yip

    Full Text Available FDA-cleared ovarian cancer biomarkers are limited to CA-125 and HE4 for monitoring and recurrence and OVA1, a multivariate panel consisting of CA-125 and four additional biomarkers, for referring patients to a specialist. Due to relatively poor performance of these tests, more accurate and broadly applicable biomarkers are needed. We evaluated the dysregulation of 259 candidate cancer markers in serum samples from 499 patients. Sera were collected prospectively at 11 monitored sites under a single well-defined protocol. All stages of ovarian cancer and common benign gynecological conditions were represented. To ensure consistency and comparability of biomarker comparisons, all measurements were performed on a single platform, at a single site, using a panel of rigorously calibrated, qualified, high-throughput, multiplexed immunoassays and all analyses were conducted using the same software. Each marker was evaluated independently for its ability to differentiate ovarian cancer from benign conditions. A total of 175 markers were dysregulated in the cancer samples. HE4 (AUC=0.933 and CA-125 (AUC=0.907 were the most informative biomarkers, followed by IL-2 receptor α, α1-antitrypsin, C-reactive protein, YKL-40, cellular fibronectin, CA-72-4 and prostasin (AUC>0.800. To improve the discrimination between cancer and benign conditions, a simple multivariate combination of markers was explored using logistic regression. When combined into a single panel, the nine most informative individual biomarkers yielded an AUC value of 0.950, significantly higher than obtained when combining the markers in the OVA1 panel (AUC 0.912. Additionally, at a threshold sensitivity of 90%, the combination of the top 9 markers gave 88.9% specificity compared to 63.4% specificity for the OVA1 markers. Although a blinded validation study has not yet been performed, these results indicate that alternative biomarker combinations might lead to significant improvements in the

  3. Variations in clinicopathologic characteristics of thyroid cancer among racial ethnic groups: analysis of a large public city hospital and the SEER database.

    Science.gov (United States)

    Moo-Young, Tricia A; Panergo, Jessel; Wang, Chih E; Patel, Subhash; Duh, Hong Yan; Winchester, David J; Prinz, Richard A; Fogelfeld, Leon

    2013-11-01

    Clinicopathologic variables influence the treatment and prognosis of patients with thyroid cancer. A retrospective analysis of public hospital thyroid cancer database and the Surveillance, Epidemiology and End Results 17 database was conducted. Demographic, clinical, and pathologic data were compared across ethnic groups. Within the public hospital database, Hispanics versus non-Hispanic whites were younger and had more lymph node involvement (34% vs 17%, P ethnic groups. Similar findings were demonstrated within the Surveillance, Epidemiology and End Results database. African Americans aged ethnic groups. Such disparities persist within an equal-access health care system. These findings suggest that factors beyond socioeconomics may contribute to such differences. Copyright © 2013 Elsevier Inc. All rights reserved.

  4. Comprehensive spectrum of BRCA1 and BRCA2 deleterious mutations in breast cancer in Asian countries

    Science.gov (United States)

    Kwong, Ava; Shin, Vivian Y; Ho, John C W; Kang, Eunyoung; Nakamura, Seigo; Teo, Soo-Hwang; Lee, Ann S G; Sng, Jen-Hwei; Ginsburg, Ophira M; Kurian, Allison W; Weitzel, Jeffrey N; Siu, Man-Ting; Law, Fian B F; Chan, Tsun-Leung; Narod, Steven A; Ford, James M; Ma, Edmond S K; Kim, Sung-Won

    2015-01-01

    Approximately 5%–10% of breast cancers are due to genetic predisposition caused by germline mutations; the most commonly tested genes are BRCA1 and BRCA2 mutations. Some mutations are unique to one family and others are recurrent; the spectrum of BRCA1/BRCA2 mutations varies depending on the geographical origins, populations or ethnic groups. In this review, we compiled data from 11 participating Asian countries (Bangladesh, Mainland China, Hong Kong SAR, Indonesia, Japan, Korea, Malaysia, Philippines, Singapore, Thailand and Vietnam), and from ethnic Asians residing in Canada and the USA. We have additionally conducted a literature review to include other Asian countries mainly in Central and Western Asia. We present the current pathogenic mutation spectrum of BRCA1/BRCA2 genes in patients with breast cancer in various Asian populations. Understanding BRCA1/BRCA2 mutations in Asians will help provide better risk assessment and clinical management of breast cancer. PMID:26187060

  5. Comprehensive clinical study of concurrent chemotherapy breathing IMRT middle part of locally advanced esophageal cancer

    International Nuclear Information System (INIS)

    Jung, Jae Hong; Moon, Seong Kwon; Kim, Seung Chul

    2015-01-01

    The standard treatment of locally advanced type of mid-esophageal cancer is concurrent chemoradiation therapy (CRT). We evaluated the feasibility of chemotherapy with adding docetaxel to the classical basic regimens of cisplatin plus 5-fluorouracil (5-FU) and radiotherapy up to 70.2 Gy using dose escalations for esophageal cancer. It was possible to escalate radiation treatment dose up to 70.2 Gy by the respiratory-gated intensity- modulated radiotherapy (gated-IMRT) based on the 4DCT-simulation, with improving target coverage and normal tissue (ex., lung, heart, and spinal cord) sparing. This study suggested that the definitive chemo-radiotherapy with docetaxel, cisplatin, and 5-fluorouracil (i.e., DCF-R) and gating IMRT is tolerable and active in patients with locally advanced mid-esophageal cancer (AEC)

  6. Lung cancer gene expression database analysis incorporating prior knowledge with support vector machine-based classification method

    Directory of Open Access Journals (Sweden)

    Huang Desheng

    2009-07-01

    Full Text Available Abstract Background A reliable and precise classification is essential for successful diagnosis and treatment of cancer. Gene expression microarrays have provided the high-throughput platform to discover genomic biomarkers for cancer diagnosis and prognosis. Rational use of the available bioinformation can not only effectively remove or suppress noise in gene chips, but also avoid one-sided results of separate experiment. However, only some studies have been aware of the importance of prior information in cancer classification. Methods Together with the application of support vector machine as the discriminant approach, we proposed one modified method that incorporated prior knowledge into cancer classification based on gene expression data to improve accuracy. A public well-known dataset, Malignant pleural mesothelioma and lung adenocarcinoma gene expression database, was used in this study. Prior knowledge is viewed here as a means of directing the classifier using known lung adenocarcinoma related genes. The procedures were performed by software R 2.80. Results The modified method performed better after incorporating prior knowledge. Accuracy of the modified method improved from 98.86% to 100% in training set and from 98.51% to 99.06% in test set. The standard deviations of the modified method decreased from 0.26% to 0 in training set and from 3.04% to 2.10% in test set. Conclusion The method that incorporates prior knowledge into discriminant analysis could effectively improve the capacity and reduce the impact of noise. This idea may have good future not only in practice but also in methodology.

  7. Metformin, other antidiabetic drugs, and endometrial cancer risk: a nested case-control study within Italian healthcare utilization databases.

    Science.gov (United States)

    Franchi, Matteo; Asciutto, Rosario; Nicotra, Federica; Merlino, Luca; La Vecchia, Carlo; Corrao, Giovanni; Bosetti, Cristina

    2017-05-01

    Metformin may reduce the risk of endometrial cancer whereas other drugs for the treatment of type 2 diabetes mellitus appear to increase it, although the evidence is still limited. We investigated this issue using data from a nested case-control study within the healthcare utilization databases of the Lombardy Region, Italy. This study included 376 diabetic women with endometrial cancer and 7485 diabetic controls matched for cases on age, date at cohort entry, and duration of follow-up. We used conditional logistic regression models to estimate the odds ratio (OR) of endometrial cancer in relation to use of antidiabetic drugs, adjusted for the Charlson's comorbidity index, selected medical conditions, prescription of selected drugs, and concomitant use of other antidiabetic drugs. At cohort entry, no significant associations were observed for metformin [OR=0.99, 95% confidence interval (CI) 0.80-1.23], sulfonylureas (OR=1.14, 95% CI 0.91-1.42), insulin (OR=0.72, 95% CI 0.34-1.56), and other antidiabetic drugs (OR=1.21, 95% CI 0.75-1.95). When we considered use during follow-up, a borderline significant excess risk was found for metformin (OR=1.30, 95% CI 1.00-1.70). However, this estimate decreased to 1.07 (95% CI 0.82-1.41) when taking into account BMI using a Monte Carlo sensitivity analysis. No significant associations were found for sulfonylureas (OR=1.16, 95% CI 0.91-1.47), thiazolidinediones (OR=0.77, 95% CI 0.48-1.24), repaglinide (OR=1.32, 95% CI 0.94-1.87), incretins (OR=1.21, 95% CI 0.63-2.32), and insulin (OR=1.19, 95% CI 0.82-1.71). Our data indicate that metformin, insulin, and other antidiabetic drugs did not meaningfully affect the risk of endometrial cancer.

  8. Marital status and survival in patients with rectal cancer: An analysis of the Surveillance, Epidemiology and End Results (SEER) database.

    Science.gov (United States)

    Wang, Xiangyang; Cao, Weilan; Zheng, Chenguo; Hu, Wanle; Liu, Changbao

    2018-06-01

    Marital status has been validated as an independent prognostic factor for survival in several cancer types, but is controversial in rectal cancer (RC). The objective of this study was to investigate the impact of marital status on the survival outcomes of patients with RC. We extracted data of 27,498 eligible patients diagnosed with RC between 2004 and 2009 from the Surveillance, Epidemiology and End Results (SEER) database. Patients were categorized into married, never married, divorced/separated and widowed groups.We used Chi-square tests to compare characteristics of patients with different marital status.Rectal cancer specific survival was compared using the Kaplan-Meier method,and multivariate Cox regression analyses was used to analyze the survival outcome risk factors in different marital status. The widowed group had the highest percentage of elderly patients and women,higher proportion of adenocarcinomas, and more stage I/II in tumor stage (P married group (76.7% VS 85.4%). Compared with the married patients, the never married (HR 1.40), widowed (HR 1.61,) and divorced/separated patients (HR 1.16) had an increased overall 5-year mortality. A further analysis showed that widowed patients had an increased overall 5-year cause-specific survival(CSS) compared with married patients at stage I(HR 1.92),stage II (HR 1.65),stage III (HR 1.73),and stage IV (HR 1.38). Our study showed marriage was associated with better outcomes of RC patients, but unmarried RC patients, especially widowed patients,are at greater risk of cancer specific mortality. Copyright © 2018 Elsevier Ltd. All rights reserved.

  9. Human Papillomavirus Vaccine as an Anti-cancer Vaccine: Collaborative Efforts to Promote HPV Vaccine in the National Comprehensive Cancer Control Program

    Science.gov (United States)

    Townsend, Julie S.; Steele, C. Brooke; Hayes, Nikki; Bhatt, Achal; Moore, Angela R.

    2018-01-01

    Background Widespread use of the HPV vaccine has the potential to reduce incidence from HPV-associated cancers. However, vaccine uptake among adolescents remains well below the Healthy People 2020 targets. The Centers for Disease Control and Prevention (CDC)’s National Comprehensive Cancer Control Program awardees (NCCCP) are well positioned to work with immunization programs to increase vaccine uptake. Methods CDC’s chronic disease management information system was queried for objectives and activities associated with HPV vaccine that were reported by NCCCP awardees from 2013 – 2016 as part of program reporting requirements. A content analysis was conducted on the query results to categorize interventions according to strategies outlined in The Guide to Community Preventive Services and the 2014 President’s Cancer Panel report. Results Sixty-two percent of NCCCP awardees had planned or implemented at least one activity since 2013 to address low HPV vaccination coverage in their jurisdictions. Most NCCCP awardees (86%) reported community education activities, while 65% reported activities associated with provider education. Systems-based strategies such as client reminders or provider assessment and feedback were each reported by less than 25% of NCCCP awardees. Conclusion Many NCCCP awardees report planning or implementing activities to address low HPV vaccination coverage, often in conjunction with state immunization programs. NCCCP awardees can play a role in increasing HPV vaccination coverage through their cancer prevention and control expertise and access to partners in the health care community. PMID:28263672

  10. Does implementation matter if comprehension is lacking? A qualitative investigation into perceptions of advance care planning in people with cancer.

    Science.gov (United States)

    Ugalde, Anna; O'Callaghan, Clare; Byard, Clem; Brean, Samantha; MacKay, Jenelle; Boltong, Anna; Davoren, Sondra; Lawson, Deborah; Parente, Phillip; Michael, Natasha; Livingston, Patricia

    2018-05-11

    While advance care planning holds promise, uptake is variable and it is unclear how well people engage with or comprehend advance care planning. The objective of this study was to explore how people with cancer comprehended advance care plans and examine how accurately advance care planning documentation represented patient wishes. This study used a qualitative descriptive design. Data collection comprised interviews and an examination of participants' existing advance care planning documentation. Participants included those who had any diagnosis of cancer with an advance care plan recorded: Refusal of Treatment Certificate, Statement of Choices, and/or Enduring Power of Attorney (Medical Treatment) at one cancer treatment centre. Fourteen participants were involved in the study. Twelve participants were female (86%). The mean age was 77 (range: 61-91), and participants had completed their advance care planning documentation between 8 and 72 weeks prior to the interview (mean 33 weeks). Three themes were evident from the data: incomplete advance care planning understanding and confidence, limited congruence for attitude and documentation, advance care planning can enable peace of mind. Complete advance care planning understanding was unusual; most participants demonstrated partial comprehension of their own advance care plan, and some indicated very limited understanding. Participants' attitudes and their written document congruence were limited, but advance care planning was seen as helpful. This study highlighted advance care planning was not a completely accurate representation of patient wishes. There is opportunity to improve how patients comprehend their own advance care planning documentation.

  11. Managing Rock and Paleomagnetic Data Flow with the MagIC Database: from Measurement and Analysis to Comprehensive Archive and Visualization

    Science.gov (United States)

    Koppers, A. A.; Minnett, R. C.; Tauxe, L.; Constable, C.; Donadini, F.

    2008-12-01

    The Magnetics Information Consortium (MagIC) is commissioned to implement and maintain an online portal to a relational database populated by rock and paleomagnetic data. The goal of MagIC is to archive all measurements and derived properties for studies of paleomagnetic directions (inclination, declination) and intensities, and for rock magnetic experiments (hysteresis, remanence, susceptibility, anisotropy). Organizing data for presentation in peer-reviewed publications or for ingestion into databases is a time-consuming task, and to facilitate these activities, three tightly integrated tools have been developed: MagIC-PY, the MagIC Console Software, and the MagIC Online Database. A suite of Python scripts is available to help users port their data into the MagIC data format. They allow the user to add important metadata, perform basic interpretations, and average results at the specimen, sample and site levels. These scripts have been validated for use as Open Source software under the UNIX, Linux, PC and Macintosh© operating systems. We have also developed the MagIC Console Software program to assist in collating rock and paleomagnetic data for upload to the MagIC database. The program runs in Microsoft Excel© on both Macintosh© computers and PCs. It performs routine consistency checks on data entries, and assists users in preparing data for uploading into the online MagIC database. The MagIC website is hosted under EarthRef.org at http://earthref.org/MAGIC/ and has two search nodes, one for paleomagnetism and one for rock magnetism. Both nodes provide query building based on location, reference, methods applied, material type and geological age, as well as a visual FlashMap interface to browse and select locations. Users can also browse the database by data type (inclination, intensity, VGP, hysteresis, susceptibility) or by data compilation to view all contributions associated with previous databases, such as PINT, GMPDB or TAFI or other user

  12. Database-augmented Mass Spectrometry Analysis of Exosomes Identifies Claudin 3 as a Putative Prostate Cancer Biomarker.

    Science.gov (United States)

    Worst, Thomas Stefan; von Hardenberg, Jost; Gross, Julia Christina; Erben, Philipp; Schnölzer, Martina; Hausser, Ingrid; Bugert, Peter; Michel, Maurice Stephan; Boutros, Michael

    2017-06-01

    In prostate cancer and other malignancies sensitive and robust biomarkers are lacking or have relevant limitations. Prostate specific antigen (PSA), the only biomarker widely used in prostate cancer, is suffering from low specificity. Exosomes offer new perspectives in the discovery of blood-based biomarkers. Here we present a proof-of principle study for a proteomics-based identification pipeline, implementing existing data sources, to exemplarily identify exosome-based biomarker candidates in prostate cancer.Exosomes from malignant PC3 and benign PNT1A cells and from FBS-containing medium were isolated using sequential ultracentrifugation. Exosome and control samples were analyzed on an LTQ-Orbitrap XL mass spectrometer. Proteomic data is available via ProteomeXchange with identifier PXD003651. We developed a scoring scheme to rank 64 proteins exclusively found in PC3 exosomes, integrating data from four public databases and published mass spectrometry data sets. Among the top candidates, we focused on the tight junction protein claudin 3. Retests under serum-free conditions using immunoblotting and immunogold labeling confirmed the presence of claudin 3 on PC3 exosomes. Claudin 3 levels were determined in the blood plasma of patients with localized ( n = 58; 42 with Gleason score 6-7, 16 with Gleason score ≥8) and metastatic prostate cancer ( n = 11) compared with patients with benign prostatic hyperplasia ( n = 15) and healthy individuals ( n = 15) using ELISA, without prior laborious exosome isolation. ANOVA showed different CLDN3 plasma levels in these groups ( p = 0.004). CLDN3 levels were higher in patients with Gleason ≥8 tumors compared with patients with benign prostatic hyperplasia ( p = 0.012) and Gleason 6-7 tumors ( p = 0.029). In patients with localized tumors CLDN3 levels predicted a Gleason score ≥ 8 (AUC = 0.705; p = 0.016) and did not correlate with serum PSA.By using the described workflow claudin 3 was identified and validated as a

  13. The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

    NARCIS (Netherlands)

