WorldWideScience

Sample records for bioinformatics early radiation

  1. Applications in Bioastronautics and Bioinformatics: Early Radiation Cataracts Detected by Noninvasive, Quantitative, and Remote Means

    Science.gov (United States)

    Ansari, Rafat R.; King, James F.; Giblin, Frank J.

    2000-01-01

    Human exploration of Mars is a key goal in NASA's exploration planning in the next 20 years. Maintaining crew health and good vision is certainly an important aspect of achieving a successful mission. Continuous radiation exposure is a risk factor for radiation-induced cataracts in astronauts because radiation exposure in space travel has the potential of accelerating the aging process (ref. 1). A patented compact device (ref. 2) based on the technique of dynamic light scattering (DLS) was designed for monitoring an astronaut's ocular health during long-duration space travel. This capability of early diagnosis, unmatched by any other clinical technique in use today, may enable prompt initiation of preventive/curative therapy. An Internet web-based system integrating photon correlation data and controlling the hardware to monitor cataract development in vivo at a remote site in real time (teleophthalmology) is currently being developed. The new technology detects cataracts very early (at the molecular level). Cataract studies onboard the International Space Station will be helpful in quantifying any adverse effect of radiation to ocular health. The normal lens in a human eye, situated behind the cornea, is a transparent tissue. It contains 35 wt % protein and 65 wt % water. Aging, disease (e.g., diabetes), smoking, dehydration, malnutrition, and exposure to ultraviolet light and ionizing radiation can cause agglomeration of the lens proteins. Protein aggregation can take place anywhere in the lens, causing lens opacity. The aggregation and opacification could produce nuclear (central portion of the lens) or cortical (peripheral) cataracts. Nuclear and posterior subcapsular (the membrane's capsule surrounds the whole lens) cataracts, being on the visual optical axis of the eye, cause visual impairment that can finally lead to blindness. The lens proteins, in their native state, are small in size. As a cataract develops, this size grows from a few nanometers

  2. Non-Invasive, Quantitative, and Remote Detection of Early Radiation Cataracts for Applications in Bio-Astronautics and Bio-Informatics

    Science.gov (United States)

    Ansari, Rafat R.; Giblin, Frank J.; King, James F.; Singh, B. (Technical Monitor)

    2002-01-01

    Human exploration of Mars may be a possibility in the next twenty years. Maintaining good vision is an essential aspect of achieving a successful mission. Continuous radiation exposure is a risk factor for radiation-induced cataracts in astronauts. A compact device based on the technique of dynamic light scattering (DLS) is designed for monitoring an astronaut's ocular health during long-duration space travel. Preliminary data on the simulated effects of ionizing radiation exposure to the ocular tissues of nonhuman animals and results on the sensitivity of DLS over established clinical procedures in investigating cataracts are presented. This capability of early diagnosis, unmatched by any other clinical technique in use today, may enable prompt initiation of preventive/curative therapy. An internet web based system integrating photon correlation data and controlling the hardware to monitor cataract development in vivo at a remote site in real time (teleophthalmology) is currently being developed. Cataract studies on-board the International Space Station (ISS) will be helpful in designing better protective radiation shields for future space vehicles and space suits.

  3. Bioinformatics

    DEFF Research Database (Denmark)

    Baldi, Pierre; Brunak, Søren

    , and medicine will be particularly affected by the new results and the increased understanding of life at the molecular level. Bioinformatics is the development and application of computer methods for analysis, interpretation, and prediction, as well as for the design of experiments. It has emerged...

  4. A Virtual Bioinformatics Knowledge Environment for Early Cancer Detection

    Science.gov (United States)

    Crichton, Daniel; Srivastava, Sudhir; Johnsey, Donald

    2003-01-01

    Discovery of disease biomarkers for cancer is a leading focus of early detection. The National Cancer Institute created a network of collaborating institutions focused on the discovery and validation of cancer biomarkers called the Early Detection Research Network (EDRN). Informatics plays a key role in enabling a virtual knowledge environment that provides scientists real time access to distributed data sets located at research institutions across the nation. The distributed and heterogeneous nature of the collaboration makes data sharing across institutions very difficult. EDRN has developed a comprehensive informatics effort focused on developing a national infrastructure enabling seamless access, sharing and discovery of science data resources across all EDRN sites. This paper will discuss the EDRN knowledge system architecture, its objectives and its accomplishments.

  5. Radiation early warning system

    International Nuclear Information System (INIS)

    Schmitzer, C.; Kloesch, W.; Stadtmann, H.

    1993-01-01

    A prototype station for a Radiation Early Warning Network has been designed and set up at the Austrian Research Centre Seibersdorf. This unit was developed to measure all relevant parameters necessary to detect and track radioactive contamination at an early stage. The station consists of the following components: Radiation measuring channel for ambient gamma dose rate. Meteorological measurement channels for air temperature and humidity, wind direction and wind speed, and precipitation. Data processing and storage unit. The system is capable of unattended operation and data acquisition even under adverse environmental conditions. Connection to a central processing platform may be achieved via leased line, dial up over public switched telephone network (PSTN), or radio-frequency transmission. The remote station will continue acquiring and storing data for at least a month, even if the communications link is broken. Multiple stations can be combined to form a network, providing detailed information about radiological and meteorological data at each site. Thus increased ambient radiation levels may be discovered, tracked, and forecasted based on calculations using current and local weather data

  6. Integrative Bioinformatic Analysis of Transcriptomic Data Identifies Conserved Molecular Pathways Underlying Ionizing Radiation-Induced Bystander Effects (RIBE

    Directory of Open Access Journals (Sweden)

    Constantinos Yeles

    2017-11-01

    Full Text Available Ionizing radiation-induced bystander effects (RIBE encompass a number of effects with potential for a plethora of damages in adjacent non-irradiated tissue. The cascade of molecular events is initiated in response to the exposure to ionizing radiation (IR, something that may occur during diagnostic or therapeutic medical applications. In order to better investigate these complex response mechanisms, we employed a unified framework integrating statistical microarray analysis, signal normalization, and translational bioinformatics functional analysis techniques. This approach was applied to several microarray datasets from Gene Expression Omnibus (GEO related to RIBE. The analysis produced lists of differentially expressed genes, contrasting bystander and irradiated samples versus sham-irradiated controls. Furthermore, comparative molecular analysis through BioInfoMiner, which integrates advanced statistical enrichment and prioritization methodologies, revealed discrete biological processes, at the cellular level. For example, the negative regulation of growth, cellular response to Zn2+-Cd2+, and Wnt and NIK/NF-kappaB signaling, thus refining the description of the phenotypic landscape of RIBE. Our results provide a more solid understanding of RIBE cell-specific response patterns, especially in the case of high-LET radiations, like α-particles and carbon-ions.

  7. Radiodiagnosis of early radiation intestinal changes

    International Nuclear Information System (INIS)

    Volodina, G.I.; Abdulkhakova, D.A.

    1987-01-01

    X-ray examination of the colon in 102 patients and of the small intestine in 62 was performed during combined radiation therapy of cervical cancer and at different time after its discontinuation. Early radiation functional and morphological changes in the ileum and colon were detected. Radiation changes in the ileac mucosa were noted in 52% of the patients, changes of various degree in the rectal, sigmoid and cecal mucosa were noted in 41.2%. Moderate radiation changes in the ascending, descending and horizontal parts of the colon were noted in 10.7%. Early radiation intestinal injuries in the form of erosions and ulcers were revealed in 5.8% of the patients. In most of the patients radiation intestinal changes were without noticeable clinical manifestations. All these patients could be defined as a group at risk of developing late radiation changes

  8. Deep learning in bioinformatics.

    Science.gov (United States)

    Min, Seonwoo; Lee, Byunghan; Yoon, Sungroh

    2017-09-01

    In the era of big data, transformation of biomedical big data into valuable knowledge has been one of the most important challenges in bioinformatics. Deep learning has advanced rapidly since the early 2000s and now demonstrates state-of-the-art performance in various fields. Accordingly, application of deep learning in bioinformatics to gain insight from data has been emphasized in both academia and industry. Here, we review deep learning in bioinformatics, presenting examples of current research. To provide a useful and comprehensive perspective, we categorize research both by the bioinformatics domain (i.e. omics, biomedical imaging, biomedical signal processing) and deep learning architecture (i.e. deep neural networks, convolutional neural networks, recurrent neural networks, emergent architectures) and present brief descriptions of each study. Additionally, we discuss theoretical and practical issues of deep learning in bioinformatics and suggest future research directions. We believe that this review will provide valuable insights and serve as a starting point for researchers to apply deep learning approaches in their bioinformatics studies. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  9. Bioinformatics Methods for Learning Radiation-Induced Lung Inflammation from Heterogeneous Retrospective and Prospective Data

    Science.gov (United States)

    Spencer, Sarah J.; Almiron Bonnin, Damian; Deasy, Joseph O.; Bradley, Jeffrey D.; El Naqa, Issam

    2009-01-01

    Radiotherapy outcomes are determined by complex interactions between physical and biological factors, reflecting both treatment conditions and underlying genetics. Recent advances in radiotherapy and biotechnology provide new opportunities and challenges for predicting radiation-induced toxicities, particularly radiation pneumonitis (RP), in lung cancer patients. In this work, we utilize datamining methods based on machine learning to build a predictive model of lung injury by retrospective analysis of treatment planning archives. In addition, biomarkers for this model are extracted from a prospective clinical trial that collects blood serum samples at multiple time points. We utilize a 3-way proteomics methodology to screen for differentially expressed proteins that are related to RP. Our preliminary results demonstrate that kernel methods can capture nonlinear dose-volume interactions, but fail to address missing biological factors. Our proteomics strategy yielded promising protein candidates, but their role in RP as well as their interactions with dose-volume metrics remain to be determined. PMID:19704920

  10. Early-delayed radiation rhombencephalopathy

    International Nuclear Information System (INIS)

    Nightingale, S.; Dawes, P.J.D.K.; Cartlidge, N.E.F.; Newcastle upon Tyne Univ.

    1982-01-01

    A 37-year-old woman developed an early-delayed rhombencephalopathy 7 weeks after completing a course of radiotherapy to a glomus jugulare tumour. The clinical features, comprising nystagmus, skew strabismus, unilateral facial weakness, dysarthria and ataxia, are compared with four previously reported patients with this syndrome. (author)

  11. Possible Biomarkers for the Early Detection of HIV-associated Heart Diseases: A Proteomics and Bioinformatics Prediction

    Directory of Open Access Journals (Sweden)

    Suraiya Rasheed

    2015-01-01

    Full Text Available The frequency of cardiovascular disorders is increasing in HIV-infected individuals despite a significant reduction in the viral load by antiretroviral therapies (ART. Since the CD4+ T-cells are responsible for the viral load as well as immunological responses, we hypothesized that chronic HIV-infection of T-cells produces novel proteins/enzymes that cause cardiac dysfunctions. To identify specific factors that might cause cardiac disorders without the influence of numerous cofactors produced by other pathogenic microorganisms that co-inhabit most HIV-infected individuals, we analyzed genome-wide proteomes of a CD4+ T-cell line at different stages of HIV replication and cell growth over >6 months. Subtractive analyses of several hundred differentially regulated proteins from HIV-infected and uninfected counterpart cells and comparisons with proteins expressed from the same cells after treating with the antiviral drug Zidovudine/AZT and inhibiting virus replication, identified a well-coordinated network of 12 soluble/diffusible proteins in HIV-infected cells. Functional categorization, bioinformatics and statistical analyses of each protein predicted that the expression of cardiac-specific Ca2+ kinase together with multiple Ca2+ release channels causes a sustained overload of Ca2+ in the heart which induces fetal/cardiac myosin heavy chains (MYH6 and MYH7 and a myosin light-chain kinase. Each of these proteins has been shown to cause cardiac stress, arrhythmia, hypertrophic signaling, cardiomyopathy and heart failure (p = 8 × 10−11. Translational studies using the newly discovered proteins produced by HIV infection alone would provide additional biomarkers that could be added to the conventional markers for an early diagnosis and/or development of specific therapeutic interventions for heart diseases in HIV-infected individuals.

  12. Transcriptomic and bioinformatics analysis of the early time-course of the response to prostaglandin F2 alpha in the bovine corpus luteum

    Directory of Open Access Journals (Sweden)

    Heather Talbott

    2017-10-01

    Full Text Available RNA expression analysis was performed on the corpus luteum tissue at five time points after prostaglandin F2 alpha treatment of midcycle cows using an Affymetrix Bovine Gene v1 Array. The normalized linear microarray data was uploaded to the NCBI GEO repository (GSE94069. Subsequent statistical analysis determined differentially expressed transcripts ± 1.5-fold change from saline control with P ≤ 0.05. Gene ontology of differentially expressed transcripts was annotated by DAVID and Panther. Physiological characteristics of the study animals are presented in a figure. Bioinformatic analysis by Ingenuity Pathway Analysis was curated, compiled, and presented in tables. A dataset comparison with similar microarray analyses was performed and bioinformatics analysis by Ingenuity Pathway Analysis, DAVID, Panther, and String of differentially expressed genes from each dataset as well as the differentially expressed genes common to all three datasets were curated, compiled, and presented in tables. Finally, a table comparing four bioinformatics tools’ predictions of functions associated with genes common to all three datasets is presented. These data have been further analyzed and interpreted in the companion article “Early transcriptome responses of the bovine mid-cycle corpus luteum to prostaglandin F2 alpha includes cytokine signaling” [1].

  13. Radiation therapy of early glottic cancer

    International Nuclear Information System (INIS)

    Neri, S.

    1987-01-01

    The control of early glottic cancer is equally satisfactory with either surgical resection or radiation therapy; this last method gives the patient good functional results. During the period from 1/1978 to 12/1985, 73 patients with early glottic carcinoma (T1 N0 M0) were treated in the Institute of Radiotherapy L. Galvani, University of Bologna; 45 were stage T1a (tumor limited to one vocal cord) and 28 were stage T1b (tumor of both vocal cords or involving anterior commissure); radiation treatment utilized a 60 Co machine and 5x5 cm fields; the median dose was 67.2 Gy (range 50-76) with conventional fractionation. Ten patients had local recurrence; the median time of recurrence was 13.4 months; 9/10 were treated by surgery and 2/10 died, so the overall control by radiotherapy with surgery in reserve was 100% in T1a tumers and 90.6% in T1b ones. The 5-years disease free survival rate was 93.1% in T1a tumors and 69% in T1b; lesions involving anterior commissure had the worst prognosis, independent of the dose and time-dose factor (3/10 recurrences in the group treated with TDF less than 110 and 4/18 recurrences in the group with TDF more than 110)

  14. The Telemetric Early Warning Environmental Radiation Monitoring System of Cyprus

    Energy Technology Data Exchange (ETDEWEB)

    Christofides, S [Medical Physics Department, Nicosia General Hospital, Nicosia (Cyprus)

    1998-12-31

    This paper presents the hardware design, the development of the software and the use of the Telemetric Early Warning Environmental Radiation Monitoring System (TEWERMS) of Cyprus. (author). 3 refs, 6 figs.

  15. A case of early-onset radiation retinopathy

    International Nuclear Information System (INIS)

    Sato, Yoko; Den, Seika; Shimizu, Kazuhiro; Ikeda, Tsunehiko

    2001-01-01

    We encountered a 27-year-old male early caused by radiation retinopathy five months after radiotherapy (51 Gy) for astrocytoma. The retinopathy was the proliferative retinopathy, with several dot and blot hemorrhages, hard and soft exudate, increased capillary permeability, macula edema and avasucular areas. So it was treated with panretial photocoagulation like diabetic retinopathy. Now hemorrhage, exudate, edema and avascular areas were improved. Photocoagulation treatment is effective to stop the progression of radiation retinopathy. Radiation retinopathy is sometimes early caused, therefore long-term follow up is recommended on starting radiotherapy. (author)

  16. A case of early-onset radiation retinopathy

    Energy Technology Data Exchange (ETDEWEB)

    Sato, Yoko; Den, Seika; Shimizu, Kazuhiro; Ikeda, Tsunehiko [Osaka Medical Coll., Takatsuki (Japan)

    2001-12-01

    We encountered a 27-year-old male early caused by radiation retinopathy five months after radiotherapy (51 Gy) for astrocytoma. The retinopathy was the proliferative retinopathy, with several dot and blot hemorrhages, hard and soft exudate, increased capillary permeability, macula edema and avasucular areas. So it was treated with panretial photocoagulation like diabetic retinopathy. Now hemorrhage, exudate, edema and avascular areas were improved. Photocoagulation treatment is effective to stop the progression of radiation retinopathy. Radiation retinopathy is sometimes early caused, therefore long-term follow up is recommended on starting radiotherapy. (author)

  17. Biggest challenges in bioinformatics.

    Science.gov (United States)

    Fuller, Jonathan C; Khoueiry, Pierre; Dinkel, Holger; Forslund, Kristoffer; Stamatakis, Alexandros; Barry, Joseph; Budd, Aidan; Soldatos, Theodoros G; Linssen, Katja; Rajput, Abdul Mateen

    2013-04-01

    The third Heidelberg Unseminars in Bioinformatics (HUB) was held on 18th October 2012, at Heidelberg University, Germany. HUB brought together around 40 bioinformaticians from academia and industry to discuss the 'Biggest Challenges in Bioinformatics' in a 'World Café' style event.

  18. Biggest challenges in bioinformatics

    OpenAIRE

    Fuller, Jonathan C; Khoueiry, Pierre; Dinkel, Holger; Forslund, Kristoffer; Stamatakis, Alexandros; Barry, Joseph; Budd, Aidan; Soldatos, Theodoros G; Linssen, Katja; Rajput, Abdul Mateen

    2013-01-01

    The third Heidelberg Unseminars in Bioinformatics (HUB) was held in October at Heidelberg University in Germany. HUB brought together around 40 bioinformaticians from academia and industry to discuss the ‘Biggest Challenges in Bioinformatics' in a ‘World Café' style event.

  19. A bioinformatics potpourri.

    Science.gov (United States)

    Schönbach, Christian; Li, Jinyan; Ma, Lan; Horton, Paul; Sjaugi, Muhammad Farhan; Ranganathan, Shoba

    2018-01-19

    The 16th International Conference on Bioinformatics (InCoB) was held at Tsinghua University, Shenzhen from September 20 to 22, 2017. The annual conference of the Asia-Pacific Bioinformatics Network featured six keynotes, two invited talks, a panel discussion on big data driven bioinformatics and precision medicine, and 66 oral presentations of accepted research articles or posters. Fifty-seven articles comprising a topic assortment of algorithms, biomolecular networks, cancer and disease informatics, drug-target interactions and drug efficacy, gene regulation and expression, imaging, immunoinformatics, metagenomics, next generation sequencing for genomics and transcriptomics, ontologies, post-translational modification, and structural bioinformatics are the subject of this editorial for the InCoB2017 supplement issues in BMC Genomics, BMC Bioinformatics, BMC Systems Biology and BMC Medical Genomics. New Delhi will be the location of InCoB2018, scheduled for September 26-28, 2018.

  20. Radiation induced early maturing mutants in barley

    International Nuclear Information System (INIS)

    Kumar, R.; Chauhan, S.V.S.; Sharma, R.P.

    1978-01-01

    In M 2 generation, two early maturing plants were screened from a single spike progeny of a plant obtained from 20 kR of gamma-ray irradiation of a six-rowed barley (Hordeum vulgare L. var. Jyoti). Their true breeding nature was confirmed in M 3 generation. These mutants flower and mature 38 and 22 days earlier than those of control. (auth.)

  1. Bioinformatics and Cancer

    Science.gov (United States)

    Researchers take on challenges and opportunities to mine "Big Data" for answers to complex biological questions. Learn how bioinformatics uses advanced computing, mathematics, and technological platforms to store, manage, analyze, and understand data.

  2. Radiation therapy planning for early-stage Hodgkin lymphoma

    DEFF Research Database (Denmark)

    Maraldo, Maja V; Dabaja, Bouthaina S; Filippi, Andrea R

    2015-01-01

    PURPOSE: Early-stage Hodgkin lymphoma (HL) is a rare disease, and the location of lymphoma varies considerably between patients. Here, we evaluate the variability of radiation therapy (RT) plans among 5 International Lymphoma Radiation Oncology Group (ILROG) centers with regard to beam arrangements...... axillary disease, and 1 had disease in the neck only. The median age at diagnosis was 34 years (range, 21-74 years), and 5 patients were male. Of the resulting 50 treatment plans, 15 were planned with volumetric modulated arc therapy (1-4 arcs), 16 with intensity modulated RT (3-9 fields), and 19 with 3...

  3. Radiation pneumonitis: a complication resulting from combined radiation and chemotherapy for early breast cancer

    International Nuclear Information System (INIS)

    Gez, E.; Sulkes, A.; Isacson, R.; Catane, R.; Weshler, Z.

    1985-01-01

    Described is a patient with early breast carcinoma who developed clinical radiation pneumonitis during primary radiation therapy and concomitant chemotherapy that included prednisone. This syndrome developed three days following abrupt steroid withdrawal. Retrieval of steroids brought complete resolution of the clinical and radiological findings. Although this syndrome is rare, it is recommended that steroid therapy in a patient previously irradiated to the chest be avoided

  4. The communications in early warning network for radiation monitoring

    International Nuclear Information System (INIS)

    Oyoun, M.B.; Al-Hussin, Mohamad; Fares, Adnan; Al-Oulabi, Yasser; Othman, Ibrahim

    1992-07-01

    The objectives of early warning network are: The determination of gamma radiation (background) levels in air which depend on location and time, evaluation of any situation resulting from radiation or nuclear accident out of boarder, and after that reporting the emergency situation to relevant authorities on the national and international levels. Monitoring stations were installed using Gm tubes to cover boarder lines from south to north and east to west as follows: Damascus, Darra, Latakia, Tartous, Aleppo, Kamishly, Ragaa, and Qunitra. The following modes of communication: Telephone line, leased line, direct connection, and Syrian data network were used in the Syrian early network. This project was carried out in cooperation with IAEA under project no. RER/9/003. (author). 22 figs., 1 tab

  5. Early test facilities and analytic methods for radiation shielding: Proceedings

    International Nuclear Information System (INIS)

    Ingersoll, D.T.; Ingersoll, J.K.

    1992-11-01

    This report represents a compilation of eight papers presented at the 1992 American Nuclear Society/European Nuclear Society International Meeting. The meeting is of special significance since it commemorates the fiftieth anniversary of the first controlled nuclear chain reaction. The papers contained in this report were presented in a special session organized by the Radiation Protection and Shielding Division in keeping with the historical theme of the meeting. The paper titles are good indicators of their content and are: (1) The origin of radiation shielding research: The Oak Ridge experience, (2) Shielding research at the hanford site, (3) Aircraft shielding experiments at General Dynamics Fort Worth, 1950-1962, (4) Where have the neutrons gone?, a history of the tower shielding facility, (5) History and evolution of buildup factors, (6) Early shielding research at Bettis atomic power laboratory, (7) UK reactor shielding: then and now, (8) A very personal view of the development of radiation shielding theory

  6. Risk estimation of radiation exposure in early pregnancy

    International Nuclear Information System (INIS)

    Neumeister, K.; Waesser, S.

    1977-01-01

    The biomedical effects of radiation exposure (occupational, by X-ray diagnosis or examinations in nuclear medicine) to low doses on early pregnancy have been subject of a research work dealing with the dose level which, in case of exceeding, may lead to somatic damage (1.5 to 10 rem), and with the type of radiation injuries (malformations, functional disorder, cancer induction, increase in morbidity rate, genetic damage). A pilot study was the basis for the programme which will record such cases from all over the GDR. Within the scope of the health centre at the National Board of Nuclear Safety and Radiation Protection of the GDR, medical opinion on the interruption or preservation of pregnancy at its early stage, after exposure, was delivered in more than 50 cases. Exposure of the foetus was exactly determined. These children were re-investigated at the age of 1 to 3 years by applying pediatric and genetic examinations. The latter were based on clinical and biochemical methods as well as chromosome analyses. From these results, the risk of exposure in early pregnancy is estimated and adequate dose limits are suggested. In case these limits are exceeded, an interruption should be advised

  7. Introduction to bioinformatics.

    Science.gov (United States)

    Can, Tolga

    2014-01-01

    Bioinformatics is an interdisciplinary field mainly involving molecular biology and genetics, computer science, mathematics, and statistics. Data intensive, large-scale biological problems are addressed from a computational point of view. The most common problems are modeling biological processes at the molecular level and making inferences from collected data. A bioinformatics solution usually involves the following steps: Collect statistics from biological data. Build a computational model. Solve a computational modeling problem. Test and evaluate a computational algorithm. This chapter gives a brief introduction to bioinformatics by first providing an introduction to biological terminology and then discussing some classical bioinformatics problems organized by the types of data sources. Sequence analysis is the analysis of DNA and protein sequences for clues regarding function and includes subproblems such as identification of homologs, multiple sequence alignment, searching sequence patterns, and evolutionary analyses. Protein structures are three-dimensional data and the associated problems are structure prediction (secondary and tertiary), analysis of protein structures for clues regarding function, and structural alignment. Gene expression data is usually represented as matrices and analysis of microarray data mostly involves statistics analysis, classification, and clustering approaches. Biological networks such as gene regulatory networks, metabolic pathways, and protein-protein interaction networks are usually modeled as graphs and graph theoretic approaches are used to solve associated problems such as construction and analysis of large-scale networks.

  8. Solar Radiation as Driving Force In Early Evolution

    Science.gov (United States)

    Rothschild, Lynn J.; Peterson, David L. (Technical Monitor)

    2002-01-01

    Ultraviolet radiation (UVR) has provided an evolutionary challenge to life on Earth in that it is both an agent of mutation and as well as a selective force. Today surface fluxes of UVR vary diurnally, seasonally, etc. Still, the UVR flux was probably substantially higher during the early phases of evolution, suggesting that its role in evolution was even more prominent during this time. In this presentation, the creative role of UVR in evolution is discussed, specifically in connection with the role that UVR may have played in the evolution of early microbial ecosystems. The presentation will include discussions of the direct influence of UVR on such processes as photosynthesis and genetic damage, as well as the indirect influence of UVR as mediated through the production of reactive oxygen species. These biological effects of UVR will be viewed against the backdrop of the physical nature of the early Earth, surely a very different place then than now.

  9. Laboratory contamination in the early period of radiation research

    International Nuclear Information System (INIS)

    Rona, E.

    1979-01-01

    Meagre records exist of the levels of contamination and human exposure encountered by those who took part in the early research on radioactive materials. In order to throw some light on the nature and extent of the problem the author presents some recollections of the conditions of the laboratories in which she worked from 1924-1940. These include the Kaiser Wilhelm Institute, the Radium Institute of Vienna and the Curie Institute. The health, radiation injuries and causes of death of some early workers are discussed. Although the effects of acute exposure were recognised early on, there was less awareness of the possible effects of chronic exposure, and lack of prompt clinical signs of injury encouraged complacency. Laboratory contamination was often seen more as a problem affecting experimental results than as a health hazard. (author)

  10. Radiation induced early onset of neuro-cognitive changes

    International Nuclear Information System (INIS)

    Kumar, Mayank; Haridas, Seenu; Gupta, Mamta; Trivedi, Richa; Khushu, Subhash; Manda, Kailash

    2012-01-01

    Exposure to ionizing radiations has been shown to cause many detrimental effects. Primarily, the effects observed are broadly classified into hematopoietic syndrome at lower doses, gastrointestinal syndrome and central nervous system dysfunctions at high doses. However, recent studies reported that even at lower doses, there is an effect seen on the nervous system which can be observed as a decline in cognitive abilities. This has been reported in patients undergoing radiotherapy. The cognitive decline, especially in young patients affects development and has been shown to persist for years after the therapy. Thus, the aim of this study was to study and consolidate the early effects of radiation exposure which result in behavioural alterations and cognitive decline. Since, radiation-induced early changes in behavioural functions are poorly understood, therefore, the present investigation aimed to conceptualize and design behavioural test batteries in order to systematically study the immediate alterations in behavioural function following irradiation with a-rays. The behavioural alterations were correlated to changes in the different area of brain like hippocampus, thalamus, hypothalamus and corpus callosum using Diffusion Tensor Imaging (DTI) studies. Present study reported profound changes in behaviour, as well as alterations in the morphology of the brain tissue as perceived by DTI, 48 hours after exposure to ionizing radiations. These changes need to be correlated and clarified further to understand the mechanisms behind the cognitive dysfunctions occurring immediately after radiation exposure as well as to find out a therapeutic window to counteract or reduce the effect of long term cognitive changes following irradiation. (author)

  11. Bioinformatics for Exploration

    Science.gov (United States)

    Johnson, Kathy A.

    2006-01-01

    For the purpose of this paper, bioinformatics is defined as the application of computer technology to the management of biological information. It can be thought of as the science of developing computer databases and algorithms to facilitate and expedite biological research. This is a crosscutting capability that supports nearly all human health areas ranging from computational modeling, to pharmacodynamics research projects, to decision support systems within autonomous medical care. Bioinformatics serves to increase the efficiency and effectiveness of the life sciences research program. It provides data, information, and knowledge capture which further supports management of the bioastronautics research roadmap - identifying gaps that still remain and enabling the determination of which risks have been addressed.

  12. Advance in structural bioinformatics

    CERN Document Server

    Wei, Dongqing; Zhao, Tangzhen; Dai, Hao

    2014-01-01

    This text examines in detail mathematical and physical modeling, computational methods and systems for obtaining and analyzing biological structures, using pioneering research cases as examples. As such, it emphasizes programming and problem-solving skills. It provides information on structure bioinformatics at various levels, with individual chapters covering introductory to advanced aspects, from fundamental methods and guidelines on acquiring and analyzing genomics and proteomics sequences, the structures of protein, DNA and RNA, to the basics of physical simulations and methods for conform

  13. Crowdsourcing for bioinformatics.

    Science.gov (United States)

    Good, Benjamin M; Su, Andrew I

    2013-08-15

    Bioinformatics is faced with a variety of problems that require human involvement. Tasks like genome annotation, image analysis, knowledge-base population and protein structure determination all benefit from human input. In some cases, people are needed in vast quantities, whereas in others, we need just a few with rare abilities. Crowdsourcing encompasses an emerging collection of approaches for harnessing such distributed human intelligence. Recently, the bioinformatics community has begun to apply crowdsourcing in a variety of contexts, yet few resources are available that describe how these human-powered systems work and how to use them effectively in scientific domains. Here, we provide a framework for understanding and applying several different types of crowdsourcing. The framework considers two broad classes: systems for solving large-volume 'microtasks' and systems for solving high-difficulty 'megatasks'. Within these classes, we discuss system types, including volunteer labor, games with a purpose, microtask markets and open innovation contests. We illustrate each system type with successful examples in bioinformatics and conclude with a guide for matching problems to crowdsourcing solutions that highlights the positives and negatives of different approaches.

  14. Phylogenetic trees in bioinformatics

    Energy Technology Data Exchange (ETDEWEB)

    Burr, Tom L [Los Alamos National Laboratory

    2008-01-01

    Genetic data is often used to infer evolutionary relationships among a collection of viruses, bacteria, animal or plant species, or other operational taxonomic units (OTU). A phylogenetic tree depicts such relationships and provides a visual representation of the estimated branching order of the OTUs. Tree estimation is unique for several reasons, including: the types of data used to represent each OTU; the use ofprobabilistic nucleotide substitution models; the inference goals involving both tree topology and branch length, and the huge number of possible trees for a given sample of a very modest number of OTUs, which implies that fmding the best tree(s) to describe the genetic data for each OTU is computationally demanding. Bioinformatics is too large a field to review here. We focus on that aspect of bioinformatics that includes study of similarities in genetic data from multiple OTUs. Although research questions are diverse, a common underlying challenge is to estimate the evolutionary history of the OTUs. Therefore, this paper reviews the role of phylogenetic tree estimation in bioinformatics, available methods and software, and identifies areas for additional research and development.

  15. Data mining for bioinformatics applications

    CERN Document Server

    Zengyou, He

    2015-01-01

    Data Mining for Bioinformatics Applications provides valuable information on the data mining methods have been widely used for solving real bioinformatics problems, including problem definition, data collection, data preprocessing, modeling, and validation. The text uses an example-based method to illustrate how to apply data mining techniques to solve real bioinformatics problems, containing 45 bioinformatics problems that have been investigated in recent research. For each example, the entire data mining process is described, ranging from data preprocessing to modeling and result validation. Provides valuable information on the data mining methods have been widely used for solving real bioinformatics problems Uses an example-based method to illustrate how to apply data mining techniques to solve real bioinformatics problems Contains 45 bioinformatics problems that have been investigated in recent research.

  16. Analysis of radiation pneumonitis outside the radiation field in breast conserving therapy for early breast cancer

    International Nuclear Information System (INIS)

    Ogo, Etsuyo; Fujimoto, Kiminori; Hayabuchi, Naofumi

    2002-01-01

    In a retrospective study of radiation-induced pulmonary changes for patients with breast conserving therapy for early breast cancer, we sent questionnaires to the main hospitals in Japan. In this study, we analyzed pulmonary changes after tangential whole-breast irradiation. The purpose of this study was to determine the incidence and risk factors for radiation pneumonitis outside the radiation field. The questionnaires included patients data, therapy data, and lung injury information between August 1999 and May 2000. On the first questionnaires, answer letters were received from 107 institutions out of 158 (67.7%). On the second questionnaires, response rate (hospitals which had radiation pneumonitis outside the radiation field) was 21.7% (23/106). We could find no risk factors of this type of pneumonitis. We suggested that lung irradiation might trigger this type of pneumonitis which is clinically similar to BOOP (bronchiolitis obliterans organizing pneumonia). It developed in 1.5-2.1% among the patients with breast conserving surgery and tangential whole-breast irradiation. And it is likely appeared within 6 months after radiotherapy. (author)

  17. COMPARISON OF POPULAR BIOINFORMATICS DATABASES

    OpenAIRE

    Abdulganiyu Abdu Yusuf; Zahraddeen Sufyanu; Kabir Yusuf Mamman; Abubakar Umar Suleiman

    2016-01-01

    Bioinformatics is the application of computational tools to capture and interpret biological data. It has wide applications in drug development, crop improvement, agricultural biotechnology and forensic DNA analysis. There are various databases available to researchers in bioinformatics. These databases are customized for a specific need and are ranged in size, scope, and purpose. The main drawbacks of bioinformatics databases include redundant information, constant change, data spread over m...

  18. Bioinformatics-Aided Venomics

    Directory of Open Access Journals (Sweden)

    Quentin Kaas

    2015-06-01

    Full Text Available Venomics is a modern approach that combines transcriptomics and proteomics to explore the toxin content of venoms. This review will give an overview of computational approaches that have been created to classify and consolidate venomics data, as well as algorithms that have helped discovery and analysis of toxin nucleic acid and protein sequences, toxin three-dimensional structures and toxin functions. Bioinformatics is used to tackle specific challenges associated with the identification and annotations of toxins. Recognizing toxin transcript sequences among second generation sequencing data cannot rely only on basic sequence similarity because toxins are highly divergent. Mass spectrometry sequencing of mature toxins is challenging because toxins can display a large number of post-translational modifications. Identifying the mature toxin region in toxin precursor sequences requires the prediction of the cleavage sites of proprotein convertases, most of which are unknown or not well characterized. Tracing the evolutionary relationships between toxins should consider specific mechanisms of rapid evolution as well as interactions between predatory animals and prey. Rapidly determining the activity of toxins is the main bottleneck in venomics discovery, but some recent bioinformatics and molecular modeling approaches give hope that accurate predictions of toxin specificity could be made in the near future.

  19. Emergent Computation Emphasizing Bioinformatics

    CERN Document Server

    Simon, Matthew

    2005-01-01

    Emergent Computation is concerned with recent applications of Mathematical Linguistics or Automata Theory. This subject has a primary focus upon "Bioinformatics" (the Genome and arising interest in the Proteome), but the closing chapter also examines applications in Biology, Medicine, Anthropology, etc. The book is composed of an organized examination of DNA, RNA, and the assembly of amino acids into proteins. Rather than examine these areas from a purely mathematical viewpoint (that excludes much of the biochemical reality), the author uses scientific papers written mostly by biochemists based upon their laboratory observations. Thus while DNA may exist in its double stranded form, triple stranded forms are not excluded. Similarly, while bases exist in Watson-Crick complements, mismatched bases and abasic pairs are not excluded, nor are Hoogsteen bonds. Just as there are four bases naturally found in DNA, the existence of additional bases is not ignored, nor amino acids in addition to the usual complement of...

  20. Bioinformatics and moonlighting proteins

    Directory of Open Access Journals (Sweden)

    Sergio eHernández

    2015-06-01

    Full Text Available Multitasking or moonlighting is the capability of some proteins to execute two or more biochemical functions. Usually, moonlighting proteins are experimentally revealed by serendipity. For this reason, it would be helpful that Bioinformatics could predict this multifunctionality, especially because of the large amounts of sequences from genome projects. In the present work, we analyse and describe several approaches that use sequences, structures, interactomics and current bioinformatics algorithms and programs to try to overcome this problem. Among these approaches are: a remote homology searches using Psi-Blast, b detection of functional motifs and domains, c analysis of data from protein-protein interaction databases (PPIs, d match the query protein sequence to 3D databases (i.e., algorithms as PISITE, e mutation correlation analysis between amino acids by algorithms as MISTIC. Programs designed to identify functional motif/domains detect mainly the canonical function but usually fail in the detection of the moonlighting one, Pfam and ProDom being the best methods. Remote homology search by Psi-Blast combined with data from interactomics databases (PPIs have the best performance. Structural information and mutation correlation analysis can help us to map the functional sites. Mutation correlation analysis can only be used in very specific situations –it requires the existence of multialigned family protein sequences - but can suggest how the evolutionary process of second function acquisition took place. The multitasking protein database MultitaskProtDB (http://wallace.uab.es/multitask/, previously published by our group, has been used as a benchmark for the all of the analyses.

  1. Interdisciplinary Introductory Course in Bioinformatics

    Science.gov (United States)

    Kortsarts, Yana; Morris, Robert W.; Utell, Janine M.

    2010-01-01

    Bioinformatics is a relatively new interdisciplinary field that integrates computer science, mathematics, biology, and information technology to manage, analyze, and understand biological, biochemical and biophysical information. We present our experience in teaching an interdisciplinary course, Introduction to Bioinformatics, which was developed…

  2. Virtual Bioinformatics Distance Learning Suite

    Science.gov (United States)

    Tolvanen, Martti; Vihinen, Mauno

    2004-01-01

    Distance learning as a computer-aided concept allows students to take courses from anywhere at any time. In bioinformatics, computers are needed to collect, store, process, and analyze massive amounts of biological and biomedical data. We have applied the concept of distance learning in virtual bioinformatics to provide university course material…

  3. External radiation therapy in early stage prostate cancer

    International Nuclear Information System (INIS)

    Sandler, Howard M.

    1996-01-01

    Optimal therapy for adenocarcinoma of the prostate is controversial. Numerous options are available, however, comparison of results is difficult in view of the insufficiency of phase III randomized trials comparing alternative treatment strategies. These options include such strategies as no curative therapy (so-called watchful waiting), radiotherapy (external and/or internal), cryotherapy, or radical prostatectomy. Clearly, a broad spectrum of clinical approaches. When reported experiences involving radiation therapy and radical prostatectomy are compared, surgical patients tend to be younger, of earlier stage, of higher performance status, and have lower pre-therapy PSA. These prognostic factors influence the probability of disease control, and since patient selection can have a profound impact on results reporting, these issues need to be carefully controlled. A review of patients who are potentially candidates for surgery at the University of Michigan treated with conformal therapy external beam treatment, indicates that these relatively early patients are doing well. These issues will be elaborated upon further during the presentation

  4. Screening for early detection of radiation-associated thyroid cancer

    International Nuclear Information System (INIS)

    Ron, E.; Modan, B.; Lubin, E.

    1984-01-01

    In the 1950s, approximately 20,000 Israeli children received scalp irradiation as treatment for tinea capitis (ringworm of the scalp). To evaluate the necessity and feasibility of early screening of these individuals for thyroid cancer, a small pilot program was undertaken. The examination consisted of a thorough palpation of the thyroid gland and the surrounding area. A sup(99m)Tc thyroid scan and thyroid function tests were performed on individuals in whom palpation suggested a nodular abnormality. A multidisciplinary committee then made a recommendation for or against surgery. A total of 443 persons were screened, and nodular abnormalities of the thyroid were detected in 24 (5.4%). Of these persons, nine displayed symptomatology or reported knowledge of a thyroid condition; despite this, three of them were not receiving treatment. This left 18 subjects - 15 new cases and 3 previously untreated patients - needing follow-up care. Altogether nine persons were recommended for surgery, but one refused. All eight of the excised lesions were benign: four colloid nodules and four adenomas. While the screening program was feasible, the fact that no cancers were detected suggested that in a population exposed to a very low dose of radiation, thyroid screening may not be justified on a large scale.

  5. Microbial bioinformatics 2020.

    Science.gov (United States)

    Pallen, Mark J

    2016-09-01

    Microbial bioinformatics in 2020 will remain a vibrant, creative discipline, adding value to the ever-growing flood of new sequence data, while embracing novel technologies and fresh approaches. Databases and search strategies will struggle to cope and manual curation will not be sustainable during the scale-up to the million-microbial-genome era. Microbial taxonomy will have to adapt to a situation in which most microorganisms are discovered and characterised through the analysis of sequences. Genome sequencing will become a routine approach in clinical and research laboratories, with fresh demands for interpretable user-friendly outputs. The "internet of things" will penetrate healthcare systems, so that even a piece of hospital plumbing might have its own IP address that can be integrated with pathogen genome sequences. Microbiome mania will continue, but the tide will turn from molecular barcoding towards metagenomics. Crowd-sourced analyses will collide with cloud computing, but eternal vigilance will be the price of preventing the misinterpretation and overselling of microbial sequence data. Output from hand-held sequencers will be analysed on mobile devices. Open-source training materials will address the need for the development of a skilled labour force. As we boldly go into the third decade of the twenty-first century, microbial sequence space will remain the final frontier! © 2016 The Author. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  6. Engineering bioinformatics: building reliability, performance and productivity into bioinformatics software.

    Science.gov (United States)

    Lawlor, Brendan; Walsh, Paul

    2015-01-01

    There is a lack of software engineering skills in bioinformatic contexts. We discuss the consequences of this lack, examine existing explanations and remedies to the problem, point out their shortcomings, and propose alternatives. Previous analyses of the problem have tended to treat the use of software in scientific contexts as categorically different from the general application of software engineering in commercial settings. In contrast, we describe bioinformatic software engineering as a specialization of general software engineering, and examine how it should be practiced. Specifically, we highlight the difference between programming and software engineering, list elements of the latter and present the results of a survey of bioinformatic practitioners which quantifies the extent to which those elements are employed in bioinformatics. We propose that the ideal way to bring engineering values into research projects is to bring engineers themselves. We identify the role of Bioinformatic Engineer and describe how such a role would work within bioinformatic research teams. We conclude by recommending an educational emphasis on cross-training software engineers into life sciences, and propose research on Domain Specific Languages to facilitate collaboration between engineers and bioinformaticians.

  7. Engineering bioinformatics: building reliability, performance and productivity into bioinformatics software

    Science.gov (United States)

    Lawlor, Brendan; Walsh, Paul

    2015-01-01

    There is a lack of software engineering skills in bioinformatic contexts. We discuss the consequences of this lack, examine existing explanations and remedies to the problem, point out their shortcomings, and propose alternatives. Previous analyses of the problem have tended to treat the use of software in scientific contexts as categorically different from the general application of software engineering in commercial settings. In contrast, we describe bioinformatic software engineering as a specialization of general software engineering, and examine how it should be practiced. Specifically, we highlight the difference between programming and software engineering, list elements of the latter and present the results of a survey of bioinformatic practitioners which quantifies the extent to which those elements are employed in bioinformatics. We propose that the ideal way to bring engineering values into research projects is to bring engineers themselves. We identify the role of Bioinformatic Engineer and describe how such a role would work within bioinformatic research teams. We conclude by recommending an educational emphasis on cross-training software engineers into life sciences, and propose research on Domain Specific Languages to facilitate collaboration between engineers and bioinformaticians. PMID:25996054

  8. Radiation therapy for early stages of Morbus Ledderhose

    Energy Technology Data Exchange (ETDEWEB)

    Heyd, Reinhard [Dept. of Radiotherapy, Klinikum Offenbach (Germany); Dorn, Anne Pia; Mueller-Schimpfle, Marcus [Central Inst. of Radiology, Municipal Hospitals, Frankfurt/Main-Hoechst (Germany); Herkstroeter, Markus [Radiotherapeutic Practice at the Municipal Hospitals, Frankfurt/Main-Hoechst (Germany); Roedel, Claus; Fraunholz, Ingeborg [Dept. of Radiotherapy and Oncology, Univ. Hospital Frankfurt/Main (Germany)

    2010-01-15

    Purpose: To evaluate the efficacy of radiation therapy (RT) in the treatment of early stages of benign plantar fibromatosis (Morbus Ledderhose [ML]). Patients and Methods: From 2003 to 2008, 24 patients (33 sites) with a mean age of 52 years received RT for symptomatic ML. Prior to RT, 19 patients complained of pain and 15 had walking difficulties. 21 patients (28 sites) were irradiated with orthovolt-age X-rays and three (five sites) received electron-beam irradiation. The RT protocol consisted of five weekly fractions of 3.0 Gy (15 Gy), repeated after 6 weeks to a total dose of 30 Gy in 20 patients (28 sites). In four patients (five sites), two single fractions of 4.0 Gy were applied, repeated at intervals of 4 weeks to total doses of 24-32 Gy. Primary study endpoints were the prevention of disease progression and the avoidance of a surgical intervention. Secondary endpoints were pain relief, improvement of gait, and patients' subjective satisfaction measured with a linear analog scale (LAS). Results: After a median follow-up of 22.5 months, none of the patients experienced a progression of number and size of the lesions or the clinical symptoms. In eleven sites (33.3%) complete remission of cords or nodules occurred, in 18 (54.5%) a reduced number or size was noted, and four sites (12.1%) were unchanged. Pain relief was achieved in 13/19 patients (68.4%), and an improvement of gait abnormalities was noted in 11/15 patients (73.3%). The patients' subjective satisfaction measured by means of the LAS revealed a median improvement of 3.5 points in 22/24 patients (91.6%). Skin or soft tissues toxicities RTOG grade > 2 were not noted. Conclusion: RT is effective for treatment of the early stages of ML and may obviate the need for a surgical intervention. Long-term follow-up studies including a larger number of patients are required to define the role of RT in the management of this disorder. (orig.)

  9. Radiation therapy for early stages of Morbus Ledderhose

    International Nuclear Information System (INIS)

    Heyd, Reinhard; Dorn, Anne Pia; Mueller-Schimpfle, Marcus; Herkstroeter, Markus; Roedel, Claus; Fraunholz, Ingeborg

    2010-01-01

    Purpose: To evaluate the efficacy of radiation therapy (RT) in the treatment of early stages of benign plantar fibromatosis (Morbus Ledderhose [ML]). Patients and Methods: From 2003 to 2008, 24 patients (33 sites) with a mean age of 52 years received RT for symptomatic ML. Prior to RT, 19 patients complained of pain and 15 had walking difficulties. 21 patients (28 sites) were irradiated with orthovolt-age X-rays and three (five sites) received electron-beam irradiation. The RT protocol consisted of five weekly fractions of 3.0 Gy (15 Gy), repeated after 6 weeks to a total dose of 30 Gy in 20 patients (28 sites). In four patients (five sites), two single fractions of 4.0 Gy were applied, repeated at intervals of 4 weeks to total doses of 24-32 Gy. Primary study endpoints were the prevention of disease progression and the avoidance of a surgical intervention. Secondary endpoints were pain relief, improvement of gait, and patients' subjective satisfaction measured with a linear analog scale (LAS). Results: After a median follow-up of 22.5 months, none of the patients experienced a progression of number and size of the lesions or the clinical symptoms. In eleven sites (33.3%) complete remission of cords or nodules occurred, in 18 (54.5%) a reduced number or size was noted, and four sites (12.1%) were unchanged. Pain relief was achieved in 13/19 patients (68.4%), and an improvement of gait abnormalities was noted in 11/15 patients (73.3%). The patients' subjective satisfaction measured by means of the LAS revealed a median improvement of 3.5 points in 22/24 patients (91.6%). Skin or soft tissues toxicities RTOG grade > 2 were not noted. Conclusion: RT is effective for treatment of the early stages of ML and may obviate the need for a surgical intervention. Long-term follow-up studies including a larger number of patients are required to define the role of RT in the management of this disorder. (orig.)

  10. Designing XML schemas for bioinformatics.

    Science.gov (United States)

    Bruhn, Russel Elton; Burton, Philip John

    2003-06-01

    Data interchange bioinformatics databases will, in the future, most likely take place using extensible markup language (XML). The document structure will be described by an XML Schema rather than a document type definition (DTD). To ensure flexibility, the XML Schema must incorporate aspects of Object-Oriented Modeling. This impinges on the choice of the data model, which, in turn, is based on the organization of bioinformatics data by biologists. Thus, there is a need for the general bioinformatics community to be aware of the design issues relating to XML Schema. This paper, which is aimed at a general bioinformatics audience, uses examples to describe the differences between a DTD and an XML Schema and indicates how Unified Modeling Language diagrams may be used to incorporate Object-Oriented Modeling in the design of schema.

  11. When process mining meets bioinformatics

    NARCIS (Netherlands)

    Jagadeesh Chandra Bose, R.P.; Aalst, van der W.M.P.; Nurcan, S.

    2011-01-01

    Process mining techniques can be used to extract non-trivial process related knowledge and thus generate interesting insights from event logs. Similarly, bioinformatics aims at increasing the understanding of biological processes through the analysis of information associated with biological

  12. Early mechanisms in radiation-induced biological damage

    International Nuclear Information System (INIS)

    Powers, E.L.

    1983-01-01

    An introduction to the mechanisms of radiation action in biological systems is presented. Several questions about the nature of the radiation damage process are discussed, including recognition of the oxygen effects, dose-response relationships, and the importance of the hydroxyl radical

  13. Taking Bioinformatics to Systems Medicine.

    Science.gov (United States)

    van Kampen, Antoine H C; Moerland, Perry D

    2016-01-01

    Systems medicine promotes a range of approaches and strategies to study human health and disease at a systems level with the aim of improving the overall well-being of (healthy) individuals, and preventing, diagnosing, or curing disease. In this chapter we discuss how bioinformatics critically contributes to systems medicine. First, we explain the role of bioinformatics in the management and analysis of data. In particular we show the importance of publicly available biological and clinical repositories to support systems medicine studies. Second, we discuss how the integration and analysis of multiple types of omics data through integrative bioinformatics may facilitate the determination of more predictive and robust disease signatures, lead to a better understanding of (patho)physiological molecular mechanisms, and facilitate personalized medicine. Third, we focus on network analysis and discuss how gene networks can be constructed from omics data and how these networks can be decomposed into smaller modules. We discuss how the resulting modules can be used to generate experimentally testable hypotheses, provide insight into disease mechanisms, and lead to predictive models. Throughout, we provide several examples demonstrating how bioinformatics contributes to systems medicine and discuss future challenges in bioinformatics that need to be addressed to enable the advancement of systems medicine.

  14. Generalized Centroid Estimators in Bioinformatics

    Science.gov (United States)

    Hamada, Michiaki; Kiryu, Hisanori; Iwasaki, Wataru; Asai, Kiyoshi

    2011-01-01

    In a number of estimation problems in bioinformatics, accuracy measures of the target problem are usually given, and it is important to design estimators that are suitable to those accuracy measures. However, there is often a discrepancy between an employed estimator and a given accuracy measure of the problem. In this study, we introduce a general class of efficient estimators for estimation problems on high-dimensional binary spaces, which represent many fundamental problems in bioinformatics. Theoretical analysis reveals that the proposed estimators generally fit with commonly-used accuracy measures (e.g. sensitivity, PPV, MCC and F-score) as well as it can be computed efficiently in many cases, and cover a wide range of problems in bioinformatics from the viewpoint of the principle of maximum expected accuracy (MEA). It is also shown that some important algorithms in bioinformatics can be interpreted in a unified manner. Not only the concept presented in this paper gives a useful framework to design MEA-based estimators but also it is highly extendable and sheds new light on many problems in bioinformatics. PMID:21365017

  15. Stereotactic body radiation therapy versus conventional radiation therapy in patients with early stage non-small cell lung cancer

    DEFF Research Database (Denmark)

    Jeppesen, Stefan Starup; Schytte, Tine; Jensen, Henrik R

    2013-01-01

    Abstract Introduction. Stereotactic body radiation therapy (SBRT) for early stage non-small cell lung cancer (NSCLC) is now an accepted and patient friendly treatment, but still controversy exists about its comparability to conventional radiation therapy (RT). The purpose of this single...... and SBRT predicted improved prognosis. However, staging procedure, confirmation procedure of recurrence and technical improvements of radiation treatment is likely to influence outcomes. However, SBRT seems to be as efficient as conventional RT and is a more convenient treatment for the patients....

  16. Bioinformatics in translational drug discovery.

    Science.gov (United States)

    Wooller, Sarah K; Benstead-Hume, Graeme; Chen, Xiangrong; Ali, Yusuf; Pearl, Frances M G

    2017-08-31

    Bioinformatics approaches are becoming ever more essential in translational drug discovery both in academia and within the pharmaceutical industry. Computational exploitation of the increasing volumes of data generated during all phases of drug discovery is enabling key challenges of the process to be addressed. Here, we highlight some of the areas in which bioinformatics resources and methods are being developed to support the drug discovery pipeline. These include the creation of large data warehouses, bioinformatics algorithms to analyse 'big data' that identify novel drug targets and/or biomarkers, programs to assess the tractability of targets, and prediction of repositioning opportunities that use licensed drugs to treat additional indications. © 2017 The Author(s).

  17. Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers

    DEFF Research Database (Denmark)

    Schneider, Maria V.; Walter, Peter; Blatter, Marie-Claude

    2012-01-01

    and clearly tagged in relation to target audiences, learning objectives, etc. Ideally, they would also be peer reviewed, and easily and efficiently accessible for downloading. Here, we present the Bioinformatics Training Network (BTN), a new enterprise that has been initiated to address these needs and review...

  18. Some effects of radiation therapy during early childhood on facial growth and tooth development

    International Nuclear Information System (INIS)

    Harris, A.M.P.; Nortje, C.J.; Lucchesi, M.V.

    1986-01-01

    Case histories of the dental examinations of 2 children who were treated by radiation therapy for retinoblastomas in early childhood are discussed. The evidence presented here seems to indicate that in both patients early irradiation of the orbits and, as a result thereof, the jaws, could be partly responsible for the underdevelopment of this region

  19. Bioinformatics decoding the genome

    CERN Multimedia

    CERN. Geneva; Deutsch, Sam; Michielin, Olivier; Thomas, Arthur; Descombes, Patrick

    2006-01-01

    Extracting the fundamental genomic sequence from the DNA From Genome to Sequence : Biology in the early 21st century has been radically transformed by the availability of the full genome sequences of an ever increasing number of life forms, from bacteria to major crop plants and to humans. The lecture will concentrate on the computational challenges associated with the production, storage and analysis of genome sequence data, with an emphasis on mammalian genomes. The quality and usability of genome sequences is increasingly conditioned by the careful integration of strategies for data collection and computational analysis, from the construction of maps and libraries to the assembly of raw data into sequence contigs and chromosome-sized scaffolds. Once the sequence is assembled, a major challenge is the mapping of biologically relevant information onto this sequence: promoters, introns and exons of protein-encoding genes, regulatory elements, functional RNAs, pseudogenes, transposons, etc. The methodological ...

  20. Radiation induced early delayed changes in mice brain: a 1h MRS and behavioral evaluation study

    International Nuclear Information System (INIS)

    Gupta, Mamta; Rana, Poonam; Haridas, Seenu; Manda, Kailash; Hemanth Kumar, B.S.; Khushu, Subash

    2014-01-01

    Radiation induced CNS injury can be classified as acute, early delayed and late delayed. Most of the studies suggest that acute injury is reversible whereas early delayed and late delayed injury is irreversible leading to metabolic and cognitive impairment. Extensive research has been carried out on cranial radiation induced early and late delayed changes, there are no reports on whole body radiation induced early and delayed changes. The present study was designed to observe early delayed effects of radiation during whole body radiation exposure. A total of 20 C57 male mice were divided in two groups of 10 animals each. One group was exposed to a dose of 5 Gy whole body radiation through Tele 60 Co irradiation facility with source operating at 2.496 Gy/min, while other group served as sham irradiated control. Behavioral and MR spectroscopy was carried out 3 months post irradiation. Behavioral parameters such as locomotor activity and working memory were evaluated first then followed by MR spectroscopy at 7T animal MRI system. For MRS, voxel was localised in the cortex-hippocampus region of mouse brain. MR spectra were acquired using PRESS sequence, FID was processed using LC model for quantitation. The data showed impaired cognitive functions and altered metabolite levels during early delayed phase of whole body radiation induced injury. In behavioural experiments, there was a significant impairment in the cognitive as well as exploratory functions at 3 months post irradiation in irradiated group as compared to controls. MRS results explained changes in mI, glutamine and glx levels in irradiated animals compared to controls. Altered mI level has been found to be associated with reduced cognitive abilities in many brain disorders including MCI and Alzheimer's disease. The findings of this study suggest that whole body radiation exposure may have long lasting effect on the cognitive performance. (author)

  1. Peer Mentoring for Bioinformatics presentation

    OpenAIRE

    Budd, Aidan

    2014-01-01

    A handout used in a HUB (Heidelberg Unseminars in Bioinformatics) meeting focused on career development for bioinformaticians. It describes an activity for use to help introduce the idea of peer mentoring, potnetially acting as an opportunity to create peer-mentoring groups.

  2. Reproducible Bioinformatics Research for Biologists

    Science.gov (United States)

    This book chapter describes the current Big Data problem in Bioinformatics and the resulting issues with performing reproducible computational research. The core of the chapter provides guidelines and summaries of current tools/techniques that a noncomputational researcher would need to learn to pe...

  3. Taking Bioinformatics to Systems Medicine

    NARCIS (Netherlands)

    van Kampen, Antoine H. C.; Moerland, Perry D.

    2016-01-01

    Systems medicine promotes a range of approaches and strategies to study human health and disease at a systems level with the aim of improving the overall well-being of (healthy) individuals, and preventing, diagnosing, or curing disease. In this chapter we discuss how bioinformatics critically

  4. Bioinformatics and the Undergraduate Curriculum

    Science.gov (United States)

    Maloney, Mark; Parker, Jeffrey; LeBlanc, Mark; Woodard, Craig T.; Glackin, Mary; Hanrahan, Michael

    2010-01-01

    Recent advances involving high-throughput techniques for data generation and analysis have made familiarity with basic bioinformatics concepts and programs a necessity in the biological sciences. Undergraduate students increasingly need training in methods related to finding and retrieving information stored in vast databases. The rapid rise of…

  5. Bioinformatics of genomic association mapping

    NARCIS (Netherlands)

    Vaez Barzani, Ahmad

    2015-01-01

    In this thesis we present an overview of bioinformatics-based approaches for genomic association mapping, with emphasis on human quantitative traits and their contribution to complex diseases. We aim to provide a comprehensive walk-through of the classic steps of genomic association mapping

  6. Health risks (early, delayed and genetic) from the present radiation level

    International Nuclear Information System (INIS)

    Stranden, E.

    1981-01-01

    A general survey is given of the risks of early, delayed and genetic injuries from present radiation environment. Brief data is presented on some industrial and medical accidents. It is stated that in Norway there are 5-10 incidents per year in industrial radiography, none of which have led to radiation syndrome. Delayed radiation effects are discussed and figures quoted for risk due to mining, industrial and medical radiography and natural sources. Genetic effects are similarly discussed and genetically significant doses from similar sources are quoted. It is concluded that the health risk from the radiation environment is very small compared with other risks. (JIW)

  7. The Evaluation of Melatonin Effect Against The Early Effect of Ionizing Radiation Induced Lung Injury

    Directory of Open Access Journals (Sweden)

    raziyeh tahamtan

    2014-06-01

    Results: the results indicated that radiation increases the collapse and fibrosis and cause the abundance of macrophage compared to control group (p<0.05. Oral administration of melatonin before radiation therapy significantly increased the lymphocyte and macrophage frequency (p<0.001 and decreased the RBC (p<0.05 frequency compared to the radiation group. Conclusion: According to the results, melatonin can prevent early damages in irradiated lungs. Free radicals cause cytotoxicity and melatonin can directly decrease the radiation induced cell damages by converting the free radicals to non- toxic compounds and also through the activation of the major antioxidant enzymes.

  8. Bioinformatics for cancer immunotherapy target discovery

    DEFF Research Database (Denmark)

    Olsen, Lars Rønn; Campos, Benito; Barnkob, Mike Stein

    2014-01-01

    therapy target discovery in a bioinformatics analysis pipeline. We describe specialized bioinformatics tools and databases for three main bottlenecks in immunotherapy target discovery: the cataloging of potentially antigenic proteins, the identification of potential HLA binders, and the selection epitopes...

  9. EURASIP journal on bioinformatics & systems biology

    National Research Council Canada - National Science Library

    2006-01-01

    "The overall aim of "EURASIP Journal on Bioinformatics and Systems Biology" is to publish research results related to signal processing and bioinformatics theories and techniques relevant to a wide...

  10. GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training.

    Science.gov (United States)

    Attwood, Teresa K; Atwood, Teresa K; Bongcam-Rudloff, Erik; Brazas, Michelle E; Corpas, Manuel; Gaudet, Pascale; Lewitter, Fran; Mulder, Nicola; Palagi, Patricia M; Schneider, Maria Victoria; van Gelder, Celia W G

    2015-04-01

    In recent years, high-throughput technologies have brought big data to the life sciences. The march of progress has been rapid, leaving in its wake a demand for courses in data analysis, data stewardship, computing fundamentals, etc., a need that universities have not yet been able to satisfy--paradoxically, many are actually closing "niche" bioinformatics courses at a time of critical need. The impact of this is being felt across continents, as many students and early-stage researchers are being left without appropriate skills to manage, analyse, and interpret their data with confidence. This situation has galvanised a group of scientists to address the problems on an international scale. For the first time, bioinformatics educators and trainers across the globe have come together to address common needs, rising above institutional and international boundaries to cooperate in sharing bioinformatics training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all.

  11. Results of primary radiation therapy in early vocal cord cancers

    International Nuclear Information System (INIS)

    Mehta, S.A.; Sarkar, S.; Mehta, M.S.; Marfatia, P.T.; Choudhary, A.J.; Mehta, A.R.

    1991-01-01

    Results of 74 patients treated by primary radiation therapy with curative intent at the Tata Memorial Hospital between January 1980 and December 1984 are reported. Thirty three (44.6%) were classified as TlaNO, twenty five (33.8%) as TlbNO, ten (13.5%) as T2NO and six(8.1%) as TisNO. The 5-year actuarial survival was 92% and disease-free survival was 85%. Thirteen patients (17.5%) failed locally, seven (53.8%) of whom were salvaged by surgery. Radiation side-effects were minimal and there were no long term complications. Anterior commissure involvement did not affect the local recurrence rates. (author). 19 refs., 1 tabs

  12. Early estimates of UK radiation doses from the Chernobyl reactor

    International Nuclear Information System (INIS)

    Fry, F.A.; Clarke, R.H.; O'Riordan, M.C.

    1986-01-01

    The plume of radioactive material from the Chernobyl reactor accident passed over the United Kingdom and will increase the radiation dose to the population in the coming year. The increase above the normal annual dose from natural radiation, averaged over persons of all ages, will be about 15% in the north and 1% in the south of the country. Averaged over all ages and areas, the increase will be about 4%. This excess dose will decrease substantially in subsequent years. The accident at the nuclear power station in Chernobyl, near Kiev, on or after 26 April 1986, led to substantial quantities of radioactive material being released to the atmosphere. Wind initially transported the material towards northern and western Europe. Activity was first detected in the southern United Kingdom, some ∼ 2,000 km away, on 2 May. The National Radiological Protection Board (NRPB), the operators of nuclear installations and the regulating authorities, had anticipated this eventuality and had intensified their normal programmes of environmental monitoring. During the following days many measurements were made and a considerable amount of data was generated throughout the country. NRPB was assigned responsibility for collating and evaluating these results; the initial information is used here to make a preliminary estimate of the radiation doses to the population of the United Kingdom

  13. New clade of enigmatic early archosaurs yields insights into early pseudosuchian phylogeny and the biogeography of the archosaur radiation.

    Science.gov (United States)

    Butler, Richard J; Sullivan, Corwin; Ezcurra, Martín D; Liu, Jun; Lecuona, Agustina; Sookias, Roland B

    2014-06-10

    The origin and early radiation of archosaurs and closely related taxa (Archosauriformes) during the Triassic was a critical event in the evolutionary history of tetrapods. This radiation led to the dinosaur-dominated ecosystems of the Jurassic and Cretaceous, and the high present-day archosaur diversity that includes around 10,000 bird and crocodylian species. The timing and dynamics of this evolutionary radiation are currently obscured by the poorly constrained phylogenetic positions of several key early archosauriform taxa, including several species from the Middle Triassic of Argentina (Gracilisuchus stipanicicorum) and China (Turfanosuchus dabanensis, Yonghesuchus sangbiensis). These species act as unstable 'wildcards' in morphological phylogenetic analyses, reducing phylogenetic resolution. We present new anatomical data for the type specimens of G. stipanicicorum, T. dabanensis, and Y. sangbiensis, and carry out a new morphological phylogenetic analysis of early archosaur relationships. Our results indicate that these three previously enigmatic taxa form a well-supported clade of Middle Triassic archosaurs that we refer to as Gracilisuchidae. Gracilisuchidae is placed basally within Suchia, among the pseudosuchian (crocodile-line) archosaurs. The approximately contemporaneous and morphologically similar G. stipanicicorum and Y. sangbiensis may be sister taxa within Gracilisuchidae. Our results provide increased resolution of the previously poorly constrained relationships of early archosaurs, with increased levels of phylogenetic support for several key early pseudosuchian clades. Moreover, they falsify previous hypotheses suggesting that T. dabanensis and Y. sangbiensis are not members of the archosaur crown group. The recognition of Gracilisuchidae provides further support for a rapid phylogenetic diversification of crown archosaurs by the Middle Triassic. The disjunct distribution of the gracilisuchid clade in China and Argentina demonstrates that early

  14. Preface to Introduction to Structural Bioinformatics

    NARCIS (Netherlands)

    Feenstra, K. Anton; Abeln, Sanne

    2018-01-01

    While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introduction into Structural Bioinformatics, which

  15. Early reionization by decaying particles and cosmic microwave background radiation

    International Nuclear Information System (INIS)

    Kasuya, S.; Kawasaki, M.

    2004-01-01

    We study the reionization scenario in which ionizing UV photons emitted from decaying particle, in addition to usual contributions from stars and quasars, ionize the universe. It is found that the scenario is consistent with both the first year data of the Wilkinson Microwave Anisotropy Probe and the fact that the universe is not fully ionized until z∼6 as observed by Sloan Digital Sky Survey. Likelihood analysis revealed that rather broad parameter space can be chosen. This scenario will be discriminated by future observations, especially by the EE polarization power spectrum of cosmic microwave background radiation

  16. The results of radiation therapy for early glottic carcinoma

    International Nuclear Information System (INIS)

    Yamamoto, Michinori; Hada, Yoshihiro; Shirane, Makoto

    2000-01-01

    To analyze various parameters affect local control, we reviewed the results of radiotherapy for early glottic carcinoma. Between 1977 and 1997, 64 patients with untreated early glottic carcinoma and four patients with recurrent early glottic carcinoma were analyzed retrospectively. All tumors were classified as follows; T1 (n=56), T2 (n=12); well differentiated (n=33), moderately (n=25), poorly (n=1), unknown (n=9); very small tumor (VST) (n=46), small tumor (ST) (n=22). All patients were treated utilizing a cobalt-60 unit to a total dose that ranged from 56 Gy to 64 Gy (mean 60 Gy). The mean treatment time was 44 days (range 38-49). The local control rates at 2 years and 5 years for all patients were 85% and 78%, respectively. On univariate analysis, tumor size (p=0.0146) and recurrent or untreated tumor (p=0.0226) affected local control. On multivariate analysis, tumor size (p=0.0273) and recurrent or untreated tumor (p=0.0495) were also significant factors that affected local control. (author)

  17. Reduction of radiation-induced early skin damage (mouse foot) by 0-(β-hydroxyaethyl)-rutoside

    International Nuclear Information System (INIS)

    Fritz-Niggli, H.; Froehlich, E.

    1980-01-01

    The effect of a bioflavonoid, 0-(β-hydroxyethyl)-rutoside (HR) on early radiation-induced skin damage was examined, using the mouse foot system; the response to radiation is not species specific and comparison with the clinical situation is therefore possible. The aim was to see whether HR, which is highly effective in protecting against late damage, is also able to reduce early effects. Early reactions were considered to be erythema, swelling and ulceration and occurring up to 30 days after irradiation. It was found that HR significantly reduces early damage, both after a single dose and after fractionated irradiation with low doses. A single pre-treatment dose of HR and pre-treatment together with 30 days post-treatment administration were both found to be effective. The protective effect became more marked with increasing radiation dose (single irradiation). Reduction of late effects is produced iptimally by an interval of 0.25 hours between application of HR and irradiation, and this is also true for early skin damage. The early effects are partly reversible, but there is possibly an interesting correlation between these and irreversible late effects (such as loss of toes); a similar mechanism, presumably affecting the vascular system, may therefore be postulated. The protective action of this well tolesated, highly effective substance, which apparently protects normal tissues from early and late injury, is discussed. (orig.) [de

  18. A Bioinformatics Facility for NASA

    Science.gov (United States)

    Schweighofer, Karl; Pohorille, Andrew

    2006-01-01

    Building on an existing prototype, we have fielded a facility with bioinformatics technologies that will help NASA meet its unique requirements for biological research. This facility consists of a cluster of computers capable of performing computationally intensive tasks, software tools, databases and knowledge management systems. Novel computational technologies for analyzing and integrating new biological data and already existing knowledge have been developed. With continued development and support, the facility will fulfill strategic NASA s bioinformatics needs in astrobiology and space exploration. . As a demonstration of these capabilities, we will present a detailed analysis of how spaceflight factors impact gene expression in the liver and kidney for mice flown aboard shuttle flight STS-108. We have found that many genes involved in signal transduction, cell cycle, and development respond to changes in microgravity, but that most metabolic pathways appear unchanged.

  19. Regulation of early and delayed radiation responses in rat small intestine by capsaicin-sensitive nerves

    International Nuclear Information System (INIS)

    Wang Junru; Zheng Huaien; Kulkarni, Ashwini; Ou Xuemei; Hauer-Jensen, Martin

    2006-01-01

    Purpose: Mast cells protect against the early manifestations of intestinal radiation toxicity, but promote chronic intestinal wall fibrosis. Intestinal sensory nerves are closely associated with mast cells, both anatomically and functionally, and serve an important role in the regulation of mucosal homeostasis. This study examined the effect of sensory nerve ablation on the intestinal radiation response in an established rat model. Methods and Materials: Rats underwent sensory nerve ablation with capsaicin or sham ablation. Two weeks later, a localized segment of ileum was X-irradiated or sham irradiated. Structural, cellular, and molecular changes were examined 2 weeks (early injury) and 26 weeks (chronic injury) after irradiation. The mast cell dependence of the effect of sensory nerve ablation on intestinal radiation injury was assessed using c-kit mutant (Ws/Ws) mast cell-deficient rats. Results: Capsaicin treatment caused a baseline reduction in mucosal mast cell density, crypt cell proliferation, and expression of substance P and calcitonin gene-related peptide, two neuropeptides released by sensory neurons. Sensory nerve ablation strikingly exacerbated early intestinal radiation toxicity (loss of mucosal surface area, inflammation, intestinal wall thickening), but attenuated the development of chronic intestinal radiation fibrosis (collagen I accumulation and transforming growth factor β immunoreactivity). In mast cell-deficient rats, capsaicin treatment exacerbated postradiation epithelial injury (loss of mucosal surface area), but none of the other aspects of radiation injury were affected by capsaicin treatment. Conclusions: Ablation of capsaicin-sensitive enteric neurons exacerbates early intestinal radiation toxicity, but attenuates development of chronic fibroproliferative changes. The effect of capsaicin treatment on the intestinal radiation response is partly mast cell dependent

  20. Efficiency of early application of immunomodulators in combined effect of radiation and thermal injury

    International Nuclear Information System (INIS)

    Makarov, G.F.

    1989-01-01

    Medical effect of thymus preparations (thymoline, thymoptine) and levamysole under combined radiation-thermal injury is studied. Experimental results have shown that early application of certain immunostimulators under combined radiation-thermal injury of medium criticality is low-efficient. Their ability to sufficiently increase the antibody synthesis is manifested only under combined action of burns and irradiation in non-lethal doses. 5 refs

  1. Establishing bioinformatics research in the Asia Pacific

    OpenAIRE

    Ranganathan, Shoba; Tammi, Martti; Gribskov, Michael; Tan, Tin Wee

    2006-01-01

    Abstract In 1998, the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation was set up to champion the advancement of bioinformatics in the Asia Pacific. By 2002, APBioNet was able to gain sufficient critical mass to initiate the first International Conference on Bioinformatics (InCoB) bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2006 Conference was organized as the 5th annual conference of the Asia-...

