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. 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

  6. Proteomics and bioinformatics analysis of altered protein expression in the placental villous tissue from early recurrent miscarriage patients.

    Science.gov (United States)

    Pan, Hai-Tao; Ding, Hai-Gang; Fang, Min; Yu, Bin; Cheng, Yi; Tan, Ya-Jing; Fu, Qi-Qin; Lu, Bo; Cai, Hong-Guang; Jin, Xin; Xia, Xian-Qing; Zhang, Tao

    2018-01-01

    Recurrent miscarriage (RM) affects 5% of women, it has an adverse emotional impact on women. Because of the complexities of early development, the mechanism of recurrent miscarriage is still unclear. We hypothesized that abnormal placenta leads to early recurrent miscarriage (ERM). The aim of this study was to identify ERM associated factors in human placenta villous tissue using proteomics. Investigation of these differences in protein expression in parallel profiling is essential to understand the comprehensive pathophysiological mechanism underlying recurrent miscarriage (RM). To gain more insight into mechanisms of recurrent miscarriage (RM), a comparative proteome profile of the human placenta villous tissue in normal and RM pregnancies was analyzed using iTRAQ technology and bioinformatics analysis used by Ingenuity Pathway Analysis (IPA) software. In this study, we employed an iTRAQ based proteomics analysis of four placental villous tissues from patients with early recurrent miscarriage (ERM) and four from normal pregnant women. Finally, we identified 2805 proteins and 79,998 peptides between patients with RM and normal matched group. Further analysis identified 314 differentially expressed proteins in placental villous tissue (≥1.3-fold, Student's t-test, p embryo. Furthermore, network analysis show that Angiotensinogen (AGT), MAPK14 and Prothrombin (F2) are core factors in early embryonic development. We used another 8 independent samples (4 cases and 4 controls) to cross validation of the proteomic data. This study has identified several proteins that are associated with early development, these results may supply new insight into mechanisms behind recurrent miscarriage. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. 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

  8. 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)

  9. Early-delayed radiation rhombencephalopathy

    Energy Technology Data Exchange (ETDEWEB)

    Nightingale, S.; Dawes, P.J.D.K.; Cartlidge, N.E.F. (Royal Victoria Infirmary, Newcastle upon Tyne (UK); Newcastle upon Tyne Univ. (UK). Newcastle General Hospital)

    1982-03-01

    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.

  10. Early radiographic changes in radiation bone injury

    Energy Technology Data Exchange (ETDEWEB)

    Fujita, M.; Tanimoto, K.; Wada, T.

    1986-06-01

    A chronologic series of periapical radiographs was evaluated for the purpose of detecting damage to bone and tooth-supporting tissues in a patient receiving radiation therapy for a basal cell carcinoma of the mandibular gingiva. Widening of the periodontal space was one of the early radiographic changes observed. It is suggested, from the sequence of radiographic changes, that radiation-induced changed in the circulatory system of the bone might be primarily responsible for the resulting changes.

  11. Early radiographic changes in radiation bone injury

    International Nuclear Information System (INIS)

    Fujita, M.; Tanimoto, K.; Wada, T.

    1986-01-01

    A chronologic series of periapical radiographs was evaluated for the purpose of detecting damage to bone and tooth-supporting tissues in a patient receiving radiation therapy for a basal cell carcinoma of the mandibular gingiva. Widening of the periodontal space was one of the early radiographic changes observed. It is suggested, from the sequence of radiographic changes, that radiation-induced changed in the circulatory system of the bone might be primarily responsible for the resulting changes

  12. 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.

  13. Aptamer Bioinformatics

    Directory of Open Access Journals (Sweden)

    Andrew B. Kinghorn

    2017-11-01

    Full Text Available Aptamers are short nucleic acid sequences capable of specific, high-affinity molecular binding. They are isolated via SELEX (Systematic Evolution of Ligands by Exponential Enrichment, an evolutionary process that involves iterative rounds of selection and amplification before sequencing and aptamer characterization. As aptamers are genetic in nature, bioinformatic approaches have been used to improve both aptamers and their selection. This review will discuss the advancements made in several enclaves of aptamer bioinformatics, including simulation of aptamer selection, fragment-based aptamer design, patterning of libraries, identification of lead aptamers from high-throughput sequencing (HTS data and in silico aptamer optimization.

  14. 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.

  15. 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].

  16. The origin and early radiation of dinosaurs

    Science.gov (United States)

    Brusatte, Stephen L.; Nesbitt, Sterling J.; Irmis, Randall B.; Butler, Richard J.; Benton, Michael J.; Norell, Mark A.

    2010-07-01

    Dinosaurs were remarkably successful during the Mesozoic and one subgroup, birds, remain an important component of modern ecosystems. Although the extinction of non-avian dinosaurs at the end of the Cretaceous has been the subject of intense debate, comparatively little attention has been given to the origin and early evolution of dinosaurs during the Late Triassic and Early Jurassic, one of the most important evolutionary radiations in earth history. Our understanding of this keystone event has dramatically changed over the past 25 years, thanks to an influx of new fossil discoveries, reinterpretations of long-ignored specimens, and quantitative macroevolutionary analyses that synthesize anatomical and geological data. Here we provide an overview of the first 50 million years of dinosaur history, with a focus on the large-scale patterns that characterize the ascent of dinosaurs from a small, almost marginal group of reptiles in the Late Triassic to the preeminent terrestrial vertebrates of the Jurassic and Cretaceous. We provide both a biological and geological background for early dinosaur history. Dinosaurs are deeply nested among the archosaurian reptiles, diagnosed by only a small number of characters, and are subdivided into a number of major lineages. The first unequivocal dinosaurs are known from the late Carnian of South America, but the presence of their sister group in the Middle Triassic implies that dinosaurs possibly originated much earlier. The three major dinosaur lineages, theropods, sauropodomorphs, and ornithischians, are all known from the Triassic, when continents were joined into the supercontinent Pangaea and global climates were hot and arid. Although many researchers have long suggested that dinosaurs outcompeted other reptile groups during the Triassic, we argue that the ascent of dinosaurs was more of a matter of contingency and opportunism. Dinosaurs were overshadowed in most Late Triassic ecosystems by crocodile-line archosaurs and

  17. 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)

  18. 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)

  19. Radiation detection and wireless networked early warning

    Science.gov (United States)

    Burns, David A.; Litz, Marc S.; Carroll, James J.; Katsis, Dimosthenis

    2012-06-01

    We have designed a compact, wireless, GPS-enabled array of inexpensive radiation sensors based on scintillation counting. Each sensor has a scintillator, photomultiplier tube, and pulse-counting circuit that includes a comparator, digital potentiometer and microcontroller. This design provides a high level of sensitivity and reliability. A 0.2 m2 PV panel powers each sensor providing a maintenance-free 24/7 energy source. The sensor can be mounted within a roadway light-post and monitor radiological activity along transport routes. Each sensor wirelessly transmits real-time data (as counts per second) up to 2 miles with a XBee radio module, and the data is received by a XBee receive-module on a computer. Data collection software logs the information from all sensors and provides real-time identification of radiation events. Measurements performed to-date demonstrate the ability of a sensor to detect a 20 μCi source at 3.5 meters when packaged with a PVT (plastic) scintillator, and 7 meters for a sensor with a CsI crystal (more expensive but ~5 times more sensitive). It is calculated that the sensor-architecture can detect sources moving as fast as 130 km/h based on the current data rate and statistical bounds of 3-sigma threshold detection. The sensor array is suitable for identifying and tracking a radiation threat from a dirty bomb along roadways.

  20. Design And Construction Of Early Warning Environmental Radiation Monitoring Station

    International Nuclear Information System (INIS)

    Early Warning Environmental Radiation Monitoring Station, used ONLINE environmental radiation monitoring and early warning network, has high sensitive radiation detection and it can send the alarm signal quickly by the Internet network to the emergency management office. Its gamma Probes are one NaI(Tl) detector and three GM detectors. The NaI(Tl) detector is used to monitor Spectrum environmental radiation and identify the Isotopes, the other are used to detect high dose rate of gamma rays. This instrument must tolerate a wide range of ambient temperature and strong temperature slopes when used in outdoor. However, the gain of photomultiplier tube, amplifier and ADC must be stabilized by pulsed LEDs used as precision reference light sources. (author)

  1. 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.)

  2. Radiation versus immunity in early breast cancer

    International Nuclear Information System (INIS)

    Turnbull, A.R.; Turner, D.T.L.; Jones, B.M.; Wright, R.

    1979-01-01

    Comparison of various in-vitro immunological tests has been made in patients with early breast cancer undergoing simple mastectomy alone or simple mastectomy with additional radical radiotherapy to the chest wall and regional lymphatics. Radiotherapy caused a depletion of both T and B lymphocytes in the peripheral blood, but did not substantially alter the proportions of these two cell populations. The response to certain mitogens was also depressed for at least 12 months, but the sensitivity of the leucocytes to tumour antigens in the leucocyte migration inhibition test was preserved, following irradiation. (author)

  3. 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.

  4. 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.

  5. 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.

  6. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    Ingersoll, D T [comp.; Oak Ridge National Lab., TN (United States); Ingersoll, J K [comp.; Tec-Com, Knoxville, TN (United States)

    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.

  8. Biochemical investigation of earliness in radiation induced early flowering mutantlines of jute Corchorus capsularis L

    International Nuclear Information System (INIS)

    Islam, M.S.; Ilias, M.; Biswas, A.K.; Naznin, S.

    1980-01-01

    With the help of radiation induced early and late flowering mutantlines of jute, studies have been made to determine the biochemical factors which could regulate the induction and expression of genes for the flowering processes in this plant. Comparative biochemical investigations were done with the parameters like : plant pigments (Chlorophyl a, b and carotenoides), auxin/antiauxin, and gibberellin/anti-gibberellin type of substances. Quantitative as well as qualitative differences of plant pigments were observed between the early and late flowering lines. Extracts of early flowering lines have been found to induce earliness in the late flowering mother variety of jute (D-154). Re-isolated growth inhibitors of early flowering lines have also been found to induce earliness in the late flowering mother variety (D-154). (author)

  9. Far-UV Radiation of the Early Sun

    Science.gov (United States)

    Heap, Sally

    2005-01-01

    Far-UV radiation is responsible for the photolysis of important greenhouse gases such as CO2, NH3 (ammonia), CH4 (methane) and more generally, the global UV photochemistry of the early atmosphere. In our project, we are concentrating on the young Sun's effect on methane, since UV sunlight (lambda less than 1450 Angstroms) was the main destruction mechanism for methane in the early Earth's atmosphere. Since the UV luminosity of the early Sun cannot be calculated a priori; it can only be estimated from observations of stars similar to the young Sun. We report our results based on Hubble + FUSE spectra of stars selected from Gaidos (1998) Catalog of Nearby Young Solar Analogs (YSA's).

  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. 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......, 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...... 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...

  12. Teaching bioinformatics to engineers.

    Science.gov (United States)

    Mihalas, George I; Tudor, Anca; Paralescu, Sorin; Andor, Minodora; Stoicu-Tivadar, Lacramioara

    2014-01-01

    The paper refers to our methodology and experience in establishing the content of the course in bioinformatics introduced to the school of "Information Systems in Healthcare" (SIIS), master level. The syllabi of both lectures and laboratory works are presented and discussed.

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. Flow cytometry bioinformatics.

    Directory of Open Access Journals (Sweden)

    Kieran O'Neill

    Full Text Available Flow cytometry bioinformatics is the application of bioinformatics to flow cytometry data, which involves storing, retrieving, organizing, and analyzing flow cytometry data using extensive computational resources and tools. Flow cytometry bioinformatics requires extensive use of and contributes to the development of techniques from computational statistics and machine learning. Flow cytometry and related methods allow the quantification of multiple independent biomarkers on large numbers of single cells. The rapid growth in the multidimensionality and throughput of flow cytometry data, particularly in the 2000s, has led to the creation of a variety of computational analysis methods, data standards, and public databases for the sharing of results. Computational methods exist to assist in the preprocessing of flow cytometry data, identifying cell populations within it, matching those cell populations across samples, and performing diagnosis and discovery using the results of previous steps. For preprocessing, this includes compensating for spectral overlap, transforming data onto scales conducive to visualization and analysis, assessing data for quality, and normalizing data across samples and experiments. For population identification, tools are available to aid traditional manual identification of populations in two-dimensional scatter plots (gating, to use dimensionality reduction to aid gating, and to find populations automatically in higher dimensional space in a variety of ways. It is also possible to characterize data in more comprehensive ways, such as the density-guided binary space partitioning technique known as probability binning, or by combinatorial gating. Finally, diagnosis using flow cytometry data can be aided by supervised learning techniques, and discovery of new cell types of biological importance by high-throughput statistical methods, as part of pipelines incorporating all of the aforementioned methods. Open standards, data

  18. 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

  19. 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.

  20. Triassic origin and early radiation of multicellular volvocine algae.

    Science.gov (United States)

    Herron, Matthew D; Hackett, Jeremiah D; Aylward, Frank O; Michod, Richard E

    2009-03-03

    Evolutionary transitions in individuality (ETIs) underlie the watershed events in the history of life on Earth, including the origins of cells, eukaryotes, plants, animals, and fungi. Each of these events constitutes an increase in the level of complexity, as groups of individuals become individuals in their own right. Among the best-studied ETIs is the origin of multicellularity in the green alga Volvox, a model system for the evolution of multicellularity and cellular differentiation. Since its divergence from unicellular ancestors, Volvox has evolved into a highly integrated multicellular organism with cellular specialization, a complex developmental program, and a high degree of coordination among cells. Remarkably, all of these changes were previously thought to have occurred in the last 50-75 million years. Here we estimate divergence times using a multigene data set with multiple fossil calibrations and use these estimates to infer the times of developmental changes relevant to the evolution of multicellularity. Our results show that Volvox diverged from unicellular ancestors at least 200 million years ago. Two key innovations resulting from an early cycle of cooperation, conflict and conflict mediation led to a rapid integration and radiation of multicellular forms in this group. This is the only ETI for which a detailed timeline has been established, but multilevel selection theory predicts that similar changes must have occurred during other ETIs.