    Ricketts, Christopher J.; De Cubas, Aguirre A.; Fan, Huihui; Smith, Christof C.; Lang, Martin; Reznik, Ed; Bowlby, Reanne; Gibb, Ewan A.; Akbani, Rehan; Beroukhim, Rameen; Bottaro, Donald P.; Choueiri, Toni K.; Gibbs, Richard A.; Godwin, Andrew K.; Haake, Scott; Hakimi, A. Ari; Henske, Elizabeth P.; Hsieh, James J.; Ho, Thai H.; Kanchi, Rupa S.; Krishnan, Bhavani; Kwaitkowski, David J.; Lui, Wembin; Merino, Maria J.; Mills, Gordon B.; Myers, Jerome; Nickerson, Michael L.; Reuter, Victor E.; Schmidt, Laura S.; Shelley, Carl Simon; Shen, Hui; Shuch, Brian; Signoretti, Sabina; Srinivasan, Ramaprasad; Tamboli, Pheroze; Thomas, George; Vincent, Benjamin G.; Vocke, Cathy D.; Wheeler, David A.; Yang, Lixing; Kim, William T.; Robertson, A. Gordon; Caesar-Johnson, Samantha J.; Demchok, John A.; Felau, Ina; Kasapi, Melpomeni; Ferguson, Martin L.; Hutter, Carolyn M.; Sofia, Heidi J.; Tarnuzzer, Roy; Wang, Zhining; Yang, Liming; Zenklusen, Jean C.; Zhang, Jiashan (Julia); Chudamani, Sudha; Liu, Jia; Lolla, Laxmi; Naresh, Rashi; Pihl, Todd; Sun, Qiang; Wan, Yunhu; Wu, Ye; Cho, Juok; DeFreitas, Timothy; Frazer, Scott; Gehlenborg, Nils; Getz, Gad; Heiman, David I.; Kim, Jaegil; Lawrence, Michael S.; Lin, Pei; Meier, Sam; Noble, Michael S.; Saksena, Gordon; Voet, Doug; Zhang, Hailei; Bernard, Brady; Chambwe, Nyasha; Dhankani, Varsha; Knijnenburg, Theo; Kramer, Roger; Leinonen, Kalle; Liu, Yuexin; Miller, Michael; Reynolds, Sheila; Shmulevich, Ilya; Thorsson, Vesteinn; Zhang, Wei; Akbani, Rehan; Broom, Bradley M.; Hegde, Apurva M.; Ju, Zhenlin; Kanchi, Rupa S.; Korkut, Anil; Li, Jun; Liang, Han; Ling, Shiyun; Liu, Wenbin; Lu, Yiling; Mills, Gordon B.; Ng, Kwok Shing; Rao, Arvind; Ryan, Michael; Wang, Jing; Weinstein, John N.; Zhang, Jiexin; Abeshouse, Adam; Armenia, Joshua; Chakravarty, Debyani; Chatila, Walid K.; de Bruijn, Ino; Gao, Jianjiong; Gross, Benjamin E.; Heins, Zachary J.; Kundra, Ritika; La, Konnor; Ladanyi, Marc; Luna, Augustin; Nissan, Moriah G.; Ochoa, Angelica; Phillips, Sarah M.; Reznik, Ed; Sanchez-Vega, Francisco; Sander, Chris; Schultz, Nikolaus; Sheridan, Robert; Sumer, S. Onur; Sun, Yichao; Taylor, Barry S.; Wang, Jioajiao; Zhang, Hongxin; Anur, Pavana; Peto, Myron; Spellman, Paul; Benz, Christopher; Stuart, Joshua M.; Wong, Christopher K.; Yau, Christina; Hayes, D. Neil; Parker, Joel S.; Wilkerson, Matthew D.; Ally, Adrian; Balasundaram, Miruna; Bowlby, Reanne; Brooks, Denise; Carlsen, Rebecca; Chuah, Eric; Dhalla, Noreen; Holt, Robert; Jones, Steven J.M.; Kasaian, Katayoon; Lee, Darlene; Ma, Yussanne; Marra, Marco A.; Mayo, Michael; Moore, Richard A.; Mungall, Andrew J.; Mungall, Karen; Robertson, A. Gordon; Sadeghi, Sara; Schein, Jacqueline E.; Sipahimalani, Payal; Tam, Angela; Thiessen, Nina; Tse, Kane; Wong, Tina; Berger, Ashton C.; Beroukhim, Rameen; Cherniack, Andrew D.; Cibulskis, Carrie; Gabriel, Stacey B.; Gao, Galen F.; Ha, Gavin; Meyerson, Matthew; Schumacher, Steven E.; Shih, Juliann; Kucherlapati, Melanie H.; Kucherlapati, Raju S.; Baylin, Stephen; Cope, Leslie; Danilova, Ludmila; Bootwalla, Moiz S.; Lai, Phillip H.; Maglinte, Dennis T.; Van Den Berg, David J.; Weisenberger, Daniel J.; Auman, J. Todd; Balu, Saianand; Bodenheimer, Tom; Fan, Cheng; Hoadley, Katherine A.; Hoyle, Alan P.; Jefferys, Stuart R.; Jones, Corbin D.; Meng, Shaowu; Mieczkowski, Piotr A.; Mose, Lisle E.; Perou, Amy H.; Perou, Charles M.; Roach, Jeffrey; Shi, Yan; Simons, Janae V.; Skelly, Tara; Soloway, Matthew G.; Tan, Donghui; Veluvolu, Umadevi; Fan, Huihui; Hinoue, Toshinori; Laird, Peter W.; Shen, Hui; Zhou, Wanding; Bellair, Michelle; Chang, Kyle; Covington, Kyle; Creighton, Chad J.; Dinh, Huyen; Doddapaneni, Harsha Vardhan; Donehower, Lawrence A.; Drummond, Jennifer; Gibbs, Richard A.; Glenn, Robert; Hale, Walker; Han, Yi; Hu, Jianhong; Korchina, Viktoriya; Lee, Sandra; Lewis, Lora; Li, Wei; Liu, Xiuping; Morgan, Margaret; Morton, Donna; Muzny, Donna; Santibanez, Jireh; Sheth, Margi; Shinbrot, Eve; Wang, Linghua; Wang, Min; Wheeler, David A.; Xi, Liu; Zhao, Fengmei; Hess, Julian; Appelbaum, Elizabeth L.; Bailey, Matthew; Cordes, Matthew G.; Ding, Li; Fronick, Catrina C.; Fulton, Lucinda A.; Fulton, Robert S.; Kandoth, Cyriac; Mardis, Elaine R.; McLellan, Michael D.; Miller, Christopher A.; Schmidt, Heather K.; Wilson, Richard K.; Crain, Daniel; Curley, Erin; Gardner, Johanna; Lau, Kevin; Mallery, David; Morris, Scott; Paulauskis, Joseph; Penny, Robert; Shelton, Candace; Shelton, Troy; Sherman, Mark; Thompson, Eric; Yena, Peggy; Bowen, Jay; Gastier-Foster, Julie M.; Gerken, Mark; Leraas, Kristen M.; Lichtenberg, Tara M.; Ramirez, Nilsa C.; Wise, Lisa; Zmuda, Erik; Corcoran, Niall; Costello, Tony; Hovens, Christopher; Carvalho, Andre L.; de Carvalho, Ana C.; Fregnani, José H.; Longatto-Filho, Adhemar; Reis, Rui M.; Scapulatempo-Neto, Cristovam; Silveira, Henrique C.S.; Vidal, Daniel O.; Burnette, Andrew; Eschbacher, Jennifer; Hermes, Beth; Noss, Ardene; Singh, Rosy; Anderson, Matthew L.; Castro, Patricia D.; Ittmann, Michael; Huntsman, David; Kohl, Bernard; Le, Xuan; Thorp, Richard; Andry, Chris; Duffy, Elizabeth R.; Lyadov, Vladimir; Paklina, Oxana; Setdikova, Galiya; Shabunin, Alexey; Tavobilov, Mikhail; McPherson, Christopher; Warnick, Ronald; Berkowitz, Ross; Cramer, Daniel; Feltmate, Colleen; Horowitz, Neil; Kibel, Adam; Muto, Michael; Raut, Chandrajit P.; Malykh, Andrei; Barnholtz-Sloan, Jill S.; Barrett, Wendi; Devine, Karen; Fulop, Jordonna; Ostrom, Quinn T.; Shimmel, Kristen; Wolinsky, Yingli; Sloan, Andrew E.; De Rose, Agostino; Giuliante, Felice; Goodman, Marc; Karlan, Beth Y.; Hagedorn, Curt H.; Eckman, John; Harr, Jodi; Myers, Jerome; Tucker, Kelinda; Zach, Leigh Anne; Deyarmin, Brenda; Hu, Hai; Kvecher, Leonid; Larson, Caroline; Mural, Richard J.; Somiari, Stella; Vicha, Ales; Zelinka, Tomas; Bennett, Joseph; Iacocca, Mary; Rabeno, Brenda; Swanson, Patricia; Latour, Mathieu; Lacombe, Louis; Têtu, Bernard; Bergeron, Alain; McGraw, Mary; Staugaitis, Susan M.; Chabot, John; Hibshoosh, Hanina; Sepulveda, Antonia; Su, Tao; Wang, Timothy; Potapova, Olga; Voronina, Olga; Desjardins, Laurence; Mariani, Odette; Roman-Roman, Sergio; Sastre, Xavier; Stern, Marc Henri; Cheng, Feixiong; Signoretti, Sabina; Berchuck, Andrew; Bigner, Darell; Lipp, Eric; Marks, Jeffrey; McCall, Shannon; McLendon, Roger; Secord, Angeles; Sharp, Alexis; Behera, Madhusmita; Brat, Daniel J.; Chen, Amy; Delman, Keith; Force, Seth; Khuri, Fadlo; Magliocca, Kelly; Maithel, Shishir; Olson, Jeffrey J.; Owonikoko, Taofeek; Pickens, Alan; Ramalingam, Suresh; Shin, Dong M.; Sica, Gabriel; Van Meir, Erwin G.; Zhang, Hongzheng; Eijckenboom, Wil; Gillis, Ad; Korpershoek, Esther; Looijenga, Leendert; Oosterhuis, Wolter; Stoop, Hans; van Kessel, Kim E.; Zwarthoff, Ellen C.; Calatozzolo, Chiara; Cuppini, Lucia; Cuzzubbo, Stefania; DiMeco, Francesco; Finocchiaro, Gaetano; Mattei, Luca; Perin, Alessandro; Pollo, Bianca; Chen, Chu; Houck, John; Lohavanichbutr, Pawadee; Hartmann, Arndt; Stoehr, Christine; Stoehr, Robert; Taubert, Helge; Wach, Sven; Wullich, Bernd; Kycler, Witold; Murawa, Dawid; Wiznerowicz, Maciej; Chung, Ki; Edenfield, W. Jeffrey; Martin, Julie; Baudin, Eric; Bubley, Glenn; Bueno, Raphael; De Rienzo, Assunta; Richards, William G.; Kalkanis, Steven; Mikkelsen, Tom; Noushmehr, Houtan; Scarpace, Lisa; Girard, Nicolas; Aymerich, Marta; Campo, Elias; Giné, Eva; Guillermo, Armando López; Van Bang, Nguyen; Hanh, Phan Thi; Phu, Bui Duc; Tang, Yufang; Colman, Howard; Evason, Kimberley; Dottino, Peter R.; Martignetti, John A.; Gabra, Hani; Juhl, Hartmut; Akeredolu, Teniola; Stepa, Serghei; Hoon, Dave; Ahn, Keunsoo; Kang, Koo Jeong; Beuschlein, Felix; Breggia, Anne; Birrer, Michael; Bell, Debra; Borad, Mitesh; Bryce, Alan H.; Castle, Erik; Chandan, Vishal; Cheville, John; Copland, John A.; Farnell, Michael; Flotte, Thomas; Giama, Nasra; Ho, Thai; Kendrick, Michael; Kocher, Jean Pierre; Kopp, Karla; Moser, Catherine; Nagorney, David; O'Brien, Daniel; O'Neill, Brian Patrick; Patel, Tushar; Petersen, Gloria; Que, Florencia; Rivera, Michael; Roberts, Lewis; Smallridge, Robert; Smyrk, Thomas; Stanton, Melissa; Thompson, R. Houston; Torbenson, Michael; Yang, Ju Dong; Zhang, Lizhi; Brimo, Fadi; Ajani, Jaffer A.; Gonzalez, Ana Maria Angulo; Behrens, Carmen; Bondaruk, Jolanta; Broaddus, Russell; Czerniak, Bogdan; Esmaeli, Bita; Fujimoto, Junya; Gershenwald, Jeffrey; Guo, Charles; Lazar, Alexander J.; Logothetis, Christopher; Meric-Bernstam, Funda; Moran, Cesar; Ramondetta, Lois; Rice, David; Sood, Anil; Tamboli, Pheroze; Thompson, Timothy; Troncoso, Patricia; Tsao, Anne; Wistuba, Ignacio; Carter, Candace; Haydu, Lauren; Hersey, Peter; Jakrot, Valerie; Kakavand, Hojabr; Kefford, Richard; Lee, Kenneth; Long, Georgina; Mann, Graham; Quinn, Michael; Saw, Robyn; Scolyer, Richard; Shannon, Kerwin; Spillane, Andrew; Stretch, onathan; Synott, Maria; Thompson, John; Wilmott, James; Al-Ahmadie, Hikmat; Chan, Timothy A.; Ghossein, Ronald; Gopalan, Anuradha; Levine, Douglas A.; Reuter, Victor; Singer, Samuel; Singh, Bhuvanesh; Tien, Nguyen Viet; Broudy, Thomas; Mirsaidi, Cyrus; Nair, Praveen; Drwiega, Paul; Miller, Judy; Smith, Jennifer; Zaren, Howard; Park, Joong Won; Hung, Nguyen Phi; Kebebew, Electron; Linehan, W. Marston; Metwalli, Adam R.; Pacak, Karel; Pinto, Peter A.; Schiffman, Mark; Schmidt, Laura S.; Vocke, Cathy D.; Wentzensen, Nicolas; Worrell, Robert; Yang, Hannah; Moncrieff, Marc; Goparaju, Chandra; Melamed, Jonathan; Pass, Harvey; Botnariuc, Natalia; Caraman, Irina; Cernat, Mircea; Chemencedji, Inga; Clipca, Adrian; Doruc, Serghei; Gorincioi, Ghenadie; Mura, Sergiu; Pirtac, Maria; Stancul, Irina; Tcaciuc, Diana; Albert, Monique; Alexopoulou, Iakovina; Arnaout, Angel; Bartlett, John; Engel, Jay; Gilbert, Sebastien; Parfitt, Jeremy; Sekhon, Harman; Thomas, George; Rassl, Doris M.; Rintoul, Robert C.; Bifulco, Carlo; Tamakawa, Raina; Urba, Walter; Hayward, Nicholas; Timmers, Henri; Antenucci, Anna; Facciolo, Francesco; Grazi, Gianluca; Marino, Mirella; Merola, Roberta; de Krijger, Ronald; Gimenez-Roqueplo, Anne Paule; Piché, Alain; Chevalier, Simone; McKercher, Ginette; Birsoy, Kivanc; Barnett, Gene; Brewer, Cathy; Farver, Carol; Naska, Theresa; Pennell, Nathan A.; Raymond, Daniel; Schilero, Cathy; Smolenski, Kathy; Williams, Felicia; Morrison, Carl; Borgia, Jeffrey A.; Liptay, Michael J.; Pool, Mark; Seder, Christopher W.; Junker, Kerstin; Omberg, Larsson; Dinkin, Mikhail; Manikhas, George; Alvaro, Domenico; Bragazzi, Maria Consiglia; Cardinale, Vincenzo; Carpino, Guido; Gaudio, Eugenio; Chesla, David; Cottingham, Sandra; Dubina, Michael; Moiseenko, Fedor; Dhanasekaran, Renumathy; Becker, Karl Friedrich; Janssen, Klaus Peter; Slotta-Huspenina, Julia; Abdel-Rahman, Mohamed H.; Aziz, Dina; Bell, Sue; Cebulla, Colleen M.; Davis, Amy; Duell, Rebecca; Elder, J. Bradley; Hilty, Joe; Kumar, Bahavna; Lang, James; Lehman, Norman L.; Mandt, Randy; Nguyen, Phuong; Pilarski, Robert; Rai, Karan; Schoenfield, Lynn; Senecal, Kelly; Wakely, Paul; Hansen, Paul; Lechan, Ronald; Powers, James; Tischler, Arthur; Grizzle, William E.; Sexton, Katherine C.; Kastl, Alison; Henderson, Joel; Porten, Sima; Waldmann, Jens; Fassnacht, Martin; Asa, Sylvia L.; Schadendorf, Dirk; Couce, Marta; Graefen, Markus; Huland, Hartwig; Sauter, Guido; Schlomm, Thorsten; Simon, Ronald; Tennstedt, Pierre; Olabode, Oluwole; Nelson, Mark; Bathe, Oliver; Carroll, Peter R.; Chan, June M.; Disaia, Philip; Glenn, Pat; Kelley, Robin K.; Landen, Charles N.; Phillips, Joanna; Prados, Michael; Simko, Jeffry; Smith-McCune, Karen; VandenBerg, Scott; Roggin, Kevin; Fehrenbach, Ashley; Kendler, Ady; Sifri, Suzanne; Steele, Ruth; Jimeno, Antonio; Carey, Francis; Forgie, Ian; Mannelli, Massimo; Carney, Michael; Hernandez, Brenda; Campos, Benito; Herold-Mende, Christel; Jungk, Christin; Unterberg, Andreas; von Deimling, Andreas; Bossler, Aaron; Galbraith, Joseph; Jacobus, Laura; Knudson, Michael; Knutson, Tina; Ma, Deqin; Milhem, Mohammed; Sigmund, Rita; Godwin, Andrew K.; Madan, Rashna; Rosenthal, Howard G.; Adebamowo, Clement; Adebamowo, Sally N.; Boussioutas, Alex; Beer, David; Giordano, Thomas; Mes-Masson, Anne Marie; Saad, Fred; Bocklage, Therese; Landrum, Lisa; Mannel, Robert; Moore, Kathleen; Moxley, Katherine; Postier, Russel; Walker, Joan; Zuna, Rosemary; Feldman, Michael; Valdivieso, Federico; Dhir, Rajiv; Luketich, James; Pinero, Edna M.Mora; Quintero-Aguilo, Mario; Carlotti, Carlos Gilberto; Dos Santos, Jose Sebastião; Kemp, Rafael; Sankarankuty, Ajith; Tirapelli, Daniela; Catto, James; Agnew, Kathy; Swisher, Elizabeth; Creaney, Jenette; Robinson, Bruce; Shelley, Carl Simon; Godwin, Eryn M.; Kendall, Sara; Shipman, Cassaundra; Bradford, Carol; Carey, Thomas; Haddad, Andrea; Moyer, Jeffey; Peterson, Lisa; Prince, Mark; Rozek, Laura; Wolf, Gregory; Bowman, Rayleen; Fong, Kwun M.; Yang, Ian; Korst, Robert; Rathmell, W. Kimryn; Fantacone-Campbell, J. Leigh; Hooke, Jeffrey A.; Kovatich, Albert J.; Shriver, Craig D.; DiPersio, John; Drake, Bettina; Govindan, Ramaswamy; Heath, Sharon; Ley, Timothy; Van Tine, Brian; Westervelt, Peter; Rubin, Mark A.; Lee, Jung Il; Aredes, Natália D.; Mariamidze, Armaz; Spellman, Paul T.; Rathmell, W. Kimryn; Linehan, W. Marston

    2018-01-01

    Renal cell carcinoma (RCC) is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and therapeutic responses. The current study evaluated 843 RCC from the three major histologic subtypes, including 488 clear cell RCC, 274 papillary RCC,

  14. Frequency of venous thromboembolism events during acute inpatient rehabilitation in a comprehensive cancer centre

    Directory of Open Access Journals (Sweden)

    Amy H. Ng

    2017-09-01

    Conclusion: Cancer patients with low FIM transfer scores and lower extremity oedema are at higher risk of venous thromboembolism. Patients with these clinical findings at admission may require measures for more aggressive surveillance for the presence of venous thromboembolism. Patients with venous thromboembolism had an increased length of stay in rehabilitation, but ultimately did not have significant differences in FIM score changes.

  15. Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer

    NARCIS (Netherlands)

    Wang, Kai; Yuen, Siu Tsan; Xu, Jiangchun; Lee, Siu Po; Yan, Helen H N; Shi, Stephanie T; Siu, Hoi Cheong; Deng, Shibing; Chu, Kent Man; Law, Simon; Chan, Kok Hoe; Chan, Annie S Y; Tsui, Wai Yin; Ho, Siu Lun; Chan, Anthony K W; Man, Jonathan L K; Foglizzo, Valentina; Ng, Man Kin; Chan, April S; Ching, Yick Pang; Cheng, Grace H W; Xie, Tao; Fernandez, Julio; Li, Vivian S W; Clevers, Hans; Rejto, Paul A; Mao, Mao; Leung, Suet Yi

    Gastric cancer is a heterogeneous disease with diverse molecular and histological subtypes. We performed whole-genome sequencing in 100 tumor-normal pairs, along with DNA copy number, gene expression and methylation profiling, for integrative genomic analysis. We found subtype-specific genetic and

  16. Sleep in children with cancer: case review of 70 children evaluated in a comprehensive pediatric sleep center.

    Science.gov (United States)

    Rosen, Gerald; Brand, Sarah R

    2011-07-01

    The goal of this study was to characterize the sleep problems of children with cancer who were referred for a comprehensive sleep evaluation. A retrospective case series review was conducted of all children with cancer referred to the pediatric sleep clinic from 1994 to 2009 for evaluation of a sleep problem. Seventy children were seen and evaluated during this interval; all had a complete sleep history taken, and further objective sleep evaluations were performed as part of their evaluation only when clinically indicated. An overnight polysomnogram was performed in 53 children. In 36 children with a history of excessive daytime sleepiness (EDS), a multiple sleep latency study was performed the following day. Seven children had a 3-4-week actigraphic study. Children with neoplasms of central nervous system (CNS) involving the hypothalamus, thalamus, and brainstem were the most commonly referred children and had the most frequent and severe sleep problems. Excessive daytime sleepiness was the most common sleep problem, seen in 60% of children with cancer and in 80% of children with CNS neoplasms involving the hypothalamus, thalamus, and brainstem. Sleep disordered breathing (SDB) was present in 40% of the entire group of children with cancer and 46% of children with neoplasms involving the hypothalamus, thalamus, and brainstem. Children with CNS neoplasms often had more than one sleep problem, most commonly EDS and SDB. In these children, correction of the SDB often did not eliminate the EDS. In children with leukemia, insomnia was the most common sleep problem identified, present in 39%. The causes of the sleep problems were varied and included neurologic injury caused by the neoplasm and/or the CNS-directed treatments; seizures, adenotonsillar hypertrophy, medication side effects, obesity, pain, anxiety, and drug abuse. Some of the sleep problems were present before the diagnosis of cancer, though most developed after treatment was begun. A wide range of

  17. HPV Involvement in Head and Neck Cancers: Comprehensive Assessment of Biomarkers in 3680 Patients.

    Science.gov (United States)

    Castellsagué, Xavier; Alemany, Laia; Quer, Miquel; Halec, Gordana; Quirós, Beatriz; Tous, Sara; Clavero, Omar; Alòs, Llúcia; Biegner, Thorsten; Szafarowski, Tomasz; Alejo, Maria; Holzinger, Dana; Cadena, Enrique; Claros, Edith; Hall, Gillian; Laco, Jan; Poljak, Mario; Benevolo, Maria; Kasamatsu, Elena; Mehanna, Hisham; Ndiaye, Cathy; Guimerà, Núria; Lloveras, Belen; León, Xavier; Ruiz-Cabezas, Juan C; Alvarado-Cabrero, Isabel; Kang, Chang-Suk; Oh, Jin-Kyoung; Garcia-Rojo, Marcial; Iljazovic, Ermina; Ajayi, Oluseyi F; Duarte, Flora; Nessa, Ashrafun; Tinoco, Leopoldo; Duran-Padilla, Marco A; Pirog, Edyta C; Viarheichyk, Halina; Morales, Hesler; Costes, Valérie; Félix, Ana; Germar, Maria Julieta V; Mena, Marisa; Ruacan, Arzu; Jain, Asha; Mehrotra, Ravi; Goodman, Marc T; Lombardi, Luis Estuardo; Ferrera, Annabelle; Malami, Sani; Albanesi, Estela I; Dabed, Pablo; Molina, Carla; López-Revilla, Rubén; Mandys, Václav; González, Manuel E; Velasco, Julio; Bravo, Ignacio G; Quint, Wim; Pawlita, Michael; Muñoz, Nubia; de Sanjosé, Silvia; Xavier Bosch, F

    2016-06-01

    We conducted a large international study to estimate fractions of head and neck cancers (HNCs) attributable to human papillomavirus (HPV-AFs) using six HPV-related biomarkers of viral detection, transcription, and cellular transformation. Formalin-fixed, paraffin-embedded cancer tissues of the oral cavity (OC), pharynx, and larynx were collected from pathology archives in 29 countries. All samples were subject to histopathological evaluation, DNA quality control, and HPV-DNA detection. Samples containing HPV-DNA were further subject to HPV E6*I mRNA detection and to p16(INK4a), pRb, p53, and Cyclin D1 immunohistochemistry. Final estimates of HPV-AFs were based on HPV-DNA, HPV E6*I mRNA, and/or p16(INK4a) results. A total of 3680 samples yielded valid results: 1374 pharyngeal, 1264 OC, and 1042 laryngeal cancers. HPV-AF estimates based on positivity for HPV-DNA, and for either HPV E6*I mRNA or p16(INK4a), were 22.4%, 4.4%, and 3.5% for cancers of the oropharynx, OC, and larynx, respectively, and 18.5%, 3.0%, and 1.5% when requiring simultaneous positivity for all three markers. HPV16 was largely the most common type. Estimates of HPV-AF in the oropharynx were highest in South America, Central and Eastern Europe, and Northern Europe, and lowest in Southern Europe. Women showed higher HPV-AFs than men for cancers of the oropharynx in Europe and for the larynx in Central-South America. HPV contribution to HNCs is substantial but highly heterogeneous by cancer site, region, and sex. This study, the largest exploring HPV attribution in HNCs, confirms the important role of HPVs in oropharyngeal cancer and drastically downplays the previously reported involvement of HPVs in the other HNCs. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  18. The role of the Hedgehog signaling pathway in cancer: A comprehensive review

    Directory of Open Access Journals (Sweden)

    Ana Marija Skoda

    2018-02-01

    Full Text Available The Hedgehog (Hh signaling pathway was first identified in the common fruit fly. It is a highly conserved evolutionary pathway of signal transmission from the cell membrane to the nucleus. The Hh signaling pathway plays an important role in the embryonic development. It exerts its biological effects through a signaling cascade that culminates in a change of balance between activator and repressor forms of glioma-associated oncogene (Gli transcription factors. The components of the Hh signaling pathway involved in the signaling transfer to the Gli transcription factors include Hedgehog ligands (Sonic Hh [SHh], Indian Hh [IHh], and Desert Hh [DHh], Patched receptor (Ptch1, Ptch2, Smoothened receptor (Smo, Suppressor of fused homolog (Sufu, kinesin protein Kif7, protein kinase A (PKA, and cyclic adenosine monophosphate (cAMP. The activator form of Gli travels to the nucleus and stimulates the transcription of the target genes by binding to their promoters. The main target genes of the Hh signaling pathway are PTCH1, PTCH2, and GLI1. Deregulation of the Hh signaling pathway is associated with developmental anomalies and cancer, including Gorlin syndrome, and sporadic cancers, such as basal cell carcinoma, medulloblastoma, pancreatic, breast, colon, ovarian, and small-cell lung carcinomas. The aberrant activation of the Hh signaling pathway is caused by mutations in the related genes (ligand-independent signaling or by the excessive expression of the Hh signaling molecules (ligand-dependent signaling – autocrine or paracrine. Several Hh signaling pathway inhibitors, such as vismodegib and sonidegib, have been developed for cancer treatment. These drugs are regarded as promising cancer therapies, especially for patients with refractory/advanced cancers.

  19. Treatment and survival of patients with non-small cell lung cancer Stage IIIA diagnosed in 1989-1994: a study in the region of the Comprehensive Cancer Centre East, The Netherlands.

    NARCIS (Netherlands)

    Dijck, J.A.A.M. van; Festen, J.; Kleijn, E.M.H.A. de; Kramer, G.W.P.M.; Tjan-Heijnen, V.C.; Verbeek, A.L.M.

    2001-01-01

    The purpose of this study was to gain insight into the treatment policy and survival of patients with non-small cell lung cancer (NSCLC) clinical stage IIIA in daily practice. We selected 212 patients, who had been diagnosed between 1989 and 1994 and registered by the Cancer Registry, Comprehensive

  20. The impact of database restriction on pharmacovigilance signal detection of selected cancer therapies.

    Science.gov (United States)

    Hauben, Manfred; Hung, Eric; Wood, Jennifer; Soitkar, Amit; Reshef, Daniel

    2017-05-01

    The aim of this study was to investigate whether database restriction can improve oncology drug pharmacovigilance signal detection performance. We used spontaneous adverse event (AE) reports in the United States (US) Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) database. Positive control (PC) drug medical concept (DMC) pairs were selected from safety information not included in the product's first label but subsequently added as label changes. These medical concepts (MCs) were mapped to the Medical Dictionary for Regulatory Activities (MedDRA) preferred terms (PTs) used in FAERS to code AEs. Negative controls (NC) were MCs with circumscribed PTs not included in the corresponding US package insert (USPI). We calculated shrinkage-adjusted observed-to-expected (O/E) reporting frequencies for the aforementioned drug-PT pairs. We also formulated an adjudication framework to calculate performance at the MC level. Performance metrics [sensitivity, specificity, positive and negative predictive value (PPV, NPV), signal/noise (S/N), F and Matthews correlation coefficient (MCC)] were calculated for each analysis and compared. The PC reference set consisted of 11 drugs, 487 PTs, 27 MCs, 37 drug-MC combinations and 638 drug-event combinations (DECs). The NC reference set consisted of 11 drugs, 9 PTs, 5 MCs, 40 drug-MC combinations and 67 DECs. Most drug-event pairs were not highlighted by either analysis. A small percentage of signals of disproportionate reporting were lost, more noise than signal, with no gains. Specificity and PPV improved whereas sensitivity, NPV, F and MCC decreased, but all changes were small relative to the decrease in sensitivity. The overall S/N improved. This oncology drug restricted analysis improved the S/N ratio, removing proportionately more noise than signal, but with significant credible signal loss. Without broader experience and a calculus of costs and utilities of correct versus incorrect classifications in

  1. Genetic variation in the TP53 pathway and bladder cancer risk. a comprehensive analysis.

    Directory of Open Access Journals (Sweden)

    Silvia Pineda

    Full Text Available Germline variants in TP63 have been consistently associated with several tumors, including bladder cancer, indicating the importance of TP53 pathway in cancer genetic susceptibility. However, variants in other related genes, including TP53 rs1042522 (Arg72Pro, still present controversial results. We carried out an in depth assessment of associations between common germline variants in the TP53 pathway and bladder cancer risk.We investigated 184 tagSNPs from 18 genes in 1,058 cases and 1,138 controls from the Spanish Bladder Cancer/EPICURO Study. Cases were newly-diagnosed bladder cancer patients during 1998-2001. Hospital controls were age-gender, and area matched to cases. SNPs were genotyped in blood DNA using Illumina Golden Gate and TaqMan assays. Cases were subphenotyped according to stage/grade and tumor p53 expression. We applied classical tests to assess individual SNP associations and the Least Absolute Shrinkage and Selection Operator (LASSO-penalized logistic regression analysis to assess multiple SNPs simultaneously.Based on classical analyses, SNPs in BAK1 (1, IGF1R (5, P53AIP1 (1, PMAIP1 (2, SERINPB5 (3, TP63 (3, and TP73 (1 showed significant associations at p-value≤0.05. However, no evidence of association, either with overall risk or with specific disease subtypes, was observed after correction for multiple testing (p-value≥0.8. LASSO selected the SNP rs6567355 in SERPINB5 with 83% of reproducibility. This SNP provided an OR = 1.21, 95%CI 1.05-1.38, p-value = 0.006, and a corrected p-value = 0.5 when controlling for over-estimation.We found no strong evidence that common variants in the TP53 pathway are associated with bladder cancer susceptibility. Our study suggests that it is unlikely that TP53 Arg72Pro is implicated in the UCB in white Europeans. SERPINB5 and TP63 variation deserve further exploration in extended studies.

  2. Predictors of circumferential resection margin involvement in surgically resected rectal cancer: A retrospective review of 23,464 patients in the US National Cancer Database.

    Science.gov (United States)

    Al-Sukhni, Eisar; Attwood, Kristopher; Gabriel, Emmanuel; Nurkin, Steven J

    2016-04-01

    The circumferential resection margin (CRM) is a key prognostic factor after rectal cancer resection. We sought to identify factors associated with CRM involvement (CRM+). A retrospective review was performed of the National Cancer Database, 2004-2011. Patients with rectal cancer who underwent radical resection and had a recorded CRM were included. Multivariable analysis of the association between clinicopathologic characteristics and CRM was performed. Tumor CRM+. Of 23,464 eligible patients, 13.3% were CRM+. Factors associated with CRM+ were diagnosis later in the study period, lack of insurance, advanced stage, higher grade, undergoing APR, and receiving radiation. Nearly half of CRM+ patients did not receive neoadjuvant therapy. CRM+ patients who did not receive neoadjuvant therapy were more likely to be female, older, with more comorbidities, smaller tumors, earlier clinical stage, advanced pathologic stage, and CEA-negative disease compared to those who received it. Factors associated with CRM+ include features of advanced disease, undergoing APR, and lack of health insurance. Half of CRM+ patients did not receive neoadjuvant treatment. These represent cases where CRM status may be modifiable with appropriate pre-operative selection and multidisciplinary management. Copyright © 2016 IJS Publishing Group Limited. Published by Elsevier Ltd. All rights reserved.

  3. UMD-USHbases: a comprehensive set of databases to record and analyse pathogenic mutations and unclassified variants in seven Usher syndrome causing genes.