  2. Pyrimetin therapy of early symptoms of radiation sickness in dogs

    International Nuclear Information System (INIS)

    Lehky, F.; Dobsinska, E.

    1975-01-01

    The antiemetic effect of Pyrimetin in dogs whole-body irradiated with gamma rays at a dose of 500 R, administered per os, intramuscularly, and subcutaneously, immediately before the exposure and after it in the course of the initial symptoms of radiation sickness was studied. A decreased emesis occurred after per os administration of Pyrimetin immediately before whole-body irradiation of the dogs. After the intramuscular application before whole-body irradiation two dogs vomitted, and in the case of the intramuscular administration after whole-body irradiation one dog vomitted. The subcutaneous application of Pyrimetin to dogs before whole-body irradiation and also after it produced only a 30% therapeutic effect. (author)

  3. Bioinformatics for Next Generation Sequencing Data

    Directory of Open Access Journals (Sweden)

    Alberto Magi

    2010-09-01

    Full Text Available The emergence of next-generation sequencing (NGS platforms imposes increasing demands on statistical methods and bioinformatic tools for the analysis and the management of the huge amounts of data generated by these technologies. Even at the early stages of their commercial availability, a large number of softwares already exist for analyzing NGS data. These tools can be fit into many general categories including alignment of sequence reads to a reference, base-calling and/or polymorphism detection, de novo assembly from paired or unpaired reads, structural variant detection and genome browsing. This manuscript aims to guide readers in the choice of the available computational tools that can be used to face the several steps of the data analysis workflow.

  4. Early remodeling of nasal mucosa in rat model after radiation injury

    International Nuclear Information System (INIS)

    Xiao Mang; Tang Jianguo; Luo Baozhen; Zhao Li'na; Shi Guozhi

    2008-01-01

    features of remodeling in the rats model of early radiation injury. (authors)

  5. Radiation Exposure and Mortality from Cardiovascular Disease and Cancer in Early NASA Astronauts: Space for Exploration

    Science.gov (United States)

    Elgart, S. R.; Little, M. P.; Campbell, L. J.; Milder, C. M.; Shavers, M. R.; Huff, J. L.; Patel, Z. S.

    2018-01-01

    Of the many possible health challenges posed during extended exploratory missions to space, the effects of space radiation on cardiovascular disease and cancer are of particular concern. There are unique challenges to estimating those radiation risks; care and appropriate and rigorous methodology should be applied when considering small cohorts such as the NASA astronaut population. The objective of this work was to establish whether there is evidence for excess cardiovascular disease or cancer mortality in an early NASA astronaut cohort and determine if a correlation exists between space radiation exposure and mortality.

  6. Radiation therapy and patient age in the survival from early-stage breast cancer

    International Nuclear Information System (INIS)

    Joslyn, Sue A.

    1999-01-01

    Purpose: To analyze the use of radiation therapy following local excision of invasive localized breast cancer and subsequent survival by 5-year age category. Methods: Data for 27,399 women diagnosed with localized stage of breast cancer and treated with local excision surgery from 1983 through 1992 were collected and provided by the national Surveillance, Epidemiology, and End Results (SEER) program. Use of radiation therapy was analyzed by race, ethnic background, geographic location, and age at diagnosis. Survival for women treated with local excision plus radiation therapy was compared to that of women treated with local excision alone for each 5-year age category. Results: Subjects in older age groups were significantly less likely (p < 0.001) to receive radiation following local excision compared to younger age groups. Statistically significant survival advantages were conferred on women receiving radiation therapy in each 5-year age category from age 35 to 84 years (ranging from p = 0.02 to p < 0.0001). Conclusion: While the use of radiation therapy following local excision of early-stage breast tumors drops significantly in older age groups, women aged 35-84 years receiving radiation therapy had significant reductions in mortality. These results did not appear to be influenced by the presence of mortal comorbid conditions. These results strongly suggest the need to consider carefully patient characteristics other than age in deciding the course of treatment for early-stage breast cancer

  7. Early radiation effects in highly apoptotic murine lymphoma xenografts monitored by 31P magnetic resonance spectroscopy

    International Nuclear Information System (INIS)

    Sakurai, Hideyuki; Mitsuhashi, Norio; Murata, Osamu; Kitamoto, Yoshizumi; Saito, Yoshihiro; Hasegawa, Masatoshi; Akimoto, Tetsuo; Takahashi, Takeo; Nasu, Sachiko; Niibe, Hideo

    1998-01-01

    Purpose: Phosphorus-31 magnetic resonance spectra ( 31 P-MRS) were obtained from highly apoptotic murine lymphoma xenografts before and up to 24 hr following graded doses of radiation ranging from 2 to 30 Gy. Radiation-induced apoptosis was also estimated up to 24 hr by scoring apoptotic cells in tumor tissue. Methods and Materials: Highly apoptotic murine lymphoma cells, EL4, were subcutaneously transplanted into C57/BL mice. At 7 days after transplantation, radiation was given to the tumor with a single dose at 3, 10, and 30 Gy. The β-ATP/Pi, PME/Pi, and β-ATP/PME values were calculated from the peak area of each spectrum. Radiation-induced apoptosis was scored with counting apoptotic cells on hematoxylin and eosin stained specimens (%apoptosis). Results: The values of % apoptosis 4, 8, and 24 hr after radiation were 21.8, 19.6, and 4.6% at 3 Gy, 35.1, 25.6, and 14.8% at 10 Gy, 38.4, 38.0, and 30.6% at 30 Gy, respectively (cf. 4.4% in control). There was no correlation between early change in β-ATP/Pi and % apoptosis at 4 hr after radiation when most of the apoptosis occurred. An early decrease in PME/Pi was observed at 4 hr after radiation dose at 30 Gy. For each dose, the values of β-ATP/Pi 24 hr after radiation were inversely related to radiation dose. Conclusion: The increase in β-ATP/Pi observed by 31 P-MRS was linked to the degree of histological recovery from radiation-induced apoptosis

  8. Significance of endothelial dysfunction in the pathogenesis of early and delayed radiation enteropathy

    Institute of Scientific and Technical Information of China (English)

    Junru Wang; Marjan Boerma; Qiang Fu; Martin Hauer-Jensen

    2007-01-01

    This review summarizes the current state of knowledge regarding the role of endothelial dysfunction in the pathogenesis of early and delayed intestinal radiation toxicity and discusses various endothelial-oriented interventions aimed at reducing the risk of radiation enteropathy. Studies published in the biomedical literature during the past four decades and cited in PubMed, as well as clinical and laboratory data from our own research program are reviewed. The risk of injury to normal tissues limits the cancer cure rates that can be achieved with radiation therapy. During treatment of abdominal and pelvic tumors, the intestine is frequently a major dose-limiting factor. Microvascular injury is a prominent feature of both early (inflammatory), as well as delayed (fibroproliferative) radiation injuries in the intestine and in many other normal tissues. Evidence from our and other laboratories suggests that endothelial dysfunction, notably a deficiency of endothelial thrombomodulin, plays a key role in the pathogenesis of these radiation responses. Deficient levels of thrombomodulin cause loss of vascular thromboresistance, excessive activation of cellular thrombin receptors by thrombin, and insufficient activation of protein C, a plasma protein with anticoagulant, anti-inflammatory, and cytoprotective properties. These changes are presumed to be critically involved in many aspects of early intestinal radiation toxicity and may sustain the fibroproliferative processes that lead to delayed intestinal dysfunction, fibrosis, and clinical complications. In conclusion, injury of vascular endothelium is important in the pathogenesis of the intestinal radiation response. Endothelial-oriented interventions are appealing strategies to prevent or treat normal tissue toxicity associated with radiation treatment of cancer.

  9. Problems arising from effects of low radiation doses in early pregnancy

    International Nuclear Information System (INIS)

    Neumeister, K.

    1976-01-01

    From 1970 to 1974, 37 expert opinions concerning interruption of pregnancy because of radiation stress of the foetus had to be given at the Centre for Clinical Radiobiology of the Karl-Marx University, Leipzig. In the cases investigated, radiation stress occurred between the first and tenth week of pregnancy at a maximum amount of approximately 20 R. X-ray diagnostic measures had been taken in the abdominal range or a tumour radiotherapy had been made, all in cases of unknown pregnancy. The individual determination of the foetal dose showed that different doses result, depending on the setting technique of photographs, physico-technical conditions and body size. In no case did anamnesis show special features. At the given doses an interruption seemed necessary only in one case (radiotherapy). According to this survey, diagnostic radiation stresses in early pregnancy almost always show radiation doses which, at the present stage of knowledge, do not make an interruption seem necessary. Individual differences of dose values for the same exposures, however, make it necessary to calculate exactly the radiation stress of the foetus in each case and to make the corresponding decision. As recent literature agrees in negating a so-called threshold dose for early damage, it is, apart from genetic considerations, necessary to avoid radiation stresses in early pregnancy for this reason also. In the author's opinion, an indication for an interruption is given at doses above 10 R (see also Hammer-Jacobsen, 1959). At lower radiation stresses, an interruption should be recommended in case of simultaneous additional noxae. This paper communicates the results of the check-ups of children who had been subject to a radiation stress of below 7 R in utero in the above cases. (author)

  10. Regulation of radiation-induced apoptosis by early growth response-1 gene in solid tumors

    International Nuclear Information System (INIS)

    Ahmed, M.

    2003-01-01

    Ionizing radiation exposure is associated with activation of certain immediate-early genes that function as transcription factors. These include members of jun or fos and early growth response (EGR) gene families. In particular, the functional role of EGR-1 in radiation-induced signaling is pivotal since the promoter of EGR-1 contains radiation-inducible CArG DNA sequences. The Egr-1 gene belongs to a family of Egr genes that includes EGR-2, EGR-3, EGR-4, EGR-α and the tumor suppressor, Wilms' tumor gene product, WT1. The Egr-1 gene product, EGR-1, is a nuclear protein that contains three zinc fingers of the C 2 H 2 subtype. The EGR-1 GC-rich consensus target sequence, 5'-GCGT/GGGGCG-3' or 5'-TCCT/ACCTCCTCC-3', has been identified in the promoter regions of transcription factors, growth factors, receptors, cell cycle regulators and pro-apoptotic genes. The gene targets mediated by Egr-1 in response to ionizing radiation include TNF-α , p53, Rb and Bax, all these are effectors of apoptosis. Based on these targets, Egr-1 is a pivotal gene that initiates early signal transduction events in response to ionizing radiation leading to either growth arrest or cell death in tumor cells. There are two potential application of Egr-1 gene in therapy of cancer. First, the Egr-1 promoter contains information for appropriate spatial and temporal expression in-vivo that can be regulated by ionizing radiation to control transcription of genes that have pro-apoptotic and suicidal function. Secondly, EGR-1 protein can eliminate 'induced-radiation resistance' by inhibiting the functions of radiation-induced pro-survival genes (NFκB activity and bcl-2 expression) and activate pro-apoptotic genes (such as bax) to confer a significant radio-sensitizing effect. Together, the reported findings from my laboratory demonstrate clearly that EGR-1 is an early central gene that confers radiation sensitivity and its pro-apoptotic functions are synergized by abrogation of induced radiation

  11. Radiation technique to determine early peopling of Brazil

    International Nuclear Information System (INIS)

    Watanabe, Shigueo; Ayta, Walter E.F.; Callata, Henry J.C.; Farias, Thiago M.B.; Gennari, Roseli F.; Etchevarne, Carlos A.

    2009-01-01

    Peopling American Continent and in particular of Brazil has been subject of research for a long time. With the results of dating of several pertinent materials many theories have been proposed. In Brazil, there is a National Park (Serra da Capivara Park) which is worldwide known due to thousands of wall paintings, most of them in rockshelters. N. Guidon, head of the Serra da Capivara National Park, found charcoal pellets in several archaeological sites and they were dated by radiocarbon technique. Ages ranging from 6 to 48 ka have been found. In one of the shelter a thin white covering was found that was proved to be calcite. This calcite was dated by Thermoluminescence and Electron Paramagnetic Resonance techniques and ages of 35 to 36 ka were obtained. In 2007, thin calcite covering wall paintings found in Iraquara County, Bahia state, has been dated. Ages of 50 ka have been obtained. The proposal of this work is that the early settlers crossed Atlantic Ocean from westernmost point of African Continent to easternmost point in Brazil more than 50000 years ago. The theory here proposed is possible once the distance between these two points is less than 3000 km distance far shorter than from Siberia to South America as proposed by other researchers.(author)

  12. Multidisciplinary approach of early breast cancer: The biology applied to radiation oncology

    International Nuclear Information System (INIS)

    Bourgier, Céline; Ozsahin, Mahmut; Azria, David

    2010-01-01

    Early breast cancer treatment is based on a multimodality approach with the application of clinical and histological prognostic factors to determine locoregional and systemic treatments. The entire scientific community is strongly involved in the management of this disease: radiologists for screening and early diagnosis, gynecologists, surgical oncologists and radiation oncologists for locoregional treatment, pathologists and biologists for personalized characterization, genetic counselors for BRCA mutation history and medical oncologists for systemic therapies. Recently, new biological tools have established various prognostic subsets of breast cancer and developed predictive markers for miscellaneous treatments. The aim of this article is to highlight the contribution of biological tools in the locoregional management of early breast cancer

  13. Preliminary early evaluation of radiation acute syndrome severity in an animal model

    Energy Technology Data Exchange (ETDEWEB)

    Gimenez, J.C.; Nasazzi, N.B.; Taja, M.R. [Comision Nacional de Energia Atomica, (Argentina); Nagle, C. [Centro de Educacion Medica e Investigaciones Clinicas (Argentina); Dubner, D. [Comision Nacional de Energia Atomica, (Argentina); Di Rizzio, C. [Academia Nacional de Medicina (Argentina)

    1992-07-01

    To improve the knowledge of Radiation Acute Syndrome radiopathological picture, whole body x-rays irradiation at 2Gy of a primate (Cebus apella paraguayanus) used as model has been performed. Early evaluations of clinical symptoms and dose and damage biological indicators have shown that this primate has given out similar responses to those of man. (author)

  14. Preliminary early evaluation of radiation acute syndrome severity in an animal model

    International Nuclear Information System (INIS)

    Gimenez, J.C.; Nasazzi, N.B.; Taja, M.R.; Nagle, C.; Dubner, D.; Di Rizzio, C.

    1992-01-01

    To improve the knowledge of Radiation Acute Syndrome radiopathological picture, whole body x-rays irradiation at 2Gy of a primate (Cebus apella paraguayanus) used as model has been performed. Early evaluations of clinical symptoms and dose and damage biological indicators have shown that this primate has given out similar responses to those of man. (author)

  15. Stimulation effect of early growth in crops by low dose radiation

    International Nuclear Information System (INIS)

    Kim, J.S.; Song, H.S.; Kim, J.K.; Lee, Y.K.; Lee, Y.B.

    1998-01-01

    Germination rate and early growth in crop such as rice,soybean,and perilla were observed after irradiation of γ-ray (Co-60) in order to determine the effects of low does radiation. The low dose radiation was able to improve the early growth in crops and their agricultural characters. Germination rate of 2Gy-irradiatied rice seeds was high and also were seeding height and fresh weight of the 0.5 Gy-irradiated. Germination rate and early growth of soybean were high in 4Gy-irradiated group. Perilla gew of so promisingly after after low dose irradiation, however there slightly increasing effects on germination rate, seeding height and fresh weight at 2Gt-, 1Gy-, and 1Gy irradiated group, respectively. (author)

  16. Effects of low dose gamma radiation on the early growth of red pepper and the resistance to subsquent high dose of radiation

    Energy Technology Data Exchange (ETDEWEB)

    Kim, J. S.; Baek, M. H.; Kim, D. H.; Lee, Y. K. [KAERI, Taejon (Korea, Republic of); Lee, Y. B. [Chungnam National Univ., Taejon (Korea, Republic of)

    2001-05-01

    Red pepper (capsicum annuum L. cv. Jokwang and cv. Johong) seeds were irradiated with the dose of 0{approx}50 Gy to investigated the effect of the low dose gamma radiation on the early growth and resistance to subsequent high dose of radiation. The effect of the low dose gamma radiation on the early growth and resistance to subsequenct high dose of radiation were enhanced in Johong cultivar but not in Jokwang cultivar. Germination rate and early growth of Johong cultivar were noticeably increased at 4 Gy-, 8 Gy- and 20 Gy irradiation group. Resistance to subsequent high dose of radiation of Johong cultivar were increased at almost all of the low dose irradiation group. Especially it was highest at 4 Gy irradiation group. The carotenoid contents and enzyme activity on the resistance to subsequent high dose of radiation of Johong cultivar were increased at the 4 Gy and 8 Gy irradiation group.

  17. Establishing bioinformatics research in the Asia Pacific

    Directory of Open Access Journals (Sweden)

    Tammi Martti

    2006-12-01

    Full Text Available Abstract In 1998, the Asia Pacific Bioinformatics Network (APBioNet, Asia's oldest bioinformatics organisation was set up to champion the advancement of bioinformatics in the Asia Pacific. By 2002, APBioNet was able to gain sufficient critical mass to initiate the first International Conference on Bioinformatics (InCoB bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2006 Conference was organized as the 5th annual conference of the Asia-Pacific Bioinformatics Network, on Dec. 18–20, 2006 in New Delhi, India, following a series of successful events in Bangkok (Thailand, Penang (Malaysia, Auckland (New Zealand and Busan (South Korea. This Introduction provides a brief overview of the peer-reviewed manuscripts accepted for publication in this Supplement. It exemplifies a typical snapshot of the growing research excellence in bioinformatics of the region as we embark on a trajectory of establishing a solid bioinformatics research culture in the Asia Pacific that is able to contribute fully to the global bioinformatics community.

  18. Emerging strengths in Asia Pacific bioinformatics.

    Science.gov (United States)

    Ranganathan, Shoba; Hsu, Wen-Lian; Yang, Ueng-Cheng; Tan, Tin Wee

    2008-12-12

    The 2008 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998, was organized as the 7th International Conference on Bioinformatics (InCoB), jointly with the Bioinformatics and Systems Biology in Taiwan (BIT 2008) Conference, Oct. 20-23, 2008 at Taipei, Taiwan. Besides bringing together scientists from the field of bioinformatics in this region, InCoB is actively involving researchers from the area of systems biology, to facilitate greater synergy between these two groups. Marking the 10th Anniversary of APBioNet, this InCoB 2008 meeting followed on from a series of successful annual events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea), New Delhi (India) and Hong Kong. Additionally, tutorials and the Workshop on Education in Bioinformatics and Computational Biology (WEBCB) immediately prior to the 20th Federation of Asian and Oceanian Biochemists and Molecular Biologists (FAOBMB) Taipei Conference provided ample opportunity for inducting mainstream biochemists and molecular biologists from the region into a greater level of awareness of the importance of bioinformatics in their craft. In this editorial, we provide a brief overview of the peer-reviewed manuscripts accepted for publication herein, grouped into thematic areas. As the regional research expertise in bioinformatics matures, the papers fall into thematic areas, illustrating the specific contributions made by APBioNet to global bioinformatics efforts.

  19. Assessment of early radiation effects on the liver. Comparison of SPECT and MR

    International Nuclear Information System (INIS)

    Masui, T.

    1996-01-01

    Purpose: To evaluate the early effects of radiation on the liver using single photon emission CT (SPECT) with 99m Tc-phytate combined with a pinhole collimator and MR imaging with superparamagnetic iron oxide (SPIO) and to compare 2 modalities regarding the assessment of the reticuloendothelial cell function. Material and Methods: The right sides of the livers of 12 anesthetized rats were irradiated with X-rays (4000 Cgy). On the 3rd and 4th days postirradiation, SPECT and MR imaging pre- and postcontrast were performed. Results: On SPECT, the irradiated areas appeared as areas with reduced 99m Tc-phytate uptake in 9 rats. In the remaining 3 rats, irradiated lesions were not evident on SPECT. On the early postcontrast MR images, differential negative enhancement of the irradiated and nonirradiated areas in the same 9 rats as on SPECT was apparent. However, on the later postcontrast images of 3 of these rats, the irradiated areas, which were brighter than the nonirradiated areas, were visually less clear than those on the earlier postcontrast images. In the remaining 3 rats, no radiation damag was evident on MR images. Conclusion: SPECT with 99m Tc-phytate and early postcontrast MR imaging with SPIO can show early radiation damage of the liver. The serial assessment of the postcontrast MR images provides functional information on the Kupffer cells. (orig.)

  20. Geographic access to radiation therapy facilities and disparities of early-stage breast cancer treatment

    Directory of Open Access Journals (Sweden)

    Yan Lin

    2018-05-01

    Full Text Available Few studies of breast cancer treatment have focused on the Northern Plains of the United States, an area with a high mastectomy rate. This study examined the association between geographic access to radiation therapy facilities and receipt of breast cancer treatments among early-stage breast cancer patients in South Dakota. Based on 4,209 early-stage breast cancer patients diagnosed between 2001 and 2012 in South Dakota, the study measured geographic proximity to radiation therapy facilities using the shortest travel time for patients to the closest radiation therapy facility. Two-level logistic regression models were used to estimate for early stage cases i the odds of mastectomy versus breast conserving surgery (BCS; ii the odds of not receiving radiation therapy after BCS versus receiving follow-up radiation therapy. Covariates included race/ethnicity, age at diagnosis, tumour grade, tumour sequence, year of diagnosis, census tract-level poverty rate and urban/rural residence. The spatial scan statistic method was used to identify geographic areas with significantly higher likelihood of experiencing mastectomy. The study found that geographic accessibility to radiation therapy facilities was negatively associated with the likelihood of receiving mastectomy after adjustment for other covariates, but not associated with radiation therapy use among patients receiving BCS. Compared with patients travelling less than 30 minutes to a radiation therapy facility, patients travelling more than 90 minutes were about 1.5 times more likely to receive mastectomy (odds ratio, 1.51; 95% confidence interval, 1.08-2.11 and patients travelling more than 120 minutes were 1.7 times more likely to receive mastectomy (odds ratio, 1.70; 95% confidence interval, 1.19-2.42. The study also identified a statistically significant cluster of patients receiving mastectomy who were located in south-eastern South Dakota, after adjustment for other factors. Because

  1. Assimilation of spatio-temporal distribution of radionuclides in early phase of radiation accident

    Czech Academy of Sciences Publication Activity Database

    Hofman, Radek; Šmídl, Václav

    2010-01-01

    Roč. 18, 7/8 (2010), s. 226-228 ISSN 1210-7085 R&D Projects: GA MŠk(CZ) 1M0572; GA ČR(CZ) GA102/07/1596 Institutional research plan: CEZ:AV0Z10750506 Keywords : decision support * early phase * Gaussian model * radioactive pollution transport Subject RIV: DL - Nuclear Waste, Radioactive Pollution ; Quality http://library.utia.cas.cz/separaty/2010/AS/hofman-assimilation of spatio-temporal distribution of radionuclides in early phase of radiation accident .pdf

  2. The secondary metabolite bioinformatics portal

    DEFF Research Database (Denmark)

    Weber, Tilmann; Kim, Hyun Uk

    2016-01-01

    . In this context, this review gives a summary of tools and databases that currently are available to mine, identify and characterize natural product biosynthesis pathways and their producers based on ‘omics data. A web portal called Secondary Metabolite Bioinformatics Portal (SMBP at http...... analytical and chemical methods gave access to this group of compounds, nowadays genomics-based methods offer complementary approaches to find, identify and characterize such molecules. This paradigm shift also resulted in a high demand for computational tools to assist researchers in their daily work......Natural products are among the most important sources of lead molecules for drug discovery. With the development of affordable whole-genome sequencing technologies and other ‘omics tools, the field of natural products research is currently undergoing a shift in paradigms. While, for decades, mainly...

  3. Sensitivity to UV radiation in early life stages of the Mediterranean sea urchin Sphaerechinus granularis (Lamarck)

    Energy Technology Data Exchange (ETDEWEB)

    Nahon, Sarah [UPMC Univ Paris 06, UMR 7621, LOBB, Observatoire Oceanologique, F-66651, Banyuls/mer (France); CNRS, UMR 7621, LOBB, Observatoire Oceanologique, F-66651, Banyuls/mer (France); Castro Porras, Viviana A. [UPMC Univ Paris 06, UMR 7621, LOBB, Observatoire Oceanologique, F-66651, Banyuls/mer (France); Pruski, Audrey M. [UPMC Univ Paris 06, UMR 7621, LOBB, Observatoire Oceanologique, F-66651, Banyuls/mer (France); CNRS, UMR 7621, LOBB, Observatoire Oceanologique, F-66651, Banyuls/mer (France); Charles, Francois [UPMC Univ Paris 06, UMR 7621, LOBB, Observatoire Oceanologique, F-66651, Banyuls/mer (France); CNRS, UMR 7621, LOBB, Observatoire Oceanologique, F-66651, Banyuls/mer (France)], E-mail: charles@obs-banyuls.fr

    2009-03-01

    The sea urchin Sphaerechinus granularis was used to investigate the impact of relevant levels of UV-B radiation on the early life stages of a common Mediterranean free spawning benthic species. Sperm, eggs and embryos were exposed to a range of UV radiation doses. The resulting endpoints were evaluated in terms of fertilisation success, development and survival rates. Above a weighted UV radiation dose of 0.0029 kJ m{sup -2}, fertilisation capability of irradiated sperm decreased rapidly. The exposure of the eggs to 0.0175 kJ m{sup -2} and more led to delayed and inhibited development with ensuing embryonic morphological abnormalities. One-day old larvae remained strongly sensitive to UV radiation as shown by the 50% decrease of the larval survival rate for a dose of 0.025 kJ m{sup -2} UVR. The elevated sensitivity of embryos to experimental UVR went along with a lack of significant amount of sunscreen compounds (e.g., mycosporine-like amino acids) in the eggs. The present results demonstrated that gamete viability and embryonic development may be significantly impaired by solar UV radiation in S. granularis, compromising in this way the reproduction of the species. Unless adaptive behavioural reproductive strategies exist, the influence of ambient UV radiation appears as a selective force for population dynamics of broadcast spawners in the shallow benthic Mediterranean environment.

  4. Early notification of the environmental radiation monitoring system to a radioactive event

    International Nuclear Information System (INIS)

    Haquin, G.; Ne'eman, F; Brenner, S.

    1997-01-01

    The National Environmental Radiation Monitoring System managed by the Radiation Safety Division of the Ministry of tile Environment has been completed and is composed of a network of 10 stations; 6 terrestrial stations, 3 waterside stations and one mobile. The system was built by Rotem Co. and the control center is located at the Unit of Environmental Resources of the Ministry of the Environment in Tel Aviv University. Each station consists of a wide range Geiger Mueller detector and ambient dose rate meter that provides the level of the environmental dose rate. Low level radioactive particles are detected by air sampling with devices that collect suspended and settling particles . Each station is connected to the control center through telephone lines and RF communication system providing 24 hour a day the level of the environmental radiation. The background radiation dose rate level depends on the location of the station and varies from 8 - 16 μR/h. The system has proved its efficiency in a 'simulation like event' early detecting an unregistered gamma radiography work in the proximity of two stations performed in June 96 in Ashdod port and in December 96 at Maspenot Israel in Haifa. During the events the radiation level increased up to 20 times above the background level. Survey teams of the Ashdod port and Maspenot Israel were sent to place to check the sources for the radiation level increase. These teams found workers performing radiography work in the area of the stations. (authors)

  5. Sensitivity to UV radiation in early life stages of the Mediterranean sea urchin Sphaerechinus granularis (Lamarck)

    International Nuclear Information System (INIS)

    Nahon, Sarah; Castro Porras, Viviana A.; Pruski, Audrey M.; Charles, Francois

    2009-01-01

    The sea urchin Sphaerechinus granularis was used to investigate the impact of relevant levels of UV-B radiation on the early life stages of a common Mediterranean free spawning benthic species. Sperm, eggs and embryos were exposed to a range of UV radiation doses. The resulting endpoints were evaluated in terms of fertilisation success, development and survival rates. Above a weighted UV radiation dose of 0.0029 kJ m -2 , fertilisation capability of irradiated sperm decreased rapidly. The exposure of the eggs to 0.0175 kJ m -2 and more led to delayed and inhibited development with ensuing embryonic morphological abnormalities. One-day old larvae remained strongly sensitive to UV radiation as shown by the 50% decrease of the larval survival rate for a dose of 0.025 kJ m -2 UVR. The elevated sensitivity of embryos to experimental UVR went along with a lack of significant amount of sunscreen compounds (e.g., mycosporine-like amino acids) in the eggs. The present results demonstrated that gamete viability and embryonic development may be significantly impaired by solar UV radiation in S. granularis, compromising in this way the reproduction of the species. Unless adaptive behavioural reproductive strategies exist, the influence of ambient UV radiation appears as a selective force for population dynamics of broadcast spawners in the shallow benthic Mediterranean environment

  6. The importance of early-school radioactivity education in cultivating proper reflexive judgement on radiation

    International Nuclear Information System (INIS)

    Nishina, Kojiro

    1999-01-01

    An attempt is made to draw a preliminary conclusion on the effectiveness of early-school education on radioactivity, based on two cases of student responses. The first is the returns of questionnaires circulated at two colleges, which were typical of an engineering college and a liberal-arts college, respectively. The second is the reactions of liberal arts students to observed, unexpected levels of radiation in their environment. Their reaction was dominated by their preoccupation on radiation, rather than by the quantitative data they themselves collected on the spot. Thus classes in early schooldays are considered to play a vital role in cultivating proper judgement they are to rely on as general citizens. (author)

  7. The importance of early-school radioactivity education in cultivating proper reflexive judgement on radiation

    Energy Technology Data Exchange (ETDEWEB)

    Nishina, Kojiro [Aichi Shukutoku Univ., The College of Contemporary Social Studies, Nagakute, Aichi (Japan)

    1999-09-01

    An attempt is made to draw a preliminary conclusion on the effectiveness of early-school education on radioactivity, based on two cases of student responses. The first is the returns of questionnaires circulated at two colleges, which were typical of an engineering college and a liberal-arts college, respectively. The second is the reactions of liberal arts students to observed, unexpected levels of radiation in their environment. Their reaction was dominated by their preoccupation on radiation, rather than by the quantitative data they themselves collected on the spot. Thus classes in early schooldays are considered to play a vital role in cultivating proper judgement they are to rely on as general citizens. (author)

  8. Primary radiation therapy for early breast cancer: the experience at the joint center for radiation therapy

    International Nuclear Information System (INIS)

    Harris, J.R.; Botnick, L.; Bloomer, W.D.; Chaffey, J.T.; Hellman, S.

    1981-01-01

    The results of primary radiation therapy in 176 consecutive patients with clinical State I and II carcinoma of the breast were reviewed. Median follow-up time was 47 months. The overall breast relapse rate was 7%. Patients undergoing interstitial implantation had a significantly lower breast relapse rate (1%) than patients not undergoing implantation (11%). Breast relapse was more common in patients undergoing incisional or needle biopsy (17%), compared to patients treated after excisional biopsy (5%). In patients undergoing excisional biopsy, but not interstitial implantation, breast relapse was related to external beam dose. Twelve percent of the patients who received less than 1600 ret dose relapsed in the breast, compared to none of the 19 patients who received more than 1700 ret dose. These results imply that supplemental irradiation to the primary tumor area is required following excisional biopsy of a primary breast cancer when 4500-5000 rad is delivered to the entire breast

  9. Biology in 'silico': The Bioinformatics Revolution.

    Science.gov (United States)

    Bloom, Mark

    2001-01-01

    Explains the Human Genome Project (HGP) and efforts to sequence the human genome. Describes the role of bioinformatics in the project and considers it the genetics Swiss Army Knife, which has many different uses, for use in forensic science, medicine, agriculture, and environmental sciences. Discusses the use of bioinformatics in the high school…

  10. Using "Arabidopsis" Genetic Sequences to Teach Bioinformatics

    Science.gov (United States)

    Zhang, Xiaorong

    2009-01-01

    This article describes a new approach to teaching bioinformatics using "Arabidopsis" genetic sequences. Several open-ended and inquiry-based laboratory exercises have been designed to help students grasp key concepts and gain practical skills in bioinformatics, using "Arabidopsis" leucine-rich repeat receptor-like kinase (LRR…

  11. A Mathematical Optimization Problem in Bioinformatics

    Science.gov (United States)

    Heyer, Laurie J.

    2008-01-01

    This article describes the sequence alignment problem in bioinformatics. Through examples, we formulate sequence alignment as an optimization problem and show how to compute the optimal alignment with dynamic programming. The examples and sample exercises have been used by the author in a specialized course in bioinformatics, but could be adapted…

  12. Online Bioinformatics Tutorials | Office of Cancer Genomics

    Science.gov (United States)

    Bioinformatics is a scientific discipline that applies computer science and information technology to help understand biological processes. The NIH provides a list of free online bioinformatics tutorials, either generated by the NIH Library or other institutes, which includes introductory lectures and "how to" videos on using various tools.

  13. Fuzzy Logic in Medicine and Bioinformatics

    Directory of Open Access Journals (Sweden)

    Angela Torres

    2006-01-01

    Full Text Available The purpose of this paper is to present a general view of the current applications of fuzzy logic in medicine and bioinformatics. We particularly review the medical literature using fuzzy logic. We then recall the geometrical interpretation of fuzzy sets as points in a fuzzy hypercube and present two concrete illustrations in medicine (drug addictions and in bioinformatics (comparison of genomes.

  14. Prospective Study of Local Control and Late Radiation Toxicity After Intraoperative Radiation Therapy Boost for Early Breast Cancer

    International Nuclear Information System (INIS)

    Chang, David W.; Marvelde, Luc te; Chua, Boon H.

    2014-01-01

    Purpose: To report the local recurrence rate and late toxicity of intraoperative radiation therapy (IORT) boost to the tumor bed using the Intrabeam System followed by external-beam whole-breast irradiation (WBI) in women with early-stage breast cancer in a prospective single-institution study. Methods and Materials: Women with breast cancer ≤3 cm were recruited between February 2003 and May 2005. After breast-conserving surgery, a single dose of 5 Gy IORT boost was delivered using 50-kV x-rays to a depth of 10 mm from the applicator surface. This was followed by WBI to a total dose of 50 Gy in 25 fractions. Patients were reviewed at regular, predefined intervals. Late toxicities were recorded using the Radiation Therapy Oncology Group/European Organization for Research and Treatment of Cancer Late Radiation Morbidity Scoring systems. Results: Fifty-five patients completed both IORT boost and external-beam WBI. Median follow-up was 3.3 years (range, 1.4-4.1 years). There was no reported locoregional recurrence or death. One patient developed distant metastases. Grade 2 and 3 subcutaneous fibrosis was detected in 29 (53%) and 8 patients (15%), respectively. Conclusions: The use of IORT as a tumor bed boost using kV x-rays in breast-conserving therapy was associated with good local control but a clinically significant rate of grade 2 and 3 subcutaneous fibrosis

  15. A case of early recurred tentorial meningioma after subtotal removal and postoperative radiation

    International Nuclear Information System (INIS)

    Kim, Han Sik; Kim, Young Baeg; Kim, Mi Kyung; Hwang, Sung Nam; Suk, Jong Sik; Choi, Duck Young

    1995-01-01

    Postoperative radiation has been given to prevent or delay recurrence of subtotally resected meningioma in recent years. However, the authors experienced early recurred tentorial meningioma 10 months after subtotal resection and postoperative radiation. This 70-year-old man was found to have a large stradling mass on the left petrous pyramid, extending to the middle fossa and cerebellopontine angle(CPA). A subtotal resection was performed at initial surgery, remaining some residual tumor along the lateral tentorium and he received 5580 Gy of radiation over the following 5 weeks. He did well until 10 months after the irradiation, when he presented with left mastoid pain, facial palsy, and left hearing loss. MRI confirmed recurrence of tumor and gross total tumor resection was performed via presigmoid retrolabyrinthine approach. The histology of the recurrent tumor was basically identical with that of the primary lesion, except for the slightly increased celluarity and mild pleomorphism

  16. Rising Strengths Hong Kong SAR in Bioinformatics.

    Science.gov (United States)

    Chakraborty, Chiranjib; George Priya Doss, C; Zhu, Hailong; Agoramoorthy, Govindasamy

    2017-06-01

    Hong Kong's bioinformatics sector is attaining new heights in combination with its economic boom and the predominance of the working-age group in its population. Factors such as a knowledge-based and free-market economy have contributed towards a prominent position on the world map of bioinformatics. In this review, we have considered the educational measures, landmark research activities and the achievements of bioinformatics companies and the role of the Hong Kong government in the establishment of bioinformatics as strength. However, several hurdles remain. New government policies will assist computational biologists to overcome these hurdles and further raise the profile of the field. There is a high expectation that bioinformatics in Hong Kong will be a promising area for the next generation.

  17. Bioinformatics clouds for big data manipulation

    Directory of Open Access Journals (Sweden)

    Dai Lin

    2012-11-01

    Full Text Available Abstract As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computing infrastructure into utility-supplied cloud computing delivered over the Internet, in order to handle the vast quantities of biological data generated by high-throughput experimental technologies. Albeit relatively new, cloud computing promises to address big data storage and analysis issues in the bioinformatics field. Here we review extant cloud-based services in bioinformatics, classify them into Data as a Service (DaaS, Software as a Service (SaaS, Platform as a Service (PaaS, and Infrastructure as a Service (IaaS, and present our perspectives on the adoption of cloud computing in bioinformatics. Reviewers This article was reviewed by Frank Eisenhaber, Igor Zhulin, and Sandor Pongor.

  18. The 2016 Bioinformatics Open Source Conference (BOSC).

    Science.gov (United States)

    Harris, Nomi L; Cock, Peter J A; Chapman, Brad; Fields, Christopher J; Hokamp, Karsten; Lapp, Hilmar; Muñoz-Torres, Monica; Wiencko, Heather

    2016-01-01

    Message from the ISCB: The Bioinformatics Open Source Conference (BOSC) is a yearly meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. BOSC has been run since 2000 as a two-day Special Interest Group (SIG) before the annual ISMB conference. The 17th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2016) took place in Orlando, Florida in July 2016. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community. The conference brought together nearly 100 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, and open and reproducible science.

  19. Bioinformatics clouds for big data manipulation

    KAUST Repository

    Dai, Lin

    2012-11-28

    As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computing infrastructure into utility-supplied cloud computing delivered over the Internet, in order to handle the vast quantities of biological data generated by high-throughput experimental technologies. Albeit relatively new, cloud computing promises to address big data storage and analysis issues in the bioinformatics field. Here we review extant cloud-based services in bioinformatics, classify them into Data as a Service (DaaS), Software as a Service (SaaS), Platform as a Service (PaaS), and Infrastructure as a Service (IaaS), and present our perspectives on the adoption of cloud computing in bioinformatics.This article was reviewed by Frank Eisenhaber, Igor Zhulin, and Sandor Pongor. 2012 Dai et al.; licensee BioMed Central Ltd.

  20. Bioinformatics clouds for big data manipulation.

    Science.gov (United States)

    Dai, Lin; Gao, Xin; Guo, Yan; Xiao, Jingfa; Zhang, Zhang

    2012-11-28

    As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computing infrastructure into utility-supplied cloud computing delivered over the Internet, in order to handle the vast quantities of biological data generated by high-throughput experimental technologies. Albeit relatively new, cloud computing promises to address big data storage and analysis issues in the bioinformatics field. Here we review extant cloud-based services in bioinformatics, classify them into Data as a Service (DaaS), Software as a Service (SaaS), Platform as a Service (PaaS), and Infrastructure as a Service (IaaS), and present our perspectives on the adoption of cloud computing in bioinformatics. This article was reviewed by Frank Eisenhaber, Igor Zhulin, and Sandor Pongor.

  1. Radiation induction of developmental effects during the very early stages of pregnancy

    International Nuclear Information System (INIS)

    Jacquet, P.

    2009-01-01

    Various studies have shown that early embryos of several mouse strains are sensitive to radiation-induction of congenital anomalies. The presence of mutations in particular genes seems to increase the sensitivity of embryos to such effects, but studies in that field are extremely limited. The aim of these studies is to determine (1) whether the sensitivity to radiation-induction of congenital anomalies during very early stages of gestation is transmitted to the following generation; (2) how mutations in genes involved in important cellular processes, like DNA repair, cell cycle regulation and apoptosis (cell suicide of a damaged cell), can influence the radiation sensitivity of the mammalian embryo during sensitive stages of early pregnancy. Emphasis is put on heterozygous mutations (in which only one of the two copies of the gene is mutated), which are relatively numerous in the human population and do not affect the viability and the fertility of individuals carrying them. The studies under way in that field are supported by contracts with the European Union and the Federal Agency for Nuclear Control (FANC-AFCN)

  2. Early effects of 16O radiation on neuronal morphology and cognition in a murine model

    Science.gov (United States)

    Carr, Hannah; Alexander, Tyler C.; Groves, Thomas; Kiffer, Frederico; Wang, Jing; Price, Elvin; Boerma, Marjan; Allen, Antiño R.

    2018-05-01

    Astronauts exposed to high linear energy transfer radiation may experience cognitive injury. The pathogenesis of this injury is unknown but may involve glutamate receptors or modifications to dendritic structure and/or dendritic spine density and morphology. Glutamate is the major excitatory neurotransmitter in the central nervous system, where it acts on ionotropic and metabotropic glutamate receptors located at the presynaptic terminal and in the postsynaptic membrane at synapses in the hippocampus. Dendritic spines are sites of excitatory synaptic transmission, and changes in spine structure and dendrite morphology are thought to be morphological correlates of altered brain function associated with hippocampal-dependent learning and memory. The aim of the current study is to assess whether behavior, glutamate receptor gene expression, and dendritic structure in the hippocampus are altered in mice after early exposure to 16O radiation in mice. Two weeks post-irradiation, animals were tested for hippocampus-dependent cognitive performance in the Y-maze. During Y-maze testing, mice exposed to 0.1 Gy and 0.25 Gy radiation failed to distinguish the novel arm, spending approximately the same amount of time in all 3 arms during the retention trial. Exposure to 16O significantly reduced the expression of Nr1 and GluR1 in the hippocampus and modulated spine morphology in the dentate gyrus and cornu Ammon 1 within the hippocampus. The present data provide evidence that 16O radiation has early deleterious effects on mature neurons that are associated with hippocampal learning and memory.

  3. Early development and characterization of a DNA-based radiation dosimeter

    Science.gov (United States)

    Avarmaa, Kirsten A.

    It is the priority of first responders to minimize damage to persons and infrastructure in the case of a nuclear emergency due to an accident or deliberate terrorist attack -- if this emergency includes a radioactive hazard, first responders require a simple-to-use, accurate and complete dosimeter for radiation protection purposes in order to minimize the health risk to these individuals and the general population at large. This work consists of the early evaluation of the design and performance of a biologically relevant dosimeter which uses DNA material that can respond to the radiation of any particle type. The construct consists of fluorescently tagged strands of DNA. The signalling components of this dosimeter are also investigated for their sensitivity to radiation damage and light exposure. The dual-labelled dosimeter that is evaluated in this work gave a measurable response to gamma radiation at dose levels of 10 Gy for the given detector design and experimental setup. Further testing outside of this work confirmed this finding and indicated a working range of 100 mGy to 10 Gy using a custom-built fluorimeter as part of a larger CRTI initiative. Characterization of the chromatic components of the dosimeter showed that photobleaching is not expected to have an effect on dosimeter performance, but that radiation can damage the non-DNA signalling components at higher dose levels, although this damage is minimal at lower doses over the expected operating ranges. This work therefore describes the early steps in the quantification of the behaviour of the DNA dosimeter as a potential biologically-based device to measure radiation dose.

  4. Information Needs of Older Women With Early-Stage Breast Cancer When Making Radiation Therapy Decisions.

    Science.gov (United States)

    Wang, Shi-Yi; Kelly, Gabrielle; Gross, Cary; Killelea, Brigid K; Mougalian, Sarah; Presley, Carolyn; Fraenkel, Liana; Evans, Suzanne B

    2017-07-15

    To identify the information older women with early-stage breast cancer need when making radiation therapy decisions, and who patients identify as the main decision maker. We surveyed (through face-to-face interview, telephone, or mail) women aged ≥65 years who received lumpectomy and were considering or receiving adjuvant radiation therapy for early-stage breast cancer. The survey instrument was constructed with input from patient and professional advisory committees, including breast cancer survivors, advocates of breast cancer care and aging, clinicians, and researchers. Participants rated the importance (on a 4-point scale) of 24 statements describing the benefits, side effects, impact on daily life, and other issues of radiation therapy in relation to radiation therapy decision making. Participants also designated who was considered the key decision maker. The response rate was 56.4% (93 of 165). Mean age was 72.5 years, ranging from 65 to 93 years. More than 96% of participants indicated they were the main decision maker on receiving radiation therapy. There was wide variation in information needs regarding radiation therapy decision making. Participants rated a mean of 18 (range, 3-24) items as "essential." Participants rated items related to benefits highest, followed by side effects. Participants who were older than 75 years rated 13.9 questions as essential, whereas participants aged ≤74 years rated 18.7 as essential (P=.018). Older women desire information and have more agency and input in the decision-making process than prior literature would suggest. The variation in information needs indicates that future decision support tools should provide options to select what information would be of interest to the participants. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. Biochemical and Radiobiological Factors in the Early Detection of Radiation Injury in Mammals

    Energy Technology Data Exchange (ETDEWEB)

    Cole, L. J. [Life Sciences Division, Stanford Research Institute, Menlo Park, CA (United States)

    1971-03-15

    In considering the body of radiobiological knowledge upon which the present possibilities for the development of an objective quantitative laboratory procedure for early detection of radiation injury depend, it is evident that there are at least three general categories of radiation effects which are relevant to this objective: (1) Products of the enzymatic-chemical breakdown of macromolecules, and lysis of killed or dying cells from radiosensitive tissues, for example deoxypolynucleotides from lymphoid tissues and bone marrow; (2) Radiation-induced inhibition of synthesis of deoxyribonucleic acid (DNA) and/or other macromolecules, eliciting alterations in tissue and blood concentrations and pool size of metabolic intermediates in the synthesis, for example, deoxycytidine; (3) Radiation-induced alterations, suppression, or cessation of specialized cell function; of particular interest here is the immunological functions of lymphocytes, including those in the circulating blood. For rodents, the exquisite radiosensitivity of bone-marrow-stem cells as well as of lymphocytes has been precisely measured by modern cellular radiobiological techniques: the colony-forming technique of Till and McCulloch, yielding a D{sub 0} for bone-marrow cells of about 80 R; and the graft-versus-host reactivity of transplanted lymphocytes yielding a similar D{sub 0} value. In our own hands, a modified colony-formation technique for dog bone-marrow cells irradiated in.vitro and in vivo give D{sub 0} values of {approx}100 R. Thus, on the basis of radiation sensitivity and the time-relationships for interphase cell death for lymphocytes, it appears that this cell class is probably the best ''candidate'' source for an early radiation-injury detection system. However,- the important report by Zicha and Buric indicates that extrapolation of biochemical data on radiation dosimetry from rodents to man is not necessarily feasible, at least in the. case of the urinary excretion of deoxycytidine

  6. Bioinformatics in cancer therapy and drug design

    International Nuclear Information System (INIS)

    Horbach, D.Y.; Usanov, S.A.

    2005-01-01

    One of the mechanisms of external signal transduction (ionizing radiation, toxicants, stress) to the target cell is the existence of membrane and intracellular proteins with intrinsic tyrosine kinase activity. No wonder that etiology of malignant growth links to abnormalities in signal transduction through tyrosine kinases. The epidermal growth factor receptor (EGFR) tyrosine kinases play fundamental roles in development, proliferation and differentiation of tissues of epithelial, mesenchymal and neuronal origin. There are four types of EGFR: EGF receptor (ErbB1/HER1), ErbB2/Neu/HER2, ErbB3/HER3 and ErbB4/HER4. Abnormal expression of EGFR, appearance of receptor mutants with changed ability to protein-protein interactions or increased tyrosine kinase activity have been implicated in the malignancy of different types of human tumors. Bioinformatics is currently using in investigation on design and selection of drugs that can make alterations in structure or competitively bind with receptors and so display antagonistic characteristics. (authors)

  7. Bioinformatics in cancer therapy and drug design

    Energy Technology Data Exchange (ETDEWEB)

    Horbach, D Y [International A. Sakharov environmental univ., Minsk (Belarus); Usanov, S A [Inst. of bioorganic chemistry, National academy of sciences of Belarus, Minsk (Belarus)

    2005-05-15

    One of the mechanisms of external signal transduction (ionizing radiation, toxicants, stress) to the target cell is the existence of membrane and intracellular proteins with intrinsic tyrosine kinase activity. No wonder that etiology of malignant growth links to abnormalities in signal transduction through tyrosine kinases. The epidermal growth factor receptor (EGFR) tyrosine kinases play fundamental roles in development, proliferation and differentiation of tissues of epithelial, mesenchymal and neuronal origin. There are four types of EGFR: EGF receptor (ErbB1/HER1), ErbB2/Neu/HER2, ErbB3/HER3 and ErbB4/HER4. Abnormal expression of EGFR, appearance of receptor mutants with changed ability to protein-protein interactions or increased tyrosine kinase activity have been implicated in the malignancy of different types of human tumors. Bioinformatics is currently using in investigation on design and selection of drugs that can make alterations in structure or competitively bind with receptors and so display antagonistic characteristics. (authors)

  8. Hyperspectral Imaging as an Early Biomarker for Radiation Exposure and Microcirculatory Damage

    Directory of Open Access Journals (Sweden)

    Michael S. Chin

    2015-10-01

    Full Text Available BACKGROUND: Radiation exposure can lead to detrimental effects in skin microcirculation. The precise relationship between radiation dose received and its effect on cutaneous perfusion still remains controversial. Previously, we have shown that hyperspectral imaging (HSI is able to demonstrate long-term reductions in cutaneous perfusion secondary to chronic microvascular injury. This study characterizes the changes in skin microcirculation in response to varying doses of ionizing radiation and investigates these microcirculatory changes as a possible early non-invasive biomarker that may correlate with the extent of long-term microvascular damage.METHODS: Immunocompetent hairless mice (n=66 were exposed to single fractions of superficial beta-irradiation in doses of 0, 5, 10, 20, 35, or 50 Gy. A HSI device was utilized to measure deoxygenated hemoglobin levels in irradiated and control areas. HSI measurements were performed at baseline before radiation exposure and for the first three days post-irradiation. Maximum macroscopic skin reactions were graded, and histological assessment of cutaneous microvascular densities at four weeks post-irradiation was performed in harvested tissue by CD31 immunohistochemistry.RESULTS: CD31 immunohistochemistry demonstrated a significant correlation (r=0.90, p<0.0001 between dose and vessel density reduction at four weeks. Using HSI analysis, early changes in deoxygenated hemoglobin levels were observed during the first three days post-irradiation in all groups. These deoxygenated hemoglobin changes varied proportionally with dose (r=0.98, p<0.0001 and skin reactions (r=0.98, p<0.0001. There was a highly significant correlation (r= 0.91, p<0.0001 between these early changes in deoxygenated hemoglobin and late vascular injury severity assessed at the end of four weeks.CONCLUSIONS: Radiation dose is directly correlated with cutaneous microvascular injury severity at four weeks in our model. Early post

  9. The role of repopulation in early and late radiation reactions in pig skin

    International Nuclear Information System (INIS)

    Redpath, J.L.; Peel, D.M.; Dodd, P.; Simmonds, R.H.; Hopewell, J.W.

    1984-01-01

    The role of repopulation in early and late radiation reactions in pig skin has been assessed by comparing split dose recovery doses (D/sub 2/-D/sub 1/) for a 1-day interval and a 28-day interval. For a 1-day interval, repair of sublethal damage is the major contribution to any recovery observed, whereas for a 28-day interval, repopulation may also play a role. The early reaction studied was moist desquamation and the late reactions studied were a later dermal erythema and necrosis. The data show that over a 28-day interval, repopulation contributes -- 7.0 Gy to a total D/sub 2/-D/sub 1/, of --14.0 Gy for the early moist desquamation (epidermal) reaction. Data for the role of repopulation in the late (dermal) reactions are also presented

  10. Radiation protection program for early detection of breast cancer in a mammography facility

    International Nuclear Information System (INIS)

    Mariana, Villagomez Casimiro; Cesar, Ruiz Trejo; Ruby, Espejo Fonseca

    2014-01-01

    Mammography is the best tool for early detection of Breast Cancer. In this diagnostic radiology modality it is necessary to establish the criteria to ensure the proper use and operation of the equipment used to obtain mammographic images in order to contribute to the safe use of ionizing radiation. The aim of the work was to implement at FUCAM-AC the radiation protection program which must be established for patients and radiation workers according to Mexican standards [1–4]. To achieve this goal, radiation protection and quality control manuals were elaborated [5]. Furthermore, a quality control program (QCP) in the mammography systems (analog/digital), darkroom included, has been implemented. Daily sensitometry, non-variability of the image quality, visualizing artifacts, revision of the equipment mechanical stability, compression force and analysis of repetition studies are some of the QCP routine tests that must be performed by radiological technicians of this institution as a set of actions to ensure the protection of patients. Image quality and patients dose assessment were performed on 4 analog equipment installed in 2 mobile units. In relation to dose assessment, all equipment passed the acceptance criteria (<3 mGy per projection). The image quality test showed that most images (70%)– presented artifacts. A brief summary of the results of quality control tests applied to the equipment and film processor are presented. To maintain an adequate level of quality and safety at FUCAM-AC is necessary that the proposed radiation protection program in this work is applied

  11. Radiation protection program for early detection of breast cancer in a mammography facility

    Energy Technology Data Exchange (ETDEWEB)

    Mariana, Villagomez Casimiro, E-mail: marjim10-66@ciencias.unam.mx, E-mail: cesar@fisica.unam.mx; Cesar, Ruiz Trejo, E-mail: marjim10-66@ciencias.unam.mx, E-mail: cesar@fisica.unam.mx [Instituto de Física, UNAM. Cd. Universitaria, CP 04510 (Mexico); Ruby, Espejo Fonseca [Instituto de Enfermedades de la Mama FUCAM-AC, CP 04980 (Mexico)

    2014-11-07

    Mammography is the best tool for early detection of Breast Cancer. In this diagnostic radiology modality it is necessary to establish the criteria to ensure the proper use and operation of the equipment used to obtain mammographic images in order to contribute to the safe use of ionizing radiation. The aim of the work was to implement at FUCAM-AC the radiation protection program which must be established for patients and radiation workers according to Mexican standards [1–4]. To achieve this goal, radiation protection and quality control manuals were elaborated [5]. Furthermore, a quality control program (QCP) in the mammography systems (analog/digital), darkroom included, has been implemented. Daily sensitometry, non-variability of the image quality, visualizing artifacts, revision of the equipment mechanical stability, compression force and analysis of repetition studies are some of the QCP routine tests that must be performed by radiological technicians of this institution as a set of actions to ensure the protection of patients. Image quality and patients dose assessment were performed on 4 analog equipment installed in 2 mobile units. In relation to dose assessment, all equipment passed the acceptance criteria (<3 mGy per projection). The image quality test showed that most images (70%)– presented artifacts. A brief summary of the results of quality control tests applied to the equipment and film processor are presented. To maintain an adequate level of quality and safety at FUCAM-AC is necessary that the proposed radiation protection program in this work is applied.

  12. Radiation protection program for early detection of breast cancer in a mammography facility

    Science.gov (United States)

    Villagomez Casimiro, Mariana; Ruiz Trejo, Cesar; Espejo Fonseca, Ruby

    2014-11-01

    Mammography is the best tool for early detection of Breast Cancer. In this diagnostic radiology modality it is necessary to establish the criteria to ensure the proper use and operation of the equipment used to obtain mammographic images in order to contribute to the safe use of ionizing radiation. The aim of the work was to implement at FUCAM-AC the radiation protection program which must be established for patients and radiation workers according to Mexican standards [1-4]. To achieve this goal, radiation protection and quality control manuals were elaborated [5]. Furthermore, a quality control program (QCP) in the mammography systems (analog/digital), darkroom included, has been implemented. Daily sensitometry, non-variability of the image quality, visualizing artifacts, revision of the equipment mechanical stability, compression force and analysis of repetition studies are some of the QCP routine tests that must be performed by radiological technicians of this institution as a set of actions to ensure the protection of patients. Image quality and patients dose assessment were performed on 4 analog equipment installed in 2 mobile units. In relation to dose assessment, all equipment passed the acceptance criteria (radiation protection program in this work is applied.

  13. Effect of ozone oxidative preconditioning in preventing early radiation-induced lung injury in rats

    Energy Technology Data Exchange (ETDEWEB)

    Bakkal, B.H. [Department of Radiation Oncology, School of Medicine, Bulent Ecevit University, Kozlu, Zonguldak (Turkey); Gultekin, F.A. [Department of General Surgery, School of Medicine, Bulent Ecevit University, Kozlu, Zonguldak (Turkey); Guven, B. [Department of Biochemistry, School of Medicine, Bulent Ecevit University, Kozlu, Zonguldak (Turkey); Turkcu, U.O. [Mugla School of Health Sciences, Mugla Sitki Kocman University, Mugla (Turkey); Bektas, S. [Department of Pathology, School of Medicine, Bulent Ecevit University, Kozlu, Zonguldak (Turkey); Can, M. [Department of Biochemistry, School of Medicine, Bulent Ecevit University, Kozlu, Zonguldak (Turkey)

    2013-09-27

    Ionizing radiation causes its biological effects mainly through oxidative damage induced by reactive oxygen species. Previous studies showed that ozone oxidative preconditioning attenuated pathophysiological events mediated by reactive oxygen species. As inhalation of ozone induces lung injury, the aim of this study was to examine whether ozone oxidative preconditioning potentiates or attenuates the effects of irradiation on the lung. Rats were subjected to total body irradiation, with or without treatment with ozone oxidative preconditioning (0.72 mg/kg). Serum proinflammatory cytokine levels, oxidative damage markers, and histopathological analysis were compared at 6 and 72 h after total body irradiation. Irradiation significantly increased lung malondialdehyde levels as an end-product of lipoperoxidation. Irradiation also significantly decreased lung superoxide dismutase activity, which is an indicator of the generation of oxidative stress and an early protective response to oxidative damage. Ozone oxidative preconditioning plus irradiation significantly decreased malondialdehyde levels and increased the activity of superoxide dismutase, which might indicate protection of the lung from radiation-induced lung injury. Serum tumor necrosis factor alpha and interleukin-1 beta levels, which increased significantly following total body irradiation, were decreased with ozone oxidative preconditioning. Moreover, ozone oxidative preconditioning was able to ameliorate radiation-induced lung injury assessed by histopathological evaluation. In conclusion, ozone oxidative preconditioning, repeated low-dose intraperitoneal administration of ozone, did not exacerbate radiation-induced lung injury, and, on the contrary, it provided protection against radiation-induced lung damage.

  14. Diversification rates indicate an early role of adaptive radiations at the origin of modern echinoid fauna.

    Directory of Open Access Journals (Sweden)

    Simon Boivin

    Full Text Available Evolutionary radiations are fascinating phenomena corresponding to a dramatic diversification of taxa and a burst of cladogenesis over short periods of time. Most evolutionary radiations have long been regarded as adaptive but this has seldom been demonstrated with large-scale comparative datasets including fossil data. Originating in the Early Jurassic, irregular echinoids are emblematic of the spectacular diversification of mobile marine faunas during the Mesozoic Marine Revolution. They diversified as they colonized various habitats, and now constitute the main component of echinoid fauna in modern seas. The evolutionary radiation of irregular echinoids has long been considered as adaptive but this hypothesis has never been tested. In the present work we analyze the evolution of echinoid species richness and morphological disparity over 37 million years based on an extensive fossil dataset. Our results demonstrate that morphological and functional diversifications in certain clades of irregular echinoids were exceptionally high compared to other clades and that they were associated with the evolution of new modes of life and so can be defined as adaptive radiations. The role played by ecological opportunities in the diversification of these clades was critical, with the evolution of the infaunal mode of life promoting the adaptive radiation of irregular echinoids.

  15. Effect of ozone oxidative preconditioning in preventing early radiation-induced lung injury in rats

    International Nuclear Information System (INIS)

    Bakkal, B.H.; Gultekin, F.A.; Guven, B.; Turkcu, U.O.; Bektas, S.; Can, M.

    2013-01-01

    Ionizing radiation causes its biological effects mainly through oxidative damage induced by reactive oxygen species. Previous studies showed that ozone oxidative preconditioning attenuated pathophysiological events mediated by reactive oxygen species. As inhalation of ozone induces lung injury, the aim of this study was to examine whether ozone oxidative preconditioning potentiates or attenuates the effects of irradiation on the lung. Rats were subjected to total body irradiation, with or without treatment with ozone oxidative preconditioning (0.72 mg/kg). Serum proinflammatory cytokine levels, oxidative damage markers, and histopathological analysis were compared at 6 and 72 h after total body irradiation. Irradiation significantly increased lung malondialdehyde levels as an end-product of lipoperoxidation. Irradiation also significantly decreased lung superoxide dismutase activity, which is an indicator of the generation of oxidative stress and an early protective response to oxidative damage. Ozone oxidative preconditioning plus irradiation significantly decreased malondialdehyde levels and increased the activity of superoxide dismutase, which might indicate protection of the lung from radiation-induced lung injury. Serum tumor necrosis factor alpha and interleukin-1 beta levels, which increased significantly following total body irradiation, were decreased with ozone oxidative preconditioning. Moreover, ozone oxidative preconditioning was able to ameliorate radiation-induced lung injury assessed by histopathological evaluation. In conclusion, ozone oxidative preconditioning, repeated low-dose intraperitoneal administration of ozone, did not exacerbate radiation-induced lung injury, and, on the contrary, it provided protection against radiation-induced lung damage

  16. Computational biology and bioinformatics in Nigeria.

    Science.gov (United States)

    Fatumo, Segun A; Adoga, Moses P; Ojo, Opeolu O; Oluwagbemi, Olugbenga; Adeoye, Tolulope; Ewejobi, Itunuoluwa; Adebiyi, Marion; Adebiyi, Ezekiel; Bewaji, Clement; Nashiru, Oyekanmi

    2014-04-01

    Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries.

  17. Computational biology and bioinformatics in Nigeria.

    Directory of Open Access Journals (Sweden)

    Segun A Fatumo

    2014-04-01

    Full Text Available Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries.

  18. When cloud computing meets bioinformatics: a review.

    Science.gov (United States)

    Zhou, Shuigeng; Liao, Ruiqi; Guan, Jihong

    2013-10-01

    In the past decades, with the rapid development of high-throughput technologies, biology research has generated an unprecedented amount of data. In order to store and process such a great amount of data, cloud computing and MapReduce were applied to many fields of bioinformatics. In this paper, we first introduce the basic concepts of cloud computing and MapReduce, and their applications in bioinformatics. We then highlight some problems challenging the applications of cloud computing and MapReduce to bioinformatics. Finally, we give a brief guideline for using cloud computing in biology research.

  19. Application of machine learning methods in bioinformatics

    Science.gov (United States)

    Yang, Haoyu; An, Zheng; Zhou, Haotian; Hou, Yawen

    2018-05-01

    Faced with the development of bioinformatics, high-throughput genomic technology have enabled biology to enter the era of big data. [1] Bioinformatics is an interdisciplinary, including the acquisition, management, analysis, interpretation and application of biological information, etc. It derives from the Human Genome Project. The field of machine learning, which aims to develop computer algorithms that improve with experience, holds promise to enable computers to assist humans in the analysis of large, complex data sets.[2]. This paper analyzes and compares various algorithms of machine learning and their applications in bioinformatics.

  20. Limits on dark radiation, early dark energy, and relativistic degrees of freedom

    International Nuclear Information System (INIS)

    Calabrese, Erminia; Melchiorri, Alessandro; Huterer, Dragan; Linder, Eric V.; Pagano, Luca

    2011-01-01

    Recent cosmological data analyses hint at the presence of an extra relativistic energy component in the early universe. This component is often parametrized as an excess of the effective neutrino number N eff over the standard value of 3.046. The excess relativistic energy could be an indication for an extra (sterile) neutrino, but early dark energy and barotropic dark energy also contribute to the relativistic degrees of freedom. We examine the capabilities of current and future data to constrain and discriminate between these explanations, and to detect the early dark energy density associated with them. We find that while early dark energy does not alter the current constraints on N eff , a dark radiation component, such as that provided by barotropic dark energy models, can substantially change current constraints on N eff , bringing its value back to agreement with the theoretical prediction. Both dark energy models also have implications for the primordial mass fraction of Helium Y p and the scalar perturbation index n s . The ongoing Planck satellite mission will be able to further discriminate between sterile neutrinos and early dark energy.

  1. Observing the Cosmic Microwave Background Radiation: A Unique Window on the Early Universe

    Science.gov (United States)

    Hinshaw, Gary; Fisher, Richard R. (Technical Monitor)

    2001-01-01

    The cosmic microwave background radiation is the remnant heat from the Big Bang. It provides us with a unique probe of conditions in the early universe, long before any organized structures had yet formed. The anisotropy in the radiation's brightness yields important clues about primordial structure and additionally provides a wealth of information about the physics,of the early universe. Within the framework of inflationary dark matter models observations of the anisotropy on sub-degree angular scales will reveal the signatures of acoustic oscillations of the photon-baryon fluid at a redshift of approx. 1100. The validity of inflationary models will be tested and, if agreement is found, accurate values for most of the key cosmological parameters will result. If disagreement is found, we will need to rethink our basic ideas about the physics of the early universe. I will present an overview of the physical processes at work in forming the anisotropy and discuss what we have already learned from current observations. I will conclude with a brief overview of the recently launched Microwave Anisotropy Probe (MAP) mission which will observe the anisotropy over the full sky with 0.21 degree angular resolution. At the time of this meeting, MAP will have just arrived at the L2 Lagrange point, marking the start of its observing campaign. The MAP hardware is being produced by Goddard in partnership with Princeton University.

  2. Early Cognitive Outcomes Following Proton Radiation in Pediatric Patients With Brain and Central Nervous System Tumors

    International Nuclear Information System (INIS)

    Pulsifer, Margaret B.; Sethi, Roshan V.; Kuhlthau, Karen A.; MacDonald, Shannon M.; Tarbell, Nancy J.; Yock, Torunn I.

    2015-01-01

    Purpose: To report, from a longitudinal study, cognitive outcome in pediatric patients treated with proton radiation therapy (PRT) for central nervous system (CNS) tumors. Methods and Materials: Sixty patients receiving PRT for medulloblastoma (38.3%), gliomas (18.3%), craniopharyngioma (15.0%), ependymoma (11.7%), and other CNS tumors (16.7%) were administered age-appropriate measures of cognitive abilities at or near PRT initiation (baseline) and afterward (follow-up). Patients were aged ≥6 years at baseline to ensure consistency in neurocognitive measures. Results: Mean age was 12.3 years at baseline; mean follow-up interval was 2.5 years. Treatment included prior surgical resection (76.7%) and chemotherapy (61.7%). Proton radiation therapy included craniospinal irradiation (46.7%) and partial brain radiation (53.3%). At baseline, mean Wechsler Full Scale IQ was 104.6; means of all 4 Index scores were also in the average range. At follow-up, no significant change was observed in mean Wechsler Full Scale IQ, Verbal Comprehension, Perceptual Reasoning/Organization, or Working Memory. However, Processing Speed scores declined significantly (mean 5.2 points), with a significantly greater decline for subjects aged <12 years at baseline and those with the highest baseline scores. Cognitive outcome was not significantly related to gender, extent of radiation, radiation dose, tumor location, histology, socioeconomic status, chemotherapy, or history of surgical resection. Conclusions: Early cognitive outcomes after PRT for pediatric CNS tumors are encouraging, compared with published outcomes from photon radiation therapy

  3. Early Cognitive Outcomes Following Proton Radiation in Pediatric Patients With Brain and Central Nervous System Tumors

    Energy Technology Data Exchange (ETDEWEB)

    Pulsifer, Margaret B., E-mail: mpulsifer@mgh.harvard.edu [Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts (United States); Sethi, Roshan V. [Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts (United States); Kuhlthau, Karen A. [Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts (United States); MacDonald, Shannon M.; Tarbell, Nancy J.; Yock, Torunn I. [Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts (United States)

    2015-10-01

    Purpose: To report, from a longitudinal study, cognitive outcome in pediatric patients treated with proton radiation therapy (PRT) for central nervous system (CNS) tumors. Methods and Materials: Sixty patients receiving PRT for medulloblastoma (38.3%), gliomas (18.3%), craniopharyngioma (15.0%), ependymoma (11.7%), and other CNS tumors (16.7%) were administered age-appropriate measures of cognitive abilities at or near PRT initiation (baseline) and afterward (follow-up). Patients were aged ≥6 years at baseline to ensure consistency in neurocognitive measures. Results: Mean age was 12.3 years at baseline; mean follow-up interval was 2.5 years. Treatment included prior surgical resection (76.7%) and chemotherapy (61.7%). Proton radiation therapy included craniospinal irradiation (46.7%) and partial brain radiation (53.3%). At baseline, mean Wechsler Full Scale IQ was 104.6; means of all 4 Index scores were also in the average range. At follow-up, no significant change was observed in mean Wechsler Full Scale IQ, Verbal Comprehension, Perceptual Reasoning/Organization, or Working Memory. However, Processing Speed scores declined significantly (mean 5.2 points), with a significantly greater decline for subjects aged <12 years at baseline and those with the highest baseline scores. Cognitive outcome was not significantly related to gender, extent of radiation, radiation dose, tumor location, histology, socioeconomic status, chemotherapy, or history of surgical resection. Conclusions: Early cognitive outcomes after PRT for pediatric CNS tumors are encouraging, compared with published outcomes from photon radiation therapy.

  4. Remembrances of the early fifteen years of radiation protection at the National Atomic Energy Commission. Part 2

    International Nuclear Information System (INIS)

    Placer, Alejandro E.

    2005-01-01

    Personal memories on the origin of radiation protection activities in Argentina. This second part covers the period from 1957 to the early sixties and describes the persons and facts that led to the future development of radiation protection in the country [es

  5. The early effects of ionizing radiation on pancreatic endocrine cells in mouse: an immunocytochemistry study

    International Nuclear Information System (INIS)

    Kosanlavit, Rachian; McCullough, Stephen

    2003-06-01

    Prodromal radiation sickness can occur within 30 minutes following irradiation. The early sign is a fatigue, accompanied by other symptoms including diarrhoea, intestinal cramps, nausea and vomiting. This event is often very significant. The contribution of pancreatic damage towards these post-irradiation symptoms is not clear. This study is to assess the volume density, by using the point counting method, of insulin-, glucagon-, somatostatin-, and pancreatic polypeptide-containing cells of mouse pancreas following X-irradiation with doses of 5 and 10 Gy. It uses an in vitro system sampled at 30 minutes, 1 and 3 hours. A radiation dose of 10 Gy significantly decreased the volume density of glucagon-containing cells at 1 hour incubation time and radiation doses of 5 and 10 Gy slightly decreased the volume density of somatostatin-containing cells at all time points. These changes may result in disturbances in metabolism of nutrients, which possibly lead to several symptoms (e.g. fatigue and weight loss) associated with prodromal radiation sickness

  6. Radiation exposure and disease questionnaires of early entrants after the Hiroshima bombing

    International Nuclear Information System (INIS)

    Imanaka, T.; Endo, S.; Kawano, N.; Tanaka, K.

    2012-01-01

    It is popularly known that people who entered into the ground-zero area shortly after the atomic bombings in Hiroshima and Nagasaki suffered from various syndromes similar to acute radiation effects. External exposures from neutron-induced radionuclides in soil have recently been reassessed based on DS02 calculations as functions of both distance from the hypo-centres and elapsed time after the explosions. Significant exposure due to induced radiation can be determined for those who entered the area within 1000 m from the hypo-centres shortly after the bombing. Although it was impossible to track the action of each of the survivors over the days or weeks following the bombings in order to make reliable dose estimates for their exposures to soil activation or fallout, four individuals among those early entrants were investigated here to describe useful information of what happened shortly after the bombing. (authors)

  7. GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training

    Science.gov (United States)

    Atwood, Teresa K.; Bongcam-Rudloff, Erik; Brazas, Michelle E.; Corpas, Manuel; Gaudet, Pascale; Lewitter, Fran; Mulder, Nicola; Palagi, Patricia M.; Schneider, Maria Victoria; van Gelder, Celia W. G.

    2015-01-01

    In recent years, high-throughput technologies have brought big data to the life sciences. The march of progress has been rapid, leaving in its wake a demand for courses in data analysis, data stewardship, computing fundamentals, etc., a need that universities have not yet been able to satisfy—paradoxically, many are actually closing “niche” bioinformatics courses at a time of critical need. The impact of this is being felt across continents, as many students and early-stage researchers are being left without appropriate skills to manage, analyse, and interpret their data with confidence. This situation has galvanised a group of scientists to address the problems on an international scale. For the first time, bioinformatics educators and trainers across the globe have come together to address common needs, rising above institutional and international boundaries to cooperate in sharing bioinformatics training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all. PMID:25856076

  8. Bioinformatic tools for PCR Primer design

    African Journals Online (AJOL)

    ES

    Bioinformatics is an emerging scientific discipline that uses information ... complex biological questions. ... and computer programs for various purposes of primer ..... polymerase chain reaction: Human Immunodeficiency Virus 1 model studies.