  1. 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...

  2. Bioinformatics meets parasitology.

    Science.gov (United States)

    Cantacessi, C; Campbell, B E; Jex, A R; Young, N D; Hall, R S; Ranganathan, S; Gasser, R B

    2012-05-01

    The advent and integration of high-throughput '-omics' technologies (e.g. genomics, transcriptomics, proteomics, metabolomics, glycomics and lipidomics) are revolutionizing the way biology is done, allowing the systems biology of organisms to be explored. These technologies are now providing unique opportunities for global, molecular investigations of parasites. For example, studies of a transcriptome (all transcripts in an organism, tissue or cell) have become instrumental in providing insights into aspects of gene expression, regulation and function in a parasite, which is a major step to understanding its biology. The purpose of this article was to review recent applications of next-generation sequencing technologies and bioinformatic tools to large-scale investigations of the transcriptomes of parasitic nematodes of socio-economic significance (particularly key species of the order Strongylida) and to indicate the prospects and implications of these explorations for developing novel methods of parasite intervention. © 2011 Blackwell Publishing Ltd.

  3. 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…

  4. 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…

  5. 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.)

  6. Early radiation effects in electron and gamma teletherapy of patients with carcinoma of the larynx

    International Nuclear Information System (INIS)

    Motorina, L.I.

    1979-01-01

    The early radiation effects in 141 patients treated with gamma radiation and in 64 patients treated with fast electrons for carcinoma of the larynx were subjected to a comparative analysis. Thus is could be stated that the early radiation effects did not differ essentially between the two groups. An island-like epithelitis of the laryngeal mucosa occured more frequently after gamma therapy, skin reactions, however, after electron therapy. Because of the considerably lower radiation doses of the surrounding tissue, electron therapy is to be preferred

  7. 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.

  8. 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....

  9. 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.

  10. DELAYED EFFECTS OF RADIATION ON THE HUMAN CENTRAL NERVOUS SYSTEM. EARLY AND LATE DELAYED REACTIONS,

    Science.gov (United States)

    Two cases of delayed effects of radiation on the central nervous system of man are reported. One demonstrates the rare early delayed reaction which...involvement. This patient is an extreme example of the well-documented late delayed effects of radiation and is presented for contrast with the patient in

  11. How to test bioinformatics software?

    Science.gov (United States)

    Kamali, Amir Hossein; Giannoulatou, Eleni; Chen, Tsong Yueh; Charleston, Michael A; McEwan, Alistair L; Ho, Joshua W K

    2015-09-01

    Bioinformatics is the application of computational, mathematical and statistical techniques to solve problems in biology and medicine. Bioinformatics programs developed for computational simulation and large-scale data analysis are widely used in almost all areas of biophysics. The appropriate choice of algorithms and correct implementation of these algorithms are critical for obtaining reliable computational results. Nonetheless, it is often very difficult to systematically test these programs as it is often hard to verify the correctness of the output, and to effectively generate failure-revealing test cases. Software testing is an important process of verification and validation of scientific software, but very few studies have directly dealt with the issues of bioinformatics software testing. In this work, we review important concepts and state-of-the-art methods in the field of software testing. We also discuss recent reports on adapting and implementing software testing methodologies in the bioinformatics field, with specific examples drawn from systems biology and genomic medicine.

  12. 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.

  13. Genome Exploitation and Bioinformatics Tools

    Science.gov (United States)

    de Jong, Anne; van Heel, Auke J.; Kuipers, Oscar P.

    Bioinformatic tools can greatly improve the efficiency of bacteriocin screening efforts by limiting the amount of strains. Different classes of bacteriocins can be detected in genomes by looking at different features. Finding small bacteriocins can be especially challenging due to low homology and because small open reading frames (ORFs) are often omitted from annotations. In this chapter, several bioinformatic tools/strategies to identify bacteriocins in genomes are discussed.

  14. 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

  15. Emerging strengths in Asia Pacific bioinformatics

    OpenAIRE

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

    2008-01-01

    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,...

  16. 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.

  17. 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

  18. 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

  19. 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).

  20. 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......://www.secondarymetabolites.org) is introduced to provide a one-stop catalog and links to these bioinformatics resources. In addition, an outlook is presented how the existing tools and those to be developed will influence synthetic biology approaches in the natural products field....

  1. 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 ...

  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. 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. 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...

  6. The Aspergillus Mine - publishing bioinformatics

    DEFF Research Database (Denmark)

    Vesth, Tammi Camilla; Rasmussen, Jane Lind Nybo; Theobald, Sebastian

    with the Joint Genome Institute. The Aspergillus Mine is not intended as a genomic data sharing service but instead focuses on creating an environment where the results of bioinformatic analysis is made available for inspection. The data and code is public upon request and figures can be obtained directly from...

  7. 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

  8. Computational intelligence techniques in bioinformatics.

    Science.gov (United States)

    Hassanien, Aboul Ella; Al-Shammari, Eiman Tamah; Ghali, Neveen I

    2013-12-01

    Computational intelligence (CI) is a well-established paradigm with current systems having many of the characteristics of biological computers and capable of performing a variety of tasks that are difficult to do using conventional techniques. It is a methodology involving adaptive mechanisms and/or an ability to learn that facilitate intelligent behavior in complex and changing environments, such that the system is perceived to possess one or more attributes of reason, such as generalization, discovery, association and abstraction. The objective of this article is to present to the CI and bioinformatics research communities some of the state-of-the-art in CI applications to bioinformatics and motivate research in new trend-setting directions. In this article, we present an overview of the CI techniques in bioinformatics. We will show how CI techniques including neural networks, restricted Boltzmann machine, deep belief network, fuzzy logic, rough sets, evolutionary algorithms (EA), genetic algorithms (GA), swarm intelligence, artificial immune systems and support vector machines, could be successfully employed to tackle various problems such as gene expression clustering and classification, protein sequence classification, gene selection, DNA fragment assembly, multiple sequence alignment, and protein function prediction and its structure. We discuss some representative methods to provide inspiring examples to illustrate how CI can be utilized to address these problems and how bioinformatics data can be characterized by CI. Challenges to be addressed and future directions of research are also presented and an extensive bibliography is included. Copyright © 2013 Elsevier Ltd. All rights reserved.

  9. 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.

  10. 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

  11. 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

  12. 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...

  13. 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.

  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. Bioinformatics in the information age

    Energy Technology Data Exchange (ETDEWEB)

    Spengler, Sylvia J.

    2000-02-01

    There is a well-known story about the blind man examining the elephant: the part of the elephant examined determines his perception of the whole beast. Perhaps bioinformatics--the shotgun marriage between biology and mathematics, computer science, and engineering--is like an elephant that occupies a large chair in the scientific living room. Given the demand for and shortage of researchers with the computer skills to handle large volumes of biological data, where exactly does the bioinformatics elephant sit? There are probably many biologists who feel that a major product of this bioinformatics elephant is large piles of waste material. If you have tried to plow through Web sites and software packages in search of a specific tool for analyzing and collating large amounts of research data, you may well feel the same way. But there has been progress with major initiatives to develop more computing power, educate biologists about computers, increase funding, and set standards. For our purposes, bioinformatics is not simply a biologically inclined rehash of information theory (1) nor is it a hodgepodge of computer science techniques for building, updating, and accessing biological data. Rather bioinformatics incorporates both of these capabilities into a broad interdisciplinary science that involves both conceptual and practical tools for the understanding, generation, processing, and propagation of biological information. As such, bioinformatics is the sine qua non of 21st-century biology. Analyzing gene expression using cDNA microarrays immobilized on slides or other solid supports (gene chips) is set to revolutionize biology and medicine and, in so doing, generate vast quantities of data that have to be accurately interpreted (Fig. 1). As discussed at a meeting a few months ago (Microarray Algorithms and Statistical Analysis: Methods and Standards; Tahoe City, California; 9-12 November 1999), experiments with cDNA arrays must be subjected to quality control

  16. Radiation from early black holes - I. Effects on the neutral intergalactic medium

    NARCIS (Netherlands)

    Ripamonti, E.; Mapelli, M.; Zaroubi, S.

    2008-01-01

    In the pre-reionization Universe, the regions of the intergalactic medium (IGM) which are far from luminous sources are the last to undergo reionization. Until then, they should be scarcely affected by stellar radiation; instead, the X-ray emission from an early black hole (BH) population can have

  17. 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)

  18. 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)

  19. Utility library for structural bioinformatics.

    Science.gov (United States)

    Gront, Dominik; Kolinski, Andrzej

    2008-02-15

    In this Note we present a new software library for structural bioinformatics. The library contains programs, computing sequence- and profile-based alignments and a variety of structural calculations with user-friendly handling of various data formats. The software organization is very flexible. Algorithms are written in Java language and may be used by Java programs. Moreover the modules can be accessed from Jython (Python scripting language implemented in Java) scripts. Finally, the new version of BioShell delivers several utility programs that can do typical bioinformatics task from a command-line level. Availability The software is available for download free of charge from its website: http://bioshell.chem.uw.edu.pl. This website provides also numerous examples, code snippets and API documentation.

  20. 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.

  1. 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)

  2. Cytokines as remedies for early pathogenetic therapy of radiation injuries. Efficiency and mechanism

    International Nuclear Information System (INIS)

    Legeza, V.I.; Chigireva, N.G.; Abdul', Yu.A.; Galeev, I.Sh.

    2000-01-01

    The efficiency of applying interleukins in the case of early pathogenetic therapy of the acute radiation disease is studied in experiments with mice, rats and dogs. The animal were subjected to the gamma-radiation with the dose rate of 1.5 Gy/min. It is shown that administration of human recombinant interleukins 1α and 1β separately (to mice and rats) or in combination with antibiotic therapy (dogs) during the first hours after irradiation essentially increases the survival rate, facilitates more rapid regeneration of the cellular content of the bone marrow and peripheral blood, intensifies the processes of endogenic colony formation and DNA synthesis in the bone marrow and liver and decreases the expressivity of radiation-induced endotoxemia. The importance of using cytokines in the system of remedial measures by radiation pathology is discussed [ru

  3. Early and Late Damages in Chromosome 3 of Human Lymphocytes After Radiation Exposure

    Science.gov (United States)

    Sunagawa, Mayumi; Mangala, Lingegowda; Zhang, Ye; Kahdim, Munira; Wilson, Bobby; Cucinotta, Francis A.; Wu, Honglu

    2011-01-01

    Tumor formation in humans or animals is a multi-step process. An early stage of cancer development is believed to be genomic instability (GI) which accelerates the mutation rate in the descendants of the cells surviving radiation exposure. GI is defined as elevated or persistent genetic damages occurring many generations after the cells are exposed. While early studies have demonstrated radiation-induced GI in several cell types as detected in endpoints such as mutation, apoptosis and damages in chromosomes, the dependence of GI on the quality of radiation remains uncertain. To investigate GI in human lymphocytes induced by both low- and high-LET radiation, we initially exposed white blood cells collected from healthy subjects to gamma rays in vitro, and cultured the cells for multiple generations. Chromosome aberrations were analyzed in cells collected at first mitosis post irradiation and at several intervals during the culture period. Among a number of biological endpoints planned for the project, the multi-color banding fluorescent in situ hybridization (mBAND) allows identification of inversions that were expected to be stable. We present here early and late chromosome aberrations detected with mBAND in chromosome 3 after gamma exposure. Comparison of chromosome damages in between human lymphocytes and human epithelial cells is also discussed

  4. Early administration of IL-6RA does not prevent radiation-induced lung injury in mice

    Directory of Open Access Journals (Sweden)

    Inoue Takehiro

    2010-04-01

    Full Text Available Abstract Background Radiation pneumonia and subsequent radiation lung fibrosis are major dose-limiting complications for patients undergoing thoracic radiotherapy. Interleukin-6 (IL-6 is a pleiotropic cytokine and plays important roles in the regulation of immune response and inflammation. The purpose of this study was to investigate whether anti-IL-6 monoclonal receptor antibody (IL-6RA could ameliorate radiation-induced lung injury in mice. Methods BALB/cAnNCrj mice having received thoracic irradiation of 21 Gy were injected intraperitoneally with IL-6RA (MR16-1 or control rat IgG twice, immediately and seven days after irradiation. Enzyme-linked immunosorbent assay was used to examine the plasma level of IL-6 and serum amyloid A (SAA. Lung injury was assessed by histological staining with haematoxylin and eosin or Azan, measuring lung weight, and hydroxyproline. Results The mice treated with IL-6RA did not survive significantly longer than the rat IgG control. We observed marked up-regulation of IL-6 in mice treated with IL-6RA 150 days after irradiation, whereas IL-6RA temporarily suppressed early radiation-induced increase in the IL-6 release level. Histopathologic assessment showed no differences in lung section or lung weight between mice treated with IL-6RA and control. Conclusions Our findings suggest that early treatment with IL-6RA after irradiation alone does not protect against radiation-induced lung injury.

  5. 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.)

  6. Early radiation swelling remains a problem in the management of paediatric brain tumours

    International Nuclear Information System (INIS)

    Plowman, P.N.; Fuentos, J.; Harnett, A.N.