    Science.gov (United States)

    Baux, David; Faugère, Valérie; Larrieu, Lise; Le Guédard-Méreuze, Sandie; Hamroun, Dalil; Béroud, Christophe; Malcolm, Sue; Claustres, Mireille; Roux, Anne-Françoise

    2008-08-01

    Using the Universal Mutation Database (UMD) software, we have constructed "UMD-USHbases", a set of relational databases of nucleotide variations for seven genes involved in Usher syndrome (MYO7A, CDH23, PCDH15, USH1C, USH1G, USH3A and USH2A). Mutations in the Usher syndrome type I causing genes are also recorded in non-syndromic hearing loss cases and mutations in USH2A in non-syndromic retinitis pigmentosa. Usher syndrome provides a particular challenge for molecular diagnostics because of the clinical and molecular heterogeneity. As many mutations are missense changes, and all the genes also contain apparently non-pathogenic polymorphisms, well-curated databases are crucial for accurate interpretation of pathogenicity. Tools are provided to assess the pathogenicity of mutations, including conservation of amino acids and analysis of splice-sites. Reference amino acid alignments are provided. Apparently non-pathogenic variants in patients with Usher syndrome, at both the nucleotide and amino acid level, are included. The UMD-USHbases currently contain more than 2,830 entries including disease causing mutations, unclassified variants or non-pathogenic polymorphisms identified in over 938 patients. In addition to data collected from 89 publications, 15 novel mutations identified in our laboratory are recorded in MYO7A (6), CDH23 (8), or PCDH15 (1) genes. Information is given on the relative involvement of the seven genes, the number and distribution of variants in each gene. UMD-USHbases give access to a software package that provides specific routines and optimized multicriteria research and sorting tools. These databases should assist clinicians and geneticists seeking information about mutations responsible for Usher syndrome.

  4. Economic, racial and ethnic disparities in breast cancer in the US: towards a more comprehensive model.

    Science.gov (United States)

    Campbell, Richard T; Li, Xue; Dolecek, Therese A; Barrett, Richard E; Weaver, Kathryn E; Warnecke, Richard B

    2009-09-01

    Using cancer registry data, we focus on racial and ethnic disparities in stage of breast cancer diagnosis in Cook County, IL. The county health system is the "last resort" health-care provider for low-income persons. Socioeconomic status is measured using empirical Bayes estimates of tract-level poverty, specific to non-Hispanic whites, non-Hispanic blacks or Hispanics in one of three age groups. We use ordinal logistic regression with non-proportional odds to model stage. Blacks and Hispanics are at greater risk for regional and distant stage diagnosis, but the disparity declines with age. Women in high-poverty areas are at substantially greater risk for late-stage diagnosis. The effects of poverty do not differ by age or across racial and ethnic groups.

  5. Translational database selection and multiplexed sequence capture for up front filtering of reliable breast cancer biomarker candidates.

    Directory of Open Access Journals (Sweden)

    Patrik L Ståhl

    Full Text Available Biomarker identification is of utmost importance for the development of novel diagnostics and therapeutics. Here we make use of a translational database selection strategy, utilizing data from the Human Protein Atlas (HPA on differentially expressed protein patterns in healthy and breast cancer tissues as a means to filter out potential biomarkers for underlying genetic causatives of the disease. DNA was isolated from ten breast cancer biopsies, and the protein coding and flanking non-coding genomic regions corresponding to the selected proteins were extracted in a multiplexed format from the samples using a single DNA sequence capture array. Deep sequencing revealed an even enrichment of the multiplexed samples and a great variation of genetic alterations in the tumors of the sampled individuals. Benefiting from the upstream filtering method, the final set of biomarker candidates could be completely verified through bidirectional Sanger sequencing, revealing a 40 percent false positive rate despite high read coverage. Of the variants encountered in translated regions, nine novel non-synonymous variations were identified and verified, two of which were present in more than one of the ten tumor samples.

  6. Proteomic biomarkers for ovarian cancer risk in women with polycystic ovary syndrome: a systematic review and biomarker database integration.

    Science.gov (United States)

    Galazis, Nicolas; Olaleye, Olalekan; Haoula, Zeina; Layfield, Robert; Atiomo, William

    2012-12-01

    To review and identify possible biomarkers for ovarian cancer (OC) in women with polycystic ovary syndrome (PCOS). Systematic literature searches of MEDLINE, EMBASE, and Cochrane using the search terms "proteomics," "proteomic," and "ovarian cancer" or "ovarian carcinoma." Proteomic biomarkers for OC were then integrated with an updated previously published database of all proteomic biomarkers identified to date in patients with PCOS. Academic department of obstetrics and gynecology in the United Kingdom. A total of 180 women identified in the six studies. Tissue samples from women with OC vs. tissue samples from women without OC. Proteomic biomarkers, proteomic technique used, and methodologic quality score. A panel of six biomarkers was overexpressed both in women with OC and in women with PCOS. These biomarkers include calreticulin, fibrinogen-γ, superoxide dismutase, vimentin, malate dehydrogenase, and lamin B2. These biomarkers could help improve our understanding of the links between PCOS and OC and could potentially be used to identify subgroups of women with PCOS at increased risk of OC. More studies are required to further evaluate the role these biomarkers play in women with PCOS and OC. Copyright © 2012 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  7. First postoperative PSA is associated with outcomes in patients with node positive prostate cancer: Results from the SEARCH database.

    Science.gov (United States)

    McDonald, Michelle L; Howard, Lauren E; Aronson, William J; Terris, Martha K; Cooperberg, Matthew R; Amling, Christopher L; Freedland, Stephen J; Kane, Christopher J

    2018-05-01

    To analyze factors associated with metastases, prostate cancer-specific mortality, and all-cause mortality in pN1 patients. We analyzed 3,642 radical prostatectomy patients within the Shared Equal Access Regional Cancer Hospital (SEARCH) database. Pathologic Gleason grade, number of lymph nodes (LN) removed, and first postoperative prostate-specific antigen (PSA) (PSA. Of 3,642 patients, 124 (3.4%) had pN1. There were 71 (60%) patients with 1 positive LN, 32 (27%) with 2 positive LNs, and 15 (13%) with ≥3. Among men with pN1, first postoperative PSA wasPSA ≥0.2 ng/ml (P = 0.005) were associated with metastases. First postoperative PSA ≥0.2ng/ml was associated with metastasis on multivariable analysis (P = 0.046). Log-rank analysis revealed a more favorable metastases-free survival in patients with a first postoperative PSAPSAPSA ≥0.2ng/ml were more likely to develop metastases. First postoperative PSA may be useful in identifying pN1 patients who harbor distant disease and aid in secondary treatment decisions. Copyright © 2018 Elsevier Inc. All rights reserved.

  8. Association of cetuximab with adverse pulmonary events in cancer patients: a comprehensive review

    Directory of Open Access Journals (Sweden)

    Lu Jason

    2009-08-01

    Full Text Available Abstract Compounds derived from biologic sources, or biologicals, are increasingly utilized as therapeutic agents in malignancy. Development of anti-cancer targeted therapies from biologics is increasingly being utilized. Cetuximab, a chimeric monoclonal antibody, is one such anti-cancer targeted therapeutic that has shown efficacy in quelling the rate of patient decline in colorectal, head/neck, and non-small cell lung cancer. However, due to the relatively recent addition of biologic compounds to the therapeutic arsenal, information related to adverse reactions is less well known than those seen in traditional chemotherapeutics. Dermatologic reactions have been demonstrated as the most frequent side effect cited during cetuximab therapy for malignancy; however, other effects may lead to greater morbidity. In general, pulmonary complications of therapeutics can lead to significant morbidity and mortality. The purpose of this review is to compile the various pulmonary side effects seen in patients treated with cetuximab for various malignancies, and to compare the incidence of these adverse reactions to standard therapies.

  9. Recruitment Methods and Show Rates to a Prostate Cancer Early Detection Program for High-Risk Men: A Comprehensive Analysis

    Science.gov (United States)

    Giri, Veda N.; Coups, Elliot J.; Ruth, Karen; Goplerud, Julia; Raysor, Susan; Kim, Taylor Y.; Bagden, Loretta; Mastalski, Kathleen; Zakrzewski, Debra; Leimkuhler, Suzanne; Watkins-Bruner, Deborah

    2009-01-01

    Purpose Men with a family history (FH) of prostate cancer (PCA) and African American (AA) men are at higher risk for PCA. Recruitment and retention of these high-risk men into early detection programs has been challenging. We report a comprehensive analysis on recruitment methods, show rates, and participant factors from the Prostate Cancer Risk Assessment Program (PRAP), which is a prospective, longitudinal PCA screening study. Materials and Methods Men 35–69 years are eligible if they have a FH of PCA, are AA, or have a BRCA1/2 mutation. Recruitment methods were analyzed with respect to participant demographics and show to the first PRAP appointment using standard statistical methods Results Out of 707 men recruited, 64.9% showed to the initial PRAP appointment. More individuals were recruited via radio than from referral or other methods (χ2 = 298.13, p < .0001). Men recruited via radio were more likely to be AA (p<0.001), less educated (p=0.003), not married or partnered (p=0.007), and have no FH of PCA (p<0.001). Men recruited via referrals had higher incomes (p=0.007). Men recruited via referral were more likely to attend their initial PRAP visit than those recruited by radio or other methods (χ2 = 27.08, p < .0001). Conclusions This comprehensive analysis finds that radio leads to higher recruitment of AA men with lower socioeconomic status. However, these are the high-risk men that have lower show rates for PCA screening. Targeted motivational measures need to be studied to improve show rates for PCA risk assessment for these high-risk men. PMID:19758657

  10. Comprehensive analysis of copy number aberrations in microsatellite stable colon cancer in view of stromal component.

    Science.gov (United States)

    Alonso, M Henar; Aussó, Susanna; Lopez-Doriga, Adriana; Cordero, David; Guinó, Elisabet; Solé, Xavier; Barenys, Mercè; de Oca, Javier; Capella, Gabriel; Salazar, Ramón; Sanz-Pamplona, Rebeca; Moreno, Victor

    2017-07-25

    Somatic copy number aberrations (CNAs) are common acquired changes in cancer cells having an important role in the progression of colon cancer (colorectal cancer, CRC). This study aimed to perform a characterisation of CNA and their impact in gene expression. Copy number aberrations were inferred from SNP array data in a series of 99 CRC. Copy number aberration events were calculated and used to assess the association between copy number dosage, clinical and molecular characteristics of the tumours, and gene expression changes. All analyses were adjusted for the quantity of stroma in each sample, which was inferred from gene expression data. High heterogeneity among samples was observed; the proportion of altered genome ranged between 0.04 and 26.6%. Recurrent CNA regions with gains were frequent in chromosomes 7p, 8q, 13q, and 20, whereas 8p, 17p, and 18 cumulated losses. A significant positive correlation was observed between the number of somatic mutations and total CNA (Spearman's r=0.42, P=0.006). Approximately 37% of genes located in CNA regions changed their level of expression and the average partial correlation (adjusted for stromal content) with copy number was 0.54 (interquartile range 0.20 to 0.81). Altered genes showed enrichment in pathways relevant for CRC. Tumours classified as CMS2 and CMS4 by the consensus molecular subtyping showed higher frequency of CNA. Losses of one small region in 1p36.33, with gene CDK11B, were associated with poor prognosis. More than 66% of the recurrent CNA were validated in the The Cancer Genome Atlas (TCGA) data when analysed with the same procedure. Furthermore, 79% of the genes with altered expression in our data were validated in the TCGA. Although CNA are frequent events in microsatellite stable CRC, few focal recurrent regions were found. These aberrations have strong effects on gene expression and contribute to deregulate relevant cancer pathways. Owing to the diploid nature of stromal cells, it is important to

  11. The surgical management of male breast cancer: Time for an easy access national reporting database?

    Directory of Open Access Journals (Sweden)

    Robert M.T. Staruch

    2016-08-01

    Discussion: We report a series of seven cases of male breast cancer encountered over three years, evaluating patient demographics as well as treatment and outcomes. In our series patients were managed with mastectomy. New evidence is questioning the role of mastectomy against breast conserving surgery in male patients. Furthermore there is a lack of reporting infrastructure for national data capture of the benefits of surgical modalities. Literature review highlights the varied clinical experience between units that remains reported as podium presentation but not published. The establishment of an online international reporting registry would allow for efficient analysis of surgical outcomes to improve patient care from smaller single centres. This would facilitate large scale meta analysis by larger academic surgical centres.

  12. Cloud-Based NoSQL Open Database of Pulmonary Nodules for Computer-Aided Lung Cancer Diagnosis and Reproducible Research.

    Science.gov (United States)

    Ferreira Junior, José Raniery; Oliveira, Marcelo Costa; de Azevedo-Marques, Paulo Mazzoncini

    2016-12-01

    Lung cancer is the leading cause of cancer-related deaths in the world, and its main manifestation is pulmonary nodules. Detection and classification of pulmonary nodules are challenging tasks that must be done by qualified specialists, but image interpretation errors make those tasks difficult. In order to aid radiologists on those hard tasks, it is important to integrate the computer-based tools with the lesion detection, pathology diagnosis, and image interpretation processes. However, computer-aided diagnosis research faces the problem of not having enough shared medical reference data for the development, testing, and evaluation of computational methods for diagnosis. In order to minimize this problem, this paper presents a public nonrelational document-oriented cloud-based database of pulmonary nodules characterized by 3D texture attributes, identified by experienced radiologists and classified in nine different subjective characteristics by the same specialists. Our goal with the development of this database is to improve computer-aided lung cancer diagnosis and pulmonary nodule detection and classification research through the deployment of this database in a cloud Database as a Service framework. Pulmonary nodule data was provided by the Lung Image Database Consortium and Image Database Resource Initiative (LIDC-IDRI), image descriptors were acquired by a volumetric texture analysis, and database schema was developed using a document-oriented Not only Structured Query Language (NoSQL) approach. The proposed database is now with 379 exams, 838 nodules, and 8237 images, 4029 of them are CT scans and 4208 manually segmented nodules, and it is allocated in a MongoDB instance on a cloud infrastructure.

  13. Trends in healthcare utilization among older Americans with colorectal cancer: A retrospective database analysis

    Directory of Open Access Journals (Sweden)

    Earle Craig C

    2009-12-01

    Full Text Available Abstract Background Analyses of utilization trends (cost drivers allow us to understand changes in colorectal cancer (CRC costs over time, better predict future costs, identify changes in the use of specific types of care (eg, hospice, and provide inputs for cost-effectiveness models. This retrospective cohort study evaluated healthcare resource use among US Medicare beneficiaries diagnosed with CRC between 1992 and 2002. Methods Cohorts included patients aged 66+ newly diagnosed with adenocarcinoma of the colon (n = 52,371 or rectum (n = 18,619 between 1992 and 2002 and matched patients from the general Medicare population, followed until death or December 31, 2005. Demographic and clinical characteristics were evaluated by cancer subsite. Resource use, including the percentage that used each type of resource, number of hospitalizations, and number of hospital and skilled nursing facility days, was evaluated by stage and subsite. The number of office, outpatient, and inpatient visits per person-year was calculated for each cohort, and was described by year of service, subsite, and treatment phase. Hospice use rates in the last year of life were calculated by year of service, stage, and subsite for CRC patients who died of CRC. Results CRC patients (mean age: 77.3 years; 44.9% male used more resources than controls in every category (P Conclusion Use of hospice care among CRC decedents increased substantially over the study period, while other resource use remained generally steady. Our findings may be useful for understanding CRC cost drivers, tracking trends, and forecasting resource needs for CRC patients in the future.

  14. Guidelines of the National Comprehensive Cancer Network on the use of myeloid growth factors with cancer chemotherapy: a review of the evidence.

    Science.gov (United States)

    Lyman, Gary H

    2005-07-01

    The prophylactic use of myeloid growth factors reduces the risk of chemotherapy-induced neutropenia and its complications, including febrile neutropenia and infection-related mortality. Perhaps most importantly, the prophylactic use of colony-stimulating factors (CSFs) has been shown to reduce the need for chemotherapy dose reductions and delays that may limit chemotherapy dose intensity, thereby increasing the potential for prolonged disease-free and overall survival in the curative setting. National surveys have shown that the majority of patients with potentially curable breast cancer or non-Hodgkin's lymphoma (NHL) do not receive prophylactic CSF support. In this issue, the National Comprehensive Cancer Network presents guidelines for the use of myeloid growth factors in patients with cancer. These guidelines recommend a balanced clinical evaluation of the potential benefits and harms associated with chemotherapy to define the treatment intention, followed by a careful assessment of the individual patient's risk for febrile neutropenia and its complications. The decision to use prophylactic CSFs is then based on the patient's risk and potential benefit from such treatment. The routine prophylactic use of CSFs in patients receiving systemic chemotherapy is recommended in patients at high risk (>20%) of developing febrile neutropenia or related complications that may compromise treatment. Where compelling clinical indications are absent, the potential for CSF prophylaxis to reduce or offset costs by preventing hospitalization for FN should be considered. The clinical, economic, and quality of life data in support of these recommendations are reviewed, and important areas of ongoing research are highlighted.

  15. Comprehensive two-dimensional PC-3 prostate cancer cell membrane chromatography for screening anti-tumor components from Radix Sophorae flavescentis.

    Science.gov (United States)

    Wang, Qiang; Xu, Junnan; Li, Xiang; Zhang, Dawei; Han, Yong; Zhang, Xu

    2017-07-01

    Radix Sophorae flavescentis is generally used for the treatment of different stages of prostate cancer in China. It has ideal effects when combined with surgical treatment and chemotherapy. However, its active components are still ambiguous. We devised a comprehensive two-dimensional PC-3 prostate cancer cell membrane chromatography system for screening anti-prostate cancer components in Radix Sophorae flavescentis. Gefitinib and dexamethasone were chosen as positive and negative drugs respectively for validation and optimization the selectivity and suitability of the comprehensive two-dimensional chromatographic system. Five compounds, sophocarpine, matrine, oxymatrine, oxysophocarpine, and xanthohumol were found to have significant retention behaviors on the PC-3 cell membrane chromatography and were unambiguously identified by time-of-flight mass spectrometry. Cell proliferation and apoptosis assays confirmed that all five compounds had anti-prostate cancer effects. Matrine and xanthohumol had good inhibitory effects, with half maximal inhibitory concentration values of 0.893 and 0.137 mg/mL, respectively. Our comprehensive two-dimensional PC-3 prostate cancer cell membrane chromatographic system promotes the efficient recognition and rapid analysis of drug candidates, and it will be practical for the discovery of prostate cancer drugs from complex traditional Chinese medicines. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Methods of comprehensive geriatric assessment of older patients with rectal cancer

    Directory of Open Access Journals (Sweden)

    S. S. Gordeev

    2017-01-01

    Full Text Available The article presents a literature review on application of modern risk predictors of complications and morbidity necessary for selection of oncologically justified treatment methods for older patients with rectal cancer taking into account advancement of the disease and concomitant pathology. Use of modern scales, calculators, and questionnaires for evaluation of functional and physical status of this complex patient category by a multidisciplinary team allows to personalize therapy approach, minimize complications and morbidity after specific treatment. Application of the developed algorithms of assessment of older patients creates satisfactory conditions for their treatment based on oncological adequacy, functionality, and safety.  

  17. Comprehensive detection of diverse exon 19 deletion mutations of EGFR in lung Cancer by a single probe set.

    Science.gov (United States)

    Bae, Jin Ho; Jo, Seong-Min; Kim, Hak-Sung

    2015-12-15

    Detection of exon 19 deletion mutation of EGFR, one of the most frequently occurring mutations in lung cancer, provides the crucial information for diagnosis and treatment guideline in non-small-cell lung cancer (NSCLC). Here, we demonstrate a simple and efficient method to detect various exon 19 deletion mutations of EGFR using a single probe set comprising of an oligo-quencher (oligo-Q) and a molecular beacon (MB). While the MB hybridizes to both the wild and mutant target DNA, the oligo-Q only binds to the wild target DNA, leading to a fluorescent signal in case of deletion mutation. This enables the comprehensive detection of the diverse exon 19 deletion mutations using a single probe set. We demonstrated the utility and efficiency of the approach by detecting the frequent exon 19 deletion mutations of EGFR through a real-time PCR and in situ fluorescence imaging. Our approach enabled the detection of genomic DNA as low as 0.02 ng, showing a detection limit of 2% in a heterogeneous DNA mixture, and could be used for detecting mutations in a single cell level. The present MB and oligo-Q dual probe system can be used for diagnosis and treatment guideline in NSCLC. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. A Comprehensive Workflow of Mass Spectrometry-Based Untargeted Metabolomics in Cancer Metabolic Biomarker Discovery Using Human Plasma and Urine

    Directory of Open Access Journals (Sweden)

    Jianwen She

    2013-09-01

    Full Text Available Current available biomarkers lack sensitivity and/or specificity for early detection of cancer. To address this challenge, a robust and complete workflow for metabolic profiling and data mining is described in details. Three independent and complementary analytical techniques for metabolic profiling are applied: hydrophilic interaction liquid chromatography (HILIC–LC, reversed-phase liquid chromatography (RP–LC, and gas chromatography (GC. All three techniques are coupled to a mass spectrometer (MS in the full scan acquisition mode, and both unsupervised and supervised methods are used for data mining. The univariate and multivariate feature selection are used to determine subsets of potentially discriminative predictors. These predictors are further identified by obtaining accurate masses and isotopic ratios using selected ion monitoring (SIM and data-dependent MS/MS and/or accurate mass MSn ion tree scans utilizing high resolution MS. A list combining all of the identified potential biomarkers generated from different platforms and algorithms is used for pathway analysis. Such a workflow combining comprehensive metabolic profiling and advanced data mining techniques may provide a powerful approach for metabolic pathway analysis and biomarker discovery in cancer research. Two case studies with previous published data are adapted and included in the context to elucidate the application of the workflow.

  19. [Organisational diagnosis of a home care-coordinating unit in oncology: which choices for the comprehensive cancer center of Lyon?].

    Science.gov (United States)

    Chvetzoff, Gisèle; Chvetzoff, Roland; Devaux, Yves; Teil, A; Chalencon, J; Lancry, L; Kante, V; Poncelas, C; Sontag, P; Tretiakoff, C; Philip, T

    2006-10-01

    Lyon comprehensive cancer center developed a home care-coordinating unit (HCCU) allowing a wide range of cancer care at home. We present the results of an organisational and strategical analysis of the unit, in relation with internal and external contexts. We describe the functioning of the unit, modelled from the daily follow-up of professionnels. Patient discharge is initiated by the oncologist at the inpatient clinic, at the day-hospital or at outpatient visit. After consent of the patient and relatives, the HCCU (nurses and medical oncologists) evaluates patient's needs, organises hospital discharge (contacts with community nurses and general practitioner, supply of medical appliances and drugs), and provides follow-up and counselling to patient and caregivers. The HCCU works in a challenging environment, with both partners and competitors. Within the hospital, it collaborates with all other units. Outside the hospital, partners are, besides patients themselves; general practitioners and community nurses home care agencies and network services, private medical appliance providers, and public health authorities. The unit might evolve towards formal home hospitalisation or community-hospital network. Collaboration of both structure closely associated with hospital could allow to provide continuous and graduated care by the same caregivers even if administrative structures change.

  20. SITE COMPREHENSIVE LISTING (CERCLIS) (Superfund)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Comprehensive Environmental Response, Compensation and Liability Information System (CERCLIS) (Superfund) Public Access Database contains a selected set of...

  1. Biomarkers in Urachal Cancer and Adenocarcinomas in the Bladder: A Comprehensive Review Supplemented by Own Data

    Directory of Open Access Journals (Sweden)

    Henning Reis

    2018-01-01

    Full Text Available Urachal cancer (UrC is a rare but aggressive cancer. Due to overlapping histomorphology, discrimination of urachal from primary bladder adenocarcinomas (PBAC and adenocarcinomas secondarily involving the bladder (particularly colorectal adenocarcinomas, CRC can be challenging. Therefore, we aimed to give an overview of helpful (immunohistochemical biomarkers and clinicopathological factors in addition to survival analyses and included institutional data from 12 urachal adenocarcinomas. A PubMed search yielded 319 suitable studies since 1930 in the English literature with 1984 cases of UrC including 1834 adenocarcinomas (92% and 150 nonadenocarcinomas (8%. UrC was more common in men (63%, showed a median age at diagnosis of 50.8 years and a median tumor size of 6.0 cm. No associations were noted for overall survival and progression-free survival (PFS and clinicopathological factors beside a favorable PFS in male patients (p=0.047. The immunohistochemical markers found to be potentially helpful in the differential diagnostic situation are AMACR and CK34βE12 (UrC versus CRC and PBAC, CK7, β-Catenin and CD15 (UrC and PBAC versus CRC, and CEA and GATA3 (UrC and CRC versus PBAC. Serum markers like CEA, CA19-9 and CA125 might additionally be useful in the follow-up and monitoring of UrC.

  2. Joint Estimation of Cardiac Toxicity and Recurrence Risks After Comprehensive Nodal Photon Versus Proton Therapy for Breast Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Stick, Line B., E-mail: line.bjerregaard.stick@regionh.dk [Department of Clinical Oncology, Rigshospitalet, University of Copenhagen, Copenhagen (Denmark); Niels Bohr Institute, Faculty of Science, University of Copenhagen, Copenhagen (Denmark); Yu, Jen [Maryland Proton Treatment Center, University of Maryland School of Medicine, Baltimore, Maryland (United States); Maraldo, Maja V. [Department of Clinical Oncology, Rigshospitalet, University of Copenhagen, Copenhagen (Denmark); Aznar, Marianne C. [Department of Clinical Oncology, Rigshospitalet, University of Copenhagen, Copenhagen (Denmark); Nuffield Department of Population Health, University of Oxford, Oxford (United Kingdom); Pedersen, Anders N. [Department of Clinical Oncology, Rigshospitalet, University of Copenhagen, Copenhagen (Denmark); Bentzen, Søren M. [Department of Clinical Oncology, Rigshospitalet, University of Copenhagen, Copenhagen (Denmark); Maryland Proton Treatment Center, University of Maryland School of Medicine, Baltimore, Maryland (United States); Greenebaum Comprehensive Cancer Center and Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland (United States); Vogelius, Ivan R. [Department of Clinical Oncology, Rigshospitalet, University of Copenhagen, Copenhagen (Denmark)

    2017-03-15

    Purpose: The study aims to perform joint estimation of the risk of recurrence caused by inadequate radiation dose coverage of lymph node targets and the risk of cardiac toxicity caused by radiation exposure to the heart. Delivered photon plans are compared with realistic proton plans, thereby providing evidence-based estimates of the heterogeneity of treatment effects in consecutive cases for the 2 radiation treatment modalities. Methods and Materials: Forty-one patients referred for postlumpectomy comprehensive nodal photon irradiation for left-sided breast cancer were included. Comparative proton plans were optimized by a spot scanning technique with single-field optimization from 2 en face beams. Cardiotoxicity risk was estimated with the model of Darby et al, and risk of recurrence following a compromise of lymph node coverage was estimated by a linear dose-response model fitted to the recurrence data from the recently published EORTC (European Organisation for Research and Treatment of Cancer) 22922/10925 and NCIC-CTG (National Cancer Institute of Canada Clinical Trials Group) MA.20 randomized controlled trials. Results: Excess absolute risk of cardiac morbidity was small with photon therapy at an attained age of 80 years, with median values of 1.0% (range, 0.2%-2.9%) and 0.5% (range, 0.03%-1.0%) with and without cardiac risk factors, respectively, but even lower with proton therapy (0.13% [range, 0.02%-0.5%] and 0.06% [range, 0.004%-0.3%], respectively). The median estimated excess absolute risk of breast cancer recurrence after 10 years was 0.10% (range, 0.0%-0.9%) with photons and 0.02% (range, 0.0%-0.07%) with protons. The association between age of the patient and benefit from proton therapy was weak, almost non-existing (Spearman rank correlations of −0.15 and −0.30 with and without cardiac risk factors, respectively). Conclusions: Modern photon therapy yields limited risk of cardiac toxicity in most patients, but proton therapy can reduce the

  3. Comprehensive profiling of DNA repair defects in breast cancer identifies a novel class of endocrine therapy resistance drivers.