  9. Challenge: A Multidisciplinary Degree Program in Bioinformatics

    Directory of Open Access Journals (Sweden)

    Mudasser Fraz Wyne

    2006-06-01

    Full Text Available Bioinformatics is a new field that is poorly served by any of the traditional science programs in Biology, Computer science or Biochemistry. Known to be a rapidly evolving discipline, Bioinformatics has emerged from experimental molecular biology and biochemistry as well as from the artificial intelligence, database, pattern recognition, and algorithms disciplines of computer science. While institutions are responding to this increased demand by establishing graduate programs in bioinformatics, entrance barriers for these programs are high, largely due to the significant prerequisite knowledge which is required, both in the fields of biochemistry and computer science. Although many schools currently have or are proposing graduate programs in bioinformatics, few are actually developing new undergraduate programs. In this paper I explore the blend of a multidisciplinary approach, discuss the response of academia and highlight challenges faced by this emerging field.

  10. Deciphering psoriasis. A bioinformatic approach.

    Science.gov (United States)

    Melero, Juan L; Andrades, Sergi; Arola, Lluís; Romeu, Antoni

    2018-02-01

    Psoriasis is an immune-mediated, inflammatory and hyperproliferative disease of the skin and joints. The cause of psoriasis is still unknown. The fundamental feature of the disease is the hyperproliferation of keratinocytes and the recruitment of cells from the immune system in the region of the affected skin, which leads to deregulation of many well-known gene expressions. Based on data mining and bioinformatic scripting, here we show a new dimension of the effect of psoriasis at the genomic level. Using our own pipeline of scripts in Perl and MySql and based on the freely available NCBI Gene Expression Omnibus (GEO) database: DataSet Record GDS4602 (Series GSE13355), we explore the extent of the effect of psoriasis on gene expression in the affected tissue. We give greater insight into the effects of psoriasis on the up-regulation of some genes in the cell cycle (CCNB1, CCNA2, CCNE2, CDK1) or the dynamin system (GBPs, MXs, MFN1), as well as the down-regulation of typical antioxidant genes (catalase, CAT; superoxide dismutases, SOD1-3; and glutathione reductase, GSR). We also provide a complete list of the human genes and how they respond in a state of psoriasis. Our results show that psoriasis affects all chromosomes and many biological functions. If we further consider the stable and mitotically inheritable character of the psoriasis phenotype, and the influence of environmental factors, then it seems that psoriasis has an epigenetic origin. This fit well with the strong hereditary character of the disease as well as its complex genetic background. Copyright © 2017 Japanese Society for Investigative Dermatology. Published by Elsevier B.V. All rights reserved.

  11. Concepts and introduction to RNA bioinformatics

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Hofacker, Ivo L.; Ruzzo, Walter L.

    2014-01-01

    RNA bioinformatics and computational RNA biology have emerged from implementing methods for predicting the secondary structure of single sequences. The field has evolved to exploit multiple sequences to take evolutionary information into account, such as compensating (and structure preserving) base...... for interactions between RNA and proteins.Here, we introduce the basic concepts of predicting RNA secondary structure relevant to the further analyses of RNA sequences. We also provide pointers to methods addressing various aspects of RNA bioinformatics and computational RNA biology....

  12. Early and late radiation response of human skin following chronic exposure of the hands

    International Nuclear Information System (INIS)

    Lenz, U.; Arndt, D.; Thormann, T.

    1979-01-01

    Clinical examinations on 45 radiation workers with chronical low-level exposures to their hands revealed that accumulated doses in the range of 15 to 30 Sv (1500 to 3000 rem) may already produce macroscopically unconspicuous early alterations of the vessel system within the corium as well as epidermal hyperplasia. Therefore, the annual permissible dose equivalent of 0.75 Sv (75 rem) recommended by ICRP for the skin of the extremities appears unjustifiably high and should be reduced to 0.30 Sv (30 rem), the limit valid for the remaining areas of skin. (author)

  13. Bioinformatics meets user-centred design: a perspective.

    Directory of Open Access Journals (Sweden)

    Katrina Pavelin

    Full Text Available Designers have a saying that "the joy of an early release lasts but a short time. The bitterness of an unusable system lasts for years." It is indeed disappointing to discover that your data resources are not being used to their full potential. Not only have you invested your time, effort, and research grant on the project, but you may face costly redesigns if you want to improve the system later. This scenario would be less likely if the product was designed to provide users with exactly what they need, so that it is fit for purpose before its launch. We work at EMBL-European Bioinformatics Institute (EMBL-EBI, and we consult extensively with life science researchers to find out what they need from biological data resources. We have found that although users believe that the bioinformatics community is providing accurate and valuable data, they often find the interfaces to these resources tricky to use and navigate. We believe that if you can find out what your users want even before you create the first mock-up of a system, the final product will provide a better user experience. This would encourage more people to use the resource and they would have greater access to the data, which could ultimately lead to more scientific discoveries. In this paper, we explore the need for a user-centred design (UCD strategy when designing bioinformatics resources and illustrate this with examples from our work at EMBL-EBI. Our aim is to introduce the reader to how selected UCD techniques may be successfully applied to software design for bioinformatics.

  14. Treatment-time-dependence models of early and delayed radiation injury in rat small intestine

    International Nuclear Information System (INIS)

    Denham, James W.; Hauer-Jensen, Martin; Kron, Tomas; Langberg, Carl W.

    2000-01-01

    Background: The present study modeled data from a large series of experiments originally designed to investigate the influence of time, dose, and fractionation on early and late pathologic endpoints in rat small intestine after localized irradiation. The objective was to obtain satisfactory descriptions of the regenerative response to injury together with the possible relationships between early and late endpoints. Methods: Two- and 26-week pathologic radiation injury data in groups of Sprague-Dawley rats irradiated with 27 different fractionation schedules were modeled using the incomplete repair (IR) version of the linear-quadratic model with or without various time correction models. The following time correction models were tested: (1) No time correction; (2) A simple exponential (SE) regenerative response beginning at an arbitrary time after starting treatment; and (3) A bi-exponential response with its commencement linked to accumulated cellular depletion and fraction size (the 'intelligent response model' [INTR]). Goodness of fit of the various models was assessed by correlating the predicted biological effective dose for each dose group with the observed radiation injury score. Results: (1) The incomplete repair model without time correction did not provide a satisfactory description of either the 2- or 26-week data. (2) The models using SE time correction performed better, providing modest descriptions of the data. (3) The INTR model provided reasonable descriptions of both the 2- and 26-week data, confirming a treatment time dependence of both early and late pathological endpoints. (4) The most satisfactory descriptions of the data by the INTR model were obtained when the regenerative response was assumed to cease 2 weeks after irradiation rather than at the end of irradiation. A fraction-size-dependent delay of the regenerative response was also suggested in the best fitting models. (5) Late endpoints were associated with low-fractionation sensitivity

  15. Effect of age on radiation-induced early changes of rat rectum. A histological time sequence

    International Nuclear Information System (INIS)

    Olofsen-van Acht, Manouk J.J.; Hooije, Christel M.C. van; Aardweg, Gerard J.M.J. van den; Levendag, Peter C.; Velthuysen, Marie Louise F. van

    2001-01-01

    Background and purpose: Radiation treatment of the elderly (>75 years) is often modified due to an assumed decrease in normal tissue tolerance in this age group. Since more radiobiological data concerning normal tissue toxicity as a function of age are needed, a histological study of age-related radiation changes of the rectum was performed. Materials and methods: The rectum of young and old female Wistar rats (12 and 78 weeks, respectively) was irradiated with single doses of 22 and 39 Gy. The field size was 1.5x2.0 cm. The animals were sacrificed at 1, 2, 4 and 10 weeks after treatment. To evaluate radiation damage, 12 histological parameters were scored in four areas of the rectum. A total radiation injury score was calculated. The number of proliferative epithelial cells was evaluated by 5-bromo-2'-deoxyuridine labeling. Results: Some age-related histological differences were observed; especially, the incidence of ulceration and vascular occlusion was higher in the older group. In the low dose group of the older animals, 60% showed ulceration, which was 0% for the young low dose animals. Severe vascular changes occurred early and were more extensive in older animals (4 weeks) than in the younger group (10 weeks). In the area adjacent to the treatment field, cell proliferation increased significantly in older rats at 1 week after 22 Gy, which did not occur in the young group. Conclusions: Discrete radiation-induced histological differences were observed between the rectum of young and old Wistar rats, especially in the development of ulceration and vascular changes. Although the survival of these Wistar rats in earlier studies was not affected by age, the impact of the observed histological differences for their importance in the long-term is currently being investigated

  16. Radiation Therapy Planning for Early-Stage Hodgkin Lymphoma: Experience of the International Lymphoma Radiation Oncology Group

    International Nuclear Information System (INIS)

    Maraldo, Maja V.; Dabaja, Bouthaina S.; Filippi, Andrea R.; Illidge, Tim; Tsang, Richard; Ricardi, Umberto; Petersen, Peter M.; Schut, Deborah A.; Garcia, John; Headley, Jayne; Parent, Amy; Guibord, Benoit; Ragona, Riccardo; Specht, Lena

    2015-01-01

    Purpose: Early-stage Hodgkin lymphoma (HL) is a rare disease, and the location of lymphoma varies considerably between patients. Here, we evaluate the variability of radiation therapy (RT) plans among 5 International Lymphoma Radiation Oncology Group (ILROG) centers with regard to beam arrangements, planning parameters, and estimated doses to the critical organs at risk (OARs). Methods: Ten patients with stage I-II classic HL with masses of different sizes and locations were selected. On the basis of the clinical information, 5 ILROG centers were asked to create RT plans to a prescribed dose of 30.6 Gy. A postchemotherapy computed tomography scan with precontoured clinical target volume (CTV) and OARs was provided for each patient. The treatment technique and planning methods were chosen according to each center's best practice in 2013. Results: Seven patients had mediastinal disease, 2 had axillary disease, and 1 had disease in the neck only. The median age at diagnosis was 34 years (range, 21-74 years), and 5 patients were male. Of the resulting 50 treatment plans, 15 were planned with volumetric modulated arc therapy (1-4 arcs), 16 with intensity modulated RT (3-9 fields), and 19 with 3-dimensional conformal RT (2-4 fields). The variations in CTV-to-planning target volume margins (5-15 mm), maximum tolerated dose (31.4-40 Gy), and plan conformity (conformity index 0-3.6) were significant. However, estimated doses to OARs were comparable between centers for each patient. Conclusions: RT planning for HL is challenging because of the heterogeneity in size and location of disease and, additionally, to the variation in choice of treatment techniques and field arrangements. Adopting ILROG guidelines and implementing universal dose objectives could further standardize treatment techniques and contribute to lowering the dose to the surrounding OARs

  17. The Cosmic Microwave Background Radiation-A Unique Window on the Early Universe

    Science.gov (United States)

    Hinshaw, Gary

    2010-01-01

    The cosmic microwave background radiation is the remnant heat from the Big Bang. It provides us with a unique probe of conditions in the early universe, long before any organized structures had yet formed. The anisotropy in the radiation's brightness yields important clues about primordial structure and additionally provides a wealth of information about the physics of the early universe. Within the framework of inflationary dark matter models, observations of the anisotropy on sub-degree angular scales reveals the signatures of acoustic oscillations of the photon-baryon fluid at a redshift of 11 00. Data from the first seven years of operation of the Wilkinson Microwave Anisotropy Probe (WMAP) satellite provide detailed full-sky maps of the cosmic microwave background temperature and polarization anisotropy. Together, the data provide a wealth of cosmological information, including the age of the universe, the epoch when the first stars formed, and the overall composition of baryonic matter, dark matter, and dark energy. The results also provide constraints on the period of inflationary expansion in the very first moments of time. WMAP, part of NASA's Explorers program, was launched on June 30, 2001. The WMAP satellite was produced in a partnership between the Goddard Space Flight Center and Princeton University. The WMAP team also includes researchers at the Johns Hopkins University; the Canadian Institute of Theoretical Astrophysics; University of Texas; Oxford University; University of Chicago; Brown University; University of British Columbia; and University of California, Los Angeles.

  18. A web based on-line radiation early warning system for emergency preparedness and response centre

    International Nuclear Information System (INIS)

    Bhujbal, Vaibhav; Saindane, Shashank S.; Narasaiah, M.V.R.; Murali, S.

    2018-01-01

    The topography of the Bhabha Atomic Research Centre, Trombay site, where all major components of nuclear fuel cycle activities are located is very complex in nature. The assessment of the radiological impact, if any, due to atmospheric releases from these facilities within BARC site is being carried out by using a Local Area Network (LAN) based Radiation Early Warning System and meteorological parameters. The upgraded system is aimed at providing data during normal operation of the various facilities at site and for providing early warning to decision makers in case of any onset of an emergency. It is carried out by acquiring both on-line and off-line data on releases from the plants, the environmental radiation dose rate at selected locations and other related parameters. The monitors placed at these selected locations including strategic point around the BARC site can also help in detecting any attempt of unauthorized trafficking of the radioactive sources. This paper explains different aspects of the system operating at BARC

  19. Cutaneous radiation syndrome: applicability of comet assay for early assessment of irradiation consequences

    International Nuclear Information System (INIS)

    Di Giorgio, Marina; Taja, Maria R.; Bolgiani, A.; Bustos, N.; Cavalieri, H.

    2002-01-01

    Many accidental overexposures to ionizing radiation lead to an inhomogeneous irradiation of the body. Skin and mucous membranes resulted exposed to very high local radiation doses, which may be survivable because bone marrow is less severely exposed. Under these circumstances, the skin becomes an important organ in determining clinical prognosis, being dosimetric assessment a necessary requirement. There is increasing interest in the assessment of biological markers that permit the detection of radiation induced damage in the localized irradiations. The 'Comet Assay' (single cell gel electrophoresis) is a sensitive, rapid and relatively inexpensive method for measuring DNA damage in individual cells. Single cells are embedded in agarose on microscope slides, lysed to remove the majority of the proteins, electrophoreses, then stained with ethidium bromide in order to visualize the DNA. Following radiation damage, the smaller the fragment size and the grater the number of fragments of DNA, the grater the percentage of DNA that it is able to migrate in an electric field, forming a comet image. The assay can be performed under alkaline conditions to examine DNA single strand breaks (SSBs), or in non denaturing (neutral) conditions to measure double strand breaks (DSBs) in individual cells. In order to get information to be applied on the evaluation of skin biopsies without culture for an early assessment of irradiation consequences in locally irradiated individuals, we have evaluated the alkaline comet assay (for doses 5 Gy), neutral comet assay has been applied to keratinocytes from primary and secondary cultures and to a suspension of epidermal cells obtained from biopsies irradiated in vitro and afterwards processed to obtain the mentioned cellular suspension, in order to reproduce the closest condition to in vivo overexposure. Our results suggest that comet assay can be applied for the early assessment of gamma radiation induced damage in skin biopsies without

  20. Predictors of delay in starting radiation treatment for patients with early stage breast cancer

    International Nuclear Information System (INIS)

    Benk, Veronique; Ho, Vivian; Fortin, Paul R.; Zhang, G.; Levinton, Carey; Freeman, C.R.

    1998-01-01

    Purpose: To describe the factors predicting waiting time for radiation treatment in early breast cancer. Materials and Methods: Between January 1992 and December 1993, 739 patients with Stage I and II breast cancer were treated with conservative treatment at three McGill University Hospitals. Waiting time was defined as the interval between the date of surgery and the date of the first radiation treatment. Delay was defined as a waiting time of more than 7 weeks for women who did not receive chemotherapy (Group NC, n 478), and as a waiting time of more than 24 weeks for those who received chemotherapy (Group C, n = 261). We analyzed predictive factors related to the patient (age, stage, treatment on protocol, income by postal code) and to the referring hospital (university or community hospital). Results: For the entire population, 54% of patients were delayed, 72% in Group NC and 21.4% in Group C. Univariate analysis showed an impact of referring hospital in both groups, and of stage and treatment on protocol in Group C (all p = 0.001). Multivariate analysis showed that delays were significantly less in Group NC for women referred from a community hospital (p = 0.001) and in Group C for women with Stage I disease (p = 0.06), those treated on protocol, and those referred from a university hospital (p = 0.001). Conclusion: More than half of patients with early breast cancer waited more than the recommended intervals for radiation therapy. However, lower income breast cancer patients did not wait longer for treatment than higher income patients, possibly a result of the Canadian Medicare system which provides universal access to health care

  1. Navigating the changing learning landscape: perspective from bioinformatics.ca

    OpenAIRE

    Brazas, Michelle D.; Ouellette, B. F. Francis

    2013-01-01

    With the advent of YouTube channels in bioinformatics, open platforms for problem solving in bioinformatics, active web forums in computing analyses and online resources for learning to code or use a bioinformatics tool, the more traditional continuing education bioinformatics training programs have had to adapt. Bioinformatics training programs that solely rely on traditional didactic methods are being superseded by these newer resources. Yet such face-to-face instruction is still invaluable...

  2. Adoption of Intensity Modulated Radiation Therapy For Early-Stage Breast Cancer From 2004 Through 2011

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Elyn H. [Yale School of Medicine, New Haven, Connecticut (United States); Mougalian, Sarah S. [Yale School of Medicine, New Haven, Connecticut (United States); Yale Cancer Center, New Haven, Connecticut (United States); Cancer Outcomes, Public Policy, and Effectiveness Research Center at Yale, New Haven, Connecticut (United States); Soulos, Pamela R. [Yale School of Medicine, New Haven, Connecticut (United States); Cancer Outcomes, Public Policy, and Effectiveness Research Center at Yale, New Haven, Connecticut (United States); Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut (United States); Smith, Benjamin D. [Department of Radiation Oncology, MD Anderson Cancer Center, Houston, Texas (United States); Haffty, Bruce G. [Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey (United States); Gross, Cary P. [Yale School of Medicine, New Haven, Connecticut (United States); Cancer Outcomes, Public Policy, and Effectiveness Research Center at Yale, New Haven, Connecticut (United States); Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut (United States); Yu, James B., E-mail: james.b.yu@yale.edu [Yale School of Medicine, New Haven, Connecticut (United States); Cancer Outcomes, Public Policy, and Effectiveness Research Center at Yale, New Haven, Connecticut (United States); Department of Therapeutic Radiology, Yale School of Medicine, New Haven, Connecticut (United States)

    2015-02-01

    Purpose: Intensity modulated radiation therapy (IMRT) is a newer method of radiation therapy (RT) that has been increasingly adopted as an adjuvant treatment after breast-conserving surgery (BCS). IMRT may result in improved cosmesis compared to standard RT, although at greater expense. To investigate the adoption of IMRT, we examined trends and factors associated with IMRT in women under the age of 65 with early stage breast cancer. Methods and Materials: We performed a retrospective study of early stage breast cancer patients treated with BCS followed by whole-breast irradiation (WBI) who were ≤65 years old in the National Cancer Data Base from 2004 to 2011. We used logistic regression to identify factors associated with receipt of IMRT (vs standard RT). Results: We identified 11,089 women with early breast cancer (9.6%) who were treated with IMRT and 104,448 (90.4%) who were treated with standard RT, after BCS. The proportion of WBI patients receiving IMRT increased yearly from 2004 to 2009, with 5.3% of WBI patients receiving IMRT in 2004 and 11.6% receiving IMRT in 2009. Further use of IMRT declined afterward, with the proportion remaining steady at 11.0% and 10.7% in 2010 and 2011, respectively. Patients treated in nonacademic community centers were more likely to receive IMRT (odds ratio [OR], 1.36; 95% confidence interval [CI], 1.30-1.43 for nonacademic vs academic center). Compared to privately insured patients, the uninsured patients (OR, 0.81; 95% CI, 0.70-0.95) and those with Medicaid insurance (OR, 0.87; 95% CI, 0.79-0.95) were less likely to receive IMRT. Conclusions: The use of IMRT rose from 2004 to 2009 and then stabilized. Important nonclinical factors associated with IMRT use included facility type and insurance status.

  3. Adoption of Intensity Modulated Radiation Therapy For Early-Stage Breast Cancer From 2004 Through 2011

    International Nuclear Information System (INIS)

    Wang, Elyn H.; Mougalian, Sarah S.; Soulos, Pamela R.; Smith, Benjamin D.; Haffty, Bruce G.; Gross, Cary P.; Yu, James B.

    2015-01-01

    Purpose: Intensity modulated radiation therapy (IMRT) is a newer method of radiation therapy (RT) that has been increasingly adopted as an adjuvant treatment after breast-conserving surgery (BCS). IMRT may result in improved cosmesis compared to standard RT, although at greater expense. To investigate the adoption of IMRT, we examined trends and factors associated with IMRT in women under the age of 65 with early stage breast cancer. Methods and Materials: We performed a retrospective study of early stage breast cancer patients treated with BCS followed by whole-breast irradiation (WBI) who were ≤65 years old in the National Cancer Data Base from 2004 to 2011. We used logistic regression to identify factors associated with receipt of IMRT (vs standard RT). Results: We identified 11,089 women with early breast cancer (9.6%) who were treated with IMRT and 104,448 (90.4%) who were treated with standard RT, after BCS. The proportion of WBI patients receiving IMRT increased yearly from 2004 to 2009, with 5.3% of WBI patients receiving IMRT in 2004 and 11.6% receiving IMRT in 2009. Further use of IMRT declined afterward, with the proportion remaining steady at 11.0% and 10.7% in 2010 and 2011, respectively. Patients treated in nonacademic community centers were more likely to receive IMRT (odds ratio [OR], 1.36; 95% confidence interval [CI], 1.30-1.43 for nonacademic vs academic center). Compared to privately insured patients, the uninsured patients (OR, 0.81; 95% CI, 0.70-0.95) and those with Medicaid insurance (OR, 0.87; 95% CI, 0.79-0.95) were less likely to receive IMRT. Conclusions: The use of IMRT rose from 2004 to 2009 and then stabilized. Important nonclinical factors associated with IMRT use included facility type and insurance status

  4. Survival rate of patients with differentiated thyroid cancer without early postoperative external radiation of the neck

    International Nuclear Information System (INIS)

    Saur, H.B.; Lerch, H.; Schober, O.

    1996-01-01

    Results of survival rates in differentiated thyroid carcinoma and comparison with a review of literature are given. Four hundred and sixty-four patients with differentiated cancer of the thyroid (354 female, 110 male, range: 6 to 84 years, median: 46.8 years; 275 patients with papillary and 190 with follicular cancer) were analyzed retrospectively. All patients were treated with ablative doses of radioiodine after thyroidectomy including compartment oriented lymphadenectomy in 27 patients. All patients passed an individual systematic follow-up according to risk: 'Low risk' pT≤3NxM0 vs. 'high risk' pT4 and/or M1. Early postoperative radiation was not included even in patients with local invasion (pT4). The corrected 5- and 10-year survival rates for papillary cancer are 0.91 and 0.91, for follicular cancer 0.94 resp. 0.78 (p=0.55), age (≤40 years 0.96 and 0.96, >40 years 0.90 and 0.80; p=0.008), gender (female 0.93 and 0.92, male 0.90 and 0.70; p=0.06) and invasion/distant metastases (pT4 and/or M1 0.83 and 0.71, other 0.97 and 0.97; p=0.0001). A systematic follow-up with an individually adapted standardized scheme is associated with high survival rates in patients with differentiated cancer of the thyroid. Early diagnosis of recurrences, locoregional lymph node and distant metastases with early surgical treatment including compartment oriented lymphadenectomy and radioiodine therapy yield high survival even without external radiation. (orig./MG) [de

  5. Development of Bioinformatics Infrastructure for Genomics Research.

    Science.gov (United States)

    Mulder, Nicola J; Adebiyi, Ezekiel; Adebiyi, Marion; Adeyemi, Seun; Ahmed, Azza; Ahmed, Rehab; Akanle, Bola; Alibi, Mohamed; Armstrong, Don L; Aron, Shaun; Ashano, Efejiro; Baichoo, Shakuntala; Benkahla, Alia; Brown, David K; Chimusa, Emile R; Fadlelmola, Faisal M; Falola, Dare; Fatumo, Segun; Ghedira, Kais; Ghouila, Amel; Hazelhurst, Scott; Isewon, Itunuoluwa; Jung, Segun; Kassim, Samar Kamal; Kayondo, Jonathan K; Mbiyavanga, Mamana; Meintjes, Ayton; Mohammed, Somia; Mosaku, Abayomi; Moussa, Ahmed; Muhammd, Mustafa; Mungloo-Dilmohamud, Zahra; Nashiru, Oyekanmi; Odia, Trust; Okafor, Adaobi; Oladipo, Olaleye; Osamor, Victor; Oyelade, Jellili; Sadki, Khalid; Salifu, Samson Pandam; Soyemi, Jumoke; Panji, Sumir; Radouani, Fouzia; Souiai, Oussama; Tastan Bishop, Özlem

    2017-06-01

    Although pockets of bioinformatics excellence have developed in Africa, generally, large-scale genomic data analysis has been limited by the availability of expertise and infrastructure. H3ABioNet, a pan-African bioinformatics network, was established to build capacity specifically to enable H3Africa (Human Heredity and Health in Africa) researchers to analyze their data in Africa. Since the inception of the H3Africa initiative, H3ABioNet's role has evolved in response to changing needs from the consortium and the African bioinformatics community. H3ABioNet set out to develop core bioinformatics infrastructure and capacity for genomics research in various aspects of data collection, transfer, storage, and analysis. Various resources have been developed to address genomic data management and analysis needs of H3Africa researchers and other scientific communities on the continent. NetMap was developed and used to build an accurate picture of network performance within Africa and between Africa and the rest of the world, and Globus Online has been rolled out to facilitate data transfer. A participant recruitment database was developed to monitor participant enrollment, and data is being harmonized through the use of ontologies and controlled vocabularies. The standardized metadata will be integrated to provide a search facility for H3Africa data and biospecimens. Because H3Africa projects are generating large-scale genomic data, facilities for analysis and interpretation are critical. H3ABioNet is implementing several data analysis platforms that provide a large range of bioinformatics tools or workflows, such as Galaxy, the Job Management System, and eBiokits. A set of reproducible, portable, and cloud-scalable pipelines to support the multiple H3Africa data types are also being developed and dockerized to enable execution on multiple computing infrastructures. In addition, new tools have been developed for analysis of the uniquely divergent African data and for

  6. Risk of Fatal Cerebrovascular Accidents after External Beam Radiation Therapy for Early Stage Glottic Larynx Cancer

    Science.gov (United States)

    Swisher-McClure, Samuel; Mitra, Nandita; Lin, Alexander; Ahn, Peter; Wan, Fei; O’Malley, Bert; Weinstein, Gregory S.; Bekelman, Justin E.

    2013-01-01

    Background This study compared the risk of fatal cerebrovascular accidents (CVA) in patients with early stage glottic larynx cancer receiving surgery or external beam radiation therapy (EBRT). Methods and Materials Using a competing risks survival analysis, we compared the risk of death due to CVA among patients with early stage glottic larynx cancer receiving surgery or EBRT in the SEER database. Results The cumulative incidence of fatal CVA at 15 years was higher in patients receiving EBRT (2.8 %; 95% CI 2.3%–3.4%) compared to surgery (1.5 %; 95% CI 0.8 %–2.3%, p= 0.024). In multivariable competing risks regression models, EBRT remained associated with an increased risk of fatal CVA compared to surgery (adjusted HR 1.75; 95% CI 1.04–2.96, p= 0.037). Conclusion Treatment of early stage glottic larynx cancer with EBRT was associated with a small increase in the risk of late fatal CVA events relative to surgery. PMID:23595858

  7. Radiation therapy alone for early stage non-small cell carcinoma of the lung

    International Nuclear Information System (INIS)

    Chun, Ha Chung; Lee, Myung Za

    2002-01-01

    To evaluate the outcome of early stage non-small cell lung cancer patients who were treated with radiation therapy along and define the optimal radiotherapeutic regimen for these patients. A retrospective review was performed on patients with sage I or II non-small cell carcinoma of the lung that were treated at our institution between June, 1987 and May, 2000. A total of 21 patients treated definitively with radiation therapy alone were included in this study. The age of the patients ranged from 53 to 81 years with a median of 66 years. All the patients were male. The medical reasons for inoperability were lack of pulmonary reserve, cardiovascular disease, poor performance status, old age, and patient refusal in the decreasing order. Pathological evidence was not adequate to characterize the non-small cell subtype in two patients. Of the remaining 19 patients, 16 had squamous cell carcinoma and 3 had adenocarcinoma. Treatment was given with conventional fractionation, once a day, five times a week. The doses to the primary site ranged from 56 Gy to 69 Gy. No patients were lost to follow-up. The overall survival rates for the entire group at 2, 3 and 5 years were 41, 30 and 21%, respectively. The cause specific survivals at 2, 3 and 5 years were 55, 36 and 25%, respectively. An intercurrent disease was the cause of death in two patients. The cumulative local failure rate at 5 years was 43%. Nine of the 21 patients had treatment failures after the curative radiotherapy was attempted. Local recurrences as the first site of failure were documented in 7 patients. Therefore, local failure alone represented 78% of the total failures. Those patients whose tumor sizes were less than 4 cm had a significantly better 5 year disease free survival than those with tumors greater than 4 cm (0% vs 36%). Those patients with a Karnofsky performance status less than 70 did not differ significantly with respect to actuarial survival when compared to those with a status greater than 70

  8. Translational Bioinformatics and Clinical Research (Biomedical) Informatics.

    Science.gov (United States)

    Sirintrapun, S Joseph; Zehir, Ahmet; Syed, Aijazuddin; Gao, JianJiong; Schultz, Nikolaus; Cheng, Donavan T

    2015-06-01

    Translational bioinformatics and clinical research (biomedical) informatics are the primary domains related to informatics activities that support translational research. Translational bioinformatics focuses on computational techniques in genetics, molecular biology, and systems biology. Clinical research (biomedical) informatics involves the use of informatics in discovery and management of new knowledge relating to health and disease. This article details 3 projects that are hybrid applications of translational bioinformatics and clinical research (biomedical) informatics: The Cancer Genome Atlas, the cBioPortal for Cancer Genomics, and the Memorial Sloan Kettering Cancer Center clinical variants and results database, all designed to facilitate insights into cancer biology and clinical/therapeutic correlations. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. Planning bioinformatics workflows using an expert system

    Science.gov (United States)

    Chen, Xiaoling; Chang, Jeffrey T.

    2017-01-01

    Abstract Motivation: Bioinformatic analyses are becoming formidably more complex due to the increasing number of steps required to process the data, as well as the proliferation of methods that can be used in each step. To alleviate this difficulty, pipelines are commonly employed. However, pipelines are typically implemented to automate a specific analysis, and thus are difficult to use for exploratory analyses requiring systematic changes to the software or parameters used. Results: To automate the development of pipelines, we have investigated expert systems. We created the Bioinformatics ExperT SYstem (BETSY) that includes a knowledge base where the capabilities of bioinformatics software is explicitly and formally encoded. BETSY is a backwards-chaining rule-based expert system comprised of a data model that can capture the richness of biological data, and an inference engine that reasons on the knowledge base to produce workflows. Currently, the knowledge base is populated with rules to analyze microarray and next generation sequencing data. We evaluated BETSY and found that it could generate workflows that reproduce and go beyond previously published bioinformatics results. Finally, a meta-investigation of the workflows generated from the knowledge base produced a quantitative measure of the technical burden imposed by each step of bioinformatics analyses, revealing the large number of steps devoted to the pre-processing of data. In sum, an expert system approach can facilitate exploratory bioinformatic analysis by automating the development of workflows, a task that requires significant domain expertise. Availability and Implementation: https://github.com/jefftc/changlab Contact: jeffrey.t.chang@uth.tmc.edu PMID:28052928

  10. The GMOD Drupal Bioinformatic Server Framework

    Science.gov (United States)

    Papanicolaou, Alexie; Heckel, David G.

    2010-01-01

    Motivation: Next-generation sequencing technologies have led to the widespread use of -omic applications. As a result, there is now a pronounced bioinformatic bottleneck. The general model organism database (GMOD) tool kit (http://gmod.org) has produced a number of resources aimed at addressing this issue. It lacks, however, a robust online solution that can deploy heterogeneous data and software within a Web content management system (CMS). Results: We present a bioinformatic framework for the Drupal CMS. It consists of three modules. First, GMOD-DBSF is an application programming interface module for the Drupal CMS that simplifies the programming of bioinformatic Drupal modules. Second, the Drupal Bioinformatic Software Bench (biosoftware_bench) allows for a rapid and secure deployment of bioinformatic software. An innovative graphical user interface (GUI) guides both use and administration of the software, including the secure provision of pre-publication datasets. Third, we present genes4all_experiment, which exemplifies how our work supports the wider research community. Conclusion: Given the infrastructure presented here, the Drupal CMS may become a powerful new tool set for bioinformaticians. The GMOD-DBSF base module is an expandable community resource that decreases development time of Drupal modules for bioinformatics. The biosoftware_bench module can already enhance biologists' ability to mine their own data. The genes4all_experiment module has already been responsible for archiving of more than 150 studies of RNAi from Lepidoptera, which were previously unpublished. Availability and implementation: Implemented in PHP and Perl. Freely available under the GNU Public License 2 or later from http://gmod-dbsf.googlecode.com Contact: alexie@butterflybase.org PMID:20971988

  11. The GMOD Drupal bioinformatic server framework.

    Science.gov (United States)

    Papanicolaou, Alexie; Heckel, David G

    2010-12-15

    Next-generation sequencing technologies have led to the widespread use of -omic applications. As a result, there is now a pronounced bioinformatic bottleneck. The general model organism database (GMOD) tool kit (http://gmod.org) has produced a number of resources aimed at addressing this issue. It lacks, however, a robust online solution that can deploy heterogeneous data and software within a Web content management system (CMS). We present a bioinformatic framework for the Drupal CMS. It consists of three modules. First, GMOD-DBSF is an application programming interface module for the Drupal CMS that simplifies the programming of bioinformatic Drupal modules. Second, the Drupal Bioinformatic Software Bench (biosoftware_bench) allows for a rapid and secure deployment of bioinformatic software. An innovative graphical user interface (GUI) guides both use and administration of the software, including the secure provision of pre-publication datasets. Third, we present genes4all_experiment, which exemplifies how our work supports the wider research community. Given the infrastructure presented here, the Drupal CMS may become a powerful new tool set for bioinformaticians. The GMOD-DBSF base module is an expandable community resource that decreases development time of Drupal modules for bioinformatics. The biosoftware_bench module can already enhance biologists' ability to mine their own data. The genes4all_experiment module has already been responsible for archiving of more than 150 studies of RNAi from Lepidoptera, which were previously unpublished. Implemented in PHP and Perl. Freely available under the GNU Public License 2 or later from http://gmod-dbsf.googlecode.com.

  12. Human radiation studies: Remembering the early years. Oral history of Julie Langham Grilly, February 3, 1995

    International Nuclear Information System (INIS)

    1995-09-01

    Julie Langham Grilly was interviewed by representatives of the US DOE Office of Human Radiation Experiments (OHRE) being the widow of Dr. Wright Langham, an investigator of principal interest of the committee. Her extensive experience with research at LANL was also of interest to the committee. Following a brief biographical sketch, Ms. Grilly relates her early postwar experience and her knowledge of Wright Langham's involvement in animal research at Los Alamos, radiolanthanum tests on monkeys, Eniwetok tissue examinations, research on tritium uptake in humans, plutonium injections, tritium injections, EDTA, and etc. In addition to illuminating her former husband as a researcher and as an individual, she also relates her remembrances of Louis Hempelman, Enrico Fermi, Oppenheimer, Edward Teller, and many others

  13. Human radiation studies: Remembering the early years. Oral history of Julie Langham Grilly, February 3, 1995

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-09-01

    Julie Langham Grilly was interviewed by representatives of the US DOE Office of Human Radiation Experiments (OHRE) being the widow of Dr. Wright Langham, an investigator of principal interest of the committee. Her extensive experience with research at LANL was also of interest to the committee. Following a brief biographical sketch, Ms. Grilly relates her early postwar experience and her knowledge of Wright Langham`s involvement in animal research at Los Alamos, radiolanthanum tests on monkeys, Eniwetok tissue examinations, research on tritium uptake in humans, plutonium injections, tritium injections, EDTA, and etc. In addition to illuminating her former husband as a researcher and as an individual, she also relates her remembrances of Louis Hempelman, Enrico Fermi, Oppenheimer, Edward Teller, and many others.

  14. Hematopoietic cell crisis: An early stage of evolving myeloid leukemia following radiation exposure

    International Nuclear Information System (INIS)

    Seed, T.M.

    1990-01-01

    Under select radiological conditions, chronic radiation exposure elicits a high incidence of myeloproliferative disease, principally myeloid leukemia (ML), in beagles. Previously we demonstrated that for full ML expression, a four-stage preclinical sequence is required, namely (1) suppression, (2) recovery, (3) accommodation, and (4) preleukemic transition. Within this pathological sequence, a critical early event has been identified as the acquisition of radioresistance by hematopoietic progenitors that serves to mediate a newfound regenerative hematopoietic capacity. As such, this event ''sets the stage'' for preleukemic progression by initiating progression from preclinical phase 1 to 2. Due to the nature of target cell suppression, the induction of crisis, and the outgrowth of progenitors with altered phenotypes, this preleukemic event resembles the ''immortalization'' step of the in vitro transformation sequence following induction with either physical and chemical carcinogens. The radiological, temporal, and biological dictates governing this event have been extensively evaluated and will be discussed in light of their role in the induction and progression of chronic radiation leukemia. 35 refs., 2 tabs

  15. Early radiation changes of normal dog brain following internal and external brain irradiation: A preliminary report

    International Nuclear Information System (INIS)

    Chin, H.; Maruyama, Y.; Markesbery, W.; Goldstein, S.; Wang, P.; Tibbs, P.; Young, B.; Feola, J.; Beach, L.

    1984-01-01

    To examine radiation-induced changes in the normal brain, internal or external radiation was given to normal dog brain. Seven medium-sized dogs were used in this study. Two dogs were controls and an ice-pick (plastic implant applicator) was placed in the right frontal lobe for about 5 hours but no irradiation. Two dogs underwent Cs-137 brain implantation for 4 and 5 hours, respectively using an ice-pick technique. Two dogs were given internal neutron irradiation using the same technique of intracerebral ice-pick brachytherapy. One dog received an external photon irradiation using 6-Mev Linear Accelerator. Postmortem microscopic examination was made to study the early cerebral changes to irradiation in three dogs: one control with no irradiation; one received intracerebral Cesium implantation; and one external photon irradiation. Vascular change was the most prominent microscopic finding. There were hemorrhage, endothelial proliferation and fibrinoid changes of small vessel wall. Most of the changes were localized in the white matter and the cortex remained intact. Details (CT, NMR and histological studies) are discussed

  16. Hematopoietic cell crisis: An early stage of evolving myeloid leukemia following radiation exposure

    Energy Technology Data Exchange (ETDEWEB)

    Seed, T.M.

    1990-01-01

    Under select radiological conditions, chronic radiation exposure elicits a high incidence of myeloproliferative disease, principally myeloid leukemia (ML), in beagles. Previously we demonstrated that for full ML expression, a four-stage preclinical sequence is required, namely (1) suppression, (2) recovery, (3) accommodation, and (4) preleukemic transition. Within this pathological sequence, a critical early event has been identified as the acquisition of radioresistance by hematopoietic progenitors that serves to mediate a newfound regenerative hematopoietic capacity. As such, this event sets the stage'' for preleukemic progression by initiating progression from preclinical phase 1 to 2. Due to the nature of target cell suppression, the induction of crisis, and the outgrowth of progenitors with altered phenotypes, this preleukemic event resembles the immortalization'' step of the in vitro transformation sequence following induction with either physical and chemical carcinogens. The radiological, temporal, and biological dictates governing this event have been extensively evaluated and will be discussed in light of their role in the induction and progression of chronic radiation leukemia. 35 refs., 2 tabs.

  17. Human radiation studies: Remembering the early years. Oral history of biochemist John Randolph Totter, Ph.D., January 23, 1995

    International Nuclear Information System (INIS)

    1995-09-01

    This document is a transcript of an interview of Dr. John Randolph Tottler by representatives of the US DOE Office of Human Radiation Experiments. Dr. Tottler was selected for this interview because of his career with the Atomic Energy Commission Division of Biology and Medicine (DBM), particularly as its director from 1967 to 1972. After a short biographical sketch Dr. Tottler discusses his remembrances on a wide range topics including nucleic acid and leukemia research at Oak Ridge, AEC biochemistry training in South America, DBM's research focus on radiation effects, early leadership of DBM, relations with the US Public Health Service, controversies on low-level radiation, iodine from fallout, on John Gofman, and Project Plowshare, funding for AEC Research Programs and for international research, testicular irradiation of prisoners in Washington State and Oregon, Plutonium injections, ethics of government radiation research, and opinions of public misperceptions about radiation and cancer

  18. Low-Dose Consolidation Radiation Therapy for Early Stage Unfavorable Hodgkin Lymphoma

    Energy Technology Data Exchange (ETDEWEB)

    Torok, Jordan A., E-mail: jordan.torok@dm.duke.edu [Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina (United States); Wu, Yuan [Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina (United States); Prosnitz, Leonard R.; Kim, Grace J. [Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina (United States); Beaven, Anne W.; Diehl, Louis F. [Division of Hematologic Malignancy and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, North Carolina (United States); Kelsey, Chris R. [Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina (United States)

    2015-05-01

    Purpose: The German Hodgkin Study Group (GHSG) trial HD11 established 4 cycles of doxorubicin, bleomycin, vinblastine, and dacarbazine (ABVD) and 30 Gy of radiation therapy (RT) as a standard for early stage (I, II), unfavorable Hodgkin lymphoma (HL). Additional cycles of ABVD may allow for a reduction in RT dose and improved toxicity profile. Methods and Materials: Patients treated with combined modality therapy at the Duke Cancer Institute for early stage, unfavorable HL by GHSG criteria from 1994 to 2012 were included. Patients who did not undergo post-chemotherapy functional imaging (positron emission tomography or gallium imaging) or who failed to achieve a complete response were excluded. Clinical outcomes were estimated using the Kaplan-Meier method. Late effects were also evaluated. Results: A total of 90 patients met inclusion criteria for analysis. Median follow-up was 5 years. Chemotherapy consisted primarily of ABVD (88%) with a median number of 6 cycles. The median dose of consolidation RT was 23.4 Gy. Four patients had relapses, 2 of which were in-field. Ten-year progression-free survival (PFS) and overall survival (OS) were 93% (95% confidence interval [CI]: 0.82-0.97) and 98% (95% CI: 0.92-0.99), respectively. For the subset of patients (n=46) who received 5 to 6 cycles of chemotherapy and ≤24 Gy, the 10-year PFS and OS values were 88% (95% CI: 70%-96%) and 98% (95% CI: 85% - 99%), respectively. The most common late effect was hypothyroidism (20%) with no cardiac complications. Seven secondary malignancies were diagnosed, with only 1 arising within the RT field. Conclusions: Lower doses of RT may be sufficient when combined with more than 4 cycles of ABVD for early stage, unfavorable HL and may result in a more favorable toxicity profile than 4 cycles of ABVD and 30 Gy of RT.

  19. Bioinformatic tools for PCR Primer design

    African Journals Online (AJOL)

    ES

    reaction (PCR), oligo hybridization and DNA sequencing. Proper primer design is actually one of the most important factors/steps in successful DNA sequencing. Various bioinformatics programs are available for selection of primer pairs from a template sequence. The plethora programs for PCR primer design reflects the.

  20. "Extreme Programming" in a Bioinformatics Class

    Science.gov (United States)

    Kelley, Scott; Alger, Christianna; Deutschman, Douglas

    2009-01-01

    The importance of Bioinformatics tools and methodology in modern biological research underscores the need for robust and effective courses at the college level. This paper describes such a course designed on the principles of cooperative learning based on a computer software industry production model called "Extreme Programming" (EP).…

  1. Bioinformatics: A History of Evolution "In Silico"

    Science.gov (United States)

    Ondrej, Vladan; Dvorak, Petr

    2012-01-01

    Bioinformatics, biological databases, and the worldwide use of computers have accelerated biological research in many fields, such as evolutionary biology. Here, we describe a primer of nucleotide sequence management and the construction of a phylogenetic tree with two examples; the two selected are from completely different groups of organisms:…

  2. Protein raftophilicity. How bioinformatics can help membranologists

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Sperotto, Maria Maddalena

    )-based bioinformatics approach. The ANN was trained to recognize feature-based patterns in proteins that are considered to be associated with lipid rafts. The trained ANN was then used to predict protein raftophilicity. We found that, in the case of α-helical membrane proteins, their hydrophobic length does not affect...

  3. Bioinformatics in Undergraduate Education: Practical Examples

    Science.gov (United States)

    Boyle, John A.

    2004-01-01

    Bioinformatics has emerged as an important research tool in recent years. The ability to mine large databases for relevant information has become increasingly central to many different aspects of biochemistry and molecular biology. It is important that undergraduates be introduced to the available information and methodologies. We present a…

  4. Implementing bioinformatic workflows within the bioextract server

    Science.gov (United States)

    Computational workflows in bioinformatics are becoming increasingly important in the achievement of scientific advances. These workflows typically require the integrated use of multiple, distributed data sources and analytic tools. The BioExtract Server (http://bioextract.org) is a distributed servi...

  5. Privacy Preserving PCA on Distributed Bioinformatics Datasets

    Science.gov (United States)

    Li, Xin

    2011-01-01

    In recent years, new bioinformatics technologies, such as gene expression microarray, genome-wide association study, proteomics, and metabolomics, have been widely used to simultaneously identify a huge number of human genomic/genetic biomarkers, generate a tremendously large amount of data, and dramatically increase the knowledge on human…

  6. Bioboxes: standardised containers for interchangeable bioinformatics software.

    Science.gov (United States)

    Belmann, Peter; Dröge, Johannes; Bremges, Andreas; McHardy, Alice C; Sczyrba, Alexander; Barton, Michael D

    2015-01-01

    Software is now both central and essential to modern biology, yet lack of availability, difficult installations, and complex user interfaces make software hard to obtain and use. Containerisation, as exemplified by the Docker platform, has the potential to solve the problems associated with sharing software. We propose bioboxes: containers with standardised interfaces to make bioinformatics software interchangeable.

  7. Development and implementation of a bioinformatics online ...

    African Journals Online (AJOL)

    Thus, there is the need for appropriate strategies of introducing the basic components of this emerging scientific field to part of the African populace through the development of an online distance education learning tool. This study involved the design of a bioinformatics online distance educative tool an implementation of ...

  8. SPECIES DATABASES AND THE BIOINFORMATICS REVOLUTION.

    Science.gov (United States)

    Biological databases are having a growth spurt. Much of this results from research in genetics and biodiversity, coupled with fast-paced developments in information technology. The revolution in bioinformatics, defined by Sugden and Pennisi (2000) as the "tools and techniques for...

  9. Probable reasons for the lower effectiveness of remedies for early treatment of acute radiation sickness accompanied by combination of radiation and thermal injuries

    International Nuclear Information System (INIS)

    Budagov, R.S.; Ul'yanova, L.P.

    2001-01-01

    Mechanism underlying a lower effectiveness of remedies for early treatment of acute radiation sickness in the case of combined radiation and thermal injuries are studied. Experiments were carried out on mice. Animals had been subjected to either a 3B degree thermal burn covering 10% of the body surface or a single whole body gamma-irradiation of 7 Gy dose or a combined injury (radiation exposure + burn), and changes of the blood serum level of interleukin-6 (IL-6) were investigated by means of ELISA kits. Modifying influence of remedies for early therapy (a synthetic analogue of dicorynomycolate trehalose and a preparation based on killed Lacobacillus acidophilus) on the endogenous serum level of IL-6 and on the 30-day survival was evaluated. In accordance with the degree and duration of increased levels of IL-6 in blood serum, the investigated groups of animals were ranged as follows: combined action > burn only > irradiation only. L. acidophilus based preparation rendered a transient modifying action on the IL-6 level at the combined injury and contributed to increasing the 30-day survival. Lower effectiveness of remedies for early treatment of acute radiation sickness may be associated with too excessive levels of IL-6 in the blood serum [ru

  10. Experimental studies on pathogenesis of the brain radiation injury in early stage

    International Nuclear Information System (INIS)

    Ye Tian; Shiyao Bao; Weibo Yin; Chunfeng Liu; Zhilin Zhang

    2000-01-01

    To investigate the pathogenesis of the brain radiation injury in the early stage, a series of experiments were performed as below. The SD rats halfbrain were irradiated by the single dose of 10, 20, and 30 Gy of 4 MeV electron, all those experiments were performed in 1 day to 3 months after radiation. The neurological symptoms, the weight and the skin response inside the field of all the rats were evaluated sequentially. The measurement of regional cerebral blood flow (rCBF) using hydrogen gas generated by electrolysis, the calculation of the brain water content percentage with wet-dry weight formula. The DNA contents and the quantities of bcl-2 protein were analyzed by flow cytometry. The brain histological sections were scanned to assess the present or absence of white matter necrosis in the region of hippocampus, and then the hippocampus region was observed for the morphological changes of the blood vessel, neuroglial, and the neurons. Some of the data were analyzed by the Student t test. Intra-portal alopecia was observed in all rats which received 30 Gy and some rats which received 20 Gy, the abnormal neurological signs were not found in all the rats, but the tend of weight increase was less pronounced in 1-3 months in the irradiated rats than those unirradiated. By comparison the unirradiated hemisphere, the rCBF of the contralateral brain decreased in most of the rats. In 20 Gy and 30 Gy groups, rCBF decreased areas expand gradually along with the prolong of observation time, from the nucleus caudate putamen, to the frontal cortex and then the hippocampus, the rCBF of whole the irradiated hemibrain was reduced significantly at 3 month after radiation. The water content of the irradiated halfbrain increased progressively, it means the brain edema exists in the meantime. By comparison the unirradiation halfbrain, the apoptosis of the hippocampus cells in the irradiated brain increased, and the expression of bcl-2 protein decreased at the meantime, and those

  11. Experimental studies on pathogenesis of the brain radiation injury in early stage

    Energy Technology Data Exchange (ETDEWEB)

    Ye Tian [Suzhou Medical Coll., Jiangsu (China). 2nd Affiliated Hospital; Shiyao Bao; Weibo Yin; Chunfeng Liu; Zhilin Zhang

    2000-05-01

    To investigate the pathogenesis of the brain radiation injury in the early stage, a series of experiments were performed as below. The SD rats halfbrain were irradiated by the single dose of 10, 20, and 30 Gy of 4 MeV electron, all those experiments were performed in 1 day to 3 months after radiation. The neurological symptoms, the weight and the skin response inside the field of all the rats were evaluated sequentially. The measurement of regional cerebral blood flow (rCBF) using hydrogen gas generated by electrolysis, the calculation of the brain water content percentage with wet-dry weight formula. The DNA contents and the quantities of bcl-2 protein were analyzed by flow cytometry. The brain histological sections were scanned to assess the present or absence of white matter necrosis in the region of hippocampus, and then the hippocampus region was observed for the morphological changes of the blood vessel, neuroglial, and the neurons. Some of the data were analyzed by the Student t test. Intra-portal alopecia was observed in all rats which received 30 Gy and some rats which received 20 Gy, the abnormal neurological signs were not found in all the rats, but the tend of weight increase was less pronounced in 1-3 months in the irradiated rats than those unirradiated. By comparison the unirradiated hemisphere, the rCBF of the contralateral brain decreased in most of the rats. In 20 Gy and 30 Gy groups, rCBF decreased areas expand gradually along with the prolong of observation time, from the nucleus caudate putamen, to the frontal cortex and then the hippocampus, the rCBF of whole the irradiated hemibrain was reduced significantly at 3 month after radiation. The water content of the irradiated halfbrain increased progressively, it means the brain edema exists in the meantime. By comparison the unirradiation halfbrain, the apoptosis of the hippocampus cells in the irradiated brain increased, and the expression of bcl-2 protein decreased at the meantime, and those

  12. Radiation

    International Nuclear Information System (INIS)

    2013-01-01

    The chapter one presents the composition of matter and atomic theory; matter structure; transitions; origin of radiation; radioactivity; nuclear radiation; interactions in decay processes; radiation produced by the interaction of radiation with matter

  13. Navigating the changing learning landscape: perspective from bioinformatics.ca.

    Science.gov (United States)

    Brazas, Michelle D; Ouellette, B F Francis

    2013-09-01

    With the advent of YouTube channels in bioinformatics, open platforms for problem solving in bioinformatics, active web forums in computing analyses and online resources for learning to code or use a bioinformatics tool, the more traditional continuing education bioinformatics training programs have had to adapt. Bioinformatics training programs that solely rely on traditional didactic methods are being superseded by these newer resources. Yet such face-to-face instruction is still invaluable in the learning continuum. Bioinformatics.ca, which hosts the Canadian Bioinformatics Workshops, has blended more traditional learning styles with current online and social learning styles. Here we share our growing experiences over the past 12 years and look toward what the future holds for bioinformatics training programs.

  14. The Sail-Backed Reptile Ctenosauriscus from the Latest Early Triassic of Germany and the Timing and Biogeography of the Early Archosaur Radiation

    Science.gov (United States)

    Butler, Richard J.; Brusatte, Stephen L.; Reich, Mike; Nesbitt, Sterling J.; Schoch, Rainer R.; Hornung, Jahn J.

    2011-01-01

    Background Archosaurs (birds, crocodilians and their extinct relatives including dinosaurs) dominated Mesozoic continental ecosystems from the Late Triassic onwards, and still form a major component of modern ecosystems (>10,000 species). The earliest diverse archosaur faunal assemblages are known from the Middle Triassic (c. 244 Ma), implying that the archosaur radiation began in the Early Triassic (252.3–247.2 Ma). Understanding of this radiation is currently limited by the poor early fossil record of the group in terms of skeletal remains. Methodology/Principal Findings We redescribe the anatomy and stratigraphic position of the type specimen of Ctenosauriscus koeneni (Huene), a sail-backed reptile from the Early Triassic (late Olenekian) Solling Formation of northern Germany that potentially represents the oldest known archosaur. We critically discuss previous biomechanical work on the ‘sail’ of Ctenosauriscus, which is formed by a series of elongated neural spines. In addition, we describe Ctenosauriscus-like postcranial material from the earliest Middle Triassic (early Anisian) Röt Formation of Waldhaus, southwestern Germany. Finally, we review the spatial and temporal distribution of the earliest archosaur fossils and their implications for understanding the dynamics of the archosaur radiation. Conclusions/Significance Comprehensive numerical phylogenetic analyses demonstrate that both Ctenosauriscus and the Waldhaus taxon are members of a monophyletic grouping of poposauroid archosaurs, Ctenosauriscidae, characterised by greatly elongated neural spines in the posterior cervical to anterior caudal vertebrae. The earliest archosaurs, including Ctenosauriscus, appear in the body fossil record just prior to the Olenekian/Anisian boundary (c. 248 Ma), less than 5 million years after the Permian–Triassic mass extinction. These earliest archosaur assemblages are dominated by ctenosauriscids, which were broadly distributed across northern Pangea and which

  15. The sail-backed reptile Ctenosauriscus from the latest Early Triassic of Germany and the timing and biogeography of the early archosaur radiation.

    Science.gov (United States)

    Butler, Richard J; Brusatte, Stephen L; Reich, Mike; Nesbitt, Sterling J; Schoch, Rainer R; Hornung, Jahn J

    2011-01-01

    Archosaurs (birds, crocodilians and their extinct relatives including dinosaurs) dominated Mesozoic continental ecosystems from the Late Triassic onwards, and still form a major component of modern ecosystems (>10,000 species). The earliest diverse archosaur faunal assemblages are known from the Middle Triassic (c. 244 Ma), implying that the archosaur radiation began in the Early Triassic (252.3-247.2 Ma). Understanding of this radiation is currently limited by the poor early fossil record of the group in terms of skeletal remains. We redescribe the anatomy and stratigraphic position of the type specimen of Ctenosauriscus koeneni (Huene), a sail-backed reptile from the Early Triassic (late Olenekian) Solling Formation of northern Germany that potentially represents the oldest known archosaur. We critically discuss previous biomechanical work on the 'sail' of Ctenosauriscus, which is formed by a series of elongated neural spines. In addition, we describe Ctenosauriscus-like postcranial material from the earliest Middle Triassic (early Anisian) Röt Formation of Waldhaus, southwestern Germany. Finally, we review the spatial and temporal distribution of the earliest archosaur fossils and their implications for understanding the dynamics of the archosaur radiation. Comprehensive numerical phylogenetic analyses demonstrate that both Ctenosauriscus and the Waldhaus taxon are members of a monophyletic grouping of poposauroid archosaurs, Ctenosauriscidae, characterised by greatly elongated neural spines in the posterior cervical to anterior caudal vertebrae. The earliest archosaurs, including Ctenosauriscus, appear in the body fossil record just prior to the Olenekian/Anisian boundary (c. 248 Ma), less than 5 million years after the Permian-Triassic mass extinction. These earliest archosaur assemblages are dominated by ctenosauriscids, which were broadly distributed across northern Pangea and which appear to have been the first global radiation of archosaurs.

  16. The sail-backed reptile Ctenosauriscus from the latest Early Triassic of Germany and the timing and biogeography of the early archosaur radiation.

    Directory of Open Access Journals (Sweden)

    Richard J Butler

    Full Text Available BACKGROUND: Archosaurs (birds, crocodilians and their extinct relatives including dinosaurs dominated Mesozoic continental ecosystems from the Late Triassic onwards, and still form a major component of modern ecosystems (>10,000 species. The earliest diverse archosaur faunal assemblages are known from the Middle Triassic (c. 244 Ma, implying that the archosaur radiation began in the Early Triassic (252.3-247.2 Ma. Understanding of this radiation is currently limited by the poor early fossil record of the group in terms of skeletal remains. METHODOLOGY/PRINCIPAL FINDINGS: We redescribe the anatomy and stratigraphic position of the type specimen of Ctenosauriscus koeneni (Huene, a sail-backed reptile from the Early Triassic (late Olenekian Solling Formation of northern Germany that potentially represents the oldest known archosaur. We critically discuss previous biomechanical work on the 'sail' of Ctenosauriscus, which is formed by a series of elongated neural spines. In addition, we describe Ctenosauriscus-like postcranial material from the earliest Middle Triassic (early Anisian Röt Formation of Waldhaus, southwestern Germany. Finally, we review the spatial and temporal distribution of the earliest archosaur fossils and their implications for understanding the dynamics of the archosaur radiation. CONCLUSIONS/SIGNIFICANCE: Comprehensive numerical phylogenetic analyses demonstrate that both Ctenosauriscus and the Waldhaus taxon are members of a monophyletic grouping of poposauroid archosaurs, Ctenosauriscidae, characterised by greatly elongated neural spines in the posterior cervical to anterior caudal vertebrae. The earliest archosaurs, including Ctenosauriscus, appear in the body fossil record just prior to the Olenekian/Anisian boundary (c. 248 Ma, less than 5 million years after the Permian-Triassic mass extinction. These earliest archosaur assemblages are dominated by ctenosauriscids, which were broadly distributed across northern Pangea and

  17. Early inflammatory changes in radiation-induced oral mucositis. Effect of pentoxifylline in a mouse model

    Energy Technology Data Exchange (ETDEWEB)

    Gruber, Sylvia; Bozsaky, Eva; Roitinger, Eva; Schwarz, Karoline [Medical University/AKH Vienna, Applied and Translational Radiobiology, Dept. Radiation Oncology/CD Lab. Med. Radiation Research for Radiation Oncology, Vienna (Austria); Schmidt, Margret [Technische Universitaet Dresden, Dept. Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Dresden (Germany); Technische Universitaet Dresden, Helmholtz-Zentrum Dresden - Rossendorf, OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Dresden (Germany); Doerr, Wolfgang [Medical University/AKH Vienna, Applied and Translational Radiobiology, Dept. Radiation Oncology/CD Lab. Med. Radiation Research for Radiation Oncology, Vienna (Austria); Technische Universitaet Dresden, Dept. Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Dresden (Germany); Technische Universitaet Dresden, Helmholtz-Zentrum Dresden - Rossendorf, OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Dresden (Germany)

    2017-06-15

    Early inflammation is a major factor of mucosal reactions to radiotherapy. Pentoxifylline administration resulted in a significant amelioration of radiation-induced oral mucositis in the mouse tongue model. The underlying mechanisms may be related to the immunomodulatory properties of the drug. The present study hence focuses on the manifestation of early inflammatory changes in mouse tongue during daily fractionated irradiation and their potential modulation by pentoxifylline. Daily fractionated irradiation with 5 fractions of 3 Gy/week (days 0-4, 7-11) was given to the snouts of mice. Groups of 3 animals per day were euthanized every second day between day 0 and 14. Pentoxifylline (15 mg/kg, s. c.) was administered daily from day 5 to the day before sacrifice. The expression of the inflammatory proteins TNFα, NF-κB, and IL-1β were analysed. Fractionated irradiation increased the expression of all inflammatory markers. Pentoxifylline significantly reduced the expression of TNFα and IL-1β, but not NF-κB. Early inflammation, as indicated by the expression of the inflammatory markers TNFα, NF-κB, and IL-1β, is an essential component of early radiogenic oral mucositis. Pentoxifylline differentially modulated the expression of different inflammatory markers. The mucoprotective effect of pentoxifylline does not appear to be based on modulation of NF-κB-associated inflammation. (orig.) [German] Fruehe entzuendliche Veraenderungen sind ein bedeutender Faktor waehrend der Strahlenreaktion der Schleimhaut. Die Behandlung mit Pentoxifyllin erzielte eine signifikante Minderung strahleninduzierter oraler Mukositis im Mauszungenmodel. Die zugrundeliegenden Mechanismen sind potenziell auf die immunomodulatorischen Eigenschaften des Wirkstoffs zurueckzufuehren. Die vorliegenden Untersuchungen fokussieren daher auf die Manifestation frueher entzuendlicher Veraenderungen in der Mauszunge waehrend taeglich fraktionierter Bestrahlung und deren potenzieller Modifikation

  18. Human radiation studies: Remembering the early years: Oral history of pathologist Clarence Lushbaugh, M.D., conducted October 5, 1994

    International Nuclear Information System (INIS)

    1995-04-01

    This report provides a transcript of an interview with Dr. Clarance Lushbaugh by representatives of the DOE Office of Human Radiation Experiments. Dr. Lushbaugh was chosen for this interview because of his research involving experimental use of irradiation with human beings at Los Alamos and at the Oak Ridge Institute of Nuclear Science (ORINS). After a brief biographical sketch Dr. Lushbaugh and his assistant Mrs. Ann Swipe defend their use of total body irradiation using the LETBI (Low Exposure Total Body Irradiation) and the LETBI (Medium Energy Total Body Irradiator). Dr. Lushbaugh also discusses his earlier experiments involving use of nitrogen mustards in chemotherapy application, his early interest in the LD50 for man, his early impressions of low-level spray radiation as introduced by Heubline, anedotal information for his duties a pathologist for Los Alamos, and his developing interest in establishing safer radiation limits for human exposure

  19. The induced expression of heat shock proteins as a part of the early cellular response to gamma radiation

    International Nuclear Information System (INIS)

    Stankova, K.; Ivanova, K.; Georgieva, R.; Rupova, I.; Boteva, R.

    2008-01-01

    A variety of stressful stimuli including gamma radiation can induce increase in the synthesis of heat shock proteins (Hsp). This family of molecular chaperones includes members with molecular masses ranging from 10 to 150 kDa and has been identified in all organisms from bacteria to humans. Hsp70 chaperones are very important. The present study aimed to characterize the radiation-induced changes in Hsp70 synthesis in human lymphocytes as a part of the early cellular response to gamma irradiation. The expression of Hsp70 was determined with Western blot and the radiation-induced apoptotic changes were registered by staining with fluorescent dyes. Part of the experiments were performed in the presence of the organic solvent DMSO. At low concentrations this reagent shows antioxidant activity and can reduce the level of the radiation-induced oxidant stress which determines the predominant biological effects of the ionizing radiation. Irradiation with 0.5 to 8 Gy caused statistically significant increase in the synthesis of Hsp70 which was strongest after irradiation with 4 Gy. In the range 0.5-2 Gy the enhancement of the radiation-induced synthesis of Hsp70 reached 60%. Our experimental results characterize changes in the Hsp70 synthesis after gamma irradiation as a part of the early cellular stress response in lymphocytes. (authors)

  20. Radiation Segmentectomy versus Selective Chemoembolization in the Treatment of Early-Stage Hepatocellular Carcinoma.

    Science.gov (United States)

    Biederman, Derek M; Titano, Joseph J; Korff, Ricki A; Fischman, Aaron M; Patel, Rahul S; Nowakowski, Francis S; Lookstein, Robert A; Kim, Edward

    2018-01-01

    To compare outcomes of radiation segmentectomy (RS) and segmental transarterial chemoembolization in treatment of unresectable, solitary hepatocellular carcinoma (HCC) ≤ 3 cm. From January 2012 to January 2016, 534 and 877 patients were treated with radioembolization and transarterial chemoembolization, respectively. A cohort of 112 (radiation segmentectomy [RS], 55; chemoembolization, 57) locoregional therapy-naïve patients with solitary HCC ≤ 3 cm without vascular invasion or metastasis was retrospectively identified and stratified according to baseline patient demographics, tumor characteristics, and laboratory values. Propensity score matching (PSM) was conducted using a nearest neighbor algorithm (1:1). Outcomes analyzed included laboratory toxicities, imaging response, time to secondary therapy (TTST), and overall survival. Before PSM, complete response (CR) rate was 81.2% for RS and 49.1% for chemoembolization (odds ratio 2.2; 95% confidence interval [CI], 1.4-3.3; P < .001). Median (95% CI) TTST after initial therapy was 246 days (135-250 d) in chemoembolization group and 700 days (308-812 d) in RS group (hazard ratio 0.71; 95% CI, 0.55-0.92; P = .009). Overall survival before PSM was not significantly different between the 2 groups (P = .29). Overall CR rate after PSM was 92.1% in RS group and 52.6% in chemoembolization group (P = .005). Median (95% CI) TTST after matching was 161 days (76-350 d) in chemoembolization group and 812 days (363-812 d) in RS group (P = .001). Overall survival after matching was not significantly different between the 2 groups (P = .71). RS results in improved imaging response and longer TTST compared with transarterial chemoembolization in treatment of early-stage HCC. Copyright © 2017 SIR. Published by Elsevier Inc. All rights reserved.

  1. Lack of Bystander Effects From High LET Radiation For Early Cytogenetic Endpoints.

    Energy Technology Data Exchange (ETDEWEB)

    Groesser, Torsten; Cooper, Brian; Rydberg, Bjorn

    2008-05-07

    The aim of this work was to study radiation-induced bystander effects for early cytogenetic end points in various cell lines using the medium transfer technique after exposure to high- and low-LET radiation. Cells were exposed to 20 MeV/ nucleon nitrogen ions, 968 MeV/nucleon iron ions, or 575 MeV/nucleon iron ions followed by transfer of the conditioned medium from the irradiated cells to unirradiated test cells. The effects studied included DNA double-strand break induction, {gamma}-H2AX focus formation, induction of chromatid breaks in prematurely condensed chromosomes, and micronucleus formation using DNA repair-proficient and -deficient hamster and human cell lines (xrs6, V79, SW48, MO59K and MO59J). Cell survival was also measured in SW48 bystander cells using X rays. Although it was occasionally possible to detect an increase in chromatid break levels using nitrogen ions and to see a higher number of {gamma}-H2AX foci using nitrogen and iron ions in xrs6 bystander cells in single experiments, the results were not reproducible. After we pooled all the data, we could not verify a significant bystander effect for any of these end points. Also, we did not detect a significant bystander effect for DSB induction or micronucleus formation in these cell lines or for clonogenic survival in SW48 cells. The data suggest that DNA damage and cytogenetic changes are not induced in bystander cells. In contrast, data in the literature show pronounced bystander effects in a variety of cell lines, including clonogenic survival in SW48 cells and induction of chromatid breaks and micronuclei in hamster cells. To reconcile these conflicting data, it is possible that the epigenetic status of the specific cell line or the precise culture conditions and medium supplements, such as serum, may be critical for inducing bystander effects.

  2. Lack of Bystander Effects From High-LET Radiation For Early Cytogenetic End Points

    International Nuclear Information System (INIS)

    Groesser, Torsten; Cooper, Brian; Rydberg, Bjorn

    2008-01-01

    The aim of this work was to study radiation-induced bystander effects for early cytogenetic end points in various cell lines using the medium transfer technique after exposure to high- and low-LET radiation. Cells were exposed to 20 MeV/ nucleon nitrogen ions, 968 MeV/nucleon iron ions, or 575 MeV/nucleon iron ions followed by transfer of the conditioned medium from the irradiated cells to unirradiated test cells. The effects studied included DNA double-strand break induction, γ-H2AX focus formation, induction of chromatid breaks in prematurely condensed chromosomes, and micronucleus formation using DNA repair-proficient and -deficient hamster and human cell lines (xrs6, V79, SW48, MO59K and MO59J). Cell survival was also measured in SW48 bystander cells using X rays. Although it was occasionally possible to detect an increase in chromatid break levels using nitrogen ions and to see a higher number of γ-H2AX foci using nitrogen and iron ions in xrs6 bystander cells in single experiments, the results were not reproducible. After we pooled all the data, we could not verify a significant bystander effect for any of these end points. Also, we did not detect a significant bystander effect for DSB induction or micronucleus formation in these cell lines or for clonogenic survival in SW48 cells. The data suggest that DNA damage and cytogenetic changes are not induced in bystander cells. In contrast, data in the literature show pronounced bystander effects in a variety of cell lines, including clonogenic survival in SW48 cells and induction of chromatid breaks and micronuclei in hamster cells. To reconcile these conflicting data, it is possible that the epigenetic status of the specific cell line or the precise culture conditions and medium supplements, such as serum, may be critical for inducing bystander effects.

  3. An evaluation of early countermeasures to reduce the risk of internal radiation exposure after the Fukushima nuclear incident in Japan.

    Science.gov (United States)

    Nomura, Shuhei; Tsubokura, Masaharu; Gilmour, Stuart; Hayano, Ryugo S; Watanabe, Yuni N; Kami, Masahiro; Kanazawa, Yukio; Oikawa, Tomoyoshi

    2016-05-01

    After a radiation-release incident, intake of radionuclides in the initial stage immediately following the incident may be the major contributor to total internal radiation exposure for individuals in affected areas. However, evaluation of early internal contamination risk is greatly lacking. This study assessed the relationship between initial stage evacuation/indoor sheltering and internal radiation contamination levels 4 months after the 2011 Fukushima nuclear incident in Japan and estimated potential pathways of the contamination. The study population comprised 525 participants in the internal radiation screening program at Minamisoma Municipal General Hospital, 23 km north of the Fukushima nuclear plant. The analysed dataset included the results of a screening performed in July 2011, 4 months after the incident, and of a questionnaire on early-incident response behaviours, such as sheltering indoors and evacuations, completed by participants. Association between such early countermeasures and internal contamination levels of cesium-134 were assessed using Tobit multiple regression analyses. Our study shows that individuals who evacuated to areas outside Fukushima Prefecture had similar contamination levels of cesium-134 to individuals who stayed in Fukushima (relative risk: 0.86; 95% confidence interval: 0.74-0.99). Time spent outdoors had no significant relationship with contamination levels. The effects of inhalation from radiological plumes released from the nuclear plant on total internal radiation contamination might be so low as to be undetectable by the whole-body counting unit used to examine participants. Given the apparent limited effectiveness of evacuation and indoor sheltering on internal contamination, the decision to implement such early responses to a radiation-release incident should be made by carefully balancing their potential benefits and health risks. © The Author 2015. Published by Oxford University Press. All rights reserved. For

  4. Component-Based Approach for Educating Students in Bioinformatics

    Science.gov (United States)

    Poe, D.; Venkatraman, N.; Hansen, C.; Singh, G.