    1987-01-01

    Deteriorating neurological signs following the first fractions of radiotherapy for central nervous system tumours have long been recognised and categorised as 'early radiation swelling'/oedema (Rubin and Casaret, 1968; Young et al, 1974), perhaps of vascular origin, comparable with primary radiation erythema of skin. However, with dexamethasone therapy and the relatively low daily fractional doses prescribed for paediatric brain tumours, it is now uncommon to commence treatment with very low dose fractions. Several authorities (Kramer, 1968; Sheline, 1980) argue such practice is unnecessary. Two cases are described arguing for individual assessment. (author)

  7. Early Signs of Oxidative Stress Induced by Environmental Pollutants and Radiation Exposure in Rats

    International Nuclear Information System (INIS)

    Noaman, E.; Gharib, O.A.

    2005-01-01

    The current study examines the early effects of whole body y-radiation exposure with single dose of (6.5 Gy) and acute single dose (2250 mg/Kg b. wt.) of 1,4-dioxane, which is considered the most common environmental contaminants used. Rats were sacrificed after one and twenty-four h after radiation exposure and/or 1,4-dioxane administration. The significant elevation in lipid peroxidation concentration, measured as malonaldehydoyl (MDA) was observed only after 24 h in radiation/1,4-dioxane group. The results showed that Glutathione (GSH) concentration was significantly decreased after 1 h followed by enhancement significantly after 24 h in radiation/1,4-dioxane group. Elevation in superoxide dismutase (SOD) activity was detected early (after 1 h) and continued elevation after twenty-four h recorded highly significant increase in radiation and/or 1,4-dioxane groups. The hematological parameters revealed more or less non-significant changes in red blood cells (RBCs) counts, hemoglobin concentration (Hbg) and haematocrit value (PVC), while significant increase in white blood cell counts (WBCs) count after one and 24 h post irradiation with or without 1,4-dioxane administration were recorded. In general 1,4-dioxane acted as a debilitator, which enhanced the overall effect of ionizing radiation when applied as the second insult. Antioxidants are the body's primary defense against free radicals and reactive oxygen species (ROS). Free radicals can cause tissue damage by reacting with polyunsaturated fatty acids in cellular membrane, nucleotides, in DNA and critical sulfhydryl bonds in protein. The over production of ROS in both intra-and extra cellular spaces upon exposure of living subjects to certain chemicals, radiation or local tissue inflammation, results in oxidative stress defined as the imbalance between pro- oxidation and antioxidants

  8. 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.

  9. 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

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

    Science.gov (United States)

    Schneider, Maria V; Walter, Peter; Blatter, Marie-Claude; Watson, James; Brazas, Michelle D; Rother, Kristian; Budd, Aidan; Via, Allegra; van Gelder, Celia W G; Jacob, Joachim; Fernandes, Pedro; Nyrönen, Tommi H; De Las Rivas, Javier; Blicher, Thomas; Jimenez, Rafael C; Loveland, Jane; McDowall, Jennifer; Jones, Phil; Vaughan, Brendan W; Lopez, Rodrigo; Attwood, Teresa K; Brooksbank, Catherine

    2012-05-01

    Funding bodies are increasingly recognizing the need to provide graduates and researchers with access to short intensive courses in a variety of disciplines, in order both to improve the general skills base and to provide solid foundations on which researchers may build their careers. In response to the development of 'high-throughput biology', the need for training in the field of bioinformatics, in particular, is seeing a resurgence: it has been defined as a key priority by many Institutions and research programmes and is now an important component of many grant proposals. Nevertheless, when it comes to planning and preparing to meet such training needs, tension arises between the reward structures that predominate in the scientific community which compel individuals to publish or perish, and the time that must be devoted to the design, delivery and maintenance of high-quality training materials. Conversely, there is much relevant teaching material and training expertise available worldwide that, were it properly organized, could be exploited by anyone who needs to provide training or needs to set up a new course. To do this, however, the materials would have to be centralized in a database 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 it, respectively, to similar initiatives and collections.

  11. 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

  12. 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)

  13. 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)

  14. Cell phone radiations affect early growth of Vigna radiata (mung bean) through biochemical alterations.

    Science.gov (United States)

    Sharma, Ved Parkash; Singh, Harminder Pal; Batish, Daizy Rani; Kohli, Ravinder Kumar

    2010-01-01

    The indiscriminate use of wireless technologies, particularly of cell phones, has increased the health risks among living organisms including plants. We investigated the impact of cell phone electromagentic field (EMF) radiations (power density, 8.55 microW cm(-2)) on germination, early growth, proteins and carbohydrate contents, and activities of some enzymes in Vigna radiata. Cell phone EMF radiations significantly reduced the seedling length and dry weight of V radiata after exposure for 0.5, 1, 2, and 4 h. Furthermore, the contents of proteins and carbohydrates were reduced in EMF-exposed plants. However, the activities of proteases, alpha-amylases, beta-amylases, polyphenol oxidases, and peroxidases were enhanced in EMF-exposed radicles indicating their role in providing protection against EMF-induced stress. The study concludes that cell phone EMFs impair early growth of V radiata seedlings by inducing biochemical changes.

  15. GAMMA-1: a first step towards a radiation early warning system for Belarus and the Ukraine

    International Nuclear Information System (INIS)

    With assistance from the European Commission, the governments of Belarus and the Ukraine have planned a radiation early warning system to detect faults and incidents which may arise in nuclear plants. The objective is to in stall a GAMMA curtain ultimately covering the whole of the former Soviet Union and to include nationwide radiation measurement networks in Belarus and the Ukraine. A pilot system, GAMMA-1, will be commissioned shortly with the primary objectives of: detecting significant changes in radiation levels in three critical pilot areas; alerting the national authorities to any significant change; providing information on which warnings to the population may be based; assisting in counter measures to protect populations and the environment; testing and evaluating key elements of the overall system. The fixed and roving response systems, the gamma monitoring stations and the response centres are described in outline. (UK)

  16. Post-surgery radiation in early breast cancer: survival analysis of registry data

    OpenAIRE

    Vinh-Hung, Vincent; BURZYKOWSKI, Tomasz; Van de Steene, Jan; Storme, Guy; Soete, Guy

    2002-01-01

    BACKGROUND AND PURPOSE: Overviews of randomized trials have shown a small survival advantage with post-surgery radiation in early breast cancer. The present study attempts to extend this observation through a systematic analysis of population data.Materials and METHODS: This retrospective cohort study used the Surveillance, Epidemiology, and End Results (SEER) data on 83,776 women with breast cancer diagnosed between 1988 and 1997, stage T1-T2, node negative or node positive. The analysis was...

  17. 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.

  18. Involved Node Radiation Therapy: An Effective Alternative in Early-Stage Hodgkin Lymphoma

    Energy Technology Data Exchange (ETDEWEB)

    Maraldo, Maja V., E-mail: dra.maraldo@gmail.com [Department of Radiation Oncology, The Finsen Center, Rigshospitalet, Copenhagen (Denmark); Aznar, Marianne C. [Department of Radiation Oncology, The Finsen Center, Rigshospitalet, Copenhagen (Denmark); Faculty of Health Sciences, University of Copenhagen, Copenhagen (Denmark); Vogelius, Ivan R.; Petersen, Peter M. [Department of Radiation Oncology, The Finsen Center, Rigshospitalet, Copenhagen (Denmark); Specht, Lena [Department of Radiation Oncology, The Finsen Center, Rigshospitalet, Copenhagen (Denmark); Faculty of Health Sciences, University of Copenhagen, Copenhagen (Denmark)

    2013-03-15

    Purpose: The involved node radiation therapy (INRT) strategy was introduced for patients with Hodgkin lymphoma (HL) to reduce the risk of late effects. With INRT, only the originally involved lymph nodes are irradiated. We present treatment outcome in a retrospective analysis using this strategy in a cohort of 97 clinical stage I-II HL patients. Methods and Materials: Patients were staged with positron emission tomography/computed tomography scans, treated with adriamycin, bleomycin, vinblastine, and dacarbazine chemotherapy, and given INRT (prechemotherapy involved nodes to 30 Gy, residual masses to 36 Gy). Patients attended regular follow-up visits until 5 years after therapy. Results: The 4-year freedom from disease progression was 96.4% (95% confidence interval: 92.4%-100.4%), median follow-up of 50 months (range: 4-71 months). Three relapses occurred: 2 within the previous radiation field, and 1 in a previously uninvolved region. The 4-year overall survival was 94% (95% confidence interval: 88.8%-99.1%), median follow-up of 58 months (range: 4-91 months). Early radiation therapy toxicity was limited to grade 1 (23.4%) and grade 2 (13.8%). During follow-up, 8 patients died, none from HL, 7 malignancies were diagnosed, and 5 patients developed heart disease. Conclusions: INRT offers excellent tumor control and represents an effective alternative to more extended radiation therapy in the combined modality treatment for early-stage HL.

  19. Bioinformatics in Africa: The Rise of Ghana?

    Directory of Open Access Journals (Sweden)

    Thomas K Karikari

    2015-09-01

    Full Text Available Until recently, bioinformatics, an important discipline in the biological sciences, was largely limited to countries with advanced scientific resources. Nonetheless, several developing countries have lately been making progress in bioinformatics training and applications. In Africa, leading countries in the discipline include South Africa, Nigeria, and Kenya. However, one country that is less known when it comes to bioinformatics is Ghana. Here, I provide a first description of the development of bioinformatics activities in Ghana and how these activities contribute to the overall development of the discipline in Africa. Over the past decade, scientists in Ghana have been involved in publications incorporating bioinformatics analyses, aimed at addressing research questions in biomedical science and agriculture. Scarce research funding and inadequate training opportunities are some of the challenges that need to be addressed for Ghanaian scientists to continue developing their expertise in bioinformatics.

  20. Bioinformatics in Africa: The Rise of Ghana?

    Science.gov (United States)

    Karikari, Thomas K

    2015-09-01

    Until recently, bioinformatics, an important discipline in the biological sciences, was largely limited to countries with advanced scientific resources. Nonetheless, several developing countries have lately been making progress in bioinformatics training and applications. In Africa, leading countries in the discipline include South Africa, Nigeria, and Kenya. However, one country that is less known when it comes to bioinformatics is Ghana. Here, I provide a first description of the development of bioinformatics activities in Ghana and how these activities contribute to the overall development of the discipline in Africa. Over the past decade, scientists in Ghana have been involved in publications incorporating bioinformatics analyses, aimed at addressing research questions in biomedical science and agriculture. Scarce research funding and inadequate training opportunities are some of the challenges that need to be addressed for Ghanaian scientists to continue developing their expertise in bioinformatics.

  1. Search strategies in structural bioinformatics.

    Science.gov (United States)

    Oakley, Mark T; Barthel, Daniel; Bykov, Yuri; Garibaldi, Jonathan M; Burke, Edmund K; Krasnogor, Natalio; Hirst, Jonathan D

    2008-06-01

    Optimisation problems pervade structural bioinformatics. In this review, we describe recent work addressing a selection of bioinformatics challenges. We begin with a discussion of research into protein structure comparison, and highlight the utility of Kolmogorov complexity as a measure of structural similarity. We then turn to research into de novo protein structure prediction, in which structures are generated from first principles. In this endeavour, there is a compromise between the detail of the model and the extent to which the conformational space of the protein can be sampled. We discuss some developments in this area, including off-lattice structure prediction using the great deluge algorithm. One strategy to reduce the size of the search space is to restrict the protein chain to sites on a regular lattice. In this context, we highlight the use of memetic algorithms, which combine genetic algorithms with local optimisation, to the study of simple protein models on the two-dimensional square lattice and the face-centred cubic lattice.

  2. BIOINFORMATICS SOFTWARE FROM INDIA: CURRENT STATUS AND CHALLENGES

    Directory of Open Access Journals (Sweden)

    Deepti D. Deobagkar

    2017-09-01

    Full Text Available Bioinformatics software and visualisation tools have been a key factor in the rapid and phenomenal advances in genomics, proteomics, medicine, drug discovery, systems approaches and in fact in every area of new development. Indian scientists have also made a mark in a few specific areas. India has an advantage of an early start and extensive and organised network in the Bioinformatics education and research with substantial inputs from the Indian government. India has a strong hold in computation and IT and has a pool of bright and young talent with demographic dividend along with experienced and excellent mentors and researchers. Although small in number and scale, Bioinformatics Industry also has a presence and is making its mark in India. There are a number of high throughput and extremely useful resources available which are critical in biological data analysis and interpretation. This has made a paradigm shift in the way research can be carried out and discoveries can be made in any area of biological, biochemical and chemical research. This article summarises the current status and contributions from India in the development of software and web servers for Bioinformatics applications.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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

    Funding bodies are increasingly recognizing the need to provide graduates and researchers with access to short intensive courses in a variety of disciplines, in order both to improve the general skills base and to provide solid foundations on which researchers may build their careers. In response...... to the development of ‘high-throughput biology’, the need for training in the field of bioinformatics, in particular, is seeing a resurgence: it has been defined as a key priority by many Institutions and research programmes and is now an important component of many grant proposals. Nevertheless, when it comes...... to planning and preparing to meet such training needs, tension arises between the reward structures that predominate in the scientific community which compel individuals to publish or perish, and the time that must be devoted to the design, delivery and maintenance of high-quality training materials...

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

    Directory of Open Access Journals (Sweden)

    Azria David

    2010-01-01

    Full Text Available Abstract 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.