    Science.gov (United States)

    Anurag, Meenakshi; Punturi, Nindo; Hoog, Jeremy; Bainbridge, Matthew N; Ellis, Matthew J; Haricharan, Svasti

    2018-05-23

    This study was undertaken to conduct a comprehensive investigation of the role of DNA damage repair (DDR) defects in poor outcome ER+ disease. Expression and mutational status of DDR genes in ER+ breast tumors were correlated with proliferative response in neoadjuvant aromatase inhibitor therapy trials (discovery data set), with outcomes in METABRIC, TCGA and Loi data sets (validation data sets), and in patient derived xenografts. A causal relationship between candidate DDR genes and endocrine treatment response, and the underlying mechanism, was then tested in ER+ breast cancer cell lines. Correlations between loss of expression of three genes: CETN2 (p<0.001) and ERCC1 (p=0.01) from the nucleotide excision repair (NER) and NEIL2 (p=0.04) from the base excision repair (BER) pathways were associated with endocrine treatment resistance in discovery data sets, and subsequently validated in independent patient cohorts. Complementary mutation analysis supported associations between mutations in NER and BER pathways and reduced endocrine treatment response. A causal role for CETN2, NEIL2 and ERCC1 loss in intrinsic endocrine resistance was experimentally validated in ER+ breast cancer cell lines, and in ER+ patient-derived xenograft models. Loss of CETN2, NEIL2 or ERCC1 induced endocrine treatment response by dysregulating G1/S transition, and therefore, increased sensitivity to CDK4/6 inhibitors. A combined DDR signature score was developed that predicted poor outcome in multiple patient cohorts. This report identifies DDR defects as a new class of endocrine treatment resistance drivers and indicates new avenues for predicting efficacy of CDK4/6 inhibition in the adjuvant treatment setting. Copyright ©2018, American Association for Cancer Research.

  4. Specialist Bibliographic Databases

    OpenAIRE

    Gasparyan, Armen Yuri; Yessirkepov, Marlen; Voronov, Alexander A.; Trukhachev, Vladimir I.; Kostyukova, Elena I.; Gerasimov, Alexey N.; Kitas, George D.

    2016-01-01

    Specialist bibliographic databases offer essential online tools for researchers and authors who work on specific subjects and perform comprehensive and systematic syntheses of evidence. This article presents examples of the established specialist databases, which may be of interest to those engaged in multidisciplinary science communication. Access to most specialist databases is through subscription schemes and membership in professional associations. Several aggregators of information and d...

  5. Supply Chain Initiatives Database

    Energy Technology Data Exchange (ETDEWEB)

    None

    2012-11-01

    The Supply Chain Initiatives Database (SCID) presents innovative approaches to engaging industrial suppliers in efforts to save energy, increase productivity and improve environmental performance. This comprehensive and freely-accessible database was developed by the Institute for Industrial Productivity (IIP). IIP acknowledges Ecofys for their valuable contributions. The database contains case studies searchable according to the types of activities buyers are undertaking to motivate suppliers, target sector, organization leading the initiative, and program or partnership linkages.

  6. Nine breast angiosarcomas after conservative treatment for breast carcinoma: a survey from French Comprehensive Cancer Centers

    International Nuclear Information System (INIS)

    Marchal, Christian; Weber, Beatrice; Lafontan, Brigitte de; Resbeut, Michel; Mignotte, Herve; Pabot du Chatelard, Pierre; Cutuli, Bruno; Reme-saumon, Monique; Broussier-leroux, Agnes; Chaplain, Gilles; Lesaunier, Francois; Dilhuydy, Jean-Marie; Lagrange, Jean Leon

    1999-01-01

    Objectives: To conduct a survey of the angiosarcomas developing after breast conservation for carcinoma in the French Cancer Centers, to study the evolution of these cases in detail, and to review literature in an attempt to propose an optimal treatment scheme. Material and Methods: Eleven of the 20 French Cancer Centers agreed to research and retrospectively analyze all angiosarcomas discovered in patients previously treated by conservative treatment. The majority of the patients were node negative, T1N0M0. The mean age of the patients at the time of primary breast cancer treatment was 62.5 years, and 69 years at the diagnosis of the angiosarcoma. Results: During the last two decades, nearly 20,000 patients have been treated conservatively in these 11 centers, and only 9 cases of angiosarcoma were found. The median latency period between the treatment of the breast carcinoma and the diagnosis of the breast angiosarcoma was approximately 74 months, with a range of 57-108 months. Mastectomy was performed as the main treatment of this angiosarcoma. All recurrences after mastectomy for the angiosarcoma appeared within 16 months after the mastectomy. A median time of recurrence was found to be 7.5 months, regardless of the treatment. The angiosarcomas appeared to be very aggressive, and chemotherapy, radiotherapy, and sometimes hyperthermia could only palliate the condition for a short time. After the diagnosis of angiosarcoma, the median survival was 15.5 months, showing a particularly poor prognosis. Only 1 patient of 9 is alive without progressive disease at 32 months after salvage mastectomy for the recurrence of the angiosarcoma. Precise data obtained from 11 centers show that, of 18115 breast carcinomas treated conservatively, only 9 breast angiosarcomas are reported, which represents a prevalence of 5 cases of angiosarcoma per 10,000, which is the same prevalence for primary breast angiosarcomas occurring in healthy breasts. Conclusion: Angiosarcoma developing

  7. Patterns of care and treatment outcomes of patients with Craniopharyngioma in the national cancer database.

    Science.gov (United States)

    Rao, Yuan J; Hassanzadeh, Comron; Fischer-Valuck, Benjamin; Chicoine, Michael R; Kim, Albert H; Perkins, Stephanie M; Huang, Jiayi

    2017-03-01

    To investigate the patterns of care and outcomes in patients with craniopharyngioma in the National Cancer Data Base (NCDB). This study included 697 patients (166 pediatric and 531 adult cases) treated for craniopharyngioma between 2004 and 2012 in the NCDB. Adjuvant radiotherapy (RT) was defined if within 6 months of surgery. Limited surgery (LS) was defined as biopsy or subtotal resection. Proportional-hazards models were used to evaluate associations between covariates and overall survival (OS). A time-dependent analysis of RT was performed to account for early deaths after surgery. Median follow-up was 46 months. Overall, 21% of patients received adjuvant RT. Of patients with known surgical extent (n = 195), 71% had LS. Utilization of adjuvant RT increased from 18% in 2004-2007 to 24% in 2008-2012. Patterns of care regarding adjuvant RT or LS were not significantly different between adult and pediatric patients. Tumor size, low comorbidity, and LS were associated with increased utilization of adjuvant RT. The 5-year OS among patients treated with LS, LS+RT, and gross total resection were 75, 85, and 82% (p = 0.02). On multivariate analysis of the 195 patients with known surgical extent, LS+RT was associated with improved OS compared to LS (HR 0.22, 95% CI 0.05-0.99, p = 0.04), but was not significant when early deaths (craniopharyngiomas. Immortal-time bias may confound assessment of OS for adjuvant RT. Prospective studies comparing adjuvant RT versus observation after LS are warranted.

  8. Associations Between Nutritional Parameters and Clinicopathologic Factors in Patients with Gastric Cancer: A Comprehensive Study.

    Science.gov (United States)

    Brewczyński, Adam; Jabłońska, Beata; Pawlicki, Krzysztof

    2017-07-01

    The aim of this study was to assess and analyze the nutritional status of gastric cancer (GC) patients. The analysis included 207 patients with GC treated in a large center of oncology. Patients were divided into two groups according to the cutoff value of the mean prognostic nutritional index (PNI): those with a PNI 10% (P = 0.000031). Body mass index (BMI) after disease recognition, albumin and total protein (0.003) levels, total lymphocyte count, and PNI were significantly lower in patients with nutritional risk. Significantly lower BMI before disease and BMI after disease recognition were noted in smoking patients. Significantly higher total lymphocyte count was observed in smoking patients (P nutritional status using PNI calculation should be the standard management of patients with GC before treatment.

  9. A comprehensive survey of the mutagenic impact of common cancer cytotoxics

    DEFF Research Database (Denmark)

    Szikriszt, Bernadett; Poti, Adam; Pipek, Orsolya

    2016-01-01

    system, is well suited to accurately assay genomic mutations. Results: We use whole genome sequencing of multiple DT40 clones to determine the mutagenic effect of eight common cytotoxics used for the treatment of millions of patients worldwide. We determine the spontaneous mutagenesis rate at 2.3 x 10......-10 per base per cell division and find that cisplatin, cyclophosphamide and etoposide induce extra base substitutions with distinct spectra. After four cycles of exposure, cisplatin induces 0.8 mutations per Mb, equivalent to the median mutational burden in common leukaemias. Cisplatin-induced mutations......, hydroxyurea, doxorubicin and paclitaxel have no measurable mutagenic effect. The cisplatin-induced mutation spectrum shows good correlation with cancer mutation signatures attributed to smoking and other sources of guanine-directed base damage. Conclusion: This study provides support for the use of cell line...

  10. Database supported electronic retrospective analyses in radiation oncology. Establishing a workflow using the example of pancreatic cancer

    International Nuclear Information System (INIS)

    Kessel, K.A.; Habermehl, D.; Bougatf, N.; Debus, J.; Combs, S.E.; Jaeger, A.; Floca, R.O.; Zhang, L.; Bendl, R.

    2012-01-01

    Purpose: Especially in the field of radiation oncology, handling a large variety of voluminous datasets from various information systems in different documentation styles efficiently is crucial for patient care and research. To date, conducting retrospective clinical analyses is rather difficult and time consuming. With the example of patients with pancreatic cancer treated with radio-chemotherapy, we performed a therapy evaluation by using an analysis system connected with a documentation system. Materials and methods: A total number of 783 patients have been documented into a professional, database-based documentation system. Information about radiation therapy, diagnostic images and dose distributions have been imported into the web-based system. Results: For 36 patients with disease progression after neoadjuvant chemoradiation, we designed and established an analysis workflow. After an automatic registration of the radiation plans with the follow-up images, the recurrence volumes are segmented manually. Based on these volumes the DVH (dose volume histogram) statistic is calculated, followed by the determination of the dose applied to the region of recurrence. All results are saved in the database and included in statistical calculations. Conclusion: The main goal of using an automatic analysis tool is to reduce time and effort conducting clinical analyses, especially with large patient groups. We showed a first approach and use of some existing tools, however manual interaction is still necessary. Further steps need to be taken to enhance automation. Already, it has become apparent that the benefits of digital data management and analysis lie in the central storage of data and reusability of the results. Therefore, we intend to adapt the analysis system to other types of tumors in radiation oncology. (orig.)

  11. A comprehensive DNA barcode database for Central European beetles with a focus on Germany: adding more than 3500 identified species to BOLD.

    Science.gov (United States)

    Hendrich, Lars; Morinière, Jérôme; Haszprunar, Gerhard; Hebert, Paul D N; Hausmann, Axel; Köhler, Frank; Balke, Michael

    2015-07-01

    Beetles are the most diverse group of animals and are crucial for ecosystem functioning. In many countries, they are well established for environmental impact assessment, but even in the well-studied Central European fauna, species identification can be very difficult. A comprehensive and taxonomically well-curated DNA barcode library could remedy this deficit and could also link hundreds of years of traditional knowledge with next generation sequencing technology. However, such a beetle library is missing to date. This study provides the globally largest DNA barcode reference library for Coleoptera for 15 948 individuals belonging to 3514 well-identified species (53% of the German fauna) with representatives from 97 of 103 families (94%). This study is the first comprehensive regional test of the efficiency of DNA barcoding for beetles with a focus on Germany. Sequences ≥500 bp were recovered from 63% of the specimens analysed (15 948 of 25 294) with short sequences from another 997 specimens. Whereas most specimens (92.2%) could be unambiguously assigned to a single known species by sequence diversity at CO1, 1089 specimens (6.8%) were assigned to more than one Barcode Index Number (BIN), creating 395 BINs which need further study to ascertain if they represent cryptic species, mitochondrial introgression, or simply regional variation in widespread species. We found 409 specimens (2.6%) that shared a BIN assignment with another species, most involving a pair of closely allied species as 43 BINs were involved. Most of these taxa were separated by barcodes although sequence divergences were low. Only 155 specimens (0.97%) show identical or overlapping clusters. © 2014 John Wiley & Sons Ltd.

  12. Comprehensive analysis of miRNAs expression profiles revealed potential key miRNA/mRNAs regulating colorectal cancer stem cell self-renewal.

    Science.gov (United States)

    Xu, Peng; Wang, Junhua; Sun, Bo; Xiao, Zhongdang

    2018-05-20

    Self-renewal is essential for the malignant biological behaviors of colorectal cancer stem cells. While the self-renewal molecular mechanisms of colorectal cancer stem cells are not yet fully understood. Recently, miRNAs are reported to be relevant to the self-renewal ability of cancer stem cells. In this study, we first isolated colorectal cancer stem cell from colorectal cancer cell line HCT-116 by 1% low serum culture. Then we conducted a comprehensive analysis based on the miRNAs profiles data of both colorectal cancer stem cells and normal cultured colorectal cancer cells. Pathway analysis revealed multiple pathways including Jak-STAT, TGF-beta, PI3K-Akt and MAPK signaling pathway that are correlated to colorectal cancer. Further, we constructed a miRNA-mRNA network, based on which, several miRNA/mRNA pairs were ranked according to their impact index to the self-renewal of colorectal cancer stem cells. Further biological experiment showed that up-regulation of miR-92a-3p led to cell cycle arrest and reduced colony formation. This work provides clues to find the new potential biomarkers for colorectal cancer stem cell diagnosis and select effective miRNAs for targeted therapy. Copyright © 2018 Elsevier B.V. All rights reserved.

  13. What is the gold standard for comprehensive interinstitutional communication of perioperative information for thyroid cancer patients? A comparison of existing electronic health records with the current American Thyroid Association recommendations.

    Science.gov (United States)

    Dos Reis, Laura L; Tuttle, R Michael; Alon, Eran; Bergman, Donald A; Bernet, Victor; Brett, Elise M; Cobin, Rhoda; Doherty, Gerard; Harris, Jeffrey R; Klopper, Joshua; Lee, Stephanie L; Lupo, Mark; Milas, Mira; Machac, Josef; Mechanick, Jeffrey I; Orloff, Lisa; Randolph, Gregory; Ross, Douglas S; Smallridge, Robert C; Terris, David James; Tufano, Ralph P; Mehra, Saral; Scherl, Sophie; Clain, Jason B; Urken, Mark L

    2014-10-01

    effective reporting of the specific domains that they cover in the management of thyroid cancer, as recommended by the ATA. However, the TCCC format is the most comprehensive. The TCCC is a new Web-based disease-specific database to enhance communication of patient information between clinicians in a Health Insurance Portability and Accountability Act (HIPAA)-compliant manner. We believe the easy-to-use TCCC format will enhance clinician communication while providing portability of thyroid cancer information for patients.

  14. Propensity Score Matched Comparison of Intensity Modulated Radiation Therapy vs Stereotactic Body Radiation Therapy for Localized Prostate Cancer: A Survival Analysis from the National Cancer Database

    Directory of Open Access Journals (Sweden)

    Anthony Ricco

    2017-08-01

    Full Text Available PurposeNo direct comparisons between extreme hypofractionation and conventional fractionation have been reported in randomized trials for the treatment of localized prostate cancer. The goal of this study is to use a propensity score matched (PSM analysis with the National Cancer Database (NCDB for the comparison of stereotactic body radiation therapy (SBRT and intensity modulated radiation therapy (IMRT for organ confined prostate cancer.MethodsMen with localized prostate cancer treated with radiation dose ≥72 Gy for IMRT and ≥35 Gy for SBRT to the prostate only were abstracted from the NCDB. Men treated with previous surgery, brachytherapy, or proton therapy were excluded. Matching was performed to eliminate confounding variables via PSM. Simple 1–1 nearest neighbor matching resulted in a matched sample of 5,430 (2,715 in each group. Subset analyses of men with prostate-specific antigen (PSA > 10, GS = 7, and GS > 7 yielded matched samples of 1,020, 2,194, and 247, respectively.ResultsNo difference in survival was noted between IMRT and SBRT at 8 years (p = 0.65. Subset analyses of higher risk men with PSA > 10 or GS = 7 histology or GS > 7 histology revealed no difference in survival between IMRT and SBRT (p = 0.58, p = 0.68, and p = 0.62, respectively. Variables significant for survival for the matched group included: age (p < 0.0001, primary payor (p = 0.0001, Charlson/Deyo Score (p = 0.0002, PSA (p = 0.0013, Gleason score (p < 0.0001, and use of hormone therapy (p = 0.02.ConclusionUtilizing the NCDB, there is no difference in survival at 8 years comparing IMRT to SBRT in the treatment of localized prostate cancer. Subset analysis confirmed no difference in survival even for intermediate- and high-risk patients based on Gleason Score and PSA.

  15. Association between African American race and outcomes in patients with nonmetastatic triple-negative breast cancer: a retrospective analysis by using results from the Georgia Cancer Specialist Database.

    Science.gov (United States)

    Christiansen, Neal; Chen, Lei; Gilmore, James; Pechar, David; Szabo, Stephen

    2012-08-01

    The objective of this study was to evaluate, in a real-world context, the impact of race on disease recurrence and survival in patients with nonmetastatic triple-negative breast cancer (TNBC) treated with adjuvant chemotherapy. The study selected patients from the 2003-2008 Georgia Cancer Specialist Database with stage I-III confirmed TNBC who had received adjuvant chemotherapy. These patients were followed-up from initial diagnosis to death, cancer recurrence, or loss to follow-up. The primary outcome was disease-free survival (DFS). Kaplan-Meier curves compared DFS and recurrence between African American and non-African American groups. The impact of African American status was examined further through multivariate Cox models by adjusting for age, comorbidity, body mass index (BMI), smoking status, initial TNBC stage, surgery, and radiation therapy. Among 209 patients with TNBC, 89 (42.6%) were African American. The 2 groups (African American vs. non-African American) were similar in mean age at diagnosis (53.2 vs. 54.4 years; P =.487) and with surgery and radiation rates (98.9% vs. 100%; P = .244; 68.5% vs. 62.5%; P = .365, respectively). Compared with non-African Americans, African American patients had a higher BMI (30.4 vs. 28.6 kg/m(2); P = .0477) and were less likely to be diagnosed at stage I (31.5% vs. 51.7%; P = .0107). The African American patients had a lower 5-year DFS rate (45.2% vs. 79.7%; P = .0005) and a higher 5-year recurrence rate (42.5% vs. 7.0%; P = .0005) compared with the non-African American patients. Among patients with TNBC treated with adjuvant chemotherapy, African American race was associated with a worse outcome irrespective of later stage at presentation or higher BMI. Copyright © 2012 Elsevier Inc. All rights reserved.

  16. Comprehensive analysis of sexual function outcome in prostate cancer patients after robot-assisted radical prostatectomy.

    Science.gov (United States)

    Woo, Seung Hyo; Kang, Dong Il; Ha, Yun-Sok; Salmasi, Amirali Hassanzadeh; Kim, Jeong Hyun; Lee, Dong-Hyeon; Kim, Wun-Jae; Kim, Isaac Yi

    2014-02-01

    The recovery of potency following radical prostatectomy is complex and has a very wide range. In this study, we analyzed in detail the precise pattern of recovery of potency following robot-assisted radical prostatectomy (RARP). Prospectively collected database of patients with a minimum follow-up of 1 year after RARP were evaluated retrospectively. Of 503 patients identified, 483 patients completed the sexual health inventory for men (SHIM) preoperatively and postoperatively every 3 months for the first 12 months. Overall potency, usage of phosphodiesterase type-5 (PDE-5) inhibitors, and return to baseline erectile function were evaluated. Potency was defined as having erection that is sufficient for sexual intercourse more than 50% of attempts, while quality potency was defined as being potent without the use of PDE-5 inhibitors. Preoperatively, the overall potency and quality potency rate were 67.1% and 48.1%, respectively. Postoperatively, the overall potency rate was 61.4%, while the quality potency rate was 37.2%. In multivariate regression analysis, independent predictors of potency recovery were young age (21, the overall potency and quality potency rate were 79.7% and 41.2%, respectively. More importantly, only 21.4% of the men with normal erection preoperatively (SHIM>21) returned to baseline erectile function (SHIM>21) 12 months after surgery. This study indicates that young age (<60), preoperative potency, and bilateral preservation of NVBs were positive predictors of potency recovery following RARP. However, an overwhelming majority of men experience a deterioration in the overall quality of erection after RARP.

  17. Comprehensive irradiation of head and neck cancer using conformal multisegmental fields: assessment of target coverage and noninvolved tissue sparing

    International Nuclear Information System (INIS)

    Eisbruch, Avraham; Marsh, Lon H.; Martel, Mary K.; Ship, Jonathan A.; Haken, Randall ten; Pu, Anthony T.; Fraass, Benedick A.; Lichter, Allen S.

    1998-01-01

    Purpose: Conformal treatment using static multisegmental intensity modulation was developed for patients requiring comprehensive irradiation for head and neck cancer. The major aim is sparing major salivary gland function while adequately treating the targets. To assess the adequacy of the conformal plans regarding target coverage and dose homogeneity, they were compared with standard irradiation plans. Methods and Materials: Fifteen patients with stage III/IV head and neck cancer requiring comprehensive, bilateral neck irradiation participated in this study. CT-based treatment plans included five to six nonopposed fields, each having two to four in-field segments. Fields and segments were devised using beam's eye views of the planning target volumes (PTVs), noninvolved organs, and isodose surfaces, to achieve homogeneous dose distribution that encompassed the targets and spared major salivary gland tissue. For comparison, standard three-field radiation plans were devised retrospectively for each patient, with the same CT-derived targets used for the clinical (conformal) plans. Saliva flow rates from each major salivary gland were measured before and periodically after treatment. Results: On average, the minimal dose to the primary PTVs in the conformal plans [95.2% of the prescribed dose, standard deviation (SD) 4%] was higher than in the standard plans (91%, SD 7%; p = 0.02), and target volumes receiving <95% or <90% of the prescribed dose were smaller in the conformal plans (p = 0.004 and 0.02, respectively). Similar advantages of the conformal plans compared to standard plans were found in ipsilateral jugular nodes PTV coverage. The reason for underdosing in the standard treatment plans was primarily failure of electron beams to fully encompass targets. No significant differences were found in contralateral jugular or posterior neck nodes coverage. The minimal dose to the retropharyngeal nodes was higher in the standard plans. However, all conformal plans

  18. A comprehensive comparison of random forests and support vector machines for microarray-based cancer classification

    Directory of Open Access Journals (Sweden)

    Wang Lily

    2008-07-01

    Full Text Available Abstract Background Cancer diagnosis and clinical outcome prediction are among the most important emerging applications of gene expression microarray technology with several molecular signatures on their way toward clinical deployment. Use of the most accurate classification algorithms available for microarray gene expression data is a critical ingredient in order to develop the best possible molecular signatures for patient care. As suggested by a large body of literature to date, support vector machines can be considered "best of class" algorithms for classification of such data. Recent work, however, suggests that random forest classifiers may outperform support vector machines in this domain. Results In the present paper we identify methodological biases of prior work comparing random forests and support vector machines and conduct a new rigorous evaluation of the two algorithms that corrects these limitations. Our experiments use 22 diagnostic and prognostic datasets and show that support vector machines outperform random forests, often by a large margin. Our data also underlines the importance of sound research design in benchmarking and comparison of bioinformatics algorithms. Conclusion We found that both on average and in the majority of microarray datasets, random forests are outperformed by support vector machines both in the settings when no gene selection is performed and when several popular gene selection methods are used.

  19. Bibliographic survey on methodologies for development of health database of the population in case of cancer occurrences; Levantamento bibliografico sobre metodologias para elaboracao de um banco de dados da saude da populacao em casos de ocorrencias de cancer

    Energy Technology Data Exchange (ETDEWEB)

    Cavinato, Christianne C.; Andrade, Delvonei A. de; Sabundjian, Gaiane, E-mail: christiannecobellocavinato@gmail.com, E-mail: delvonei@ipen.br, E-mail: gdjian@ipen.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil); Diz, Maria Del Pilar E., E-mail: maria.pilar@icesp.org.br [Instituto do Cancer do Estado de Sao Paulo (ICESP), Sao Paulo, SP (Brazil)

    2014-07-01

    The objective is to make a survey of existing methodologies and for the development of public health database, focusing on health (fatal and nonfatal cancer) of the population surrounding a nuclear facility, for purposes of calculating the environmental cost of the same. From methodologies found to develop this type of database, a methodology will be developed to be applied to the internal public of IPEN/CNEN-SP, Brazil, as a pre-test for the acquisition of health information desired.

  20. Comprehensive comparison of in silico MS/MS fragmentation tools of the CASMI contest: database boosting is needed to achieve 93% accuracy.