    2009-01-01

    There is an increasing need for an effective method of teaching bioinformatics. Increased progress and availability of computer-based tools for educating students have led to the implementation of a computer-based system for teaching bioinformatics as described in this paper. Bioinformatics is a recent, hybrid field of study combining elements of…

  5. Environmental exposure to low-doses of ionizing radiation. Effects on early nephrotoxicity in mice.

    Science.gov (United States)

    Bellés, Montserrat; Gonzalo, Sergio; Serra, Noemí; Esplugas, Roser; Arenas, Meritxell; Domingo, José Luis; Linares, Victoria

    2017-07-01

    Nuclear accidents of tremendous magnitude, such as those of Chernobyl (1986) and Fukushima (2011), mean that individuals living in the contaminated areas are potentially exposed to ionizing radiation (IR). However, the dose-response relationship for effects of low doses of radiation is not still established. The present study was aimed at investigating in mice the early effects of low-dose internal radiation exposure on the kidney. Adult male (C57BL/6J) mice were divided into three groups. Two groups received a single subcutaneous (s.c.) doses of cesium ( 137 Cs) with activities of 4000 and 8000Bq/kg bw. A third group (control group) received a single s.c. injection of 0.9% saline. To evaluate acute and subacute effects, mice (one-half of each group) were euthanized at 72h and 10 days post-exposure to 137 Cs, respectively. Urine samples were collected for biochemical analysis, including the measurement of F2-isoprostane (F2-IsoP) and kidney injury molecule-1 (KIM-1) levels. Moreover, the concentrations of 8-hydroxy-2'-deoxyguanosine (8-OHdG), a sensitive marker of oxidative DNA damage, were measured in renal tissue. Urinary excretion of total protein significantly increased at 72h in mice exposed to Cs4000. Uric acid and lactate dehydrogenase (LDH) decreased significantly at both times post-exposure in animals exposed to Cs8000. After 72h and 10d of exposure to Cs4000, a significant increase in the γ-glutamil transferase (GGT) and N-acetyl-β-D-glucosaminidase (NAG) activities was observed. In turn, F2-IsoP levels increased -mainly in the Cs4000 group- at 72h post-exposure. Following irradiation ( 137 Cs), the highest level of KIM-1 was corresponded to the Cs4000 group at 72h. Likewise, the main DNA damage was detected in mice exposed to Cs4000, mainly at 10d after irradiation. The alterations observed in several biomarkers suggest an immediate renal damage following exposure to low doses of IR (given as 137 Cs). Further investigations are required to clarify the

  6. Analysis of early initiating event(s) in radiation-induced thymic lymphomagenesis

    International Nuclear Information System (INIS)

    Muto, Masahiro; Ying Chen; Kubo, Eiko; Mita, Kazuei

    1996-01-01

    Since the T cell receptor rearrangement is a sequential process and unique to the progeny of each clone, we investigated the early initiating events in radiation-induced thymic lymphomagenesis by comparing the oncogenic alterations with the pattern of γ T cell receptor (TCR) rearrangements. We reported previously that after leukemogenic irradiation, preneoplastic cells developed, albeit infrequently, from thymic leukemia antigen-2 + (TL-2 + ) thymocytes. Limited numbers of TL-2 + cells from individual irradiated B10.Thy-1.1 mice were injected into B10.Thy-1.2 mice intrathymically, and the common genetic changes among the donor-type T cell lymphomas were investigated with regard to p53 gene and chromosome aberrations. The results indicated that some mutations in the p53 gene had taken place in these lymphomas, but there was no common mutation among the donor-type lymphomas from individual irradiated mice, suggesting that these mutations were late-occurring events in the process of oncogenesis. On the other hand, there were common chromosome aberrations or translocations such as trisomy 15, t(7F; 10C), t(1A; 13D) or t(6A; XB) among the donor-type lymphomas derived from half of the individual irradiated mice. This indicated that the aberrations/translocations, which occurred in single progenitor cells at the early T cell differentiation either just before or after γ T cell receptor rearrangements, might be important candidates for initiating events. In the donor-type lymphomas from the other half of the individual irradiated mice, microgenetic changes were suggested to be initial events and also might take place in single progenitor cells just before or right after γ TCR rearrangements. (author)

  7. The use of discriminant analysis for evaluation of early-response multiple biomarkers of radiation exposure using non-human primate 6-Gy whole-body radiation model

    Energy Technology Data Exchange (ETDEWEB)

    Ossetrova, N.I. [Armed Forces Radiobiology Research Institute, 8901 Wisconsin Avenue, Bethesda, MD 20889-5603 (United States)], E-mail: ossetrova@afrri.usuhs.mil; Farese, A.M.; MacVittie, T.J. [Marlene and Stewart Greenebaum Cancer Center, Bressler Research Building, Room 7-039, University of Maryland-Baltimore, 655 West Baltimore Street, Baltimore, MD 21201 (United States); Manglapus, G.L.; Blakely, W.F. [Armed Forces Radiobiology Research Institute, 8901 Wisconsin Avenue, Bethesda, MD 20889-5603 (United States)

    2007-07-15

    The present need to rapidly identify severely irradiated individuals in mass-casualty and population-monitoring scenarios prompted an evaluation of potential protein biomarkers to provide early diagnostic information after exposure. The level of specific proteins measured using immunodiagnostic technologies may be useful as protein biomarkers to provide early diagnostic information for acute radiation exposures. Herein we present results from on-going studies using a non-human primate (NHP) 6-Gy X-rays ( 0.13Gymin{sup -1}) whole-body radiation model. Protein targets were measured by enzyme-linked immunosorbent assay (ELISA) in blood plasma before, 1, and 2 days after exposure. Exposure of 10 NHPs to 6 Gy resulted in the up-regulation of plasma levels of (a) p21 WAF1/CIP1, (b) interleukin 6 (IL-6), (c) tissue enzyme salivary {alpha}-amylase, and (d) C-reactive protein. Data presented show the potential utility of protein biomarkers selected from distinctly different pathways to detect radiation exposure. A correlation analysis demonstrated strong correlations among different combinations of four candidate radiation-responsive blood protein biomarkers. Data analyzed with use of multivariate discriminant analysis established very successful separation of NHP groups: 100% discrimination power for animals with correct classification for separation between groups before and 1 day after irradiation, and 95% discrimination power for separation between groups before and 2 days after irradiation. These results also demonstrate proof-in-concept that multiple protein biomarkers provide early diagnostic information to the medical community, along with classical biodosimetric methodologies, to effectively manage radiation casualty incidents.

  8. Bioinformatics and systems biology research update from the 15th International Conference on Bioinformatics (InCoB2016).

    Science.gov (United States)

    Schönbach, Christian; Verma, Chandra; Bond, Peter J; Ranganathan, Shoba

    2016-12-22

    The International Conference on Bioinformatics (InCoB) has been publishing peer-reviewed conference papers in BMC Bioinformatics since 2006. Of the 44 articles accepted for publication in supplement issues of BMC Bioinformatics, BMC Genomics, BMC Medical Genomics and BMC Systems Biology, 24 articles with a bioinformatics or systems biology focus are reviewed in this editorial. InCoB2017 is scheduled to be held in Shenzen, China, September 20-22, 2017.

  9. Bioinformatics in New Generation Flavivirus Vaccines

    Directory of Open Access Journals (Sweden)

    Penelope Koraka

    2010-01-01

    Full Text Available Flavivirus infections are the most prevalent arthropod-borne infections world wide, often causing severe disease especially among children, the elderly, and the immunocompromised. In the absence of effective antiviral treatment, prevention through vaccination would greatly reduce morbidity and mortality associated with flavivirus infections. Despite the success of the empirically developed vaccines against yellow fever virus, Japanese encephalitis virus and tick-borne encephalitis virus, there is an increasing need for a more rational design and development of safe and effective vaccines. Several bioinformatic tools are available to support such rational vaccine design. In doing so, several parameters have to be taken into account, such as safety for the target population, overall immunogenicity of the candidate vaccine, and efficacy and longevity of the immune responses triggered. Examples of how bio-informatics is applied to assist in the rational design and improvements of vaccines, particularly flavivirus vaccines, are presented and discussed.

  10. Seasonal Variation in Solar Ultra Violet Radiation and Early Mortality in Extremely Preterm Infants.

    Science.gov (United States)

    Salas, Ariel A; Smith, Kelly A; Rodgers, Mackenzie D; Phillips, Vivien; Ambalavanan, Namasivayam

    2015-11-01

    Vitamin D production during pregnancy promotes fetal lung development, a major determinant of infant survival after preterm birth. Because vitamin D synthesis in humans is regulated by solar ultraviolet B (UVB) radiation, we hypothesized that seasonal variation in solar UVB doses during fetal development would be associated with variation in neonatal mortality rates. This cohort study included infants born alive with gestational age (GA) between 23 and 28 weeks gestation admitted to a neonatal unit between 1996 and 2010. Three infant cohort groups were defined according to increasing intensities of solar UVB doses at 17 and 22 weeks gestation. The primary outcome was death during the first 28 days after birth. Outcome data of 2,319 infants were analyzed. Mean birth weight was 830 ± 230 g and median gestational age was 26 weeks. Mortality rates were significantly different across groups (p = 0.04). High-intensity solar UVB doses were associated with lower mortality when compared with normal intensity solar UVB doses (hazard ratio: 0.70; 95% confidence interval: 0.54-0.91; p = 0.01). High-intensity solar UVB doses during fetal development seem to be associated with risk reduction of early mortality in preterm infants. Prospective studies are needed to validate these preliminary findings. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

  11. Role of MMP-12 on tissue remodeling at early stage of radiation-induced pulmonary injury

    International Nuclear Information System (INIS)

    Li Ming; Song Liangwen; Diao Ruiying; Wang Shaoxia; Xu Xinping; Luo Qingliang

    2008-01-01

    Objective: To explore the role of MMP-12 on tissue remodeling at early stage of radiation- induced pulmonary injury. Methods: Wistar rats irradiated by 60 Co γ-rays to the whole lungs were sacrificed at 1, 2, 4 weeks. MMP-12 mRNA expression was detected by RT-PCR. MMP-2, MMP-9, MMP-12 activities were determined by zymography. The degradation and collapse of elastin were determined by tissue elastin particular staining; the 'cross talking' phenomenon between alveolar type II cells and mesenchymal cells was observed under electron microscope; the expression of TGF-β1 and TNF-α in BALF was detected by ELISA. The expression of α-SMA was determined by immunohistochemistry. Results: The mRNA expression of MMP-12 displayed a significant elevation at 1, 2, 4 weeks after irradiation. MMP-12 activity increased at 2, 4 weeks after irradiation. Elastin began to degrade and collapse at 1 week, which became worst 4 weeks after irradiation. The cross talking phenomenon was found under electron microscope. The expression of TGF-β1, TNF-α and α-SMA was increased gradually as time elapse after irradiation. Conclusions: 60 Co γ-ray irradiation can promote pulmonary MMP-12 expression, initiate pulmonary tissue remodeling by degradation of elastin, and make the pulmonary injury develop towards pulmonary fibrosis eventually. (authors)

  12. Early Treatment of radiation-Induced Heart Damage in Rats by Caffeic acid phenethyl Ester

    International Nuclear Information System (INIS)

    Tawfik, S.S.; Mansour, H. H.

    2012-12-01

    The study designed to determine the therapeutic effect of caffeic acid phenethyl ester (CAPE) in minimising radiation-induced injuries in rats. Rats were exposed to 7 Gy γ-rays, 30 minutes later; rats were injected with CAPE (10μmol/ kg body, i.p.) for 7 consecutive days. Rats were sacrificed at 8 and 15 days after starting the experiment. Gamma-irradiation induced significant increase in malonaldehyde (MDA) level and xanthine oxidase (XO) and adenosine deaminase (ADA) activities, and significant decrease in total nitrate/nitrate (NO (x)) level and glutathione peroxidise (Gpx), superoxide dismutase (SOD)and catalase (CAT) activities in heart tissue and augmented activities of lactate dehydrogenase (LDH), creatine phosphokinase (CPK) and aspartate transaminase (AST) in serum. Irradiated rats early treated with CAPE showed significant decrease in MDA, XO and ADA and significant increase in group. Cardiac enzymes were restored. Conclusion, CAPE could exhibits curable effect on gamma irradiation-induced cardiac-oxidative impairment in rats. (Author)

  13. Cytokines, Fatigue, and Cutaneous Erythema in Early Stage Breast Cancer Patients Receiving Adjuvant Radiation Therapy

    Directory of Open Access Journals (Sweden)

    Vitaliana De Sanctis

    2014-01-01

    Full Text Available We investigated the hypothesis that patients developing high-grade erythema of the breast skin during radiation treatment could be more likely to present increased levels of proinflammatory cytokines which may lead, in turn, to associated fatigue. Forty women with early stage breast cancer who received adjuvant radiotherapy were enrolled from 2007 to 2010. Fatigue symptoms, erythema, and cytokine levels (IL-1β, IL-2, IL6, IL-8, TNF-α, and MCP-1 were registered at baseline, during treatment, and after radiotherapy completion. Seven (17.5% patients presented fatigue without associated depression/anxiety. Grade ≥2 erythema was observed in 5 of these 7 patients. IL-1β, IL-2, IL-6, and TNF-α were statistically increased 4 weeks after radiotherapy (P<0.05. After the Heckman two-step analysis, a statistically significant influence of skin erythema on proinflammatory markers increase (P = 0.00001 was recorded; in the second step, these blood markers showed a significant impact on fatigue (P = 0.026. A seeming increase of fatigue, erythema, and proinflammatory markers was observed between the fourth and the fifth week of treatment followed by a decrease after RT. There were no significant effects of hormone therapy, breast volume, and anemia on fatigue. Our study seems to suggest that fatigue is related to high-grade breast skin erythema during radiotherapy through the increase of cytokines levels.

  14. Chronological observation in early radiation myelopathy of the cervical spinal cord

    International Nuclear Information System (INIS)

    Hirota, Saeko; Yoshida, Shoji; Soejima, Toshinori

    1993-01-01

    Gd-enhanced MR images of two patients with clinically and histopathologically diagnosed chronic progressive radiation myelitis (CPRM) were observed chronologically. One of them had had nasopharyngeal cancer and received radiotherapy at a dose of 100 Gy to the C1-2 level of the spinal cord. She developed CPRM 25 months after the termination of radiotherapy. The other had had malignant lymphoma originating from the tonsil and received chemoradiotherapy. The dose delivered to her cervical spinal cord was 40 Gy, and she developed CPRM 30 months later. Gd-enhanced MRI in the early phase revealed a small crescent-shaped nidus with or without a very small central nonenhanced area in both cases. Enhancement was not great. At that time, patients noticed only the inability to perceive pain and temperature or paresthesia in the opposite side. In a few months, MRI revealed a much more strongly enhanced and larger nidus with enlargement of a central nonenhanced area accompanied by long segmental cord enlargement. The patients' neurological symptoms had also progressed, with hemiparesis developing, for example. (author)

  15. The growing need for microservices in bioinformatics

    Directory of Open Access Journals (Sweden)

    Christopher L Williams

    2016-01-01

    Full Text Available Objective: Within the information technology (IT industry, best practices and standards are constantly evolving and being refined. In contrast, computer technology utilized within the healthcare industry often evolves at a glacial pace, with reduced opportunities for justified innovation. Although the use of timely technology refreshes within an enterprise′s overall technology stack can be costly, thoughtful adoption of select technologies with a demonstrated return on investment can be very effective in increasing productivity and at the same time, reducing the burden of maintenance often associated with older and legacy systems. In this brief technical communication, we introduce the concept of microservices as applied to the ecosystem of data analysis pipelines. Microservice architecture is a framework for dividing complex systems into easily managed parts. Each individual service is limited in functional scope, thereby conferring a higher measure of functional isolation and reliability to the collective solution. Moreover, maintenance challenges are greatly simplified by virtue of the reduced architectural complexity of each constitutive module. This fact notwithstanding, rendered overall solutions utilizing a microservices-based approach provide equal or greater levels of functionality as compared to conventional programming approaches. Bioinformatics, with its ever-increasing demand for performance and new testing algorithms, is the perfect use-case for such a solution. Moreover, if promulgated within the greater development community as an open-source solution, such an approach holds potential to be transformative to current bioinformatics software development. Context: Bioinformatics relies on nimble IT framework which can adapt to changing requirements. Aims: To present a well-established software design and deployment strategy as a solution for current challenges within bioinformatics Conclusions: Use of the microservices framework

  16. The growing need for microservices in bioinformatics.

    Science.gov (United States)

    Williams, Christopher L; Sica, Jeffrey C; Killen, Robert T; Balis, Ulysses G J

    2016-01-01

    Within the information technology (IT) industry, best practices and standards are constantly evolving and being refined. In contrast, computer technology utilized within the healthcare industry often evolves at a glacial pace, with reduced opportunities for justified innovation. Although the use of timely technology refreshes within an enterprise's overall technology stack can be costly, thoughtful adoption of select technologies with a demonstrated return on investment can be very effective in increasing productivity and at the same time, reducing the burden of maintenance often associated with older and legacy systems. In this brief technical communication, we introduce the concept of microservices as applied to the ecosystem of data analysis pipelines. Microservice architecture is a framework for dividing complex systems into easily managed parts. Each individual service is limited in functional scope, thereby conferring a higher measure of functional isolation and reliability to the collective solution. Moreover, maintenance challenges are greatly simplified by virtue of the reduced architectural complexity of each constitutive module. This fact notwithstanding, rendered overall solutions utilizing a microservices-based approach provide equal or greater levels of functionality as compared to conventional programming approaches. Bioinformatics, with its ever-increasing demand for performance and new testing algorithms, is the perfect use-case for such a solution. Moreover, if promulgated within the greater development community as an open-source solution, such an approach holds potential to be transformative to current bioinformatics software development. Bioinformatics relies on nimble IT framework which can adapt to changing requirements. To present a well-established software design and deployment strategy as a solution for current challenges within bioinformatics. Use of the microservices framework is an effective methodology for the fabrication and

  17. The growing need for microservices in bioinformatics

    Science.gov (United States)

    Williams, Christopher L.; Sica, Jeffrey C.; Killen, Robert T.; Balis, Ulysses G. J.

    2016-01-01

    Objective: Within the information technology (IT) industry, best practices and standards are constantly evolving and being refined. In contrast, computer technology utilized within the healthcare industry often evolves at a glacial pace, with reduced opportunities for justified innovation. Although the use of timely technology refreshes within an enterprise's overall technology stack can be costly, thoughtful adoption of select technologies with a demonstrated return on investment can be very effective in increasing productivity and at the same time, reducing the burden of maintenance often associated with older and legacy systems. In this brief technical communication, we introduce the concept of microservices as applied to the ecosystem of data analysis pipelines. Microservice architecture is a framework for dividing complex systems into easily managed parts. Each individual service is limited in functional scope, thereby conferring a higher measure of functional isolation and reliability to the collective solution. Moreover, maintenance challenges are greatly simplified by virtue of the reduced architectural complexity of each constitutive module. This fact notwithstanding, rendered overall solutions utilizing a microservices-based approach provide equal or greater levels of functionality as compared to conventional programming approaches. Bioinformatics, with its ever-increasing demand for performance and new testing algorithms, is the perfect use-case for such a solution. Moreover, if promulgated within the greater development community as an open-source solution, such an approach holds potential to be transformative to current bioinformatics software development. Context: Bioinformatics relies on nimble IT framework which can adapt to changing requirements. Aims: To present a well-established software design and deployment strategy as a solution for current challenges within bioinformatics Conclusions: Use of the microservices framework is an effective

  18. Bioinformatics of cardiovascular miRNA biology.

    Science.gov (United States)

    Kunz, Meik; Xiao, Ke; Liang, Chunguang; Viereck, Janika; Pachel, Christina; Frantz, Stefan; Thum, Thomas; Dandekar, Thomas

    2015-12-01

    MicroRNAs (miRNAs) are small ~22 nucleotide non-coding RNAs and are highly conserved among species. Moreover, miRNAs regulate gene expression of a large number of genes associated with important biological functions and signaling pathways. Recently, several miRNAs have been found to be associated with cardiovascular diseases. Thus, investigating the complex regulatory effect of miRNAs may lead to a better understanding of their functional role in the heart. To achieve this, bioinformatics approaches have to be coupled with validation and screening experiments to understand the complex interactions of miRNAs with the genome. This will boost the subsequent development of diagnostic markers and our understanding of the physiological and therapeutic role of miRNAs in cardiac remodeling. In this review, we focus on and explain different bioinformatics strategies and algorithms for the identification and analysis of miRNAs and their regulatory elements to better understand cardiac miRNA biology. Starting with the biogenesis of miRNAs, we present approaches such as LocARNA and miRBase for combining sequence and structure analysis including phylogenetic comparisons as well as detailed analysis of RNA folding patterns, functional target prediction, signaling pathway as well as functional analysis. We also show how far bioinformatics helps to tackle the unprecedented level of complexity and systemic effects by miRNA, underlining the strong therapeutic potential of miRNA and miRNA target structures in cardiovascular disease. In addition, we discuss drawbacks and limitations of bioinformatics algorithms and the necessity of experimental approaches for miRNA target identification. This article is part of a Special Issue entitled 'Non-coding RNAs'. Copyright © 2014 Elsevier Ltd. All rights reserved.

  19. Comprehensive decision tree models in bioinformatics.

    Directory of Open Access Journals (Sweden)

    Gregor Stiglic

    Full Text Available PURPOSE: Classification is an important and widely used machine learning technique in bioinformatics. Researchers and other end-users of machine learning software often prefer to work with comprehensible models where knowledge extraction and explanation of reasoning behind the classification model are possible. METHODS: This paper presents an extension to an existing machine learning environment and a study on visual tuning of decision tree classifiers. The motivation for this research comes from the need to build effective and easily interpretable decision tree models by so called one-button data mining approach where no parameter tuning is needed. To avoid bias in classification, no classification performance measure is used during the tuning of the model that is constrained exclusively by the dimensions of the produced decision tree. RESULTS: The proposed visual tuning of decision trees was evaluated on 40 datasets containing classical machine learning problems and 31 datasets from the field of bioinformatics. Although we did not expected significant differences in classification performance, the results demonstrate a significant increase of accuracy in less complex visually tuned decision trees. In contrast to classical machine learning benchmarking datasets, we observe higher accuracy gains in bioinformatics datasets. Additionally, a user study was carried out to confirm the assumption that the tree tuning times are significantly lower for the proposed method in comparison to manual tuning of the decision tree. CONCLUSIONS: The empirical results demonstrate that by building simple models constrained by predefined visual boundaries, one not only achieves good comprehensibility, but also very good classification performance that does not differ from usually more complex models built using default settings of the classical decision tree algorithm. In addition, our study demonstrates the suitability of visually tuned decision trees for datasets

  20. Comprehensive decision tree models in bioinformatics.

    Science.gov (United States)

    Stiglic, Gregor; Kocbek, Simon; Pernek, Igor; Kokol, Peter

    2012-01-01

    Classification is an important and widely used machine learning technique in bioinformatics. Researchers and other end-users of machine learning software often prefer to work with comprehensible models where knowledge extraction and explanation of reasoning behind the classification model are possible. This paper presents an extension to an existing machine learning environment and a study on visual tuning of decision tree classifiers. The motivation for this research comes from the need to build effective and easily interpretable decision tree models by so called one-button data mining approach where no parameter tuning is needed. To avoid bias in classification, no classification performance measure is used during the tuning of the model that is constrained exclusively by the dimensions of the produced decision tree. The proposed visual tuning of decision trees was evaluated on 40 datasets containing classical machine learning problems and 31 datasets from the field of bioinformatics. Although we did not expected significant differences in classification performance, the results demonstrate a significant increase of accuracy in less complex visually tuned decision trees. In contrast to classical machine learning benchmarking datasets, we observe higher accuracy gains in bioinformatics datasets. Additionally, a user study was carried out to confirm the assumption that the tree tuning times are significantly lower for the proposed method in comparison to manual tuning of the decision tree. The empirical results demonstrate that by building simple models constrained by predefined visual boundaries, one not only achieves good comprehensibility, but also very good classification performance that does not differ from usually more complex models built using default settings of the classical decision tree algorithm. In addition, our study demonstrates the suitability of visually tuned decision trees for datasets with binary class attributes and a high number of possibly

  1. Penalized feature selection and classification in bioinformatics

    OpenAIRE

    Ma, Shuangge; Huang, Jian

    2008-01-01

    In bioinformatics studies, supervised classification with high-dimensional input variables is frequently encountered. Examples routinely arise in genomic, epigenetic and proteomic studies. Feature selection can be employed along with classifier construction to avoid over-fitting, to generate more reliable classifier and to provide more insights into the underlying causal relationships. In this article, we provide a review of several recently developed penalized feature selection and classific...

  2. Bioinformatics Training: A Review of Challenges, Actions and Support Requirements

    DEFF Research Database (Denmark)

    Schneider, M.V.; Watson, J.; Attwood, T.

    2010-01-01

    As bioinformatics becomes increasingly central to research in the molecular life sciences, the need to train non-bioinformaticians to make the most of bioinformatics resources is growing. Here, we review the key challenges and pitfalls to providing effective training for users of bioinformatics...... services, and discuss successful training strategies shared by a diverse set of bioinformatics trainers. We also identify steps that trainers in bioinformatics could take together to advance the state of the art in current training practices. The ideas presented in this article derive from the first...

  3. Adapting bioinformatics curricula for big data.

    Science.gov (United States)

    Greene, Anna C; Giffin, Kristine A; Greene, Casey S; Moore, Jason H

    2016-01-01

    Modern technologies are capable of generating enormous amounts of data that measure complex biological systems. Computational biologists and bioinformatics scientists are increasingly being asked to use these data to reveal key systems-level properties. We review the extent to which curricula are changing in the era of big data. We identify key competencies that scientists dealing with big data are expected to possess across fields, and we use this information to propose courses to meet these growing needs. While bioinformatics programs have traditionally trained students in data-intensive science, we identify areas of particular biological, computational and statistical emphasis important for this era that can be incorporated into existing curricula. For each area, we propose a course structured around these topics, which can be adapted in whole or in parts into existing curricula. In summary, specific challenges associated with big data provide an important opportunity to update existing curricula, but we do not foresee a wholesale redesign of bioinformatics training programs. © The Author 2015. Published by Oxford University Press.

  4. Bioinformatics on the Cloud Computing Platform Azure

    Science.gov (United States)

    Shanahan, Hugh P.; Owen, Anne M.; Harrison, Andrew P.

    2014-01-01

    We discuss the applicability of the Microsoft cloud computing platform, Azure, for bioinformatics. We focus on the usability of the resource rather than its performance. We provide an example of how R can be used on Azure to analyse a large amount of microarray expression data deposited at the public database ArrayExpress. We provide a walk through to demonstrate explicitly how Azure can be used to perform these analyses in Appendix S1 and we offer a comparison with a local computation. We note that the use of the Platform as a Service (PaaS) offering of Azure can represent a steep learning curve for bioinformatics developers who will usually have a Linux and scripting language background. On the other hand, the presence of an additional set of libraries makes it easier to deploy software in a parallel (scalable) fashion and explicitly manage such a production run with only a few hundred lines of code, most of which can be incorporated from a template. We propose that this environment is best suited for running stable bioinformatics software by users not involved with its development. PMID:25050811

  5. Application of Bioinformatics in Chronobiology Research

    Directory of Open Access Journals (Sweden)

    Robson da Silva Lopes

    2013-01-01

    Full Text Available Bioinformatics and other well-established sciences, such as molecular biology, genetics, and biochemistry, provide a scientific approach for the analysis of data generated through “omics” projects that may be used in studies of chronobiology. The results of studies that apply these techniques demonstrate how they significantly aided the understanding of chronobiology. However, bioinformatics tools alone cannot eliminate the need for an understanding of the field of research or the data to be considered, nor can such tools replace analysts and researchers. It is often necessary to conduct an evaluation of the results of a data mining effort to determine the degree of reliability. To this end, familiarity with the field of investigation is necessary. It is evident that the knowledge that has been accumulated through chronobiology and the use of tools derived from bioinformatics has contributed to the recognition and understanding of the patterns and biological rhythms found in living organisms. The current work aims to develop new and important applications in the near future through chronobiology research.

  6. Chapter 16: text mining for translational bioinformatics.

    Science.gov (United States)

    Cohen, K Bretonnel; Hunter, Lawrence E

    2013-04-01

    Text mining for translational bioinformatics is a new field with tremendous research potential. It is a subfield of biomedical natural language processing that concerns itself directly with the problem of relating basic biomedical research to clinical practice, and vice versa. Applications of text mining fall both into the category of T1 translational research-translating basic science results into new interventions-and T2 translational research, or translational research for public health. Potential use cases include better phenotyping of research subjects, and pharmacogenomic research. A variety of methods for evaluating text mining applications exist, including corpora, structured test suites, and post hoc judging. Two basic principles of linguistic structure are relevant for building text mining applications. One is that linguistic structure consists of multiple levels. The other is that every level of linguistic structure is characterized by ambiguity. There are two basic approaches to text mining: rule-based, also known as knowledge-based; and machine-learning-based, also known as statistical. Many systems are hybrids of the two approaches. Shared tasks have had a strong effect on the direction of the field. Like all translational bioinformatics software, text mining software for translational bioinformatics can be considered health-critical and should be subject to the strictest standards of quality assurance and software testing.

  7. Bringing Web 2.0 to bioinformatics.

    Science.gov (United States)

    Zhang, Zhang; Cheung, Kei-Hoi; Townsend, Jeffrey P

    2009-01-01

    Enabling deft data integration from numerous, voluminous and heterogeneous data sources is a major bioinformatic challenge. Several approaches have been proposed to address this challenge, including data warehousing and federated databasing. Yet despite the rise of these approaches, integration of data from multiple sources remains problematic and toilsome. These two approaches follow a user-to-computer communication model for data exchange, and do not facilitate a broader concept of data sharing or collaboration among users. In this report, we discuss the potential of Web 2.0 technologies to transcend this model and enhance bioinformatics research. We propose a Web 2.0-based Scientific Social Community (SSC) model for the implementation of these technologies. By establishing a social, collective and collaborative platform for data creation, sharing and integration, we promote a web services-based pipeline featuring web services for computer-to-computer data exchange as users add value. This pipeline aims to simplify data integration and creation, to realize automatic analysis, and to facilitate reuse and sharing of data. SSC can foster collaboration and harness collective intelligence to create and discover new knowledge. In addition to its research potential, we also describe its potential role as an e-learning platform in education. We discuss lessons from information technology, predict the next generation of Web (Web 3.0), and describe its potential impact on the future of bioinformatics studies.

  8. Adapting bioinformatics curricula for big data

    Science.gov (United States)

    Greene, Anna C.; Giffin, Kristine A.; Greene, Casey S.

    2016-01-01

    Modern technologies are capable of generating enormous amounts of data that measure complex biological systems. Computational biologists and bioinformatics scientists are increasingly being asked to use these data to reveal key systems-level properties. We review the extent to which curricula are changing in the era of big data. We identify key competencies that scientists dealing with big data are expected to possess across fields, and we use this information to propose courses to meet these growing needs. While bioinformatics programs have traditionally trained students in data-intensive science, we identify areas of particular biological, computational and statistical emphasis important for this era that can be incorporated into existing curricula. For each area, we propose a course structured around these topics, which can be adapted in whole or in parts into existing curricula. In summary, specific challenges associated with big data provide an important opportunity to update existing curricula, but we do not foresee a wholesale redesign of bioinformatics training programs. PMID:25829469

  9. A case of central type early stage lung cancer receiving 60Co high dose-rate postoperative endobronchial radiation

    International Nuclear Information System (INIS)

    Nakamori, Syouji; Kodama, Ken; Kurokawa, Eiji; Doi, Osamu; Terasawa, Toshio; Chatani, Masashi; Inoue, Toshihiko; Tateishi, Ryuhei

    1985-01-01

    Right middle-lower lobectomy and mediastinal lymph node dissection were performed for a case of central type early stage lung cancer. Tumor extended very closely to the line of incision margin of the resected specimen, appearing as carcinoma in situ. To inprove curativity, postoperative radiation therapy was performed with 60 Co high dose-rate endobronchial radiation by a remote afterloading system. A total dose of 40Gy was administered to the target area without any severe side effects. The patient is healthy and has no evidence of metastasis. This procedure is considered to be an effective treatment for postoperative lung cancer with possible residual malignancy. (author)

  10. Sci—Fri AM: Mountain — 04: Label-free Raman spectroscopy of single tumour cells detects early radiation-induced glycogen synthesis associated with increased radiation resistance

    International Nuclear Information System (INIS)

    Matthews, Q; Lum, JJ; Isabelle, M; Harder, S; Jirasek, A; Brolo, AG

    2014-01-01

    Purpose: To use label-free Raman spectroscopy (RS) for early treatment monitoring of tumour cell radioresistance. Methods: Three human tumour cell lines, two radioresistant (H460, SF 2 = 0.57 and MCF7, SF 2 = 0.70) and one radiosensitive (LNCaP, SF 2 = 0.36), were irradiated with single fractions of 2, 4, 6, 8 or 10 Gy. In additional experiments, H460 and MCF7 cells were irradiated under co-treatment with the anti-diabetic drug metformin, a known radiosensitizing agent. Treated and control cultures were analyzed with RS daily for 3 days post-treatment. Single-cell Raman spectra were acquired from 20 live cells per sample, and experiments were repeated in triplicate. The combined data sets were analyzed with principal component analysis using standard algorithms. Cells from each culture were also subjected to standard assays for viability, proliferation, cell cycle, and radiation clonogenic survival. Results: The radioresistant cells (H460, MCF7) exhibited a RS molecular radiation response signature, detectable as early as 1 day post-treatment, of which radiation-induced glycogen synthesis is a significant contributor. The radiosensitive cells (LNCaP) exhibited negligible glycogen synthesis. Co-treatment with metformin in MCF7 cells blocked glycogen synthesis, reduced viability and proliferation, and increased radiosensitivity. Conversely, metformin co-treatment in H460 cells did not produce these same effects; importantly, both radiation-induced synthesis of glycogen and radiosensitivity were unaffected. Conclusions: Label-free RS can detect early glycogen synthesis post-irradiation, a previously undocumented metabolic mechanism associated with tumour cell radioresistance that can be targeted to increase radiosensitivity. RS monitoring of intratumoral glycogen may provide new opportunities for personalized combined modality radiotherapy treatments

  11. Sci—Fri AM: Mountain — 04: Label-free Raman spectroscopy of single tumour cells detects early radiation-induced glycogen synthesis associated with increased radiation resistance

    Energy Technology Data Exchange (ETDEWEB)

    Matthews, Q; Lum, JJ [BC Cancer Agency — Vancouver Island Centre (Canada); Isabelle, M; Harder, S; Jirasek, A [Physics and Astronomy, University of Victoria (Australia); Brolo, AG [Chemistry, University of Victoria (Australia)

    2014-08-15

    Purpose: To use label-free Raman spectroscopy (RS) for early treatment monitoring of tumour cell radioresistance. Methods: Three human tumour cell lines, two radioresistant (H460, SF{sub 2} = 0.57 and MCF7, SF{sub 2} = 0.70) and one radiosensitive (LNCaP, SF{sub 2} = 0.36), were irradiated with single fractions of 2, 4, 6, 8 or 10 Gy. In additional experiments, H460 and MCF7 cells were irradiated under co-treatment with the anti-diabetic drug metformin, a known radiosensitizing agent. Treated and control cultures were analyzed with RS daily for 3 days post-treatment. Single-cell Raman spectra were acquired from 20 live cells per sample, and experiments were repeated in triplicate. The combined data sets were analyzed with principal component analysis using standard algorithms. Cells from each culture were also subjected to standard assays for viability, proliferation, cell cycle, and radiation clonogenic survival. Results: The radioresistant cells (H460, MCF7) exhibited a RS molecular radiation response signature, detectable as early as 1 day post-treatment, of which radiation-induced glycogen synthesis is a significant contributor. The radiosensitive cells (LNCaP) exhibited negligible glycogen synthesis. Co-treatment with metformin in MCF7 cells blocked glycogen synthesis, reduced viability and proliferation, and increased radiosensitivity. Conversely, metformin co-treatment in H460 cells did not produce these same effects; importantly, both radiation-induced synthesis of glycogen and radiosensitivity were unaffected. Conclusions: Label-free RS can detect early glycogen synthesis post-irradiation, a previously undocumented metabolic mechanism associated with tumour cell radioresistance that can be targeted to increase radiosensitivity. RS monitoring of intratumoral glycogen may provide new opportunities for personalized combined modality radiotherapy treatments.

  12. Ray Guns and Radium: Radiation in the Public Imagination as Reflected in Early American Science Fiction

    Science.gov (United States)

    Slaughter, Aimee

    2014-01-01

    The 1920s and 1930s were a period which saw great popular interest in radiation and radioactivity in America, and the establishment of a new genre of pulp literature, science fiction. Radiation was prevalent in American popular culture at the time, and sf stories were dependent upon radiation for much of their color and excitement. In this case…

  13. Early effect of external beam radiation therapy on the anal sphincter: A study using anal manometry and transrectal ultrasound

    International Nuclear Information System (INIS)

    Birnbaum, E.H.; Dreznik, Z.; Myerson, R.J.; Lacey, D.L.; Fry, R.D.; Kodner, I.J.; Fleshman, J.W.

    1992-01-01

    The early of pelvic irradiation on the anal sphincter has not been previously investigated. This study prospectively evaluated the acute effect of preoperative radiation on anal function. Twenty patients with rectal carcinoma received 4,500 cGy of preoperative external beam radiation. The field of radiation included the sphincter in 10 patients and was delivered above the anorectal ring in 10 patients. Anal manometry and transrectal ultrasound were performed before and four weeks after radiotherapy. No significant difference in mean maximal squeeze or resting pressure was found after radiation therapy. An increase in mean minimal sensory threshold was significant. Histologic examination revealed minimal radiation changes at the distal margin in 8 of 10 patients who underwent low anterior resection and in 1 of 3 patients who underwent abdominoperineal resection. The authors conclude that preoperative radiation therapy has minimal immediate effect on the anal sphincter and is not a major contributing factor to postoperative incontinence in patients after sphincter-saving operations for rectal cancer

  14. The environmental radiation monitoring system and in-situ measurements for early notification and OIL (Operational Intervention Levels) calculations

    International Nuclear Information System (INIS)

    Haquin, G.; Ne'eman, E.; Brenner, S.; Lavi, N.

    1997-01-01

    The efficiency of the environmental radiation monitoring, low level laboratory and in-situ gamma-ray spectrometry are evaluated as the systems for early notification and for determination of dose rate in air, surface contamination and activity concentration in food during emergencies for Operational Intervention Levels (OIL) recalculation.The National Environmental Radiation Monitoring System has proved its efficiency in the early detection of unregistered radiography work. A mobile station of the network can be used for absorbed dose rate measurement during emergencies in contaminated areas. The calibrated in-situ gamma-ray spectrometry system in an open phosphate ore mine has showed the efficiency of this technique for fast and accurate determination of soil activity concentration. The calibration for an uniform depth distribution can be easily mathematically converted to an exponential depth distribution in cases of radioactive material fallout

  15. Prognosis after local recurrence after conservative surgery and radiation for early-stage breast cancer

    International Nuclear Information System (INIS)

    Galper, Sharon; Blood, Emily; Gelman, Rebecca; Abner, Anthony; Recht, Abram; Kohli, Anita; Wong, Julia S.; Smith, Darrell; Bellon, Jennifer; Connolly, James; Schnitt, Stuart; Winer, Eric; Silver, Barbara B.A.; Harris, Jay R.

    2005-01-01

    Purpose: To determine the long-term prognosis of patients who develop a local recurrence (LR) after conservative surgery (CS) and radiation therapy (RT) for early-stage invasive breast cancer. Methods and materials: Between 1970 and 1987, 2102 patients with clinical Stage I-II breast cancer were treated with CS+RT. LR was defined as any recurrence within the ipsilateral breast with or without simultaneous regional nodal or distant metastasis. Patients were at risk for a LR until the first of distant metastases, second nonbreast malignancy, or death (DF/S/D). The final study population comprised 341 patients with LR. The median time to LR was 72 months. The median follow-up time after LR was 85 months. A proportional hazards model of time from LR to DF/S/D was done to investigate the influence of factors at initial diagnosis and at LR on subsequent outcome. Results: The actuarial freedom from DF/S/D 5 years after LR was 65% and the survival was 81%. Variables significantly associated with time to DF/S/D were: LR histology (invasive vs. ductal carcinoma in situ, hazard ratio [HR] = 4.1, p 5 years, HR = 2.6, p 5 years, HR = 1.8, p = 0.006); and age at initial diagnosis (≥60 vs. < 60, HR = 1.6, p = 0.01). Conclusions: Many patients with LR after CS+RT have prolonged distant disease-free survival, particularly those able to be treated with mastectomy. Patients with a noninvasive LR, longer interval to LR, or age <60 had a longer time to distant failure, second malignancy, or death than other patients

  16. Aspirin and Statin Nonuse Associated With Early Biochemical Failure After Prostate Radiation Therapy

    Energy Technology Data Exchange (ETDEWEB)

    Zaorsky, Nicholas G. [Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania (United States); Buyyounouski, Mark K., E-mail: mark.buyyounouski@fccc.edu [Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania (United States); Li, Tianyu [Department of Biostatistics, Fox Chase Cancer Center, Philadelphia, Pennsylvania (United States); Horwitz, Eric M. [Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania (United States)

    2012-09-01

    Purpose: To present the largest retrospective series investigating the effect of aspirin and statins, which are hypothesized to have antineoplastic properties, on biochemical failure (nadir plus 2 ng/mL) after prostate radiation therapy (RT). Methods and Materials: Between 1989 and 2006, 2051 men with clinically localized prostate cancer received definitive RT alone (median dose, 76 Gy). The rates of aspirin use and statin use (defined as any use at the time of RT or during follow-up) were 36% and 34%, respectively. The primary endpoint of the study was an interval to biochemical failure (IBF) of less than 18 months, which has been shown to be the single strongest predictor of distant metastasis, prostate cancer survival, and overall survival after RT. Patient demographic characteristics and tumor staging factors were assessed with regard to associations with the endpoint. Univariate analysis was performed with the {chi}{sup 2} test for categorical variables and the Wilcoxon test for continuous variables. Multivariable analysis was performed with a multiple logistic regression. Results: The median follow-up was 75 months. Univariate analysis showed that an IBF of less than 18 months was associated with aspirin nonuse (P<.0001), statin nonuse (P<.0001), anticoagulant nonuse (P=.0006), cardiovascular disease (P=.0008), and prostate-specific antigen (continuous) (P=.008) but not with Gleason score, age, RT dose, or T stage. On multivariate analysis, only aspirin nonuse (P=.0012; odds ratio, 2.052 [95% confidence interval, 1.328-3.172]) and statin nonuse (P=.0002; odds ratio, 2.465 [95% confidence interval, 1.529-3.974]) were associated with an IBF of less than 18 months. Conclusions: In patients who received RT for prostate cancer, aspirin or statin nonuse was associated with early biochemical failure, a harbinger of distant metastasis and death. Further study is needed to confirm these findings and to determine the optimal dosing and schedule, as well as the relative

  17. Aspirin and Statin Nonuse Associated With Early Biochemical Failure After Prostate Radiation Therapy

    International Nuclear Information System (INIS)

    Zaorsky, Nicholas G.; Buyyounouski, Mark K.; Li, Tianyu; Horwitz, Eric M.

    2012-01-01

    Purpose: To present the largest retrospective series investigating the effect of aspirin and statins, which are hypothesized to have antineoplastic properties, on biochemical failure (nadir plus 2 ng/mL) after prostate radiation therapy (RT). Methods and Materials: Between 1989 and 2006, 2051 men with clinically localized prostate cancer received definitive RT alone (median dose, 76 Gy). The rates of aspirin use and statin use (defined as any use at the time of RT or during follow-up) were 36% and 34%, respectively. The primary endpoint of the study was an interval to biochemical failure (IBF) of less than 18 months, which has been shown to be the single strongest predictor of distant metastasis, prostate cancer survival, and overall survival after RT. Patient demographic characteristics and tumor staging factors were assessed with regard to associations with the endpoint. Univariate analysis was performed with the χ 2 test for categorical variables and the Wilcoxon test for continuous variables. Multivariable analysis was performed with a multiple logistic regression. Results: The median follow-up was 75 months. Univariate analysis showed that an IBF of less than 18 months was associated with aspirin nonuse (P<.0001), statin nonuse (P<.0001), anticoagulant nonuse (P=.0006), cardiovascular disease (P=.0008), and prostate-specific antigen (continuous) (P=.008) but not with Gleason score, age, RT dose, or T stage. On multivariate analysis, only aspirin nonuse (P=.0012; odds ratio, 2.052 [95% confidence interval, 1.328-3.172]) and statin nonuse (P=.0002; odds ratio, 2.465 [95% confidence interval, 1.529-3.974]) were associated with an IBF of less than 18 months. Conclusions: In patients who received RT for prostate cancer, aspirin or statin nonuse was associated with early biochemical failure, a harbinger of distant metastasis and death. Further study is needed to confirm these findings and to determine the optimal dosing and schedule, as well as the relative

  18. Stereotactic body radiation therapy (S.B.R.T.) for early-stage lung cancer

    International Nuclear Information System (INIS)

    Hiraok, M.; Matsuo, Y.; Nagata, Y.

    2007-01-01

    Stereotactic body radiation therapy (SBRT) is a new treatment modality for early stage non-small-cell lung cancer, and has been developed in the United States, the European Union, and Japan. We started a feasibility study of this therapy in July 1998, using a stereotactic body frame. The eligibility criteria for primary lung cancer were: 1) solitary tumor less than 4 cm (T1-3NOM); 2) inoperable, or the patient refused operation; 3) no necessity for oxygen support; 4) performance status equal to or less than 2; 5) the peripheral tumor which dose constraints of mediastinal organs are maintained. A total dose of 48 Gy was delivered in four fractions in 2 weeks in most patients. Lung toxicity was minimal. No grade II toxicities for spinal cord, bronchus, pulmonary artery, or esophagus were observed. The 3 years overall survival for 32 patients with stage IA, and 13 patients with stage IB were 83% and 72%, respectively. Only one local recurrence was observed in a follow-up of 6 1 months. We retrospectively analyzed 241 patients from 13 Japanese institutions. The local recurrence rate was 20% when the biological equivalent dose (BED) was less than 100 Gy, and 6.5% when the BED was over 100 Gy. Overall survival at 3 years was 42% when the BED was less than 100 Gy, and 46% when it was over 100 Gy. In tumors, which received a BED of more than 100 Gy, overall survival at 3 years was 91% for operable patients, and 50% for inoperable patients. Long-term results, in terms of local control, regional recurrence, survival, and complications, are not yet evaluated. However, this treatment modality is highly expected to be a standard treatment for inoperable patients, and it may be an alternative to lobectomy for operative patients. A prospective trial, which is now ongoing, will, answer these questions. (author)

  19. Radiation therapy for early stage Hodgkin's disease: Australasian patterns of care

    Energy Technology Data Exchange (ETDEWEB)

    Barton, Michael; Boyages, John; Crennan, Elizabeth; Davis, Sidney; Fisher, Richard J; Hook, Carolyn; Johnson, Neva; Joseph, David; Liew, Kuen H; Morgan, Graeme; O' Brien, Peter; Pendlebury, Sue; Pratt, Gary; Quong, George; Thornton, Deborah; Walker, Quenten; Wallington, Margaret; Trotter, Grant

    1995-01-15

    Purpose: Analysis of treatment outcome for Stage I-IIA supradiaphragmatic Hodgkin's disease treated solely by irradiation in Australia and New Zealand. Methods and Materials: Patients with supradiaphragmatic Hodgkin's disease only who were treated by irradiation alone with curative intent between 1969 to 1988 were retrospectively reviewed. Ten radiation oncology departments in Australia and New Zealand contributed patient data to the study. Patient, tumor, and treatment variables were recorded. Disease-free interval, survival, and complications were analyzed. Results: Eight hundred and twenty patients were reviewed. The median age was 29 years. There were 437 men and 383 women. The distribution of 310 clinically staged patients was 170 stage IA, 5 IB, and 135 IIA. Five hundred and ten patients received laparotomies, and pathologic staging was as follows: IA 214, IB 13, IIA 283. The 10-year acturial disease-free rate was 69% and overall survival rate was 79%. Increasing age, male sex, higher number of involved sites, the use of involved field irradiation, no staging laparotomy, and earlier year of treatment were significantly associated with an increased risk of relapse and lower survival. Actuarial 10-year survival following recurrence was 48%. Acute complications requiring interruption to treatment occurred in 46 patients (6%), but < 1% had their treatment permanently suspended. Actuarial complication rates at 10 years were: cardiac 2%, pulmonary 3% and thyroid 5%. There were 44 second malignancies including 10 non-Hodgkin's lymphomas, 3 leukemias, 7 lung, and 6 breast cancers. Mean delay to the development of a second cancer was 6 years. The 10-year actuarial rate of second malignancy was 5%. Conclusions: The Australasian experience of early stage Hodgkin's disease is consistent with the results in the published literature and confirms that irradiation produces a high cure rate with minimal toxicity.

  20. Radiation therapy for early stage Hodgkin's disease: Australasian patterns of care

    International Nuclear Information System (INIS)

    Barton, Michael; Boyages, John; Crennan, Elizabeth; Davis, Sidney; Fisher, Richard J.; Hook, Carolyn; Johnson, Neva; Joseph, David; Liew, Kuen H.; Morgan, Graeme; O'Brien, Peter; Pendlebury, Sue; Pratt, Gary; Quong, George; Thornton, Deborah; Walker, Quenten; Wallington, Margaret; Trotter, Grant

    1995-01-01

    Purpose: Analysis of treatment outcome for Stage I-IIA supradiaphragmatic Hodgkin's disease treated solely by irradiation in Australia and New Zealand. Methods and Materials: Patients with supradiaphragmatic Hodgkin's disease only who were treated by irradiation alone with curative intent between 1969 to 1988 were retrospectively reviewed. Ten radiation oncology departments in Australia and New Zealand contributed patient data to the study. Patient, tumor, and treatment variables were recorded. Disease-free interval, survival, and complications were analyzed. Results: Eight hundred and twenty patients were reviewed. The median age was 29 years. There were 437 men and 383 women. The distribution of 310 clinically staged patients was 170 stage IA, 5 IB, and 135 IIA. Five hundred and ten patients received laparotomies, and pathologic staging was as follows: IA 214, IB 13, IIA 283. The 10-year acturial disease-free rate was 69% and overall survival rate was 79%. Increasing age, male sex, higher number of involved sites, the use of involved field irradiation, no staging laparotomy, and earlier year of treatment were significantly associated with an increased risk of relapse and lower survival. Actuarial 10-year survival following recurrence was 48%. Acute complications requiring interruption to treatment occurred in 46 patients (6%), but < 1% had their treatment permanently suspended. Actuarial complication rates at 10 years were: cardiac 2%, pulmonary 3% and thyroid 5%. There were 44 second malignancies including 10 non-Hodgkin's lymphomas, 3 leukemias, 7 lung, and 6 breast cancers. Mean delay to the development of a second cancer was 6 years. The 10-year actuarial rate of second malignancy was 5%. Conclusions: The Australasian experience of early stage Hodgkin's disease is consistent with the results in the published literature and confirms that irradiation produces a high cure rate with minimal toxicity

  1. Enhanced adhesion of early endothelial progenitor cells to radiation-induced senescence-like vascular endothelial cells in vitro

    International Nuclear Information System (INIS)

    Sermsathanasawadi, N.; Inoue, Yoshinori; Iwai, Takehisa; Ishii, Hideto; Yoshida, Masayuki; Igarashi, Kaori; Miura, Masahiko

    2009-01-01

    The effects of ionizing radiation (IR) on tumor neovascularization are still unclear. We previously reported that vascular endothelial cells (ECs) expressing the IR-induced senescence-like (IRSL) phenotype exhibit a significant decrease in angiogenic activity in vitro. In this study, we examined the effects of the IRSL phenotype on adhesion to early endothelial progenitor cells (early EPCs). Adhesion of human peripheral blood-derived early EPCs to human umbilical vein endothelial cells (HUVECs) expressing the IRSL phenotype was evaluated by an adhesion assay under static conditions. It was revealed that the IRSL HUVECs supported significantly more adhesion of early EPCs than normal HUVECs. Expressions of ICAM-1, VCAM-1 and E-selectin were up-regulated in IRSL HUVECs. Pre-treatment of IRSL HUVECs with adhesion-blocking monoclonal antibodies against E-selectin and VCAM-1 significantly reduced early EPC adhesion to IRSL HUVECs, suggesting a potential role for the E-selectin and VCAM-1 in the adhesion between IRSL ECs and early EPCs. Therefore, the IRSL phenotype expressed in ECs may enhance neovascularization via increased homing of early EPCs. Our findings are first to implicate the complex effects of this phenotype on tumor neovascularization following irradiation. (author)

  2. Selection towards different adaptive optima drove the early diversification of locomotor phenotypes in the radiation of Neotropical geophagine cichlids.

    Science.gov (United States)

    Astudillo-Clavijo, Viviana; Arbour, Jessica H; López-Fernández, Hernán

    2015-05-01

    Simpson envisaged a conceptual model of adaptive radiation in which lineages diversify into "adaptive zones" within a macroevolutionary adaptive landscape. However, only a handful of studies have empirically investigated this adaptive landscape and its consequences for our interpretation of the underlying mechanisms of phenotypic evolution. In fish radiations the evolution of locomotor phenotypes may represent an important dimension of ecomorphological diversification given the implications of locomotion for feeding and habitat use. Neotropical geophagine cichlids represent a newly identified adaptive radiation and provide a useful system for studying patterns of locomotor diversification and the implications of selective constraints on phenotypic divergence in general. We use multivariate ordination, models of phenotypic evolution and posterior predictive approaches to investigate the macroevolutionary adaptive landscape and test for evidence of early divergence of locomotor phenotypes in Geophagini. The evolution of locomotor phenotypes was characterized by selection towards at least two distinct adaptive peaks and the early divergence of modern morphological disparity. One adaptive peak included the benthic and epibenthic invertivores and was characterized by fishes with deep, laterally compressed bodies that optimize precise, slow-swimming manoeuvres. The second adaptive peak resulted from a shift in adaptive optima in the species-rich ram-feeding/rheophilic Crenicichla-Teleocichla clade and was characterized by species with streamlined bodies that optimize fast starts and rapid manoeuvres. Evolutionary models and posterior predictive approaches favoured an early shift to a new adaptive peak over decreasing rates of evolution as the underlying process driving the early divergence of locomotor phenotypes. The influence of multiple adaptive peaks on the divergence of locomotor phenotypes in Geophagini is compatible with the expectations of an ecologically driven

  3. Second Malignancies After Adjuvant Radiation Therapy for Early Stage Breast Cancer: Is There Increased Risk With Addition of Regional Radiation to Local Radiation?

    Energy Technology Data Exchange (ETDEWEB)

    Hamilton, Sarah Nicole [Department of Surgery, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia (Canada); Department of Radiation Oncology, British Columbia Cancer Agency-Vancouver Centre, Vancouver, British Columbia (Canada); Tyldesley, Scott, E-mail: styldesl@bccancer.bc.ca [Department of Surgery, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia (Canada); Department of Radiation Oncology, British Columbia Cancer Agency-Vancouver Centre, Vancouver, British Columbia (Canada); Li, Dongdong [Cancer Control Research Department, British Columbia Cancer Agency-Vancouver Centre, Vancouver, British Columbia (Canada); Olson, Robert [Department of Radiation Oncology, British Columbia Cancer Agency-Centre for the North, Prince George, British Columbia (Canada); McBride, Mary [Cancer Control Research Department, British Columbia Cancer Agency-Vancouver Centre, Vancouver, British Columbia (Canada)

    2015-04-01

    Purpose: This study was undertaken to determine whether there was an increased risk of second malignancies (SM), particularly lung cancer, in early stage breast cancer patients treated with the addition of nodal fields to breast and/or chest wall radiation therapy (RT). Materials and Methods: Subjects were stage I/II female breast cancer patients 20 to 79 years of age, diagnosed between 1989 and 2005 and treated with adjuvant RT at our institution. Patients were included if they survived and did not have SM within 3 years of diagnosis. Standardized incidence ratios (SIR) with 95% confidence intervals (CI) were calculated to compare SM incidence to cancer incidence in the general sex- and age-matched populations. Secondary malignancy risks in patients treated with local RT (LRT) to the breast/chest wall were compared to those in patients treated with locoregional RT (LRRT) to the breast/chest wall and regional nodes, using multivariate regression analysis (MVA) to account for covariates. Results: The cohort included 12,836 patients with a median follow-up of 8.4 years. LRRT was used in 18% of patients. The SIR comparing patients treated with LRT to the general population was 1.29 (CI: 1.21-1.38). No statistically significant increased incidence of in-field malignancies (SIR, 1.04; CI: 0.87-1.23) and lung cancers (SIR, 1.06; CI: 0.88-1.26) was detected. The SIR comparing patients treated with LRRT to the general population was 1.39 (CI: 1.17-1.64). No statistically significant increased incidence of in-field malignancies (SIR, 1.26; CI: 0.77-1.94) and lung cancers (SIR, 1.27; CI: 0.76-1.98) was detected. On MVA comparing LRRT to LRT, the adjusted hazard ratio was 1.20 for in-field malignancies (CI: 0.68-2.16) and 1.26 for lung cancer (CI: 0.67-2.36). The excess attributable risk (EAR) to regional RT was 3.1 per 10,000 person years (CI: −8.7 to 9.9). Conclusions: No statistically significant increased risk of second malignancy was detected after LRRT relative to

  4. Modern bioinformatics meets traditional Chinese medicine.

    Science.gov (United States)

    Gu, Peiqin; Chen, Huajun

    2014-11-01

    Traditional Chinese medicine (TCM) is gaining increasing attention with the emergence of integrative medicine and personalized medicine, characterized by pattern differentiation on individual variance and treatments based on natural herbal synergism. Investigating the effectiveness and safety of the potential mechanisms of TCM and the combination principles of drug therapies will bridge the cultural gap with Western medicine and improve the development of integrative medicine. Dealing with rapidly growing amounts of biomedical data and their heterogeneous nature are two important tasks among modern biomedical communities. Bioinformatics, as an emerging interdisciplinary field of computer science and biology, has become a useful tool for easing the data deluge pressure by automating the computation processes with informatics methods. Using these methods to retrieve, store and analyze the biomedical data can effectively reveal the associated knowledge hidden in the data, and thus promote the discovery of integrated information. Recently, these techniques of bioinformatics have been used for facilitating the interactional effects of both Western medicine and TCM. The analysis of TCM data using computational technologies provides biological evidence for the basic understanding of TCM mechanisms, safety and efficacy of TCM treatments. At the same time, the carrier and targets associated with TCM remedies can inspire the rethinking of modern drug development. This review summarizes the significant achievements of applying bioinformatics techniques to many aspects of the research in TCM, such as analysis of TCM-related '-omics' data and techniques for analyzing biological processes and pharmaceutical mechanisms of TCM, which have shown certain potential of bringing new thoughts to both sides. © The Author 2013. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  5. Multiobjective optimization in bioinformatics and computational biology.

    Science.gov (United States)

    Handl, Julia; Kell, Douglas B; Knowles, Joshua

    2007-01-01

    This paper reviews the application of multiobjective optimization in the fields of bioinformatics and computational biology. A survey of existing work, organized by application area, forms the main body of the review, following an introduction to the key concepts in multiobjective optimization. An original contribution of the review is the identification of five distinct "contexts," giving rise to multiple objectives: These are used to explain the reasons behind the use of multiobjective optimization in each application area and also to point the way to potential future uses of the technique.

  6. Robust Bioinformatics Recognition with VLSI Biochip Microsystem

    Science.gov (United States)

    Lue, Jaw-Chyng L.; Fang, Wai-Chi

    2006-01-01

    A microsystem architecture for real-time, on-site, robust bioinformatic patterns recognition and analysis has been proposed. This system is compatible with on-chip DNA analysis means such as polymerase chain reaction (PCR)amplification. A corresponding novel artificial neural network (ANN) learning algorithm using new sigmoid-logarithmic transfer function based on error backpropagation (EBP) algorithm is invented. Our results show the trained new ANN can recognize low fluorescence patterns better than the conventional sigmoidal ANN does. A differential logarithmic imaging chip is designed for calculating logarithm of relative intensities of fluorescence signals. The single-rail logarithmic circuit and a prototype ANN chip are designed, fabricated and characterized.

  7. Introducing bioinformatics, the biosciences' genomic revolution

    CERN Document Server

    Zanella, Paolo

    1999-01-01

    The general audience for these lectures is mainly physicists, computer scientists, engineers or the general public wanting to know more about what’s going on in the biosciences. What’s bioinformatics and why is all this fuss being made about it ? What’s this revolution triggered by the human genome project ? Are there any results yet ? What are the problems ? What new avenues of research have been opened up ? What about the technology ? These new developments will be compared with what happened at CERN earlier in its evolution, and it is hoped that the similiraties and contrasts will stimulate new curiosity and provoke new thoughts.

  8. A Survey of Scholarly Literature Describing the Field of Bioinformatics Education and Bioinformatics Educational Research

    Science.gov (United States)

    Magana, Alejandra J.; Taleyarkhan, Manaz; Alvarado, Daniela Rivera; Kane, Michael; Springer, John; Clase, Kari

    2014-01-01

    Bioinformatics education can be broadly defined as the teaching and learning of the use of computer and information technology, along with mathematical and statistical analysis for gathering, storing, analyzing, interpreting, and integrating data to solve biological problems. The recent surge of genomics, proteomics, and structural biology in the…

  9. Early urinary diversion with ileal conduit and vesicovaginostomy in the treatment of radiation cystitis due to carcinoma cervix: a study from a tertiary care hospital in South India.

    Science.gov (United States)

    Banerji, John Samuel; Devasia, Antony; Kekre, Nitin Sudhakar; Chacko, Ninan

    2015-10-01

    To study the magnitude of radiation cystitis following radiation therapy for carcinoma cervix, and propose an algorithm to decide on early diversion, with or without vesicovaginostomy. Women who developed radiation cystitis following radiotherapy for carcinoma cervix from January 1998 to December 2011 were included in this retrospective study. Electronic hospital records were analysed to document the presence of radiation cystitis. All women who developed evidence of radiation-induced cystitis, according to the common toxicity and Radiation Therapy Oncology Group criteria, were included in the study. We looked at transfusion requirements, number of hospital admissions, quality of life and cost involved. Chi-square tests were done where applicable. SPSS version 16 was used for analysis. Of the 902 patients who received radiation for carcinoma cervix in the 13-year period, 62 (6.87%) developed grade 3/4 cystitis. Twenty-eight of them underwent ileal conduit diversion, with 18 undergoing concomitant vesicovaginostomy. When compared with the patients who did not have diversion, the transfusion requirements, number of hospital admissions and quality of life had a statistically significant difference. Cost analysis of early diversion too showed a marginal benefit with early diversion. The limitation of the study was that it was retrospective in nature. In radiation cystitis, multiple hospital admissions and consequential increase in cost is the norm. In severe disease, early diversion is a prudent, cost-effective approach with good quality of life and early return to normal activity. © 2014 Royal Australasian College of Surgeons.

  10. Bioinformatics Database Tools in Analysis of Genetics of Neurodevelopmental Disorders

    Directory of Open Access Journals (Sweden)

    Dibyashree Mallik

    2017-10-01

    Full Text Available Bioinformatics tools are recently used in various sectors of biology. Many questions regarding Neurodevelopmental disorder which arises as a major health issue recently can be solved by using various bioinformatics databases. Schizophrenia is such a mental disorder which is now arises as a major threat in young age people because it is mostly seen in case of people during their late adolescence or early adulthood period. Databases like DISGENET, GWAS, PHARMGKB, and DRUGBANK have huge repository of genes associated with schizophrenia. We found a lot of genes are being associated with schizophrenia, but approximately 200 genes are found to be present in any of these databases. After further screening out process 20 genes are found to be highly associated with each other and are also a common genes in many other diseases also. It is also found that they all are serves as a common targeting gene in many antipsychotic drugs. After analysis of various biological properties, molecular function it is found that these 20 genes are mostly involved in biological regulation process and are having receptor activity. They are belonging mainly to receptor protein class. Among these 20 genes CYP2C9, CYP3A4, DRD2, HTR1A, HTR2A are shown to be a main targeting genes of most of the antipsychotic drugs and are associated with  more than 40% diseases. The basic findings of the present study enumerated that a suitable combined drug can be design by targeting these genes which can be used for the better treatment of schizophrenia.

  11. Spectrum of the cosmic background radiation: early and recent measurements from the White Mountain Research Station

    International Nuclear Information System (INIS)

    Smoot, G.F.

    1985-09-01

    The White Mountain Research Station has provided a support facility at a high, dry, radio-quiet site for measurements that have established the blackbody character of the cosmic microwave background radiation. This finding has confirmed the interpretation of the radiation as a relic of the primeval fireball and helped to establish the hot Big Bang theory as the standard cosmological model

  12. Early bilateral radiation-induced optic neuropathy with follow-up MRI

    International Nuclear Information System (INIS)

    McClellan, R.L.; El Gammal, T.; Kline, L.B.

    1995-01-01

    Most documented cases of radiation-induced optic neuropathy are unilateral and occur more than 1 year after radiotherapy to the sellar region. We describe a patient with bilateral radiation optic neuropathy 3 months following the completion of radiotherapy. MRI 13 months after the onset of visual failure showed bilateral optic atrophy with residual gadolinium enhancement. (orig.)

  13. Early bilateral radiation-induced optic neuropathy with follow-up MRI

    Energy Technology Data Exchange (ETDEWEB)

    McClellan, R.L. [Alabama Univ., Birmingham (United States). Dept. of Radiology; El Gammal, T. [Alabama Univ., Birmingham (United States). Dept. of Radiology; Kline, L.B. [Alabama Univ., Birmingham (United States). Dept. of Radiology

    1995-02-01

    Most documented cases of radiation-induced optic neuropathy are unilateral and occur more than 1 year after radiotherapy to the sellar region. We describe a patient with bilateral radiation optic neuropathy 3 months following the completion of radiotherapy. MRI 13 months after the onset of visual failure showed bilateral optic atrophy with residual gadolinium enhancement. (orig.)

  14. Human radiation studies: Remembering the early years. Oral history of Merril Eisenbud, January 26, 1995

    International Nuclear Information System (INIS)

    1995-05-01

    Merril Eisenbud was interviewed on January 26, 1995 by representatives of the US DOE Office of Human Radiation Experiments. Following a brief biographical sketch, Mr. Eisenbud relates his remembrances as the AEC's first industrial hygienist, the setting up of AEC's Health and Safety Laboratory, monitoring radioactive fallout, and use or exposure of humans to radiation

  15. Distance to Radiation Facility and Treatment Choice in Early-Stage Breast Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Acharya, Sahaja; Hsieh, Samantha; Michalski, Jeff M. [Department of Radiation Oncology, Washington University School of Medicine-St. Louis, St. Louis, Missouri (United States); Shinohara, Eric T. [Department of Radiation Oncology, Vanderbilt University School of Medicine, Nashville, Tennessee (United States); Perkins, Stephanie M., E-mail: sperkins@radonc.wustl.edu [Department of Radiation Oncology, Washington University School of Medicine-St. Louis, St. Louis, Missouri (United States)

    2016-03-15

    Purpose: Breast-conserving therapy (BCT) is a recommended alternative to mastectomy (MT) for early-stage breast cancer. Limited access to radiation therapy (RT) may result in higher rates of MT. We assessed the association between distance to the nearest RT facility and the use of MT, in a modern cohort of women. Methods and Materials: Women with stage 0-II breast cancer eligible for BCT diagnosed from 2004 to 2010 were identified from the Florida Cancer Data System (FCDS). Distances from patient census tracts to the nearest RT facility census tract were calculated. Multivariate logistic regression was used to identify explanatory variables that influenced MT use. Results: Of the 27,489 eligible women, 32.1% (n=8841) underwent MT, and 67.8% (n=18,648) underwent BCS. Thirty-two percent of patients lived in a census tract that was >5 miles from an RT facility. MT use increased with increasing distance to RT facility (31.1% at ≤5 miles, 33.8% at >5 to <15 miles, 34.9% at 15 to <40 miles, and 51% at ≥40 miles, P<.001). The likelihood was that MT was independently associated with increasing distance to RT facility on multivariate analysis (P<.001). Compared to patients living <5 miles away from an RT facility, patients living 15 to <40 miles away were 1.2 times more likely to be treated with MT (odds ratio [OR]: 1.19, 95% confidence interval [CI]: 1.05-1.35, P<.01), and those living ≥40 miles away were more than twice as likely to be treated with MT (OR: 2.17, 95% CI: 1.48-3.17, P<.001). However, in patients younger than 50 years (n=5179), MT use was not associated with distance to RT facility (P=.235). Conclusions: MT use in a modern cohort of women is independently associated with distance to RT facility. However, for young patients, distance to RT is not a significant explanatory variable for MT use.

  16. Impact of radiation therapy fraction size on local control of early glottic carcinoma

    International Nuclear Information System (INIS)

    Yu, Edward; Shenouda, George; Beaudet, Marie P.; Black, Martin J.

    1997-01-01

    Purpose: Different radiotherapy fractionation schedules were used over a 10-year period to treat patients with early squamous cell carcinoma of the vocal cords at McGill University. A retrospective analysis was performed to study the effect of fraction size on local control in this group of patients. Methods and Materials: A total of 126 previously untreated patients with T1 invasive squamous cell carcinoma of the true vocal cords were irradiated between January 1978 and December 1988 in the Department of Radiation Oncology at McGill University. All patients received megavoltage irradiation, 94 patients received daily fractions > 2 Gy (64 patients received 50 Gy with once-daily 2.5-Gy fractions, and 30 received 65.25 Gy in 29 fractions of 2.25 Gy each), and 32 patients were treated to a dose of 66 Gy in 33 fractions with 2 Gy/fraction. Patients' characteristics of prognostic importance were equally distributed between the two fractionation groups. Results: At a median follow-up of 84 months, the 10-year disease-free survival and overall survival were 76% and 93%, respectively. Local control for patients treated with > 2 Gy fraction was 84%, compared to 65.6% for those treated with 2-Gy fractions (p = 0.026). Among the prognostic factors tested, such as gender, age, stage, anterior and posterior commissure involvement, smoking history, and fraction size, the latter was the only significant predictor of local control for the whole group of patients in univariate (p = 0.041) and multivariate (p = 0.023) analysis. There was no observed difference in the incidence of complications between the two fraction groups. Conclusions: From the results of this retrospective review of patients treated with radiotherapy for T1 true vocal cord cancer, and within the range of total doses and overall treatment times used in our patients, it was found that fractionation schedules using daily fraction size > 2 Gy are associated with a better local control than schedules delivering 2 Gy

  17. OpenHelix: bioinformatics education outside of a different box.

    Science.gov (United States)

    Williams, Jennifer M; Mangan, Mary E; Perreault-Micale, Cynthia; Lathe, Scott; Sirohi, Neeraj; Lathe, Warren C

    2010-11-01

    The amount of biological data is increasing rapidly, and will continue to increase as new rapid technologies are developed. Professionals in every area of bioscience will have data management needs that require publicly available bioinformatics resources. Not all scientists desire a formal bioinformatics education but would benefit from more informal educational sources of learning. Effective bioinformatics education formats will address a broad range of scientific needs, will be aimed at a variety of user skill levels, and will be delivered in a number of different formats to address different learning styles. Informal sources of bioinformatics education that are effective are available, and will be explored in this review.

  18. Dependence of Early and Late Chromosomal Aberrations on Radiation Quality and Cell Types

    Science.gov (United States)

    Lu, Tao; Zhang, Ye; Krieger, Stephanie; Yeshitla, Samrawit; Goss, Rosalin; Bowler, Deborah; Kadhim, Munira; Wilson, Bobby; Rohde, Larry; Wu, Honglu

    2017-01-01

    Exposure to radiation induces different types of DNA damage, increases mutation and chromosome aberration rates, and increases cellular transformation in vitro and in vivo. The susceptibility of cells to radiation depends on genetic background and growth condition of cells, as well as types of radiation. Mammalian cells of different tissue types and with different genetic background are known to have different survival rate and different mutation rate after cytogenetic insults. Genomic instability, induced by various genetic, metabolic, and environmental factors including radiation, is the driving force of tumorigenesis. Accurate measurements of the relative biological effectiveness (RBE) is important for estimating radiation-related risks. To further understand genomic instability induced by charged particles and their RBE, we exposed human lymphocytes ex vivo, human fibroblast AG1522, human mammary epithelial cells (CH184B5F5/M10), and bone marrow cells isolated from CBA/CaH(CBA) and C57BL/6 (C57) mice to high energy protons and Fe ions. Normal human fibroblasts AG1522 have apparently normal DNA damage response and repair mechanisms, while mammary epithelial cells (M10) are deficient in the repair of DNA DSBs. Mouse strain CBA is radio-sensitive while C57 is radio-resistant. Metaphase chromosomes at different cell divisions after radiation exposure were collected and chromosome aberrations were analyzed as RBE for different cell lines exposed to different radiations at various time points up to one month post irradiation.