  9. Long-term Results of Breast-conserving Surgery and Radiation Therapy in Early Breast Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jin Hee; Byun, Sang Jun [Dongsan Medical Center, Daegu (Korea, Republic of)

    2009-09-15

    To evaluate the long-term results after breast-conserving surgery and radiation therapy in early breast cancer in terms of failure, survival, and cosmesis. One hundred fifty-four patients with stage I and II breast cancer were treated with conservative surgery plus radiotherapy between January 1992 and December 2002 at the Keimyung University Dongsan Medical Center. According to TNM stage, 93 patients were stage I, 50 were IIa, and 11 were IIb. The affected breasts were irradiated with 6 MV photons to 50.4 Gy in 28 fractions over 5.5 weeks with a boost irradiation dose of 10{approx}16 Gy to the excision site. Chemotherapy was administered in 75 patients and hormonal therapy in 92 patients with tamoxifen. Follow-up periods were 13{approx}179 months, with a median of 92.5 months. The 5- and 10-year overall survival rates were 97.3% and 94.5%, respectively. The 5- and 10-year disease-free survival (5YDFS and 10YDFS, respectively) rates were 92.5% and 88.9%, respectively; the ultimate 5YDFS and 10YDFS rates after salvage treatment were 93.9% and 90.2%, respectively. Based on multivariate analysis, only the interval between surgery and radiation therapy ({<=}6 weeks vs. >6 weeks, p=0.017) was a statistically significant prognostic factor for DFS. The major type of treatment failure was distant failure (78.5%) and the most common distant metastatic site was the lungs. The cosmetic results were good-to-excellent in 96 patients (80.7%). Conservative surgery and radiation for early stage invasive breast cancer yielded excellent survival and cosmetic results. Radiation therapy should be started as soon as possible after breast-conserving surgery in patients with early breast cancer, ideally within 6 weeks.

  10. Prognostic factors for local control in early glottic cancer treated with radiation therapy

    Energy Technology Data Exchange (ETDEWEB)

    Chung, Woong Ki; Ahn, Sung Ja; Nam, Taek Keun; Nah, Byung Sik; Cho, Jae Shik; Lim, Sang Chull [College of Medicine, Chonnam National Univ, Kwangju (Korea, Republic of)

    2000-12-01

    This study was performed to find out the prognostic factors affecting local control in early glottic cancer treated with radiation therapy alone. We analysed 37 patients of histologically confirmed early glottic cancer treated at Chonnam National University Hospital between July 1986 and December 1995, retrospectively. Age of patients ranged from 30 to 73 years (median; 59 years). Thirty-five (95%) patients were male. Histological type was all squamous cell carcinoma. According to the staging system of 1997 American Joint Committee on Cancer, 37 patients were restaged as follows: T1a; 27 (73%), T1b; 3 (8%), T2; 7 (19%). Radiation therapy was done using 6 MV X-ray of linear accelerator. The range of total radiation dose delivered to the glottic lesion was between 5,040 cGy and 7,020 cGy (median; 6,600 cGy). Median follow-up period was 80 months. Local control rates were calculated by Kaplan-Meier method. Generalized Wilcoxon test was used to evaluate the difference of control rates between comparable groups. Multivariate analysis using Cox proportional hazard model was done to find out prognostic factors affecting local control. 5 year survival rate of 37 patients was 89%. Local control rate of 37 patients was 74% in 5 years. We included age, T -stage, anterior commissure involvement, fraction size, total radiation dose, treatment time of radiotherapy as potential prognostic factors in univariate and multivariate analysis. As a result, treatment time had statistical significance in local control rate in both univariate (p=0.026) and multivariate (p=0.017) analysis. Complication was not recorded except one patient with hypothyroidism. This study revealed that overall treatment time of radiation was a significant factor affecting local control rate.

  11. 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

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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…

  17. 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…

  18. 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

  19. 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)

  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. 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.

  2. 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.

  3. Bioinformatics clouds for big data manipulation

    Science.gov (United States)

    2012-01-01

    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. PMID:23190475

  4. 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.

  5. 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.

  6. Early exposure to ultraviolet-B radiation decreases immune function later in life.

    Science.gov (United States)

    Ceccato, Emma; Cramp, Rebecca L; Seebacher, Frank; Franklin, Craig E

    2016-01-01

    Amphibians have declined dramatically worldwide. Many of these declines are occurring in areas where no obvious anthropogenic stressors are present. It is proposed that in these areas, environmental factors such as elevated solar ultraviolet-B (UV-B) radiation could be responsible. Ultraviolet-B levels have increased in many parts of the world as a consequence of the anthropogenic destruction of the ozone layer. Amphibian tadpoles are particularly sensitive to the damaging effects of UV-B radiation, with exposure disrupting growth and fitness in many species. Given that UV-B can disrupt immune function in other animals, we tested the hypothesis that early UV-B exposure suppresses the immune responses of amphibian tadpoles and subsequent juvenile frogs. We exposed Limnodynastes peronii tadpoles to sublethal levels of UV-B radiation for 6 weeks after hatching, then examined indices of immune function in both the tadpoles and the subsequent metamorphs. There was no significant effect of UV-B on tadpole leucocyte counts or on their response to an acute antigen (phytohaemagglutinin) challenge. However, early UV-B exposure resulted in a significant reduction in both metamorph leucocyte abundance and their response to an acute phytohaemagglutinin challenge. These data demonstrate that early UV-B exposure can have carry-over effects on later life-history traits even if the applied stressor has no immediately discernible effect. These findings have important implications for our understanding of the effects of UV-B exposure on amphibian health and susceptibility to diseases such as chytridiomycosis.

  7. Personalized medicine: challenges and opportunities for translational bioinformatics.

    Science.gov (United States)

    Overby, Casey Lynnette; Tarczy-Hornoch, Peter

    2013-07-01

    Personalized medicine can be defined broadly as a model of healthcare that is predictive, personalized, preventive and participatory. Two US President's Council of Advisors on Science and Technology reports illustrate challenges in personalized medicine (in a 2008 report) and in use of health information technology (in a 2010 report). Translational bioinformatics is a field that can help address these challenges and is defined by the American Medical Informatics Association as "the development of storage, analytic and interpretive methods to optimize the transformation of increasing voluminous biomedical data into proactive, predictive, preventative and participatory health." This article discusses barriers to implementing genomics applications and current progress toward overcoming barriers, describes lessons learned from early experiences of institutions engaged in personalized medicine and provides example areas for translational bioinformatics research inquiry.

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

    Energy Technology Data Exchange (ETDEWEB)

    Maraldo, Maja V., E-mail: dra.maraldo@gmail.com [Departments of Clinical Oncology and Hematology, Rigshospitalet, University of Copenhagen (Denmark); Dabaja, Bouthaina S. [Department of Radiation Oncology, MD Anderson Cancer Center, Texas (United States); Filippi, Andrea R. [Department of Oncology, University of Torino School of Medicine, Torino (Italy); Illidge, Tim [Department of Oncology, Christie Hospital, Manchester (United Kingdom); Tsang, Richard [Department of Radiation Oncology, Princess Margaret Cancer Centre, Toronto, Ontario (Canada); Ricardi, Umberto [Department of Oncology, University of Torino School of Medicine, Torino (Italy); Petersen, Peter M.; Schut, Deborah A. [Departments of Clinical Oncology and Hematology, Rigshospitalet, University of Copenhagen (Denmark); Garcia, John [Department of Radiation Oncology, MD Anderson Cancer Center, Texas (United States); Headley, Jayne [Department of Oncology, Christie Hospital, Manchester (United Kingdom); Parent, Amy; Guibord, Benoit [Department of Radiation Oncology, Princess Margaret Cancer Centre, Toronto, Ontario (Canada); Ragona, Riccardo [Department of Oncology, University of Torino School of Medicine, Torino (Italy); Specht, Lena [Departments of Clinical Oncology and Hematology, Rigshospitalet, University of Copenhagen (Denmark)

    2015-05-01

    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.

  9. 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

    2014-01-01

    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. PMID:24763310

  10. 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.

  11. 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.

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

    International Nuclear Information System (INIS)

    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

  13. 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.

  14. 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

  15. Breast conserving operation and radiation therapy in early breast cancer: interim analysis

    International Nuclear Information System (INIS)

    Kim, Jin Hee; Kim, Ok Bae; Kim, You Sah

    2001-01-01

    To evaluate interim results in terms of failure, cosmetic results and survival after breast conserving operation and radiation therapy in early breast cancer. From January 1992 through December 1997, seventy two patients with early stage 0, I and II breast cancer were treated with conservative surgery plus radiotherapy at Keimyung University Dongsan Medical Center. Age distribution was 25 to 77 years old with median age of 43. Ac cording to TNM stage, five patients had stage 0, thirty three were stage I, twenty five were lIa, and nine were llb. Most patients underwent excision of all gross tumor and ipsilateral axillary dissection. Breast was irradiated through medial and lateral tangential fields of 6 MV photons to 50.4 Gy in 28 fractions over 5.5 weeks. We delivered a boost irradiation dose of 10 to 16 Gy in 1 to 2 weeks to excision site. Adjuvant chemotherapy was administered in forty one patients with CMF (cyclophosphamide, methotrexate, 5fluorouracil) regimens of 6 cycles concurrently or before radiation. Cosmetic results were assessed by questionnaire to patients grading of excellent, good, fair, poor. Follow-up periods were 22 to 91 months with median 40 months. Five year disease free survival rate (5YDFS) was 95.8%. According to stage, 5YDFS was 100%, 96.9%, 96% and 88.9% in stage 0, I, lIa and llb, respectively. Two patients had distant metastasis and one had local and distant failure. One patient with distant failure had bone and liver metastasis at 14 months after treatment and the other had lung and both supraclavicular metastasis at 21 months after treatment. Patient with local and distant failure had local recurrence on other quadrant in same breast and then salvaged with total mastectomy and chemotherapy but she died due to brain metastasis at 55 months. Complications were radiation pneumonitis in five patients (four patients of asymptomatic, one patient of symptomatic) and hand or arm edema(4 patients). Fifty nine patients answered our cosmetic

  16. 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.

  17. 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.

  18. 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

  19. Coronavirus Genomics and Bioinformatics Analysis

    Directory of Open Access Journals (Sweden)

    Kwok-Yung Yuen

    2010-08-01

    Full Text Available The drastic increase in the number of coronaviruses discovered and coronavirus genomes being sequenced have given us an unprecedented opportunity to perform genomics and bioinformatics analysis on this family of viruses. Coronaviruses possess the largest genomes (26.4 to 31.7 kb among all known RNA viruses, with G + C contents varying from 32% to 43%. Variable numbers of small ORFs are present between the various conserved genes (ORF1ab, spike, envelope, membrane and nucleocapsid and downstream to nucleocapsid gene in different coronavirus lineages. Phylogenetically, three genera, Alphacoronavirus, Betacoronavirus and Gammacoronavirus, with Betacoronavirus consisting of subgroups A, B, C and D, exist. A fourth genus, Deltacoronavirus, which includes bulbul coronavirus HKU11, thrush coronavirus HKU12 and munia coronavirus HKU13, is emerging. Molecular clock analysis using various gene loci revealed that the time of most recent common ancestor of human/civet SARS related coronavirus to be 1999-2002, with estimated substitution rate of 4´10-4 to 2´10-2 substitutions per site per year. Recombination in coronaviruses was most notable between different strains of murine hepatitis virus (MHV, between different strains of infectious bronchitis virus, between MHV and bovine coronavirus, between feline coronavirus (FCoV type I and canine coronavirus generating FCoV type II, and between the three genotypes of human coronavirus HKU1 (HCoV-HKU1. Codon usage bias in coronaviruses were observed, with HCoV-HKU1 showing the most extreme bias, and cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape such codon usage bias in coronaviruses.

  20. 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.

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

    Directory of Open Access Journals (Sweden)

    Teresa K Attwood

    2015-04-01

    Full Text Available 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.

  2. 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

  3. Bioinformatics for cancer immunotherapy target discovery

    DEFF Research Database (Denmark)

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

    2014-01-01

    cancer immunotherapies has yet to be fulfilled. The insufficient efficacy of existing treatments can be attributed to a number of biological and technical issues. In this review, we detail the current limitations of immunotherapy target selection and design, and review computational methods to streamline...... 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...

  4. 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

  5. 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.

  6. 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

  7. The Austrian early radiation warning system. Current status and new developments

    International Nuclear Information System (INIS)

    In 1995 the Austrian early radiation warning system consisted of external gamma dose rate measuring devices in 336 locations that are rather evenly distributed across Austria and of nine aerosol warning devices. The measurement devices are connected to regional warning centres via dedicated telephone lines. Now a basic change in the system is foreseen. A renewal of the air contamination warning devices is scheduled, plans are being developed to use more 'intelligent' gamma measuring devices and packet switched data transfer. A data base system will be set up, containing on-line dose rate and air contamination data as well as laboratory measurement data for various media. Communication of these data to federal and regional authorities and other institutions will be managed within a geographical information system. (R.P.)

  8. 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.

  9. 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

  10. 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.

  11. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    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.

  13. 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

  14. 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...

  15. 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

  16. 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

  17. 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

  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. Risk factors for radiation failure in early-stage glottic carcinoma: A systematic review and meta-analysis.

    Science.gov (United States)

    Eskiizmir, Görkem; Baskın, Yasemin; Yalçın, Femin; Ellidokuz, Hülya; Ferris, Robert L

    2016-11-01

    Radiotherapy is one of the main treatment modalities for early-stage glottic carcinoma. Unfortunately, local failure may occur in a group of cases with T1-T2 glottic carcinoma. This meta-analysis sought to determine risk factors for radiation failure in patients with early-stage glottic carcinoma. A systematic and comprehensive search was performed for related studies published between 1995 and 2014. The primary end-point was 5-year local control. Data extraction and analysis were performed using the software STATA/SE 13.1 for Windows. Twenty-seven studies were eligible. A higher risk of radiation failure was demonstrated in male patients [relative risk (RR): 0.927, pfailure, although a moderate to high interstudy heterogeneity was determined. A statistically significant contribution was not detected for age, presence of comorbidity, alcohol use or subglottic extension. This is the first meta-analysis which assessed the potential risk factors for radiation failure in patients with early-stage glottic carcinoma. Gender and pretreatment hemoglobin level are major influential factors associated with radiation failure in patients with early-stage glottic carcinoma. However, prospective, randomized clinical trials may permit better stratification of their relative contributions, and those who may benefit more from upfront surgery. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. 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.