    Science.gov (United States)

    Blaženović, Ivana; Kind, Tobias; Torbašinović, Hrvoje; Obrenović, Slobodan; Mehta, Sajjan S; Tsugawa, Hiroshi; Wermuth, Tobias; Schauer, Nicolas; Jahn, Martina; Biedendieck, Rebekka; Jahn, Dieter; Fiehn, Oliver

    2017-05-25

    In mass spectrometry-based untargeted metabolomics, rarely more than 30% of the compounds are identified. Without the true identity of these molecules it is impossible to draw conclusions about the biological mechanisms, pathway relationships and provenance of compounds. The only way at present to address this discrepancy is to use in silico fragmentation software to identify unknown compounds by comparing and ranking theoretical MS/MS fragmentations from target structures to experimental tandem mass spectra (MS/MS). We compared the performance of four publicly available in silico fragmentation algorithms (MetFragCL, CFM-ID, MAGMa+ and MS-FINDER) that participated in the 2016 CASMI challenge. We found that optimizing the use of metadata, weighting factors and the manner of combining different tools eventually defined the ultimate outcomes of each method. We comprehensively analysed how outcomes of different tools could be combined and reached a final success rate of 93% for the training data, and 87% for the challenge data, using a combination of MAGMa+, CFM-ID and compound importance information along with MS/MS matching. Matching MS/MS spectra against the MS/MS libraries without using any in silico tool yielded 60% correct hits, showing that the use of in silico methods is still important.

  1. Building a comprehensive mill-level database for the Industrial Sectors Integrated Solutions (ISIS) model of the U.S. pulp and paper sector.

    Science.gov (United States)

    Modak, Nabanita; Spence, Kelley; Sood, Saloni; Rosati, Jacky Ann

    2015-01-01

    Air emissions from the U.S. pulp and paper sector have been federally regulated since 1978; however, regulations are periodically reviewed and revised to improve efficiency and effectiveness of existing emission standards. The Industrial Sectors Integrated Solutions (ISIS) model for the pulp and paper sector is currently under development at the U.S. Environmental Protection Agency (EPA), and can be utilized to facilitate multi-pollutant, sector-based analyses that are performed in conjunction with regulatory development. The model utilizes a multi-sector, multi-product dynamic linear modeling framework that evaluates the economic impact of emission reduction strategies for multiple air pollutants. The ISIS model considers facility-level economic, environmental, and technical parameters, as well as sector-level market data, to estimate the impacts of environmental regulations on the pulp and paper industry. Specifically, the model can be used to estimate U.S. and global market impacts of new or more stringent air regulations, such as impacts on product price, exports and imports, market demands, capital investment, and mill closures. One major challenge to developing a representative model is the need for an extensive amount of data. This article discusses the collection and processing of data for use in the model, as well as the methods used for building the ISIS pulp and paper database that facilitates the required analyses to support the air quality management of the pulp and paper sector.

  2. ACE (I/D polymorphism and response to treatment in coronary artery disease: a comprehensive database and meta-analysis involving study quality evaluation

    Directory of Open Access Journals (Sweden)

    Kitsios Georgios

    2009-06-01

    Full Text Available Abstract Background The role of angiotensin-converting enzyme (ACE gene insertion/deletion (I/D polymorphism in modifying the response to treatment modalities in coronary artery disease is controversial. Methods PubMed was searched and a database of 58 studies with detailed information regarding ACE I/D polymorphism and response to treatment in coronary artery disease was created. Eligible studies were synthesized using meta-analysis methods, including cumulative meta-analysis. Heterogeneity and study quality issues were explored. Results Forty studies involved invasive treatments (coronary angioplasty or coronary artery by-pass grafting and 18 used conservative treatment options (including anti-hypertensive drugs, lipid lowering therapy and cardiac rehabilitation procedures. Clinical outcomes were investigated by 11 studies, while 47 studies focused on surrogate endpoints. The most studied outcome was the restenosis following coronary angioplasty (34 studies. Heterogeneity among studies (p ACE I/D polymorphism on the response to treatment for the rest outcomes (coronary events, endothelial dysfunction, left ventricular remodeling, progression/regression of atherosclerosis, individual studies showed significance; however, results were discrepant and inconsistent. Conclusion In view of available evidence, genetic testing of ACE I/D polymorphism prior to clinical decision making is not currently justified. The relation between ACE genetic variation and response to treatment in CAD remains an unresolved issue. The results of long-term and properly designed prospective studies hold the promise for pharmacogenetically tailored therapy in CAD.

  3. Building a Comprehensive Mill-Level Database for the Industrial Sectors Integrated Solutions (ISIS) Model of the U.S. Pulp and Paper Sector

    Science.gov (United States)

    Modak, Nabanita; Spence, Kelley; Sood, Saloni; Rosati, Jacky Ann

    2015-01-01

    Air emissions from the U.S. pulp and paper sector have been federally regulated since 1978; however, regulations are periodically reviewed and revised to improve efficiency and effectiveness of existing emission standards. The Industrial Sectors Integrated Solutions (ISIS) model for the pulp and paper sector is currently under development at the U.S. Environmental Protection Agency (EPA), and can be utilized to facilitate multi-pollutant, sector-based analyses that are performed in conjunction with regulatory development. The model utilizes a multi-sector, multi-product dynamic linear modeling framework that evaluates the economic impact of emission reduction strategies for multiple air pollutants. The ISIS model considers facility-level economic, environmental, and technical parameters, as well as sector-level market data, to estimate the impacts of environmental regulations on the pulp and paper industry. Specifically, the model can be used to estimate U.S. and global market impacts of new or more stringent air regulations, such as impacts on product price, exports and imports, market demands, capital investment, and mill closures. One major challenge to developing a representative model is the need for an extensive amount of data. This article discusses the collection and processing of data for use in the model, as well as the methods used for building the ISIS pulp and paper database that facilitates the required analyses to support the air quality management of the pulp and paper sector. PMID:25806516

  4. Natural products against cancer: A comprehensive bibliometric study of the research projects, publications, patents and drugs

    Directory of Open Access Journals (Sweden)

    Jian Du

    2014-01-01

    Full Text Available Objectives: To analyze multi-source data including awards, publications, patents and drugs, and try to draw the whole landscape of the research and development community in the area of natural products (NPs against cancer. Materials and Methods: Awards, publications, patents and drugs data from National Institute of Health/Natural Science Foundation of China (NIH/NSFC, PubMed, Derwent Innovation Index and Cortellis were collected. Bibliometric methodologies and technology are used to investigate publications/patents/drugs, their contents and relationships. Results: NIH and NSFC respectively demonstrated a stable and sustained expenditure growth in this area. The number of publications is continuously increasing. Yet the annual patent applications worldwide and FDA drug approvals were little changed or not obviously fluctuated in 2003-2013. USA and several Asia-pacific countries/territories are important contributing powers. We described the evolution of major research topics by those MeSH Major Topics indexed in PubMed with the largest growth range in three intervals, and analyzed hot research topics in the recent 10 years which include NPs or NPs derivatives, cell line/animal model, laboratory technologies and activation mechanisms. Conclusions: China published the most publications and received the most patent applications, but drug discovery performance is no better than USA and Japan. Research on anti-neoplastic structures and compounds originated from Chinese traditional medicine (TCM, medicinal plants, herbal medicine and marine NPs are major research topics in the recent 10 years. There still exits translational gap between basic research and drug discovery. Translational research should be undertaken to strengthen the applicability of NPs.

  5. Internal Audit of a Comprehensive IMRT Program for Prostate Cancer: A Model for Centers in Developing Countries?

    International Nuclear Information System (INIS)

    Koh, Wee Yao; Ren Wei; Mukherjee, Rahul K.; Chung, Hans T.

    2009-01-01

    Purpose: With improving regional prosperity, significant capital investments have been made to rapidly expand radiotherapy capacity across Southeast Asia. Yet little has been reported on the implementation of adequate quality assurance (QA) in patient management. The objective of this study is to perform an in-depth QA assessment of our definitive intensity-modulated radiotherapy (IMRT) program for prostate cancer since its inception. Methods and Materials: The department's prostate IMRT program was modeled after that of University of California San Francisco. A departmental protocol consisting of radiotherapy volume/dose and hormone sequencing/duration and a set of 18 dose objectives to the target and critical organs were developed, and all plans were presented at the weekly departmental QA rounds. All patients treated with definitive IMRT for nonmetastatic prostate cancer were retrospectively reviewed. Protocol adherence, dosimetry data, toxicities, and outcomes were evaluated. Results: Since 2005, 76 patients received IMRT: 54 with whole-pelvis and 22 with prostate-only treatment. Of the 1,140 recorded dosimetric end points, 39 (3.3%) did not meet the protocol criteria. At QA rounds, no plans required a revision. Only one major protocol violation was observed. Two and two cases of Grade 3-4 acute and late toxicities, respectively, were observed. Five (8.8%) patients developed proctitis, but only one required argon laser therapy. Conclusions: Our comprehensive, practice-adapted QA measures appeared to ensure that we were able to consistently generate conforming IMRT plans with acceptable toxicities. These measures can be easily integrated into other clinics contemplating on developing such a program.

  6. Delphi consensus of an expert committee in oncogeriatrics regarding comprehensive geriatric assessment in seniors with cancer in Spain.

    Science.gov (United States)

    Molina-Garrido, Maria-Jose; Guillén-Ponce, Carmen; Blanco, Remei; Saldaña, Juana; Feliú, Jaime; Antonio, Maite; López-Mongil, Rosa; Ramos Cordero, Primitivo; Gironés, Regina

    2018-07-01

    The aim of this work was to reach a national consensus in Spain regarding the Comprehensive Geriatric Assessment (CGA) domains in older oncological patients and the CGA scales to be used as a foundation for widespread use. The Delphi method was implemented to attain consensus. Representatives of the panel were chosen from among the members of the Oncogeriatric Working Group of the Spanish Society of Medical Oncology (SEOM). Consensus was defined as ≥66.7% coincidence in responses and by the stability of said coincidence (changes ≤15% between rounds). The study was conducted between July and December 2016. Of the 17 people invited to participate, 16 agreed. The panel concluded by consensus that the following domains should be included in the CGA:(and the scales to evaluate them): functional (Barthel Index, Lawton-Brody scale, gait speed), cognitive (Pfeiffer questionnaire), nutritional (Mini Nutritional Assessment - MNA), psychological/mood (Yesavage scale), social-familial (Gijon scale), comorbidity (Charlson index), medications, and geriatric syndromes (urinary and/or fecal incontinence, low auditory and/or visual acuity, presence of falls, pressure sores, insomnia, and abuse). Also by consensus, the CGA should be administered to older patients with cancer for whom there is a subsequent therapeutic intent and who scored positive on a previous frailty-screening questionnaire. After 3 rounds, consensus was reached regarding CGA domains to be used in older patients with cancer, the scales to be administered for each of these domains, as well as the timeline to be followed during consultation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Database principles programming performance

    CERN Document Server

    O'Neil, Patrick

    2014-01-01

    Database: Principles Programming Performance provides an introduction to the fundamental principles of database systems. This book focuses on database programming and the relationships between principles, programming, and performance.Organized into 10 chapters, this book begins with an overview of database design principles and presents a comprehensive introduction to the concepts used by a DBA. This text then provides grounding in many abstract concepts of the relational model. Other chapters introduce SQL, describing its capabilities and covering the statements and functions of the programmi

  8. The Utility of Expert Diagnosis in Surgical Neuropathology: Analysis of Consultations Reviewed at 5 National Comprehensive Cancer Network Institutions.

    Science.gov (United States)

    Bruner, Janet M; Louis, David N; McLendon, Roger; Rosenblum, Marc K; Archambault, W Tad; Most, Susan; Tihan, Tarik

    2017-03-01

    The aim of this study was to characterize the type and degree of discrepancies between non-expert and expert diagnoses of CNS tumors to identify the value of consultations in surgical neuropathology. Neuropathology experts from 5 National Comprehensive Cancer Network (NCCN) member institutions participated in the review of 1281 consultations selected based on inclusion criteria. The consultation cases were re-reviewed at the NCCN headquarters to determine concordance with the original diagnoses. Among all consultations, 249 (19.4%) were submitted for expert diagnoses without final diagnoses from the submitting institution. Within the remaining 1032 patients, the serious/major discrepancy rate was 4.8%, and less serious and minor discrepancies were seen in 19.4% of the cases. The discrepancy rate was higher among patients who were referred to NCCN institutions for consultation compared to those who were referred for treatment only. The discrepancy rates, patient demographics, type of consultations and submitting institutions varied among participating NCCN institutions. Expert consultations identified a subset of cases with significant diagnostic discrepancies, and constituted the initial diagnoses in some cases. These data indicate that expert consultations in glial tumors and all types of pediatric CNS tumors can improve accurate diagnosis and enable appropriate management. © 2017 American Association of Neuropathologists, Inc. All rights reserved.

  9. Comprehensive biostatistical analysis of CpG island methylator phenotype in colorectal cancer using a large population-based sample.

    Directory of Open Access Journals (Sweden)

    Katsuhiko Nosho

    Full Text Available The CpG island methylator phenotype (CIMP is a distinct phenotype associated with microsatellite instability (MSI and BRAF mutation in colon cancer. Recent investigations have selected 5 promoters (CACNA1G, IGF2, NEUROG1, RUNX3 and SOCS1 as surrogate markers for CIMP-high. However, no study has comprehensively evaluated an expanded set of methylation markers (including these 5 markers using a large number of tumors, or deciphered the complex clinical and molecular associations with CIMP-high determined by the validated marker panel. METHOLODOLOGY/PRINCIPAL FINDINGS: DNA methylation at 16 CpG islands [the above 5 plus CDKN2A (p16, CHFR, CRABP1, HIC1, IGFBP3, MGMT, MINT1, MINT31, MLH1, p14 (CDKN2A/ARF and WRN] was quantified in 904 colorectal cancers by real-time PCR (MethyLight. In unsupervised hierarchical clustering analysis, the 5 markers (CACNA1G, IGF2, NEUROG1, RUNX3 and SOCS1, CDKN2A, CRABP1, MINT31, MLH1, p14 and WRN were generally clustered with each other and with MSI and BRAF mutation. KRAS mutation was not clustered with any methylation marker, suggesting its association with a random methylation pattern in CIMP-low tumors. Utilizing the validated CIMP marker panel (including the 5 markers, multivariate logistic regression demonstrated that CIMP-high was independently associated with older age, proximal location, poor differentiation, MSI-high, BRAF mutation, and inversely with LINE-1 hypomethylation and beta-catenin (CTNNB1 activation. Mucinous feature, signet ring cells, and p53-negativity were associated with CIMP-high in only univariate analysis. In stratified analyses, the relations of CIMP-high with poor differentiation, KRAS mutation and LINE-1 hypomethylation significantly differed according to MSI status.Our study provides valuable data for standardization of the use of CIMP-high-specific methylation markers. CIMP-high is independently associated with clinical and key molecular features in colorectal cancer. Our data also

  10. Comprehensive Care

    Science.gov (United States)

    ... Comprehensive Care Share this page Facebook Twitter Email Comprehensive Care Understand the importance of comprehensive MS care ... In this article A complex disease requires a comprehensive approach Today multiple sclerosis (MS) is not a ...

  11. Adjuvant chemotherapy versus chemoradiotherapy for small cell lung cancer with lymph node metastasis: a retrospective observational study with use of a national database in Japan

    OpenAIRE

    Urushiyama, Hirokazu; Jo, Taisuke; Yasunaga, Hideo; Yamauchi, Yasuhiro; Matsui, Hiroki; Hasegawa, Wakae; Takeshima, Hideyuki; Hiraishi, Yoshihisa; Mitani, Akihisa; Fushimi, Kiyohide; Nagase, Takahide

    2017-01-01

    Background The optimal postoperative treatment strategy for small cell lung cancer (SCLC) remains unclear, especially in patients with lymph node metastasis. We aimed to compare the outcomes of patients with SCLC and lymph node metastasis treated with postoperative adjuvant chemotherapy or chemoradiotherapy. Methods We retrospectively collected data on patients with postoperative SCLC diagnosed with N1 and N2 lymph node metastasis from the Diagnosis Procedure Combination database in Japan, be...

  12. Causes of death and competing risk analysis of the associated factors for non-small cell lung cancer using the Surveillance, Epidemiology, and End Results database.

    Science.gov (United States)

    Wei, Shenhai; Tian, Jintao; Song, Xiaoping; Wu, Bingqun; Liu, Limin

    2018-01-01

    To investigate the probability of death (POD) from any causes by time after diagnosis of non-small cell lung cancer (NSCLC) and the factors associated with survival for NSCLC patients. A total of 202,914 patients with NSCLC from 2004 to 2013 were identified from the Surveillance, Epidemiology, and End Results (SEER) database. The overall survival (OS) and lung cancer-specific survival (LCSS) were calculated and POD from any causes at different time periods after diagnosis was explored. The predictive factors for OS, LCSS and survival from non-lung cancer deaths were investigated using multivariate analysis with Cox proportional hazards regression and competing risk regression analysis. The 5- and 10-year OS were 20.4% and 11.5%, accordingly that for LCSS were 25.5% and 18.4%, respectively. Lung cancer contributed 88.3% (n = 128,402) of the deaths. The POD from lung cancer decreased with time after diagnosis. In multivariate analysis, advanced age and advanced stage of NSCLC were associated with decreased OS and LCSS. Comparing to no surgery, any kind of resection conferred lower risk of death from lung cancer and higher risk of dying from non-lung cancer conditions except lobectomy or bilobectomy, which was associated with lower risk of death from both lung cancer and non-lung cancer conditions. Most of the patients with NSCLC died from lung cancer. Rational surveillance and treatment policies should be made for them. Early stage and lobectomy or bilobectomy were associated with improved OS and LCSS. It is reasonable to focus on early detection and optimal surgical treatment for NSCLC.

  13. Management and cost analysis of cancer patients treated with G-CSF: a cohort study based on the French national healthcare insurance database.

    Science.gov (United States)

    Tilleul, Patrick; Jacot, William; Emery, Corinne; Lafuma, Antoine; Gourmelen, Julie

    2017-12-01

    To describe the management and costs associated with G-CSF therapy in cancer patients in France. This study analyzed a representative random population sample from the French national healthcare insurance database, focusing on 1,612 patients with hematological or solid malignancies who were reimbursed in 2013 or 2014 for at least one G-CSF treatment dispensed in a retail pharmacy. Patient characteristics and treatment costs were analyzed according to the type of cancer. Then the costs and characteristics of patients associated with the use of different G-CSF products were analyzed in the sub-set of breast cancer patients. The most frequent malignancies in the database population were breast cancer (23.3%), hematological malignancies (22.2%), and lung cancer (12.4%). The reimbursed G-CSF was pegfilgrastim in 34.1% of cases, lenograstim in 26.7%, and filgrastim in 17.9%. More than one G-CSF product was reimbursed to 21.3% of patients. The total annual reimbursed health expenses per patient, according to the type of G-CSF, were €27,001, €24,511, and €20,802 for patients treated with filgrastim, lenograstim, and pegfilgrastim, respectively. Ambulatory care accounted for, respectively, 35%, 38%, and 41% of those costs. In patients with breast cancer, ambulatory care cost was €7,915 with filgrastim, €7,750 with lenograstim, and €6,989 with pegfilgrastim, and the respective cost of G-CSF was €1,733, €1,559, and €3,668. All available G-CSF products have been shown to be effective in cancer patients, and both daily G-CSFs and pegylated G-CSF are recommended in international guidelines. Nevertheless, this analysis of G-CSF reimbursement indicates that the choice of product can markedly affect the total cost of ambulatory care.

  14. Outcome in Advanced Ovarian Cancer following an Appropriate and Comprehensive Effort at Upfront Cytoreduction: A Twenty-Year Experience in a Single Cancer Institute

    Directory of Open Access Journals (Sweden)

    Anne Marszalek

    2010-01-01

    Full Text Available Objectives. The purpose of this retrospective evaluation of advanced-stage ovarian cancer patients was to compare outcome with published findings from other centers and to discuss future options for the management of advanced ovarian carcinoma patients. Methods. A retrospective series of 340 patients with a mean age of 58 years (range: 17–88 treated for FIGO stage III and IV ovarian cancer between January 1985 and January 2005 was reviewed. All patients had primary cytoreductive surgery, without extensive bowel, peritoneal, or systematic lymph node resection, thereby allowing initiation of chemotherapy without delay. Chemotherapy consisted of cisplatin-based chemotherapy in combination with alkylating agents before 2000, whereas carboplatin and paclitaxel regimes were generally used after 1999-2000. Overall survival and disease-free survival were analyzed by the Kaplan-Meier method and the log-rank test. Results. With a mean followup of 101 months (range: 5 to 203, 280 events (recurrence or death were observed and 245 patients (72% had died. The mortality and morbidity related to surgery were low. The main prognostic factor for overall survival was postoperative residual disease (P<.0002, while the main prognostic factor for disease-free survival was histological tumor type (P<.0007. Multivariate analysis identified three significant risk factors: optimal surgery (RR=2.2 for suboptimal surgery, menopausal status (RR=1.47 for postmenopausal women, and presence of a taxane in the chemotherapy combination (RR=0.72. Conclusion. These results confirm that optimal surgery defined by an appropriate and comprehensive effort at upfront cytoreduction limits morbidity related to the surgical procedure and allows initiation of chemotherapy without any negative impact on survival. The impact of neoadjuvant chemotherapy to improve resectability while lowering the morbidity of the surgical procedure is discussed.

  15. A proposal for a comprehensive risk scoring system for predicting postoperative complications in octogenarian patients with medically operable lung cancer: JACS1303.

    Science.gov (United States)

    Saji, Hisashi; Ueno, Takahiko; Nakamura, Hiroshige; Okumura, Norihito; Tsuchida, Masanori; Sonobe, Makoto; Miyazaki, Takuro; Aokage, Keiju; Nakao, Masayuki; Haruki, Tomohiro; Ito, Hiroyuki; Kataoka, Kazuhiko; Okabe, Kazunori; Tomizawa, Kenji; Yoshimoto, Kentaro; Horio, Hirotoshi; Sugio, Kenji; Ode, Yasuhisa; Takao, Motoshi; Okada, Morihito; Chida, Masayuki

    2018-04-01

    Although some retrospective studies have reported clinicopathological scoring systems for predicting postoperative complications and survival outcomes for elderly lung cancer patients, optimized scoring systems remain controversial. The Japanese Association for Chest Surgery (JACS) conducted a nationwide multicentre prospective cohort and enrolled a total of 1019 octogenarians with medically operable lung cancer. Details of the clinical factors, comorbidities and comprehensive geriatric assessment were recorded for 895 patients to develop a comprehensive risk scoring (RS) system capable of predicting severe complications. Operative (30 days) and hospital mortality rates were 1.0% and 1.6%, respectively. Complications were observed in 308 (34%) patients, of whom 81 (8.4%) had Grade 3-4 severe complications. Pneumonia was the most common severe complication, observed in 27 (3.0%) patients. Five predictive factors, gender, comprehensive geriatric assessment75: memory and Simplified Comorbidity Score (SCS): diabetes mellitus, albumin and percentage vital capacity, were identified as independent predictive factors for severe postoperative complications (odds ratio = 2.73, 1.86, 1.54, 1.66 and 1.61, respectively) through univariate and multivariate analyses. A 5-fold cross-validation was performed as an internal validation to reconfirm these 5 predictive factors (average area under the curve 0.70). We developed a simplified RS system as follows: RS = 3 (gender: male) + 2 (comprehensive geriatric assessment 75: memory: yes) + 2 (albumin: <3.8 ng/ml) + 1 (percentage vital capacity: ≤90) + 1 (SCS: diabetes mellitus: yes). The current series shows that octogenarians can be successfully treated for lung cancer with surgical resection with an acceptable rate of severe complications and mortality. We propose a simplified RS system to predict severe complications in octogenarian patients with medically operative lung cancer. JACS1303 (UMIN000016756).

  16. Rate of Clinical Complete Response for 1 Year or More in Bone-Metastatic Breast Cancer after Comprehensive Treatments including Autologous Formalin-Fixed Tumor Vaccine.

    Science.gov (United States)

    Kuranishi, Fumito; Imaoka, Yuki; Sumi, Yuusuke; Uemae, Yoji; Yasuda-Kurihara, Hiroko; Ishihara, Takeshi; Miyazaki, Tsubasa; Ohno, Tadao

    2018-01-01

    No effective treatment has been developed for bone-metastatic breast cancer. We found 3 cases with clinical complete response (cCR) of the bone metastasis and longer overall survival of the retrospectively examined cohort treated comprehensively including autologous formalin-fixed tumor vaccine (AFTV). AFTV was prepared individually for each patient from their own formalin-fixed and paraffin-embedded breast cancer tissues. Three patients maintained cCR status of the bone metastasis for 17 months or more. Rate of cCR for 1 year or more appeared to be 15% (3/20) after comprehensive treatments including AFTV. The median overall survival time (60.0 months) and the 3- to 8-year survival rates after diagnosis of bone metastasis were greater than those of historical control cohorts in Japan (1988-2002) and in the nationwide population-based cohort study of Denmark (1999-2007). Bone-metastatic breast cancer may be curable after comprehensive treatments including AFTV, although larger scale clinical trial is required.

  17. Rate of Clinical Complete Response for 1 Year or More in Bone-Metastatic Breast Cancer after Comprehensive Treatments including Autologous Formalin-Fixed Tumor Vaccine

    Directory of Open Access Journals (Sweden)

    Fumito Kuranishi

    2018-01-01

    Full Text Available Introduction. No effective treatment has been developed for bone-metastatic breast cancer. We found 3 cases with clinical complete response (cCR of the bone metastasis and longer overall survival of the retrospectively examined cohort treated comprehensively including autologous formalin-fixed tumor vaccine (AFTV. Patients and Methods. AFTV was prepared individually for each patient from their own formalin-fixed and paraffin-embedded breast cancer tissues. Results. Three patients maintained cCR status of the bone metastasis for 17 months or more. Rate of cCR for 1 year or more appeared to be 15% (3/20 after comprehensive treatments including AFTV. The median overall survival time (60.0 months and the 3- to 8-year survival rates after diagnosis of bone metastasis were greater than those of historical control cohorts in Japan (1988–2002 and in the nationwide population-based cohort study of Denmark (1999–2007. Conclusion. Bone-metastatic breast cancer may be curable after comprehensive treatments including AFTV, although larger scale clinical trial is required.