  19. Early Tissue Effects of Stereotactic Body Radiation Therapy for Spinal Metastases

    NARCIS (Netherlands)

    Steverink, Jasper G.; Willems, Stefan M.; Philippens, Marielle E.P.; Kasperts, Nicolien; Eppinga, Wietse S.C.; Versteeg, Anne L.; van der Velden, Joanne M.; Faruqi, Salman; Sahgal, Arjun; Verlaan, Jorrit Jan

    2018-01-01

    Purpose: Stereotactic body radiation therapy (SBRT) is a highly effective and potentially ablative treatment for complex spinal metastases. Recent data have suggested radiobiologic effects of SBRT that expand beyond the traditional concept of DNA damage. Antitumor immunity, vascular damage leading

  20. New Patagonian Cretaceous theropod sheds light about the early radiation of Coelurosauria

    Directory of Open Access Journals (Sweden)

    Fernando E Novas

    2012-06-01

    Full Text Available Here we describe a new theropod, Bicentenaria argentina nov. gen. et nov. sp., from the early Late Cretaceous of Patagonia. It is represented by more than a hundred bones belonging to different sized individuals, which were buried together in disarticulation after little transportation. The available association of skeletal elements suggests a gregarious behaviour for Bicentenaria, an ethological trait also recorded among other theropod clades. Increasing documentation of monospecific assemblages of different groups of theropods suggests that a gregarious behaviour may have constituted the ancestral condition for Theropoda, at least. Bicentenaria characterizes for the surangular bone with a high dorsal margin and a prominent lateral shelf, a retroarticular process that is low, wide and spoon-shaped, and quadrate bone with its lateral condyle larger than the medial one. Phylogenetic analysis found the Chinese Tugulusaurus and the Patagonian Bicentenaria as successive sister taxa of all other coelurosaurs, thus revealing the importance of the new taxon in the understanding of the early diversification of Coelurosauria. In particular, Bicentenaria amplifies the array of basal coelurosaurs that inhabited Gondwana during the Cretaceous, also including compsognathids, Aniksosaurus and Santanaraptor. Although still restricted to a handful of forms, available information indicates that Gondwana was a cradle for the evolution of different lineages of basal coelurosaurs, different from those documented in Upper Cretaceous beds in the northern landmasses. Analysis of body size distribution in averostran theropods results in the identification of two main episodes of drastic size reduction in the evolutionary history of Coelurosauria: one occurred at the initial radiation of the group (as represented by Bicentenaria, Zuolong, Tugulusaurus, compsognathids, and Aniksosaurus, and a second episode occurred at the early diverification of Paraves or avialans

  1. TP53inp1 Gene Is Implicated in Early Radiation Response in Human Fibroblast Cells

    Directory of Open Access Journals (Sweden)

    Nikolett Sándor

    2015-10-01

    Full Text Available Tumor protein 53-induced nuclear protein-1 (TP53inp1 is expressed by activation via p53 and p73. The purpose of our study was to investigate the role of TP53inp1 in response of fibroblasts to ionizing radiation. γ-Ray radiation dose-dependently induces the expression of TP53inp1 in human immortalized fibroblast (F11hT cells. Stable silencing of TP53inp1 was done via lentiviral transfection of shRNA in F11hT cells. After irradiation the clonogenic survival of TP53inp1 knockdown (F11hT-shTP cells was compared to cells transfected with non-targeting (NT shRNA. Radiation-induced senescence was measured by SA-β-Gal staining and autophagy was detected by Acridine Orange dye and microtubule-associated protein-1 light chain 3 (LC3B immunostaining. The expression of TP53inp1, GDF-15, and CDKN1A and alterations in radiation induced mitochondrial DNA deletions were evaluated by qPCR. TP53inp1 was required for radiation (IR induced maximal elevation of CDKN1A and GDF-15 expressions. Mitochondrial DNA deletions were increased and autophagy was deregulated following irradiation in the absence of TP53inp1. Finally, we showed that silencing of TP53inp1 enhances the radiation sensitivity of fibroblast cells. These data suggest functional roles for TP53inp1 in radiation-induced autophagy and survival. Taken together, we suppose that silencing of TP53inp1 leads radiation induced autophagy impairment and induces accumulation of damaged mitochondria in primary human fibroblasts.

  2. Long-term follow-up of testicular function following radiation therapy for early-stage Hodgkin's disease

    International Nuclear Information System (INIS)

    Kinsella, T.J.; Trivette, G.; Rowland, J.; Sorace, R.; Miller, R.; Fraass, B.; Steinberg, S.M.; Glatstein, E.; Sherins, R.J.

    1989-01-01

    Seventeen male patients with pathological staged I-IIIA1 Hodgkin's disease were followed prospectively for radiation damage to the testes from low-dose scattered irradiation. During conventionally fractionated radiation therapy, the testicular dose ranged from 6 to 70 cGy. Testicular function was measured in a prospective fashion by repeated analyses (every 6 to 12 months) of serum follicle-stimulating hormone (FSH), luteinizing hormone (LH), and testosterone. Patients were also followed by serial semen analyses and by a questionnaire on fertility. The follow-up period ranged from 3 to 7 years after completion of radiation therapy. In patients receiving greater than or equal to 20 cGy, there was a dose-dependent increase in serum FSH values following irradiation, with the maximum difference at 6 months compared with pretreatment levels. All patients showed a return to normal FSH values within 12 to 24 months following irradiation. No significant changes in LH and testosterone were observed in this patient group. Eight patients with a normal pretreatment semen analysis provided serial semen samples and two patients showed transient oligospermia with complete recovery by 18 months following treatment. Four patients have fathered normal offspring following radiation therapy. We conclude that low doses (greater than 20 cGy) of scatter irradiation during treatment for Hodgkin's disease can result in transient injury to the seminiferous tubule as manifested by elevations of FSH for 6 to 24 months following treatment. Below 20 cGy, FSH values remained in the normal range. No evidence of Leydig cell injury (using LH and testosterone) was seen in this dose range (up to 70 cGy). Thus, patients with early-stage Hodgkin's disease can be treated with radiation therapy with little to no risk of irreversible testicular injury. Radiation treatment techniques to shield the testes are discussed

  3. Apoptosis is signalled early by low doses of ionising radiation in a radiation-induced bystander effect

    International Nuclear Information System (INIS)

    Furlong, Hayley; Mothersill, Carmel; Lyng, Fiona M.; Howe, Orla

    2013-01-01

    Highlights: ► Molecular mechanisms involved in the production of a radiation induced bystander effect are not well known. ► We investigate gene expression changes in apoptotic genes in both direct and bystander responses. ► We demonstrate initiation of the apoptotic cascade in a bystander response. ► Lower doses reveal a specific but differential response related to apoptosis compared to higher doses. - Abstract: It is known that ionising radiation (IR) induces a complex signalling apoptotic cascade post-exposure to low doses ultimately to remove damaged cells from a population, specifically via the intrinsic pathway. Therefore, it was hypothesised that bystander reporter cells may initiate a similar apoptotic response if exposed to low doses of IR (0.05 Gy and 0.5 Gy) and compared to directly irradiated cells. Key apoptotic genes were selected according to their role in the apoptotic cascade; tumour suppressor gene TP53, pro-apoptotic Bax and anti-apoptotic Bcl2, pro-apoptotic JNK and anti-apoptotic ERK, initiator caspase 2 and 9 and effector caspase 3, 6 and 7. The data generated consolidated the role of apoptosis following direct IR exposure for all doses and time points as pro-apoptotic genes such as Bax and JNK as well as initiator caspase 7 and effector caspase 3 and 9 were up-regulated. However, the gene expression profile for the bystander response was quite different and more complex in comparison to the direct response. The 0.05 Gy dose point had a more significant apoptosis gene expression profile compared to the 0.5 Gy dose point and genes were not always expressed within 1 h but were sometimes expressed 24 h later. The bystander data clearly demonstrates initiation of the apoptotic cascade by the up-regulation of TP53, Bax, Bcl-2, initiator caspase 2 and effector caspase 6. The effector caspases 3 and 7 of the bystander samples demonstrated down-regulation in their gene expression levels at 0.05 Gy and 0.5 Gy at both time points therefore not

  4. Apoptosis is signalled early by low doses of ionising radiation in a radiation-induced bystander effect

    Energy Technology Data Exchange (ETDEWEB)

    Furlong, Hayley, E-mail: hayley.furlong@dit.ie [DIT Centre for Radiation and Environmental Science, Focas Research Institute, Dublin Institute of Technology, Kevin St, Dublin 8 (Ireland); School of Biological Sciences, College of Sciences and Health, Dublin Institute of Technology, Kevin St, Dublin 8 (Ireland); Mothersill, Carmel [Medical Physics and Applied Radiation Sciences, Nuclear Research Building, 1280 Hamilton, Ontario L8S 4K1 (Canada); Lyng, Fiona M. [DIT Centre for Radiation and Environmental Science, Focas Research Institute, Dublin Institute of Technology, Kevin St, Dublin 8 (Ireland); Howe, Orla [DIT Centre for Radiation and Environmental Science, Focas Research Institute, Dublin Institute of Technology, Kevin St, Dublin 8 (Ireland); School of Biological Sciences, College of Sciences and Health, Dublin Institute of Technology, Kevin St, Dublin 8 (Ireland)

    2013-01-15

    Highlights: ► Molecular mechanisms involved in the production of a radiation induced bystander effect are not well known. ► We investigate gene expression changes in apoptotic genes in both direct and bystander responses. ► We demonstrate initiation of the apoptotic cascade in a bystander response. ► Lower doses reveal a specific but differential response related to apoptosis compared to higher doses. - Abstract: It is known that ionising radiation (IR) induces a complex signalling apoptotic cascade post-exposure to low doses ultimately to remove damaged cells from a population, specifically via the intrinsic pathway. Therefore, it was hypothesised that bystander reporter cells may initiate a similar apoptotic response if exposed to low doses of IR (0.05 Gy and 0.5 Gy) and compared to directly irradiated cells. Key apoptotic genes were selected according to their role in the apoptotic cascade; tumour suppressor gene TP53, pro-apoptotic Bax and anti-apoptotic Bcl2, pro-apoptotic JNK and anti-apoptotic ERK, initiator caspase 2 and 9 and effector caspase 3, 6 and 7. The data generated consolidated the role of apoptosis following direct IR exposure for all doses and time points as pro-apoptotic genes such as Bax and JNK as well as initiator caspase 7 and effector caspase 3 and 9 were up-regulated. However, the gene expression profile for the bystander response was quite different and more complex in comparison to the direct response. The 0.05 Gy dose point had a more significant apoptosis gene expression profile compared to the 0.5 Gy dose point and genes were not always expressed within 1 h but were sometimes expressed 24 h later. The bystander data clearly demonstrates initiation of the apoptotic cascade by the up-regulation of TP53, Bax, Bcl-2, initiator caspase 2 and effector caspase 6. The effector caspases 3 and 7 of the bystander samples demonstrated down-regulation in their gene expression levels at 0.05 Gy and 0.5 Gy at both time points therefore not

  5. Bioinformatic Analysis of Strawberry GSTF12 Gene

    Science.gov (United States)

    Wang, Xiran; Jiang, Leiyu; Tang, Haoru

    2018-01-01

    GSTF12 has always been known as a key factor of proanthocyanins accumulate in plant testa. Through bioinformatics analysis of the nucleotide and encoded protein sequence of GSTF12, it is more advantageous to the study of genes related to anthocyanin biosynthesis accumulation pathway. Therefore, we chosen GSTF12 gene of 11 kinds species, downloaded their nucleotide and protein sequence from NCBI as the research object, found strawberry GSTF12 gene via bioinformation analyse, constructed phylogenetic tree. At the same time, we analysed the strawberry GSTF12 gene of physical and chemical properties and its protein structure and so on. The phylogenetic tree showed that Strawberry and petunia were closest relative. By the protein prediction, we found that the protein owed one proper signal peptide without obvious transmembrane regions.

  6. Combining multiple decisions: applications to bioinformatics

    International Nuclear Information System (INIS)

    Yukinawa, N; Ishii, S; Takenouchi, T; Oba, S

    2008-01-01

    Multi-class classification is one of the fundamental tasks in bioinformatics and typically arises in cancer diagnosis studies by gene expression profiling. This article reviews two recent approaches to multi-class classification by combining multiple binary classifiers, which are formulated based on a unified framework of error-correcting output coding (ECOC). The first approach is to construct a multi-class classifier in which each binary classifier to be aggregated has a weight value to be optimally tuned based on the observed data. In the second approach, misclassification of each binary classifier is formulated as a bit inversion error with a probabilistic model by making an analogy to the context of information transmission theory. Experimental studies using various real-world datasets including cancer classification problems reveal that both of the new methods are superior or comparable to other multi-class classification methods

  7. Data mining in bioinformatics using Weka.

    Science.gov (United States)

    Frank, Eibe; Hall, Mark; Trigg, Len; Holmes, Geoffrey; Witten, Ian H

    2004-10-12

    The Weka machine learning workbench provides a general-purpose environment for automatic classification, regression, clustering and feature selection-common data mining problems in bioinformatics research. It contains an extensive collection of machine learning algorithms and data pre-processing methods complemented by graphical user interfaces for data exploration and the experimental comparison of different machine learning techniques on the same problem. Weka can process data given in the form of a single relational table. Its main objectives are to (a) assist users in extracting useful information from data and (b) enable them to easily identify a suitable algorithm for generating an accurate predictive model from it. http://www.cs.waikato.ac.nz/ml/weka.

  8. Bioinformatic and Biometric Methods in Plant Morphology

    Directory of Open Access Journals (Sweden)

    Surangi W. Punyasena

    2014-08-01

    Full Text Available Recent advances in microscopy, imaging, and data analyses have permitted both the greater application of quantitative methods and the collection of large data sets that can be used to investigate plant morphology. This special issue, the first for Applications in Plant Sciences, presents a collection of papers highlighting recent methods in the quantitative study of plant form. These emerging biometric and bioinformatic approaches to plant sciences are critical for better understanding how morphology relates to ecology, physiology, genotype, and evolutionary and phylogenetic history. From microscopic pollen grains and charcoal particles, to macroscopic leaves and whole root systems, the methods presented include automated classification and identification, geometric morphometrics, and skeleton networks, as well as tests of the limits of human assessment. All demonstrate a clear need for these computational and morphometric approaches in order to increase the consistency, objectivity, and throughput of plant morphological studies.

  9. Academic Training - Bioinformatics: Decoding the Genome

    CERN Multimedia

    Chris Jones

    2006-01-01

    ACADEMIC TRAINING LECTURE SERIES 27, 28 February 1, 2, 3 March 2006 from 11:00 to 12:00 - Auditorium, bldg. 500 Decoding the Genome A special series of 5 lectures on: Recent extraordinary advances in the life sciences arising through new detection technologies and bioinformatics The past five years have seen an extraordinary change in the information and tools available in the life sciences. The sequencing of the human genome, the discovery that we possess far fewer genes than foreseen, the measurement of the tiny changes in the genomes that differentiate us, the sequencing of the genomes of many pathogens that lead to diseases such as malaria are all examples of completely new information that is now available in the quest for improved healthcare. New tools have allowed similar strides in the discovery of the associated protein structures, providing invaluable information for those searching for new drugs. New DNA microarray chips permit simultaneous measurement of the state of expression of tens...

  10. Italian news coverage of radiation in the early decades of the twentieth century: A qualitative and quantitative analysis.

    Science.gov (United States)

    Candela, Andrea; Pasquarè Mariotto, Federico

    2016-02-01

    This work uses a qualitative approach coupled with a quantitative software-based methodology to examine the Italian news media coverage of radiation in the early decades of the twentieth century. We analyze 80 news stories from two of the most influential Italian newspapers from that time: La Stampa (a daily newspaper) and La Domenica del Corriere (an Italian Sunday supplement). While much of previous research on media coverage of scientific topics was generally focused on present-day news, our work revolves around the ground-breaking discovery of X-rays and radioactivity at the dawn of the last century. Our analysis aims to identify journalistic frames in the news coverage of radiation that journalists might have used to emphasize the benefits (or the risks) of the new discoveries. We also hypothesize how this kind of news coverage might have influenced public perception of technological, commercial, and public health applications of the new scientific advancements. © The Author(s) 2014.

  11. Adjuvant radiation use in older women with early-stage breast cancer at Johns Hopkins.

    Science.gov (United States)

    Pollock, YaoYao G; Blackford, Amanda L; Jeter, Stacie C; Wright, Jean; Cimino-Mathews, Ashley; Camp, Melissa; Harvey, Susan; Asrari, Fariba; Schoenborn, Nancy L; Stearns, Vered

    2016-11-01

    In 2004, The National Comprehensive Cancer Network (NCCN) Guidelines incorporated omission of radiation therapy after breast-conservation surgery in women ≥70 years old with stage I, estrogen receptor-positive breast cancer who plan to receive endocrine therapy. One study demonstrated wide variation in implementing this change across 13 NCCN institutions. We evaluated the practice pattern at our institution. We identified women ≥70 years old treated at our institution from 2009 to 2014. We calculated radiation therapy omission rate in those meeting the guidelines. We explored associations between radiation therapy omission, year of diagnosis, and patient characteristics with Wilcoxon rank sum tests and Fisher's exact tests. A total of 667 women met the inclusion criteria, and 117 (18 %) were candidates for radiation therapy omission. Mean age among the 117 was 76.3 years (Range: 70-95). Overall radiation therapy omission rate was 36.8 %, but varied greatly by year of diagnosis (Range: 7.7-54.5 %). This variation persisted after excluding women who did not receive endocrine therapy (Mean: 39.0 %, Range: 0.0-75.0 %). Factors associated with higher radiation therapy omission rates included older age and not having pathological nodal evaluation. The radiation therapy omission rate did not vary by race, tumor type, grade, or size. The implementation of the NCCN guideline has not been consistent at our institution. Our data suggest that other tools should be considered to apply the guidelines more consistently. We have implemented a quality improvement protocol that incorporates life expectancy estimate and geriatric assessment in women meeting the NCCN guideline at our institution.

  12. Long-term tolerance and outcomes for dose escalation in early salvage post-prostatectomy radiation therapy

    International Nuclear Information System (INIS)

    Safdieh, Joseph; Schwartz, David; Weiner, Joseph; Weiss, Jeffrey P.; Madeb, Isaac; Rotman, Marvin; Schreiber, David; Rineer, Justin

    2014-01-01

    To study the long-term outcomes and tolerance in our patients who received dose escalated radiotherapy in the early salvage post-prostatectomy setting. The medical records of 54 consecutive patients who underwent radical prostatectomy subsequently followed by salvage radiation therapy (SRT) to the prostate bed between 2003-2010 were analyzed. Patients included were required to have a pre-radiation prostate specific antigen level (PSA) of 2 ng/mL or less. The median SRT dose was 70.2 Gy. Biochemical failure after salvage radiation was defined as a PSA level >0.2 ng/mL. Biochemical control and survival endpoints were analyzed using the Kaplan-Meier method. Univariate and multivariate Cox regression analysis were used to identify the potential impact of confounding factors on outcomes. The median pre-SRT PSA was 0.45 ng/mL and the median follow-up time was 71 months. The 4- and 7-year actuarial biochemical control rates were 75.7% and 63.2%, respectively. The actuarial 4- and 7-year distant metastasis-free survival was 93.7% and 87.0%, respectively, and the actuarial 7-year prostate cancer specific survival was 94.9%. Grade 3 late genitourinary toxicity developed in 14 patients (25.9%), while grade 4 late genitourinary toxicity developed in 2 patients (3.7%). Grade 3 late gastrointestinal toxicity developed in 1 patient (1.9%), and grade 4 late gastrointestinal toxicity developed in 1 patient (1.9%). In this series with long-term follow-up, early SRT provided outcomes and toxicity profiles similar to those reported from the three major randomized trials studying adjuvant radiation therapy.

  13. Evaluating an Inquiry-Based Bioinformatics Course Using Q Methodology

    Science.gov (United States)

    Ramlo, Susan E.; McConnell, David; Duan, Zhong-Hui; Moore, Francisco B.

    2008-01-01

    Faculty at a Midwestern metropolitan public university recently developed a course on bioinformatics that emphasized collaboration and inquiry. Bioinformatics, essentially the application of computational tools to biological data, is inherently interdisciplinary. Thus part of the challenge of creating this course was serving the needs and…

  14. Bioinformatics education dissemination with an evolutionary problem solving perspective.

    Science.gov (United States)

    Jungck, John R; Donovan, Samuel S; Weisstein, Anton E; Khiripet, Noppadon; Everse, Stephen J

    2010-11-01

    Bioinformatics is central to biology education in the 21st century. With the generation of terabytes of data per day, the application of computer-based tools to stored and distributed data is fundamentally changing research and its application to problems in medicine, agriculture, conservation and forensics. In light of this 'information revolution,' undergraduate biology curricula must be redesigned to prepare the next generation of informed citizens as well as those who will pursue careers in the life sciences. The BEDROCK initiative (Bioinformatics Education Dissemination: Reaching Out, Connecting and Knitting together) has fostered an international community of bioinformatics educators. The initiative's goals are to: (i) Identify and support faculty who can take leadership roles in bioinformatics education; (ii) Highlight and distribute innovative approaches to incorporating evolutionary bioinformatics data and techniques throughout undergraduate education; (iii) Establish mechanisms for the broad dissemination of bioinformatics resource materials and teaching models; (iv) Emphasize phylogenetic thinking and problem solving; and (v) Develop and publish new software tools to help students develop and test evolutionary hypotheses. Since 2002, BEDROCK has offered more than 50 faculty workshops around the world, published many resources and supported an environment for developing and sharing bioinformatics education approaches. The BEDROCK initiative builds on the established pedagogical philosophy and academic community of the BioQUEST Curriculum Consortium to assemble the diverse intellectual and human resources required to sustain an international reform effort in undergraduate bioinformatics education.

  15. Bioinformatics and its application in animal health: a review | Soetan ...

    African Journals Online (AJOL)

    Bioinformatics is an interdisciplinary subject, which uses computer application, statistics, mathematics and engineering for the analysis and management of biological information. It has become an important tool for basic and applied research in veterinary sciences. Bioinformatics has brought about advancements into ...

  16. Recent developments in life sciences research: Role of bioinformatics

    African Journals Online (AJOL)

    Life sciences research and development has opened up new challenges and opportunities for bioinformatics. The contribution of bioinformatics advances made possible the mapping of the entire human genome and genomes of many other organisms in just over a decade. These discoveries, along with current efforts to ...

  17. Generative Topic Modeling in Image Data Mining and Bioinformatics Studies

    Science.gov (United States)

    Chen, Xin

    2012-01-01

    Probabilistic topic models have been developed for applications in various domains such as text mining, information retrieval and computer vision and bioinformatics domain. In this thesis, we focus on developing novel probabilistic topic models for image mining and bioinformatics studies. Specifically, a probabilistic topic-connection (PTC) model…

  18. Assessment of a Bioinformatics across Life Science Curricula Initiative

    Science.gov (United States)

    Howard, David R.; Miskowski, Jennifer A.; Grunwald, Sandra K.; Abler, Michael L.

    2007-01-01

    At the University of Wisconsin-La Crosse, we have undertaken a program to integrate the study of bioinformatics across the undergraduate life science curricula. Our efforts have included incorporating bioinformatics exercises into courses in the biology, microbiology, and chemistry departments, as well as coordinating the efforts of faculty within…

  19. Concepts Of Bioinformatics And Its Application In Veterinary ...

    African Journals Online (AJOL)

    Bioinformatics has advanced the course of research and future veterinary vaccines development because it has provided new tools for identification of vaccine targets from sequenced biological data of organisms. In Nigeria, there is lack of bioinformatics training in the universities, expect for short training courses in which ...

  20. Current status and future perspectives of bioinformatics in Tanzania ...

    African Journals Online (AJOL)

    The main bottleneck in advancing genomics in present times is the lack of expertise in using bioinformatics tools and approaches for data mining in raw DNA sequences generated by modern high throughput technologies such as next generation sequencing. Although bioinformatics has been making major progress and ...

  1. The 2015 Bioinformatics Open Source Conference (BOSC 2015).

    Science.gov (United States)

    Harris, Nomi L; Cock, Peter J A; Lapp, Hilmar; Chapman, Brad; Davey, Rob; Fields, Christopher; Hokamp, Karsten; Munoz-Torres, Monica

    2016-02-01

    The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included "Data Science;" "Standards and Interoperability;" "Open Science and Reproducibility;" "Translational Bioinformatics;" "Visualization;" and "Bioinformatics Open Source Project Updates". In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled "Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community," that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule.

  2. Is there room for ethics within bioinformatics education?

    Science.gov (United States)

    Taneri, Bahar

    2011-07-01

    When bioinformatics education is considered, several issues are addressed. At the undergraduate level, the main issue revolves around conveying information from two main and different fields: biology and computer science. At the graduate level, the main issue is bridging the gap between biology students and computer science students. However, there is an educational component that is rarely addressed within the context of bioinformatics education: the ethics component. Here, a different perspective is provided on bioinformatics education, and the current status of ethics is analyzed within the existing bioinformatics programs. Analysis of the existing undergraduate and graduate programs, in both Europe and the United States, reveals the minimal attention given to ethics within bioinformatics education. Given that bioinformaticians speedily and effectively shape the biomedical sciences and hence their implications for society, here redesigning of the bioinformatics curricula is suggested in order to integrate the necessary ethics education. Unique ethical problems awaiting bioinformaticians and bioinformatics ethics as a separate field of study are discussed. In addition, a template for an "Ethics in Bioinformatics" course is provided.

  3. The Results and Prognostic Factors of Postoperative Radiation Therapy in the Early Stages of Endometrial Cancer

    International Nuclear Information System (INIS)

    Lee, Kyung Ja

    2008-01-01

    To evaluate the results and prognostic factors for postoperative adjuvant radiation therapy in patients at stages I and II of endometrial cancer. Materials and Methods: Between January 1991 and December 2006, 35 patients with FIGO stages I and II disease, who received adjuvant radiation therapy following surgery for endometrial cancer at Ewha Womans University Hospital, were enrolled in this study. A total of 17 patients received postoperative pelvic external beam radiation therapy; whereas, 12 patients received vaginal brachytherapy alone, and 6 patients received both pelvic radiation therapy and vaginal brachytherapy. Results: The median follow-up period for all patients was 54 months. The 5-yr overall survival and disease-free survival rates for all patients were 91.4% and 81.7%, respectively. The 5-yr overall survival rates for low-risk, intermediate-risk, and high-risk groups were 100%, 100% and 55.6%, respectively. In addition, the 5-yr disease-free survival rates were 100%, 70.0%, and 45.7%, respectively. Although no locoregional relapses were identified, distant metastases were observed in 5 patients (14%). The most common site of distant metastases was the lung, followed by bone, liver, adrenal gland, and peritoneum. A univariate analysis revealed a significant correlation between distant metastases and risk-group (p=0.018), pathology type (p=0.001), and grade (p=0.019). A multivariate analysis also revealed that distant metastases were correlated with pathology type (p=0.009). Papillary, serous and clear cell carcinoma cases demonstrated a poor patient survival rate compared to cases of endometrioid adenocarcinoma or adenosquamous carcinoma. The most common complication of pelvic external beam radiation therapy was enteritis (30%), followed by proctitis, leucopenia, and lymphedema. All these complications were of RTOG grades 1 and 2; no grades 3 and 4 were observed. Conclusion: For the low-risk and intermediate-risk groups (stages 1 and 2) endometrial

  4. 4273π: bioinformatics education on low cost ARM hardware.

    Science.gov (United States)

    Barker, Daniel; Ferrier, David Ek; Holland, Peter Wh; Mitchell, John Bo; Plaisier, Heleen; Ritchie, Michael G; Smart, Steven D

    2013-08-12

    Teaching bioinformatics at universities is complicated by typical computer classroom settings. As well as running software locally and online, students should gain experience of systems administration. For a future career in biology or bioinformatics, the installation of software is a useful skill. We propose that this may be taught by running the course on GNU/Linux running on inexpensive Raspberry Pi computer hardware, for which students may be granted full administrator access. We release 4273π, an operating system image for Raspberry Pi based on Raspbian Linux. This includes minor customisations for classroom use and includes our Open Access bioinformatics course, 4273π Bioinformatics for Biologists. This is based on the final-year undergraduate module BL4273, run on Raspberry Pi computers at the University of St Andrews, Semester 1, academic year 2012-2013. 4273π is a means to teach bioinformatics, including systems administration tasks, to undergraduates at low cost.

  5. LXtoo: an integrated live Linux distribution for the bioinformatics community.

    Science.gov (United States)

    Yu, Guangchuang; Wang, Li-Gen; Meng, Xiao-Hua; He, Qing-Yu

    2012-07-19

    Recent advances in high-throughput technologies dramatically increase biological data generation. However, many research groups lack computing facilities and specialists. This is an obstacle that remains to be addressed. Here, we present a Linux distribution, LXtoo, to provide a flexible computing platform for bioinformatics analysis. Unlike most of the existing live Linux distributions for bioinformatics limiting their usage to sequence analysis and protein structure prediction, LXtoo incorporates a comprehensive collection of bioinformatics software, including data mining tools for microarray and proteomics, protein-protein interaction analysis, and computationally complex tasks like molecular dynamics. Moreover, most of the programs have been configured and optimized for high performance computing. LXtoo aims to provide well-supported computing environment tailored for bioinformatics research, reducing duplication of efforts in building computing infrastructure. LXtoo is distributed as a Live DVD and freely available at http://bioinformatics.jnu.edu.cn/LXtoo.

  6. The development and application of bioinformatics core competencies to improve bioinformatics training and education.

    Science.gov (United States)

    Mulder, Nicola; Schwartz, Russell; Brazas, Michelle D; Brooksbank, Cath; Gaeta, Bruno; Morgan, Sarah L; Pauley, Mark A; Rosenwald, Anne; Rustici, Gabriella; Sierk, Michael; Warnow, Tandy; Welch, Lonnie

    2018-02-01

    Bioinformatics is recognized as part of the essential knowledge base of numerous career paths in biomedical research and healthcare. However, there is little agreement in the field over what that knowledge entails or how best to provide it. These disagreements are compounded by the wide range of populations in need of bioinformatics training, with divergent prior backgrounds and intended application areas. The Curriculum Task Force of the International Society of Computational Biology (ISCB) Education Committee has sought to provide a framework for training needs and curricula in terms of a set of bioinformatics core competencies that cut across many user personas and training programs. The initial competencies developed based on surveys of employers and training programs have since been refined through a multiyear process of community engagement. This report describes the current status of the competencies and presents a series of use cases illustrating how they are being applied in diverse training contexts. These use cases are intended to demonstrate how others can make use of the competencies and engage in the process of their continuing refinement and application. The report concludes with a consideration of remaining challenges and future plans.

  7. The development and application of bioinformatics core competencies to improve bioinformatics training and education

    Science.gov (United States)

    Brooksbank, Cath; Morgan, Sarah L.; Rosenwald, Anne; Warnow, Tandy; Welch, Lonnie

    2018-01-01

    Bioinformatics is recognized as part of the essential knowledge base of numerous career paths in biomedical research and healthcare. However, there is little agreement in the field over what that knowledge entails or how best to provide it. These disagreements are compounded by the wide range of populations in need of bioinformatics training, with divergent prior backgrounds and intended application areas. The Curriculum Task Force of the International Society of Computational Biology (ISCB) Education Committee has sought to provide a framework for training needs and curricula in terms of a set of bioinformatics core competencies that cut across many user personas and training programs. The initial competencies developed based on surveys of employers and training programs have since been refined through a multiyear process of community engagement. This report describes the current status of the competencies and presents a series of use cases illustrating how they are being applied in diverse training contexts. These use cases are intended to demonstrate how others can make use of the competencies and engage in the process of their continuing refinement and application. The report concludes with a consideration of remaining challenges and future plans. PMID:29390004

  8. Determination of the Risk of Radiation-Associated Circulatory and Cancer Disease Mortality in a NASA Early Astronaut Cohort

    Science.gov (United States)

    Elgart, S. R.; Chappell, L.; Milder, C. M.; Shavers, M. R.; Huff, J. L.; Little, M.; Patel, Z. S.

    2017-01-01

    Of the many possible health challenges posed during extended exploratory missions to space, the effects of space radiation on cardiovascular disease and cancer are of particular concern. There are unique challenges to estimating those radiation risks; care and appropriate and rigorous methodology should be applied when considering small cohorts such as the NASA astronaut population. The objective of this work was to determine if there was sufficient evidence for excess risk of cardiovascular disease and cancer in early NASA astronaut cohorts. NASA astronauts in selection groups 1-7 were chosen; this relatively homogeneous cohort consists of 73 white males, who unlike today's astronauts, maintained similar smoking and drinking habits to the general US population, and have published radiation doses. The participants flew in space on missions Mercury through Shuttle and received space radiation doses between 0-74.1 milligrays. Cause of death information was obtained from the Lifetime Surveillance of Astronaut Health (LSAH) program at NASA Johnson Space Center. Mortality was compared with the US male population. Trends of mortality with dose were assessed using a logistic model, fitted by maximum likelihood. Only 32 (43.84 percent) of the 73 early astronauts have died. Standard mortality ratios (SMRs) for cancer (n=7, SMR=43.4, 95 percent CI 17.8, 84.9), all circulatory disease (n=7, SMR=33.2, 95 percent CI 13.7, 65.0), and ischemic heart disease (IHD) (n=5, SMR=40.1, 95 percent CI 13.2, 89.4) were significantly lower than for the US white male population. For cerebrovascular disease, the upper confidence interval for SMR included 100, indicating it was not significantly different from the US population (n=2, SMR = 77.0, 95 percent CI 9.4, 268.2). The power of the study is low and remains below 10 percent even when risks 10 times those reported in the literature are assumed. Due to small sample size, there is currently insufficient statistical power to evaluate space

  9. Radiation Therapy Overcomes Adverse Prognostic Role of Cyclooxygenase-2 Expression on Reed-Sternberg Cells in Early Hodgkin Lymphoma

    Energy Technology Data Exchange (ETDEWEB)

    Mestre, Francisco [Service of Radiation Therapy, University Hospital Son Espases, Instituto de Investigación Sanitaria de Palma, Palma de Mallorca (Spain); Gutiérrez, Antonio, E-mail: antoniom.gutierrez@ssib.es [Service of Hematology, University Hospital Son Espases, Instituto de Investigación Sanitaria de Palma, Palma de Mallorca (Spain); Rodriguez, Jose [MD Anderson Cancer Center, Madrid (Spain); Ramos, Rafael [Service of Pathology, University Hospital Son Espases, Instituto de Investigación Sanitaria de Palma, Palma de Mallorca (Spain); Garcia, Juan Fernando [Spanish National Cancer Research Centre, Madrid (Spain); Martinez-Serra, Jordi [Service of Hematology, University Hospital Son Espases, Instituto de Investigación Sanitaria de Palma, Palma de Mallorca (Spain); Casasus, Marta; Nicolau, Cristina [Service of Radiation Therapy, Policlinica Miramar, Palma de Mallorca (Spain); Bento, Leyre; Herraez, Ines [Service of Hematology, University Hospital Son Espases, Instituto de Investigación Sanitaria de Palma, Palma de Mallorca (Spain); Lopez-Perezagua, Paloma [Service of Radiology, IDISPA, Palma de Mallorca (Spain); Daumal, Jaime [Service of Nuclear Medicine, IDISPA, Palma de Mallorca (Spain); Besalduch, Joan [Service of Hematology, University Hospital Son Espases, Instituto de Investigación Sanitaria de Palma, Palma de Mallorca (Spain)

    2015-05-01

    Purpose: To analyze the role of radiation therapy (RT) on the adverse prognostic influence of cyclooxygenase-2 (COX-2) expression on Reed-Sternberg (RS) cells, in the setting of early Hodgkin lymphoma (HL) treated with ABVD (adriamycin, vinblastine, bleomycin, dacarbazine). Methods and Materials: In the present study we retrospectively investigated the prognostic value of COX-2 expression in a large (n=143), uniformly treated early HL population from the Spanish Network of HL using tissue microarrays. Univariate and multivariate analyses were done, including the most recognized clinical variables and the potential role of administration of adjuvant RT. Results: Median age was 31 years; the expression of COX-2 defined a subgroup with significantly worse prognosis. Considering COX-2{sup +} patients, those who received RT had significantly better 5-year progression-free survival (PFS) (80% vs 54% if no RT; P=.008). In contrast, COX-2{sup −} patients only had a modest, nonsignificant benefit from RT in terms of 5-year PFS (90% vs 79%; P=.13). When we compared the outcome of patients receiving RT considering the expression of COX-2 on RS cells, we found a nonsignificant 10% difference in terms of PFS between COX-2{sup +} and COX-2{sup −} patients (P=.09), whereas the difference between the 2 groups was important (25%) in patients not receiving RT (P=.04). Conclusions: Cyclooxygenase-2 RS cell expression is an adverse independent prognostic factor in early HL. Radiation therapy overcomes the worse prognosis associated with COX-2 expression on RS cells, acting in a chemotherapy-independent way. Cyclooxygenase-2 RS cell expression may be useful for determining patient candidates with early HL to receive consolidation with RT.

  10. Radiation therapy for early stage (T1 - T2) sarcomatoid carcinoma of true vocal cords: outcomes and patterns of failure

    International Nuclear Information System (INIS)

    Ballo, Matthew T.; Garden, Adam S.; El-Naggar, Adel K.; Morrison, William H.; Ang, K. Kian

    1997-01-01

    Objectives/hypothesis: Sarcomatoid carcinoma of head and neck mucosal sites is a rare malignancy surrounded with much controversy. One factor consistently reported yet not well supported throughout the literature is their relative radioresistance and a general belief that surgery is the treatment of choice. Our objective was to determine if patients treated with radiation for early glottic carcinoma with this histologic diagnosis had worse outcomes than typical squamous cell carcinoma of similar stage. Materials and Methods: Twenty-eight cases of early stage sarcomatoid carcinoma of the larynx treated with definitive doses of megavoltage irradiation between 1969 and 1995 at the University of Texas M.D. Anderson Cancer Center form the cohort for this analysis. All pathologic material was reviewed to confirm the diagnosis. Follow-up ranged from 1.5 - 24 years (median, 10 years). Results: Twenty-one patients were staged T1 and 7 patients had stage T2 disease. Sixteen tumors had the more typical polypoid morphology of sarcomatoid carcinoma. All patients were treated with small laryngeal fields, median size 20 cm2, and to a median dose of 65 Gy. Four patients (14%) had local disease recurrence. All 4 patients had salvage total laryngectomies and remained free of local disease. Only one patient manifested regional and distant disease. The 10-year actuarial survival rate was 63%. Conclusions: Patients with early staged sarcomatoid carcinoma of the glottis treated with radiation had similar control rates to irradiated patients with similar volume disease with the more typical squamous cell carcinoma. We do not believe that the histologic diagnosis of sarcomatoid carcinoma by itself should influence the decision to not treat a patient with early staged glottic disease with irradiation

  11. Radiation Therapy Overcomes Adverse Prognostic Role of Cyclooxygenase-2 Expression on Reed-Sternberg Cells in Early Hodgkin Lymphoma

    International Nuclear Information System (INIS)

    Mestre, Francisco; Gutiérrez, Antonio; Rodriguez, Jose; Ramos, Rafael; Garcia, Juan Fernando; Martinez-Serra, Jordi; Casasus, Marta; Nicolau, Cristina; Bento, Leyre; Herraez, Ines; Lopez-Perezagua, Paloma; Daumal, Jaime; Besalduch, Joan

    2015-01-01

    Purpose: To analyze the role of radiation therapy (RT) on the adverse prognostic influence of cyclooxygenase-2 (COX-2) expression on Reed-Sternberg (RS) cells, in the setting of early Hodgkin lymphoma (HL) treated with ABVD (adriamycin, vinblastine, bleomycin, dacarbazine). Methods and Materials: In the present study we retrospectively investigated the prognostic value of COX-2 expression in a large (n=143), uniformly treated early HL population from the Spanish Network of HL using tissue microarrays. Univariate and multivariate analyses were done, including the most recognized clinical variables and the potential role of administration of adjuvant RT. Results: Median age was 31 years; the expression of COX-2 defined a subgroup with significantly worse prognosis. Considering COX-2 + patients, those who received RT had significantly better 5-year progression-free survival (PFS) (80% vs 54% if no RT; P=.008). In contrast, COX-2 − patients only had a modest, nonsignificant benefit from RT in terms of 5-year PFS (90% vs 79%; P=.13). When we compared the outcome of patients receiving RT considering the expression of COX-2 on RS cells, we found a nonsignificant 10% difference in terms of PFS between COX-2 + and COX-2 − patients (P=.09), whereas the difference between the 2 groups was important (25%) in patients not receiving RT (P=.04). Conclusions: Cyclooxygenase-2 RS cell expression is an adverse independent prognostic factor in early HL. Radiation therapy overcomes the worse prognosis associated with COX-2 expression on RS cells, acting in a chemotherapy-independent way. Cyclooxygenase-2 RS cell expression may be useful for determining patient candidates with early HL to receive consolidation with RT

  12. The types and genetic analysis of radiation induced early maturity mutants of rice

    International Nuclear Information System (INIS)

    Yang Hefeng; Chen Xiulan; He Zhengtian; Gu Shiliang; Xu Chenwu

    1989-01-01

    Observation and correlation analysis were made for 50 early mutant lines,The early mutant lines fall into late type of early-maturity rice, and early type of mid- maturity rice, some of which are valuable as materials of rice breeding.With shorter growing period, the mutants have less inter-nodes and leaf numbers on main culm, shorter leaf and panicle length, and less filled grains and yield per plant, but have higher Protein content.Among 20 traits observed, 7 were significantly correlated with the length of growing period.The genetic parameter analysis for the mutant lines indicates that the length of growing period, plant height, grain number per panicle, 1000-grain weight have high heritability, Non-filled grain rate, secondary branch, number of panicle, grain number per panicle have larger genetic coefficient of variation and larger gain of selection

  13. Proliferative compensation of residual radiation damage in the compartment of hematopoietic early progenitor cells of the mouse

    International Nuclear Information System (INIS)

    Huebner, G.E.; Wangenheim, K.H. von; Feinendegen, L.E.

    1984-01-01

    The rate of cell entry from the compartment of hematopoietic early progenitor cells into differentiation was determined in sublethally irradiated mice. By use of the criterion of repopulating ability, transplantation of 5-( 125 I) iodo-2'-deoxyuridine labeled bone marrow cells into fatally irradiated syngeneic recipients allows to measure the relative number of early progenitor cells lodging in the spleen and the turnover of these cells in the donors. Following 450 rad the relative number of transplantable early progenitor cells in S-phase recovers to normal within 2 weeks and stabilizes after 5 weeks. At this time, the labeled progenitors turn over with a half-time of 1.4-2.2 days; the respective times for unirradiated mice are 1.5-1.8 days. This, quantitative and qualitative residual radiation damage that is known to exist in the compartment of CFU-S, is disguised within 2-5 weeks after irradiation by proliferative compensation in the entirety of early hemopoietic precursor cells which are here defined by their capacity of selfrenewal and delivery of differentiated cells and of seeding to spleens of lethally irradiated recipients. (orig.)

  14. Does sucralfate reduce early side effects of pelvic radiation? A double-blind randomized trial.

    Science.gov (United States)

    Stellamans, Karin; Lievens, Yolande; Lambin, Philippe; Van den Weyngaert, Danielle; Van den Bogaert, Walter; Scalliet, Pierre; Hutsebaut, Liesbeth; Haustermans, Karin

    2002-11-01

    STUDY AND METHODS: A double-blind placebo-controlled study randomized 108 patients to investigate the effect of sucralfate on gastrointestinal side effects of pelvic radiation. Overall, pelvic radiation with the administered doses and fields and performed according to nowadays technical standards, was well tolerated. Comparison of the mean scores and the peak reactions for radiotherapy discomfort, diarrhoea and number of stools per day in the 80 evaluable patients showed no statistically significant difference between sucralfate and placebo. Based on these results, the use of sucralfate can not be recommended as standard practice.

  15. Does sucralfate reduce early side effects of pelvic radiation? A double-blind randomized trial

    International Nuclear Information System (INIS)

    Stellamans, Karin; Lievens, Yolande; Lambin, Philippe; Van den Weyngaert, Danielle; Van den Bogaert, Walter; Scalliet, Pierre; Hutsebaut, Liesbeth; Haustermans, Karin

    2002-01-01

    Study and methods: A double-blind placebo-controlled study randomized 108 patients to investigate the effect of sucralfate on gastrointestinal side effects of pelvic radiation. Results: Overall, pelvic radiation with the administered doses and fields and performed according to nowadays technical standards, was well tolerated. Comparison of the mean scores and the peak reactions for radiotherapy discomfort, diarrhoea and number of stools per day in the 80 evaluable patients showed no statistically significant difference between sucralfate and placebo. Conclusion: Based on these results, the use of sucralfate can not be recommended as standard practice

  16. Study on the early and late mutants of radiation induced rice

    International Nuclear Information System (INIS)

    Yang Hefeng; Chen Xiulan; He Zhentian; Gu Shiliang; Xu Chenwu

    1990-12-01

    After three years of consecutive experiments for the irradiated M 2 generations of 53 different varieties of rice, the following results have been obtained: (1) The average of early mutant plant rate is 1.4%. The rate in the early-maturing varieties is lower than that in the late-maturing varieties. It is in proportion to the length of growing period of these varieties tested. The shortened days of growing period of early mutants are 3 to 32 days (the average was 9.5 days), and it is increasing as the growing period increases. (2) In the irradiated M 2 generation of same variety, the early mutants and late mutants could be simultaneously happened, but the rate of the late mutants is 2.67%, which is higher than the rate of early mutants (1.39%). The shortened and prolonged days of growing period are 11.5 and 10.5 days respectively. These early and late mutants have some changes, both good and bad, in agronomical traits such as plant height, weight per kilo-grains and grains number per tassel. In some extent these changes are significant

  17. The early effects of radiation on in vitro explants of mouse pancreas. A morphological and immunocytochemical study

    International Nuclear Information System (INIS)

    Kosanlavit, R.

    2001-01-01

    Prodromal radiation sickness involving the digestive system may occur less than an hour following whole-body or abdominal irradiation, and may be of such severity as to prevent cancer patients from completing their course of radiotherapy. The contribution of radiation-induced pancreatic damage to radiation sickness is poorly understood. This study seeks to demonstrate the early effects of X-rays (0.5-10 Gy) on mouse pancreas in vitro. The response of exocrine acinar cells, and endocrine cells from the islets of Langerhans was examined using immunocytochemistry, light and transmission electron microscopy, and morphometric analysis. There was an approximate 50% decrease in the mean number of zymogen granules in acinar cells following 10 Gy irradiation at 1 hour, which may have been due to the acceleration of enzyme secretion or the interruption of enzyme synthesis or a combination of both. The frequency distributions of zymogen granules diameter showed minor change. The gross structure of acinar cells appeared not to be affected by irradiation at the doses and times used. Following 5 and 10 Gy irradiation a few pancreatic endocrine cells within each islet lost their chromogranin A-immunoreactivity whereas other islet cells showed more intense immunostaining for chromogranin A. A dose of 10 Gy significantly decreased the volume density of glucagon-containing cells at 1 hour. Doses of 5 and 10 Gy slightly decreased the volume density of somatostatin-containing cells from 30 minutes to 3 hours. Such changes in the expression of endocrine products from these cells are likely to have profound physiological effects. Radiation induced no changes in the volume density of insulin and PP-containing cells. The results of the present study suggest that X-irradiation induce changes to exocrine and endocrine pancreatic cells, and that this may contribute to some of the symptoms of radiation sickness. (author)

  18. The effect of early radiation in N-body simulations of cosmic structure formation

    DEFF Research Database (Denmark)

    Adamek, Julian; Brandbyge, Jacob; Fidler, Christian

    2017-01-01

    Newtonian N-body simulations have been employed successfully over the past decades for the simulation of the cosmological large-scale structure. Such simulations usually ignore radiation perturbations (photons and massless neutrinos) and the impact of general relativity (GR) beyond the background...

  19. Ten scenarios from early radiation to late time acceleration with a minimally coupled dark energy

    Energy Technology Data Exchange (ETDEWEB)

    Fay, Stéphane, E-mail: steph.fay@gmail.com [Palais de la Découverte, Astronomy Department, Avenue Franklin Roosevelt, 75008 Paris (France)

    2013-09-01

    We consider General Relativity with matter, radiation and a minimally coupled dark energy defined by an equation of state w. Using dynamical system method, we find the equilibrium points of such a theory assuming an expanding Universe and a positive dark energy density. Two of these points correspond to classical radiation and matter dominated epochs for the Universe. For the other points, dark energy mimics matter, radiation or accelerates Universe expansion. We then look for possible sequences of epochs describing a Universe starting with some radiation dominated epoch(s) (mimicked or not by dark energy), then matter dominated epoch(s) (mimicked or not by dark energy) and ending with an accelerated expansion. We find ten sequences able to follow this Universe history without singular behaviour of w at some saddle points. Most of them are new in dark energy literature. To get more than these ten sequences, w has to be singular at some specific saddle equilibrium points. This is an unusual mathematical property of the equation of state in dark energy literature, whose physical consequences tend to be discarded by observations. This thus distinguishes the ten above sequences from an infinity of ways to describe Universe expansion.

  20. Ten scenarios from early radiation to late time acceleration with a minimally coupled dark energy

    International Nuclear Information System (INIS)

    Fay, Stéphane

    2013-01-01

    We consider General Relativity with matter, radiation and a minimally coupled dark energy defined by an equation of state w. Using dynamical system method, we find the equilibrium points of such a theory assuming an expanding Universe and a positive dark energy density. Two of these points correspond to classical radiation and matter dominated epochs for the Universe. For the other points, dark energy mimics matter, radiation or accelerates Universe expansion. We then look for possible sequences of epochs describing a Universe starting with some radiation dominated epoch(s) (mimicked or not by dark energy), then matter dominated epoch(s) (mimicked or not by dark energy) and ending with an accelerated expansion. We find ten sequences able to follow this Universe history without singular behaviour of w at some saddle points. Most of them are new in dark energy literature. To get more than these ten sequences, w has to be singular at some specific saddle equilibrium points. This is an unusual mathematical property of the equation of state in dark energy literature, whose physical consequences tend to be discarded by observations. This thus distinguishes the ten above sequences from an infinity of ways to describe Universe expansion

  1. Morphological correlates of fractionated radiation of the mouse lung: Early and late effects

    International Nuclear Information System (INIS)

    Penney, D.P.; Siemann, D.W.; Rubin, P.; Maltby, K.

    1994-01-01

    The definition and quantitation of radiation-induced morphologic alterations in murine lungs is presented. The extent of injury to the lung, which is the dose-limiting organ in the thorax, may be reduced by fractionating the total radiation exposure to permit partial repair of radiation-induced damage between fraction administration and also to permit a larger total exposure to be administered. The authors previously reported that, following fractionated radiation exposures, as the dose/fraction decreases, the total dose to reach an isoeffect increases, with an α/β ratio of 3.2 and 3.0 for breathing rates and lethality, respectively. In the present report, they provide comparative morphologic evaluation of the effects of weekly fractionated, daily fractionated, and hyperfractionated radiation exposures. The doses administered within each group were uniform. To determine morphologic alterations, LAF1 mice were irradiated with 3, 15, and 30 fractions delivered in 19 days overall treatment time. In the hyperfractionation schedule, the two fractions per day were separated by a 6-h time interval. Total doses were as follows: 15-21 Gy for weekly fractionation, 30-41.5 Gy for daily fractionation, and 30-49.5 Gy for hyperfractionated schedules. Lung tissue, recovered either 24 or 72 weeks following the final exposure, was evaluated by transmission and scanning electron microscopy and light microscopy. Morphological damage was not uniform throughout the exposed lung and tended to be concentrated in lobes or portions of lobes. In the three fractionation regimens studied, there is progressive sparing of the lung with increased fractionation during the pnuemonitic state (24 weeks postirradiation). Both daily and twice daily fractionations provide increased sparing over weekly fractionation during the fibrotic stages (72 weeks postirradiation), but were not markedly different from each other (i.e. weekly < daily = twice daily). 41 refs., 15 figs., 2 tabs

  2. Intensity-modulated radiation therapy for pediatric medulloblastoma: early report on the reduction of ototoxicity

    International Nuclear Information System (INIS)

    Huang, Eugene; Teh, Bin S.; Strother, Douglas R.; Davis, Quillin G.; Chiu, J. Kam; Lu, Hsin H.; Carpenter, L. Steven; Mai Weiyuan; Chintagumpala, Murali M.; South, Michael; Grant, Walter H. III; Butler, E. Brian; Woo, Shiao Y.

    2002-01-01

    Purpose: The combination of cisplatin chemotherapy and radiation therapy for the treatment of medulloblastoma has been shown to cause significant ototoxicity, impairing a child's cognitive function and quality of life. Our purpose is to determine whether the new conformal technique of intensity-modulated radiation therapy (IMRT) can achieve lower rates of hearing loss by decreasing the radiation dose delivered to the cochlea and eighth cranial nerve (auditory apparatus). Patients and Methods: Twenty-six pediatric patients treated for medulloblastoma were retrospectively divided into two groups that received either conventional radiotherapy (Conventional-RT Group) or IMRT (IMRT Group). One hundred thirteen pure-tone audiograms were evaluated retrospectively, and hearing function was graded on a scale of 0 to 4 according to the Pediatric Oncology Group's toxicity criteria. Statistical analysis comparing the rates of ototoxicity was performed using Fisher's exact test with two-tailed analysis. Results: When compared to conventional radiotherapy, IMRT delivered 68% of the radiation dose to the auditory apparatus (mean dose: 36.7 vs. 54.2 Gy). Audiometric evaluation showed that mean decibel hearing thresholds of the IMRT Group were lower at every frequency compared to those of the Conventional-RT Group, despite having higher cumulative doses of cisplatin. The overall incidence of ototoxicity was lower in the IMRT Group. Thirteen percent of the IMRT Group had Grade 3 or 4 hearing loss, compared to 64% of the Conventional-RT Group (p<0.014). Conclusion: The conformal technique of IMRT delivered much lower doses of radiation to the auditory apparatus, while still delivering full doses to the desired target volume. Our findings suggest that, despite higher doses of cisplatin, and despite radiotherapy before cisplatin therapy, treatment with IMRT can achieve a lower rate of hearing loss

  3. The environmental radiation monitoring system and in-situ measurements for early notification and OIL (Operational Intervention Levels) calculations

    Energy Technology Data Exchange (ETDEWEB)

    Haquin, G.; Ne`eman, E.; Brenner, S.; Lavi, N. [Tel Aviv Univ. (Israel). Sackler School of Medicine. Inst. for Environmental Research

    1997-12-31

    The efficiency of the environmental radiation monitoring, low level laboratory and in-situ gamma-ray spectrometry are evaluated as the systems for early notification and for determination of dose rate in air, surface contamination and activity concentration in food during emergencies for Operational Intervention Levels (OIL) recalculation.The National Environmental Radiation Monitoring System has proved its efficiency in the early detection of unregistered radiography work. A mobile station of the network can be used for absorbed dose rate measurement during emergencies in contaminated areas. The calibrated in-situ gamma-ray spectrometry system in an open phosphate ore mine has showed the efficiency of this technique for fast and accurate determination of soil activity concentration. The calibration for an uniform depth distribution can be easily mathematically converted to an exponential depth distribution in cases of radioactive material fallout 7 refs., 3 figs., 1 tab.; e-mail: envirad at post.tau.ac.il; env{sub r}ad at netvision,net.il

  4. The genetic basis of strain-dependent differences in the early phase of radiation injury in mouse lung

    International Nuclear Information System (INIS)

    Franko, A.J.; Sharplin, J.; Ward, W.F.; Hinz, J.M.

    1991-01-01

    Substantial differences between mouse strains have been reported in the lesions present in the lung during the early phase of radiation injury. Some strains show only classical pneumonitis, while other strains develop substantial fibrosis and hyaline membranes which contribute appreciably to respiratory insufficiency, in addition to pneumonitis. Other strains are intermediate between these extremes. These differences correlate with intrinsic differences in activities of lung plasminogen activator and angiotensin converting enzyme. The genetic basis of these differences was assessed by examining histologically the early reaction in lungs of seven murine hybrids available commercially after whole-thorax irradiation. Crosses between fibrosing and nonfibrosing parents were uniformly nonfibrosing, and crosses between fibrosing and intermediate parents were uniformly intermediate. No evidence of sex linkage was seen. Thus the phenotype in which fibrosis is found is controlled by autosomal recessive determinants. Strains prone to radiation-induced pulmonary fibrosis and hyaline membranes exhibited intrinsically lower activities of lung plasminogen activator and angiotensin converting enzyme than either the nonfibrosing strains or the nonfibrosing hybrid crosses. The median time of death of the hybrids was genetically determined primarily by the longest-lived parent regardless of the types of lesions expressed

  5. Cosmetic Outcome and Seroma Formation After Breast-Conserving Surgery With Intraoperative Radiation Therapy Boost for Early Breast Cancer

    International Nuclear Information System (INIS)

    Senthi, Sashendra; Link, Emma; Chua, Boon H.

    2012-01-01

    Purpose: To evaluate cosmetic outcome and its association with breast wound seroma after breast-conserving surgery (BCS) with targeted intraoperative radiation therapy (tIORT) boost for early breast cancer. Methods and Materials: An analysis of a single-arm prospective study of 55 patients with early breast cancer treated with BCS and tIORT boost followed by conventional whole breast radiation therapy (WBRT) between August 2003 and January 2006 was performed. A seroma was defined as a fluid collection at the primary tumor resection site identified clinically or radiologically. Cosmetic assessments using the European Organization for Research and Treatment of Cancer rating system were performed at baseline before BCS and 30 months after WBRT was completed. Results: Twenty-eight patients (51%) developed a seroma, with 18 patients (33%) requiring at least 1 aspiration. Tumor location was significantly associated with seroma formation (P=.001). Ten of 11 patients with an upper inner quadrant tumor developed a seroma. Excellent or good overall cosmetic outcome at 30 months was observed in 34 patients (62%, 95% confidence interval 53%-80%). Seroma formation was not associated with the overall cosmetic result (P=.54). Conclusion: BCS with tIORT boost followed by WBRT was associated with an acceptable cosmetic outcome. Seroma formation was not significantly associated with an adverse cosmetic outcome.

  6. Early Assessment of Treatment Responses During Radiation Therapy for Lung Cancer Using Quantitative Analysis of Daily Computed Tomography

    Energy Technology Data Exchange (ETDEWEB)

    Paul, Jijo; Yang, Cungeng [Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin (United States); Wu, Hui [Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin (United States); The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou (China); Tai, An [Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin (United States); Dalah, Entesar [Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin (United States); Department of Medical Diagnostic Imaging, College of Health Science, University of Sharjah (United Arab Emirates); Zheng, Cheng [Biostatistics, Joseph. J. Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin (United States); Johnstone, Candice [Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin (United States); Kong, Feng-Ming [Department of Radiation Oncology, Indiana University, Indianapolis, Indiana (United States); Gore, Elizabeth [Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin (United States); Li, X. Allen, E-mail: ali@mcw.edu [Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin (United States)

    2017-06-01

    Purpose: To investigate early tumor and normal tissue responses during the course of radiation therapy (RT) for lung cancer using quantitative analysis of daily computed tomography (CT) scans. Methods and Materials: Daily diagnostic-quality CT scans acquired using CT-on-rails during CT-guided RT for 20 lung cancer patients were quantitatively analyzed. On each daily CT set, the contours of the gross tumor volume (GTV) and lungs were generated and the radiation dose delivered was reconstructed. The changes in CT image intensity (Hounsfield unit [HU]) features in the GTV and the multiple normal lung tissue shells around the GTV were extracted from the daily CT scans. The associations between the changes in the mean HUs, GTV, accumulated dose during RT delivery, and patient survival rate were analyzed. Results: During the RT course, radiation can induce substantial changes in the HU histogram features on the daily CT scans, with reductions in the GTV mean HUs (dH) observed in the range of 11 to 48 HU (median 30). The dH is statistically related to the accumulated GTV dose (R{sup 2} > 0.99) and correlates weakly with the change in GTV (R{sup 2} = 0.3481). Statistically significant increases in patient survival rates (P=.038) were observed for patients with a higher dH in the GTV. In the normal lung, the 4 regions proximal to the GTV showed statistically significant (P<.001) HU reductions from the first to last fraction. Conclusion: Quantitative analysis of the daily CT scans indicated that the mean HUs in lung tumor and surrounding normal tissue were reduced during RT delivery. This reduction was observed in the early phase of the treatment, is patient specific, and correlated with the delivered dose. A larger HU reduction in the GTV correlated significantly with greater patient survival. The changes in daily CT features, such as the mean HU, can be used for early assessment of the radiation response during RT delivery for lung cancer.

  7. Effect of radiation on the early period of gametogenesis in Tilapia mossambika Peters

    International Nuclear Information System (INIS)

    Chmilevskij, D.A.; Ivojlov, A.A.

    1978-01-01

    Tilapia mossambica Peters larvae 10 days after hatching were X-irradiated at 350 R, and the number of germinative cells at different stages of development was followed. In the control, 10-day larvae possessed primordial germ cells and gonia; 15-day larvae had mostly gonia; in 20-day larvae some gonia were entering early prophase of meiosis; 25-day larvae possessed gonia and early meiotic prophase oocytes; and 30-day larvae had oogonia, oocytes at early prophase and at the previtellogenesis stage. After the irradiation, 13- and 14-day larvae showed some mitotic disturbances; however the mass death of germ cells was observed after their entering the pachytene stage in fishes 25 days old

  8. Radiation Induced Apoptosis of Murine Bone Marrow Cells Is Independent of Early Growth Response 1 (EGR1.

    Directory of Open Access Journals (Sweden)

    Karine Z Oben

    Full Text Available An understanding of how each individual 5q chromosome critical deleted region (CDR gene contributes to malignant transformation would foster the development of much needed targeted therapies for the treatment of therapy related myeloid neoplasms (t-MNs. Early Growth Response 1 (EGR1 is a key transcriptional regulator of myeloid differentiation located within the 5q chromosome CDR that has been shown to regulate HSC (hematopoietic stem cell quiescence as well as the master regulator of apoptosis-p53. Since resistance to apoptosis is a hallmark of malignant transformation, we investigated the role of EGR1 in apoptosis of bone marrow cells; a cell population from which myeloid malignancies arise. We evaluated radiation induced apoptosis of Egr1+/+ and Egr1-/- bone marrow cells in vitro and in vivo. EGR1 is not required for radiation induced apoptosis of murine bone marrow cells. Neither p53 mRNA (messenger RNA nor protein expression is regulated by EGR1 in these cells. Radiation induced apoptosis of bone marrow cells by double strand DNA breaks induced p53 activation. These results suggest EGR1 dependent signaling mechanisms do not contribute to aberrant apoptosis of malignant cells in myeloid malignancies.

  9. Experimental study of Gadofluorine M enhancement in early diagnosis of radiation brain injury by MRI in rats

    International Nuclear Information System (INIS)

    Bai Shoumin; Liao Chengde; Guo Ruomi; Huang Ying; Liang Biling; Shen Jun; Lu Taixiang

    2011-01-01

    Objective: To explore the value of Gadofluorine M, a novel MRI enhancement agent,in the diagnosis the early radiation brain injury. Methods: Seventy-two Wistar rats were randomly divided into 5 equal groups. To establish the radiation injury model, the rat's posterior brain was irradiated with 0 (blank controls), 25, 35, 45, 55, and 65 Gy, respectively. After irradiation MR plain scanning and Gadofluorine M enhancement scanning (after the T1WI and T2WI scanning Gf at the dosage of 0.1 mmol/kg was injected intravenously and scanning was performed again 12 h later) were performed once a week for 8 weeks. Another 12 rats were randomly divided into 2 equal groups to exposure to 55 and 65 Gy, respectively, and MR scanning was performed once a week for 8 weeks since the third week after MR. After T1WI and T2WI scanning Gd-DTPA was injected intravenously, MR was conducted again 30 min later, and Gf was injected intravenously (Gd-DTPA enhancement and Gf enhancement contrast). The MR image and the pixel count were compared. Since the third week 2 rats from the Gf enhancement scanning group and 1 rat from the Gd-DTPA enhancement and Gf enhancement contrast were killed after MR with their brains taken out to undergo pathological examination. Results: No abnormal signal changes were found in MRI in 25 and 35 Gy groups within 2 months after irradiation. A high signal in the Gf enhancement T1WI image was found in 45, 55, and 65 Gy groups within the period of 4-6 weeks after radiation. The signal intensity was significantly higher than that of the control, 25, and 35 Gy groups (F=2.15, P<0.05). The emerge time of this signal was negatively correlated with the dose of radiation (r =-0.62, P<0.05). When there was no obvious change was found by Gd-DTPA enhancement, a high signal representing change of injury could be found in Gf enhancement in the same rat. The signal intensity was significantly enhanced in Gf enhancement compared to the Gd-DTPA enhancement (F=2.74, P<0

  10. Amelioration of both early and late radiation-induced damage to pig skin by essential fatty acids

    International Nuclear Information System (INIS)

    Hopewell, J.W.; Van den Aardweg, G.J.M.J.; Morris, G.M.

    1994-01-01

    To evaluate the possible role of essential fatty acids, specifically gamma-linolenic and eicosapentaenoic acid, in the amelioration of early and late radiation damage to the skin. Skin sites on the flank of 22-25 kg female large white pigs were irradiated with either single or fractionated doses (20 F/28 days) of β-rays from 22.5 mm diameter 90 Sr/ 90 Y plaques at a dose rate of ∼3 Gy/min. Essential fatty acids were administered orally in the form of two open-quotes activeclose quotes oils, So-1100 and So-5407, which contained gamma-linolenic acid and a mixture of that oil with eicosapentaenoic acid, respectively. Oils (1.5-6.0 ml) were given daily for 4 weeks prior, both 4 weeks prior and 10-16 weeks after, or in the case of one single dose study, just for 10 weeks after irradiation. Control animals received a open-quotes placeboclose quotes oil, So-1129, containing no gamma linolenic acid or eicosapentaenoic acid over similar time scales before and after irradiation. Acute and late skin reactions were assessed visually and the dose-related incidence of a specific reaction used to compare the effects of different treatment schedules. A reduction in the severity of both the early and late radiation reactions in the skin was only observed when open-quotes activeclose quotes oils were given over the time course of the expression of radiation damage. Prior treatment with oils did not modify the radiation reaction. A 3.0 ml daily dose of either So-1100 or So-5407 given prior to, but also after irradiation with single and fractionated doses of β-rays produced the most significant modification to the radiation reactions, effects consistent with dose modification factors between 1.06-1.24 for the acute reactions of bright red erythema and/or moist desquamation, and of 1.14-1.35 for the late reactions of dusky/mauve erythema and dermal necrosis. 38 refs., 5 tabs

  11. Radiation and chemotherapy bystander effects induce early genomic instability events: telomere shortening and bridge formation coupled with mitochondrial dysfunction.

    LENUS (Irish Health Repository)

    Gorman, Sheeona

    2012-02-01

    The bridge breakage fusion cycle is a chromosomal instability mechanism responsible for genomic changes. Radiation bystander effects induce genomic instability; however, the mechanism driving this instability is unknown. We examined if radiation and chemotherapy bystander effects induce early genomic instability events such as telomere shortening and bridge formation using a human colon cancer explant model. We assessed telomere lengths, bridge formations, mitochondrial membrane potential and levels of reactive oxygen species in bystander cells exposed to medium from irradiated and chemotherapy-treated explant tissues. Bystander cells exposed to media from 2Gy, 5Gy, FOLFOX treated tumor and matching normal tissue showed a significant reduction in telomere lengths (all p values <0.018) and an increase in bridge formations (all p values <0.017) compared to bystander cells treated with media from unirradiated tissue (0Gy) at 24h. There was no significant difference between 2Gy and 5Gy treatments, or between effects elicited by tumor versus matched normal tissue. Bystander cells exposed to media from 2Gy irradiated tumor tissue showed significant depolarisation of the mitochondrial membrane potential (p=0.012) and an increase in reactive oxygen species levels. We also used bystander cells overexpressing a mitochondrial antioxidant manganese superoxide dismutase (MnSOD) to examine if this antioxidant could rescue the mitochondrial changes and subsequently influence nuclear instability events. In MnSOD cells, ROS levels were reduced (p=0.02) and mitochondrial membrane potential increased (p=0.04). These events were coupled with a decrease in percentage of cells with anaphase bridges and a decrease in the number of cells undergoing telomere length shortening (p values 0.01 and 0.028 respectively). We demonstrate that radiation and chemotherapy bystander responses induce early genomic instability coupled with defects in mitochondrial function. Restoring mitochondrial

  12. Early-Stage Classic Hodgkin Lymphoma: The Utilization of Radiation Therapy and Its Impact on Overall Survival

    Energy Technology Data Exchange (ETDEWEB)

    Parikh, Rahul R., E-mail: rparikh@chpnet.org [Department of Radiation Oncology, Mount Sinai Beth Israel Medical Center and Mount Sinai St. Luke' s-Roosevelt Hospitals, Mount Sinai Health System, Icahn School of Medicine at Mount Sinai, New York, New York (United States); Grossbard, Michael L. [Division of Hematology-Oncology, Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, New York (United States); Harrison, Louis B. [Department of Radiation Oncology, Moffitt Cancer Center and Research Institute, Tampa, Florida (United States); Yahalom, Joachim [Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York (United States)

    2015-11-01

    Purpose: To examine the association between radiation therapy (RT) utilization and overall survival (OS) for patients with early-stage Hodgkin lymphoma (HL). Methods and Materials: Using the National Cancer Database, we evaluated clinical features and survival outcomes among patients diagnosed with stage I/II HL from 1998 to 2011. The association between RT use, covariables, and outcome was assessed in a Cox proportional hazards regression model. Propensity score matching was performed to balance observed confounding factors. Survival was estimated using the Kaplan-Meier method. Results: Among the 41,943 patients in the National Cancer Database with stage I/II HL, 29,752 patients were analyzed for this study. Radiation therapy use was associated with younger age (≤40 years), favorable insured status, higher socioeconomic status (income, education), and treatment at comprehensive community cancer centers (all P<.05). Five-year OS for patients receiving RT was 94.5%, versus 88.9% for those not receiving RT (P<.01). Radiation therapy use was a significant predictor of OS in the “As-Treated” cohort (hazard ratio 0.53, 95% confidence interval 0.49-0.58, P<.01) and intention-to-treat analysis (P<.01). After propensity score matching based on clinicopathologic characteristics, RT use remained associated with improved OS (hazard ratio 0.46, 95% confidence interval 0.38-0.56, P<.01). Over the study period, RT utilization for this cohort decreased from 55% to 44%, most commonly because it was not part of the planned initial treatment strategy. Conclusions: Consolidation RT was associated with improved OS for patients with early-stage classic HL. We also have identified patient-specific variations in the use of RT that may be targeted to improve patient access to care.

  13. Early alterations in extracellular matrix and transforming growth factor β gene expression in mouse lung indicative of late radiation fibrosis

    International Nuclear Information System (INIS)

    Finkelstein, J.N.; Johnston, C.J.; Baggs, R.; Rubin, P.

    1994-01-01

    Fibrosis, characterized by the accumulation of collagen, is a late result of thoracic irradiation. The expression of late radiation injury can be found immediately after irradiation by measuring messenger RNA (mRNA) abundance. To determine if extracellular matrix mRNA and transforming growth factor beta abundance was affected acutely after irradiation, the authors measured mRNA levels of collagen I (CI), collagen III (CIII), collagen IV (CIV), fibronectin (FN), and transforming growth factor β (TGFβ 1,2ampersand3 ) in mouse lungs on day 1 and day 14 after graded doses of radiation. C57BL/6 female mice were irradiated with a single dose to the thorax of 5 or 12.5 Gy. Total lung RNA was prepared and immobilized by Northern and slot blotting and hybridized with radiolabelled cDNA probes for CI, CIII, CIV, FN, TGFβ 1,2ampersand3 and a control probe encoding for glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Autoradiographic data were quantified by video densitometry and results normalized to GAPDH. Changes in the expression of CI, CIII, CIV, FN and TGFβ 1,2ampersand3 were observed as early as 1 day after exposure. Through 14 days, changes in mRNA up to 5-fold were seen for any one dose. Dose related changes as high as 10-fold were also evident. The CI:CIII ratio increased gradually for the 5 Gy dose at 14 days postirradiation while the CI:CII ratio for the 12.5 Gy dose decreased by approximately 4-fold as compared to the control. These studies suggest that alterations in expression of extracellular matrix and TGFβ mRNA occur very early after radiation injury even at low doses and may play a role in the development of chronic fibrosis. 37 refs., 6 figs

  14. Bioinformatic Prediction of WSSV-Host Protein-Protein Interaction

    Directory of Open Access Journals (Sweden)

    Zheng Sun

    2014-01-01

    Full Text Available WSSV is one of the most dangerous pathogens in shrimp aquaculture. However, the molecular mechanism of how WSSV interacts with shrimp is still not very clear. In the present study, bioinformatic approaches were used to predict interactions between proteins from WSSV and shrimp. The genome data of WSSV (NC_003225.1 and the constructed transcriptome data of F. chinensis were used to screen potentially interacting proteins by searching in protein interaction databases, including STRING, Reactome, and DIP. Forty-four pairs of proteins were suggested to have interactions between WSSV and the shrimp. Gene ontology analysis revealed that 6 pairs of these interacting proteins were classified into “extracellular region” or “receptor complex” GO-terms. KEGG pathway analysis showed that they were involved in the “ECM-receptor interaction pathway.” In the 6 pairs of interacting proteins, an envelope protein called “collagen-like protein” (WSSV-CLP encoded by an early virus gene “wsv001” in WSSV interacted with 6 deduced proteins from the shrimp, including three integrin alpha (ITGA, two integrin beta (ITGB, and one syndecan (SDC. Sequence analysis on WSSV-CLP, ITGA, ITGB, and SDC revealed that they possessed the sequence features for protein-protein interactions. This study might provide new insights into the interaction mechanisms between WSSV and shrimp.

  15. Bioinformatics research in the Asia Pacific: a 2007 update.

    Science.gov (United States)

    Ranganathan, Shoba; Gribskov, Michael; Tan, Tin Wee

    2008-01-01

    We provide a 2007 update on the bioinformatics research in the Asia-Pacific from the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998. From 2002, APBioNet has organized the first International Conference on Bioinformatics (InCoB) bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2007 Conference was organized as the 6th annual conference of the Asia-Pacific Bioinformatics Network, on Aug. 27-30, 2007 at Hong Kong, following a series of successful events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea) and New Delhi (India). Besides a scientific meeting at Hong Kong, satellite events organized are a pre-conference training workshop at Hanoi, Vietnam and a post-conference workshop at Nansha, China. This Introduction provides a brief overview of the peer-reviewed manuscripts accepted for publication in this Supplement. We have organized the papers into thematic areas, highlighting the growing contribution of research excellence from this region, to global bioinformatics endeavours.