  1. 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

  2. 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)

  3. Planning bioinformatics workflows using an expert system.

    Science.gov (United States)

    Chen, Xiaoling; Chang, Jeffrey T

    2017-04-15

    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. 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. https://github.com/jefftc/changlab. jeffrey.t.chang@uth.tmc.edu. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  4. 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

  5. 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.

  6. 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

  7. Soluble ferric iron as an effective protective agent against UV radiation: Implications for early life

    Science.gov (United States)

    Gómez, Felipe; Aguilera, Angeles; Amils, Ricardo

    2007-11-01

    Some recent MER Rover Opportunity results on ancient sedimentary rocks from Mars describe sandstones originated from the chemical weathering of olivine basalts by acidic waters [Squyres, S.W., Knoll, A.H., 2005. Earth Planet. Sci. Lett. 240, 1-10]. The absence of protective components in early Mars atmosphere forced any possible primordial life forms to deal with high doses of UV radiation. A similar situation occurred on the primitive Earth during the development of early life in the Archean [Berkner, L.V., Marshall, L.C., 1965. J. Atmos. Sci. 22 (3), 225-261; Kasting, J.F., 1993. Science 259, 920-926]. It is known that some cellular and/or external components can shield organisms from damaging UV radiation or quench its toxic effects [Olson, J.M., Pierson, B.K., 1986. Photosynth. Res. 9, 251-259; García-Pichel, F., 1998. Origins Life Evol. B 28, 321-347; Cockell, C., Rettberg, P., Horneck, G., Scherer, K., Stokes, M.D., 2003. Polar Biol. 26, 62-69]. The effectiveness of iron minerals for UV protection has also been reported [Phoenix, V.R., Konhauser, K.O., Adams, D.G., Bottrell, S.H., 2001. Geology 29 (9), 823-826], but nothing is known about the effect of iron in solution. Here we demonstrate the protective effect of soluble ferric iron against UV radiation on acidophilic photosynthetic microorganisms. These results offer an interesting alternative means of protection for life on the surface of early Mars and Earth, especially in light of the geochemical conditions in which the sedimentary minerals, jarosite and goethite, recently reported by the MER missions, were formed [Squyres, S.W., Arvidson, R.E., Bell III, J.F., Brückner, J., Cabrol, N.A., Calvin, W., Carr, M.H., Christensen, P.R., Clark, B.C., Crumpler, L., Des Marais, D.J., d'Uston, C., Economou, T., Farmer, J., Farrand, W., Folkner, W., Golombek, M., Gorevan, S., Grant, J.A., Greeley, R., Grotzinger, J., Haskin, L., Herkenhoff, K.E., Hviid, S., Johnson, J., Klingelhöfer, G., Knoll, A.H., Landis, G

  8. 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

  9. 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.

  10. 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

  11. 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

  12. 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)

  13. 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)

  14. 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.

  15. 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)

  16. A bioinformatics approach to marker development

    NARCIS (Netherlands)

    Tang, J.

    2008-01-01

    The thesis focuses on two bioinformatics research topics: the development of tools for an efficient and reliable identification of single nucleotides polymorphisms (SNPs) and polymorphic simple sequence repeats (SSRs) from expressed sequence tags (ESTs) (Chapter 2, 3 and 4), and the subsequent

  17. 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...

  18. An integrative bioinformatics pipeline for the genomewide ...

    Indian Academy of Sciences (India)

    An integrative bioinformatics pipeline for the genomewide identification of novel porcine microRNA genes. Wei Fang, Na Zhou, Dengyun Li, Zhigang Chen, Pengfei Jiang and Deli Zhang. J. Genet. 92,587 593. Figure 1. Primary sequence of the predicted SSc-mir-2053 precursor and locations of some terms in the secondary ...

  19. Novel bioinformatic developments for exome sequencing

    NARCIS (Netherlands)

    Lelieveld, S.H.; Veltman, J.A.; Gilissen, C.F.

    2016-01-01

    With the widespread adoption of next generation sequencing technologies by the genetics community and the rapid decrease in costs per base, exome sequencing has become a standard within the repertoire of genetic experiments for both research and diagnostics. Although bioinformatics now offers

  20. An integrative bioinformatics pipeline for the genomewide ...

    Indian Academy of Sciences (India)

    2013-12-06

    Dec 6, 2013 ... The majority of miRNAs in pig (Sus scrofa), an impor- tant domestic animal, remain unknown. From this perspec- tive, we attempted the genomewide identification of novel porcine miRNAs. Here, we propose a novel integrative bioinformatics pipeline to identify conservative and non- conservative novel ...

  1. 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 ...

  2. 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.

  3. 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...

  4. "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).…

  5. 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...

  6. 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:…

  7. 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…

  8. 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…

  9. Bioinformatics applications in proteomics data analysis

    NARCIS (Netherlands)

    Peng, M.

    2015-01-01

    In this thesis, I detail my 4-year efforts in developing bioinformatics tools and algorithms to address the growing demands of current proteomics endeavors, covering a range of facets such as large-scale protein expression profiling, charting post-translation modifications as well as

  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

    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.

  11. Agile parallel bioinformatics workflow management using Pwrake.

    Science.gov (United States)

    Mishima, Hiroyuki; Sasaki, Kensaku; Tanaka, Masahiro; Tatebe, Osamu; Yoshiura, Koh-Ichiro

    2011-09-08

    In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error.Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows. We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK) and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows. Pwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows. Furthermore, readability and maintainability of rakefiles

  12. Agile parallel bioinformatics workflow management using Pwrake

    Science.gov (United States)

    2011-01-01

    Background In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error. Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows. Findings We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK) and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows. Conclusions Pwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows. Furthermore, readability

  13. 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…

  14. 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.

  15. A Bioinformatics Reference Model: Towards a Framework for Developing and Organising Bioinformatic Resources

    Science.gov (United States)

    Hiew, Hong Liang; Bellgard, Matthew

    2007-11-01

    Life Science research faces the constant challenge of how to effectively handle an ever-growing body of bioinformatics software and online resources. The users and developers of bioinformatics resources have a diverse set of competing demands on how these resources need to be developed and organised. Unfortunately, there does not exist an adequate community-wide framework to integrate such competing demands. The problems that arise from this include unstructured standards development, the emergence of tools that do not meet specific needs of researchers, and often times a communications gap between those who use the tools and those who supply them. This paper presents an overview of the different functions and needs of bioinformatics stakeholders to determine what may be required in a community-wide framework. A Bioinformatics Reference Model is proposed as a basis for such a framework. The reference model outlines the functional relationship between research usage and technical aspects of bioinformatics resources. It separates important functions into multiple structured layers, clarifies how they relate to each other, and highlights the gaps that need to be addressed for progress towards a diverse, manageable, and sustainable body of resources. The relevance of this reference model to the bioscience research community, and its implications in progress for organising our bioinformatics resources, are discussed.

  16. The early adoption of intensity-modulated radiotherapy and stereotactic body radiation treatment among older Medicare beneficiaries with prostate cancer.

    Science.gov (United States)

    Jacobs, Bruce L; Yabes, Jonathan G; Lopa, Samia H; Heron, Dwight E; Chang, Chung-Chou H; Schroeck, Florian R; Bekelman, Justin E; Kahn, Jeremy M; Nelson, Joel B; Barnato, Amber E

    2017-08-01

    Several new prostate cancer treatments have emerged since 2000, including 2 radiotherapies with similar efficacy at the time of their introduction: intensity-modulated radiotherapy (IMRT) and stereotactic body radiation therapy (SBRT). The objectives of this study were to compare their early adoption patterns and identify factors associated with their use. By using the Surveillance, Epidemiology, and End Results (SEER)-Medicare database, patients who received radiation therapy during the 5 years after IMRT introduction (2001-2005) and the 5 years after SBRT introduction (2007-2011) were identified. The outcome of interest was the receipt of new radiation therapy (ie, IMRT or SBRT) compared with the existing standard radiation therapies at that time. The authors fit a series of multivariable, hierarchical logistic regression models accounting for patients nested within health service areas to examine the factors associated with the receipt of new radiation therapy. During 2001 to 2005, 5680 men (21%) received IMRT compared with standard radiation (n = 21,555). Men who received IMRT were older, had higher grade tumors, and lived in more populated areas (P adoption rate for IMRT was substantially higher than that for SBRT (44% vs 4%; P adoption rates of IMRT and SBRT at the time of their introduction. Further investigation of the nonclinical factors associated with this difference is warranted. Cancer 2017;123:2945-54. © 2017 American Cancer Society. © 2017 American Cancer Society.

  17. 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

  18. 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 Gagne's Conditions of Learning instructional design theory. This theory, although first published in the early 1970s, is still fundamental in instructional design and instructional technology. First, top-level as well as prerequisite learning objectives for a microarray analysis workshop and a primer design workshop were defined. Then a hierarchy of objectives for each workshop was created. Hands-on tutorials were designed to meet these objectives. Finally, events of learning proposed by Gagne's theory were incorporated into the hands-on tutorials. The resultant manuals were tested on a small number of trainees, revised, and applied in 1-day bioinformatics workshops. Based on this experience and on observations made during the workshops, we conclude that Gagne's Conditions of Learning instructional design theory provides a useful framework for developing bioinformatics training, but may not be optimal as a method for teaching it.

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

    African Journals Online (AJOL)

    The aim of this review is to discuss the importance of bioinformatics and emphasize the need to acquire bioinformatics training and skills so as to maximize its potentials for improved delivery of animal health. In this review, bioinformatics is introduced, challenges to effective animal disease diagnosis, prevention and control, ...

  20. 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…

  1. 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

  2. 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

  3. 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

  4. 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.

  5. 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)

  6. Bioinformatics Approaches for Human Gut Microbiome Research

    Directory of Open Access Journals (Sweden)

    Zhijun Zheng

    2016-07-01

    Full Text Available The human microbiome has received much attention because many studies have reported that the human gut microbiome is associated with several diseases. The very large datasets that are produced by these kinds of studies means that bioinformatics approaches are crucial for their analysis. Here, we systematically reviewed bioinformatics tools that are commonly used in microbiome research, including a typical pipeline and software for sequence alignment, abundance profiling, enterotype determination, taxonomic diversity, identifying differentially abundant species/genes, gene cataloging, and functional analyses. We also summarized the algorithms and methods used to define metagenomic species and co-abundance gene groups to expand our understanding of unclassified and poorly understood gut microbes that are undocumented in the current genome databases. Additionally, we examined the methods used to identify metagenomic biomarkers based on the gut microbiome, which might help to expand the knowledge and approaches for disease detection and monitoring.

  7. 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...... changes. These methods have been developed further and applied for computational screens of genomic sequence. Furthermore, a number of additional directions have emerged. These include methods to search for RNA 3D structure, RNA-RNA interactions, and design of interfering RNAs (RNAi) as well as methods...... 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....

  8. IEEE Nuclear and Space Radiation Effects Conference: Notes on the Early Conferences

    Science.gov (United States)

    Pellish, Jonathan A.; Galloway, Kenneth F.

    2013-01-01

    This paper gathers the remembrances of several key contributors who participated in the earliest Institute of Electrical and Electronics Engineers (IEEE) Nuclear and Space Radiation Effects Conferences (NSREC).

  9. VLSI Microsystem for Rapid Bioinformatic Pattern Recognition

    Science.gov (United States)

    Fang, Wai-Chi; Lue, Jaw-Chyng

    2009-01-01

    A system comprising very-large-scale integrated (VLSI) circuits is being developed as a means of bioinformatics-oriented analysis and recognition of patterns of fluorescence generated in a microarray in an advanced, highly miniaturized, portable genetic-expression-assay instrument. Such an instrument implements an on-chip combination of polymerase chain reactions and electrochemical transduction for amplification and detection of deoxyribonucleic acid (DNA).

  10. 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

  11. 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

  12. 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

  13. ballaxy: web services for structural bioinformatics.

    Science.gov (United States)

    Hildebrandt, Anna Katharina; Stöckel, Daniel; Fischer, Nina M; de la Garza, Luis; Krüger, Jens; Nickels, Stefan; Röttig, Marc; Schärfe, Charlotta; Schumann, Marcel; Thiel, Philipp; Lenhof, Hans-Peter; Kohlbacher, Oliver; Hildebrandt, Andreas

    2015-01-01

    Web-based workflow systems have gained considerable momentum in sequence-oriented bioinformatics. In structural bioinformatics, however, such systems are still relatively rare; while commercial stand-alone workflow applications are common in the pharmaceutical industry, academic researchers often still rely on command-line scripting to glue individual tools together. In this work, we address the problem of building a web-based system for workflows in structural bioinformatics. For the underlying molecular modelling engine, we opted for the BALL framework because of its extensive and well-tested functionality in the field of structural bioinformatics. The large number of molecular data structures and algorithms implemented in BALL allows for elegant and sophisticated development of new approaches in the field. We hence connected the versatile BALL library and its visualization and editing front end BALLView with the Galaxy workflow framework. The result, which we call ballaxy, enables the user to simply and intuitively create sophisticated pipelines for applications in structure-based computational biology, integrated into a standard tool for molecular modelling.  ballaxy consists of three parts: some minor modifications to the Galaxy system, a collection of tools and an integration into the BALL framework and the BALLView application for molecular modelling. Modifications to Galaxy will be submitted to the Galaxy project, and the BALL and BALLView integrations will be integrated in the next major BALL release. After acceptance of the modifications into the Galaxy project, we will publish all ballaxy tools via the Galaxy toolshed. In the meantime, all three components are available from http://www.ball-project.org/ballaxy. Also, docker images for ballaxy are available at https://registry.hub.docker.com/u/anhi/ballaxy/dockerfile/. ballaxy is licensed under the terms of the GPL. © The Author 2014. Published by Oxford University Press. All rights reserved. For

  14. 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

  15. 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.