  18. National Comprehensive Cancer Network

    Science.gov (United States)

    ... Congress: Hematologic Malignancies™ NCCN Global Academy for Excellence & Leadership in Oncology™ NCCN Corporate Council Next Meeting, March 22 NCCN Global Corporate Council NCCN State Oncology Society Forum NCCN Employer Forum View All Webinars NCCN 2017 Congress Webinar ...

  19. The database of chromosome imbalance regions and genes resided in lung cancer from Asian and Caucasian identified by array-comparative genomic hybridization

    Directory of Open Access Journals (Sweden)

    Lo Fang-Yi

    2012-06-01

    Full Text Available Abstract Background Cancer-related genes show racial differences. Therefore, identification and characterization of DNA copy number alteration regions in different racial groups helps to dissect the mechanism of tumorigenesis. Methods Array-comparative genomic hybridization (array-CGH was analyzed for DNA copy number profile in 40 Asian and 20 Caucasian lung cancer patients. Three methods including MetaCore analysis for disease and pathway correlations, concordance analysis between array-CGH database and the expression array database, and literature search for copy number variation genes were performed to select novel lung cancer candidate genes. Four candidate oncogenes were validated for DNA copy number and mRNA and protein expression by quantitative polymerase chain reaction (qPCR, chromogenic in situ hybridization (CISH, reverse transcriptase-qPCR (RT-qPCR, and immunohistochemistry (IHC in more patients. Results We identified 20 chromosomal imbalance regions harboring 459 genes for Caucasian and 17 regions containing 476 genes for Asian lung cancer patients. Seven common chromosomal imbalance regions harboring 117 genes, included gain on 3p13-14, 6p22.1, 9q21.13, 13q14.1, and 17p13.3; and loss on 3p22.2-22.3 and 13q13.3 were found both in Asian and Caucasian patients. Gene validation for four genes including ARHGAP19 (10q24.1 functioning in Rho activity control, FRAT2 (10q24.1 involved in Wnt signaling, PAFAH1B1 (17p13.3 functioning in motility control, and ZNF322A (6p22.1 involved in MAPK signaling was performed using qPCR and RT-qPCR. Mean gene dosage and mRNA expression level of the four candidate genes in tumor tissues were significantly higher than the corresponding normal tissues (PP=0.06. In addition, CISH analysis of patients indicated that copy number amplification indeed occurred for ARHGAP19 and ZNF322A genes in lung cancer patients. IHC analysis of paraffin blocks from Asian Caucasian patients demonstrated that the frequency of

  20. The database of chromosome imbalance regions and genes resided in lung cancer from Asian and Caucasian identified by array-comparative genomic hybridization

    International Nuclear Information System (INIS)

    Lo, Fang-Yi; Nandi, Suvobroto; Salgia, Ravi; Wang, Yi-Ching; Chang, Jer-Wei; Chang, I-Shou; Chen, Yann-Jang; Hsu, Han-Shui; Huang, Shiu-Feng Kathy; Tsai, Fang-Yu; Jiang, Shih Sheng; Kanteti, Rajani

    2012-01-01

    Cancer-related genes show racial differences. Therefore, identification and characterization of DNA copy number alteration regions in different racial groups helps to dissect the mechanism of tumorigenesis. Array-comparative genomic hybridization (array-CGH) was analyzed for DNA copy number profile in 40 Asian and 20 Caucasian lung cancer patients. Three methods including MetaCore analysis for disease and pathway correlations, concordance analysis between array-CGH database and the expression array database, and literature search for copy number variation genes were performed to select novel lung cancer candidate genes. Four candidate oncogenes were validated for DNA copy number and mRNA and protein expression by quantitative polymerase chain reaction (qPCR), chromogenic in situ hybridization (CISH), reverse transcriptase-qPCR (RT-qPCR), and immunohistochemistry (IHC) in more patients. We identified 20 chromosomal imbalance regions harboring 459 genes for Caucasian and 17 regions containing 476 genes for Asian lung cancer patients. Seven common chromosomal imbalance regions harboring 117 genes, included gain on 3p13-14, 6p22.1, 9q21.13, 13q14.1, and 17p13.3; and loss on 3p22.2-22.3 and 13q13.3 were found both in Asian and Caucasian patients. Gene validation for four genes including ARHGAP19 (10q24.1) functioning in Rho activity control, FRAT2 (10q24.1) involved in Wnt signaling, PAFAH1B1 (17p13.3) functioning in motility control, and ZNF322A (6p22.1) involved in MAPK signaling was performed using qPCR and RT-qPCR. Mean gene dosage and mRNA expression level of the four candidate genes in tumor tissues were significantly higher than the corresponding normal tissues (P<0.001~P=0.06). In addition, CISH analysis of patients indicated that copy number amplification indeed occurred for ARHGAP19 and ZNF322A genes in lung cancer patients. IHC analysis of paraffin blocks from Asian Caucasian patients demonstrated that the frequency of PAFAH1B1 protein overexpression was 68

  1. Irinotecan and Oxaliplatin Might Provide Equal Benefit as Adjuvant Chemotherapy for Patients with Resectable Synchronous Colon Cancer and Liver-confined Metastases: A Nationwide Database Study.

    Science.gov (United States)

    Liang, Yi-Hsin; Shao, Yu-Yun; Chen, Ho-Min; Cheng, Ann-Lii; Lai, Mei-Shu; Yeh, Kun-Huei

    2017-12-01

    Although irinotecan and oxaliplatin are both standard treatments for advanced colon cancer, it remains unknown whether either is effective for patients with resectable synchronous colon cancer and liver-confined metastasis (SCCLM) after curative surgery. A population-based cohort of patients diagnosed with de novo SCCLM between 2004 and 2009 was established by searching the database of the Taiwan Cancer Registry and the National Health Insurance Research Database of Taiwan. Patients who underwent curative surgery as their first therapy followed by chemotherapy doublets were classified into the irinotecan group or oxaliplatin group accordingly. Patients who received radiotherapy or did not receive chemotherapy doublets were excluded. We included 6,533 patients with de novo stage IV colon cancer. Three hundred and nine of them received chemotherapy doublets after surgery; 77 patients received irinotecan and 232 patients received oxaliplatin as adjuvant chemotherapy. The patients in both groups exhibited similar overall survival (median: not reached vs. 40.8 months, p=0.151) and time to the next line of treatment (median: 16.5 vs. 14.3 months, p=0.349) in both univariate and multivariate analyses. Additionally, patients with resectable SCCLM had significantly shorter median overall survival than patients with stage III colon cancer who underwent curative surgery and subsequent adjuvant chemotherapy, but longer median overall survival than patients with de novo stage IV colon cancer who underwent surgery only at the primary site followed by standard systemic chemotherapy (p<0.001). Irinotecan and oxaliplatin exhibited similar efficacy in patients who underwent curative surgery for resectable SCCLM. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

  2. Association of Palliative Care Consultation With Reducing Inpatient Chemotherapy Use in Elderly Patients With Cancer in Japan: Analysis Using a Nationwide Administrative Database.

    Science.gov (United States)

    Sano, Motoko; Fushimi, Kiyohide

    2017-08-01

    The administration of chemotherapy at the end of life is considered an aggressive life-prolonging treatment. The use of unnecessarily aggressive therapy in elderly patients at the end of life is an important health-care concern. To explore the impact of palliative care consultation (PCC) on chemotherapy use in geriatric oncology inpatients in Japan by analyzing data from a national database. We conducted a multicenter cohort study of patients aged ≥65 years, registered in the Japan National Administrative Healthcare Database, who died with advanced (stage ≥3) lung, stomach, colorectal, liver, or breast cancer while hospitalized between April 2010 and March 2013. The relationship between PCC and chemotherapy use in the last 2 weeks of life was analyzed using χ 2 and logistic regression analyses. We included 26 012 patients in this analysis. The mean age was 75.74 ± 6.40 years, 68.1% were men, 81.8% had recurrent cancer, 29.5% had lung cancer, and 29.5% had stomach cancer. Of these, 3134 (12%) received PCC. Among individuals who received PCC, chemotherapy was administered to 46 patients (1.5%) and was not administered to 3088 patients (98.5%). Among those not receiving PCC, chemotherapy was administered to 909 patients (4%) and was not administered to the remaining 21 978 patients (96%; odds ratio [OR], 0.35; 95% confidence interval, 0.26-0.48). The OR of chemotherapy use was higher in men, young-old, and patients with primary cancer. Palliative care consultation was associated with less chemotherapy use in elderly Japanese patients with cancer who died in the hospital setting.

  3. Identification of a comprehensive spectrum of genetic factors for hereditary breast cancer in a Chinese population by next-generation sequencing.

    Directory of Open Access Journals (Sweden)

    Xiaochen Yang

    Full Text Available The genetic etiology of hereditary breast cancer has not been fully elucidated. Although germline mutations of high-penetrance genes such as BRCA1/2 are implicated in development of hereditary breast cancers, at least half of all breast cancer families are not linked to these genes. To identify a comprehensive spectrum of genetic factors for hereditary breast cancer in a Chinese population, we performed an analysis of germline mutations in 2,165 coding exons of 152 genes associated with hereditary cancer using next-generation sequencing (NGS in 99 breast cancer patients from families of cancer patients regardless of cancer types. Forty-two deleterious germline mutations were identified in 21 genes of 34 patients, including 18 (18.2% BRCA1 or BRCA2 mutations, 3 (3% TP53 mutations, 5 (5.1% DNA mismatch repair gene mutations, 1 (1% CDH1 mutation, 6 (6.1% Fanconi anemia pathway gene mutations, and 9 (9.1% mutations in other genes. Of seven patients who carried mutations in more than one gene, 4 were BRCA1/2 mutation carriers, and their average onset age was much younger than patients with only BRCA1/2 mutations. Almost all identified high-penetrance gene mutations in those families fulfill the typical phenotypes of hereditary cancer syndromes listed in the National Comprehensive Cancer Network (NCCN guidelines, except two TP53 and three mismatch repair gene mutations. Furthermore, functional studies of MSH3 germline mutations confirmed the association between MSH3 mutation and tumorigenesis, and segregation analysis suggested antagonism between BRCA1 and MSH3. We also identified a lot of low-penetrance gene mutations. Although the clinical significance of those newly identified low-penetrance gene mutations has not been fully appreciated yet, these new findings do provide valuable epidemiological information for the future studies. Together, these findings highlight the importance of genetic testing based on NCCN guidelines and a multi-gene analysis

  4. [The human and economic burden of cancer in France in 2014, based on the Sniiram national database].

    Science.gov (United States)

    Tuppin, Philippe; Pestel, Laurence; Samson, Solène; Cuerq, Anne; Rivière, Sébastien; Tala, Stéphane; Denis, Pierre; Drouin, Jérôme; Gissot, Claude; Gastaldi-Ménager, Christelle; Fagot-Campagna, Anne

    2017-06-01

    The national health insurance information system (Sniiram) can be used to estimate the national medical and economic burden of cancer. This study reports the annual rates, characteristics and expenditure of people reimbursed for cancer. Among 57 million general health scheme beneficiaries (86% of the French population), people managed for cancer were identified using algorithms based on hospital diagnoses and full refund for long-term cancer. The reimbursed costs (euros) related to the cancer, paid off by the health insurance, were estimated. In 2014, 2.491 million people (4.4%) covered by the general health scheme had a cancer managed (men 1.1 million, 5.1%; women 1.3 million, 4.9%). The annual (2012-2014) average growth rate of patients was 0.8%. The spending related to the cancer was 13.5 billion: 5 billion for primary health care (drugs 2.3 billion), 7.5 billion for the hospital (drugs 1.3 billions) and 900 million for sick leave and invalidity pensions. Spending annual average growth rate (2012-2014) was 4% (drugs 2%). The rates of patients and the relative spending were 1.8% and 2.5 billion for the breast cancer (women), 1.5% and 1.0 billion for prostate cancer, 0.9% and 1.5 billion for the colon cancer, and 0.19% and 1.3 billion for lung cancer. Cancers establish one of the first groups of chronic diseases pathologies in terms of patients and spending. If the numbers of patients remain stables, the spending increases, mainly for medicines. Copyright © 2017 Société Française du Cancer. Published by Elsevier Masson SAS. All rights reserved.

  5. A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE).

    Science.gov (United States)

    Wu, Tsung-Jung; Shamsaddini, Amirhossein; Pan, Yang; Smith, Krista; Crichton, Daniel J; Simonyan, Vahan; Mazumder, Raja

    2014-01-01

    Years of sequence feature curation by UniProtKB/Swiss-Prot, PIR-PSD, NCBI-CDD, RefSeq and other database biocurators has led to a rich repository of information on functional sites of genes and proteins. This information along with variation-related annotation can be used to scan human short sequence reads from next-generation sequencing (NGS) pipelines for presence of non-synonymous single-nucleotide variations (nsSNVs) that affect functional sites. This and similar workflows are becoming more important because thousands of NGS data sets are being made available through projects such as The Cancer Genome Atlas (TCGA), and researchers want to evaluate their biomarkers in genomic data. BioMuta, an integrated sequence feature database, provides a framework for automated and manual curation and integration of cancer-related sequence features so that they can be used in NGS analysis pipelines. Sequence feature information in BioMuta is collected from the Catalogue of Somatic Mutations in Cancer (COSMIC), ClinVar, UniProtKB and through biocuration of information available from publications. Additionally, nsSNVs identified through automated analysis of NGS data from TCGA are also included in the database. Because of the petabytes of data and information present in NGS primary repositories, a platform HIVE (High-performance Integrated Virtual Environment) for storing, analyzing, computing and curating NGS data and associated metadata has been developed. Using HIVE, 31 979 nsSNVs were identified in TCGA-derived NGS data from breast cancer patients. All variations identified through this process are stored in a Curated Short Read archive, and the nsSNVs from the tumor samples are included in BioMuta. Currently, BioMuta has 26 cancer types with 13 896 small-scale and 308 986 large-scale study-derived variations. Integration of variation data allows identifications of novel or common nsSNVs that can be prioritized in validation studies. Database URL: BioMuta: http

  6. Developing a Comprehensive Spectral-Biogeochemical Database of Midwestern Rivers for Water Quality Retrieval Using Remote Sensing Data: A Case Study of the Wabash River and Its Tributary, Indiana

    Directory of Open Access Journals (Sweden)

    Jing Tan

    2016-06-01

    Full Text Available A comprehensive spectral-biogeochemical database was developed for the Wabash River and the Tippecanoe River in Indiana, United States. This database includes spectral measurements of river water, coincident in situ measurements of water quality parameters (chlorophyll (chl, non-algal particles (NAP, and colored dissolved organic matter (CDOM, nutrients (total nitrogen (TN, total phosphorus (TP, and dissolved organic carbon (DOC, water-column inherent optical properties (IOPs, water depths, substrate types, and bottom reflectance spectra collected in summer 2014. With this dataset, the temporal variability of water quality observations was first analyzed and studied. Second, radiative transfer models were inverted to retrieve water quality parameters using a look-up table (LUT based spectrum matching methodology. Results found that the temporal variability of water quality parameters and nutrients in the Wabash River was closely associated with hydrologic conditions. Meanwhile, there were no significant correlations found between these parameters and streamflow for the Tippecanoe River, due to the two upstream reservoirs, which increase the settling of sediment and uptake of nutrients. The poor relationship between CDOM and DOC indicates that most DOC in the rivers was from human sources such as wastewater. It was also found that the source of water (surface runoff or combined sewer overflow (CSO, water temperature, and nutrients were important factors controlling instream concentrations of phytoplankton. The LUT retrieved NAP concentrations were in good agreement with field measurements with slope close to 1.0 and the average estimation error was 4.1% of independently obtained lab measurements. The error for chl estimation was larger (37.7%, which is attributed to the fact that the specific absorption spectrum of chl was not well represented in this study. The LUT retrievals for CDOM experienced large variability, probably due to the small data

  7. Mycobacteriophage genome database.

    Science.gov (United States)

    Joseph, Jerrine; Rajendran, Vasanthi; Hassan, Sameer; Kumar, Vanaja

    2011-01-01

    Mycobacteriophage genome database (MGDB) is an exclusive repository of the 64 completely sequenced mycobacteriophages with annotated information. It is a comprehensive compilation of the various gene parameters captured from several databases pooled together to empower mycobacteriophage researchers. The MGDB (Version No.1.0) comprises of 6086 genes from 64 mycobacteriophages classified into 72 families based on ACLAME database. Manual curation was aided by information available from public databases which was enriched further by analysis. Its web interface allows browsing as well as querying the classification. The main objective is to collect and organize the complexity inherent to mycobacteriophage protein classification in a rational way. The other objective is to browse the existing and new genomes and describe their functional annotation. The database is available for free at http://mpgdb.ibioinformatics.org/mpgdb.php.

  8. Descriptive study of breast and cervix cancer, in patients treated with linear accelerator, at the Centro Medico de Radioterapia Irazu, between 2000 and 2001, and proposed a database

    International Nuclear Information System (INIS)

    Calvo Jimenez, Kattia; Marchena Mendoza, Mario

    2008-01-01

    A descriptive study of breast and cervix cancer was performed in patients who have received treatment linear accelerator, during the period 2000 - 2001 in the Centro Medico de Radioterapia Irazu. The survival of the patients was assessed to five years (2006). One proposal called database is the product of analysis performed and consistent with the objectives set. The idea to develop the database of these features in the medical center, arises because the Centre was at that time with the only linear accelerator in the country and also all the necessary information of patients was easily accessible. A population of 438 records, with a common pathology was analyzed under the following variables: type of cancer, identification of anatomic region, province, age, sex, type of radiation, number of sessions, referral hospital, physician, physician referral. This work is relevant, because breast and cervical cancers have been a major cause of mortality, ranked among the five most common malignancies in women. From there to have adequate information systems, has led policy makers and health professionals to have a better outlook for their level of management. (author) [es

  9. Multidisciplinary team-based approach for comprehensive preoperative pulmonary rehabilitation including intensive nutritional support for lung cancer patients.

    Directory of Open Access Journals (Sweden)

    Hiroaki Harada

    Full Text Available BACKGROUND: To decrease the risk of postoperative complication, improving general and pulmonary conditioning preoperatively should be considered essential for patients scheduled to undergo lung surgery. OBJECTIVE: The aim of this study is to develop a short-term beneficial program of preoperative pulmonary rehabilitation for lung cancer patients. METHODS: From June 2009, comprehensive preoperative pulmonary rehabilitation (CHPR including intensive nutritional support was performed prospectively using a multidisciplinary team-based approach. Postoperative complication rate and the transitions of pulmonary function in CHPR were compared with historical data of conventional preoperative pulmonary rehabilitation (CVPR conducted since June 2006. The study population was limited to patients who underwent standard lobectomy. RESULTS: Postoperative complication rate in the CVPR (n = 29 and CHPR (n = 21 were 48.3% and 28.6% (p = 0.2428, respectively. Those in patients with Charlson Comorbidity Index scores ≥2 were 68.8% (n = 16 and 27.3% (n = 11, respectively (p = 0.0341 and those in patients with preoperative risk score in Estimation of Physiologic Ability and Surgical Stress scores >0.3 were 57.9% (n = 19 and 21.4% (n = 14, respectively (p = 0.0362. Vital capacities of pre- and post intervention before surgery in the CHPR group were 2.63±0.65 L and 2.75±0.63 L (p = 0.0043, respectively; however, their transition in the CVPR group was not statistically significant (p = 0.6815. Forced expiratory volumes in one second of pre- and post intervention before surgery in the CHPR group were 1.73±0.46 L and 1.87±0.46 L (p = 0.0012, respectively; however, their transition in the CVPR group was not statistically significant (p = 0.6424. CONCLUSIONS: CHPR appeared to be a beneficial and effective short-term preoperative rehabilitation protocol, especially in patients with poor preoperative conditions.

  10. Multidisciplinary team-based approach for comprehensive preoperative pulmonary rehabilitation including intensive nutritional support for lung cancer patients.

    Science.gov (United States)

    Harada, Hiroaki; Yamashita, Yoshinori; Misumi, Keizo; Tsubokawa, Norifumi; Nakao, Junichi; Matsutani, Junko; Yamasaki, Miyako; Ohkawachi, Tomomi; Taniyama, Kiyomi

    2013-01-01

    To decrease the risk of postoperative complication, improving general and pulmonary conditioning preoperatively should be considered essential for patients scheduled to undergo lung surgery. The aim of this study is to develop a short-term beneficial program of preoperative pulmonary rehabilitation for lung cancer patients. From June 2009, comprehensive preoperative pulmonary rehabilitation (CHPR) including intensive nutritional support was performed prospectively using a multidisciplinary team-based approach. Postoperative complication rate and the transitions of pulmonary function in CHPR were compared with historical data of conventional preoperative pulmonary rehabilitation (CVPR) conducted since June 2006. The study population was limited to patients who underwent standard lobectomy. Postoperative complication rate in the CVPR (n = 29) and CHPR (n = 21) were 48.3% and 28.6% (p = 0.2428), respectively. Those in patients with Charlson Comorbidity Index scores ≥2 were 68.8% (n = 16) and 27.3% (n = 11), respectively (p = 0.0341) and those in patients with preoperative risk score in Estimation of Physiologic Ability and Surgical Stress scores >0.3 were 57.9% (n = 19) and 21.4% (n = 14), respectively (p = 0.0362). Vital capacities of pre- and post intervention before surgery in the CHPR group were 2.63±0.65 L and 2.75±0.63 L (p = 0.0043), respectively; however, their transition in the CVPR group was not statistically significant (p = 0.6815). Forced expiratory volumes in one second of pre- and post intervention before surgery in the CHPR group were 1.73±0.46 L and 1.87±0.46 L (p = 0.0012), respectively; however, their transition in the CVPR group was not statistically significant (p = 0.6424). CHPR appeared to be a beneficial and effective short-term preoperative rehabilitation protocol, especially in patients with poor preoperative conditions.

  11. Association study of IL10, IL1beta, and IL1RN and schizophrenia using tag SNPs from a comprehensive database: suggestive association with rs16944 at IL1beta.

    Science.gov (United States)

    Shirts, Brian H; Wood, Joel; Yolken, Robert H; Nimgaonkar, Vishwajit L

    2006-12-01

    Genetic association studies of several candidate cytokine genes have been motivated by evidence of immune dysfunction among patients with schizophrenia. Intriguing but inconsistent associations have been reported with polymorphisms of three positional candidate genes, namely IL1beta, IL1RN, and IL10. We used comprehensive sequencing data from the Seattle SNPs database to select tag SNPs that represent all common polymorphisms in the Caucasian population at these loci. Associations with 28 tag SNPs were evaluated in 478 cases and 501 unscreened control individuals, while accounting for population sub-structure using the genomic control method. The samples were also stratified by gender, diagnostic category, and exposure to infectious agents. Significant association was not detected after correcting for multiple comparisons. However, meta-analysis of our data combined with previously published association studies of rs16944 (IL1beta -511) suggests that the C allele confers modest risk for schizophrenia among individuals reporting Caucasian ancestry, but not Asians (Caucasians, n=819 cases, 1292 controls; p=0.0013, OR=1.24, 95% CI 1.09, 1.41).

  12. Incidence of and survival after subsequent cancers in carriers of pathogenic MMR variants with previous cancer : a report from the prospective Lynch syndrome database

    NARCIS (Netherlands)

    Møller, Pål; Seppälä, Toni; Bernstein, Inge; Holinski-Feder, Elke; Sala, Paola; Evans, D Gareth; Lindblom, Annika; Macrae, Finlay; Blanco, Ignacio; Sijmons, Rolf; Jeffries, Jacqueline; Vasen, Hans; Burn, John; Nakken, Sigve; Hovig, Eivind; Rødland, Einar Andreas; Tharmaratnam, Kukatharmini; de Vos Tot Nederveen Cappel, Wouter H; Hill, James; Wijnen, Juul; Jenkins, Mark; Green, Kate; Lalloo, Fiona; Sunde, Lone; Mints, Miriam; Bertario, Lucio; Pineda, Marta; Navarro, Matilde; Morak, Monika; Renkonen-Sinisalo, Laura; Frayling, Ian M; Plazzer, John-Paul; Pylvanainen, Kirsi; Genuardi, Maurizio; Mecklin, Jukka-Pekka; Möslein, Gabriela; Sampson, Julian R; Capella, Gabriel

    2016-01-01

    Objective Today most patients with Lynch syndrome (LS) survive their first cancer. There is limited information on the incidences and outcome of subsequent cancers. The present study addresses three questions: (i) what is the cumulative incidence of a subsequent cancer; (ii) in which organs do

  13. Measurement of the Inter-Rater Reliability Rate Is Mandatory for Improving the Quality of a Medical Database: Experience with the Paulista Lung Cancer Registry.

    Science.gov (United States)

    Lauricella, Leticia L; Costa, Priscila B; Salati, Michele; Pego-Fernandes, Paulo M; Terra, Ricardo M

    2018-06-01

    Database quality measurement should be considered a mandatory step to ensure an adequate level of confidence in data used for research and quality improvement. Several metrics have been described in the literature, but no standardized approach has been established. We aimed to describe a methodological approach applied to measure the quality and inter-rater reliability of a regional multicentric thoracic surgical database (Paulista Lung Cancer Registry). Data from the first 3 years of the Paulista Lung Cancer Registry underwent an audit process with 3 metrics: completeness, consistency, and inter-rater reliability. The first 2 methods were applied to the whole data set, and the last method was calculated using 100 cases randomized for direct auditing. Inter-rater reliability was evaluated using percentage of agreement between the data collector and auditor and through calculation of Cohen's κ and intraclass correlation. The overall completeness per section ranged from 0.88 to 1.00, and the overall consistency was 0.96. Inter-rater reliability showed many variables with high disagreement (>10%). For numerical variables, intraclass correlation was a better metric than inter-rater reliability. Cohen's κ showed that most variables had moderate to substantial agreement. The methodological approach applied to the Paulista Lung Cancer Registry showed that completeness and consistency metrics did not sufficiently reflect the real quality status of a database. The inter-rater reliability associated with κ and intraclass correlation was a better quality metric than completeness and consistency metrics because it could determine the reliability of specific variables used in research or benchmark reports. This report can be a paradigm for future studies of data quality measurement. Copyright © 2018 American College of Surgeons. Published by Elsevier Inc. All rights reserved.