  16. Continuing Education Workshops in Bioinformatics Positively Impact Research and Careers.

    Science.gov (United States)

    Brazas, Michelle D; Ouellette, B F Francis

    2016-06-01

    Bioinformatics.ca has been hosting continuing education programs in introductory and advanced bioinformatics topics in Canada since 1999 and has trained more than 2,000 participants to date. These workshops have been adapted over the years to keep pace with advances in both science and technology as well as the changing landscape in available learning modalities and the bioinformatics training needs of our audience. Post-workshop surveys have been a mandatory component of each workshop and are used to ensure appropriate adjustments are made to workshops to maximize learning. However, neither bioinformatics.ca nor others offering similar training programs have explored the long-term impact of bioinformatics continuing education training. Bioinformatics.ca recently initiated a look back on the impact its workshops have had on the career trajectories, research outcomes, publications, and collaborations of its participants. Using an anonymous online survey, bioinformatics.ca analyzed responses from those surveyed and discovered its workshops have had a positive impact on collaborations, research, publications, and career progression.

  17. Bioinformatics approaches for identifying new therapeutic bioactive peptides in food

    Directory of Open Access Journals (Sweden)

    Nora Khaldi

    2012-10-01

    Full Text Available ABSTRACT:The traditional methods for mining foods for bioactive peptides are tedious and long. Similar to the drug industry, the length of time to identify and deliver a commercial health ingredient that reduces disease symptoms can take anything between 5 to 10 years. Reducing this time and effort is crucial in order to create new commercially viable products with clear and important health benefits. In the past few years, bioinformatics, the science that brings together fast computational biology, and efficient genome mining, is appearing as the long awaited solution to this problem. By quickly mining food genomes for characteristics of certain food therapeutic ingredients, researchers can potentially find new ones in a matter of a few weeks. Yet, surprisingly, very little success has been achieved so far using bioinformatics in mining for food bioactives.The absence of food specific bioinformatic mining tools, the slow integration of both experimental mining and bioinformatics, and the important difference between different experimental platforms are some of the reasons for the slow progress of bioinformatics in the field of functional food and more specifically in bioactive peptide discovery.In this paper I discuss some methods that could be easily translated, using a rational peptide bioinformatics design, to food bioactive peptide mining. I highlight the need for an integrated food peptide database. I also discuss how to better integrate experimental work with bioinformatics in order to improve the mining of food for bioactive peptides, therefore achieving a higher success rates.

  18. Complications of combined radical hysterectomy-postoperative radiation therapy in women with early stage cervical cancer

    International Nuclear Information System (INIS)

    Barter, J.F.; Soong, S.J.; Shingleton, H.M.; Hatch, K.D.; Orr, J.W. Jr.

    1989-01-01

    Fifty patients with cervical cancer were treated with radical hysterectomy and lymphadenectomy followed by postoperative radiation therapy for high risk factors (nodal metastases, lymphvascular space invasion, close or involved margins) at the University of Alabama at Birmingham Medical Center from 1969 to 1984. Fifteen (30%) of the patients treated had serious complications, 8 (16%) requiring an operation, and 1 (2%) dying as a result of treatment-related problems. This combined modality approach is associated with significant complications

  19. Dynamic changes of the early protein synthesis in murine immune cells after low dose radiation

    International Nuclear Information System (INIS)

    Chen Shali; Liu Shuzheng

    1997-01-01

    It was shown that there was a marked increase in protein synthesis of thymocytes that were metabolically labelled with 3 H-Leu for 4,6,8 and 12 hours in low dose irradiated mice showing 33.26%, 51.48%, 51.54% and 34.98% increase respectively at different time intervals of incubation when the thymic and splenic cells were sampled 4 hours after whole body irradiation (WBI) with 75 mGy X-rays. The results suggest that there is an increase in protein synthesis with its peak at 6∼8 hours after radiation. Changes in protein synthesis of immune cells in mice 4 hours after radiation and incubated for 4∼12 h were observed with SDS-PAGE followed by densitometrical scanning. It is revealed that 28 kD protein synthesis was increased gradually within 12 hours of incubation and 43 kD protein synthesis was increased in the thymocytes rapidly reaching a maximum 2 hours after incubation. It was also exhibited that the synthesis of 43 kD protein and 32 kD protein was increased in the splenocytes 2 hours after incubation. These findings may have implications in the mechanism of immunoenhancement and adaptive response induced by low dose radiation

  20. ESTRO consensus guideline on target volume delineation for elective radiation therapy of early stage breast cancer

    International Nuclear Information System (INIS)

    Offersen, Birgitte V.; Boersma, Liesbeth J.; Kirkove, Carine; Hol, Sandra; Aznar, Marianne C.; Biete Sola, Albert; Kirova, Youlia M.; Pignol, Jean-Philippe; Remouchamps, Vincent; Verhoeven, Karolien; Weltens, Caroline; Arenas, Meritxell; Gabrys, Dorota; Kopek, Neil; Krause, Mechthild; Lundstedt, Dan; Marinko, Tanja

    2015-01-01

    Background and purpose: Delineation of clinical target volumes (CTVs) is a weak link in radiation therapy (RT), and large inter-observer variation is seen in breast cancer patients. Several guidelines have been proposed, but most result in larger CTVs than based on conventional simulator-based RT. The aim was to develop a delineation guideline obtained by consensus between a broad European group of radiation oncologists. Material and methods: During ESTRO teaching courses on breast cancer, teachers sought consensus on delineation of CTV through dialogue based on cases. One teacher delineated CTV on CT scans of 2 patients, followed by discussion and adaptation of the delineation. The consensus established between teachers was sent to other teams working in the same field, both locally and on a national level, for their input. This was followed by developing a broad consensus based on discussions. Results: Borders of the CTV encompassing a 5 mm margin around the large veins, running through the regional lymph node levels were agreed, and for the breast/thoracic wall other vessels were pointed out to guide delineation, with comments on margins for patients with advanced breast cancer. Conclusion: The ESTRO consensus on CTV for elective RT of breast cancer, endorsed by a broad base of the radiation oncology community, is presented to improve consistency

  1. Proteinase-activated receptors - mediators of early and delayed normal tissue radiation responses

    International Nuclear Information System (INIS)

    Hauer-Jensen, M.

    2003-01-01

    Proteinase-activated receptors (PARs) are G-protein coupled receptors that are activated by proteolytic exposure of a receptor-tethered ligand. The discovery of this receptor family represents one of the most intriguing recent developments in signal transduction. PARs are involved in the regulation of many normal and pathophysiological processes, notably inflammatory and fibroproliferative responses to injury. Preclinical studies performed in our laboratory suggest that proteinase-activated receptor-1 (PAR-1) plays a critical role in the mechanism of chronicity of radiation fibrosis, while proteinase-activated receptor-2 (PAR-2) may mediate important fibroproliferative responses in irradiated intestine. Specifically, activation of PAR-1 by thrombin, and PAR-2 by pancreatic trypsin and mast cell proteinases, appears to be involved in acute radiation-induced inflammation, as well as in subsequent extracellular matrix deposition, leading to the development of intestinal wall fibrosis and clinical complications. Pharmacological modulators of PAR-1 or PAR-2 expression or activation would be potentially useful as preventive or therapeutic agents in patients who receive radiation therapy, especially if blockade could be targeted to specific tissues or cellular compartments

  2. Bioinformatics study of the mangrove actin genes

    Science.gov (United States)

    Basyuni, M.; Wasilah, M.; Sumardi

    2017-01-01

    This study describes the bioinformatics methods to analyze eight actin genes from mangrove plants on DDBJ/EMBL/GenBank as well as predicted the structure, composition, subcellular localization, similarity, and phylogenetic. The physical and chemical properties of eight mangroves showed variation among the genes. The percentage of the secondary structure of eight mangrove actin genes followed the order of a helix > random coil > extended chain structure for BgActl, KcActl, RsActl, and A. corniculatum Act. In contrast to this observation, the remaining actin genes were random coil > extended chain structure > a helix. This study, therefore, shown the prediction of secondary structure was performed for necessary structural information. The values of chloroplast or signal peptide or mitochondrial target were too small, indicated that no chloroplast or mitochondrial transit peptide or signal peptide of secretion pathway in mangrove actin genes. These results suggested the importance of understanding the diversity and functional of properties of the different amino acids in mangrove actin genes. To clarify the relationship among the mangrove actin gene, a phylogenetic tree was constructed. Three groups of mangrove actin genes were formed, the first group contains B. gymnorrhiza BgAct and R. stylosa RsActl. The second cluster which consists of 5 actin genes the largest group, and the last branch consist of one gene, B. sexagula Act. The present study, therefore, supported the previous results that plant actin genes form distinct clusters in the tree.

  3. Parallel evolutionary computation in bioinformatics applications.

    Science.gov (United States)

    Pinho, Jorge; Sobral, João Luis; Rocha, Miguel

    2013-05-01

    A large number of optimization problems within the field of Bioinformatics require methods able to handle its inherent complexity (e.g. NP-hard problems) and also demand increased computational efforts. In this context, the use of parallel architectures is a necessity. In this work, we propose ParJECoLi, a Java based library that offers a large set of metaheuristic methods (such as Evolutionary Algorithms) and also addresses the issue of its efficient execution on a wide range of parallel architectures. The proposed approach focuses on the easiness of use, making the adaptation to distinct parallel environments (multicore, cluster, grid) transparent to the user. Indeed, this work shows how the development of the optimization library can proceed independently of its adaptation for several architectures, making use of Aspect-Oriented Programming. The pluggable nature of parallelism related modules allows the user to easily configure its environment, adding parallelism modules to the base source code when needed. The performance of the platform is validated with two case studies within biological model optimization. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  4. SU-F-R-56: Early Assessment of Treatment Response During Radiation Therapy Delivery for Esophageal Cancer Using Quantitative CT

    Energy Technology Data Exchange (ETDEWEB)

    Li, D [Henan Province Tumor Hospital, Zhengzhou, Henan (China); Chen, X; Li, X [Medical College of Wisconsin, Milwaukee, WI (United States); Wu, H [Medical college of Wisconsin, Milwaukee, WI (United States); Wang, J [Henan province Tumor hospital, Zhengzhou, Henan (China)

    2016-06-15

    Purpose: To investigate the feasibility of assessing treatment response using CTs during delivery of radiation therapy (RT) for esophageal cancer. Methods: Daily CTs acquired using a CT-on-Rails during the routine CT-guided RT for 20 patients with stage II to IV esophageal cancers were analyzed. All patients were treated with combined chemotherapy and IMRT of 45–50 Gy in 25 fractions, and were followed up for two years. Contours of GTV, spinal cord, and non-specified tissue (NST) irradiated with low dose were generated on each daily CT. A series of CT-texture metrics including Hounsfield Unit (HU) histogram, mean HU, standard derivation (STD), entropy, and energy were obtained in these contours on each daily CT. The changes of these metrics and GTV volume during RT delivery were calculated and correlated with treatment outcome. Results: Changes in CT texture (e.g., HU histogram) in GTV and spinal cord (but not in NST) were observed during RT delivery and were consistently increased with radiation dose. For the 20 cases studied, the mean HU in GTV was reduced on average by 4.0HU from the first to the last fractions, while 8 patients (responders) had larger reductions in GTV mean HU (average 7.8 HU) with an average GTV reduction of 51% and had increased consistently in GTV STD and entropy with radiation dose. The rest of 12 patients (non-responders) had lower reductions in GTV mean HU (average 1.5HU) and almost no change in STD and entropy. For the 8 responders, 2 experienced complete response, 7 (88%) survived and 1 died. In contrast, for the 12 non-responders, 4 (33%) survived and 8 died. Conclusion: Radiation can induce changes in CT texture in tumor (e.g., mean HU) during the delivery of RT for esophageal cancer. If validated with more data, such changes may be used for early prediction of RT response for esophageal cancer.

  5. Modellierung dreidimensionaler Strahlungsfelder im frühen Universum %t Modelling three dimensional radiation fields in the early universe

    Science.gov (United States)

    Meinköhn, Erik

    2002-11-01

    The present work aims at the modelling of three-dimensional radiation fields in gas clouds from the early universe, in particular as to the influence of varying distributions of density and velocity. In observations of high-redshift gas clouds, the Lyα transition from the first excited energy level to the ground state of the hydrogen atom is usually found to be the only prominent emission lines in the entire spectrum. It is a well-known assumption that high-redshifted hydrogen clouds are the precursors of present-day galaxies. Thus, the investigation of the Lyα line is of paramount importance of the theory of galaxy formation and evolution. The observed Lyα line - or rather, to be precise, its profile - reveals both the complexity of the spatial distribution and of the kinematics of the interstellar gas, and also the nature of the photon source. In this thesis we have developed a code which is capable of solving the three-dimensional frequency-dependent radiative transfer equation for arbitrarily nonrelativistically moving media. The numerical treatment of the associated partial integro-differential equation is an extremely challenging task, since radiation intensity depends on 6 variables, namely 3 space variables, 2 variables describing the direction of photon propagation, and the frequency. With the goal of a quantitative comparison with observational data in mind, the implementation of very efficient methods for a sufficiently accurate solution of the complex radiative transfer problems turned out to be a necessity. The size of the resulting linear system of equations makes the use of parallelization techniques and grid refinement strategies indispensable.

  6. Risk of fatal cerebrovascular accidents after external beam radiation therapy for early-stage glottic laryngeal cancer.

    Science.gov (United States)

    Swisher-McClure, Samuel; Mitra, Nandita; Lin, Alexander; Ahn, Peter; Wan, Fei; O'Malley, Bert; Weinstein, Gregory S; Bekelman, Justin E

    2014-05-01

    This study compared the risk of fatal cerebrovascular accidents (CVAs) in patients with early-stage glottic laryngeal cancer receiving surgery or external beam radiation therapy (EBRT). Using a competing risks survival analysis, we compared the risk of death because of CVA among patients with early-stage glottic laryngeal cancer receiving surgery or EBRT in the Surveillance, Epidemiology, and End Results (SEER) database. The cumulative incidence of fatal CVA at 15 years was higher in patients receiving EBRT (2.8%; 95% confidence interval [CI], 2.3% to 3.4%) compared to surgery (1.5%; 95% CI, 0.8% to 2.3%; p = .024). In multivariable competing risks regression models, EBRT remained associated with an increased risk of fatal CVA compared to surgery (adjusted hazard ratio [HR], 1.75; 95% CI, 1.04-2.96; p = .037). Treatment for early-stage glottic laryngeal cancer with EBRT was associated with a small increase in the risk of late fatal CVA events relative to surgery. Copyright © 2013 Wiley Periodicals, Inc.

  7. Bioconductor: open software development for computational biology and bioinformatics

    DEFF Research Database (Denmark)

    Gentleman, R.C.; Carey, V.J.; Bates, D.M.

    2004-01-01

    The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisci......The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry...... into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples....

  8. An Overview of Bioinformatics Tools and Resources in Allergy.

    Science.gov (United States)

    Fu, Zhiyan; Lin, Jing

    2017-01-01

    The rapidly increasing number of characterized allergens has created huge demands for advanced information storage, retrieval, and analysis. Bioinformatics and machine learning approaches provide useful tools for the study of allergens and epitopes prediction, which greatly complement traditional laboratory techniques. The specific applications mainly include identification of B- and T-cell epitopes, and assessment of allergenicity and cross-reactivity. In order to facilitate the work of clinical and basic researchers who are not familiar with bioinformatics, we review in this chapter the most important databases, bioinformatic tools, and methods with relevance to the study of allergens.

  9. Radiations

    International Nuclear Information System (INIS)

    Pujol Mora, J.

    1999-01-01

    The exposition to ionizing radiations is a constant fact in the life of the human being and its utilization as diagnostic and therapeutic method is generalized. However, it is notorious how as years go on, the fear to the ionizing radiation seems to persist too, and this fact is not limited to the common individual, but to the technical personnel and professional personnel that labors with them same. (S. Grainger) [es

  10. Radiation

    International Nuclear Information System (INIS)

    Davidson, J.H.

    1986-01-01

    The basic facts about radiation are explained, along with some simple and natural ways of combating its ill-effects, based on ancient healing wisdom as well as the latest biochemical and technological research. Details are also given of the diet that saved thousands of lives in Nagasaki after the Atomic bomb attack. Special comment is made on the use of radiation for food processing. (U.K.)

  11. Radiation

    International Nuclear Information System (INIS)

    Winther, J.F.; Ulbak, K.; Dreyer, L.; Pukkala, E.; Oesterlind, A.

    1997-01-01

    Exposure to solar and ionizing radiation increases the risk for cancer in humans. Some 5% of solar radiation is within the ultraviolet spectrum and may cause both malignant melanoma and non-melanocytic skin cancer; the latter is regarded as a benign disease and is accordingly not included in our estimation of avoidable cancers. Under the assumption that the rate of occurrence of malignant melanoma of the buttocks of both men and women and of the scalp of women would apply to all parts of the body in people completely unexposed to solar radiation, it was estimated that approximately 95% of all malignant melanomas arising in the Nordic populations around the year 2000 will be due to exposure to natural ultraviolet radiation, equivalent to an annual number of about 4700 cases, with 2100 in men and 2600 in women, or some 4% of all cancers notified. Exposure to ionizing radiation in the Nordic countries occurs at an average effective dose per capita per year of about 3 mSv (Iceland, 1.1 mSv) from natural sources, and about 1 mSv from man-made sources. While the natural sources are primarily radon in indoor air, natural radionuclides in food, cosmic radiation and gamma radiation from soil and building materials, the man-made sources are dominated by the diagnostic and therapeutic use of ionizing radiation. On the basis of measured levels of radon in Nordic dwellings and associated risk estimates for lung cancer derived from well-conducted epidemiological studies, we estimated that about 180 cases of lung cancer (1% of all lung cancer cases) per year could be avoided in the Nordic countries around the year 2000 if indoor exposure to radon were eliminated, and that an additional 720 cases (6%) could be avoided annually if either radon or tobacco smoking were eliminated. Similarly, it was estimated that the exposure of the Nordic populations to natural sources of ionizing radiation other than radon and to medical sources will each give rise to an annual total of 2120

  12. Relative biological effectiveness (RBE) and distal edge effects of proton radiation on early damage in vivo

    DEFF Research Database (Denmark)

    Sørensen, Brita Singers; Bassler, Niels; Nielsen, Steffen

    2017-01-01

    of the SOBP to behind the distal dose fall-off. Irradiations were performed with the same dose plan at all positions, corresponding to a dose of 31.25 Gy in the middle of the SOBP. Endpoint of the study was early skin damage of the foot, assessed by a mouse foot skin scoring system. RESULTS: The MDD50 values......, where LETd,z =1 was 3.3 keV/μm. CONCLUSIONS: Although there is a need to expand the current study to be able to calculate an exact enhancement ratio, an enhanced biological effect in vivo for early skin damage in the distal edge was demonstrated....

  13. Combined exposure to ambient UVB radiation and nitrite negatively affects survival of amphibian early life stages

    International Nuclear Information System (INIS)

    Macias, Guadalupe; Marco, Adolfo; Blaustein, Andrew R.

    2007-01-01

    Many aquatic species are sensitive to ambient levels of ultraviolet-B radiation (UVB) and chemical fertilizers. However, recent studies indicate that the interaction among multiple stressors acting simultaneously could be contributing to the population declines of some animal species. Therefore, we tested the potential synergistic effects between ambient levels of UVB and a contaminant, sodium nitrite in the larvae of two amphibian species, the common European toad Bufo bufo and the Iberian green frog Rana perezi. We studied R. perezi from both mountain and coastal populations to examine if populations of the same species varied in their response to stressors in different habitats. Both species were sensitive to the two stressors acting alone, but the interaction between the two stressors caused a multiplicative impact on tadpole survival. For B. bufo, the combination of UVB and nitrite was up to seven times more lethal than mortality for each stressor alone. In a coastal wetland, the combination of UVB and nitrite was four times more toxic for R. perezi than the sum of the effect on mortality for each stressor alone. One mg/L of nitrite killed half the population of R. perezi at Gredos Mountains at day 10 in the absence of UVB. In the presence of UVB, 50% of the tadpoles from the same experiment died at day 7. Similar toxic response were found for R. perezi in two highly contrasted environments suggesting this synergistic interaction can be a widespread phenomenon. The interaction of excess chemical fertilizers and manure with ambient UVB radiation could be contributing to the global decline of some amphibian species. We suggest that potential exposure to UVB radiation be accounted for when assessing water quality criteria regarding nitrite pollution

  14. Computed Tomography Appearance of Early Radiation Injury to the Lung: Correlation With Clinical and Dosimetric Factors

    International Nuclear Information System (INIS)

    Jenkins, Peter; Welsh, Anne

    2011-01-01

    Purpose: To systematically assess the spectrum of radiologic changes in the lung after radiation therapy for non-small-cell lung cancer. Methods and Materials: We reviewed the cases of 146 patients treated with radical radiotherapy at our institution. All patients had computed tomography (CT) scans performed 3 months after completion of therapy. Radiographic appearances were categorized using a standard grading system. The association of these abnormalities with pretreatment factors and clinical radiation pneumonitis (RP) was investigated. Results: New intrapulmonary abnormalities were seen in 92 patients (63%). These were ground-glass opacity in 16 (11%), patchy consolidation in 19 (13%), and diffuse consolidation in 57 (39%). Twenty-five patients (17%) developed clinical symptoms of RP. Although 80% of the patients with RP had areas of consolidation seen on the posttreatment CT scan, the majority (74%) of patients with such radiographic changes were asymptomatic. For patients with lung infiltrates, the minimum isodose encompassing the volume of radiologic abnormality was usually ≥27 Gy. Traditional dose-volume metrics, pulmonary function tests, and the coadministration of angiotensin converting enzyme inhibitors (ACE-I) were all strongly correlated with the presence of radiologic injury on univariate analysis (p ≤ 0.002). There was also an inverse correlation between prior smoking history and CT scan changes (p = 0.02). On multivariate analysis, dosimetric parameters and the use of ACE-I retained significance (p = 0.005). Conclusions: Our findings suggest that there is substantial interindividual variation in lung radiosensitivity. ACE-I prevented the radiologic changes seen after high-dose radiation therapy, and their role as radioprotectants warrants further investigation.

  15. Radiosensitization In Vivo by Histone Deacetylase Inhibition with No Increase in Early Normal Tissue Radiation Toxicity.

    Science.gov (United States)

    Groselj, Blaz; Ruan, Jia-Ling; Scott, Helen; Gorrill, Jessica; Nicholson, Judith; Kelly, Jacqueline; Anbalagan, Selvakumar; Thompson, James; Stratford, Michael R L; Jevons, Sarah J; Hammond, Ester M; Scudamore, Cheryl L; Kerr, Martin; Kiltie, Anne E

    2018-02-01

    As the population ages, more elderly patients require radiotherapy-based treatment for their pelvic malignancies, including muscle-invasive bladder cancer, as they are unfit for major surgery. Therefore, there is an urgent need to find radiosensitizing agents minimally toxic to normal tissues, including bowel and bladder, for such patients. We developed methods to determine normal tissue toxicity severity in intestine and bladder in vivo , using novel radiotherapy techniques on a small animal radiation research platform (SARRP). The effects of panobinostat on in vivo tumor growth delay were evaluated using subcutaneous xenografts in athymic nude mice. Panobinostat concentration levels in xenografts, plasma, and normal tissues were measured in CD1-nude mice. CD1-nude mice were treated with drug/irradiation combinations to assess acute normal tissue effects in small intestine using the intestinal crypt assay, and later effects in small and large intestine at 11 weeks by stool assessment and at 12 weeks by histologic examination. In vitro effects of panobinostat were assessed by qPCR and of panobinostat, TMP195, and mocetinostat by clonogenic assay, and Western blot analysis. Panobinostat resulted in growth delay in RT112 bladder cancer xenografts but did not significantly increase acute (3.75 days) or 12 weeks' normal tissue radiation toxicity. Radiosensitization by panobinostat was effective in hypoxic bladder cancer cells and associated with class I HDAC inhibition, and protein downregulation of HDAC2 and MRE11. Pan-HDAC inhibition is a promising strategy for radiosensitization, but more selective agents may be more useful radiosensitizers clinically, resulting in fewer systemic side effects. Mol Cancer Ther; 17(2); 381-92. ©2017 AACR See all articles in this MCT Focus section, "Developmental Therapeutics in Radiation Oncology." ©2017 American Association for Cancer Research.

  16. Combined exposure to ambient UVB radiation and nitrite negatively affects survival of amphibian early life stages

    Energy Technology Data Exchange (ETDEWEB)

    Macias, Guadalupe [Donana Biological Station, CSIC, Spanish Council for Scientific Research. P.O. Box 1056, Sevilla 41013 (Spain); Marco, Adolfo [Donana Biological Station, CSIC, Spanish Council for Scientific Research. P.O. Box 1056, Sevilla 41013 (Spain)], E-mail: amarco@ebd.csic.es; Blaustein, Andrew R. [Department of Zoology, Oregon State University, Corvallis, Oregon, 97331 (United States)

    2007-10-15

    Many aquatic species are sensitive to ambient levels of ultraviolet-B radiation (UVB) and chemical fertilizers. However, recent studies indicate that the interaction among multiple stressors acting simultaneously could be contributing to the population declines of some animal species. Therefore, we tested the potential synergistic effects between ambient levels of UVB and a contaminant, sodium nitrite in the larvae of two amphibian species, the common European toad Bufo bufo and the Iberian green frog Rana perezi. We studied R. perezi from both mountain and coastal populations to examine if populations of the same species varied in their response to stressors in different habitats. Both species were sensitive to the two stressors acting alone, but the interaction between the two stressors caused a multiplicative impact on tadpole survival. For B. bufo, the combination of UVB and nitrite was up to seven times more lethal than mortality for each stressor alone. In a coastal wetland, the combination of UVB and nitrite was four times more toxic for R. perezi than the sum of the effect on mortality for each stressor alone. One mg/L of nitrite killed half the population of R. perezi at Gredos Mountains at day 10 in the absence of UVB. In the presence of UVB, 50% of the tadpoles from the same experiment died at day 7. Similar toxic response were found for R. perezi in two highly contrasted environments suggesting this synergistic interaction can be a widespread phenomenon. The interaction of excess chemical fertilizers and manure with ambient UVB radiation could be contributing to the global decline of some amphibian species. We suggest that potential exposure to UVB radiation be accounted for when assessing water quality criteria regarding nitrite pollution.

  17. Early carcinoma of the penis treated with radiation therapy: a preliminary report

    International Nuclear Information System (INIS)

    Sur, R.K.; Babaiah, M.; Sudarshan, G.; Shah, A.M.; Ranganathan, Vanieshree

    1994-01-01

    Four patients with stage 1 carcinoma of the penis were treated with radical external beam radiotherapy using individualized wax bolus. All patients are alive and doing well at the time of this report, 2 years after treatment. No patient had local recurrence and all had preservation of the organ and its function. Radiotherapy can be used as an alternative modality to surgery especially in the early stages of penile cancers. (author). 13 refs., 1 tab

  18. Diminished lifetime reproductive capacity in the female after early radiation exposure

    International Nuclear Information System (INIS)

    Dobson, R.L.; Kwan, T.C.; Brunckhorst, B.F.; Straume, T.

    1986-01-01

    To measure effects of early tritium-induced oocyte loss on lifetime reproduction, we determined total reproductive capacity (RC) of female mice in which known oocyte deficiencies had been produced in early life by chronic exposure to 3 HOH administered to their mothers in drinking water from the day of conception to 14 days postpartum. At that time 3 HOH administration was stopped, and oocytes were enumerated in the suckling young. Over the subsequent two years, RC was determined in these young by counting the litters and offspring they produced during continuous breeding over their entire reproductive life spans. Offspring were removed at birth to avoid interrupting the breeding process. Tritium-induced diminution of RC was found to be done dependent but less than - and, interestingly, different from - diminution of oocyte number. Oocyte loss was stochastic; RC reduction, nonstochastic. Also, despite oocyte deficiencies, productivity of exposed females tended to be normal during early reproductive life but failed prematurely as oocytes ran out. 15 refs., 4 figs., 3 tabs

  19. Tissue Banking, Bioinformatics, and Electronic Medical Records: The Front-End Requirements for Personalized Medicine

    Science.gov (United States)

    Suh, K. Stephen; Sarojini, Sreeja; Youssif, Maher; Nalley, Kip; Milinovikj, Natasha; Elloumi, Fathi; Russell, Steven; Pecora, Andrew; Schecter, Elyssa; Goy, Andre

    2013-01-01

    Personalized medicine promises patient-tailored treatments that enhance patient care and decrease overall treatment costs by focusing on genetics and “-omics” data obtained from patient biospecimens and records to guide therapy choices that generate good clinical outcomes. The approach relies on diagnostic and prognostic use of novel biomarkers discovered through combinations of tissue banking, bioinformatics, and electronic medical records (EMRs). The analytical power of bioinformatic platforms combined with patient clinical data from EMRs can reveal potential biomarkers and clinical phenotypes that allow researchers to develop experimental strategies using selected patient biospecimens stored in tissue banks. For cancer, high-quality biospecimens collected at diagnosis, first relapse, and various treatment stages provide crucial resources for study designs. To enlarge biospecimen collections, patient education regarding the value of specimen donation is vital. One approach for increasing consent is to offer publically available illustrations and game-like engagements demonstrating how wider sample availability facilitates development of novel therapies. The critical value of tissue bank samples, bioinformatics, and EMR in the early stages of the biomarker discovery process for personalized medicine is often overlooked. The data obtained also require cross-disciplinary collaborations to translate experimental results into clinical practice and diagnostic and prognostic use in personalized medicine. PMID:23818899

  20. Delivery of intraoperative radiation therapy after pneumonectomy: experimental observations and early clinical results

    International Nuclear Information System (INIS)

    Pass, H.I.; Sindelar, W.F.; Kinsella, T.J.

    1987-01-01

    Intraoperative radiation therapy (IORT) is capable of delivering high doses of radiation to mediastinal structures while sparing lung parenchyma, heart, and other locoregional tissues. A canine model of pulmonary resection and IORT was investigated by performing a pneumonectomy in 15 adult foxhounds followed by 0 cGy, 2000 cGy, 3000 cGy, 4000 cGy. No clinical complications developed in 4 animals in the 2000-cGy group. However, 2 of the 8 animals given a high dose died of esophageal hemorrhage or carinal necrosis. Esophagitis occurred in 10 of 12 animals, and none of the animals experienced bronchial stump dehiscence. In a limited Phase I protocol, 4 patients with non-small cell lung cancer were treated with resection and 2500 cGy of IORT to two separate ports encompassing the superior and inferior mediastinum. Two patients experienced life-threatening bronchopleural fistulas, and 2 patients died as a consequence of esophageal problems. One patients had recurrence with brain metastases, and the 1 long-term survivor is free from disease. As opposed to the animal model of thoracic IORT, the clinical study demonstrated major toxicity with respiratory and esophageal morbidity. The therapeutic usefulness of thoracic IORT in the management of lung cancer must be questioned in view of this small but consistent series of patients. Further carefully designed clinical studies using lower doses of IORT are needed

  1. Joseph John Thomson's models of matter and radiation in the early 1890s.

    Science.gov (United States)

    Bordoni, Stefano

    In the late nineteenth century, Joseph John Thomson moved away from Maxwell's specific theoretical models of matter and energy, even though he continued to rely on the general framework of Maxwell's electromagnetic theory. In his 1893 book, he accomplished the conceptual drift towards a discrete model for matter, electricity, and fields. In Thomson's model, energy was linked to tubes of force, in particular to the aether contained in them and surrounding them: the energy was the kinetic energy of aether, of both a rotational and translational kind. Starting from Maxwell's electromagnetic fields, namely stresses propagating through a continuous solid medium, Thomson arrived at a representation of fields as a sea of discrete units carrying energy and momentum. He tried to transform Maxwell's theory into a unified picture in which atomic models of matter stood beside atomic models of fields. In 1904 his interpretation of X-rays was based on the integration between two complementary features of electromagnetic radiation, the continuity and the discreteness, and on some kind of fibrous aether. In recent secondary literature, the problematic conceptual link between J. J. Thomson's theory and contemporary theories on electromagnetic radiation has been underestimated. On the contrary, in the first half of the twentieth century, some physicists inquired into that link, and a widespread debate emerged, misunderstandings included.

  2. Development of a cloud-based Bioinformatics Training Platform.

    Science.gov (United States)

    Revote, Jerico; Watson-Haigh, Nathan S; Quenette, Steve; Bethwaite, Blair; McGrath, Annette; Shang, Catherine A

    2017-05-01

    The Bioinformatics Training Platform (BTP) has been developed to provide access to the computational infrastructure required to deliver sophisticated hands-on bioinformatics training courses. The BTP is a cloud-based solution that is in active use for delivering next-generation sequencing training to Australian researchers at geographically dispersed locations. The BTP was built to provide an easy, accessible, consistent and cost-effective approach to delivering workshops at host universities and organizations with a high demand for bioinformatics training but lacking the dedicated bioinformatics training suites required. To support broad uptake of the BTP, the platform has been made compatible with multiple cloud infrastructures. The BTP is an open-source and open-access resource. To date, 20 training workshops have been delivered to over 700 trainees at over 10 venues across Australia using the BTP. © The Author 2016. Published by Oxford University Press.

  3. Virginia Bioinformatics Institute to expand cyberinfrastructure education and outreach project

    OpenAIRE

    Whyte, Barry James

    2008-01-01

    The National Science Foundation has awarded the Virginia Bioinformatics Institute at Virginia Tech $918,000 to expand its education and outreach program in Cyberinfrastructure - Training, Education, Advancement and Mentoring, commonly known as the CI-TEAM.

  4. An Adaptive Hybrid Multiprocessor technique for bioinformatics sequence alignment

    KAUST Repository

    Bonny, Talal; Salama, Khaled N.; Zidan, Mohammed A.

    2012-01-01

    Sequence alignment algorithms such as the Smith-Waterman algorithm are among the most important applications in the development of bioinformatics. Sequence alignment algorithms must process large amounts of data which may take a long time. Here, we

  5. Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond.

    Science.gov (United States)

    Hiraoka, Satoshi; Yang, Ching-Chia; Iwasaki, Wataru

    2016-09-29

    Metagenomic approaches are now commonly used in microbial ecology to study microbial communities in more detail, including many strains that cannot be cultivated in the laboratory. Bioinformatic analyses make it possible to mine huge metagenomic datasets and discover general patterns that govern microbial ecosystems. However, the findings of typical metagenomic and bioinformatic analyses still do not completely describe the ecology and evolution of microbes in their environments. Most analyses still depend on straightforward sequence similarity searches against reference databases. We herein review the current state of metagenomics and bioinformatics in microbial ecology and discuss future directions for the field. New techniques will allow us to go beyond routine analyses and broaden our knowledge of microbial ecosystems. We need to enrich reference databases, promote platforms that enable meta- or comprehensive analyses of diverse metagenomic datasets, devise methods that utilize long-read sequence information, and develop more powerful bioinformatic methods to analyze data from diverse perspectives.

  6. Bioinformatics Education in Pathology Training: Current Scope and Future Direction

    Directory of Open Access Journals (Sweden)

    Michael R Clay

    2017-04-01

    Full Text Available Training anatomic and clinical pathology residents in the principles of bioinformatics is a challenging endeavor. Most residents receive little to no formal exposure to bioinformatics during medical education, and most of the pathology training is spent interpreting histopathology slides using light microscopy or focused on laboratory regulation, management, and interpretation of discrete laboratory data. At a minimum, residents should be familiar with data structure, data pipelines, data manipulation, and data regulations within clinical laboratories. Fellowship-level training should incorporate advanced principles unique to each subspecialty. Barriers to bioinformatics education include the clinical apprenticeship training model, ill-defined educational milestones, inadequate faculty expertise, and limited exposure during medical training. Online educational resources, case-based learning, and incorporation into molecular genomics education could serve as effective educational strategies. Overall, pathology bioinformatics training can be incorporated into pathology resident curricula, provided there is motivation to incorporate, institutional support, educational resources, and adequate faculty expertise.

  7. In silico cloning and bioinformatic analysis of PEPCK gene in ...

    African Journals Online (AJOL)

    Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. According to the relative conservation of homologous gene, a bioinformatics strategy was applied to clone Fusarium ...

  8. Best practices in bioinformatics training for life scientists.

    KAUST Repository

    Via, Allegra; Blicher, Thomas; Bongcam-Rudloff, Erik; Brazas, Michelle D; Brooksbank, Cath; Budd, Aidan; De Las Rivas, Javier; Dreyer, Jacqueline; Fernandes, Pedro L; van Gelder, Celia; Jacob, Joachim; Jimenez, Rafael C; Loveland, Jane; Moran, Federico; Mulder, Nicola; Nyrö nen, Tommi; Rother, Kristian; Schneider, Maria Victoria; Attwood, Teresa K

    2013-01-01

    concepts. Providing bioinformatics training to empower life scientists to handle and analyse their data efficiently, and progress their research, is a challenge across the globe. Delivering good training goes beyond traditional lectures and resource

  9. Microsoft Biology Initiative: .NET Bioinformatics Platform and Tools

    Science.gov (United States)

    Diaz Acosta, B.

    2011-01-01

    The Microsoft Biology Initiative (MBI) is an effort in Microsoft Research to bring new technology and tools to the area of bioinformatics and biology. This initiative is comprised of two primary components, the Microsoft Biology Foundation (MBF) and the Microsoft Biology Tools (MBT). MBF is a language-neutral bioinformatics toolkit built as an extension to the Microsoft .NET Framework—initially aimed at the area of Genomics research. Currently, it implements a range of parsers for common bioinformatics file formats; a range of algorithms for manipulating DNA, RNA, and protein sequences; and a set of connectors to biological web services such as NCBI BLAST. MBF is available under an open source license, and executables, source code, demo applications, documentation and training materials are freely downloadable from http://research.microsoft.com/bio. MBT is a collection of tools that enable biology and bioinformatics researchers to be more productive in making scientific discoveries.

  10. Bioinformatics tools for development of fast and cost effective simple ...

    African Journals Online (AJOL)

    Bioinformatics tools for development of fast and cost effective simple sequence repeat ... comparative mapping and exploration of functional genetic diversity in the ... Already, a number of computer programs have been implemented that aim at ...

  11. Skate Genome Project: Cyber-Enabled Bioinformatics Collaboration

    Science.gov (United States)

    Vincent, J.

    2011-01-01

    The Skate Genome Project, a pilot project of the North East Cyber infrastructure Consortium, aims to produce a draft genome sequence of Leucoraja erinacea, the Little Skate. The pilot project was designed to also develop expertise in large scale collaborations across the NECC region. An overview of the bioinformatics and infrastructure challenges faced during the first year of the project will be presented. Results to date and lessons learned from the perspective of a bioinformatics core will be highlighted.

  12. PubData: search engine for bioinformatics databases worldwide

    OpenAIRE

    Vand, Kasra; Wahlestedt, Thor; Khomtchouk, Kelly; Sayed, Mohammed; Wahlestedt, Claes; Khomtchouk, Bohdan

    2016-01-01

    We propose a search engine and file retrieval system for all bioinformatics databases worldwide. PubData searches biomedical data in a user-friendly fashion similar to how PubMed searches biomedical literature. PubData is built on novel network programming, natural language processing, and artificial intelligence algorithms that can patch into the file transfer protocol servers of any user-specified bioinformatics database, query its contents, retrieve files for download, and adapt to the use...

  13. An innovative approach for testing bioinformatics programs using metamorphic testing

    Directory of Open Access Journals (Sweden)

    Liu Huai

    2009-01-01

    Full Text Available Abstract Background Recent advances in experimental and computational technologies have fueled the development of many sophisticated bioinformatics programs. The correctness of such programs is crucial as incorrectly computed results may lead to wrong biological conclusion or misguide downstream experimentation. Common software testing procedures involve executing the target program with a set of test inputs and then verifying the correctness of the test outputs. However, due to the complexity of many bioinformatics programs, it is often difficult to verify the correctness of the test outputs. Therefore our ability to perform systematic software testing is greatly hindered. Results We propose to use a novel software testing technique, metamorphic testing (MT, to test a range of bioinformatics programs. Instead of requiring a mechanism to verify whether an individual test output is correct, the MT technique verifies whether a pair of test outputs conform to a set of domain specific properties, called metamorphic relations (MRs, thus greatly increases the number and variety of test cases that can be applied. To demonstrate how MT is used in practice, we applied MT to test two open-source bioinformatics programs, namely GNLab and SeqMap. In particular we show that MT is simple to implement, and is effective in detecting faults in a real-life program and some artificially fault-seeded programs. Further, we discuss how MT can be applied to test programs from various domains of bioinformatics. Conclusion This paper describes the application of a simple, effective and automated technique to systematically test a range of bioinformatics programs. We show how MT can be implemented in practice through two real-life case studies. Since many bioinformatics programs, particularly those for large scale simulation and data analysis, are hard to test systematically, their developers may benefit from using MT as part of the testing strategy. Therefore our work

  14. BOWS (bioinformatics open web services) to centralize bioinformatics tools in web services.

    Science.gov (United States)

    Velloso, Henrique; Vialle, Ricardo A; Ortega, J Miguel

    2015-06-02

    Bioinformaticians face a range of difficulties to get locally-installed tools running and producing results; they would greatly benefit from a system that could centralize most of the tools, using an easy interface for input and output. Web services, due to their universal nature and widely known interface, constitute a very good option to achieve this goal. Bioinformatics open web services (BOWS) is a system based on generic web services produced to allow programmatic access to applications running on high-performance computing (HPC) clusters. BOWS intermediates the access to registered tools by providing front-end and back-end web services. Programmers can install applications in HPC clusters in any programming language and use the back-end service to check for new jobs and their parameters, and then to send the results to BOWS. Programs running in simple computers consume the BOWS front-end service to submit new processes and read results. BOWS compiles Java clients, which encapsulate the front-end web service requisitions, and automatically creates a web page that disposes the registered applications and clients. Bioinformatics open web services registered applications can be accessed from virtually any programming language through web services, or using standard java clients. The back-end can run in HPC clusters, allowing bioinformaticians to remotely run high-processing demand applications directly from their machines.

  15. C-reactive protein and serum amyloid A as early-phase and prognostic indicators of acute radiation exposure in nonhuman primate total-body irradiation model

    Energy Technology Data Exchange (ETDEWEB)

    Ossetrova, N.I., E-mail: ossetrova@afrri.usuhs.mil [Armed Forces Radiobiology Research Institute, 8901 Wisconsin Avenue, Bldg. 42, Bethesda, MD 20889-5603 (United States); Sandgren, D.J.; Blakely, W.F. [Armed Forces Radiobiology Research Institute, 8901 Wisconsin Avenue, Bldg. 42, Bethesda, MD 20889-5603 (United States)

    2011-09-15

    Terrorist radiological attacks or nuclear accidents could expose large numbers of people to ionizing radiation. In mass-casualty radiological incidents early medical-management requires triage tools for first-responders to quantitatively identify individuals exposed to life-threatening radiation doses and for early initiation (i.e., within one day after radiation exposure) of cytokine therapy for treatment of bone marrow acute radiation syndrome. Herein, we present results from 30 rhesus macaques total-body irradiated (TBI) to a broad dose range of 1-8.5 Gy with {sup 60}Co {gamma}-rays (0.55 Gy min{sup -1}) and demonstrate dose- and time-dependent changes in blood of C-reactive protein (CRP), serum amyloid A (SAA), and interleukin 6 (IL-6) measured by enzyme linked immunosorbent assay (ELISA). CRP and SAA dose-response results are consistent with {approx}1 Gy and {approx}0.2 Gy thresholds for photon-exposure at 24 h after TBI, respectively. Highly significant elevations of CRP and SAA (p = 0.00017 and p = 0.0024, respectively) were found in animal plasma at 6 h after all TBI doses suggesting their potential use as early-phase biodosimeters. Results also show that the dynamics and content of CRP and SAA levels reflect the course and severity of the acute radiation sickness (ARS) and may function as prognostic indicators of ARS outcome. These results demonstrate proof-of-concept that these radiation-responsive proteins show promise as a complementary approach to conventional biodosimetry for early assessment of radiation exposures and may also contribute as diagnostic indices in the medical management of radiation accidents.

  16. The ''Uranium Society''. Looking at the early history of radiation protection

    International Nuclear Information System (INIS)

    Nagel, G.

    2000-01-01

    The contribution initially looks at the early days of research activities conducted inter alia under an ''atomic research programme'' of the Third Reich, highlighting essential steps and experiments in the history, the foundation of the 'Uranverein' (uranium society) and the avtivities of the group of scientists around Heisenberg. The author presents information that answers the question of whether and how the scientists in those days have been thinking of adequate protection against harmful and toxic effects of the uranium material they were handling. The first instructions for on-the-job safety and protective measures recommended at the time are reported, and are also illustrated by some pictures. (orig./CB) [de

  17. Conformal radiation therapy of localized prostate cancer: acute tolerance and early evaluation of effectiveness

    International Nuclear Information System (INIS)

    Zierhut, D.; Flentje, M.; Sroka-Perez, G.; Rudat, V.; Engenhart-Cabillic, R.; Wannenmacher, M.

    1997-01-01

    Aim: In a prospective trial early effectiveness and acute toxicity of conformal 3D-planned radiotherapy for localized prostate cancer was quantified using dose-volume-histogramms and evaluated with respect of treatment technique. Results: Eleven patients (of 32) had none, 15 mild (RTOG grade 1) and 6 moderate symptoms (RTOG grade 2, mainly diarrhoea, dysuria and polyuria). Acute complications leading to treatment interruption did not occur. In 16 patients symptoms disappeared within 6 weeks after radiotherapy. Only 2 men had symptoms which lasted longer than 3 months and were endoscopically examined. Up to now no late complications were detected. Incidence and severity of toxicity was significantly (p [de

  18. Clinical outcome and cosmetic results of conservative surgery plus radiation therapy in early stage breast cancer patients

    International Nuclear Information System (INIS)

    Jin Yening; Wang Yajie; Zhang Xiaoqing; Meng Yan; Li Rongqing; Shi Junyi

    2005-01-01

    Objective: To evaluate the clinical outcome and cosmetic results in early stage breast cancer patients treated with conservative surgery plus radiation therapy. Methods: From May 1995 to December 2002, 109 such patients were so treated. The post-operative radiotherapy consisted of whole-breast 6 MV linear accelerator irradiation with two tangential half-fields to a total dose of 45-52 Gy (mean 48.6 Gy), followed by a boost irradiation to the tumor bed. Among them, 79 patients received 10-12 Gy (DB) boost by interstitial implantation brachytherapy ( 192 Ir HDR, Nucletron), with single plane implantation for T1 and double plane implantation for T2 tumor. Thirty patients received 15 Gy boost by electron beam. Adjuvant/concurrent chemotherapy (CMF or CEF) and hormonotherapy were also used according to the patients' clinical characteristics. The cosmetic results were scored by both the doctor and the patients. Results: The overall actuarial 5-year survival was 93.8%, with local recurrence of 6.5%. No radiation-induced ulcer was observed in the breast except for acute inflammation at skin pinholes in 5 patients treated by interstitial implant brachytherapy. Among the 75 patients who had had breast examination, cosmetic result scored as good by patient and doctor were 81% and 87%, respectively. The good rate assessed by doctor in brachytherapy boost group and electron beam boost group were 81.2% (39/48) and 85.2% (23/27), There was no significant difference between these two boost techniques (P>0.05). Conclusions: Tumor bed boost irradiation by either brachytherapy or electron beam technique can provide satisfactory local control in early breast cancer treated with conservative surgery plus radiotherapy without increasing the side effects. There is no significant difference in cosmetic result between these two boost techniques. (authors)

  19. A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera

    Science.gov (United States)

    Ronquist, Fredrik; Klopfstein, Seraina; Vilhelmsen, Lars; Schulmeister, Susanne; Murray, Debra L.; Rasnitsyn, Alexandr P.

    2012-01-01

    Abstract Phylogenies are usually dated by calibrating interior nodes against the fossil record. This relies on indirect methods that, in the worst case, misrepresent the fossil information. Here, we contrast such node dating with an approach that includes fossils along with the extant taxa in a Bayesian total-evidence analysis. As a test case, we focus on the early radiation of the Hymenoptera, mostly documented by poorly preserved impression fossils that are difficult to place phylogenetically. Specifically, we compare node dating using nine calibration points derived from the fossil record with total-evidence dating based on 343 morphological characters scored for 45 fossil (4--20 complete) and 68 extant taxa. In both cases we use molecular data from seven markers (∼5 kb) for the extant taxa. Because it is difficult to model speciation, extinction, sampling, and fossil preservation realistically, we develop a simple uniform prior for clock trees with fossils, and we use relaxed clock models to accommodate rate variation across the tree. Despite considerable uncertainty in the placement of most fossils, we find that they contribute significantly to the estimation of divergence times in the total-evidence analysis. In particular, the posterior distributions on divergence times are less sensitive to prior assumptions and tend to be more precise than in node dating. The total-evidence analysis also shows that four of the seven Hymenoptera calibration points used in node dating are likely to be based on erroneous or doubtful assumptions about the fossil placement. With respect to the early radiation of Hymenoptera, our results suggest that the crown group dates back to the Carboniferous, ∼309 Ma (95% interval: 291--347 Ma), and diversified into major extant lineages much earlier than previously thought, well before the Triassic. [Bayesian inference; fossil dating; morphological evolution; relaxed clock; statistical phylogenetics.] PMID:22723471

  20. Survival Advantage With the Addition of Radiation Therapy to Chemotherapy in Early Stage Peripheral T-Cell Lymphoma, Not Otherwise Specified

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Xi-Mei [Department of Radiation Oncology, Cancer Hospital and Institution, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing (China); Department of Radiation Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin (China); Li, Ye-Xiong, E-mail: yexiong@yahoo.com [Department of Radiation Oncology, Cancer Hospital and Institution, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing (China); Wang, Wei-Hu; Jin, Jing; Wang, Shu-Lian; Liu, Yue-Ping; Song, Yong-Wen; Fang, Hui; Ren, Hua [Department of Radiation Oncology, Cancer Hospital and Institution, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing (China); Zhou, Li-Qiang [Department of Medical Oncology, Cancer Hospital and Institution, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing (China); Liu, Xin-Fan; Yu, Zi-Hao [Department of Radiation Oncology, Cancer Hospital and Institution, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing (China)

    2013-03-15

    Purpose: Early stage peripheral T-cell lymphoma, not otherwise specified (PTCL-NOS) is rare. The purpose of this study was to evaluate the outcome of treatment as well as the potential role of radiation therapy in PTCL-NOS. Methods and Materials: Thirty-five patients with early stage PTCL-NOS were included. There were 13 patients with stage I disease and 22 with stage II. All patients except 1 received doxorubicin-based chemotherapy alone (n=13) or a combination of chemotherapy and radiation therapy (CMT) (n=21). Results: The 3-year overall survival (OS) and progression-free survival (PFS) rates for the entire group were 41.3% and 25.7%, respectively. The addition of radiation therapy to chemotherapy significantly improved OS and PFS in early stage PTCL-NOS. The 3-year OS and PFS rates were 49.7% and 33.3% for CMT, compared with 23.1% (P=.042) and 15.4% (P=.035) for chemotherapy alone, respectively. The prognosis for patients who achieved a complete response (CR) was significantly better than that observed in those who did not achieve a CR. Conclusions: Despite the aggressive clinical course of early stage PTCL-NOS, additional radiation therapy has a significant impact on outcome. The integration of local radiation therapy into more effective systemic therapies may further improve survival.

  1. Survival Advantage With the Addition of Radiation Therapy to Chemotherapy in Early Stage Peripheral T-Cell Lymphoma, Not Otherwise Specified

    International Nuclear Information System (INIS)

    Zhang, Xi-Mei; Li, Ye-Xiong; Wang, Wei-Hu; Jin, Jing; Wang, Shu-Lian; Liu, Yue-Ping; Song, Yong-Wen; Fang, Hui; Ren, Hua; Zhou, Li-Qiang; Liu, Xin-Fan; Yu, Zi-Hao

    2013-01-01

    Purpose: Early stage peripheral T-cell lymphoma, not otherwise specified (PTCL-NOS) is rare. The purpose of this study was to evaluate the outcome of treatment as well as the potential role of radiation therapy in PTCL-NOS. Methods and Materials: Thirty-five patients with early stage PTCL-NOS were included. There were 13 patients with stage I disease and 22 with stage II. All patients except 1 received doxorubicin-based chemotherapy alone (n=13) or a combination of chemotherapy and radiation therapy (CMT) (n=21). Results: The 3-year overall survival (OS) and progression-free survival (PFS) rates for the entire group were 41.3% and 25.7%, respectively. The addition of radiation therapy to chemotherapy significantly improved OS and PFS in early stage PTCL-NOS. The 3-year OS and PFS rates were 49.7% and 33.3% for CMT, compared with 23.1% (P=.042) and 15.4% (P=.035) for chemotherapy alone, respectively. The prognosis for patients who achieved a complete response (CR) was significantly better than that observed in those who did not achieve a CR. Conclusions: Despite the aggressive clinical course of early stage PTCL-NOS, additional radiation therapy has a significant impact on outcome. The integration of local radiation therapy into more effective systemic therapies may further improve survival

  2. Assessment of Data Reliability of Wireless Sensor Network for Bioinformatics

    Directory of Open Access Journals (Sweden)

    Ting Dong

    2017-09-01

    Full Text Available As a focal point of biotechnology, bioinformatics integrates knowledge from biology, mathematics, physics, chemistry, computer science and information science. It generally deals with genome informatics, protein structure and drug design. However, the data or information thus acquired from the main areas of bioinformatics may not be effective. Some researchers combined bioinformatics with wireless sensor network (WSN into biosensor and other tools, and applied them to such areas as fermentation, environmental monitoring, food engineering, clinical medicine and military. In the combination, the WSN is used to collect data and information. The reliability of the WSN in bioinformatics is the prerequisite to effective utilization of information. It is greatly influenced by factors like quality, benefits, service, timeliness and stability, some of them are qualitative and some are quantitative. Hence, it is necessary to develop a method that can handle both qualitative and quantitative assessment of information. A viable option is the fuzzy linguistic method, especially 2-tuple linguistic model, which has been extensively used to cope with such issues. As a result, this paper introduces 2-tuple linguistic representation to assist experts in giving their opinions on different WSNs in bioinformatics that involve multiple factors. Moreover, the author proposes a novel way to determine attribute weights and uses the method to weigh the relative importance of different influencing factors which can be considered as attributes in the assessment of the WSN in bioinformatics. Finally, an illustrative example is given to provide a reasonable solution for the assessment.

  3. Stereotactic radiation therapy: a second gold standard in the treatment of early-stage lung cancer?

    International Nuclear Information System (INIS)

    Santini B, Alejandro; Valdez C, Cristian; Sepulveda A, Veronica; Baeza L, Ricardo; Bustos, Sergio

    2016-01-01

    Lung cancer is still the leading cause of cancer death in the world. Although in Chile this is not the case, the northern regions of the country show higher incidence and mortality rates than the other Chilean regions. In recent years screening guides for lung cancer with low-dose scanner have begun to be established, and most of the medical societies involved in this subject have already settled the selection criteria. At the same time new techniques of treatment for these patients have developed, with highly sophisticated radiotherapy such as SBRT (Stereotactic Body Radiotherapy) and SBART (Stereotactic ablative body radiation therapy) that are revealing extremely encouraging results and augur significant changes in the coming years. In the present review we analyze the current work, their results, and the future of this treatment modality

  4. Bcl2-independent chromatin cleavage is a very early event during induction of apoptosis in mouse thymocytes after treatment with either dexamethasone or ionizing radiation.

    Science.gov (United States)

    Hahn, Peter J; Lai, Zhi-Wei; Nevaldine, Barbara; Schiff, Ninel; Fiore, Nancy C; Silverstone, Allen E

    2003-11-01

    We have quantified the emergence of early chromatin breaks during the signal transduction phase of apoptosis in mouse thymocytes after treatment with either ionizing radiation or dexamethasone. Dexamethasone at 1 microM can induce significant levels of DNA breaks (equivalent to the amount induced directly by 7.5 Gy ionizing radiation) within 0.5 h of treatment. The execution phase of apoptosis was not observed until 4-6 h after the same treatment. The presence of the Bcl2 transgene under the control of the p56lck promoter almost completely inhibited apoptosis up to 24 h after treatment, but it had virtually no effect on the early chromatin cleavage occurring in the first 6 h. Ionizing radiation induced chromatin cleavage both directly by damaging DNA and indirectly with kinetics similar to the induction of chromatin cleavage by dexamethasone. The presence of the Bcl2 transgene had no effect on the direct or indirect radiation-induced cleavage in the first 6 h, but after the first 6 h, the Bcl2 gene inhibited further radiation-induced chromatin cleavage. These results suggest that endonucleases are activated within minutes of treatment with either dexamethasone or ionizing radiation as part of the very early signal transduction phase of apoptosis, and prior to the irreversible commitment to cell death.

  5. Phenotypic characterization of early events of thymus repopulation in radiation bone marrow chimeras

    International Nuclear Information System (INIS)

    Sharrow, S.O.; Singer, A.; Hammerling, U.; Mathieson, B.J.

    1983-01-01

    The phenotype of murine thymocytes repopulating the thymus of radiation bone marrow chimeras shortly after irradiation and bone marrow reconstitution was analyzed by immunofluorescence and flow microfluorometry. Thymuses in these chimeras, while essentially devoid of lymphoid cells at day 7, were repopulated by days 10 to 12 after irradiation. It was found that this initial repopulation arose from a radioresistant intrathymic precursor that expanded to an almost complete complement of host-type thymocytes. However, these host-derived thymocytes were unusual in that they were relatively deficient in Lyt 1+2- and peanut agglutinin ''dull'' cells as compared with normal thymocytes. Donor bone-marrow-derived cells first appeared in the irradiated chimeric thymuses between days 12 and 15 after irradiation and bone marrow transfer. By day 19, chimeric thymuses contained more than 98% donor cells. This course was identical for three chimeric combinations, each made across different genetic barriers. In contrast to the cells that populate the fetal thymus during normal ontogeny, the first donor bone-marrow-derived cells that can be detected within the irradiated chimeric thymuses already expressed phenotypically normal adult T cell subpopulations in that they contained significant numbers both of Lyt 1+2- and of Lyt 1+2+ thymocytes. Thus, the Lyt phenotype of donor cells that initially repopulate an adult thymus after irradiation is markedly different from the Lyt phenotype of cells that initially populate the fetal thymus. The differences between adult and fetal thymic development that are observed in radiation bone marrow chimeras may be important in our understanding of T cell differentiation in these animals

  6. [Skin cancer and sun radiation: peruvian experience in the prevention and early detection of skin cancer and melanoma].

    Science.gov (United States)

    Sordo, Carlos; Gutiérrez, César

    2013-03-01

    The excessive exposure to sun radiation, especially to ultraviolet radiation (UV), has led to various diseases, in particular to skin cancer. In 1995, the Peruvian Dermatological Association conducted the first "Campaign for Education, Prevention and Early Detection of Skin Cancer and Melanoma" called "Mole's Day". The Ministry of Health has turned it into an official event, and the Health Social Security (EsSalud) also participates. This is a free campaign that takes place every year nationwide. 118,092 people attended from 1995 to 2011 in 76 sites distributed in 18 cities throughout the country. A cutaneous lesion were malignancy was suspected was identified in 2.8% of people attending, out of which 64.9% corresponded to basal cell carcinoma, 26.7% to cutaneous melanoma, and 8.4% to squamous cell carcinoma. These campaigns are highly important not only because of the assistance given, but also because of the educational activities aimed at promoting a prevention culture in favor of the most vulnerable populations. Finally, we believe it is important to continue educating the population on skin cancer prevention, to build awareness among the authorities so that they actively participate in the performance of these activities, and to ask all physicians to coordinately join this initiative, in order to continue growing, and to improve all that has been attained for the benefit of our country.

  7. Progressive behavioral changes during the maturation of rats with early radiation-induced hypoplasia of fascia dentata granule cells

    International Nuclear Information System (INIS)

    Mickley, G.A.; Ferguson, J.L.; Mulvihill, M.A.; Nemeth, T.J.

    1989-01-01

    Localized exposure of the neonatal rat brain to X-rays produces neuronal hypoplasia specific to the granule cell layer of the hippocampal dentate gyrus. This brain damage causes locomotor hyperactivity, slowed acquisition of passive avoidance tasks and long bouts of spontaneous turning (without reversals) in a bowl apparatus. Here we report how these behavioral deficits change as a function of subject aging and behavioral test replications. Portions of the neonatal rat cerebral hemispheres were X-irradiated in order to selectively damage the granule cells of the dentate gyrus. The brains of experimental animals received a fractionated dose of X rays (13 Gy total) over postnatal days 1 to 16 and control animals were sham-irradiated. Rats between the ages of 71-462 days were tested 3 separate times on each of the following 3 behavioral tests: (1) spontaneous locomotion, (2) passive avoidance acquisition, and (3) spontaneous circling in a large plastic hemisphere. Rats with radiation-induced damage to the fascia dentata exhibited long bouts of slow turns without reversals. Once they began, irradiated subjects perseverated in turning to an extent significantly greater than sham-irradiated control subjects. This irradiation effect was significant during all test series. Moreover, in time, spontaneous perseverative turning was significantly potentiated in rats with hippocampal damage but increased only slightly in controls. Early radiation exposure produced locomotor hyperactivity in young rats. While activity levels of controls remained fairly stable throughout the course of the experiment, the hyperactivity of the irradiated animals decreased significantly as they matured

  8. Effect of calcium-binding protein S100A8 expression on early phase of radiation pulmonary fibrosis

    International Nuclear Information System (INIS)

    Rao Yalan; Li Ming; Cong Yue; Li Fengsheng; Chen Xiaohua; Dong Bo; Zhang Junquan; Gao Ling; Mao Bingzhi

    2008-01-01

    The study explores the expression and effect of calcium-binding protein S100A8 on early phase of radiation pulmonary fibrosis via in vivo and in vitro experiments. In vivo experiment, the thoracic regions of rats were irradiated under 20Gy 60 Co γ-rays to establish radiation pulmonary fibrosis. After irradiation, the lung specimens of the sacrificed rats were separately harvested by the ends of the first, second, and fourth weeks respectively. The protein expression of S100A8 was tested through immunohistochemistry, the mRNA expression of S100A8 and its heterodimeric S100A9 were investigated by RT-PCR method. In vitro experiment, RT-PCR method was also applied to measure the mRNA expression of S100A8 in mouse macrophage cell line RAW264.7 after γ-rays irradiation and/or lipopolysaccharide (LPS). It shows that the protein expression of S100A8 was increased in the plasma of lung macrophages samples and the mRNA expression of S100A8 and S100A9 was also increased in the lung tissue samples in four weeks after irradiation in vivo experiment. And in vitro experiment it shows that the cooperation between γ-rays and LPS can increase the mRNA expression of S100A8 in RAW264.7. These phenomena suggest that S100A8 can exert the chemotactic activity, participate in the inflammatory response, and influence the establishment of radiation pulmonary fibrosis. (authors)

  9. Intraoperative boost radiation effects on early wound complications in breast cancer patients undergoing breast-conserving surgery

    Science.gov (United States)

    Gülçelik, Mehmet Ali; Doğan, Lütfi; Karaman, Niyazi; Turan, Müjdat; Kahraman, Yavuz Selim; Akgül, Gökhan Giray; Özaslan, Cihangir

    2017-08-23

    Background/aim: Intraoperative radiation therapy (IORT) may pose a risk for wound complications. All technical aspects of IORT regarding early wound complications were evaluated. Materials and methods: Ninety-three consecutive patients operated on with the same surgical technique and given (study group) or not given (control group) IORT were included. Wound complications were evaluated in two groups. Results: Forty-three patients were treated with boost dose IORT and 50 patients were treated with breast-conserving surgery without IORT. When both groups were compared in terms of early postoperative complications, there were 11 (25.5%) patients with seroma in the IORT group and 3 patients (6%) in the control group (P = 0.04). While 9 (21%) patients were seen to have surgical site infection (SSI) in the IORT group, there was 1 (2%) SSI in the control group (P = 0.005). There were 15 (35%) patients with delayed wound healing in the IORT group and 4 patients (8%) in the control group (P = 0.006). Conclusion: IORT could have a negative effect on seroma formation, SSI, and delayed healing. It should be kept in mind, however, that in centers with IORT implementation, the complication rate could also increase. Necessary measures for better sterilization in the operating room should be taken, while patient wound healing should be monitored closely.

  10. Involved-Site Image-Guided Intensity Modulated Versus 3D Conformal Radiation Therapy in Early Stage Supradiaphragmatic Hodgkin Lymphoma

    Energy Technology Data Exchange (ETDEWEB)

    Filippi, Andrea Riccardo, E-mail: andreariccardo.filippi@unito.it [Department of Oncology, University of Torino, Torino (Italy); Ciammella, Patrizia [Radiation Therapy Unit, Department of Oncology and Advanced Technology, ASMN Hospital IRCCS, Reggio Emilia (Italy); Piva, Cristina; Ragona, Riccardo [Department of Oncology, University of Torino, Torino (Italy); Botto, Barbara [Hematology, Città della Salute e della Scienza, Torino (Italy); Gavarotti, Paolo [Hematology, University of Torino and Città della Salute e della Scienza, Torino (Italy); Merli, Francesco [Hematology Unit, ASMN Hospital IRCCS, Reggio Emilia (Italy); Vitolo, Umberto [Hematology, Città della Salute e della Scienza, Torino (Italy); Iotti, Cinzia [Radiation Therapy Unit, Department of Oncology and Advanced Technology, ASMN Hospital IRCCS, Reggio Emilia (Italy); Ricardi, Umberto [Department of Oncology, University of Torino, Torino (Italy)

    2014-06-01

    Purpose: Image-guided intensity modulated radiation therapy (IG-IMRT) allows for margin reduction and highly conformal dose distribution, with consistent advantages in sparing of normal tissues. The purpose of this retrospective study was to compare involved-site IG-IMRT with involved-site 3D conformal RT (3D-CRT) in the treatment of early stage Hodgkin lymphoma (HL) involving the mediastinum, with efficacy and toxicity as primary clinical endpoints. Methods and Materials: We analyzed 90 stage IIA HL patients treated with either involved-site 3D-CRT or IG-IMRT between 2005 and 2012 in 2 different institutions. Inclusion criteria were favorable or unfavorable disease (according to European Organization for Research and Treatment of Cancer criteria), complete response after 3 to 4 cycles of an adriamycin- bleomycin-vinblastine-dacarbazine (ABVD) regimen plus 30 Gy as total radiation dose. Exclusion criteria were chemotherapy other than ABVD, partial response after ABVD, total radiation dose other than 30 Gy. Clinical endpoints were relapse-free survival (RFS) and acute toxicity. Results: Forty-nine patients were treated with 3D-CRT (54.4%) and 41 with IG-IMRT (45.6%). Median follow-up time was 54.2 months for 3D-CRT and 24.1 months for IG-IMRT. No differences in RFS were observed between the 2 groups, with 1 relapse each. Three-year RFS was 98.7% for 3D-CRT and 100% for IG-IMRT. Grade 2 toxicity events, mainly mucositis, were recorded in 32.7% of 3D-CRT patients (16 of 49) and in 9.8% of IG-IMRT patients (4 of 41). IG-IMRT was significantly associated with a lower incidence of grade 2 acute toxicity (P=.043). Conclusions: RFS rates at 3 years were extremely high in both groups, albeit the median follow-up time is different. Acute tolerance profiles were better for IG-IMRT than for 3D-CRT. Our preliminary results support the clinical safety and efficacy of advanced RT planning and delivery techniques in patients affected with early stage HL, achieving complete

  11. Individualized Prediction of Overall Survival After Postoperative Radiation Therapy in Patients With Early-Stage Cervical Cancer: A Korean Radiation Oncology Group Study (KROG 13-03)

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Hyun Jin [Department of Radiation Oncology, Asan Medical Center, University of Ulsan, College of Medicine, Seoul (Korea, Republic of); Han, Seungbong [Department of Clinical Epidemiology and Biostatistics, Asan Medical Center, University of Ulsan, College of Medicine, Seoul (Korea, Republic of); Kim, Young Seok, E-mail: ysk@amc.seoul.kr [Department of Radiation Oncology, Asan Medical Center, University of Ulsan, College of Medicine, Seoul (Korea, Republic of); Nam, Joo-Hyun [Department of Obstetrics and Gynecology, Asan Medical Center, University of Ulsan, College of Medicine, Seoul (Korea, Republic of); Kim, Hak Jae [Department of Radiation Oncology, Seoul National University Hospital, Seoul (Korea, Republic of); Kim, Jae Weon [Department of Obstetrics and Gynecology, Seoul National University Hospital, Seoul (Korea, Republic of); Park, Won [Department of Radiation Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of); Kim, Byoung-Gie [Department of Obstetrics and Gynecology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of); Kim, Jin Hee [Department of Radiation Oncology, Dongsan Medical Center, Keimyung University School of Medicine, Daegu (Korea, Republic of); Cha, Soon Do [Department of Obstetrics and Gynecology, Dongsan Medical Center, Keimyung University School of Medicine, Daegu (Korea, Republic of); Kim, Juree [Department of Radiation Oncology, Cheil General Hospital and Women' s Healthcare Center, Kwandong University, College of Medicine, Seoul (Korea, Republic of); Lee, Ki-Heon [Department of Obstetrics and Gynecology, Cheil General Hospital and Women' s Healthcare Center, Kwandong University, College of Medicine, Seoul (Korea, Republic of); Yoon, Mee Sun [Department of Radiation Oncology, Chonnam National University Hwasun Hospital, Chonnam National University Medical School, Jeollanam-do (Korea, Republic of); and others

    2013-11-15

    Purpose: A nomogram is a predictive statistical model that generates the continuous probability of a clinical event such as death or recurrence. The aim of the study was to construct a nomogram to predict 5-year overall survival after postoperative radiation therapy for stage IB to IIA cervical cancer. Methods and Materials: The clinical data from 1702 patients with early-stage cervical cancer, treated at 10 participating hospitals from 1990 to 2011, were reviewed to develop a prediction nomogram based on the Cox proportional hazards model. Demographic, clinical, and pathologic variables were included and analyzed to formulate the nomogram. The discrimination and calibration power of the model was measured using a concordance index (c-index) and calibration curve. Results: The median follow-up period for surviving patients was 75.6 months, and the 5-year overall survival probability was 87.1%. The final model was constructed using the following variables: age, number of positive pelvic lymph nodes, parametrial invasion, lymphovascular invasion, and the use of concurrent chemotherapy. The nomogram predicted the 5-year overall survival with a c-index of 0.69, which was superior to the predictive power of the International Federation of Gynecology and Obstetrics (FIGO) staging system (c-index of 0.54). Conclusions: A survival-predicting nomogram that offers an accurate level of prediction and discrimination was developed based on a large multi-center study. The model may be more useful than the FIGO staging system for counseling individual patients regarding prognosis.

  12. Individualized Prediction of Overall Survival After Postoperative Radiation Therapy in Patients With Early-Stage Cervical Cancer: A Korean Radiation Oncology Group Study (KROG 13-03)

    International Nuclear Information System (INIS)

    Lee, Hyun Jin; Han, Seungbong; Kim, Young Seok; Nam, Joo-Hyun; Kim, Hak Jae; Kim, Jae Weon; Park, Won; Kim, Byoung-Gie; Kim, Jin Hee; Cha, Soon Do; Kim, Juree; Lee, Ki-Heon; Yoon, Mee Sun

    2013-01-01

    Purpose: A nomogram is a predictive statistical model that generates the continuous probability of a clinical event such as death or recurrence. The aim of the study was to construct a nomogram to predict 5-year overall survival after postoperative radiation therapy for stage IB to IIA cervical cancer. Methods and Materials: The clinical data from 1702 patients with early-stage cervical cancer, treated at 10 participating hospitals from 1990 to 2011, were reviewed to develop a prediction nomogram based on the Cox proportional hazards model. Demographic, clinical, and pathologic variables were included and analyzed to formulate the nomogram. The discrimination and calibration power of the model was measured using a concordance index (c-index) and calibration curve. Results: The median follow-up period for surviving patients was 75.6 months, and the 5-year overall survival probability was 87.1%. The final model was constructed using the following variables: age, number of positive pelvic lymph nodes, parametrial invasion, lymphovascular invasion, and the use of concurrent chemotherapy. The nomogram predicted the 5-year overall survival with a c-index of 0.69, which was superior to the predictive power of the International Federation of Gynecology and Obstetrics (FIGO) staging system (c-index of 0.54). Conclusions: A survival-predicting nomogram that offers an accurate level of prediction and discrimination was developed based on a large multi-center study. The model may be more useful than the FIGO staging system for counseling individual patients regarding prognosis

  13. ["Epistemic Negotiations" and the Pluralism of the Radiation Protection Regime: The Determination of Radiation Protection Standards for the General Population in the Early Years After World War II].