  16. Bioinformatics on the cloud computing platform Azure.

    Directory of Open Access Journals (Sweden)

    Hugh P Shanahan

    Full Text Available 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.

  17. 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.

  18. 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.

  19. Bioinformatics training: a review of challenges, actions and support requirements.

    Science.gov (United States)

    Schneider, Maria Victoria; Watson, James; Attwood, Teresa; Rother, Kristian; Budd, Aidan; McDowall, Jennifer; Via, Allegra; Fernandes, Pedro; Nyronen, Tommy; Blicher, Thomas; Jones, Phil; Blatter, Marie-Claude; De Las Rivas, Javier; Judge, David Phillip; van der Gool, Wouter; Brooksbank, Cath

    2010-11-01

    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 Trainer Networking Session held under the auspices of the EU-funded SLING Integrating Activity, which took place in November 2009.

  20. 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...

  1. 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.

  2. 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

  3. Early

    Directory of Open Access Journals (Sweden)

    Kamel Abd Elaziz Mohamed

    2014-04-01

    Conclusion: Early PDT is recommended for patients who require prolonged tracheal intubation in the ICU as outcomes like the duration of mechanical ventilation length of ICU stay and hospital stay were significantly shorter in early tracheostomy.

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

    Science.gov (United States)

    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

    2018-01-06

    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 to tumor necrosis, and increased rates of tumor apoptosis have been implied; however, in-human evidence remains scarce. The present study reports unique pathologic confirmation of SBRT-induced biological effects within spinal metastases treated with preoperative SBRT. Ten patients with spinal metastases secondary to various solid tumors were treated with preoperative single-fraction SBRT (18 Gy) to the magnetic resonance imaging-defined macroscopic metastasis, followed by spinal stabilization within 24 hours. Perioperative samples of spinal metastases were obtained, and 6 patients also had a pre-SBRT biopsy specimen available for a matched comparison. The samples were stained for tumor necrosis on routine hematoxylin-eosin-stained slices and, subsequently, immunohistochemical staining for T cells (CD3+, CD4+, CD8+), natural killer cells (CD56+), endothelium (CD31+), and apoptotic activity (caspase-3). Perioperative biopsy specimens were obtained ∼6 hours (range 4.5-7.5) or 21 hours (range 18.5-22.5) after SBRT. Necrosis was observed in 83% of the 21-hour post-SBRT samples (5 of 6) compared with 0% of pre-SBRT biopsies (0 of 6) and 6-hour post-SBRT biopsies (0 of 4). Tumor cell apoptosis had increased greatly in the 21-hour post-SBRT samples compared with before and 6 hours after SBRT. The CD31+ vessel counts decreased after SBRT, as did mitotic activity. Both of the renal cell metastases displayed major decreases in vessel density. Desmoplastic reaction was visible in 67% (4 of 6) of the pre-SBRT samples compared with 100% (10 of 10) the post-SBRT samples. The T-cell and natural killer cell counts were relatively unaffected. High-dose single-fraction SBRT induced tumor

  5. 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.

  6. 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

  7. Early Results from the Advanced Radiation Protection Thick GCR Shielding Project

    Science.gov (United States)

    Norman, Ryan B.; Clowdsley, Martha; Slaba, Tony; Heilbronn, Lawrence; Zeitlin, Cary; Kenny, Sean; Crespo, Luis; Giesy, Daniel; Warner, James; McGirl, Natalie; hide

    2017-01-01

    The Advanced Radiation Protection Thick Galactic Cosmic Ray (GCR) Shielding Project leverages experimental and modeling approaches to validate a predicted minimum in the radiation exposure versus shielding depth curve. Preliminary results of space radiation models indicate that a minimum in the dose equivalent versus aluminum shielding thickness may exist in the 20-30 g/cm2 region. For greater shield thickness, dose equivalent increases due to secondary neutron and light particle production. This result goes against the long held belief in the space radiation shielding community that increasing shielding thickness will decrease risk to crew health. A comprehensive modeling effort was undertaken to verify the preliminary modeling results using multiple Monte Carlo and deterministic space radiation transport codes. These results verified the preliminary findings of a minimum and helped drive the design of the experimental component of the project. In first-of-their-kind experiments performed at the NASA Space Radiation Laboratory, neutrons and light ions were measured between large thicknesses of aluminum shielding. Both an upstream and a downstream shield were incorporated into the experiment to represent the radiation environment inside a spacecraft. These measurements are used to validate the Monte Carlo codes and derive uncertainty distributions for exposure estimates behind thick shielding similar to that provided by spacecraft on a Mars mission. Preliminary results for all aspects of the project will be presented.

  8. Stereotactic body radiation therapy (SBRT) for early stage lung cancer delivers clinically significant radiation to the draining lymph nodes

    Science.gov (United States)

    Singh, Prabhsimranjot; Christos, Paul; Arora, Shruthi; Desai, Prashant; Wernicke, A Gabriella; Delamerced, Marylynn; Boothe, Dustin; Nori, Dattatreyudu; Chao, KSC

    2013-01-01

    Background To evaluate clinically significant radiotherapy (RT) dose to draining lymph nodes (LN) in patients treated with SBRT. Findings Early stage non-small cell lung cancer patients treated with SBRT were selected for analysis. Patients received SBRT if they were not considered eligible for surgical resection. RT plans for 29 patients (32 lesions) were analyzed. For each patient, ipsilateral and contralateral levels 2, 3, 4, 5, 6, 7 and ipsilateral hilar LN stations were contoured. Dose volume histograms and dosimetric coverage of each lymph node region were obtained for each patient. There were 14 males and 15 females. Median age was 75 (range 60-89). Clinically significant RT was received at the corresponding draining lymph node station depending on the primary tumor location. Friedman’s non-parametric test revealed a statistically significant difference in RT dose to LN stations depending on the location of the tumor (p<0.0001). Conclusion SBRT for early stage lung cancer results in significant RT dose to the draining LN. This RT dose may be sufficient to eliminate subclinical microscopic disease despite being a highly conformal treatment. Prospective studies are needed to evaluate if SBRT is comparable to lobectomy plus mediastinal lymph node dissection as a treatment option. PMID:29296376

  9. 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.)

  10. 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

  11. 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

  12. Voice Quality After Treatment of Early Vocal Cord Cancer: A Randomized Trial Comparing Laser Surgery With Radiation Therapy

    Energy Technology Data Exchange (ETDEWEB)

    Aaltonen, Leena-Maija, E-mail: leena-maija.aaltonen@hus.fi [Department of Otorhinolaryngology–Head and Neck Surgery, Helsinki University Central Hospital, and University of Helsinki, Helsinki (Finland); Rautiainen, Noora; Sellman, Jaana [Institute of Behavioural Sciences, University of Helsinki, Helsinki (Finland); Saarilahti, Kauko [Department of Oncology, Helsinki University Central Hospital, and University of Helsinki, Helsinki (Finland); Mäkitie, Antti; Rihkanen, Heikki [Department of Otorhinolaryngology–Head and Neck Surgery, Helsinki University Central Hospital, and University of Helsinki, Helsinki (Finland); Laranne, Jussi; Kleemola, Leenamaija [Department of Otorhinolaryngology–Head and Neck Surgery, Tampere University Hospital, and University of Tampere, Tampere (Finland); Wigren, Tuija [Department of Oncology, Tampere University Hospital, and University of Tampere, Tampere (Finland); Sala, Eeva [Department of Otorhinolaryngology–Head and Neck Surgery, Turku University Hospital, and University of Turku, Turku (Finland); Lindholm, Paula [Department of Oncology, Turku University Hospital, and University of Turku, Turku (Finland); Grenman, Reidar [Department of Otorhinolaryngology–Head and Neck Surgery, Turku University Hospital, and University of Turku, Turku (Finland); Joensuu, Heikki [Department of Oncology, Helsinki University Central Hospital, and University of Helsinki, Helsinki (Finland)

    2014-10-01

    Objective: Early laryngeal cancer is usually treated with either transoral laser surgery or radiation therapy. The quality of voice achieved with these treatments has not been compared in a randomized trial. Methods and Materials: Male patients with carcinoma limited to 1 mobile vocal cord (T1aN0M0) were randomly assigned to receive either laser surgery (n=32) or external beam radiation therapy (n=28). Surgery consisted of tumor excision with a CO{sub 2} laser with the patient under general anaesthesia. External beam radiation therapy to the larynx was delivered to a cumulative dose of 66 Gy in 2-Gy daily fractions over 6.5 weeks. Voice quality was assessed at baseline and 6 and 24 months after treatment. The main outcome measures were expert-rated voice quality on a grade, roughness, breathiness, asthenia, and strain (GRBAS) scale, videolaryngostroboscopic findings, and the patients' self-rated voice quality and its impact on activities of daily living. Results: Overall voice quality between the groups was rated similar, but voice was more breathy and the glottal gap was wider in patients treated with laser surgery than in those who received radiation therapy. Patients treated with radiation therapy reported less hoarseness-related inconvenience in daily living 2 years after treatment. Three patients in each group had local cancer recurrence within 2 years from randomization. Conclusions: Radiation therapy may be the treatment of choice for patients whose requirements for voice quality are demanding. Overall voice quality was similar in both treatment groups, however, indicating a need for careful consideration of patient-related factors in the choice of a treatment option.

  13. 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.

  14. Bioinformatic analysis of whole genome sequencing data

    OpenAIRE

    Maqbool, Khurram

    2014-01-01

    Evolution has shaped the life forms for billion of years. Domestication is an accelerated process that can be used as a model for evolutionary changes. The aim of this thesis project has been to carry out extensive bioinformatic analyses of whole genome sequencing data to reveal SNPs, InDels and selective sweeps in the chicken, pig and dog genome. Pig genome sequencing revealed loci under selection for elongation of back and increased number of vertebrae, associated with the NR6A1, PLAG1,...

  15. Top considerations for creating bioinformatics software documentation.

    Science.gov (United States)

    Karimzadeh, Mehran; Hoffman, Michael M

    2017-01-14

    Investing in documenting your bioinformatics software well can increase its impact and save your time. To maximize the effectiveness of your documentation, we suggest following a few guidelines we propose here. We recommend providing multiple avenues for users to use your research software, including a navigable HTML interface with a quick start, useful help messages with detailed explanation and thorough examples for each feature of your software. By following these guidelines, you can assure that your hard work maximally benefits yourself and others. © The Author 2017. Published by Oxford University Press.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Safdieh, Joseph; Schwartz, David; Weiner, Joseph; Weiss, Jeffrey P.; Madeb, Isaac; Rotman, Marvin; Schreiber, David [Dept.of Veteran Affairs, New York Harbor Healthcare System, Brooklyn (United States); Rineer, Justin [University of Florida Health Cancer Center, Orlando (United States)

    2014-09-15

    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.

  1. Cytogenetic analysis of thymocytes during early stages after irradiation in mice with different susceptibilities to radiation-induced lymphomagenesis

    International Nuclear Information System (INIS)

    Chen Ying; Kubo, Eiko; Sado, Toshihiko; Muto, Masahiro.

    1996-01-01

    To investigate the relationship between radiation-induced chromosomal instability and lymphomagenesis, the incidences of chromosome aberrations and of cells with abnormal chromosome complements in the thymuses of B10. Thy 1.1 and STS/A strains which have shown marked differences in susceptibility to radiation-induced lymphomagenesis were compared at an early time (12-33 days) after whole-body X-irradiation (1.61 Gy X 4). Numerical and structural aberrations of chromosome in B10. Thy 1.1 mice were higher than those in STS/A mice. The average incidence of trisomy 15 was 37.5% (12/32 mice) from 12 days to 32 days after irradiation in B10. Thy 1.1 mice, whereas none was found (0/38 mice) in STS/A mice. Frequencies of aberrations in chromosomes 11, 12, 15 of the thymocytes from irradiated B10. Thy 1.1 mice were higher than those from irradiated STS/A mice, and especially, the most frequent translocations occurred in the E-F regions of chromosome 12. Using B10. Thy 1 congenic mice, we found that in many cases (8/13), the chromosome aberrations detected in the thymocytes from B10. Thy 1.1 mice at an early time after irradiation could also be observed in the donor-type (Thy 1.1) lymphomas developed from recipient mice 4-5 months after intrathymic injection, suggesting that these chromosome aberrations have some role in lymphomagenesis. The difference of chromosome instability detected at an early time after irradiation might be due to genetic background with regard to genomic instability induced by radiation. (author)

  2. Teaching the ABCs of bioinformatics: a brief introduction to the Applied Bioinformatics Course.

    Science.gov (United States)

    Luo, Jingchu

    2014-11-01

    With the development of the Internet and the growth of online resources, bioinformatics training for wet-lab biologists became necessary as a part of their education. This article describes a one-semester course 'Applied Bioinformatics Course' (ABC, http://abc.cbi.pku.edu.cn/) that the author has been teaching to biological graduate students at the Peking University and the Chinese Academy of Agricultural Sciences for the past 13 years. ABC is a hands-on practical course to teach students to use online bioinformatics resources to solve biological problems related to their ongoing research projects in molecular biology. With a brief introduction to the background of the course, detailed information about the teaching strategies of the course are outlined in the 'How to teach' section. The contents of the course are briefly described in the 'What to teach' section with some real examples. The author wishes to share his teaching experiences and the online teaching materials with colleagues working in bioinformatics education both in local and international universities. © The Author 2013. Published by Oxford University Press.