  14. Reducing Disparities in Cancer Screening and Prevention through Community-Based Participatory Research Partnerships with Local Libraries: A Comprehensive Dynamic Trial.

    Science.gov (United States)

    Rapkin, Bruce D; Weiss, Elisa; Lounsbury, David; Michel, Tamara; Gordon, Alexis; Erb-Downward, Jennifer; Sabino-Laughlin, Eilleen; Carpenter, Alison; Schwartz, Carolyn E; Bulone, Linda; Kemeny, Margaret

    2017-09-01

    Reduction of cancer-related disparities requires strategies that link medically underserved communities to preventive care. In this community-based participatory research project, a public library system brought together stakeholders to plan and undertake programs to address cancer screening and risk behavior. This study was implemented over 48 months in 20 large urban neighborhoods, selected to reach diverse communities disconnected from care. In each neighborhood, Cancer Action Councils were organized to conduct a comprehensive dynamic trial, an iterative process of program planning, implementation and evaluation. This process was phased into neighborhoods in random, stepped-wedge sequence. Population-level outcomes included self-reported screening adherence and smoking cessation, based on street intercept interviews. Event-history regressions (n = 9374) demonstrated that adherence outcomes were associated with program implementation, as were mediators such as awareness of screening programs and cancer information seeking. Findings varied by ethnicity, and were strongest among respondents born outside the U.S. or least engaged in care. This intervention impacted health behavior in diverse, underserved and vulnerable neighborhoods. It has been sustained as a routine library system program for several years after conclusion of grant support. In sum, participatory research with the public library system offers a flexible, scalable approach to reduce cancer health disparities. © Society for Community Research and Action 2017.

  15. Long-term effect of the self-management comprehensive coping strategy program on quality of life in patients with breast cancer treated with high-dose chemotherapy.

    Science.gov (United States)

    Gaston-Johansson, Fannie; Fall-Dickson, Jane M; Nanda, Joy P; Sarenmalm, Elisabeth Kenne; Browall, Maria; Goldstein, Nancy

    2013-03-01

    This study aims to examine the effectiveness of a self-management multimodal comprehensive coping strategy program (CCSP) on quality of life (QOL) among breast cancer patients 1 year after treatment. Patients (n = 110) with stage II, III, or IV breast cancer scheduled to receive high dose chemotherapy and autologous hematopoietic stem cell transplantation were randomized to either CCSP treatment or control group. The CCSP intervention was taught 2 week before hospital admission with reinforcement at specified times during treatment and 3 months after discharge. The CCSP components included educational information, cognitive restructuring, coping skills enhancement, and relaxation with guided imagery. Instruments administered at baseline included the following: Quality of Life Index-Cancer Version (QOLI-CV), State-Trait Anxiety Inventory, Beck Depression Inventory, and Coping Strategies Questionnaire. At 1-year follow-up, patients (n = 73) completed and returned the follow-up QOLI-CV. Patients were mainly ≥ 40 years of age, married, Caucasian, and diagnosed with advanced breast cancer. A model measuring effectiveness of CCSP on QOL (total and subscale) at 1-year follow-up showed that the CCSP group (n = 38) had significant improvement in overall QOL (p psychological/spiritual well-being (p psychological (51%) and sleep problems (60%). The CCSP improved QOL for patients at 1-year follow-up. Patients overwhelmingly reported that CCSP was beneficial. The CCSP as an effective coping intervention has potential as a self-management program for breast cancer survivors. Copyright © 2012 John Wiley & Sons, Ltd.

  16. The REDUCE metagram: a comprehensive prediction tool for determining the utility of dutasteride chemoprevention in men at risk for prostate cancer

    Directory of Open Access Journals (Sweden)

    Carvell eNguyen

    2012-10-01

    Full Text Available Introduction: 5-alpha reductase inhibitors can reduce the risk of prostate cancer but can be associated with significant side effects. A library of nomograms which predict the risk of clinical endpoints relevant to dutasteride treatment may help determine if chemoprevention is suited to the individual patient. Methods: Data from the REDUCE trial was used to identify predictive factors for nine endpoints relevant to dutasteride treatment. Using the treatment and placebo groups from the biopsy cohort, Cox proportional hazards and competing risks regression models were used to build 18 nomograms, whose predictive ability was measured by concordance index and calibration plots. Results: A total of 18 nomograms assessing the risks of cancer, high-grade cancer, high grade prostatic intraepithelial neoplasia (HGPIN, atypical small acinar proliferation (ASAP, erectile dysfunction (ED, acute urinary retention (AUR, gynecomastia, urinary tract infection (UTI and BPH-related surgery either on or off dutasteride were created. The nomograms for cancer, high grade cancer, ED, AUR, and BPH-related surgery demonstrated good discrimination and calibration while those for gynecomastia, UTI, HGPIN, and ASAP predicted no better than random chance. Conclusions: To aid patients in determining whether the benefits of dutasteride use outweigh the risks, we have developed a comprehensive metagram that can generate individualized risks of 9 outcomes relevant to men considering chemoprevention. Better models based on more predictive markers are needed for some of the endpoints but the current metagram demonstrates potential as a tool for patient counseling and decision making that is accessible, intuitive, and clinically relevant.

  17. NOAA and MMS Marine Minerals Geochemical Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Marine Minerals Geochemical Database was created by NGDC as a part of a project to construct a comprehensive computerized bibliography and geochemical database...

  18. Post-treatment surveillance testing of patients with colorectal cancer and the association with survival: protocol for a retrospective cohort study of the Surveillance, Epidemiology, and End Results (SEER)-Medicare database.

    Science.gov (United States)

    Hines, Robert B; Jiban, Md Jibanul Haque; Choudhury, Kanak; Loerzel, Victoria; Specogna, Adrian V; Troy, Steven P; Zhang, Shunpu

    2018-04-28

    Although the colorectal cancer (CRC) mortality rate has significantly improved over the past several decades, many patients will have a recurrence following curative treatment. Despite this high risk of recurrence, adherence to CRC surveillance testing guidelines is poor which increases cancer-related morbidity and potentially, mortality. Several randomised controlled trials (RCTs) with varying surveillance strategies have yielded conflicting evidence regarding the survival benefit associated with surveillance testing. However, due to differences in study protocols and limitations of sample size and length of follow-up, the RCT may not be the best study design to evaluate this relationship. An observational comparative effectiveness research study can overcome the sample size/follow-up limitations of RCT designs while assessing real-world variability in receipt of surveillance testing to provide much needed evidence on this important clinical issue. The gap in knowledge that this study will address concerns whether adherence to National Comprehensive Cancer Network CRC surveillance guidelines improves survival. Patients with colon and rectal cancer aged 66-84 years, who have been diagnosed between 2002 and 2008 and have been included in the Surveillance, Epidemiology, and End Results-Medicare database, are eligible for this retrospective cohort study. To minimise bias, patients had to survive at least 12 months following the completion of treatment. Adherence to surveillance testing up to 5 years post-treatment will be assessed in each year of follow-up and overall. Binomial regression will be used to assess the association between patients' characteristics and adherence. Survival analysis will be conducted to assess the association between adherence and 5-year survival. This study was approved by the National Cancer Institute and the Institutional Review Board of the University of Central Florida. The results of this study will be disseminated by publishing in

  19. Relational databases

    CERN Document Server

    Bell, D A

    1986-01-01

    Relational Databases explores the major advances in relational databases and provides a balanced analysis of the state of the art in relational databases. Topics covered include capture and analysis of data placement requirements; distributed relational database systems; data dependency manipulation in database schemata; and relational database support for computer graphics and computer aided design. This book is divided into three sections and begins with an overview of the theory and practice of distributed systems, using the example of INGRES from Relational Technology as illustration. The

  20. CERCLIS (Superfund) ASCII Text Format - CPAD Database

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Comprehensive Environmental Response, Compensation and Liability Information System (CERCLIS) (Superfund) Public Access Database (CPAD) contains a selected set...

  1. Current Molecular Targeted Therapy in Advanced Gastric Cancer: A Comprehensive Review of Therapeutic Mechanism, Clinical Trials, and Practical Application

    Directory of Open Access Journals (Sweden)

    Kaichun Li

    2016-01-01

    Full Text Available Despite the great progress in the treatment of gastric cancer, it is still the third leading cause of cancer death worldwide. Patients often miss the opportunity for a surgical cure, because the cancer has already developed into advanced cancer when identified. Compared to best supportive care, chemotherapy can improve quality of life and prolong survival time, but the overall survival is often short. Due to the molecular study of gastric cancer, new molecular targeted drugs have entered the clinical use. Trastuzumab, an antibody targeting human epidermal growth factor receptor 2 (HER2, can significantly improve survival in advanced gastric cancer patients with HER2 overexpression. Second-line treatment of advanced gastric cancer with ramucirumab, an antibody targeting VEGFR-2, alone or in combination with paclitaxel, has been proved to provide a beneficial effect. The VEGFR-2 tyrosine kinase inhibitor, apatinib, can improve the survival of advanced gastric cancer patients after second-line chemotherapy failure. Unfortunately, none of the EGFR targeting antibodies (cetuximab or panitumumab, VEGF targeting monoclonal antibodies (bevacizumab, mTOR inhibitor (everolimus, or HGF/MET pathway targeting drugs has a significant survival benefit. Many other clinical trials based on molecular markers are underway. This review will summarize targeted therapies for advanced gastric cancer.

  2. In vitro anti-proliferative activity on colon cancer cell line (HT-29) of Thai medicinal plants selected from Thai/Lanna medicinal plant recipe database "MANOSROI III".

    Science.gov (United States)

    Manosroi, Aranya; Akazawa, Hiroyuki; Akihisa, Toshihiro; Jantrawut, Pensak; Kitdamrongtham, Worapong; Manosroi, Worapaka; Manosroi, Jiradej

    2015-02-23

    Thai/Lanna region has its own folklore wisdoms including the traditional medicinal plant recipes. Thai/Lanna medicinal plant recipe database "MANOSROI III" has been developed by Prof. Dr. Jiradej Manosroi. It consists of over 200,000 recipes for all diseases including cancer. To investigate the anti-proliferative and apoptotic activities on human colon cancer cell line (HT-29) as well as the cancer cell selectivity of the methanolic extracts (MEs) and fractions of the 23 selected plants from the "MANOSROI III" database. The 23 selected plants were extracted with methanol under reflux and evaluated for their anti-proliferative activity by sulforhodamine B assay. The 5 plants (Gloriosa superba, Caesalpinia sappan, Fibraurea tinctoria, Ventilago denticulata and Psophocarpus tetragonolobus) with potent anti-proliferative activity were fractionated by liquid-liquid partition to give 4 fractions including each hexane (HF), methanol-water (MF), n-butanol (BF) and water (WF) fractions. They were tested for anti-proliferative activity and cancer cell selectivity. The ME and fractions of G. superba which showed potent anti-proliferative activity were further examined for morphological changes and apoptotic activities by acridine orange (AO)/ethidium bromide (EB) staining. The ME of G. superba root showed active with the highest anti-proliferative activity at 9.17 and 1.58 folds of cisplatin and doxorubicin, respectively. After liquid-liquid partition, HF of V. denticulata, MFs of F. tinctoria, V. denticulata and BF of P. tetragonolobus showed higher anti-proliferative activities than their MEs. The MF of G. superba indicated the highest anti-proliferative activity at 7.73 and 1.34 folds of cisplatin and doxorubicin, respectively, but only 0.86 fold of its ME. The ME and HF, MF and BF of G. superba and MF of F. tinctoria demonstrated high cancer cell selectivity. At 50 µg/ml, ME, HF, MF and BF of G. superba demonstrated higher apoptotic activities than the two standard drugs

  3. Prevalence of hypercalcemia of malignancy among pediatric cancer patients in the UK Clinical Practice Research Datalink database

    Directory of Open Access Journals (Sweden)

    Jick S

    2017-06-01

    Full Text Available Susan Jick,1 Lin Li,1 Victor M Gastanaga,2 Alexander Liede,2 Rohini K Hernandez2 1Boston Collaborative Drug Surveillance Program, Boston University School of Public Health, Lexington, MA, USA; 2Center for Observational Research, Amgen Inc., Thousand Oaks and South San Francisco, CA, USA Background: The reported proportion of cancer patients who experience hypercalcemia of malignancy (HCM is low, particularly in the pediatric population, ranging between <1% and 5%. HCM can be observed with any type of tumor in children and occurs most commonly with leukemia. While HCM is a potentially fatal condition, the prevalence of HCM is not well understood in pediatric cancer patients. Methods: Using the UK Clinical Practice Research Datalink, we identified pediatric cancer patients with recorded corrected serum calcium (CSC from 2003 through 2014. Hypercalcemic patients (CSC ≥10.8 mg/dL were classified into 4 CSC levels. We estimated the annual prevalence of HCM using Byar’s method. Results: Among 517 pediatric cancer patients, leukemia, lymphoma, and brain tumors were the most frequent cancer types. The prevalence of HCM overall (grade 1 or higher ranged from 0.24% to 0.81% between 2003 and 2014. There were too few cases to compare prevalence by type of cancer. Conclusion: We provide the first systematic analysis using a UK population-based data source to estimate the number of pediatric cancer patients affected with HCM by grade. Our findings showed that the prevalence of pediatric HCM was very low (0.24%–0.81% over the 12-year study period, which is consistent with previous study of adult cancer patients in the UK (0.20%–0.67%. Keywords: hypercalcemia, pediatric, cancer, prevalence, Clinical Practice Research Datalink

  4. Biofuel Database

    Science.gov (United States)

    Biofuel Database (Web, free access)   This database brings together structural, biological, and thermodynamic data for enzymes that are either in current use or are being considered for use in the production of biofuels.

  5. Community Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This excel spreadsheet is the result of merging at the port level of several of the in-house fisheries databases in combination with other demographic databases such...

  6. Variation in cancer surgical outcomes associated with physician and nurse staffing: a retrospective observational study using the Japanese Diagnosis Procedure Combination Database

    Directory of Open Access Journals (Sweden)

    Yasunaga Hideo

    2012-05-01

    Full Text Available Abstract Background Little is known about the effects of professional staffing on cancer surgical outcomes. The present study aimed to investigate the association between cancer surgical outcomes and physician/nurse staffing in relation to hospital volume. Methods We analyzed 131,394 patients undergoing lung lobectomy, esophagectomy, gastrectomy, colorectal surgery, hepatectomy or pancreatectomy for cancer between July and December, 2007–2008, using the Japanese Diagnosis Procedure Combination database linked to the Survey of Medical Institutions data. Physician-to-bed ratio (PBR and nurse-to-bed ratio (NBR were determined for each hospital. Hospital volume was categorized into low, medium and high for each of six cancer surgeries. Failure to rescue (FTR was defined as a proportion of inhospital deaths among those with postoperative complications. Multi-level logistic regression analysis was performed to examine the association between physician/nurse staffing and FTR, adjusting for patient characteristics and hospital volume. Results Overall inhospital mortality was 1.8%, postoperative complication rate was 15.2%, and FTR rate was 11.9%. After adjustment for hospital volume, FTR rate in the group with high PBR (≥19.7 physicians per 100 beds and high NBR (≥77.0 nurses per 100 beds was significantly lower than that in the group with low PBR ( Conclusions Well-staffed hospitals confer a benefit for cancer surgical patients regarding reduced FTR, irrespective of hospital volume. These results suggest that consolidation of surgical centers linked with migration of medical professionals may improve the quality of cancer surgical management.

  7. Database Administrator

    Science.gov (United States)

    Moore, Pam

    2010-01-01

    The Internet and electronic commerce (e-commerce) generate lots of data. Data must be stored, organized, and managed. Database administrators, or DBAs, work with database software to find ways to do this. They identify user needs, set up computer databases, and test systems. They ensure that systems perform as they should and add people to the…

  8. Prognostic value of platelet-to-lymphocyte ratio in pancreatic cancer: a comprehensive meta-analysis of 17 cohort studies.

    Science.gov (United States)

    Zhou, Yongping; Cheng, Sijin; Fathy, Abdel Hamid; Qian, Haixin; Zhao, Yongzhao

    2018-01-01

    Several studies were conducted to explore the prognostic value of platelet-to-lymphocyte ratio (PLR) in pancreatic cancer and have reported contradictory results. This study aims to summarize the prognostic role of PLR in pancreatic cancer. Embase, PubMed and Cochrane Library were completely searched. The cohort studies focusing on the prognostic role of PLR in pancreatic cancer were eligible. The overall survival (OS) and progression-free survival (PFS) were analyzed. Fifteen papers containing 17 cohort studies with pancreatic cancer were identified. The results showed patients that with low PLR might have longer OS when compared to the patients with high PLR (hazard ratio=1.28, 95% CI=1.17-1.40, P analysis model, ethnicity, sample size and cut-off value. Further analyses based on the adjusted potential confounders were conducted, including CA199, neutrophil-to-lymphocyte ratio, modified Glasgow Prognostic Score, albumin, C-reactive protein, Eastern Cooperative Oncology Group, stage, tumor size, nodal involvement, tumor differentiation, margin status, age and gender, which confirmed that low PLR was a protective factor in pancreatic cancer. In addition, low PLR was significantly associated with longer PFS when compared to high PLR in pancreatic cancer (hazard ratio=1.27, 95% CI=1.03-1.57, P =0.03; I 2 =33%). In conclusion, it was found that high PLR is an unfavorable predictor of OS and PFS in patients with pancreatic cancer, and PLR is a promising prognostic biomarker for pancreatic cancer.

  9. A comprehensive custom panel design for routine hereditary cancer testing: preserving control, improving diagnostics and revealing a complex variation landscape.

    Science.gov (United States)

    Castellanos, Elisabeth; Gel, Bernat; Rosas, Inma; Tornero, Eva; Santín, Sheila; Pluvinet, Raquel; Velasco, Juan; Sumoy, Lauro; Del Valle, Jesús; Perucho, Manuel; Blanco, Ignacio; Navarro, Matilde; Brunet, Joan; Pineda, Marta; Feliubadaló, Lidia; Capellá, Gabi; Lázaro, Conxi; Serra, Eduard

    2017-01-04

    We wanted to implement an NGS strategy to globally analyze hereditary cancer with diagnostic quality while retaining the same degree of understanding and control we had in pre-NGS strategies. To do this, we developed the I2HCP panel, a custom bait library covering 122 hereditary cancer genes. We improved bait design, tested different NGS platforms and created a clinically driven custom data analysis pipeline. The I2HCP panel was developed using a training set of hereditary colorectal cancer, hereditary breast and ovarian cancer and neurofibromatosis patients and reached an accuracy, analytical sensitivity and specificity greater than 99%, which was maintained in a validation set. I2HCP changed our diagnostic approach, involving clinicians and a genetic diagnostics team from panel design to reporting. The new strategy improved diagnostic sensitivity, solved uncertain clinical diagnoses and identified mutations in new genes. We assessed the genetic variation in the complete set of hereditary cancer genes, revealing a complex variation landscape that coexists with the disease-causing mutation. We developed, validated and implemented a custom NGS-based strategy for hereditary cancer diagnostics that improved our previous workflows. Additionally, the existence of a rich genetic variation in hereditary cancer genes favors the use of this panel to investigate their role in cancer risk.

  10. A DGGE system for comprehensive mutation screening of BRCA1 and BRCA2 : Application in a Dutch cancer clinic setting

    NARCIS (Netherlands)

    van der Hout, Annemarie H.; van den Ouweland, AMW; van der Luijt, RB; Gille, HJP; Bodmer, D; Bruggenwirth, H; Mulder, IM; van der Vlies, P; Elfferich, P; Huisman, Maarten T.; ten Berge, Annelies M.; Kromosoeto, J; Jansen, RPM; van Zon, PHA; Vriesman, T; Arts, N; Lange, MBD; Oosterwijk, Jan C.; Meijers-Heijboer, H; Ausems, MGEM; Hoogerbrugge, N; Verhoef, S; Halley, DJJ; Vos, Yvonne J.; Hogervorst, F; Ligtenberg, M; Hofstra, Robert M.W.

    Rapid and reliable identification of deleterious changes in the breast cancer genes BRCA1 and BRCA2 has become one of the major issues in most DNA services laboratories. To rapidly detect all possible changes within the coding and splice site determining sequences of the breast cancer genes, we

  11. Cannabis use among patients at a comprehensive cancer center in a state with legalized medicinal and recreational use.

    Science.gov (United States)

    Pergam, Steven A; Woodfield, Maresa C; Lee, Christine M; Cheng, Guang-Shing; Baker, Kelsey K; Marquis, Sara R; Fann, Jesse R

    2017-11-15

    Cannabis is purported to alleviate symptoms related to cancer treatment, although the patterns of use among cancer patients are not well known. This study was designed to determine the prevalence and methods of use among cancer patients, the perceived benefits, and the sources of information in a state with legalized cannabis. A cross-sectional, anonymous survey of adult cancer patients was performed at a National Cancer Institute-designated cancer center in Washington State. Random urine samples for tetrahydrocannabinol provided survey validation. Nine hundred twenty-six of 2737 eligible patients (34%) completed the survey, and the median age was 58 years (interquartile range [IQR], 46-66 years). Most had a strong interest in learning about cannabis during treatment (6 on a 1-10 scale; IQR, 3-10) and wanted information from cancer providers (677 of 911 [74%]). Previous use was common (607 of 926 [66%]); 24% (222 of 926) used cannabis in the last year, and 21% (192 of 926) used cannabis in the last month. Random urine samples found similar percentages of users who reported weekly use (27 of 193 [14%] vs 164 of 926 [18%]). Active users inhaled (153 of 220 [70%]) or consumed edibles (154 of 220 [70%]); 89 (40%) used both modalities. Cannabis was used primarily for physical (165 of 219 [75%]) and neuropsychiatric symptoms (139 of 219 [63%]). Legalization significantly increased the likelihood of use in more than half of the respondents. This study of cancer patients in a state with legalized cannabis found high rates of active use across broad subgroups, and legalization was reported to be important in patients' decision to use. Cancer patients desire but are not receiving information about cannabis use during their treatment from oncology providers. Cancer 2017;123:4488-97. © 2017 The Authors. Cancer published by Wiley Periodicals, Inc. on behalf of American Cancer Society. This is an open access article under the terms of the Creative Commons Attribution

  12. Cross-cultural adaptation and psychometric assessment of the Chinese version of the comprehensive needs assessment tool for cancer caregivers (CNAT-C).

    Science.gov (United States)

    Zhang, Yin-Ping; Zhao, Xin-Shuang; Zhang, Bei; Zhang, Lu-Lu; Ni, Chun-Ping; Hao, Nan; Shi, Chang-Bei; Porr, Caroline

    2015-07-01

    The comprehensive needs assessment tool for cancer caregivers (CNAT-C) is a systematic and comprehensive needs assessment tool for the family caregivers. The purpose of this project was twofold: (1) to adapt the CNAT-C to Mainland China's cultural context and (2) to evaluate the psychometric properties of the newly adapted Chinese CNAT-C. Cross-cultural adaptation of the original CNAT-C was performed according to published guidelines. A pilot study was conducted in Mainland China with 30 Chinese family cancer caregivers. A subsequent validation study was conducted with 205 Chinese cancer caregivers from Mainland China. Construct validity was determined through exploratory and confirmatory factor analyses. Reliability was determined using internal consistency and test-retest reliability. The split-half coefficient for the overall Chinese CNAT-C scale was 0.77. Principal component analysis resulted in an eight-factor structure explaining 68.11 % of the total variance. The comparative fit index (CFI) was 0.91 from the modified model confirmatory factor analysis. The Chi-square divided by degrees of freedom was 1.98, and the root mean squared error of approximation (RMSEA) was 0.079. In relation to the known-group validation, significant differences were found in the Chinese CNAT-C scale according to various caregiver characteristics. Internal consistency was high for the Chinese CNAT-C reaching a Cronbach α value of 0.94. Test-retest reliability was 0.85. The newly adapted Chinese CNAT-C scale possesses adequate validity, test-retest reliability, and internal consistency and therefore may be used to ascertain holistic health and support needs of cancer patients' family caregivers in Mainland China.

  13. Serum miRNAs as Biomarkers for the Diagnosis and Prognosis of Thyroid Cancer: A Comprehensive Review of the Literature.

    Science.gov (United States)

    Mahmoudian-Sani, Mohammad-Reza; Mehri-Ghahfarrokhi, Ameneh; Asadi-Samani, Majid; Mobini, Gholam-Reza

    2017-07-01

    Thyroid cancer is the most common endocrine malignancy and accounts for 1% of cancers. In recent years, there has been much interest in the feasibility of using miRNAs or miRNA panels as biomarkers for the diagnosis of thyroid cancer. miRNAs are noncoding RNAs with 21-23 nucleotides that are highly conserved during evolution. They have been proposed as regulators of gene expression, apoptosis, cancer, and cell growth and differentiation. The Directory of Open Access Journals (DOAJ), Google Scholar, PubMed (NLM), LISTA (EBSCO), and Web of Science were searched. The serum level of miRNAs (miRNA-375, 34a, 145b, 221, 222, 155, Let-7, 181b) can be used as molecular markers for the diagnosis and prognosis of thyroid cancer in the serum samples of patients with thyroid glands. Given that most common methods for the screening of thyroid cancer cannot detect the disease in its early stages, identifying miRNAs that are released in the bloodstream during the gradual progression of the disease is considered a key method in the early diagnosis of thyroid cancers.

  14. Comprehensive review of genetic association studies and meta-analyses on miRNA polymorphisms and cancer risk.

    Directory of Open Access Journals (Sweden)

    Kshitij Srivastava

    Full Text Available MicroRNAs (miRNAs are small RNA molecules that regulate the expression of corresponding messenger RNAs (mRNAs. Variations in the level of expression of distinct miRNAs have been observed in the genesis, progression and prognosis of multiple human malignancies. The present study was aimed to investigate the association between four highly studied miRNA polymorphisms (mir-146a rs2910164, mir-196a2 rs11614913, mir-149 rs2292832 and mir-499 rs3746444 and cancer risk by using a two-sided meta-analytic approach.An updated meta-analysis based on 53 independent case-control studies consisting of 27573 cancer cases and 34791 controls was performed. Odds ratio (OR and 95% confidence interval (95% CI were used to investigate the strength of the association.Overall, the pooled analysis showed that mir-196a2 rs11614913 was associated with a decreased cancer risk (OR = 0.846, P = 0.004, TT vs. CC while other miRNA SNPs showed no association with overall cancer risk. Subgroup analyses based on type of cancer and ethnicity were also performed, and results indicated that there was a strong association between miR-146a rs2910164 and overall cancer risk in Caucasian population under recessive model (OR = 1.274, 95%CI = 1.096-1.481, P = 0.002. Stratified analysis by cancer type also associated mir-196a2 rs11614913 with lung and colorectal cancer at allelic and genotypic level.The present meta-analysis suggests an important role of mir-196a2 rs11614913 polymorphism with overall cancer risk especially in Asian population. Further studies with large sample size are needed to evaluate and confirm this association.