    Science.gov (United States)

    Higuchi, Toshihiro

    2015-10-01

    Radiation protection standards for the general population have constituted one of the most controversial subjects in the history of atomic energy uses. This paper reexamines the process in which the first such standards evolved in the early postwar period. While the existing literature has emphasized a "collusion" between the standard-setters and users, the paper seeks to examine the horizontal relationship among the standard-setters. It first examines a series of expert consultations between the United States and the United Kingdom. Representing a different configuration of power and interest, the two failed to agree on the assessment of genetic damage and cancer induction whose occurrence might have no threshold and therefore be dependent on the population size. This stalemate prevented the International Commission on Radiological Protection (ICRP), established in 1950, from formulating separate guidelines for the general public. Situations radically changed when the Bikini incident in 1954 led to the creation of more scientific panels. One such panel under the U.S. Academy of Sciences enabled the geneticists to bridge their internal divide, unanimously naming 100 mSv as the genetically permissible dose for the general population. Not to be outdone, ICRP publicized its own guidelines for the same purpose. The case examined in this paper shows that the standard-setting process is best understood as a series of "epistemic negotiations" among and within the standard-setters, whose agendas were determined from the outset but whose outcomes were not.

  14. Direct evidence that radiation induced micronuclei of early embryos require a mitosis for expression

    International Nuclear Information System (INIS)

    Mueller, W.U.; Schlusen, I.; Streffer, C.

    1991-01-01

    The naturally synchronous development of early mouse embryos was exploited to address the question, whether micronuclei require a mitosis for expression or whether they can be expressed in the same cell cycle, in which exposure to X-rays or caffeine took place. Experiments with 2-cell and with 4-cell embryos showed that micronulcei are expressed only if a mitosis is completed. There was no indication, even after doses up to 20 Gy, that micronuclei can be expressed before the mitosis was reached, which followed exposure. Furthermore, no nuclear fragmentation pointing to apoptosis could be detected in the cycle, in which cells were exposed. The same results were obtained when caffeine (5 mM) was used as micronucleus inducing agent. (orig.)

  15. Risk of Cerebrovascular Events in Elderly Patients After Radiation Therapy Versus Surgery for Early-Stage Glottic Cancer

    International Nuclear Information System (INIS)

    Hong, Julian C.; Kruser, Tim J.; Gondi, Vinai; Mohindra, Pranshu; Cannon, Donald M.; Harari, Paul M.; Bentzen, Søren M.

    2013-01-01

    Purpose: Comprehensive neck radiation therapy (RT) has been shown to increase cerebrovascular disease (CVD) risk in advanced-stage head-and-neck cancer. We assessed whether more limited neck RT used for early-stage (T1-T2 N0) glottic cancer is associated with increased CVD risk, using the Surveillance, Epidemiology, and End Results (SEER)-Medicare linked database. Methods and Materials: We identified patients ≥66 years of age with early-stage glottic laryngeal cancer from SEER diagnosed from 1992 to 2007. Patients treated with combined surgery and RT were excluded. Medicare CPT codes for carotid interventions, Medicare ICD-9 codes for cerebrovascular events, and SEER data for stroke as the cause of death were collected. Similarly, Medicare CPT and ICD-9 codes for peripheral vascular disease (PVD) were assessed to serve as an internal control between treatment groups. Results: A total of 1413 assessable patients (RT, n=1055; surgery, n=358) were analyzed. The actuarial 10-year risk of CVD was 56.5% (95% confidence interval 51.5%-61.5%) for the RT cohort versus 48.7% (41.1%-56.3%) in the surgery cohort (P=.27). The actuarial 10-year risk of PVD did not differ between the RT (52.7% [48.1%-57.3%]) and surgery cohorts (52.6% [45.2%-60.0%]) (P=.89). Univariate analysis showed an increased association of CVD with more recent diagnosis (P=.001) and increasing age (P=.001). On multivariate Cox analysis, increasing age (P<.001) and recent diagnosis (P=.002) remained significantly associated with a higher CVD risk, whereas the association of RT and CVD remained not statistically significant (HR=1.11 [0.91-1.37,] P=.31). Conclusions: Elderly patients with early-stage laryngeal cancer have a high burden of cerebrovascular events after surgical management or RT. RT and surgery are associated with comparable risk for subsequent CVD development after treatment in elderly patients

  16. Decreased local control following radiation therapy alone in early-stage glottic carcinoma with anterior commissure extension

    International Nuclear Information System (INIS)

    Zouhair, A.; Azria, D.; Coucke, P.; Matzinger, O.; Mirimanoff, R.O.; Ozsahin, M.; Bron, L.; Moeckli, R.; Do, H.P.

    2004-01-01

    Purpose: to assess the patterns of failure in the treatment of early-stage squamous cell carcinoma of the glottic larynx. Patients and methods: between 1983-2000, 122 consecutive patients treated for early laryngeal cancer (UICC T1N0 and T2N0) by radical radiation therapy (RT) were retrospectively studied. Male-to-female ratio was 106: 16, and median age 62 years (35-92 years). There were 68 patients with T1a, 18 with T1b, and 36 with T2 tumors. Diagnosis was made by biopsy in 104 patients, and by laser vaporization or stripping in 18. Treatment planning consisted of three-dimensional (3-D) conformal RT in 49 (40%) patients including nine patients irradiated using arytenoid protection. A median dose of 70 Gy (60-74 Gy) was given (2 Gy/fraction) over a median period of 46 days (21-79 days). Median follow-up period was 85 months. Results: the 5-year overall, cancer-specific, and disease-free survival amounted to 80%, 94%, and 70%, respectively. 5-year local control was 83%. Median time to local recurrence in 19 patients was 13 months (5-58 months). Salvage treatment consisted of surgery in 17 patients (one patient refused salvage and one was inoperable; total laryngectomy in eleven, and partial laryngectomy or cordectomy in six patients). Six patients died because of laryngeal cancer. Univariate analyses revealed that prognostic factors negatively influencing local control were anterior commissure extension, arytenoid protection, and total RT dose < 66 Gy. Among the factors analyzed, multivariate analysis (cox model) demonstrated that anterior commissure extension, arytenoid protection, and male gender were the worst independent prognostic factors in terms of local control. Conclusion: for early-stage laryngeal cancer, outcome after RT is excellent. In case of anterior commissure extension, surgery or higher RT doses are warranted. Because of a high relapse risk, arytenoid protection should not be attempted. (orig.)

  17. DNA repair efficiency in germ cells and early mouse embryos and consequences for radiation-induced transgenerational genomic damage

    Energy Technology Data Exchange (ETDEWEB)

    Marchetti, Francesco; Wyrobek, Andrew J.

    2009-01-18

    Exposure to ionizing radiation and other environmental agents can affect the genomic integrity of germ cells and induce adverse health effects in the progeny. Efficient DNA repair during gametogenesis and the early embryonic cycles after fertilization is critical for preventing transmission of DNA damage to the progeny and relies on maternal factors stored in the egg before fertilization. The ability of the maternal repair machinery to repair DNA damage in both parental genomes in the fertilizing egg is especially crucial for the fertilizing male genome that has not experienced a DNA repair-competent cellular environment for several weeks prior to fertilization. During the DNA repair-deficient period of spermatogenesis, DNA lesions may accumulate in sperm and be carried into the egg where, if not properly repaired, could result in the formation of heritable chromosomal aberrations or mutations and associated birth defects. Studies with female mice deficient in specific DNA repair genes have shown that: (i) cell cycle checkpoints are activated in the fertilized egg by DNA damage carried by the sperm; and (ii) the maternal genotype plays a major role in determining the efficiency of repairing genomic lesions in the fertilizing sperm and directly affect the risk for abnormal reproductive outcomes. There is also growing evidence that implicates DNA damage carried by the fertilizing gamete as a mediator of postfertilization processes that contribute to genomic instability in subsequent generations. Transgenerational genomic instability most likely involves epigenetic mechanisms or error-prone DNA repair processes in the early embryo. Maternal and embryonic DNA repair processes during the early phases of mammalian embryonic development can have far reaching consequences for the genomic integrity and health of subsequent generations.

  18. Risk of Cerebrovascular Events in Elderly Patients After Radiation Therapy Versus Surgery for Early-Stage Glottic Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Hong, Julian C.; Kruser, Tim J. [Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin (United States); Gondi, Vinai [Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin (United States); Central Dupage Hospital Cancer Center, Warrenville, Illinois (United States); Mohindra, Pranshu; Cannon, Donald M.; Harari, Paul M. [Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin (United States); Bentzen, Søren M., E-mail: bentzen@humonc.wisc.edu [Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin (United States)

    2013-10-01

    Purpose: Comprehensive neck radiation therapy (RT) has been shown to increase cerebrovascular disease (CVD) risk in advanced-stage head-and-neck cancer. We assessed whether more limited neck RT used for early-stage (T1-T2 N0) glottic cancer is associated with increased CVD risk, using the Surveillance, Epidemiology, and End Results (SEER)-Medicare linked database. Methods and Materials: We identified patients ≥66 years of age with early-stage glottic laryngeal cancer from SEER diagnosed from 1992 to 2007. Patients treated with combined surgery and RT were excluded. Medicare CPT codes for carotid interventions, Medicare ICD-9 codes for cerebrovascular events, and SEER data for stroke as the cause of death were collected. Similarly, Medicare CPT and ICD-9 codes for peripheral vascular disease (PVD) were assessed to serve as an internal control between treatment groups. Results: A total of 1413 assessable patients (RT, n=1055; surgery, n=358) were analyzed. The actuarial 10-year risk of CVD was 56.5% (95% confidence interval 51.5%-61.5%) for the RT cohort versus 48.7% (41.1%-56.3%) in the surgery cohort (P=.27). The actuarial 10-year risk of PVD did not differ between the RT (52.7% [48.1%-57.3%]) and surgery cohorts (52.6% [45.2%-60.0%]) (P=.89). Univariate analysis showed an increased association of CVD with more recent diagnosis (P=.001) and increasing age (P=.001). On multivariate Cox analysis, increasing age (P<.001) and recent diagnosis (P=.002) remained significantly associated with a higher CVD risk, whereas the association of RT and CVD remained not statistically significant (HR=1.11 [0.91-1.37,] P=.31). Conclusions: Elderly patients with early-stage laryngeal cancer have a high burden of cerebrovascular events after surgical management or RT. RT and surgery are associated with comparable risk for subsequent CVD development after treatment in elderly patients.

  19. Analyses of patterns-of-failure and prognostic factors according to radiation fields in early-stage Hodgkin lymphoma

    International Nuclear Information System (INIS)

    Krebs, Lorraine; Guillerm, Sophie; Menard, Jean; Hennequin, Christophe; Quero, Laurent; Amorin, Sandy; Brice, Pauline

    2017-01-01

    Doses and volumes of radiation therapy (RT) for early stages of Hodgkin lymphoma (HL) have been reduced over the last 30 years. Combined modality therapy (CMT) is currently the standard treatment for most patients with early-stage HL. The aim of this study was to analyze the site of relapse after RT according to the extent of radiation fields. Between 1987 and 2011, 427 patients were treated at our institution with RT ± chemotherapy for stage-I/II HL. Among these, 65 patients who experienced a relapse were retrospectively analyzed. Most patients had nodular sclerosis histology (86 %) and stage-II disease (75.9 %). Bulky disease was present in 21 % and 56 % of patients belonged to the unfavorable risk group according to European Organization for Research and Treatment of Cancer (EORTC)/The Lymphoma Study Association (LYSA) definitions. CMT was delivered to 91 % of patients. All patients received RT with doses ranging from 20 to 45 Gy (mean = 34 ± 5.3 Gy). The involved-field RT technique was used in 59 % of patients. The mean time between diagnosis and relapse was 4.2 years (range 0.3-24.5). Out-of-field relapses were suffered by 53 % of patients. Relapses occurred more frequently at out-of-field sites in patients with a favorable disease status, whereas in-field relapses were associated with bulky mediastinal disease. Relapses occurred later for favorable compared with the unfavorable risk group (3.5 vs. 2.9 years, p = 0.5). From multivariate analyses, neither RT dose nor RT field size were predictive for an in-field relapse (p = 0.25 and p = 0.8, respectively), only bulky disease was predictive (p = 0.018). In patients with bulky disease, RT dose and RT field size were not predictive for an in-field relapse. In this subgroup of patients, chemotherapy should be intensified. We confirmed the bad prognosis of early relapses. (orig.) [de

  20. Robotic stereotactic body radiation therapy for elderly medically inoperable early-stage non-small cell lung cancer

    Directory of Open Access Journals (Sweden)

    Karam SD

    2013-08-01

    Full Text Available Sana D Karam,1 Zachary D Horne,1 Robert L Hong,1,2 Nimrah Baig,1 Gregory J Gagnon,4 Don McRae,2 David Duhamel,3 Nadim M Nasr1,21Department of Radiation Oncology, Georgetown University Hospital, Washington, DC, USA; 2Department of Radiation Oncology, Virginia Hospital Center, Arlington, VA, USA; 3Department of Pulmonary/Critical Care Medicine, Virginia Hospital Center, Arlington, VA, USA; 4Department of Radiation Oncology, Frederick Memorial Hospital, Frederick, MD, USAIntroduction: Stereotactic body radiation therapy (SBRT is being increasingly applied in the treatment of non-small cell lung cancer (NSCLC because of its high local efficacy. This study aims to examine survival outcomes in elderly patients with inoperable stage I NSCLC treated with SBRT.Methods: A total of 31 patients with single lesions treated with fractionated SBRT from 2008 to 2011 were retrospectively analyzed. A median prescribed dose of 48 Gy was delivered to the prescription isodose line, over a median of four treatments. The median biologically effective dose (BED was 105.6 (range 37.50–180, and the median age was 73 (65–90 years. No patient received concurrent chemotherapy.Results: With a median follow up of 13 months (range, 4–40 months, the actuarial median overall survival (OS and progression-free survival (PFS were 32 months, and 19 months, respectively. The actuarial median local control (LC time was not reached. The survival outcomes at median follow up of 13 months were 80%, 68%, and 70% for LC, PFS, and OS, respectively. Univariate analysis revealed a BED of >100 Gy was associated with improved LC rates (P = 0.02, while squamous cell histology predicted for worse LC outcome at median follow up time of 13 months (P = 0.04. Increased tumor volume was a worse prognostic indicator of both LC and OS outcomes (P < 0.05. Finally, female gender was a better prognostic factor for OS than male gender (P = 0.006. There were no prognostic indicators of PFS that reached

  1. Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting.

    Science.gov (United States)

    Ibrahim, Bashar; Arkhipova, Ksenia; Andeweg, Arno C; Posada-Céspedes, Susana; Enault, François; Gruber, Arthur; Koonin, Eugene V; Kupczok, Anne; Lemey, Philippe; McHardy, Alice C; McMahon, Dino P; Pickett, Brett E; Robertson, David L; Scheuermann, Richard H; Zhernakova, Alexandra; Zwart, Mark P; Schönhuth, Alexander; Dutilh, Bas E; Marz, Manja

    2018-05-14

    The Second Annual Meeting of the European Virus Bioinformatics Center (EVBC), held in Utrecht, Netherlands, focused on computational approaches in virology, with topics including (but not limited to) virus discovery, diagnostics, (meta-)genomics, modeling, epidemiology, molecular structure, evolution, and viral ecology. The goals of the Second Annual Meeting were threefold: (i) to bring together virologists and bioinformaticians from across the academic, industrial, professional, and training sectors to share best practice; (ii) to provide a meaningful and interactive scientific environment to promote discussion and collaboration between students, postdoctoral fellows, and both new and established investigators; (iii) to inspire and suggest new research directions and questions. Approximately 120 researchers from around the world attended the Second Annual Meeting of the EVBC this year, including 15 renowned international speakers. This report presents an overview of new developments and novel research findings that emerged during the meeting.

  2. Radiation Therapy, Cardiac Risk Factors, and Cardiac Toxicity in Early-Stage Breast Cancer Patients

    International Nuclear Information System (INIS)

    Doyle, John J.; Neugut, Alfred I.; Jacobson, Judith S.; Wang Jian; McBride, Russell; Grann, Alison; Grann, Victor R.; Hershman, Dawn

    2007-01-01

    Purpose: The benefits of adjuvant radiation therapy (RT) for breast cancer may be counterbalanced by the risk of cardiac toxicity. We studied the cardiac effects of RT and the impact of pre-existing cardiac risk factors (CRFs) in a population-based sample of older patients with breast cancer. Methods and Materials: In the Surveillance, Epidemiology and End-Results (SEER)-Medicare database of women ≥65 years diagnosed with Stages I to III breast cancer from January 1, 1992 to December 31, 2000, we used multivariable logistic regression to model the associations of demographic and clinical variables with postmastectomy and postlumpectomy RT. Using Cox proportional hazards regression, we then modeled the association between treatment and myocardial infarction (MI) and ischemia in the 10 or more years after diagnosis, taking the predictors of treatment into account. Results: Among 48,353 women with breast cancer; 19,897 (42%) were treated with lumpectomy and 26,534 (55%) with mastectomy; the remainder had unknown surgery type (3%). Receipt of RT was associated with later year of diagnosis, younger age, fewer comorbidities, nonrural residence, and chemotherapy. Postlumpectomy RT was also associated with white ethnicity and no prior history of heart disease (HD). The RT did not increase the risk of MI. Presence of MI was associated with age, African American ethnicity, advanced stage, nonrural residence, more than one comorbid condition, a hormone receptor-negative tumor, CRFs and HD. Among patients who received RT, tumor laterality was not associated with MI outcome. The effect of RT on the heart was not influenced by HD or CRFs. Conclusion: It appears unlikely that RT would increase the risk of MI in elderly women with breast cancer, regardless of type of surgery, tumor laterality, or history of CRFs or HD, for at least 10 years

  3. Crop growth in early spring and radiation use efficiency in alfalfa

    International Nuclear Information System (INIS)

    Akmal, M.; Farid, U.; Asim, M.; Farhatullah, A.; Raziuddin, A.

    2011-01-01

    The study was conducted at Agronomy Research Farm, KP Agricultural University Peshawar. Fifteen alfalfa lines (M. sativa L.) were compared for crop growth rate (CGR), biomass yield and radiation use efficiency (RUE). The previous year experiment was defoliated on March, 13 2006 at ground levels about 5 cm height. Fertilizer to the crop was applied every year in first week of March to yield 30, 60, and 30 kg ha/sup -1/ N, P, and K, respectively after defoliation. Periodic samples were harvested from one meter row length at two locations and oven dried at 70 degree C for about 36 h. Before samples, periodic leaf area index (LAI) was recorded with LI-2000 (LI-COR, USA) and subsequently light measurements were made using data logger (LI-1400, LI-COR, USA) and light sensors LI-190 and LI-191 (LI-COR, USA). The CGR showed variation in shapes and asymptotes for the different alfalfa lines which resulted differences in both fresh and dry matters yield at final sampling harvest. Alfalfa line Gramma-2 was the highest in dry matter yield (110 g m-2) followed by Flewish-pop (107 g m-2). Alfalfa line Pumha with 74 g m-2 was the lowest in dry matter yield. Differences were observed in LAI (p<0.05). High dry matter yield of alfalfa line Gramma-2 was due to higher LAI which was associated to highest leaf fraction (38%). Differences in RUE were also observed among the lines. Flewish-pop was the highest in RUE (0.20 g DM MJ-2 PAR absorbed), followed by Gramma-2 (0.18 g DM MJ-2 PAR absorbed). Mean CGR and RUE of the different lines showed association with dry matter yield of which the lateral one showed a strong association compared with the earlier one. We conclude that higher RUE than CGR is important for the line/variety to get quality fodder production. (author)

  4. Strategic lesions in the anterior thalamic radiation and apathy in early Alzheimer's disease.

    Directory of Open Access Journals (Sweden)

    Mario Torso

    Full Text Available Behavioural disorders and psychological symptoms of Dementia (BPSD are commonly observed in Alzheimer's disease (AD, and strongly contribute to increasing patients' disability. Using voxel-lesion-symptom mapping (VLSM, we investigated the impact of white matter lesions (WMLs on the severity of BPSD in patients with amnestic mild cognitive impairment (a-MCI.Thirty-one a-MCI patients (with a conversion rate to AD of 32% at 2 year follow-up and 26 healthy controls underwent magnetic resonance imaging (MRI examination at 3T, including T2-weighted and fluid-attenuated-inversion-recovery images, and T1-weighted volumes. In the patient group, BPSD was assessed using the Neuropsychiatric Inventory-12. After quantitative definition of WMLs, their distribution was investigated, without an a priori anatomical hypothesis, against patients' behavioural symptoms. Unbiased regional grey matter volumetrics was also used to assess the contribution of grey matter atrophy to BPSD.Apathy, irritability, depression/dysphoria, anxiety and agitation were shown to be the most common symptoms in the patient sample. Despite a more widespread anatomical distribution, a-MCI patients did not differ from controls in WML volumes. VLSM revealed a strict association between the presence of lesions in the anterior thalamic radiations (ATRs and the severity of apathy. Regional grey matter atrophy did not account for any BPSD.This study indicates that damage to the ATRs is strategic for the occurrence of apathy in patients with a-MCI. Disconnection between the prefrontal cortex and the mediodorsal and anterior thalamic nuclei might represent the pathophysiological substrate for apathy, which is one of the most common psychopathological symptoms observed in dementia.

  5. Early national and international recommendations for X-ray and radiation protection

    International Nuclear Information System (INIS)

    Tesinska, E.

    2008-01-01

    The first three decades of pioneering work in the field of X-ray and natural radioactivity research and use took its toll all over the world because of lack of knowledge and caution. Coordinated, international cooperation in the field of X-ray and radium protection and standardization of measures was established after the World War I. The First and the Second International Congress of Radiology held in London in 1925 and in Stockholm in 1928 respectively, played a crucial role in it. Based on these congresses' initiatives and resolutions, the International X-ray Unit Committee and the International X-ray and Radium Protection Committee were established in 1828. The early recommendations on the international X-ray unit and on X-ray and radium protection, as passed by the Second International Congress of Radiology in Stockholm in 1928, are presented and compared with two related national initiatives, namely with the Memorandum No. 1 (July 1921) of the British X-ray and Radium Protection Committee, and with a draft of a legal measure regarding the X-ray and radium treatment regulation in Czechoslovakia, which was put together by the Czechoslovak Society of Radiology and the Vereinigung der deutschen Roentgenologen und Radiologen in der Tschechoslowakischen Republik in 1927 at a request of the Chamber of Doctor of Medicine for Bohemia and Moravia and in response to the international initiatives in that field. (author)

  6. Yield potential of a radiation induced early-dwarf mutant in linseed

    International Nuclear Information System (INIS)

    Nayar, G.G.

    1975-01-01

    An early maturing dwarf mutant, TL-1 was isolated in the high yielding linseed (Linum usitatissimum L.) wariety Neelum following seed irradiation with 50 kR gamma rays. The yield components of the mutant have been evaluated for its productivity in the M 7 generation. TL-1 is compact and significantly short in height (41.8 +- 2.71 cm) as compared to Neelum (79.2 +- 3.08 cm). In flowering the mutant is 30 days earlier than the parent under Trombay conditions. TL-1 and Neelum did not differ significantly in their mean number of primary branches. Although the mean seed yield per plant is lower, in 1000 seed weight the mutant is markedly superior to the parent. The oil content in TL-1 is significantly higher by 3.5 percent points than Neelum and its oil is lighter in colour. By growing more plants per unit area with reduced spacing, the yield potential of TL-1 was considerably increased. The productivity of oil per hectare per day of TL-1 was higher than Neelum. (author)

  7. Macrophage function in murine allogeneic bone marrow radiation chimeras in the early phase after transplantation

    International Nuclear Information System (INIS)

    Roesler, J.; Baccarini, M.; Vogt, B.; Lohmann-Matthes, M.L.

    1989-01-01

    We tested several of the functions of macrophages (M phi) in the early phase after allogeneic bone marrow transfer to get information about this important aspect of the nonspecific immune system in the T-cell-deficient recipient. On days 3-5 after transfer, the number of M phi was reduced in the spleen, liver, lungs, and peritoneal cavity (Pe). The phagocytosis of sheep red blood cells (SRBC) by these M phi was normal or even enhanced, as in the case of Pe-M phi. Already on days 8-12 after transfer, the number of M phi in spleen and liver exceeded that of controls, whereas the number was still reduced in lungs and Pe. We examined their ability to kill P815 tumor cells, to produce tumor necrosis factor-alpha (TNF alpha), to phagocytose SRBC, to produce reactive oxygen intermediates (ROI) in vitro and to kill Listeria monocytogenes in vivo. Most functions were normal and often even enhanced, depending on the organ origin, but the ability of Pe-M phi to produce ROI was reduced. Proliferative response to macrophage colony-stimulating factor (M-CSF) and killing of YAC-1 tumor cells revealed a high frequency of macrophage precursor cells in the spleen and liver and a high natural killer (NK) activity in the liver. Altogether, enhanced nonspecific immune function, especially preactivated M phi, may enable chimeras to survive attacks by opportunistic pathogens

  8. Early detection of lung cancer recurrence after stereotactic ablative radiation therapy: radiomics system design

    Science.gov (United States)

    Dammak, Salma; Palma, David; Mattonen, Sarah; Senan, Suresh; Ward, Aaron D.

    2018-02-01

    Stereotactic ablative radiotherapy (SABR) is the standard treatment recommendation for Stage I non-small cell lung cancer (NSCLC) patients who are inoperable or who refuse surgery. This option is well tolerated by even unfit patients and has a low recurrence risk post-treatment. However, SABR induces changes in the lung parenchyma that can appear similar to those of recurrence, and the difference between the two at an early follow-up time point is not easily distinguishable for an expert physician. We hypothesized that a radiomics signature derived from standard-of-care computed tomography (CT) imaging can detect cancer recurrence within six months of SABR treatment. This study reports on the design phase of our work, with external validation planned in future work. In this study, we performed cross-validation experiments with four feature selection approaches and seven classifiers on an 81-patient data set. We extracted 104 radiomics features from the consolidative and the peri-consolidative regions on the follow-up CT scans. The best results were achieved using the sum of estimated Mahalanobis distances (Maha) for supervised forward feature selection and a trainable automatic radial basis support vector classifier (RBSVC). This system produced an area under the receiver operating characteristic curve (AUC) of 0.84, an error rate of 16.4%, a false negative rate of 12.7%, and a false positive rate of 20.0% for leaveone patient out cross-validation. This suggests that once validated on an external data set, radiomics could reliably detect post-SABR recurrence and form the basis of a tool assisting physicians in making salvage treatment decisions.

  9. Use of the prone position in radiation treatment for women with early stage breast cancer

    International Nuclear Information System (INIS)

    Algan, Oezer; Fowble, Barbara; McNeeley, Shawn; Fein, Douglas

    1998-01-01

    Purpose: The prone position has been advocated for women with large pendulous breasts undergoing breast-conserving treatment with radiation therapy. However, there is no information in the literature regarding the coverage of the target volume with this technique. The purpose of this study was to evaluate the effectiveness of the prone treatment position in including at least the biopsy cavity with a 2-cm margin. Methods and Materials: Eleven consecutive patients who underwent CT simulation in the prone position were included in this study. Patients underwent CT simulation in the prone position using a flat platform containing an aperture for the breast to hang through in a dependent fashion. CT slices were 5-mm thick taken at 3-mm intervals. The biopsy cavity was localized and outlined on sequential CT images using the surgical clips (when present) as well as the residual seroma. A 2-cm margin was included around the biopsy cavity to define the minimal target volume (mTV). Lateral fields were used for treatment planning. The beam arrangements were considered adequate if the mTV was totally included in the lateral fields. Results: Median age of the patient population was 55 years. Bra sizes ranged from 36A-44DD. The majority of patients had mammographically detected T1 lesions. Median volume of the biopsy cavity was 48 cm 3 . Five of 11 (45%) patients underwent reexcision of the biopsy cavity, and 6 of 11 (55%) had surgical clips placed in the biopsy cavity. Overall, 8 of 11 (73%) patients did not have the entire mTV included in the lateral opposed tangential fields in the prone position. This was especially true in patients whose biopsy cavity extended down to the chest wall. There were no other clinical factors that could predict for the adequacy of coverage in the prone position. Conclusion: Special attention must be paid to the location of the surgical clips to determine the proximity of the biopsy cavity to the chest wall, or CT simulation should be performed

  10. Randomized trial on external radiation therapy alone versus external radiation therapy followed by brachytherapy in early stage nasopharyngeal carcinoma with a long term result

    International Nuclear Information System (INIS)

    Gao Li; Yuan Zhiyong; Xu Guozhen; Li Suyan; Xiao Guangli; Cai Weiming

    2004-01-01

    Objective: To compare local control and toxicity in patients treated with external beam radiotherapy followed by intracavitary brachytherapy (BT) versus external beam radiotherapy alone (RT) for locally early stage nasopharyngeal carcinoma (NPC). Methods: From 1990 to 1997, 126 NPC patients staged T1 and T2 by 1992 Fuzhou Staging System (oropharynx, carotid sheath and soft tissue around cervical vertebral involvement excluded) were randomized into RT alone and RT followed BT groups. The two groups were comparable in age, gender, stage and pathology. The median follow-up was 112 months. T1 patients were randomized before the treatment into RT alone group of 66-70 Gy and RT plus BT with the dose of 56 Gy plus 10-16 Gy BT boost to the nasopharynx. For T2 patients, if MRI or CT showed no residual lesion in parapharyngeal space after 50 Gy, they were randomized into RT alone (median dose: 72 Gy) or RT of 66 Gy followed by 8-24 Gy BT boost (1-3 fractions over 1-3 weeks). Results: In RT group, 8 patients (13.1%) failed in primary site during the follow-up period, 7 (11%) in BT group. The 5-year local control rates was 86% for RT group and 88% for BT group (P=0.47). The 5-year overall survival rates were 83% and 84% (P=0.84), respectively. Ten patients (18%) in RT group (4 of grade I, 6 of grade II) and 7 patients (11%) in BT group (4 of grade I, 3 of grade II, P=0.31) developed radiation induced encephalopathy. The incidence of trismus was much lower in BT group than in RT group (26% versus 10%, P=0.02). No soft palate perforation or sphenoid necrosis were observed. Conclusion: Compared to conventional external beam radiotherapy, planned irradiation plus intracavitary brachytherapy not only can achieve similar local control and survival rates for locally early stage nasopharyngeal carcinoma, but also decrease irradiation dose and the trismus incidence. (authors)

  11. Intraoperative Radiation Using Low-Kilovoltage X-Rays for Early Breast Cancer: A Single Site Trial.

    Science.gov (United States)

    Silverstein, Melvin J; Epstein, Melinda S; Lin, Kevin; Chen, Peter; Khan, Sadia; Snyder, Lincoln; Guerra, Lisa E; De Leon, Cristina; Mackintosh, Ralph; Coleman, Colleen; Lopez, January; Kim, Brian

    2017-10-01

    Two prospective, randomized trials, TARGIT-A and ELIOT, have shown intraoperative radiation therapy (IORT) to be a safe alternative to whole breast radiation therapy following breast-conserving surgery for selected low-risk patients. However, minimal data are available about the clinical effectiveness of this modality of treatment using the Xoft ® Axxent ® Electronic Brachytherapy (eBx ® ) System ® . A total of 201 patients with 204 early-stage breast cancers were enrolled in a prospective X-ray IORT trial from June 2010 to September 2013. All tumors were treated with breast-conserving surgery and IORT. Data were collected at 1 week, 1 month, 6 months, 1 year, and yearly thereafter. With a median follow-up of 50 months, there have been seven ipsilateral breast tumor events (IBTE), no regional or distant recurrences, and no breast cancer-related deaths. One IBTE was within the IORT field, four outside of the IORT field but within the same quadrant as the index cancer, and two were new biologically different cancers in different quadrants. Three events were in patients who deviated from the protocol criteria. Kaplan-Meier analysis projects that 2.9% of patients will recur locally at 4 years. Recurrence rates observed in this trial were comparable to those of the TARGIT-A and ELIOT trials as well as the retrospective TARGIT-R trial. The low complication rates previously reported by our group as well as the low recurrence rates reported in this study support the cautious use and continued study of IORT in selected women with low-risk breast cancer.

  12. Myocardial hydroxyproline reduced by early administration of methylprednisolone or ibuprofen to rabbits with radiation-induced heart disease

    International Nuclear Information System (INIS)

    Reeves, W.C.; Cunningham, D.; Schwiter, E.J.; Abt, A.; Skarlatos, S.; Wood, M.A.; Whitesell, L.

    1982-01-01

    The ability of methylprednisolone (MP) and ibuprofen (IB) to reduce the severity of the late state of radiation-induced heart disease was assessed in 57 New Zealand white rabbits. Before and shortly after cardiac irradiation, 15 rabbits received i.v. MP, 30 mg/kg twice daily for 3 days, and 15 others received IB, 12.5 mg/kg twice daily for 2 days. No drug administered to 14 irradiated rabbits, and neither irradiation nor drugs were administered to 13 rabbits that served as controls. All 15 rabbits treated with MP and 13 of the 15 treated with IB lived for 100 days. Only seven of the untreated, irradiated rabbits lived that long. Longevity of each treated group of rabbits was better (p < 0.01 and 0.05) than that of the untreated, irradiated rabbits. Surviving rabbits were killed 100 days after irradiation. Pericarditis (p < 0.05) and pericardial effusion (p < 0.01) were less frequent in the treated, irradiated groups than in the untreated, irradiated rabbits. At least some rabbits in each irradiated group had microscopic evidence of myocardial fibrosis. The fibrosis was quantitated by determination of myocardial hydroxyproline concentrations (MHP). MHP concentration in the untreated, irradiated rabbits was greater than in those treated with MP (p < 0.05) or IB (p < 0.01) and in the untreated, unirradiated rabbits (p < 0.01). Early administrative of MP or IB retarded the development of myocardial fibrosis, pericarditis and pericardial effusin, and improved survival in this experimental model of radiation-induced heart disease

  13. Myocardial hydroxyproline reduced by early administration of methylprednisolone or ibuprofen to rabbits with radiation-induced heart disease

    International Nuclear Information System (INIS)

    Reeves, W.C.; Cunningham, D.; Schwiter, E.J.; Abt, A.; Skarlatos, S.; Wood, M.A.; Whitesell, L.

    1982-01-01

    The ability of methylprednisolone (MP) and ibuprofen (IB) to reduce the severity of the late state of radiation-induced heart disease was assessed in 57 New Zealand white rabbits. Before and shortly after cardiac irradiation, 15 rabbits received i.v. MP, 30 mg/kg twice daily for 3 days, and 15 others received IB, 12.5 mg/kg twice daily for 2 days. No drug was administered to 14 irradiated rabbits, and neither irradiation nor drugs were administered to 13 rabbits that served as controls, All 15 rabbits treated with MP and 13 of the 15 treated with IB lived for 100 days. Only seven of the untreated, irradiated rabbits lived that long. Longevity of each treated group of rabbits was better (p less than 0.01 and 0.05) than that of the untreated, irradiated rabbits. Surviving rabbits were killed 100 days after irradiation. Pericarditis (p less than 0.05) and pericardial effusion (p less than 0.01) were less frequent in the treated, irradiated groups than in the untreated, irradiated rabbits. At least some rabbits in each irradiated group had microscopic evidence of myocardial fibrosis. The fibrosis was quantitated by determination of myocardial hydroxyproline concentrations (MHP). MHP concentration in the untreated, irradiated rabbits was greater than in those treated with MP (p less than 0.05) or IB (p less than 0.01) and in the untreated, unirradiated rabbits (p less than 0.01). Early administration of MP or IB retarded the development of myocardial fibrosis, pericarditis and pericardial effusion, and improved survival in this experimental model of radiation-induced heart disease

  14. Clinical outcomes of adjuvant radiation therapy and prognostic factors in early stage uterine cervical cancer

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Hyun Ju; Rhee, Woo Joong; Choi, Seo Hee; Kim, Gwi Eon; Kim, Yong Bae [Dept. of Radiation Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul (Korea, Republic of); Nam, EunJi; Kim, Sang Wun; Kim, Sung Hoon [Dept. of Radiation Oncology, Obstetrics and Gynecology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul (Korea, Republic of)

    2015-06-15

    significance in early uterine cervical cancer patients. More effective systemic treatments might be needed to reduce distant metastasis in these patients.

  15. Biometry, biometrics, biostatistics, bioinformatics, . . . , bio-X

    OpenAIRE

    Molenberghs, Geert

    2005-01-01

    Recent scientific evolutions force us to rethink our profession's position on the scientific map, in relation to our neighboring professions, the ones with which we traditionally have strong collaborative links as well as the newly emerging fields, but also within our own, diverse professional group. We will show that great inspiration can be drawn from our own history, in fact from the early days of the Society. A recent inspiring example has been set by the late Rob Kempton, who died sudden...

  16. Bioinformatics in the Netherlands: the value of a nationwide community.

    Science.gov (United States)

    van Gelder, Celia W G; Hooft, Rob W W; van Rijswijk, Merlijn N; van den Berg, Linda; Kok, Ruben G; Reinders, Marcel; Mons, Barend; Heringa, Jaap

    2017-09-15

    This review provides a historical overview of the inception and development of bioinformatics research in the Netherlands. Rooted in theoretical biology by foundational figures such as Paulien Hogeweg (at Utrecht University since the 1970s), the developments leading to organizational structures supporting a relatively large Dutch bioinformatics community will be reviewed. We will show that the most valuable resource that we have built over these years is the close-knit national expert community that is well engaged in basic and translational life science research programmes. The Dutch bioinformatics community is accustomed to facing the ever-changing landscape of data challenges and working towards solutions together. In addition, this community is the stable factor on the road towards sustainability, especially in times where existing funding models are challenged and change rapidly. © The Author 2017. Published by Oxford University Press.

  17. Genomics and bioinformatics resources for translational science in Rosaceae.

    Science.gov (United States)

    Jung, Sook; Main, Dorrie

    2014-01-01

    Recent technological advances in biology promise unprecedented opportunities for rapid and sustainable advancement of crop quality. Following this trend, the Rosaceae research community continues to generate large amounts of genomic, genetic and breeding data. These include annotated whole genome sequences, transcriptome and expression data, proteomic and metabolomic data, genotypic and phenotypic data, and genetic and physical maps. Analysis, storage, integration and dissemination of these data using bioinformatics tools and databases are essential to provide utility of the data for basic, translational and applied research. This review discusses the currently available genomics and bioinformatics resources for the Rosaceae family.

  18. Naturally selecting solutions: the use of genetic algorithms in bioinformatics.

    Science.gov (United States)

    Manning, Timmy; Sleator, Roy D; Walsh, Paul

    2013-01-01

    For decades, computer scientists have looked to nature for biologically inspired solutions to computational problems; ranging from robotic control to scheduling optimization. Paradoxically, as we move deeper into the post-genomics era, the reverse is occurring, as biologists and bioinformaticians look to computational techniques, to solve a variety of biological problems. One of the most common biologically inspired techniques are genetic algorithms (GAs), which take the Darwinian concept of natural selection as the driving force behind systems for solving real world problems, including those in the bioinformatics domain. Herein, we provide an overview of genetic algorithms and survey some of the most recent applications of this approach to bioinformatics based problems.

  19. Best practices in bioinformatics training for life scientists

    DEFF Research Database (Denmark)

    Via, Allegra; Blicher, Thomas; Bongcam-Rudloff, Erik

    2013-01-01

    their data efficiently, and progress their research, is a challenge across the globe. Delivering good training goes beyond traditional lectures and resource-centric demos, using interactivity, problem-solving exercises and cooperative learning to substantially enhance training quality and learning outcomes...... to environmental researchers, a common theme is the need not just to use, and gain familiarity with, bioinformatics tools and resources but also to understand their underlying fundamental theoretical and practical concepts. Providing bioinformatics training to empower life scientists to handle and analyse...

  20. Modelling dust rings in early-type galaxies through a sequence of radiative transfer simulations and 2D image fitting

    Science.gov (United States)

    Bonfini, P.; González-Martín, O.; Fritz, J.; Bitsakis, T.; Bruzual, G.; Sodi, B. Cervantes

    2018-05-01

    A large fraction of early-type galaxies (ETGs) host prominent dust features, and central dust rings are arguably the most interesting among them. We present here `Lord Of The Rings' (LOTR), a new methodology which allows to integrate the extinction by dust rings in a 2D fitting modelling of the surface brightness distribution. Our pipeline acts in two steps, first using the surface fitting software GALFIT to determine the unabsorbed stellar emission, and then adopting the radiative transfer code SKIRT to apply dust extinction. We apply our technique to NGC 4552 and NGC 4494, two nearby ETGs. We show that the extinction by a dust ring can mimic, in a surface brightness profile, a central point source (e.g. an unresolved nuclear stellar cluster or an active galactic nucleus; AGN) superimposed to a `core' (i.e. a central flattening of the stellar light commonly observed in massive ETGs). We discuss how properly accounting for dust features is of paramount importance to derive correct fluxes especially for low luminosity AGNs (LLAGNs). We suggest that the geometries of dust features are strictly connected with how relaxed is the gravitational potential, i.e. with the evolutionary stage of the host galaxy. Additionally, we find hints that the dust mass contained in the ring relates to the AGN activity.

  1. A case of perforating radiation-induced ulcer of the esophagus, 7 months after radiotherapy for early esophageal cancer

    International Nuclear Information System (INIS)

    Ikuta, Hajime; Hamabe, Yutaka; Narita, Kouichi

    1997-01-01

    The patient was a 64-year-old man. Early esophageal cancer, slightly depressed type, was diagnosed at the middle part of the intrathoracic esophagus. Radiotherapy was chosen because of severe liver cirrhosis. External and intracavitary irradiation (50 Gy and 12 Gy, respectively) were administered with uracil and futraful (300 mg/day). The result of this therapy was complete response. Six months later, endoscopy showed that the lesion of the tumor had been almost completely healed with normal mucosa, but after 7 months the patient complained of chest pain. A large ulcer with white belag had formed. One month later the ulcer perforated into the right side of the chest, and the patient died of pyothorax. We suspected that the esophageal cancer had recurred, but at autopsy a deep ulcer 4 cm in length was found to have perforated into the right side of the chest. Pathologic findings included severe vasculitis of the esophageal wall. We diagnosed perforation of a radiation-induced esophageal ulcer after radiotherapy. The esophageal cancer did not recur. (author)

  2. Chronological observation in early radiation myelopathy of the cervical spinal cord; Gadolinium-enhanced MRI findings in two cases

    Energy Technology Data Exchange (ETDEWEB)

    Hirota, Saeko; Yoshida, Shoji; Soejima, Toshinori (Hyogo Medical Center for Adults, Akashi (Japan)) (and others)

    Gd-enhanced MR images of two patients with clinically and histopathologically diagnosed chronic progressive radiation myelitis (CPRM) were observed chronologically. One of them had had nasopharyngeal cancer and received radiotherapy at a dose of 100 Gy to the C1-2 level of the spinal cord. She developed CPRM 25 months after the termination of radiotherapy. The other had had malignant lymphoma originating from the tonsil and received chemoradiotherapy. The dose delivered to her cervical spinal cord was 40 Gy, and she developed CPRM 30 months later. Gd-enhanced MRI in the early phase revealed a small crescent-shaped nidus with or without a very small central nonenhanced area in both cases. Enhancement was not great. At that time, patients noticed only the inability to perceive pain and temperature or paresthesia in the opposite side. In a few months, MRI revealed a much more strongly enhanced and larger nidus with enlargement of a central nonenhanced area accompanied by long segmental cord enlargement. The patients' neurological symptoms had also progressed, with hemiparesis developing, for example. (author).

  3. Isolated lung events following radiation for early stage breast cancer: incidence and predictors for primary lung vs metastatic breast cancer

    International Nuclear Information System (INIS)

    Van Buren, Teresa A; Harris, Jay R; Sugarbaker, David J; Schneider, Lindsey; Healey, Elizabeth A

    1995-01-01

    Purpose: 1) To define the incidence of isolated lung events in a cohort of women treated with conservative surgery (CS) and radiation therapy (RT) for early stage breast cancer. 2) Among such patients, to define the relative distribution of primary lung cancer, metastatic breast cancer, and indeterminate lesions; and to identify any predictors for a diagnosis of lung vs metastatic breast cancer. 3) To examine the cohort with respect to whether a higher than expected incidence of lung cancer is seen following breast irradiation. Materials and Methods: Between 1968 and 1986, 1865 patients with clinical stage I-II breast cancer were treated with CS and RT; the median follow-up for surviving patients is 129 months. The study population was limited to patients who developed a subsequent isolated lung event as the first site of distant disease. Isolated lung event was defined as disease limited to the thoracic cavity, without evidence of either uncontrolled local breast disease or metastatic disease elsewhere. Diagnosis of the lung event as a primary lung cancer, a metastatic breast lesion, or an indeterminate lesion was documented from the viewpoint of 1) the pathologic analysis and 2) the clinical impression at the time of the lung event. Results: Sixty six of the 1865 patients (3.5%) developed an isolated lung event. The relative distribution of the pathologic and clinical diagnoses is shown below: The 66 lung events were characterized either as a solitary pulmonary nodule (27), multiple nodules (23), pleural effusion alone (10), unknown (2), or miscellaneous other findings (4). Among the 47 patients for whom pathology was available, the diagnosis remained indeterminate for 24 (51%). For patients with a definitive pathologic diagnosis, 69% ((9(13))) of smokers had a new lung cancer compared to 20% ((2(10))) of non-smokers (p=0.036), and 67% ((10(15))) of patients with a solitary pulmonary nodule had lung cancer compared to 14% ((1(7))) for other lung presentations (p

  4. Biometry, biometrics, biostatistics, bioinformatics,..., bio-X.

    Science.gov (United States)

    Molenberghs, Geert

    2005-03-01

    Recent scientific evolutions force us to rethink our profession's position on the scientific map, in relation to our neighboring professions, the ones with which we traditionally have strong collaborative links as well as the newly emerging fields, but also within our own, diverse professional group. We will show that great inspiration can be drawn from our own history, in fact from the early days of the Society. A recent inspiring example has been set by the late Rob Kempton, who died suddenly just months before he was to become President of the International Biometric Society.

  5. Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum

    Energy Technology Data Exchange (ETDEWEB)

    Ditty, Jayna L.; Kvaal, Christopher A.; Goodner, Brad; Freyermuth, Sharyn K.; Bailey, Cheryl; Britton, Robert A.; Gordon, Stuart G.; Heinhorst, Sabine; Reed, Kelynne; Xu, Zhaohui; Sanders-Lorenz, Erin R.; Axen, Seth; Kim, Edwin; Johns, Mitrick; Scott, Kathleen; Kerfeld, Cheryl A.

    2011-08-01

    Undergraduate life sciences education needs an overhaul, as clearly described in the National Research Council of the National Academies publication BIO 2010: Transforming Undergraduate Education for Future Research Biologists. Among BIO 2010's top recommendations is the need to involve students in working with real data and tools that reflect the nature of life sciences research in the 21st century. Education research studies support the importance of utilizing primary literature, designing and implementing experiments, and analyzing results in the context of a bona fide scientific question in cultivating the analytical skills necessary to become a scientist. Incorporating these basic scientific methodologies in undergraduate education leads to increased undergraduate and post-graduate retention in the sciences. Toward this end, many undergraduate teaching organizations offer training and suggestions for faculty to update and improve their teaching approaches to help students learn as scientists, through design and discovery (e.g., Council of Undergraduate Research [www.cur.org] and Project Kaleidoscope [www.pkal.org]). With the advent of genome sequencing and bioinformatics, many scientists now formulate biological questions and interpret research results in the context of genomic information. Just as the use of bioinformatic tools and databases changed the way scientists investigate problems, it must change how scientists teach to create new opportunities for students to gain experiences reflecting the influence of genomics, proteomics, and bioinformatics on modern life sciences research. Educators have responded by incorporating bioinformatics into diverse life science curricula. While these published exercises in, and guidelines for, bioinformatics curricula are helpful and inspirational, faculty new to the area of bioinformatics inevitably need training in the theoretical underpinnings of the algorithms. Moreover, effectively integrating bioinformatics

  6. The Pattern of Use of Hypofractionated Radiation Therapy for Early-Stage Breast Cancer in New South Wales, Australia, 2008 to 2012

    Energy Technology Data Exchange (ETDEWEB)

    Delaney, Geoff P., E-mail: Geoff.delaney@swsahs.nsw.gov.au [Liverpool Cancer Therapy Centre, Liverpool, New South Wales (Australia); Collaboration for Cancer Outcomes Research and Evaluation, University of New South Wales, Sydney (Australia); Ingham Health and Medical Research Institute, Sydney (Australia); New South Wales Cancer Institute (Australia); Gandhidasan, Senthilkumar [Peter MacCallum Cancer Centre, Melbourne (Australia); Walton, Richard; Terlich, Frances; Baker, Deborah; Currow, David [New South Wales Cancer Institute (Australia)

    2016-10-01

    Purpose: Increasing phase 3 evidence has been published about the safety and efficacy of hypofractionated radiation therapy, in comparison with standard fractionation, in early-stage, node-negative breast cancer. However, uptake of hypofractionation has not been universal. The aim of this study was to investigate the hypofractionation regimen variations in practice across public radiation oncology facilities in New South Wales (NSW). Methods and Materials: Patients with early breast cancer registered in the NSW Clinical Cancer Registry who received radiation therapy for early-stage breast cancer in a publicly funded radiation therapy department between 2008 and 2012 were identified. Data extracted and analyzed included dose and fractionation type, patient age at first fraction, address (for geocoding), year of diagnosis, year of treatment, laterality, and department of treatment. A logistic regression model was used to identify factors associated with fractionation type. Results: Of the 5880 patients fulfilling the study criteria, 3209 patients (55%) received standard fractionation and 2671 patients (45%) received hypofractionation. Overall, the use of hypofractionation increased from 37% in 2008 to 48% in 2012 (range, 7%-94% across departments). Treatment facility and the radiation oncologist prescribing the treatment were the strongest independent predictors of hypofractionation. Weaker associations were also found for age, tumor site laterality, year of treatment, and distance to facility. Conclusions: Hypofractionated regimens of whole breast radiation therapy have been variably administered in the adjuvant setting in NSW despite the publication of long-term trial results and consensus guidelines. Some factors that predict the use of hypofractionation are not based on guideline recommendations, including lower rates of left-sided treatment and increasing distance from a treatment facility.

  7. Remembrances of the early fifteen years of radiation protection at the National Atomic Energy Commission. Part 3

    International Nuclear Information System (INIS)

    Placer, Alejandro E.

    2005-01-01

    Personal memories on the origin of radiation protection activities in Argentina. This third part covers the period from 1963 to 1973 and describes the persons and facts that led to the future development of radiation protection in the country [es

  8. 5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame.

    Science.gov (United States)

    Stephan, Christian; Hamacher, Michael; Blüggel, Martin; Körting, Gerhard; Chamrad, Daniel; Scheer, Christian; Marcus, Katrin; Reidegeld, Kai A; Lohaus, Christiane; Schäfer, Heike; Martens, Lennart; Jones, Philip; Müller, Michael; Auyeung, Kevin; Taylor, Chris; Binz, Pierre-Alain; Thiele, Herbert; Parkinson, David; Meyer, Helmut E; Apweiler, Rolf

    2005-09-01

    The Bioinformatics Committee of the HUPO Brain Proteome Project (HUPO BPP) meets regularly to execute the post-lab analyses of the data produced in the HUPO BPP pilot studies. On July 7, 2005 the members came together for the 5th time at the European Bioinformatics Institute (EBI) in Hinxton, UK, hosted by Rolf Apweiler. As a main result, the parameter set of the semi-automated data re-analysis of MS/MS spectra has been elaborated and the subsequent work steps have been defined.

  9. Experimental study of the role of blocking of 5-HT3 serotonin receptors and D2 dophamin receptors in the mechanism of early radiation vomiting in monkeys

    International Nuclear Information System (INIS)

    Martirosov, K.S.; Grigor'ev, Yu.G.; Zorin, V.V.; Andrianova, I.E.

    2000-01-01

    Specific activity of Latranum and Dimetphramidum is studied using experimental model of early radiation vomiting on 17 monkeys, mass 6-9 kg inherent on usual ration of vivarium. The experiments with M. fasciculata monkeys exposed to 137 Cs γ-radiation with a dose of 6.9 Gy showed that Latranum, a blocker of serotonin 5-HT 3 receptors, is a more efficient antimetric than Dimetphramidum, a D 2 dophamin lytic. This suggested by fewer animals with emetic reaction of by less severe vomiting in case they have any. The results agree well with a hypothesis that serotonin receptors are dominant in the chemoreceptor trigger zone of monkeys [ru

  10. Anti-inflammatory and Anti-apoptotic Effect of Valproic Acid and Doxycycline Independent from MMP Inhibition in Early Radiation Damage

    Directory of Open Access Journals (Sweden)

    Ferda Hoşgörler

    2016-10-01

    Full Text Available Background: Matrix metalloproteinase (MMP inhibitors decrease inflammation in normal tissues and suppress cancer progress in normal tissues. Valproic acid (VA and doxycycline (DX are MMP inhibitors that have radio-protective effects. Their ability to inhibit MMPs in irradiated tissue is unknown and the role of MMPs in radio-protective effects has not been tested to date. Aims: The purpose of this study was to examine whether administration of VA and DX to rats before irradiation affects tissue inflammation and apoptosis in the early phase of radiation, and whether the effect of these drugs is mediated by MMP inhibition. Study Design: Animal experimentation. Methods: Twenty-six Wistar rats were randomized into four groups: control (CTRL, radiation (RT, VA plus radiation (VA+RT, and DX plus radiation (DX+RT.Three study groups were exposed to a single dose of abdominal 10 Gy gamma radiation; the CTRL group received no radiation. Single doses of VA 300 mg/kg and DX 100 mg/kg were administered to each rat before radiation and all rats were sacrificed 8 hours after irradiation, at which point small intestine tissue samples were taken for analyses. Levels of inflammatory cytokines (TNF-α, IL-1β, and IL-6 and matrix metalloproteinases (MMP-2 and MMP 9 were measured by ELISA, MMP activities were measured by gelatin and casein zymography and apoptosis was assessed by terminal deoxynucleotidyl transferase dUTP nick end labeling assay. Results: VA decreased the levels of TNF-α and IL-1β proteins insignificantly and decreased apoptosis significantly in the irradiated tissue, but did not inhibit MMPs. In contrast, VA protected the basal MMP activities, which decreased in response to irradiation. No effect of DX was observed on the levels of inflammatory cytokines or activities of MMPs in the early phases of radiation apoptosis. Conclusion: Our findings indicated that VA protects against inflammation and apoptosis, and DX exhibits anti-apoptotic effects in

  11. Intrageneric Primer Design: Bringing Bioinformatics Tools to the Class

    Science.gov (United States)

    Lima, Andre O. S.; Garces, Sergio P. S.

    2006-01-01

    Bioinformatics is one of the fastest growing scientific areas over the last decade. It focuses on the use of informatics tools for the organization and analysis of biological data. An example of their importance is the availability nowadays of dozens of software programs for genomic and proteomic studies. Thus, there is a growing field (private…

  12. A BIOINFORMATIC STRATEGY TO RAPIDLY CHARACTERIZE CDNA LIBRARIES

    Science.gov (United States)

    A Bioinformatic Strategy to Rapidly Characterize cDNA LibrariesG. Charles Ostermeier1, David J. Dix2 and Stephen A. Krawetz1.1Departments of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, & Institute for Scientific Computing, Wayne State Univer...

  13. Bioinformatics in the Netherlands : The value of a nationwide community

    NARCIS (Netherlands)

    van Gelder, Celia W.G.; Hooft, Rob; van Rijswijk, Merlijn; van den Berg, Linda; Kok, Ruben; Reinders, M.J.T.; Mons, Barend; Heringa, Jaap

    2017-01-01

    This review provides a historical overview of the inception and development of bioinformatics research in the Netherlands. Rooted in theoretical biology by foundational figures such as Paulien Hogeweg (at Utrecht University since the 1970s), the developments leading to organizational structures

  14. Bioinformatic tools and guideline for PCR primer design | Abd ...

    African Journals Online (AJOL)

    Bioinformatics has become an essential tool not only for basic research but also for applied research in biotechnology and biomedical sciences. Optimal primer sequence and appropriate primer concentration are essential for maximal specificity and efficiency of PCR. A poorly designed primer can result in little or no ...

  15. CROSSWORK for Glycans: Glycan Identificatin Through Mass Spectrometry and Bioinformatics

    DEFF Research Database (Denmark)

    Rasmussen, Morten; Thaysen-Andersen, Morten; Højrup, Peter

      We have developed "GLYCANthrope " - CROSSWORKS for glycans:  a bioinformatics tool, which assists in identifying N-linked glycosylated peptides as well as their glycan moieties from MS2 data of enzymatically digested glycoproteins. The program runs either as a stand-alone application or as a plug...

  16. Learning Genetics through an Authentic Research Simulation in Bioinformatics

    Science.gov (United States)

    Gelbart, Hadas; Yarden, Anat

    2006-01-01

    Following the rationale that learning is an active process of knowledge construction as well as enculturation into a community of experts, we developed a novel web-based learning environment in bioinformatics for high-school biology majors in Israel. The learning environment enables the learners to actively participate in a guided inquiry process…

  17. Hidden in the Middle: Culture, Value and Reward in Bioinformatics

    Science.gov (United States)

    Lewis, Jamie; Bartlett, Andrew; Atkinson, Paul

    2016-01-01

    Bioinformatics--the so-called shotgun marriage between biology and computer science--is an interdiscipline. Despite interdisciplinarity being seen as a virtue, for having the capacity to solve complex problems and foster innovation, it has the potential to place projects and people in anomalous categories. For example, valorised…

  18. Bioinformatics for Undergraduates: Steps toward a Quantitative Bioscience Curriculum

    Science.gov (United States)

    Chapman, Barbara S.; Christmann, James L.; Thatcher, Eileen F.

    2006-01-01

    We describe an innovative bioinformatics course developed under grants from the National Science Foundation and the California State University Program in Research and Education in Biotechnology for undergraduate biology students. The project has been part of a continuing effort to offer students classroom experiences focused on principles and…

  19. Mathematics and evolutionary biology make bioinformatics education comprehensible

    Science.gov (United States)

    Weisstein, Anton E.

    2013-01-01

    The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes—the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software—the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a ‘two-culture’ problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses. PMID:23821621

  20. The structural bioinformatics library: modeling in biomolecular science and beyond.

    Science.gov (United States)

    Cazals, Frédéric; Dreyfus, Tom

    2017-04-01

    Software in structural bioinformatics has mainly been application driven. To favor practitioners seeking off-the-shelf applications, but also developers seeking advanced building blocks to develop novel applications, we undertook the design of the Structural Bioinformatics Library ( SBL , http://sbl.inria.fr ), a generic C ++/python cross-platform software library targeting complex problems in structural bioinformatics. Its tenet is based on a modular design offering a rich and versatile framework allowing the development of novel applications requiring well specified complex operations, without compromising robustness and performances. The SBL involves four software components (1-4 thereafter). For end-users, the SBL provides ready to use, state-of-the-art (1) applications to handle molecular models defined by unions of balls, to deal with molecular flexibility, to model macro-molecular assemblies. These applications can also be combined to tackle integrated analysis problems. For developers, the SBL provides a broad C ++ toolbox with modular design, involving core (2) algorithms , (3) biophysical models and (4) modules , the latter being especially suited to develop novel applications. The SBL comes with a thorough documentation consisting of user and reference manuals, and a bugzilla platform to handle community feedback. The SBL is available from http://sbl.inria.fr. Frederic.Cazals@inria.fr. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  1. Rapid cloning and bioinformatic analysis of spinach Y chromosome ...

    Indian Academy of Sciences (India)

    Rapid cloning and bioinformatic analysis of spinach Y chromosome- specific EST sequences. Chuan-Liang Deng, Wei-Li Zhang, Ying Cao, Shao-Jing Wang, ... Arabidopsis thaliana mRNA for mitochondrial half-ABC transporter (STA1 gene). 389 2.31E-13. 98.96. SP3−12. Betula pendula histidine kinase 3 (HK3) mRNA, ...

  2. Staff Scientist - RNA Bioinformatics | Center for Cancer Research

    Science.gov (United States)

    The newly established RNA Biology Laboratory (RBL) at the Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH) in Frederick, Maryland is recruiting a Staff Scientist with strong expertise in RNA bioinformatics to join the Intramural Research Program’s mission of high impact, high reward science. The RBL is the equivalent of an

  3. Mathematics and evolutionary biology make bioinformatics education comprehensible.

    Science.gov (United States)

    Jungck, John R; Weisstein, Anton E

    2013-09-01

    The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes-the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software-the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a 'two-culture' problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses.

  4. A bioinformatic survey of RNA-binding proteins in Plasmodium.

    Science.gov (United States)

    Reddy, B P Niranjan; Shrestha, Sony; Hart, Kevin J; Liang, Xiaoying; Kemirembe, Karen; Cui, Liwang; Lindner, Scott E

    2015-11-02

    The malaria parasites in the genus Plasmodium have a very complicated life cycle involving an invertebrate vector and a vertebrate host. RNA-binding proteins (RBPs) are critical factors involved in every aspect of the development of these parasites. However, very few RBPs have been functionally characterized to date in the human parasite Plasmodium falciparum. Using different bioinformatic methods and tools we searched P. falciparum genome to list and annotate RBPs. A representative 3D models for each of the RBD domain identified in P. falciparum was created using I-TESSAR and SWISS-MODEL. Microarray and RNAseq data analysis pertaining PfRBPs was performed using MeV software. Finally, Cytoscape was used to create protein-protein interaction network for CITH-Dozi and Caf1-CCR4-Not complexes. We report the identification of 189 putative RBP genes belonging to 13 different families in Plasmodium, which comprise 3.5% of all annotated genes. Almost 90% (169/189) of these genes belong to six prominent RBP classes, namely RNA recognition motifs, DEAD/H-box RNA helicases, K homology, Zinc finger, Puf and Alba gene families. Interestingly, almost all of the identified RNA-binding helicases and KH genes have cognate homologs in model species, suggesting their evolutionary conservation. Exploration of the existing P. falciparum blood-stage transcriptomes revealed that most RBPs have peak mRNA expression levels early during the intraerythrocytic development cycle, which taper off in later stages. Nearly 27% of RBPs have elevated expression in gametocytes, while 47 and 24% have elevated mRNA expression in ookinete and asexual stages. Comparative interactome analyses using human and Plasmodium protein-protein interaction datasets suggest extensive conservation of the PfCITH/PfDOZI and PfCaf1-CCR4-NOT complexes. The Plasmodium parasites possess a large number of putative RBPs belonging to most of RBP families identified so far, suggesting the presence of extensive post

  5. Impact of Pretreatment Tumor Growth Rate on Outcome of Early-Stage Lung Cancer Treated With Stereotactic Body Radiation Therapy

    Energy Technology Data Exchange (ETDEWEB)

    Atallah, Soha; Cho, B.C. John; Allibhai, Zishan; Taremi, Mojgan; Giuliani, Meredith [Radiation Medicine Program, Princess Margaret Cancer Centre, Toronto, Ontario (Canada); Department of Radiation Oncology, University of Toronto, Toronto, Ontario (Canada); Le, Lisa W. [Department of Biostatistics, Princess Margaret Cancer Centre, Toronto, Ontario (Canada); Brade, Anthony; Sun, Alexander; Bezjak, Andrea [Radiation Medicine Program, Princess Margaret Cancer Centre, Toronto, Ontario (Canada); Department of Radiation Oncology, University of Toronto, Toronto, Ontario (Canada); Hope, Andrew J., E-mail: andrew.hope@rmp.uhn.on.ca [Radiation Medicine Program, Princess Margaret Cancer Centre, Toronto, Ontario (Canada); Department of Radiation Oncology, University of Toronto, Toronto, Ontario (Canada)

    2014-07-01

    Purpose: To determine the influence of pretreatment tumor growth rate on outcomes in patients with early-stage non-small cell lung cancer (NSCLC) treated with stereotactic body radiation therapy (SBRT). Methods and Materials: A review was conducted on 160 patients with T1-T2N0M0 NSCLC treated with SBRT at single institution. The patient's demographic and clinical data, time interval (t) between diagnostic and planning computed tomography (CT), vital status, disease status, and cause of death were extracted from a prospectively kept database. Differences in gross tumor volume between diagnostic CT (GTV1) and planning CT (GTV2) were recorded, and growth rate was calculated by use of specific growth rate (SGR). Kaplan-Meier curves were constructed for overall survival (OS). Differences between groups were compared with a log-rank test. Multivariate analyses were performed by use of the Cox proportional hazard model with SGR and other relevant clinical factors. Cumulative incidence was calculated for local, regional, and distant failures by use of the competing risk approach and was compared with Gray's test. Results: The median time interval between diagnostic and planning CT was 82 days. The patients were divided into 2 groups, and the median SGR was used as a cut-off. The median survival times were 38.6 and 27.7 months for the low and high SGR groups, respectively (P=.03). Eastern Cooperative Oncology Group performance status (P=.01), sex (P=.04), SGR (P=.03), and GTV2 (P=.002) were predictive for OS in multivariable Cox regression analysis and, except sex, were similarly predictive for failure-free survival (FFS). The 3-year cumulative incidences of regional failure were 19.2% and 6.0% for the high and low SGR groups, respectively (P=.047). Conclusion: High SGR was correlated with both poorer OS and FFS in patients with early-stage NSCLC treated with SBRT. If validated, this measurement may be useful in identifying patients most likely to benefit from

  6. Inhaled /sup 147/Pm and/or total-body gamma radiation: Early mortality and morbidity in rats

    Energy Technology Data Exchange (ETDEWEB)

    Filipy, R.E.; Lauhala, K.E.; McGee, D.R.; Cannon, W.C.; Buschbom, R.L.; Decker, J.R.; Kuffel, E.G.; Park, J.F.; Ragan, H.A.; Yaniv, S.S.; Scott, B.R.

    1989-05-01

    Rats were given doses of /sup 60/Co gamma radiation and/or lung burdens of /sup 147/Pm (in fused aluminosilicate particles) within lethal ranges in an experiment to determine and compare morbidity and mortality responses for the radiation insults within 1 year after exposure. Radiation-induced morbidity was assessed by measuring changes in body weights, hematologic parameters, and pulmonary-function parameters. Acute mortality and morbidity from inhaled promethium were caused primarily by radiation pneumonitis and pulmonary fibrosis that occurred more than 53 days after exposure. Acute mortality and morbidity from total-body gamma irradiation occurred within 30 days of exposure and resulted from the bone-marrow radiation syndrome. Gamma radiation caused transient morbidity, reflected by immediately depressed blood cell levels and by reduced body weight gain in animals that survived the acute gamma radiation syndrome. Inhaled promethium caused a loss of body weight and diminished pulmonary function, but its only effect on blood cell levels was lymphocytopenia. Combined gamma irradiation and promethium lung burdens were synergistic, in that animals receiving both radiation insults had higher morbidity and mortality rates than would be predicted based on the effect of either kind of radiation alone. Promethium lung burdens enhanced the effect of gamma radiation in rats within the first 30 days of exposure, and gamma radiation enhanced the later effect of promethium lung burdens. 70 refs., 68 figs., 21 tabs.

  7. Influence of intestinal early enteral nutrition therapy on intestinal barrier function and immune response of patients with radiation enteritis

    International Nuclear Information System (INIS)

    Liu Guohui; Kang Xin; Chen Gong; Wang Guangyi

    2012-01-01

    Objective: To investigate the influence of early enteral nutrition therapy on the intestinal barrier function and immune response of the patients with radiation enteritis (ER) so as to find a relatively simple and effective method to treat RE. Methods: Fifty-six patients with radiation enteritis (RE) diagnosed by colonoscopy, X-rays, and pathology were randomly divided into 2 equal groups: experimental group undergoing enteral nutrition therapy, and control group undergoing conventional therapy only. Peripheral blood samples were collected 1, 11, and 21 days after admission. Plasma diamine oxidase (DAO), D-lactic acid, endotoxin, and lactulose/mannitol (L/M) ratio, and levels of IgG, IgM, and IgA, and CD4/CD8 ratio were examined. Five cases from the experimental group and 5 cases from the control group underwent second-time operation because of incomplete intestinal obstruction, intestinal stenosis, or recurrent tumor respectively. The biopsy specimens of the terminal ileum or distal descending colon taken during the first and second operations underwent pathological examination. Peripheral blood samples were collected 1, 11, and 21 days after admission. Plasma diamine oxidase (DAO), D-lactic acid, endotoxin, and lactulose/mannitol (L/M) ratio, and levels of IgG, IgM, and IgA, and CD4/CD8 ratio were examined. Results: There were no significant differences in the intestinal function and blood immunological indices between these 2 groups. The levels of DAO, D-lactic acid, and endotoxin,and the L/M ratio 11 days after admission of the experiment group were all significantly lower than those of the control group (t=2.568, 2.427, 2.143, 2.443, P<0.05), and all those indices 21 days after admission of the experiment group were all much more significantly lower in comparison with the control group (t=6.019, 12.834, 7.837, 7.997, P<0.01). The levels of IgG, IgM, and IgA, and CD4/CD8 ratio 11 days after admission of the experimental group were all significantly higher than

  8. Bioclipse: an open source workbench for chemo- and bioinformatics

    Directory of Open Access Journals (Sweden)

    Wagener Johannes

    2007-02-01

    Full Text Available Abstract Background There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no sucessful attempts have been made to integrate chemo- and bioinformatics into a single framework. Results Bioclipse is an advanced workbench for resources in chemo- and bioinformatics, such as molecules, proteins, sequences, spectra, and scripts. It provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, and much more; all fully integrated into a user-friendly desktop application. Editing supports standard functions such as cut and paste, drag and drop, and undo/redo. Bioclipse is written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plugin architecture. This gives Bioclipse an advantage over other systems as it can easily be extended with functionality in any desired direction. Conclusion Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL, an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at http://www.bioclipse.net.

  9. BioWarehouse: a bioinformatics database warehouse toolkit

    Directory of Open Access Journals (Sweden)

    Stringer-Calvert David WJ

    2006-03-01

    Full Text Available Abstract Background This article addresses the problem of interoperation of heterogeneous bioinformatics databases. Results We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. Conclusion BioWarehouse embodies significant progress on the

  10. BioWarehouse: a bioinformatics database warehouse toolkit.

    Science.gov (United States)

    Lee, Thomas J; Pouliot, Yannick; Wagner, Valerie; Gupta, Priyanka; Stringer-Calvert, David W J; Tenenbaum, Jessica D; Karp, Peter D

    2006-03-23

    This article addresses the problem of interoperation of heterogeneous bioinformatics databases. We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL) but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. BioWarehouse embodies significant progress on the database integration problem for bioinformatics.

  11. Diffuse optical measurements of head and neck tumor hemodynamics for early prediction of radiation therapy (Conference Presentation)

    Science.gov (United States)

    Dong, Lixin; Kudrimoti, Mahesh; Irwin, Daniel; Chen, Li; Shang, Yu; Li, Xingzhe; Stevens, Scott D.; Shelton, Brent J.; Yu, Guoqiang

    2016-03-01

    Radiation therapy is a principal modality for head and neck cancers and its efficacy depends on tumor hemodynamics. Our laboratory developed a hybrid diffuse optical instrument allowing for simultaneous measurements of tumor blood flow and oxygenation. In this study, the clinically involved cervical lymph node was monitored by the hybrid instrument once a week over the treatment period of seven weeks. Based on treatment outcomes within one year, patients were classified into a complete response group (CR) and an incomplete response group (IR) with remote metastasis and/or local recurrence. A linear mixed models was used to compare tumor hemodynamic responses to the treatment between the two groups. Interestingly, we found that human papilloma virus (HPV-16) status largely affected tumor hemodynamic responses. For HPV-16 negative tumors, significant differences in blood flow index (BFI, p = 0.007) and reduced scattering coefficient (μs', p = 0.0005) were observed between the two groups; IR tumors exhibited higher μs' values and a continuous increase in BFI over the treatment period. For HPV-16 positive tumors, oxygenated hemoglobin concentration ([HbO2]) and blood oxygen saturation (StO2) were significant different (p = 0.003 and 0.01, respectively); IR group showed lower [HbO2] and StO2. Our results imply HPV-16 negative tumors with higher density of vasculature (μs') and higher blood flow show poor responses to radiotherapy and HPV-16 positive tumors with lower tissue oxygenation level (lower StO2 and [HbO2]) exhibit poor treatment outcomes. Our diffuse optical measurements show the great potential for early prediction of radiotherapy in head and neck cancers.

  12. Stereotactic body radiation therapy for early-stage non-small-cell lung cancer. The Japanese experience

    International Nuclear Information System (INIS)

    Hiraoka, Masahiro; Nagata, Yasushi

    2004-01-01

    Stereotactic body radiation therapy is a new treatment modality for early-stage non-small-cell lung cancer, and is being intensively investigated in the United States, the European Union, and Japan. We started a feasibility study of this therapy in July 1998, using a stereotactic body frame. The eligibility criteria for primary lung cancer were: solitary tumor less than 4 cm; inoperable, or the patient refused operation; histologically confirmed malignancy; no necessity for oxygen support; performance status equal to or less than 2, and the tumor was not close to the spinal cord. A total dose of 48 Gy was delivered in four fractions in 2 weeks in most patients. Lung toxicity was minimal. No grade II toxicities for spinal cord, bronchus, pulmonary artery, or esophagus were observed. Overall survival for 29 patients with stage IA, and 14 patients with stage IB disease was 87% and 80%, respectively. No local recurrence was observed in a follow-up of 3-50 months. Regional lymph node recurrence developed in 1 patient, and distant metastases developed in 4 patients. We retrospectively analyzed 241 patients from 13 Japanese institutions. The local recurrence rate was 20% when the biological equivalent dose (BED) was less than 100 Gy, and 6.5% when the BED was over 100 Gy. Overall survival at 3 years was 42% when the BED was less than 100 Gy, and 46% when it was over 100 Gy. In tumors which received a BED of more than 100 Gy, overall survival at 3 years was 91% for operable patients, and 50% for inoperable patients. Long-term results, in terms of local control, regional recurrence, survival, and complications, are not yet evaluated. However, this treatment modality is highly expected to be a standard treatment for inoperable patients, and it may be an alternative to lobectomy for operative patients. A prospective trial, which is now ongoing, will, answer these questions. (author)

  13. Comparison of the early response of human embryonic stem cells and human induced pluripotent stem cells to ionizing radiation.