  3. 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…

  4. Radiation therapy after breast augmentation or reconstruction in early or recurrent breast cancer

    International Nuclear Information System (INIS)

    Ryu, J.; Yahalom, J.; Shank, B.; Chaglassian, T.A.; McCormick, B.

    1990-01-01

    Fourteen patients whose augmented or reconstructed breasts were treated with radiation therapy were analyzed. Silicone gel implants were used in 13 patients and free-injected silicone in one patient. The total radiation dose ranged from 4400 to 6200 cGy using tangential photon fields or an en face electron field by megavoltage equipment. In several cases, electron boost radiation was added to the tumor bed. The majority of the patients tolerated therapy well with minimal transient skin reactions; only three patients required a treatment break secondary to moist desquamation. Three patients developed documented implant encapsulation, although the majority retained good to excellent cosmesis. In summary, when breast carcinoma arises in the augmented or reconstructed breast, conservative management (i.e., limited surgery and definitive irradiation) is feasible without compromising the therapy or the cosmetic result. Thus, conservative management should be offered as an option to patients who are interested in breast prosthesis conservation

  5. Bioinformatics tools for predicting GPCR gene functions.

    Science.gov (United States)

    Suwa, Makiko

    2014-01-01

    The automatic classification of GPCRs by bioinformatics methodology can provide functional information for new GPCRs in the whole 'GPCR proteome' and this information is important for the development of novel drugs. Since GPCR proteome is classified hierarchically, general ways for GPCR function prediction are based on hierarchical classification. Various computational tools have been developed to predict GPCR functions; those tools use not simple sequence searches but more powerful methods, such as alignment-free methods, statistical model methods, and machine learning methods used in protein sequence analysis, based on learning datasets. The first stage of hierarchical function prediction involves the discrimination of GPCRs from non-GPCRs and the second stage involves the classification of the predicted GPCR candidates into family, subfamily, and sub-subfamily levels. Then, further classification is performed according to their protein-protein interaction type: binding G-protein type, oligomerized partner type, etc. Those methods have achieved predictive accuracies of around 90 %. Finally, I described the future subject of research of the bioinformatics technique about functional prediction of GPCR.

  6. 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.

  7. 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

  8. 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

  9. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    Senthi, Sashendra, E-mail: sashasenthi@msn.com [Department of Radiation Oncology, Peter MacCallum Cancer Centre, Melbourne (Australia); Link, Emma [Centre for Biostatistics and Clinical Trials, Peter MacCallum Cancer Centre, Melbourne (Australia); Chua, Boon H. [Department of Radiation Oncology, Peter MacCallum Cancer Centre, Melbourne (Australia); University of Melbourne, Melbourne (Australia)

    2012-10-01

    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.

  11. 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.

  12. Long-term results of forward intensity-modulated radiation therapy for patients with early-stage breast cancer

    Energy Technology Data Exchange (ETDEWEB)

    Ha, Boram; Suh, Hyun Suk; Lee, Ji Hae; Lee, Kyung Ja; Lee, Rena; Moon, Byung In [Ewha Womans University College of Medicine, Seoul (Korea, Republic of)

    2013-12-15

    To observe long-term clinical outcomes for patients with early-stage breast cancer treated with forward intensity-modulated radiation therapy (IMRT), including local control and clinical toxicities. We retrospectively analyzed a total of 214 patients with stage I-II breast cancer who were treated with breast conserving surgery followed by adjuvant breast radiation therapy between 2001 and 2008. All patients were treated using forward IMRT. The whole breast was irradiated to a dose of 50 to 50.4 Gy followed by an 8 to 12 Gy electron boost to the surgical bed. The median age was 46 years (range, 21 to 82 years) and the medial follow-up time was 7.3 years (range, 2.4 to 11.7 years). Stage T1 was 139 (65%) and T2 was 75 (35%), respectively. Ipsilateral breast recurrence was observed in 3 patients. The 5- and 10-year local control rates were 99.1% and 97.8%, respectively. The cosmetic outcome was evaluated according to the Harvard scale and 89.4% of patients were scored as excellent or good. The whole breast radiation therapy as an adjuvant treatment using a forward IMRT technique showed excellent long-term local control as well as favorable outcomes of toxicity and cosmesis.

  13. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    Hopewell, J.W.; Van den Aardweg, G.J.M.J.; Morris, G.M. [Univ. of Oxford (United Kingdom)] [and others

    1994-12-01

    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 {beta}-rays from 22.5 mm diameter {sup 90}Sr/{sup 90}Y plaques at a dose rate of {approximately}3 Gy/min. Essential fatty acids were administered orally in the form of two {open_quotes}active{close_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}placebo{close_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}active{close_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 {beta}-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.

  15. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Gorman, Sheeona; Tosetto, Miriam [Centre for Colorectal Disease, St. Vincent' s University Hospital, Elm Park, Dublin 4 (Ireland); Lyng, Fiona; Howe, Orla [Radiation and Environmental Science Centre, Dublin Institute of Technology and St. Luke' s Hospital, Dublin (Ireland); Sheahan, Kieran; O' Donoghue, Diarmuid; Hyland, John; Mulcahy, Hugh [Centre for Colorectal Disease, St. Vincent' s University Hospital, Elm Park, Dublin 4 (Ireland); O' Sullivan, Jacintha, E-mail: jacintha.osullivan@ucd.ie [Centre for Colorectal Disease, St. Vincent' s University Hospital, Elm Park, Dublin 4 (Ireland)

    2009-10-02

    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 2 Gy, 5 Gy, 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 (0 Gy) at 24 h. There was no significant difference between 2 Gy and 5 Gy treatments, or between effects elicited by tumor versus matched normal tissue. Bystander cells exposed to media from 2 Gy 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

  17. 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

  18. Radiation therapy planning with photons and protons for early and advanced breast cancer: an overview

    Directory of Open Access Journals (Sweden)

    Lomax Antony J

    2006-07-01

    Full Text Available Abstract Postoperative radiation therapy substantially decreases local relapse and moderately reduces breast cancer mortality, but can be associated with increased late mortality due to cardiovascular morbidity and secondary malignancies. Sophistication of breast irradiation techniques, including conformal radiotherapy and intensity modulated radiation therapy, has been shown to markedly reduce cardiac and lung irradiation. The delivery of more conformal treatment can also be achieved with particle beam therapy using protons. Protons have superior dose distributional qualities compared to photons, as dose deposition occurs in a modulated narrow zone, called the Bragg peak. As a result, further dose optimization in breast cancer treatment can be reasonably expected with protons. In this review, we outline the potential indications and benefits of breast cancer radiotherapy with protons. Comparative planning studies and preliminary clinical data are detailed and future developments are considered.

  19. 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

  20. Applied bioinformatics: Genome annotation and transcriptome analysis

    DEFF Research Database (Denmark)

    Gupta, Vikas

    and dhurrin, which have not previously been characterized in blueberries. There are more than 44,500 spider species with distinct habitats and unique characteristics. Spiders are masters of producing silk webs to catch prey and using venom to neutralize. The exploration of the genetics behind these properties...... japonicus (Lotus), Vaccinium corymbosum (blueberry), Stegodyphus mimosarum (spider) and Trifolium occidentale (clover). From a bioinformatics data analysis perspective, my work can be divided into three parts; genome annotation, small RNA, and gene expression analysis. Lotus is a legume of significant...... has just started. We have assembled and annotated the first two spider genomes to facilitate our understanding of spiders at the molecular level. The need for analyzing the large and increasing amount of sequencing data has increased the demand for efficient, user friendly, and broadly applicable...

  1. 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.

  2. Applied bioinformatics: Genome annotation and transcriptome analysis

    DEFF Research Database (Denmark)

    Gupta, Vikas

    japonicus (Lotus), Vaccinium corymbosum (blueberry), Stegodyphus mimosarum (spider) and Trifolium occidentale (clover). From a bioinformatics data analysis perspective, my work can be divided into three parts; genome annotation, small RNA, and gene expression analysis. Lotus is a legume of significant...... biology and genetics studies. We present an improved Lotus genome assembly and annotation, a catalog of natural variation based on re-sequencing of 29 accessions, and describe the involvement of small RNAs in the plant-bacteria symbiosis. Blueberries contain anthocyanins, other pigments and various...... polyphenolic compounds, which have been linked to protection against diabetes, cardiovascular disease and age-related cognitive decline. We present the first genome- guided approach in blueberry to identify genes involved in the synthesis of health-protective compounds. Using RNA-Seq data from five stages...

  3. 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...

  4. 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

  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. Prospective study to determine early hypertrophy of the contra-lateral liver lobe after unilobar, Yttrium-90, selective internal radiation therapy in patients with hepatocellular carcinoma.

    Science.gov (United States)

    Teo, Jin Yao; Allen, John Carson; Ng, David Chee Eng; Abdul Latiff, Julianah Bee; Choo, Su Pin; Tai, David Wai-Meng; Low, Albert Su Chong; Cheah, Foong Koon; Chang, Jason Pik Eu; Kam, Juinn Huar; Lee, Victor T W; Chung, Alexander Yaw Fui; Chan, Chung Yip; Chow, Pierce Kah Hoe; Goh, Brian K P

    2018-01-03

    Liver resection is a major curative option in patients presenting with hepatocellular carcinoma. An inadequate functional liver remnant is a major limiting factor precluding liver resection. In recent years, hypertrophy of the functional liver remnant after selective internal radiation therapy hypertrophy has been observed, but the degree of hypertrophy in the early postselective internal radiation therapy period has not been well studied. We conducted a prospective study on patients undergoing unilobar, Yttrium-90 selective internal radiation therapy for hepatocellular carcinoma to evaluate early hypertrophy at 4-6 weeks and 8-12 weeks after selective internal radiation therapy. In the study, 24 eligible patients were recruited and had serial volumetric measurements performed. The median age was 66 years (38-75 years). All patients were either Child-Pugh Class A or B, and 6/24 patients had documented, clinically relevant portal hypertension; 15 of the 24 patients were hepatitis B positive. At 4-6 weeks, modest hypertrophy was seen (median 3%; range -12 to 42%) and this increased at 8-12 weeks (median 9%; range -12 to 179%). No preprocedural factors predictive of hypertrophy were identified. Hypertrophy of the functional liver remnant after selective internal radiation therapy with Yttrium-90 occurred in a subset of patients but was modest and unpredictable in the early stages. Selective internal radiation therapy cannot be recommended as a standard treatment modality to induce early hypertrophy for patients with hepatocellular carcinoma. (Surgery 2017;160:XXX-XXX.). Copyright © 2017 Elsevier Inc. All rights reserved.

  7. 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.

  8. Rust-Bio: a fast and safe bioinformatics library

    NARCIS (Netherlands)

    J. Köster (Johannes)

    2015-01-01

    textabstractWe present Rust-Bio, the first general purpose bioinformatics library for the innovative Rust programming language. Rust-Bio leverages the unique combination of speed, memory safety and high-level syntax offered by Rust to provide a fast and safe set of bioinformatics algorithms and data

  9. 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 ...

  10. The 2015 Bioinformatics Open Source Conference (BOSC 2015.

    Directory of Open Access Journals (Sweden)

    Nomi L Harris

    2016-02-01

    Full Text Available 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.

  11. 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 ...

  12. 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.

  13. Perspectives on presentation and pedagogy in aid of bioinformatics education.

    Science.gov (United States)

    Buttigieg, Pier Luigi

    2010-11-01

    Using live presentation to communicate the interdisciplinary and abstract content of bioinformatics to its educationally diverse studentship is a sizeable challenge. This review collects a number of perspectives on multimedia presentation, visual communication and pedagogy. The aim is to encourage educators to reflect on the great potential of live presentation in facilitating bioinformatics education.

  14. 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 ...

  15. 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…

  16. 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…

  17. 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…

  18. 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.

  19. The Solar Radiation and Climate Experiment (SORCE) Mission Description and Early Results

    CERN Document Server

    Rottman, G; George, V

    2005-01-01

    This book describes the state-of-the art instruments for measuring the solar irradiance from soft x-ray to the near infrared and the total solar irradiance. Furthermore, the SORCE mission and early results on solar variability are presented along with papers that provide an overview of solar influences on Earth.

  20. 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

  1. 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.

  2. 4273π: Bioinformatics education on low cost ARM hardware

    Science.gov (United States)

    2013-01-01

    Background 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. Results 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. Conclusions 4273π is a means to teach bioinformatics, including systems administration tasks, to undergraduates at low cost. PMID:23937194

  3. 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.

  4. 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.

  5. Early radiation-induced changes evaluated by intravoxel incoherent motion in the major salivary glands.

    Science.gov (United States)

    Marzi, Simona; Forina, Chiara; Marucci, Laura; Giovinazzo, Giuseppe; Giordano, Carolina; Piludu, Francesca; Landoni, Valeria; Spriano, Giuseppe; Vidiri, Antonello

    2015-04-01

    To investigate the potential of intravoxel incoherent motion (IVIM) MRI for early evaluation of irradiated major salivary glands. Thirty-four patients with head-neck cancer were included in a prospective study. All patients underwent three serial IVIM-MRI: before, half-way through, and at the end of radiotherapy (RT). Apparent diffusion coefficient (ADC), ADClow derived in the low b-value range, perfusion fraction f, and pure diffusion coefficient D were estimated. Pretreatment values and early changes of diffusion parameters were correlated with parotid mean dose (Dmean ) and volume reduction after RT. Changes in diffusion parameters over time were all significant (P salivary glands can be noninvasively evaluated by IVIM-MRI. Perfusion-related coefficients in conjunction with dosimetric information increase our capability to predict the change in parotid volume and hence, if further validated, guide treatment strategy in RT. © 2014 Wiley Periodicals, Inc.