  15. Comprehensive Evaluation of the Role of EZH2 in the Growth, Invasion, and Aggression of a Panel of Prostate Cancer Cell Lines

    Science.gov (United States)

    Karanikolas, Breanne D.W.; Figueiredo, Marxa L.; Wu, Lily

    2010-01-01

    Background Although most prostate cancers respond well to initial treatments, a fraction of prostate cancers are more aggressive and will recur and metastasize. At that point, there are few treatment options available. Significant efforts have been made to identify biomarkers that will identify these more aggressive cancers to tailor a more vigorous treatment in order to improve outcome. Polycomb Group protein Enhancer of Zeste 2 (EZH2) was found to be overexpressed in metastatic prostate tumors, and is considered an excellent candidate for such a biomarker. Scattered studies have found that EZH2 overexpression causes neoplastic transformation, invasion, and growth of prostate cells. However, these studies utilized different systems and cell lines, and so are difficult to correlate with one another. Methods In this study, a comprehensive evaluation of the phenotypic effects of EZH2 in a panel of five prostate cancer cell lines was performed. By using multiple cell lines, and examining overexpression and knockdown of EZH2 concurrently, a broad view of EZH2's role in prostate cancer was achieved. Results Overexpression of EZH2 led to more aggressive behaviors in all prostate cell lines tested. In contrast, downregulation of EZH2 reduced invasion and tumorigenicity of androgen-independent cell lines CWR22Rv1, PC3, and DU145, but not of androgen-dependent cell lines LAPC4 and LNCaP. Conclusions Findings from this study suggest androgen-independent prostate tumors are more dependent on EZH2 expression than androgen-dependent tumors. Our observations provide an explanation for the strong correlation between EZH2 overexpression and advanced stage, aggressive prostate cancers. PMID:20087897

  16. Cannabis use among patients at a comprehensive cancer center in a state with legalized medicinal and recreational use

    Science.gov (United States)

    Woodfield, Maresa C.; Lee, Christine M.; Cheng, Guang‐Shing; Baker, Kelsey K.; Marquis, Sara R.; Fann, Jesse R.

    2017-01-01

    BACKGROUND Cannabis is purported to alleviate symptoms related to cancer treatment, although the patterns of use among cancer patients are not well known. This study was designed to determine the prevalence and methods of use among cancer patients, the perceived benefits, and the sources of information in a state with legalized cannabis. METHODS A cross‐sectional, anonymous survey of adult cancer patients was performed at a National Cancer Institute–designated cancer center in Washington State. Random urine samples for tetrahydrocannabinol provided survey validation. RESULTS Nine hundred twenty‐six of 2737 eligible patients (34%) completed the survey, and the median age was 58 years (interquartile range [IQR], 46‐66 years). Most had a strong interest in learning about cannabis during treatment (6 on a 1‐10 scale; IQR, 3‐10) and wanted information from cancer providers (677 of 911 [74%]). Previous use was common (607 of 926 [66%]); 24% (222 of 926) used cannabis in the last year, and 21% (192 of 926) used cannabis in the last month. Random urine samples found similar percentages of users who reported weekly use (27 of 193 [14%] vs 164 of 926 [18%]). Active users inhaled (153 of 220 [70%]) or consumed edibles (154 of 220 [70%]); 89 (40%) used both modalities. Cannabis was used primarily for physical (165 of 219 [75%]) and neuropsychiatric symptoms (139 of 219 [63%]). Legalization significantly increased the likelihood of use in more than half of the respondents. CONCLUSIONS This study of cancer patients in a state with legalized cannabis found high rates of active use across broad subgroups, and legalization was reported to be important in patients' decision to use. Cancer patients desire but are not receiving information about cannabis use during their treatment from oncology providers. Cancer 2017;123:4488‐97. © 2017 The Authors. Cancer published by Wiley Periodicals, Inc. on behalf of American Cancer Society. This is an open access article under the

  17. Quality of Care for Lung Cancer in Taiwan: A Pattern of Care Based on Core Measures in the Taiwan Cancer Database Registry

    Directory of Open Access Journals (Sweden)

    Chun-Ru Chien

    2008-08-01

    Conclusion: It is very likely that significant variation in QOC for lung cancer in Taiwan exists among different types but not locations of hospitals, at least in the diagnostic domain. The introduction of internal benchmarking (TCDB and core measures was associated with some changes, at least in some diagnostic domains, which may lead to improvement in QOC for lung cancer in Taiwan.

  18. The Effects of a Comprehensive Coping Strategy on Clinical Outcomes in Breast Cancer Bone Marrow Transplant Patients and Primary Caregiver

    National Research Council Canada - National Science Library

    Gaston-Johannson, Fannie

    1997-01-01

    .... Specifically, the purpose of this study was to compare descriptions of pain, psychological distress, fatigue, and perceived health status and burden of care in breast cancer patients who received...

  19. Potent anti-proliferative effects against oral and cervical cancers of Thai medicinal plants selected from the Thai/Lanna medicinal plant recipe database "MANOSROI III".

    Science.gov (United States)

    Manosroi, Aranya; Akazawa, Hiroyuki; Pattamapun, Kassara; Kitdamrongtham, Worapong; Akihisa, Toshihiro; Manosroi, Worapaka; Manosroi, Jiradej

    2015-07-01

    Thai/Lanna medicinal plant recipes have been used for the treatment of several diseases including oral and cervical cancers. To investigate anti-proliferative activity on human cervical (HeLa) and oral (KB) cancer cell lines of medicinal plants selected from Thai/Lanna medicinal plant recipe database "MANOSROI III". Twenty-three methanolic plant crude extracts were tested for phytochemicals and anti-proliferative activity on HeLa and KB cell lines for 24 h by the sulforhodamine B (SRB) assay at the doses of 1 × 10(1)-1 × 10(-6 )mg/ml. The nine extracts with the concentrations giving 50% growth inhibition (GI50) lower than 100 µg/ml were further semi-purified by liquid/liquid partition in order to evaluate and enhance the anti-proliferative potency. All extracts contained steroids/triterpenoids, but not xanthones. The methanolic extracts of Gloriosa superba L. (Colchinaceae) root and Albizia chinensis (Osbeck) Merr. (Leguminosae-Mimosoideae) wood gave the highest anti-proliferative activity on HeLa and KB cell lines with the GI50 values of 0.91 (6.0- and 0.31-fold of cisplatin and doxorubicin) and 0.16 µg/ml (28.78- and 82.29-fold of cisplatin and doxorubicin), respectively. Hexane and methanol-water fractions of G. superba exhibited the highest anti-proliferative activity on HeLa and KB cell lines with the GI50 values of 0.15 (37- and 1.9-fold of cisplatin and doxorubicin) and 0.058 µg/ml (77.45- and 221.46-fold of cisplatin and doxorubicin), respectively. This study has demonstrated the potential of plants selected from MANOSROI III database especially G. superba and A. chinensis for further development as anti-oral and cervical cancer agents.

  20. Comprehensive characterization of lncRNA-mRNA related ceRNA network across 12 major cancers

    Science.gov (United States)

    Feng, Li; Li, Feng; Sun, Zeguo; Wu, Tan; Shi, Xinrui; Li, Jing; Li, Xia

    2016-01-01

    Recent studies indicate that long noncoding RNAs (lncRNAs) can act as competing endogenous RNAs (ceRNAs) to indirectly regulate mRNAs through shared microRNAs, which represents a novel layer of RNA crosstalk and plays critical roles in the development of tumor. However, the global regulation landscape and characterization of these lncRNA related ceRNA crosstalk in cancers is still largely unknown. Here, we systematically characterized the lncRNA related ceRNA interactions across 12 major cancers and the normal physiological states by integrating multidimensional molecule profiles of more than 5000 samples. Our study suggest the large difference of ceRNA regulation between normal and tumor states and the higher similarity across similar tissue origin of tumors. The ceRNA related molecules have more conserved features in tumor networks and they play critical roles in both the normal and tumorigenesis processes. Besides, lncRNAs in the pan-cancer ceRNA network may be potential biomarkers of tumor. By exploring hub lncRNAs, we found that these conserved key lncRNAs dominate variable tumor hallmark processes across pan-cancers. Network dynamic analysis highlights the critical roles of ceRNA regulation in tumorigenesis. By analyzing conserved ceRNA interactions, we found that miRNA mediate ceRNA regulation showed different patterns across pan-cancer; while analyzing the cancer specific ceRNA interactions reveal that lncRNAs synergistically regulated tumor driver genes of cancer hallmarks. Finally, we found that ceRNA modules have the potential to predict patient survival. Overall, our study systematically dissected the lncRNA related ceRNA networks in pan-cancer that shed new light on understanding the molecular mechanism of tumorigenesis. PMID:27580177

  1. The need for a rapid and comprehensive adoption of the revised European standard population in cancer incidence comparisons.

    Science.gov (United States)

    Crocetti, Emanuele; Dyba, Tadek; Martos, Carmen; Randi, Giorgia; Rooney, Roisin; Bettio, Manola

    2017-09-01

    As cancer incidence varies according to age, it is important to rule out differences in age structures in any comparison. A common way of adjusting for these differences is using direct age standardization, which applies age-specific weights from a standard population. Eurostat has recently introduced a revised European standard population (RESP). The effect of using the new standard, in comparison with that introduced in 1976 [European standard population (ESP)], is evaluated. Cancer incidence data for prostate and testis cancer for Denmark, Finland, Sweden, Norway, and Iceland from the NORDCAN web site, and for Ireland and Italy-Genoa from Cancer Incidence in five Continents-X, were analyzed. Incidence rates were directly age standardized using ESP and RESP. The RESP conferred greater weight to adults and the elderly than the ESP. For prostate cancer, age-standardized rates computed with RESP are consistently higher by between 50 and 60% than those computed with ESP. However, the use of RESP, instead of ESP, has little impact on the pattern of time trends, the relative ranking of countries, the values of relative risks, or the percentage differences between age-standardized rates. For testis cancer, RESP and ESP provide very similar results because this cancer is more common in young men. Both ESP and RESP are in circulation. It is, therefore, important that European cancer registries reach consensus on a single standard to use to avoid erroneous comparisons of data computed with different standards. Given that Eurostat recently introduced RESP and is using this standard for data collected from the European Union Member States, it would make sense to rally behind RESP.

  2. Surgical-site infections and postoperative complications: agreement between the Danish Gynecological Cancer Database and a randomized clinical trial

    DEFF Research Database (Denmark)

    Antonsen, Sofie L; Meyhoff, Christian Sylvest; Lundvall, Lene

    2011-01-01

    between November 2006 and October 2008 and data from the DGCD. METHODS: Outcomes within 30 days from the trial and the database were compared and levels of agreements were calculated with kappa-statistics. MAIN OUTCOME MEASURES: Primary outcome was surgical-site infection. Other outcomes included re-operation...... registered in the PROXI trial, but not in the DGCD. Agreements between secondary outcomes were very varying (kappa-value 0.77 for re-operation, 0.37 for urinary tract infections, 0.19 for sepsis and 0.18 for pneumonia). CONCLUSIONS: The randomized trial reported significantly more surgical-site infections......OBJECTIVE: Surgical-site infections are serious complications and thorough follow-up is important for accurate surveillance. We aimed to compare the frequency of complications recorded in a clinical quality database with those noted in a randomized clinical trial with follow-up visits. DESIGN...

  3. Pre-operative assessment of cancer in the elderly (PACE) : A comprehensive assessment of underlying characteristics of elderly cancer patients prior to elective surgery

    NARCIS (Netherlands)

    Pope, D.; Ramesh, H.; Gennari, R.; Corsini, G.; Maffezzini, M.; Hoekstra, H. J.; Mobarak, D.; Sunouchi, K.; Stotter, A.; West, C.; Audisio, R. A.

    2006-01-01

    Background: Cancer is a disease that particularly affects the elderly and, although surgery is the first treatment choice, many elderly cancer patients do not receive standard surgery because they are considered unfit for treatment due to an inaccurate estimation of operative risk. Pre-operative

  4. Is admittance to specialised palliative care among cancer patients related to sex, age and cancer diagnosis? A nation-wide study from the Danish Palliative Care Database (DPD)

    DEFF Research Database (Denmark)

    Adsersen, Mathilde; Thygesen, Lau Caspar; Jensen, Anders Bonde

    2017-01-01

    /units. Patients with brain cancer were more often admitted to hospices, whereas patients with prostate cancer were more often admitted to hospital-based palliative care teams/units. CONCLUSION: It is unlikely that the variations in relation to sex, age and cancer diagnoses can be fully explained by differences...... to investigate whether cancer patients' admittance to SPC in Denmark varied in relation to sex, age and diagnosis, and whether the patterns differed by type of institution (hospital-based palliative care team/unit, hospice, or both). METHODS: This was a register-based study of adult patients living in Denmark......BACKGROUND: Specialised palliative care (SPC) takes place in specialised services for patients with complex symptoms and problems. Little is known about what determines the admission of patients to SPC and whether there are differences in relation to institution type. The aims of the study were...

  5. The REDUCE metagram: a comprehensive prediction tool for determining the utility of dutasteride chemoprevention in men at risk for prostate cancer

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, Carvell T.; Isariyawongse, Brandon [Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic Foundation, Cleveland, OH (United States); Yu, Changhong; Kattan, Michael W., E-mail: kattanm@ccf.org [Department of Quantitative Health Sciences, Cleveland Clinic Foundation, Cleveland, OH (United States)

    2012-10-11

    Introduction: 5-alpha reductase inhibitors can reduce the risk of prostate cancer (PCa) but can be associated with significant side effects. A library of nomograms which predict the risk of clinical endpoints relevant to dutasteride treatment may help determine if chemoprevention is suited to the individual patient. Methods: Data from the REDUCE trial was used to identify predictive factors for 9 endpoints relevant to dutasteride treatment. Using the treatment and placebo groups from the biopsy cohort, Cox proportional hazards (PH) and competing risks regression (CRR) models were used to build 18 nomograms, whose predictive ability was measured by concordance index (CI) and calibration plots. Results: A total of 18 nomograms assessing the risks of cancer, high grade cancer, high grade prostatic intraepithelial neoplasia (HGPIN), atypical small acinar proliferation (ASAP), erectile dysfunction (ED), acute urinary retention (AUR), gynecomastia, urinary tract infection (UTI) and BPH-related surgery either on or off dutasteride were created. The nomograms for cancer, high grade cancer, ED, AUR, and BPH-related surgery demonstrated good discrimination and calibration while those for gynecomastia, UTI, HGPIN, and ASAP predicted no better than random chance. Conclusions: To aid patients in determining whether the benefits of dutasteride use outweigh the risks, we have developed a comprehensive metagram that can generate individualized risks of 9 outcomes relevant to men considering chemoprevention. Better models based on more predictive markers are needed for some of the endpoints but the current metagram demonstrates potential as a tool for patient counseling and decision-making that is accessible, intuitive, and clinically relevant.

  6. Comprehensive analysis of CpG island methylator phenotype (CIMP)-high, -low, and -negative colorectal cancers based on protein marker expression and molecular features.

    Science.gov (United States)

    Zlobec, Inti; Bihl, Michel; Foerster, Anja; Rufle, Alex; Lugli, Alessandro

    2011-11-01

    CpG island methylator phenotype (CIMP) is being investigated for its role in the molecular and prognostic classification of colorectal cancer patients but is also emerging as a factor with the potential to influence clinical decision-making. We report a comprehensive analysis of clinico-pathological and molecular features (KRAS, BRAF and microsatellite instability, MSI) as well as of selected tumour- and host-related protein markers characterizing CIMP-high (CIMP-H), -low, and -negative colorectal cancers. Immunohistochemical analysis for 48 protein markers and molecular analysis of CIMP (CIMP-H: ≥ 4/5 methylated genes), MSI (MSI-H: ≥ 2 instable genes), KRAS, and BRAF were performed on 337 colorectal cancers. Simple and multiple regression analysis and receiver operating characteristic (ROC) curve analysis were performed. CIMP-H was found in 24 cases (7.1%) and linked (p CIMP-low or -negative cases. Of the 48 protein markers, decreased levels of RKIP (p = 0.0056), EphB2 (p = 0.0045), CK20 (p = 0.002), and Cdx2 (p CIMP-H, independently of MSI status. In addition to the expected clinico-pathological and molecular associations, CIMP-H colorectal cancers are characterized by a loss of protein markers associated with differentiation, and metastasis suppression, and have increased CD8+ T-lymphocytes regardless of MSI status. In particular, Cdx2 loss seems to strongly predict CIMP-H in both microsatellite-stable (MSS) and MSI-H colorectal cancers. Cdx2 is proposed as a surrogate marker for CIMP-H. Copyright © 2011 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

  7. The REDUCE metagram: a comprehensive prediction tool for determining the utility of dutasteride chemoprevention in men at risk for prostate cancer

    International Nuclear Information System (INIS)

    Nguyen, Carvell T.; Isariyawongse, Brandon; Yu, Changhong; Kattan, Michael W.

    2012-01-01

    Introduction: 5-alpha reductase inhibitors can reduce the risk of prostate cancer (PCa) but can be associated with significant side effects. A library of nomograms which predict the risk of clinical endpoints relevant to dutasteride treatment may help determine if chemoprevention is suited to the individual patient. Methods: Data from the REDUCE trial was used to identify predictive factors for 9 endpoints relevant to dutasteride treatment. Using the treatment and placebo groups from the biopsy cohort, Cox proportional hazards (PH) and competing risks regression (CRR) models were used to build 18 nomograms, whose predictive ability was measured by concordance index (CI) and calibration plots. Results: A total of 18 nomograms assessing the risks of cancer, high grade cancer, high grade prostatic intraepithelial neoplasia (HGPIN), atypical small acinar proliferation (ASAP), erectile dysfunction (ED), acute urinary retention (AUR), gynecomastia, urinary tract infection (UTI) and BPH-related surgery either on or off dutasteride were created. The nomograms for cancer, high grade cancer, ED, AUR, and BPH-related surgery demonstrated good discrimination and calibration while those for gynecomastia, UTI, HGPIN, and ASAP predicted no better than random chance. Conclusions: To aid patients in determining whether the benefits of dutasteride use outweigh the risks, we have developed a comprehensive metagram that can generate individualized risks of 9 outcomes relevant to men considering chemoprevention. Better models based on more predictive markers are needed for some of the endpoints but the current metagram demonstrates potential as a tool for patient counseling and decision-making that is accessible, intuitive, and clinically relevant.

  8. Integration of comprehensive women's health programmes into health systems: cervical cancer prevention, care and control in Rwanda.

    Science.gov (United States)

    Binagwaho, Agnes; Ngabo, Fidele; Wagner, Claire M; Mugeni, Cathy; Gatera, Maurice; Nutt, Cameron T; Nsanzimana, Sabin

    2013-09-01

    Although it is highly preventable and treatable, cervical cancer is the most common and most deadly cancer among women in Rwanda. By mobilizing a diverse coalition of partnerships, Rwanda became the first country in Africa to develop and implement a national strategic plan for cervical cancer prevention, screening and treatment. Rwanda - a small, landlocked nation in East Africa with a population of 10.4 million - is well positioned to tackle a number of "high-burden" noncommunicable diseases. The country's integrated response to infectious diseases has resulted in steep declines in premature mortality over the past decade. In 2011-2012, Rwanda vaccinated 227,246 girls with all three doses of the human papillomavirus (HPV) vaccine. Among eligible girls, three-dose coverage rates of 93.2% and 96.6% were achieved in 2011 and 2012, respectively. The country has also initiated nationwide screening and treatment programmes that are based on visual inspection of the cervix with acetic acid, testing for HPV DNA, cryotherapy, the loop electrosurgical excision procedure and various advanced treatment options. Low-income countries should begin to address cervical cancer by integrating prevention, screening and treatment into routine women's health services. This requires political will, cross-sectoral collaboration and planning, innovative partnerships and robust monitoring and evaluation. With external support and adequate planning, high nationwide coverage rates for HPV vaccination and screening for cervical cancer can be achieved within a few years.

  9. Evaluation of comorbidity in 9388 head and neck cancer patients: A national cohort study from the DAHANCA database

    DEFF Research Database (Denmark)

    Bøje, Charlotte Rotbøl; Dalton, Susanne O; Primdahl, Hanne

    2014-01-01

    diagnosed from 1992 to 2008 was identified from the DAHANCA-database. Data on comorbidity prior to HNSCC-diagnosis was obtained from the National Patient Registry and adapted to the CCI. RESULTS: By dividing the patients into two groups, we tested and validated which type of comorbidities within the CCI...... in randomized trials to avoid bias. Re-evaluation of the CCI revealed that only six conditions had an impact on survival, and a new modified index to assess comorbidity for HNSCC-patients was developed. The performance of HN-CCI to stratify patients on survival was good and HN-CCI is highly recommended...

  10. Radiation?induced mesothelioma among long?term solid cancer survivors: a longitudinal analysis of SEER database

    OpenAIRE

    Farioli, Andrea; Ottone, Marta; Morganti, Alessio G.; Compagnone, Gaetano; Romani, Fabrizio; Cammelli, Silvia; Mattioli, Stefano; Violante, Francesco S.

    2016-01-01

    Abstract We investigated the association between external beam radiotherapy (EBRT) and pleural and peritoneal mesothelioma among long?term (>5?years) solid cancer survivors. We analyzed data from the US Surveillance, Epidemiology, and End Results (SEER) program (1973?2012). We fitted survival models adjusted by age, gender, race, year, surgery, and relative risk of primary mesothelioma in the county of residence (proxy for individual asbestos exposure). We estimated hazard ratios [HR] with re...

  11. Affiliation to the work market after curative treatment of head-and-neck cancer: a population-based study from the DAHANCA database.

    Science.gov (United States)

    Kjær, Trille; Bøje, Charlotte Rotbøl; Olsen, Maja Halgren; Overgaard, Jens; Johansen, Jørgen; Ibfelt, Else; Steding-Jessen, Marianne; Johansen, Christoffer; Dalton, Susanne O

    2013-02-01

    Survivors of squamous cell carcinoma of the head and neck (HNSCC) are more severely affected in regard to affiliation to the work market than other cancer survivors. Few studies have investigated associations between socioeconomic and disease-related factors and work market affiliation after curative treatment of HNSCC. We investigated the factors for early retirement pension due to disability and unemployment in patients who had been available for work one year before diagnosis. In a nationwide, population-based cohort study, data on 2436 HNSCC patients treated curatively in 1992-2008 were obtained from the Danish Head and Neck Cancer Group database and linked to Danish administrative population-based registries to obtain demographic and socioeconomic variables. We used multivariate logistic regression models to assess associations between socioeconomic factors (education, income and cohabitating status), cancer-specific variables such as tumour site and stage, comorbidity, early retirement pension and unemployment, with adjustment for age, gender and year of diagnosis. Short education [odds ratio (OR) 4.8; 95% confidence interval (CI) 2.2-10.4], low income (OR 3.2; 95% CI 1.8-5.8), living alone (OR 3.0; 95% CI 2.1-4.4) and having a Charlson comorbidity index score of 3 or more (OR 5.9; 95% CI 3.1-11) were significantly associated with early retirement overall and in all site groups. For the subgroup of patients who were employed before diagnosis, the risk pattern was similar. Tumour stage was not associated with early retirement or unemployment. Cancer-related factors were less strongly associated with early retirement and unemployment than socioeconomic factors and comorbidity. Clinicians treating HNSCC patients should be aware of the socioeconomic factors related to work market affiliation in order to provide more intensive social support or targeted rehabilitation for this patient group.

  12. Characteristics of Epstein-Barr virus-associated gastric cancer: A study of 235 cases at a comprehensive cancer center in U.S.A

    Directory of Open Access Journals (Sweden)

    Yu Yingyan

    2009-02-01

    Full Text Available Abstract Background Epstein-Barr virus (EBV has been shown to be associated with gastric cancer. However, inconsistent findings have been reported regarding the distribution of EBV infected cells (in normal gastric epithelium vs. intestinal metaplastic cells vs. in neoplastic cells and the characteristics of EBV-associated gastric cancer. Lymph node positive EBV-associated gastric cancer has not been systematically studied. The aims of this study were to evaluate EBV-associated gastric cancer, to assess the distribution of EBV infected cells including all positive lymph nodes, and to define the characteristics of EBV-associated gastric cancer. Design The study included primary gastric cancer patients who underwent surgical resection with no preoperative treatment at M.D. Anderson Cancer Center between 1987 and 2006. Formalin-fixed paraffin-embedded tissue from these resection specimens were assessed for EBV by in situ hybridization, the gold standard for EBV detection in tissue. EBV status was analyzed along with clinicopathologic parameters including age, gender, tumor type, lymph node status, and pathologic stage of the tumor. Results Among 235 patients, 12 had intranuclear expression of EBV. EBV staining was seen only in tumor cells and no detectable EBV was observed in normal gastric mucosa, intestinal metaplasia or stromal cells. Eight of 12 patients with EBV-associated gastric cancer had regional lymph node metastasis. Of note, metastatic tumor cells in all of the involved lymph nodes of these 8 cases contained EBV. The epidemiologic data showed 11 of the 12 patients with EBV-associated gastric cancer were men, ranging in age from 54 to 78 years (mean age, 60 years; median age, 62.1 years. The age distribution for non-EBV associated gastric cancer patients ranged from 21 to 93 years (mean age, 67 years; median age, 66.4 years. Conclusion Our study demonstrated that EBV is present exclusively in gastric cancer cells. The detection of EBV in

  13. Quality of laparoscopic radical hysterectomy in developing countries: a comparison of surgical and oncologic outcomes between a comprehensive cancer center in the United States and a cancer center in Colom