    Science.gov (United States)

    Suchorska, Wiktoria Maria; Augustyniak, Ewelina; Łukjanow, Magdalena

    2017-04-01

    Despite the well-demonstrated efficacy of stem cell (SC) therapy, this approach has a number of key drawbacks. One important concern is the response of pluripotent SCs to treatment with ionizing radiation (IR), given that SCs used in regenerative medicine will eventually be exposed to IR for diagnostic or treatment‑associated purposes. Therefore, the aim of the present study was to examine and compare early IR‑induced responses of pluripotent SCs to assess their radioresistance and radiosensitivity. In the present study, 3 cell lines; human embryonic SCs (hESCs), human induced pluripotent SCs (hiPSCs) and primary human dermal fibroblasts (PHDFs); were exposed to IR at doses ranging from 0 to 15 gray (Gy). Double strand breaks (DSBs), and the gene expression of the following DNA repair genes were analyzed: P53; RAD51; BRCA2; PRKDC; and XRCC4. hiPSCs demonstrated greater radioresistance, as fewer DSBs were identified, compared with hESCs. Both pluripotent SC lines exhibited distinct gene expression profiles in the most common DNA repair genes that are involved in homologous recombination, non‑homologous end‑joining and enhanced DNA damage response following IR exposure. Although hESCs and hiPSCs are equivalent in terms of capacity for pluripotency and differentiation into 3 germ layers, the results of the present study indicate that these 2 types of SCs differ in gene expression following exposure to IR. Consequently, further research is required to determine whether hiPSCs and hESCs are equally safe for application in clinical practice. The present study contributes to a greater understanding of DNA damage response (DDR) mechanisms activated in pluripotent SCs and may aid in the future development of safe SC‑based clinical protocols.

  14. Early Clinical Outcomes Demonstrate Preserved Cognitive Function in Children With Average-Risk Medulloblastoma When Treated With Hyperfractionated Radiation Therapy

    International Nuclear Information System (INIS)

    Gupta, Tejpal; Jalali, Rakesh; Goswami, Savita; Nair, Vimoj; Moiyadi, Aliasgar; Epari, Sridhar; Sarin, Rajiv

    2012-01-01

    Purpose: To report on acute toxicity, longitudinal cognitive function, and early clinical outcomes in children with average-risk medulloblastoma. Methods and Materials: Twenty children ≥5 years of age classified as having average-risk medulloblastoma were accrued on a prospective protocol of hyperfractionated radiation therapy (HFRT) alone. Radiotherapy was delivered with two daily fractions (1 Gy/fraction, 6 to 8 hours apart, 5 days/week), initially to the neuraxis (36 Gy/36 fractions), followed by conformal tumor bed boost (32 Gy/32 fractions) for a total tumor bed dose of 68 Gy/68 fractions over 6 to 7 weeks. Cognitive function was prospectively assessed longitudinally (pretreatment and at specified posttreatment follow-up visits) with the Wechsler Intelligence Scale for Children to give verbal quotient, performance quotient, and full-scale intelligence quotient (FSIQ). Results: The median age of the study cohort was 8 years (range, 5–14 years), representing a slightly older cohort. Acute hematologic toxicity was mild and self-limiting. Eight (40%) children had subnormal intelligence (FSIQ <85), including 3 (15%) with mild mental retardation (FSIQ 56–70) even before radiotherapy. Cognitive functioning for all tested domains was preserved in children evaluable at 3 months, 1 year, and 2 years after completion of HFRT, with no significant decline over time. Age at diagnosis or baseline FSIQ did not have a significant impact on longitudinal cognitive function. At a median follow-up time of 33 months (range, 16–58 months), 3 patients had died (2 of relapse and 1 of accidental burns), resulting in 3-year relapse-free survival and overall survival of 83.5% and 83.2%, respectively. Conclusion: HFRT without upfront chemotherapy has an acceptable acute toxicity profile, without an unduly increased risk of relapse, with preserved cognitive functioning in children with average-risk medulloblastoma.

  15. Early Clinical Outcomes Demonstrate Preserved Cognitive Function in Children With Average-Risk Medulloblastoma When Treated With Hyperfractionated Radiation Therapy

    Energy Technology Data Exchange (ETDEWEB)

    Gupta, Tejpal, E-mail: tejpalgupta@rediffmail.com [Department of Radiation Oncology, Advanced Centre for Treatment Research and Education in Cancer and Tata Memorial Hospital, Mumbai (India); Jalali, Rakesh [Department of Radiation Oncology, Advanced Centre for Treatment Research and Education in Cancer and Tata Memorial Hospital, Mumbai (India); Goswami, Savita [Department of Clinical Psychology and Psychiatry Unit, Advanced Centre for Treatment Research and Education in Cancer and Tata Memorial Hospital, Mumbai (India); Nair, Vimoj [Department of Radiation Oncology, Advanced Centre for Treatment Research and Education in Cancer and Tata Memorial Hospital, Mumbai (India); Moiyadi, Aliasgar [Division of Neuro-Surgery, Department of Surgical Oncology, Advanced Centre for Treatment Research and Education in Cancer and Tata Memorial Hospital, Mumbai (India); Epari, Sridhar [Department of Pathology, Advanced Centre for Treatment Research and Education in Cancer and Tata Memorial Hospital, Mumbai (India); Sarin, Rajiv [Department of Radiation Oncology, Advanced Centre for Treatment Research and Education in Cancer and Tata Memorial Hospital, Mumbai (India)

    2012-08-01

    Purpose: To report on acute toxicity, longitudinal cognitive function, and early clinical outcomes in children with average-risk medulloblastoma. Methods and Materials: Twenty children {>=}5 years of age classified as having average-risk medulloblastoma were accrued on a prospective protocol of hyperfractionated radiation therapy (HFRT) alone. Radiotherapy was delivered with two daily fractions (1 Gy/fraction, 6 to 8 hours apart, 5 days/week), initially to the neuraxis (36 Gy/36 fractions), followed by conformal tumor bed boost (32 Gy/32 fractions) for a total tumor bed dose of 68 Gy/68 fractions over 6 to 7 weeks. Cognitive function was prospectively assessed longitudinally (pretreatment and at specified posttreatment follow-up visits) with the Wechsler Intelligence Scale for Children to give verbal quotient, performance quotient, and full-scale intelligence quotient (FSIQ). Results: The median age of the study cohort was 8 years (range, 5-14 years), representing a slightly older cohort. Acute hematologic toxicity was mild and self-limiting. Eight (40%) children had subnormal intelligence (FSIQ <85), including 3 (15%) with mild mental retardation (FSIQ 56-70) even before radiotherapy. Cognitive functioning for all tested domains was preserved in children evaluable at 3 months, 1 year, and 2 years after completion of HFRT, with no significant decline over time. Age at diagnosis or baseline FSIQ did not have a significant impact on longitudinal cognitive function. At a median follow-up time of 33 months (range, 16-58 months), 3 patients had died (2 of relapse and 1 of accidental burns), resulting in 3-year relapse-free survival and overall survival of 83.5% and 83.2%, respectively. Conclusion: HFRT without upfront chemotherapy has an acceptable acute toxicity profile, without an unduly increased risk of relapse, with preserved cognitive functioning in children with average-risk medulloblastoma.

  16. Missing "Links" in Bioinformatics Education: Expanding Students' Conceptions of Bioinformatics Using a Biodiversity Database of Living and Fossil Reef Corals

    Science.gov (United States)

    Nehm, Ross H.; Budd, Ann F.

    2006-01-01

    NMITA is a reef coral biodiversity database that we use to introduce students to the expansive realm of bioinformatics beyond genetics. We introduce a series of lessons that have students use this database, thereby accessing real data that can be used to test hypotheses about biodiversity and evolution while targeting the "National Science …

  17. Probing early tumor response to radiation therapy using hyperpolarized [1-¹³C]pyruvate in MDA-MB-231 xenografts.

    Directory of Open Access Journals (Sweden)

    Albert P Chen

    Full Text Available Following radiation therapy (RT, tumor morphology may remain unchanged for days and sometimes weeks, rendering anatomical imaging methods inadequate for early detection of therapeutic response. Changes in the hyperpolarized [1-¹³C]lactate signals observed in vivo following injection of pre-polarized [1-¹³C]pyruvate has recently been shown to be a marker for tumor progression or early treatment response. In this study, the feasibility of using ¹³C metabolic imaging with [1-¹³C]pyruvate to detect early radiation treatment response in a breast cancer xenograft model was demonstrated in vivo and in vitro. Significant decreases in hyperpolarized [1-¹³C]lactate relative to [1-¹³C]pyruvate were observed in MDA-MB-231 tumors 96 hrs following a single dose of ionizing radiation. Histopathologic data from the treated tumors showed higher cellular apoptosis and senescence; and changes in the expression of membrane monocarboxylate transporters and lactate dehydrogenase B were also observed. Hyperpolarized ¹³C metabolic imaging may be a promising new tool to develop novel and adaptive therapeutic regimens for patients undergoing RT.

  18. Identification of differentially expressed genes and signaling pathways in ovarian cancer by integrated bioinformatics analysis

    Directory of Open Access Journals (Sweden)

    Yang X

    2018-03-01

    tumor signaling pathway. The 17 most closely related genes among DEGs were identified from the PPI network. Conclusion: This study indicates that screening for DEGs and pathways in ovarian cancer using integrated bioinformatics analyses could help us understand the molecular mechanism underlying the development of ovarian cancer, be of clinical significance for the early diagnosis and prevention of ovarian cancer, and provide effective targets for the treatment of ovarian cancer. Keywords: ovarian cancer, GEO data, integrated bioinformatics, differentially expressed genes

  19. Report on the EMBER Project--A European Multimedia Bioinformatics Educational Resource

    Science.gov (United States)

    Attwood, Terri K.; Selimas, Ioannis; Buis, Rob; Altenburg, Ruud; Herzog, Robert; Ledent, Valerie; Ghita, Viorica; Fernandes, Pedro; Marques, Isabel; Brugman, Marc

    2005-01-01

    EMBER was a European project aiming to develop bioinformatics teaching materials on the Web and CD-ROM to help address the recognised skills shortage in bioinformatics. The project grew out of pilot work on the development of an interactive web-based bioinformatics tutorial and the desire to repackage that resource with the help of a professional…

  20. Applying Instructional Design Theories to Bioinformatics Education in Microarray Analysis and Primer Design Workshops

    Science.gov (United States)

    Shachak, Aviv; Ophir, Ron; Rubin, Eitan

    2005-01-01

    The need to support bioinformatics training has been widely recognized by scientists, industry, and government institutions. However, the discussion of instructional methods for teaching bioinformatics is only beginning. Here we report on a systematic attempt to design two bioinformatics workshops for graduate biology students on the basis of…

  1. Introductory Bioinformatics Exercises Utilizing Hemoglobin and Chymotrypsin to Reinforce the Protein Sequence-Structure-Function Relationship

    Science.gov (United States)

    Inlow, Jennifer K.; Miller, Paige; Pittman, Bethany

    2007-01-01

    We describe two bioinformatics exercises intended for use in a computer laboratory setting in an upper-level undergraduate biochemistry course. To introduce students to bioinformatics, the exercises incorporate several commonly used bioinformatics tools, including BLAST, that are freely available online. The exercises build upon the students'…

  2. Vertical and Horizontal Integration of Bioinformatics Education: A Modular, Interdisciplinary Approach

    Science.gov (United States)

    Furge, Laura Lowe; Stevens-Truss, Regina; Moore, D. Blaine; Langeland, James A.

    2009-01-01

    Bioinformatics education for undergraduates has been approached primarily in two ways: introduction of new courses with largely bioinformatics focus or introduction of bioinformatics experiences into existing courses. For small colleges such as Kalamazoo, creation of new courses within an already resource-stretched setting has not been an option.…

  3. Changes in intracellular K+ concentration and action potential of myocardiocytes in early stage of radiation, burn and combined radiation-burn injuries in rats

    International Nuclear Information System (INIS)

    Li Min; Xiao Jiasi; Yan Shuzhi; Wan Zibin

    1996-01-01

    K + -ISME and micro electrode were used respectively to measure the [K + ] i concentration and action potential in ventricular papillary myocardiocytes of 92 Wistar rats, which were divided into four groups: normal rats (group C), and rats receiving radiation (group R), burn (group B) and combined radiation-burn (group RB), and undergoing measurement 1,3,8 and 24 hours after respective treatment. It was found that (1) [K + ] i was reduced in groups B and RB (especially in group B), but there was no change in group R; (2) RP, APA and V max were all decreased in three injured groups; (3) APD 50 and APD 90 were shortened obviously in group B, but were prolonged in both groups R and RB (especially in group R). These results suggest that (1) radiation injury diminishes Na + inflow and K + outflow; (2) burn diminishes Na + inflow and accelerates K + outflow; (3) combined radiation-burn injury is not a simple addition of radiation and burn effects

  4. Analyses of patterns-of-failure and prognostic factors according to radiation fields in early-stage Hodgkin lymphoma

    Energy Technology Data Exchange (ETDEWEB)

    Krebs, Lorraine; Guillerm, Sophie; Menard, Jean; Hennequin, Christophe; Quero, Laurent [Saint Louis Hospital, Radiation Oncology Department, Paris (France); Amorin, Sandy; Brice, Pauline [Saint Louis Hospital, AP-HP, Hematooncology Department, Paris (France)

    2017-02-15

    Doses and volumes of radiation therapy (RT) for early stages of Hodgkin lymphoma (HL) have been reduced over the last 30 years. Combined modality therapy (CMT) is currently the standard treatment for most patients with early-stage HL. The aim of this study was to analyze the site of relapse after RT according to the extent of radiation fields. Between 1987 and 2011, 427 patients were treated at our institution with RT ± chemotherapy for stage-I/II HL. Among these, 65 patients who experienced a relapse were retrospectively analyzed. Most patients had nodular sclerosis histology (86 %) and stage-II disease (75.9 %). Bulky disease was present in 21 % and 56 % of patients belonged to the unfavorable risk group according to European Organization for Research and Treatment of Cancer (EORTC)/The Lymphoma Study Association (LYSA) definitions. CMT was delivered to 91 % of patients. All patients received RT with doses ranging from 20 to 45 Gy (mean = 34 ± 5.3 Gy). The involved-field RT technique was used in 59 % of patients. The mean time between diagnosis and relapse was 4.2 years (range 0.3-24.5). Out-of-field relapses were suffered by 53 % of patients. Relapses occurred more frequently at out-of-field sites in patients with a favorable disease status, whereas in-field relapses were associated with bulky mediastinal disease. Relapses occurred later for favorable compared with the unfavorable risk group (3.5 vs. 2.9 years, p = 0.5). From multivariate analyses, neither RT dose nor RT field size were predictive for an in-field relapse (p = 0.25 and p = 0.8, respectively), only bulky disease was predictive (p = 0.018). In patients with bulky disease, RT dose and RT field size were not predictive for an in-field relapse. In this subgroup of patients, chemotherapy should be intensified. We confirmed the bad prognosis of early relapses. (orig.) [German] Waehrend der letzten 30 Jahre wurden die Strahlentherapie-(RT-)Dosis und die RT-Volumina fuer die Behandlung der Fruehstadien

  5. Quantum Bio-Informatics II From Quantum Information to Bio-Informatics

    Science.gov (United States)

    Accardi, L.; Freudenberg, Wolfgang; Ohya, Masanori

    2009-02-01

    / H. Kamimura -- Massive collection of full-length complementary DNA clones and microarray analyses: keys to rice transcriptome analysis / S. Kikuchi -- Changes of influenza A(H5) viruses by means of entropic chaos degree / K. Sato and M. Ohya -- Basics of genome sequence analysis in bioinformatics - its fundamental ideas and problems / T. Suzuki and S. Miyazaki -- A basic introduction to gene expression studies using microarray expression data analysis / D. Wanke and J. Kilian -- Integrating biological perspectives: a quantum leap for microarray expression analysis / D. Wanke ... [et al.].

  6. Effects of low dose {gamma} radiation on early growth and physiological activities of radish (raphanus sativus L.) and the reduction of ultraviolet-B stress

    Energy Technology Data Exchange (ETDEWEB)

    Kim, J. S.; Lee, Y. K.; Lee, H. Y.; Baek, M. H.; Yoo, J. C. [KAERI, Taejon (Korea, Republic of)

    2002-10-01

    The effect of low dose {gamma} radiation on early growth and photosynthesis in radish plant was studied. The seedling height of radish was stimulated in plants grown from seeds irradiated with the low dose of 10 Gy. The O{sub 2} evolution in the 10 Gy irradiation group was 1.2 times greater than in the control. The catalase and peroxidase activity of radish leaves grown from seeds irradiated with {gamma} radiation were increased at 10 Gy irradiation group as the superoxide dismutase activity of leaves was. To investigate the effect of low dose {gamma} radiation on response to UV-B stress, UV-B was given at the intensity of 1 W{center_dot} m{sup -2} to the detached leaves. Pmax was decreased with increasing illumination time by 76% in the control, while decreased by 75% in the 10 Gy irradiation group. The photochemical yield of PSII, estimated as Fv/Fm, was decreased with increasing illumination time by 75% after 4 hours while Fv/Fm in the 10 Gy irradiation group was decreased by 69% of inhibition, indicating that the low dose {gamma} radiation retarded the deteriorative effect of UV-B on PSII. The initial fluorescence (Fo) was slightly increased with increasing illumination time, while the maximal fluorescence (Fm) was decreased. These results showed the positive effect of low dose {gamma} radiation on the seedling growth and the reduction of the deteriorative effect of UV-B stress on photosynthesis in radish plant.

  7. Radiation-induced apoptosis of neural precursors cell cultures: early modulation of the response mediated by reactive oxygen and nitrogen species (ROS/RNS)

    Energy Technology Data Exchange (ETDEWEB)

    Gisone, P.; Dubner, D.; Robello, E.; Michelin, S.; Perez, M. R.

    2004-07-01

    Apoptosis, the typical mode of radiation-induced cell death in developing Central Nervous System (CNS), is closely related with the oxidative status. Enhanced radiation-induced generation of ROS/RNS has been observed after exposures to low radiation doses leading to cellular amplification of signal transduction and further molecular and cellular radiation-responses. Moreover Nitric oxide (NO) and hydroxyl radical are implicated in dopaminergic neurotoxicity in different parading. This study is an attempt to address the participation of radiation-induced free radicals production, the contribution of endogenous NO generation, and the excitonic pathway, in the radiation-induced apoptosis of neural cortical precursors. Cortical cells obtained from at 17 gestational day (gd) were irradiated with doses from 0,2 Gy to 2 Gy at a dose-rate of 0.3 Gy/m. A significant decrease of Luminol-dependent Chemiluminescence was evident 30 m after irradiation reaching basal levels at 120 m follow for a tendency to increasing values Incubations with Superoxide Dismatuse (SOD) decreased significantly the chemiluminescence in irradiated samples NO content estimated by measuring the stable products NO{sub 2} and NO{sub 3} released to the culture medium in the same period, has shown a time-dependent accumulation from 1 h post-irradiation. the apoptosis, determined 24 h post-irradiation by flow cytometry, morphology and DNA fragmentation revealed a dose-effect relationship with significant differences from 0.4 Gy. The samples pre-treated with 10 mM of N-acetyl cysteine (NAC) a precursor of intracellular GSH synthesis, shown a significant decrease of the apoptosis. Apoptosis was significantly increased in irradiated cells after inhibition of nitric oxide synthase (NOS) byL-NAME. We conclude that ROS/RNS play a pivotal role in the early signaling pathways leading to a radiation-induced cell death. (Author) 40 refs.

  8. Radiation-induced apoptosis of neural precursors cell cultures: early modulation of the response mediated by reactive oxygen and nitrogen species (ROS/RNS)

    International Nuclear Information System (INIS)

    Gisone, P.; Dubner, D.; Robello, E.; Michelin, S.; Perez, M. R.

    2004-01-01

    Apoptosis, the typical mode of radiation-induced cell death in developing Central Nervous System (CNS), is closely related with the oxidative status. Enhanced radiation-induced generation of ROS/RNS has been observed after exposures to low radiation doses leading to cellular amplification of signal transduction and further molecular and cellular radiation-responses. Moreover Nitric oxide (NO) and hydroxyl radical are implicated in dopaminergic neurotoxicity in different parading. This study is an attempt to address the participation of radiation-induced free radicals production, the contribution of endogenous NO generation, and the excitonic pathway, in the radiation-induced apoptosis of neural cortical precursors. Cortical cells obtained from at 17 gestational day (gd) were irradiated with doses from 0,2 Gy to 2 Gy at a dose-rate of 0.3 Gy/m. A significant decrease of Luminol-dependent Chemiluminescence was evident 30 m after irradiation reaching basal levels at 120 m follow for a tendency to increasing values Incubations with Superoxide Dismatuse (SOD) decreased significantly the chemiluminescence in irradiated samples NO content estimated by measuring the stable products NO 2 and NO 3 released to the culture medium in the same period, has shown a time-dependent accumulation from 1 h post-irradiation. the apoptosis, determined 24 h post-irradiation by flow cytometry, morphology and DNA fragmentation revealed a dose-effect relationship with significant differences from 0.4 Gy. The samples pre-treated with 10 mM of N-acetyl cysteine (NAC) a precursor of intracellular GSH synthesis, shown a significant decrease of the apoptosis. Apoptosis was significantly increased in irradiated cells after inhibition of nitric oxide synthase (NOS) byL-NAME. We conclude that ROS/RNS play a pivotal role in the early signaling pathways leading to a radiation-induced cell death. (Author) 40 refs

  9. Human radiation studies: Remembering the early years: Oral history of radiation biologist Marvin Goldman, Ph.D., conducted December 22, 1994

    International Nuclear Information System (INIS)

    1995-09-01

    This report provides a transcript of an interview of Dr. Marvin Goldman by representatives of DOE's Office of Human Radiation Experiments. Dr. Goldman was chosen for this interview because of his work on bone-seeking radionuclides. After a brief biographical sketch Dr. Goldman related his experiences concerning his training and work at Rochester University, his work at Brookhaven National Laboratory, his participation in the Beagle Studies at University of California at Davis, his work with the Chernobyl Nuclear Plant Accident, his consultation work with Russian authorities on the health and ecological effects in their history, and finally his opinions and recommendations on human radiation research and the environmental cleanup of DOE sites

  10. Improved Survival Endpoints With Adjuvant Radiation Treatment in Patients With High-Risk Early-Stage Endometrial Carcinoma

    Energy Technology Data Exchange (ETDEWEB)

    Elshaikh, Mohamed A., E-mail: melshai1@hfhs.org [Department of Radiation Oncology, Henry Ford Hospital, Detroit, Michigan (United States); Vance, Sean; Suri, Jaipreet S. [Department of Radiation Oncology, Henry Ford Hospital, Detroit, Michigan (United States); Mahan, Meredith [Public Health Science, Henry Ford Hospital, Detroit, Michigan (United States); Munkarah, Adnan [Division of Gynecologic Oncology, Department of Women' s Health Services, Henry Ford Hospital, Detroit, Michigan (United States)

    2014-02-01

    Purpose/Objective(s): To determine the impact of adjuvant radiation treatment (RT) on recurrence-free survival (RFS), disease-specific survival (DSS), and overall survival (OS) in patients with high-risk 2009 International Federation of Gynecology and Obstetrics stage I-II endometrial carcinoma. Methods and Materials: We identified 382 patients with high-risk EC who underwent hysterectomy. RFS, DSS, and OS were calculated from the date of hysterectomy by use of the Kaplan-Meier method. Cox regression modeling was used to explore the risks associated with various factors on survival endpoints. Results: The median follow-up time for the study cohort was 5.4 years. The median age was 71 years. All patients underwent hysterectomy and salpingo-oophorectomy, 93% had peritoneal cytology, and 85% underwent lymphadenectomy. Patients with endometrioid histology constituted 72% of the study cohort, serous in 16%, clear cell in 7%, and mixed histology in 4%. Twenty-three percent of patients had stage II disease. Adjuvant management included RT alone in 220 patients (57%), chemotherapy alone in 25 patients (7%), and chemoradiation therapy in 27 patients (7%); 110 patients (29%) were treated with close surveillance. The 5-year RFS, DSS, and OS were 76%, 88%, and 73%, respectively. On multivariate analysis, adjuvant RT was a significant predictor of RFS (P<.001) DSS (P<.001), and OS (P=.017). Lymphovascular space involvement was a significant predictor of RFS and DSS (P<.001). High tumor grade was a significant predictor for RFS (P=.038) and DSS (P=.025). Involvement of the lower uterine segment was also a predictor of RFS (P=.049). Age at diagnosis and lymphovascular space involvement were significant predictors of OS: P<.001 and P=.002, respectively. Conclusion: In the treatment of patients with high-risk features, our study suggests that adjuvant RT significantly improves recurrence-free, disease-specific, and overall survival in patients with early-stage endometrial carcinoma

  11. Enhancing the radiation response of tumors but not early or late responding normal tissues using a vascular disrupting agent

    DEFF Research Database (Denmark)

    Horsman, Michael R

    2017-01-01

    INTRODUCTION: Vascular disrupting agents (VDAs) damage tumor vasculature and enhance tumor radiation response. In this pre-clinical study, we combined radiation with the leading VDA in clinical development, combretastatin A-4 phosphate (CA4P), and compared the effects seen in tumors and relevant...... normal tissues. MATERIAL AND METHODS: Radiation was applied locally to tissues in CDF1 mice to produce full radiation dose-response curves. CA4P (250 mg/kg) was intraperitoneally (i.p.) injected within 30 minutes after irradiating. Response of 200 mm3 foot implanted C3H mammary carcinomas was assessed......% increase in ventilation rate measured by plethysmography within 9 months). A Chi-squared test was used for statistical comparisons (significance level of p 4P. The radiation...

  12. Meeting review: 2002 O'Reilly Bioinformatics Technology Conference.

    Science.gov (United States)

    Counsell, Damian

    2002-01-01

    At the end of January I travelled to the States to speak at and attend the first O'Reilly Bioinformatics Technology Conference. It was a large, well-organized and diverse meeting with an interesting history. Although the meeting was not a typical academic conference, its style will, I am sure, become more typical of meetings in both biological and computational sciences.Speakers at the event included prominent bioinformatics researchers such as Ewan Birney, Terry Gaasterland and Lincoln Stein; authors and leaders in the open source programming community like Damian Conway and Nat Torkington; and representatives from several publishing companies including the Nature Publishing Group, Current Science Group and the President of O'Reilly himself, Tim O'Reilly. There were presentations, tutorials, debates, quizzes and even a 'jam session' for musical bioinformaticists.

  13. Open discovery: An integrated live Linux platform of Bioinformatics tools.

    Science.gov (United States)

    Vetrivel, Umashankar; Pilla, Kalabharath

    2008-01-01

    Historically, live linux distributions for Bioinformatics have paved way for portability of Bioinformatics workbench in a platform independent manner. Moreover, most of the existing live Linux distributions limit their usage to sequence analysis and basic molecular visualization programs and are devoid of data persistence. Hence, open discovery - a live linux distribution has been developed with the capability to perform complex tasks like molecular modeling, docking and molecular dynamics in a swift manner. Furthermore, it is also equipped with complete sequence analysis environment and is capable of running windows executable programs in Linux environment. Open discovery portrays the advanced customizable configuration of fedora, with data persistency accessible via USB drive or DVD. The Open Discovery is distributed free under Academic Free License (AFL) and can be downloaded from http://www.OpenDiscovery.org.in.

  14. Rise and demise of bioinformatics? Promise and progress.

    Directory of Open Access Journals (Sweden)

    Christos A Ouzounis

    Full Text Available The field of bioinformatics and computational biology has gone through a number of transformations during the past 15 years, establishing itself as a key component of new biology. This spectacular growth has been challenged by a number of disruptive changes in science and technology. Despite the apparent fatigue of the linguistic use of the term itself, bioinformatics has grown perhaps to a point beyond recognition. We explore both historical aspects and future trends and argue that as the field expands, key questions remain unanswered and acquire new meaning while at the same time the range of applications is widening to cover an ever increasing number of biological disciplines. These trends appear to be pointing to a redefinition of certain objectives, milestones, and possibly the field itself.

  15. A Survey on Evolutionary Algorithm Based Hybrid Intelligence in Bioinformatics

    Directory of Open Access Journals (Sweden)

    Shan Li

    2014-01-01

    Full Text Available With the rapid advance in genomics, proteomics, metabolomics, and other types of omics technologies during the past decades, a tremendous amount of data related to molecular biology has been produced. It is becoming a big challenge for the bioinformatists to analyze and interpret these data with conventional intelligent techniques, for example, support vector machines. Recently, the hybrid intelligent methods, which integrate several standard intelligent approaches, are becoming more and more popular due to their robustness and efficiency. Specifically, the hybrid intelligent approaches based on evolutionary algorithms (EAs are widely used in various fields due to the efficiency and robustness of EAs. In this review, we give an introduction about the applications of hybrid intelligent methods, in particular those based on evolutionary algorithm, in bioinformatics. In particular, we focus on their applications to three common problems that arise in bioinformatics, that is, feature selection, parameter estimation, and reconstruction of biological networks.

  16. Bioinformatics and Microarray Data Analysis on the Cloud.

    Science.gov (United States)

    Calabrese, Barbara; Cannataro, Mario

    2016-01-01

    High-throughput platforms such as microarray, mass spectrometry, and next-generation sequencing are producing an increasing volume of omics data that needs large data storage and computing power. Cloud computing offers massive scalable computing and storage, data sharing, on-demand anytime and anywhere access to resources and applications, and thus, it may represent the key technology for facing those issues. In fact, in the recent years it has been adopted for the deployment of different bioinformatics solutions and services both in academia and in the industry. Although this, cloud computing presents several issues regarding the security and privacy of data, that are particularly important when analyzing patients data, such as in personalized medicine. This chapter reviews main academic and industrial cloud-based bioinformatics solutions; with a special focus on microarray data analysis solutions and underlines main issues and problems related to the use of such platforms for the storage and analysis of patients data.

  17. Architecture exploration of FPGA based accelerators for bioinformatics applications

    CERN Document Server

    Varma, B Sharat Chandra; Balakrishnan, M

    2016-01-01

    This book presents an evaluation methodology to design future FPGA fabrics incorporating hard embedded blocks (HEBs) to accelerate applications. This methodology will be useful for selection of blocks to be embedded into the fabric and for evaluating the performance gain that can be achieved by such an embedding. The authors illustrate the use of their methodology by studying the impact of HEBs on two important bioinformatics applications: protein docking and genome assembly. The book also explains how the respective HEBs are designed and how hardware implementation of the application is done using these HEBs. It shows that significant speedups can be achieved over pure software implementations by using such FPGA-based accelerators. The methodology presented in this book may also be used for designing HEBs for accelerating software implementations in other domains besides bioinformatics. This book will prove useful to students, researchers, and practicing engineers alike.

  18. 2nd Colombian Congress on Computational Biology and Bioinformatics

    CERN Document Server

    Cristancho, Marco; Isaza, Gustavo; Pinzón, Andrés; Rodríguez, Juan

    2014-01-01

    This volume compiles accepted contributions for the 2nd Edition of the Colombian Computational Biology and Bioinformatics Congress CCBCOL, after a rigorous review process in which 54 papers were accepted for publication from 119 submitted contributions. Bioinformatics and Computational Biology are areas of knowledge that have emerged due to advances that have taken place in the Biological Sciences and its integration with Information Sciences. The expansion of projects involving the study of genomes has led the way in the production of vast amounts of sequence data which needs to be organized, analyzed and stored to understand phenomena associated with living organisms related to their evolution, behavior in different ecosystems, and the development of applications that can be derived from this analysis.  .

  19. Bioinformatics for whole-genome shotgun sequencing of microbial communities.

    Directory of Open Access Journals (Sweden)

    Kevin Chen

    2005-07-01

    Full Text Available The application of whole-genome shotgun sequencing to microbial communities represents a major development in metagenomics, the study of uncultured microbes via the tools of modern genomic analysis. In the past year, whole-genome shotgun sequencing projects of prokaryotic communities from an acid mine biofilm, the Sargasso Sea, Minnesota farm soil, three deep-sea whale falls, and deep-sea sediments have been reported, adding to previously published work on viral communities from marine and fecal samples. The interpretation of this new kind of data poses a wide variety of exciting and difficult bioinformatics problems. The aim of this review is to introduce the bioinformatics community to this emerging field by surveying existing techniques and promising new approaches for several of the most interesting of these computational problems.

  20. Statistical modelling in biostatistics and bioinformatics selected papers

    CERN Document Server

    Peng, Defen

    2014-01-01

    This book presents selected papers on statistical model development related mainly to the fields of Biostatistics and Bioinformatics. The coverage of the material falls squarely into the following categories: (a) Survival analysis and multivariate survival analysis, (b) Time series and longitudinal data analysis, (c) Statistical model development and (d) Applied statistical modelling. Innovations in statistical modelling are presented throughout each of the four areas, with some intriguing new ideas on hierarchical generalized non-linear models and on frailty models with structural dispersion, just to mention two examples. The contributors include distinguished international statisticians such as Philip Hougaard, John Hinde, Il Do Ha, Roger Payne and Alessandra Durio, among others, as well as promising newcomers. Some of the contributions have come from researchers working in the BIO-SI research programme on Biostatistics and Bioinformatics, centred on the Universities of Limerick and Galway in Ireland and fu...

  1. Adjuvant Hypofractionated Versus Conventional Whole Breast Radiation Therapy for Early-Stage Breast Cancer: Long-Term Hospital-Related Morbidity From Cardiac Causes

    International Nuclear Information System (INIS)

    Chan, Elisa K.; Woods, Ryan; McBride, Mary L.; Virani, Sean; Nichol, Alan; Speers, Caroline; Wai, Elaine S.; Tyldesley, Scott

    2014-01-01

    Purpose: The risk of cardiac injury with hypofractionated whole-breast/chest wall radiation therapy (HF-WBI) compared with conventional whole-breast/chest wall radiation therapy (CF-WBI) in women with left-sided breast cancer remains a concern. The purpose of this study was to determine if there is an increase in hospital-related morbidity from cardiac causes with HF-WBI relative to CF-WBI. Methods and Materials: Between 1990 and 1998, 5334 women ≤80 years of age with early-stage breast cancer were treated with postoperative radiation therapy to the breast or chest wall alone. A population-based database recorded baseline patient, tumor, and treatment factors. Hospital administrative records identified baseline cardiac risk factors and other comorbidities. Factors between radiation therapy groups were balanced using a propensity-score model. The first event of a hospital admission for cardiac causes after radiation therapy was determined from hospitalization records. Ten- and 15-year cumulative hospital-related cardiac morbidity after radiation therapy was estimated for left- and right-sided cases using a competing risk approach. Results: The median follow-up was 13.2 years. For left-sided cases, 485 women were treated with CF-WBI, and 2221 women were treated with HF-WBI. Mastectomy was more common in the HF-WBI group, whereas boost was more common in the CF-WBI group. The CF-WBI group had a higher prevalence of diabetes. The 15-year cumulative hospital-related morbidity from cardiac causes (95% confidence interval) was not different between the 2 radiation therapy regimens after propensity-score adjustment: 21% (19-22) with HF-WBI and 21% (17-25) with CF-WBI (P=.93). For right-sided cases, the 15-year cumulative hospital-related morbidity from cardiac causes was also similar between the radiation therapy groups (P=.76). Conclusions: There is no difference in morbidity leading to hospitalization from cardiac causes among women with left-sided early-stage breast

  2. Adjuvant Hypofractionated Versus Conventional Whole Breast Radiation Therapy for Early-Stage Breast Cancer: Long-Term Hospital-Related Morbidity From Cardiac Causes

    Energy Technology Data Exchange (ETDEWEB)

    Chan, Elisa K. [Department of Oncology, Saint John Regional Hospital, Saint John (Canada); Woods, Ryan; McBride, Mary L. [Cancer Control Research Department, BC Cancer Agency, Vancouver (Canada); Virani, Sean [Division of Cardiology, University of British Columbia, Vancouver (Canada); Nichol, Alan [Radiation Therapy Program, BC Cancer Agency, Vancouver (Canada); Speers, Caroline [Breast Cancer Outcomes Unit, BC Cancer Agency, Vancouver (Canada); Wai, Elaine S. [Radiation Therapy Program, BC Cancer Agency, Vancouver (Canada); Tyldesley, Scott, E-mail: styldesl@bccancer.bc.ca [Radiation Therapy Program, BC Cancer Agency, Vancouver (Canada)

    2014-03-15

    Purpose: The risk of cardiac injury with hypofractionated whole-breast/chest wall radiation therapy (HF-WBI) compared with conventional whole-breast/chest wall radiation therapy (CF-WBI) in women with left-sided breast cancer remains a concern. The purpose of this study was to determine if there is an increase in hospital-related morbidity from cardiac causes with HF-WBI relative to CF-WBI. Methods and Materials: Between 1990 and 1998, 5334 women ≤80 years of age with early-stage breast cancer were treated with postoperative radiation therapy to the breast or chest wall alone. A population-based database recorded baseline patient, tumor, and treatment factors. Hospital administrative records identified baseline cardiac risk factors and other comorbidities. Factors between radiation therapy groups were balanced using a propensity-score model. The first event of a hospital admission for cardiac causes after radiation therapy was determined from hospitalization records. Ten- and 15-year cumulative hospital-related cardiac morbidity after radiation therapy was estimated for left- and right-sided cases using a competing risk approach. Results: The median follow-up was 13.2 years. For left-sided cases, 485 women were treated with CF-WBI, and 2221 women were treated with HF-WBI. Mastectomy was more common in the HF-WBI group, whereas boost was more common in the CF-WBI group. The CF-WBI group had a higher prevalence of diabetes. The 15-year cumulative hospital-related morbidity from cardiac causes (95% confidence interval) was not different between the 2 radiation therapy regimens after propensity-score adjustment: 21% (19-22) with HF-WBI and 21% (17-25) with CF-WBI (P=.93). For right-sided cases, the 15-year cumulative hospital-related morbidity from cardiac causes was also similar between the radiation therapy groups (P=.76). Conclusions: There is no difference in morbidity leading to hospitalization from cardiac causes among women with left-sided early-stage breast

  3. Neonatal Informatics: Transforming Neonatal Care Through Translational Bioinformatics

    Science.gov (United States)

    Palma, Jonathan P.; Benitz, William E.; Tarczy-Hornoch, Peter; Butte, Atul J.; Longhurst, Christopher A.

    2012-01-01

    The future of neonatal informatics will be driven by the availability of increasingly vast amounts of clinical and genetic data. The field of translational bioinformatics is concerned with linking and learning from these data and applying new findings to clinical care to transform the data into proactive, predictive, preventive, and participatory health. As a result of advances in translational informatics, the care of neonates will become more data driven, evidence based, and personalized. PMID:22924023

  4. BIRCH: A user-oriented, locally-customizable, bioinformatics system

    Science.gov (United States)

    Fristensky, Brian

    2007-01-01

    Background Molecular biologists need sophisticated analytical tools which often demand extensive computational resources. While finding, installing, and using these tools can be challenging, pipelining data from one program to the next is particularly awkward, especially when using web-based programs. At the same time, system administrators tasked with maintaining these tools do not always appreciate the needs of research biologists. Results BIRCH (Biological Research Computing Hierarchy) is an organizational framework for delivering bioinformatics resources to a user group, scaling from a single lab to a large institution. The BIRCH core distribution includes many popular bioinformatics programs, unified within the GDE (Genetic Data Environment) graphic interface. Of equal importance, BIRCH provides the system administrator with tools that simplify the job of managing a multiuser bioinformatics system across different platforms and operating systems. These include tools for integrating locally-installed programs and databases into BIRCH, and for customizing the local BIRCH system to meet the needs of the user base. BIRCH can also act as a front end to provide a unified view of already-existing collections of bioinformatics software. Documentation for the BIRCH and locally-added programs is merged in a hierarchical set of web pages. In addition to manual pages for individual programs, BIRCH tutorials employ step by step examples, with screen shots and sample files, to illustrate both the important theoretical and practical considerations behind complex analytical tasks. Conclusion BIRCH provides a versatile organizational framework for managing software and databases, and making these accessible to a user base. Because of its network-centric design, BIRCH makes it possible for any user to do any task from anywhere. PMID:17291351

  5. A Quick Guide for Building a Successful Bioinformatics Community

    Science.gov (United States)

    Budd, Aidan; Corpas, Manuel; Brazas, Michelle D.; Fuller, Jonathan C.; Goecks, Jeremy; Mulder, Nicola J.; Michaut, Magali; Ouellette, B. F. Francis; Pawlik, Aleksandra; Blomberg, Niklas

    2015-01-01

    “Scientific community” refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role in many bioinformatics activities. Communities may be linked to a specific location or institute, or involve people working at many different institutions and locations. Education and training is typically an important component of these communities, providing a valuable context in which to develop skills and expertise, while also strengthening links and relationships within the community. Scientific communities facilitate: (i) the exchange and development of ideas and expertise; (ii) career development; (iii) coordinated funding activities; (iv) interactions and engagement with professionals from other fields; and (v) other activities beneficial to individual participants, communities, and the scientific field as a whole. It is thus beneficial at many different levels to understand the general features of successful, high-impact bioinformatics communities; how individual participants can contribute to the success of these communities; and the role of education and training within these communities. We present here a quick guide to building and maintaining a successful, high-impact bioinformatics community, along with an overview of the general benefits of participating in such communities. This article grew out of contributions made by organizers, presenters, panelists, and other participants of the ISMB/ECCB 2013 workshop “The ‘How To Guide’ for Establishing a Successful Bioinformatics Network” at the 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 12th European Conference on Computational Biology (ECCB). PMID:25654371

  6. Kubernetes as an approach for solving bioinformatic problems.

    OpenAIRE

    Markstedt, Olof

    2017-01-01

    The cluster orchestration tool Kubernetes enables easy deployment and reproducibility of life science research by utilizing the advantages of the container technology. The container technology allows for easy tool creation, sharing and runs on any Linux system once it has been built. The applicability of Kubernetes as an approach to run bioinformatic workflows was evaluated and resulted in some examples of how Kubernetes and containers could be used within the field of life science and how th...

  7. BIRCH: A user-oriented, locally-customizable, bioinformatics system

    Directory of Open Access Journals (Sweden)

    Fristensky Brian

    2007-02-01

    Full Text Available Abstract Background Molecular biologists need sophisticated analytical tools which often demand extensive computational resources. While finding, installing, and using these tools can be challenging, pipelining data from one program to the next is particularly awkward, especially when using web-based programs. At the same time, system administrators tasked with maintaining these tools do not always appreciate the needs of research biologists. Results BIRCH (Biological Research Computing Hierarchy is an organizational framework for delivering bioinformatics resources to a user group, scaling from a single lab to a large institution. The BIRCH core distribution includes many popular bioinformatics programs, unified within the GDE (Genetic Data Environment graphic interface. Of equal importance, BIRCH provides the system administrator with tools that simplify the job of managing a multiuser bioinformatics system across different platforms and operating systems. These include tools for integrating locally-installed programs and databases into BIRCH, and for customizing the local BIRCH system to meet the needs of the user base. BIRCH can also act as a front end to provide a unified view of already-existing collections of bioinformatics software. Documentation for the BIRCH and locally-added programs is merged in a hierarchical set of web pages. In addition to manual pages for individual programs, BIRCH tutorials employ step by step examples, with screen shots and sample files, to illustrate both the important theoretical and practical considerations behind complex analytical tasks. Conclusion BIRCH provides a versatile organizational framework for managing software and databases, and making these accessible to a user base. Because of its network-centric design, BIRCH makes it possible for any user to do any task from anywhere.

  8. p3d--Python module for structural bioinformatics.

    Science.gov (United States)

    Fufezan, Christian; Specht, Michael

    2009-08-21

    High-throughput bioinformatic analysis tools are needed to mine the large amount of structural data via knowledge based approaches. The development of such tools requires a robust interface to access the structural data in an easy way. For this the Python scripting language is the optimal choice since its philosophy is to write an understandable source code. p3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files). p3d's strength arises from the combination of a) very fast spatial access to the structural data due to the implementation of a binary space partitioning (BSP) tree, b) set theory and c) functions that allow to combine a and b and that use human readable language in the search queries rather than complex computer language. All these factors combined facilitate the rapid development of bioinformatic tools that can perform quick and complex analyses of protein structures. p3d is the perfect tool to quickly develop tools for structural bioinformatics using the Python scripting language.

  9. p3d – Python module for structural bioinformatics

    Directory of Open Access Journals (Sweden)

    Fufezan Christian

    2009-08-01

    Full Text Available Abstract Background High-throughput bioinformatic analysis tools are needed to mine the large amount of structural data via knowledge based approaches. The development of such tools requires a robust interface to access the structural data in an easy way. For this the Python scripting language is the optimal choice since its philosophy is to write an understandable source code. Results p3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files. p3d's strength arises from the combination of a very fast spatial access to the structural data due to the implementation of a binary space partitioning (BSP tree, b set theory and c functions that allow to combine a and b and that use human readable language in the search queries rather than complex computer language. All these factors combined facilitate the rapid development of bioinformatic tools that can perform quick and complex analyses of protein structures. Conclusion p3d is the perfect tool to quickly develop tools for structural bioinformatics using the Python scripting language.

  10. mORCA: sailing bioinformatics world with mobile devices.

    Science.gov (United States)

    Díaz-Del-Pino, Sergio; Falgueras, Juan; Perez-Wohlfeil, Esteban; Trelles, Oswaldo

    2018-03-01

    Nearly 10 years have passed since the first mobile apps appeared. Given the fact that bioinformatics is a web-based world and that mobile devices are endowed with web-browsers, it seemed natural that bioinformatics would transit from personal computers to mobile devices but nothing could be further from the truth. The transition demands new paradigms, designs and novel implementations. Throughout an in-depth analysis of requirements of existing bioinformatics applications we designed and deployed an easy-to-use web-based lightweight mobile client. Such client is able to browse, select, compose automatically interface parameters, invoke services and monitor the execution of Web Services using the service's metadata stored in catalogs or repositories. mORCA is available at http://bitlab-es.com/morca/app as a web-app. It is also available in the App store by Apple and Play Store by Google. The software will be available for at least 2 years. ortrelles@uma.es. Source code, final web-app, training material and documentation is available at http://bitlab-es.com/morca. © The Author(s) 2017. Published by Oxford University Press.

  11. Bioinformatics analysis and detection of gelatinase encoded gene in Lysinibacillussphaericus

    Science.gov (United States)

    Repin, Rul Aisyah Mat; Mutalib, Sahilah Abdul; Shahimi, Safiyyah; Khalid, Rozida Mohd.; Ayob, Mohd. Khan; Bakar, Mohd. Faizal Abu; Isa, Mohd Noor Mat

    2016-11-01

    In this study, we performed bioinformatics analysis toward genome sequence of Lysinibacillussphaericus (L. sphaericus) to determine gene encoded for gelatinase. L. sphaericus was isolated from soil and gelatinase species-specific bacterium to porcine and bovine gelatin. This bacterium offers the possibility of enzymes production which is specific to both species of meat, respectively. The main focus of this research is to identify the gelatinase encoded gene within the bacteria of L. Sphaericus using bioinformatics analysis of partially sequence genome. From the research study, three candidate gene were identified which was, gelatinase candidate gene 1 (P1), NODE_71_length_93919_cov_158.931839_21 which containing 1563 base pair (bp) in size with 520 amino acids sequence; Secondly, gelatinase candidate gene 2 (P2), NODE_23_length_52851_cov_190.061386_17 which containing 1776 bp in size with 591 amino acids sequence; and Thirdly, gelatinase candidate gene 3 (P3), NODE_106_length_32943_cov_169.147919_8 containing 1701 bp in size with 566 amino acids sequence. Three pairs of oligonucleotide primers were designed and namely as, F1, R1, F2, R2, F3 and R3 were targeted short sequences of cDNA by PCR. The amplicons were reliably results in 1563 bp in size for candidate gene P1 and 1701 bp in size for candidate gene P3. Therefore, the results of bioinformatics analysis of L. Sphaericus resulting in gene encoded gelatinase were identified.

  12. KBWS: an EMBOSS associated package for accessing bioinformatics web services.

    Science.gov (United States)

    Oshita, Kazuki; Arakawa, Kazuharu; Tomita, Masaru

    2011-04-29

    The availability of bioinformatics web-based services is rapidly proliferating, for their interoperability and ease of use. The next challenge is in the integration of these services in the form of workflows, and several projects are already underway, standardizing the syntax, semantics, and user interfaces. In order to deploy the advantages of web services with locally installed tools, here we describe a collection of proxy client tools for 42 major bioinformatics web services in the form of European Molecular Biology Open Software Suite (EMBOSS) UNIX command-line tools. EMBOSS provides sophisticated means for discoverability and interoperability for hundreds of tools, and our package, named the Keio Bioinformatics Web Service (KBWS), adds functionalities of local and multiple alignment of sequences, phylogenetic analyses, and prediction of cellular localization of proteins and RNA secondary structures. This software implemented in C is available under GPL from http://www.g-language.org/kbws/ and GitHub repository http://github.com/cory-ko/KBWS. Users can utilize the SOAP services implemented in Perl directly via WSDL file at http://soap.g-language.org/kbws.wsdl (RPC Encoded) and http://soap.g-language.org/kbws_dl.wsdl (Document/literal).

  13. Combining medical informatics and bioinformatics toward tools for personalized medicine.

    Science.gov (United States)

    Sarachan, B D; Simmons, M K; Subramanian, P; Temkin, J M

    2003-01-01

    Key bioinformatics and medical informatics research areas need to be identified to advance knowledge and understanding of disease risk factors and molecular disease pathology in the 21 st century toward new diagnoses, prognoses, and treatments. Three high-impact informatics areas are identified: predictive medicine (to identify significant correlations within clinical data using statistical and artificial intelligence methods), along with pathway informatics and cellular simulations (that combine biological knowledge with advanced informatics to elucidate molecular disease pathology). Initial predictive models have been developed for a pilot study in Huntington's disease. An initial bioinformatics platform has been developed for the reconstruction and analysis of pathways, and work has begun on pathway simulation. A bioinformatics research program has been established at GE Global Research Center as an important technology toward next generation medical diagnostics. We anticipate that 21 st century medical research will be a combination of informatics tools with traditional biology wet lab research, and that this will translate to increased use of informatics techniques in the clinic.

  14. KBWS: an EMBOSS associated package for accessing bioinformatics web services

    Directory of Open Access Journals (Sweden)

    Tomita Masaru

    2011-04-01

    Full Text Available Abstract The availability of bioinformatics web-based services is rapidly proliferating, for their interoperability and ease of use. The next challenge is in the integration of these services in the form of workflows, and several projects are already underway, standardizing the syntax, semantics, and user interfaces. In order to deploy the advantages of web services with locally installed tools, here we describe a collection of proxy client tools for 42 major bioinformatics web services in the form of European Molecular Biology Open Software Suite (EMBOSS UNIX command-line tools. EMBOSS provides sophisticated means for discoverability and interoperability for hundreds of tools, and our package, named the Keio Bioinformatics Web Service (KBWS, adds functionalities of local and multiple alignment of sequences, phylogenetic analyses, and prediction of cellular localization of proteins and RNA secondary structures. This software implemented in C is available under GPL from http://www.g-language.org/kbws/ and GitHub repository http://github.com/cory-ko/KBWS. Users can utilize the SOAP services implemented in Perl directly via WSDL file at http://soap.g-language.org/kbws.wsdl (RPC Encoded and http://soap.g-language.org/kbws_dl.wsdl (Document/literal.

  15. A comparison of common programming languages used in bioinformatics.

    Science.gov (United States)

    Fourment, Mathieu; Gillings, Michael R

    2008-02-05

    The performance of different programming languages has previously been benchmarked using abstract mathematical algorithms, but not using standard bioinformatics algorithms. We compared the memory usage and speed of execution for three standard bioinformatics methods, implemented in programs using one of six different programming languages. Programs for the Sellers algorithm, the Neighbor-Joining tree construction algorithm and an algorithm for parsing BLAST file outputs were implemented in C, C++, C#, Java, Perl and Python. Implementations in C and C++ were fastest and used the least memory. Programs in these languages generally contained more lines of code. Java and C# appeared to be a compromise between the flexibility of Perl and Python and the fast performance of C and C++. The relative performance of the tested languages did not change from Windows to Linux and no clear evidence of a faster operating system was found. Source code and additional information are available from http://www.bioinformatics.org/benchmark/. This benchmark provides a comparison of six commonly used programming languages under two different operating systems. The overall comparison shows that a developer should choose an appropriate language carefully, taking into account the performance expected and the library availability for each language.

  16. Best practices in bioinformatics training for life scientists.

    KAUST Repository

    Via, Allegra

    2013-06-25

    The mountains of data thrusting from the new landscape of modern high-throughput biology are irrevocably changing biomedical research and creating a near-insatiable demand for training in data management and manipulation and data mining and analysis. Among life scientists, from clinicians to environmental researchers, a common theme is the need not just to use, and gain familiarity with, bioinformatics tools and resources but also to understand their underlying fundamental theoretical and practical concepts. Providing bioinformatics training to empower life scientists to handle and analyse their data efficiently, and progress their research, is a challenge across the globe. Delivering good training goes beyond traditional lectures and resource-centric demos, using interactivity, problem-solving exercises and cooperative learning to substantially enhance training quality and learning outcomes. In this context, this article discusses various pragmatic criteria for identifying training needs and learning objectives, for selecting suitable trainees and trainers, for developing and maintaining training skills and evaluating training quality. Adherence to these criteria may help not only to guide course organizers and trainers on the path towards bioinformatics training excellence but, importantly, also to improve the training experience for life scientists.

  17. Bioinformatics process management: information flow via a computational journal

    Directory of Open Access Journals (Sweden)

    Lushington Gerald

    2007-12-01

    Full Text Available Abstract This paper presents the Bioinformatics Computational Journal (BCJ, a framework for conducting and managing computational experiments in bioinformatics and computational biology. These experiments often involve series of computations, data searches, filters, and annotations which can benefit from a structured environment. Systems to manage computational experiments exist, ranging from libraries with standard data models to elaborate schemes to chain together input and output between applications. Yet, although such frameworks are available, their use is not widespread–ad hoc scripts are often required to bind applications together. The BCJ explores another solution to this problem through a computer based environment suitable for on-site use, which builds on the traditional laboratory notebook paradigm. It provides an intuitive, extensible paradigm designed for expressive composition of applications. Extensive features facilitate sharing data, computational methods, and entire experiments. By focusing on the bioinformatics and computational biology domain, the scope of the computational framework was narrowed, permitting us to implement a capable set of features for this domain. This report discusses the features determined critical by our system and other projects, along with design issues. We illustrate the use of our implementation of the BCJ on two domain-specific examples.

  18. Human radiation studies: Remembering the early years. Oral history of Dr. George Voelz, M.D., November 29, 1994

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-05-01

    Dr. George Voelz was interviewed by representatives of the US DOE Office of Human Radiation Experiments (OHRE). This oral history covers Dr. Voelz`s research on Manhattan Engineering District plutonium workers, the acute and long term effects of radiation, his inhalation studies, and his activities at the 1961 INL reactor accident (SL-1 Reactor). After a brief biographical sketch, Dr. Voelz his remembrances on tissue studies of plutonium workers, the plutonium injection studies of 1945-1946, the controlled environmental radioiodine tests of 1963-1968, and tracer studies with human volunteers at Los Alamos. Dr. Voelz states his opinions concerning misconceptions about the Los Alamos Human Radiation Experiments.

  19. Human radiation studies: Remembering the early years. Oral history of Dr. George Voelz, M.D., November 29, 1994

    International Nuclear Information System (INIS)

    1995-05-01

    Dr. George Voelz was interviewed by representatives of the US DOE Office of Human Radiation Experiments (OHRE). This oral history covers Dr. Voelz's research on Manhattan Engineering District plutonium workers, the acute and long term effects of radiation, his inhalation studies, and his activities at the 1961 INL reactor accident (SL-1 Reactor). After a brief biographical sketch, Dr. Voelz his remembrances on tissue studies of plutonium workers, the plutonium injection studies of 1945-1946, the controlled environmental radioiodine tests of 1963-1968, and tracer studies with human volunteers at Los Alamos. Dr. Voelz states his opinions concerning misconceptions about the Los Alamos Human Radiation Experiments

  20. Reduction of the treated volume to involved node radiation therapy as part of combined modality treatment for early stage aggressive non-Hodgkin’s lymphoma

    International Nuclear Information System (INIS)

    Verhappen, Marieke H.; Poortmans, Philip M.P.; Raaijmakers, Esther; Raemaekers, John M.M.

    2013-01-01

    Background and purpose: This retrospective study investigated whether focused involved node radiation therapy (INRT) can safely replace involved field RT (IFRT) in patients with early stage aggressive NHL. Patients and methods: We included 258 patients with stage I/II aggressive NHL who received combined modality treatment (87%) or primary RT alone (13%). RT consisted of a total dose of 30–40 Gy in 15–20 fractions IFRT or INRT. We compared survival, relapse pattern, radiation-related toxicity and quality of life for both RT techniques. Results: Type of RT was not related to the outcome in either the uni- or multivariate survival analysis. Relapses developed in 59 of 252 patients (23%) of which 47 (80%) were documented as distant recurrence only. Failure of the INRT technique was noted in one patient. There was no significant difference in acute radiation-related toxicity between RT-groups but IFRT showed a significantly higher incidence of higher grade toxicities. Patients treated with INRT had a significantly better physical functioning and global quality of life compared to the IFRT group. Conclusions: Given the retrospective nature of this study, no solid conclusions can be drawn. However, in view of the equivalent efficacy and more favorable toxicity profile, the replacement of IFRT by INRT in combination with chemo-(immuno)-therapy looks very attractive for patients with early stage aggressive NHL

  1. A reappraisal of the reported dose equivalents at the boundary of the University of California Radiation Laboratory during the early days of Bevatron operation

    International Nuclear Information System (INIS)

    Thomas, Ralph H.; Smith, Alan R.; Zeman, Gary H.

    2000-01-01

    Accelerator-produced radiation levels at the perimeter of the Ernest Orlando Lawrence Berkeley National Laboratory (the Berkeley Laboratory) reached a maximum in 1959. Neutrons produced by the Bevatron were the dominant component of the radiation field. Radiation levels were estimated from measurements of total neutron fluence and reported in units of dose equivalent (rem). Accurate conversion from total fluence to dose equivalent demands knowledge of both the energy spectrum of accelerator-produced neutrons and the appropriate conversion coefficient functions for different irradiation geometries. At that time (circa 1960), such information was limited, and it was necessary to use judgment in the interpretation of measured data. The Health Physics Group of the Berkeley Laboratory used the best data then available and, as a matter of policy, reported the most conservative (largest) values of dose equivalent supported by their data. Since the early sixties, significant improvements in the information required to compute dose equivalent, particularly in the case of conversion coefficients, have been reported in the scientific literature. This paper reinterprets the older neutron measurements using the best conversion coefficient data available today. It is concluded that the dose equivalents reported in the early sixties would be reduced by at least a factor of two using current methods of analysis

  2. γ-H2AX foci analysis in human lymphocytes: a biological tool for assessment of early triage during mass exposure of radiation

    International Nuclear Information System (INIS)

    Nayak, Akshay Kumar A.; Mumbrekar, Kamalesh D.; Satish Rao, B.S.

    2014-01-01

    Emergence of nuclear terrorism and increased use of nuclear technology for industry, energy production, and defence purpose has also increased the risk of mass exposure to radiation. During these scenarios of mass exposure to radiation, an efficient system which would measure the dose absorbed by an individual is required for early triage management. The present study aims to establish γ-H2AX as a biomarker for management of early triage. Radiation induced DNA DSB studied in lymphocytes isolated from 10 healthy individuals and challenged with 2 Gy of X-rays in vitro showed a gradual decrease in number of foci signals. As the persistence of foci signals is important for biodosimetry, phosphatase inhibitors like Calyculin A, Fostriecin and Okadiac Acid were used. Calyculin A was found to be the better inhibitor showing a 2 fold increase in retention of foci signals at 6 hours. The dose response curve was performed in lymphocytes isolated from healthy individuals by fluorescent microscopy and flow cytometry. Although both the methods indicated a linear increase in foci signals, microscopic analysis was found to be more sensitive. Influence of age and gender on dose response curve was studied and no significant difference was found. The effect of confounding factors like genetic factors and smoking habits on the dose response curve is being investigated. (author)

  3. Dosimetric and Clinical Outcomes With Intensity Modulated Radiation Therapy After Chemotherapy for Patients With Early-Stage Diffuse Large B-cell Lymphoma of Waldeyer Ring

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Yong-Gang; Qi, Shu-Nan; Wang, Shu-Lian; Liu, Yue-Ping; Wang, Wei-Hu; Jin, Jing; Song, Yong-Wen; Ren, Hua; Fang, Hui [Department of Radiation Oncology, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (China); He, Xiao-Hui; Dong, Mei [Department of Medical Oncology, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (China); Chen, Bo; Lu, Ning-Ning; Li, Ning; Tang, Yuan; Tang, Yu; Dai, Jian-Rong [Department of Radiation Oncology, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (China); Li, Ye-Xiong, E-mail: yexiong12@163.com [Department of Radiation Oncology, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (China)

    2016-10-01

    Purpose: To assess the dosimetric benefit, prognosis, and toxicity of intensity modulated radiation therapy (IMRT) for early-stage, diffuse large B-cell lymphoma of Waldeyer ring (WR-DLBCL). Methods and Materials: Sixty-one patients with early-stage WR-DLBCL who received chemotherapy followed by IMRT were retrospectively reviewed. Dosimetric parameters for the target volume and critical normal structures were evaluated, and survival was calculated. Linear regression analysis was used to assess the effect of the mean dose (D{sub mean}) to the parotid glands on xerostomia. Results: The median conformity index and homogeneity index of the planning target volume (PTV) were 0.83 and 0.90, respectively, demonstrating very good coverage of the target volume. The mean dose to the parotid glands was 24.9 Gy. The 5-year overall survival (OS), progression-free survival (PFS), and locoregional control (LRC) were 94.7%, 93.1%, and 98.3%, respectively. Early and late toxicities were mild, and no patient experienced late grade ≥3 toxicities. The D{sub mean} to the parotid glands had a linear correlation with late grade ≥2 xerostomia. Conclusions: IMRT after chemotherapy can provide excellent dose conformity and achieve favorable survival and LRC with mild toxicities in patients with early-stage WR-DLBCL. Dose constraints for the parotid glands should be limited to <24 Gy for early-stage WR-DLBCL.

  4. MicroRNA-Related DNA Repair/Cell-Cycle Genes Independently Associated With Relapse After Radiation Therapy for Early Breast Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Gee, Harriet E., E-mail: harriet.gee@sydney.edu.au [The Kinghorn Cancer Centre & Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW (Australia); The Chris O' Brien Lifehouse, Missenden Road, Camperdown, NSW (Australia); Central Clinical School, Sydney Medical School, University of Sydney, NSW (Australia); Buffa, Francesca M.; Harris, Adrian L. [Department of Medical Oncology, The University of Oxford, Oxford (United Kingdom); Toohey, Joanne M.; Carroll, Susan L. [The Chris O' Brien Lifehouse, Missenden Road, Camperdown, NSW (Australia); Cooper, Caroline L. [Central Clinical School, Sydney Medical School, University of Sydney, NSW (Australia); Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW (Australia); Beith, Jane [The Chris O' Brien Lifehouse, Missenden Road, Camperdown, NSW (Australia); McNeil, Catriona [The Kinghorn Cancer Centre & Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW (Australia); The Chris O' Brien Lifehouse, Missenden Road, Camperdown, NSW (Australia); Carmalt, Hugh; Mak, Cindy; Warrier, Sanjay [The Chris O' Brien Lifehouse, Missenden Road, Camperdown, NSW (Australia); Holliday, Anne [The Kinghorn Cancer Centre & Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW (Australia); Selinger, Christina; Beckers, Rhiannon [Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW (Australia); Kennedy, Catherine [Central Clinical School, Sydney Medical School, University of Sydney, NSW (Australia); Graham, Peter [Department of Radiation Oncology, Cancer Care Centre, St. George Hospital, Kogarah, NSW (Australia); Swarbrick, Alexander [The Kinghorn Cancer Centre & Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW (Australia); St Vincent' s Clinical School, Faculty of Medicine, University of NSW, Kensington, NSW (Australia); and others

    2015-12-01

    Purpose: Local recurrence and distant failure after adjuvant radiation therapy for breast cancer remain significant clinical problems, incompletely predicted by conventional clinicopathologic markers. We had previously identified microRNA-139-5p and microRNA-1274a as key regulators of breast cancer radiation response in vitro. The purpose of this study was to investigate standard clinicopathologic markers of local recurrence in a contemporary series and to establish whether putative target genes of microRNAs involved in DNA repair and cell cycle control could better predict radiation therapy response in vivo. Methods and Materials: With institutional ethics board approval, local recurrence was measured in a contemporary, prospectively collected series of 458 patients treated with radiation therapy after breast-conserving surgery. Additionally, independent publicly available mRNA/microRNA microarray expression datasets totaling >1000 early-stage breast cancer patients, treated with adjuvant radiation therapy, with >10 years of follow-up, were analyzed. The expression of putative microRNA target biomarkers—TOP2A, POLQ, RAD54L, SKP2, PLK2, and RAG1—were correlated with standard clinicopathologic variables using 2-sided nonparametric tests, and to local/distant relapse and survival using Kaplan-Meier and Cox regression analysis. Results: We found a low rate of isolated local recurrence (1.95%) in our modern series, and that few clinicopathologic variables (such as lymphovascular invasion) were significantly predictive. In multiple independent datasets (n>1000), however, high expression of RAD54L, TOP2A, POLQ, and SKP2 significantly correlated with local recurrence, survival, or both in univariate and multivariate analyses (P<.001). Low RAG1 expression significantly correlated with local recurrence (multivariate, P=.008). Additionally, RAD54L, SKP2, and PLK2 may be predictive, being prognostic in radiation therapy–treated patients but not in untreated matched

  5. The Austrian system for the measurement of environmental radioactivity (ASMER) and the Austrian early radiation warning system (AERWS)

    International Nuclear Information System (INIS)

    Henrich, E.

    1988-01-01

    The two systems of environment radiation measurements complement each other. ASMER does a detailed, quantitative and nuclide specific analysis of the contaminations in the environment. AERWS's aim is to alarm the authorities in case of accident. It is aimed at higher radiation levels is not nuclide specific but quick. A short description is given of the organisations concerned, the procedures used and items surveyed by the two networks. 8 refs., 19 figs. (qui)

  6. Human radiation studies: Remembering the early years: Oral history of radiologist Hymer L. Friedell, M.D., Ph.D., conducted January 28, 1995

    International Nuclear Information System (INIS)

    Fisher, D.; Melamed, E.

    1995-07-01

    NThis report is a transcript of an interview with Hymer L. Friedell by representatives of the US DOE Office of Human Radiation Experiments. Dr. Friedell was selected for this interview because of his participation in the early stages of the medical use of radioisotopes, his important role in the Manhattan Engineer District Medical Division, and his distinguished medical career and his involvement in the distribution of isotopes and the approval for their use in humans. After a brief biographical sketch Dr. Friedell discusses his remembrances on a wide range of subjects. Topics discussed include pre-war radiation therapy, information provided to patients, the Army Medical Corps and the Manhattan Project, his work at the Chicago Metallurgical Laboratory, inspection visits of Manhattan Project facilities and proposed sites, Plutonium injection studies, and actions of the AEC Isotope Distribution Committee

  7. Modeling of the topology of energy deposits created by ionizing radiation on a nano-metric scale in cell nuclei in relation to radiation-induced early events

    International Nuclear Information System (INIS)

    Dos Santos, Morgane

    2013-01-01

    Ionizing radiations are known to induce critical damages on biological matter and especially on DNA. Among these damages, DNA double strand breaks (DSB) are considered as key precursor of lethal effects of ionizing radiations. Understand and predict how DNA double and simple strand breaks are created by ionizing radiation and repaired in cell nucleus is nowadays a major challenge in radiobiology research. This work presents the results on the simulation of the DNA double strand breaks produced from the energy deposited by the irradiation at the intracellular level. At the nano-metric scale, the only method to accurately simulate the topological details of energy deposited on the biological matter is the use of Monte Carlo codes. In this work, we used the Geant4 Monte Carlo code and, in particular, the low energy electromagnetic package extensions, referred as Geant4-DNA processes.In order to evaluate DNA radio-induced damages, the first objective of this work consisted in implementing a detailed geometry of the DNA on the Monte Carlo simulations. Two types of cell nuclei, representing a fibroblast and an endothelium, were described in order to evaluate the influence of the DNA density on the topology of the energy deposits contributing to strand breaks. Indeed, the implemented geometry allows the selection of energy transfer points that can lead to strand breaks because they are located on the backbone. Then, these energy transfer points were analysed with a clustering algorithm in order to reveal groups of aggregates and to study their location and complexity. In this work, only the physical interactions of ionizing radiations are simulated. Thus, it is not possible to achieve an absolute number of strand breaks as the creation and transportation of radical species which could lead to indirect DNA damages is not included. Nevertheless, the aim of this work was to evaluate the relative dependence of direct DNA damages with the DNA density, radiation quality, cell

  8. The effect of pentoxifylline on early and late radiation injury following fractionated irradiation in C3H mice

    Energy Technology Data Exchange (ETDEWEB)

    Dion, M.W.; Hussey, D.H.; Osborne, J.W.

    1989-07-01

    An experiment was performed to test the effectiveness of pentoxifylline in reducing late radiation injury. One hundred and four C3H mice were randomized into eight groups of 13 mice each, and the right hind limbs were irradiated with 4000, 5000, 6000, or 7000 cGy in ten fractions. Each group was treated with once daily injections of either pentoxifylline or saline for 30+ weeks. An additional ten mice received daily injections of pentoxifylline or saline, but no irradiation. The pentoxifylline animals demonstrated significantly less late injury than the saline treated animals. The most obvious differences were observed in the 5000 and 6000 cGy groups. There were seven radiation related deaths in the saline treated control groups, but only one radiation related death in the pentoxifylline treated groups. Whereas 42% (20/48) of the saline treated animals had a late injury score of 3.0 or greater, only 8% (4/51) of the pentoxifylline treated animals had a late skin score as high as 3.0. Pentoxifylline had no effect on the acute radiation injury scores. The drug was well tolerated with no toxic effects noted. Pentoxifylline is a methyl xanthine derivative that is used to treat vascular occlusive disease in humans. It improves perfusion through small capillaries by improving the deformability of red blood cells, inhibiting platelet aggregation, and stimulating the release of prostacyclin. This study shows that the prophylactic administration of pentoxifylline can modify late radiation induced injury in the mouse extremity. It may have value in the prevention or treatment of late radiation induced injury in humans, and it could be a useful tool to help define the mechanisms of late radiation injury in specific organs.

  9. The effect of pentoxifylline on early and late radiation injury following fractionated irradiation in C3H mice

    International Nuclear Information System (INIS)

    Dion, M.W.; Hussey, D.H.; Osborne, J.W.

    1989-01-01

    An experiment was performed to test the effectiveness of pentoxifylline in reducing late radiation injury. One hundred and four C3H mice were randomized into eight groups of 13 mice each, and the right hind limbs were irradiated with 4000, 5000, 6000, or 7000 cGy in ten fractions. Each group was treated with once daily injections of either pentoxifylline or saline for 30+ weeks. An additional ten mice received daily injections of pentoxifylline or saline, but no irradiation. The pentoxifylline animals demonstrated significantly less late injury than the saline treated animals. The most obvious differences were observed in the 5000 and 6000 cGy groups. There were seven radiation related deaths in the saline treated control groups, but only one radiation related death in the pentoxifylline treated groups. Whereas 42% (20/48) of the saline treated animals had a late injury score of 3.0 or greater, only 8% (4/51) of the pentoxifylline treated animals had a late skin score as high as 3.0. Pentoxifylline had no effect on the acute radiation injury scores. The drug was well tolerated with no toxic effects noted. Pentoxifylline is a methyl xanthine derivative that is used to treat vascular occlusive disease in humans. It improves perfusion through small capillaries by improving the deformability of red blood cells, inhibiting platelet aggregation, and stimulating the release of prostacyclin. This study shows that the prophylactic administration of pentoxifylline can modify late radiation induced injury in the mouse extremity. It may have value in the prevention or treatment of late radiation induced injury in humans, and it could be a useful tool to help define the mechanisms of late radiation injury in specific organs

  10. The early summertime Saharan heat low: sensitivity of the radiation budget and atmospheric heating to water vapour and dust aerosol

    Science.gov (United States)

    Alamirew, Netsanet K.; Todd, Martin C.; Ryder, Claire L.; Marsham, John H.; Wang, Yi

    2018-01-01

    The Saharan heat low (SHL) is a key component of the west African cli