  6. MRI to quantify early radiation-induced changes in the salivary glands.

    Science.gov (United States)

    Houweling, Antonetta C; Schakel, Tim; van den Berg, Cornelis A T; Philippens, Marielle E P; Roesink, Judith M; Terhaard, Chris H J; Raaijmakers, Cornelis P J

    2011-09-01

    We investigated radiation-induced changes in the salivary glands, 6 weeks after RT, using MRI. Eighteen oropharyngeal cancer patients were treated with salivary gland sparing IMRT. All patients received a 3T MRI exam before and 6 weeks after the end of RT, including a T(1)-weighted (T(1)w), a T(2)-weighted (T(2)w), and a dynamic contrast-enhanced (DCE) MRI. For both time points separately, the parotid and submandibular glands were delineated on the MR images. Differences in median signal intensity and signal variation within the glands were tested for significance. Correlations were studied between the MR changes and the planned RT dose. The volume of the glands reduced significantly by 25%. The T(1)w signal decreased by 10% and the T(2)w signal increased by 23%. The k(ep) value decreased, while the v(e) increased. A correlation of the changes in T(2)w signal with the mean dose was found in both glands. Overall radiation-induced changes and volume loss were observed in the parotid and submandibular gland using MR. The observed differences indicated an increased water content such as found in oedema. The overall changes could be related to the mean dose, with a slightly greater impact in the high dose area. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  7. 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.

  8. 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

  9. Amplification of oncogenes in early-stage, radiation-induced rat skin tumours

    International Nuclear Information System (INIS)

    Ashkenazi-Kimmel, T.

    1989-10-01

    The effect of gene amplification on tumour size and growth was investigated in 39 samples collected from 23 radiation-induced rat skin tumours. The relationships of both the time from irradiation and the time from first appearance of the tumour to gene amplification were also examined. DNA from each tumour sample was extracted and probed for abl, fos, c-myc, N-myc, H-ras, and K-ras, and amplification of all but N-myc was detected. A single amplified gene was observed in 8 of 39 samples; multiple amplified genes were found in an additional 7. The amplification of c-myc, H-ras, or K-ras was found to be associated with increase in tumour size. c-myc amplification was also associated with an increase in growth rate. Amplification of c-myc was found to occur as a late-stage event in these tumours. The results suggest that both myc and ras genes play unique roles in the growth and development of radiation tumours, and they provide new information on the temporal aspects of c-myc activation. 77 refs., 26 figs., 11 tabs

  10. 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

  11. 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

  12. The effect of ultraviolet radiation on early stages of activation of human lymphocytes: inhibition is independent of effects on DNA

    DEFF Research Database (Denmark)

    Castellanos, G; Owens, T; Rudd, C

    1982-01-01

    before mitogen was added to the cultures, but were unaffected if irradiation occurred after 16 h of culture in presence of Con A. Cells irradiated with 84 ergs/mm2 at the onset of culture with mitogen did not show the early increase of cation pump function which is a characteristic of stimulated......Low doses (30-84 ergs/mm2, 1 erg = 10(7) J) of ultraviolet radiation (UV) caused severe inhibition of the proliferation of human lymphocytes in vitro. Greatest inhibition was produced when resting cells were irradiated immediately prior to stimulation with concanavalin A (Con A); this was true...... lymphocytes, when this was measured by means of 86Rb uptake after 2-4 h culture. The mitogen-stimulated activation of cation pump function has previously been shown to be unaffected by concentrations of cycloheximide and actinomycin D which produce virtually complete inhibition of protein and RNA synthesis...

  13. 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

  14. 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

    2012-12-01

    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.].

  15. 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

  16. 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)

  17. 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

  18. 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

  19. [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.

  20. Early to mid Cretaceous vegetation of northern Gondwana - the onset of angiosperm radiation and climatic implications

    Science.gov (United States)

    Coiffard, Clément; Mohr, Barbara

    2014-05-01

    Early Cretaceous Northern Gondwana seems to be the cradle of many early flowering plants, especially mesangiosperms that include magnoliids and monocots and basal eudicots. So far our knowledge was based mostly on dispersed pollen and small flowering structures. New fossil finds from Brazil include more complete plants with attached roots, leaves and flowers. Taxonomic studies show that these fossils belonged to clades which are, based on macroscopic characters and molecular data, also considered to be rather basal, such as several members of Nymphaeales, Piperales, Laurales, Magnoliales, monocots (Araliaceae) and Ranunculales. Various parameters can be used in order to understand the physiology and habitat of these plants. Adaptations to climate and habitat are partly mirrored in their root anatomy (evidence of tap roots), leaf size and shape, leaf anatomy including presence of glands, and distribution of stomata. An important ecophysiolocical parameter is vein density as an indicator for the plants' cabability to pump water, and the stomatal pore index, representing the proportion of stomatal pore area on the leaf surface, which is related to the water vapor resistance of the leaf epidermis. During the mid-Cretaceous leaf vein density started to surpass that of gymnosperms, one factor that made angiosperms very successful in conquering many kinds of new environments. Using data on these parameters we deduce that during the late Early to mid Cretaceous angiosperms were already diverse, being represented as both herbs, with aquatic members, such as Nymphaeles, helophytes (e.g. some monocots) and plants that may have grown in shady locations. Other life forms included shrubs and perhaps already small trees (e.g. Magnoliales). These flowering plants occupied various habitats, ranging from xeric (e.g. some Magnoliales) to mesic and shady (e.g. Piperales) or aquatic (e.g. Araceae, Nymphaeales). Overall, it seems that several of these plants clearly exhibited some

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

    Science.gov (United States)

    Sørensen, Brita Singers; Bassler, Niels; Nielsen, Steffen; Horsman, Michael R; Grzanka, Leszek; Spejlborg, Harald; Swakoń, Jan; Olko, Paweł; Overgaard, Jens

    2017-11-01

    The aim of the present study was to examine the RBE for early damage in an in vivo mouse model, and the effect of the increased linear energy transfer (LET) towards the distal edge of the spread-out Bragg peak (SOBP). The lower part of the right hind limb of CDF1 mice was irradiated with single fractions of either 6 MV photons, 240 kV photons or scanning beam protons and graded doses were applied. For the proton irradiation, the leg was either placed in the middle of a 30-mm SOBP, or to assess the effect in different positions, irradiated in 4 mm intervals from the middle 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. The MDD 50 values with 95% confidence intervals were 36.1 (34.2-38.1) Gy for protons in the middle of the SOBP for score 3.5. For 6 MV photons, it was 35.9 (34.5-37.5) Gy and 32.6 (30.7-34.7) Gy for 240 kV photons for score 3.5. The corresponding RBE was 1.00 (0.94-1.05), relative to 6 MV photons and 0.9 (0.85-0.97) relative to 240 kV photons. In the mice group positioned at the SOBP distal dose fall-off, 25% of the mice developed early skin damage compared with 0-8% in other groups. LET d,z = 1 was 8.4 keV/μm at the distal dose fall-off and the physical dose delivered was 7% lower than in the central SOBP position, where LET d,z =1 was 3.3 keV/μm. 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.

  2. 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

  3. 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.

  4. 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.

  5. Bioinformatic landscapes for plant transcription factor system research.

    Science.gov (United States)

    Wang, Yijun; Lu, Wenjie; Deng, Dexiang

    2016-02-01

    Diverse bioinformatic resources have been developed for plant transcription factor (TF) research. This review presents the bioinformatic resources and methodologies for the elucidation of plant TF-mediated biological events. Such information is helpful to dissect the transcriptional regulatory systems in the three reference plants Arabidopsis , rice, and maize and translation to other plants. Transcription factors (TFs) orchestrate diverse biological programs by the modulation of spatiotemporal patterns of gene expression via binding cis-regulatory elements. Advanced sequencing platforms accompanied by emerging bioinformatic tools revolutionize the scope and extent of TF research. The system-level integration of bioinformatic resources is beneficial to the decoding of TF-involved networks. Herein, we first briefly introduce general and specialized databases for TF research in three reference plants Arabidopsis, rice, and maize. Then, as proof of concept, we identified and characterized heat shock transcription factor (HSF) members through the TF databases. Finally, we present how the integration of bioinformatic resources at -omics layers can aid the dissection of TF-mediated pathways. We also suggest ways forward to improve the bioinformatic resources of plant TFs. Leveraging these bioinformatic resources and methodologies opens new avenues for the elucidation of transcriptional regulatory systems in the three model systems and translation to other plants.

  6. 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.

  7. 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

    INTRODUCTION: The aim of the present study was to examine the RBE for early damage in an in vivo mouse model, and the effect of the increased linear energy transfer (LET) towards the distal edge of the spread-out Bragg peak (SOBP). METHOD: The lower part of the right hind limb of CDF1 mice......, 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....... was irradiated with single fractions of either 6 MV photons, 240 kV photons or scanning beam protons and graded doses were applied. For the proton irradiation, the leg was either placed in the middle of a 30-mm SOBP, or to assess the effect in different positions, irradiated in 4 mm intervals from the middle...

  8. 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

  9. Bioinformatics Tools for Extracellular Vesicles Research.

    Science.gov (United States)

    Keerthikumar, Shivakumar; Gangoda, Lahiru; Gho, Yong Song; Mathivanan, Suresh

    2017-01-01

    Extracellular vesicles (EVs) are a class of membranous vesicles that are released by multiple cell types into the extracellular environment. This unique class of extracellular organelles which play pivotal role in intercellular communication are conserved across prokaryotes and eukaryotes. Depending upon the cell origin and the functional state, the molecular cargo including proteins, lipids, and RNA within the EVs are modulated. Owing to this, EVs are considered as a subrepertoire of the host cell and are rich reservoirs of disease biomarkers. In addition, the availability of EVs in multiple bodily fluids including blood has created significant interest in biomarker and signaling research. With the advancement in high-throughput techniques, multiple EV studies have embarked on profiling the molecular cargo. To benefit the scientific community, existing free Web-based resources including ExoCarta, EVpedia, and Vesiclepedia catalog multiple datasets. These resources aid in elucidating molecular mechanism and pathophysiology underlying different disease conditions from which EVs are isolated. Here, the existing bioinformatics tools to perform integrated analysis to identify key functional components in the EV datasets are discussed.

  10. 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.

  11. Evolution of web services in bioinformatics.

    Science.gov (United States)

    Neerincx, Pieter B T; Leunissen, Jack A M

    2005-06-01

    Bioinformaticians have developed large collections of tools to make sense of the rapidly growing pool of molecular biological data. Biological systems tend to be complex and in order to understand them, it is often necessary to link many data sets and use more than one tool. Therefore, bioinformaticians have experimented with several strategies to try to integrate data sets and tools. Owing to the lack of standards for data sets and the interfaces of the tools this is not a trivial task. Over the past few years building services with web-based interfaces has become a popular way of sharing the data and tools that have resulted from many bioinformatics projects. This paper discusses the interoperability problem and how web services are being used to try to solve it, resulting in the evolution of tools with web interfaces from HTML/web form-based tools not suited for automatic workflow generation to a dynamic network of XML-based web services that can easily be used to create pipelines.

  12. 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.

  13. Explosion of red-supergiant stars: Influence of the atmospheric structure on shock breakout and early-time supernova radiation

    Science.gov (United States)

    Dessart, Luc; John Hillier, D.; Audit, Edouard

    2017-09-01

    Early-time observations of Type II supernovae (SNe) 2013cu and 2013fs have revealed an interaction of ejecta with material near the star surface. Unlike Type IIn SN 2010jl, which interacts with a dense wind for 1 yr, the interaction ebbs after 2-3 d, suggesting a dense and compact circumstellar envelope. Here, we use multi-group radiation hydrodynamics and non-local-thermodynamic-equilibrium radiative transfer to explore the properties of red-supergiant (RSG) star explosions embedded in a variety of dense envelopes. We consider the cases of an extended static atmosphere or a steady-state wind, adopting a range of mass loss rates. The shock breakout signal, luminosity and color evolution up to 10 d, and ejecta dynamics are strongly influenced by the properties of this nearby environment. This compromises the use of early-time observations to constrain R⋆. For dense circumstellar envelopes, the time-integrated luminosity over the first 10-15 d can be boosted by a factor of a few. The presence of narrow lines for 2-3 d in 2013fs and 2013cu require a cocoon of material of 0.01 M⊙ out to 5-10 R⋆. Spectral lines evolve from electron scattering to Doppler broadened with a growing blueshift of their emission peaks. Recent studies propose a super-wind phase with a mass loss rate from 0.001 up to 1 M⊙ yr-1 in the last months or years of the life of a RSG, although there is no observational constraint that this external material is a steady-state outflow. Alternatively, observations may be explained by the explosion of a RSG star inside its complex atmosphere. Indeed, spatially resolved observations reveal that RSG stars have extended atmospheres, with the presence of downflows and upflows out to several R⋆, even in a standard RSG such as Betelgeuse. Mass loading in the region intermediate between star and wind can accommodate the 0.01 M⊙ needed to explain the observations of 2013fs. Signatures of interaction in early-time spectra of RSG star explosions may

  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. 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

  16. Early Clinical Outcomes Using Proton Radiation for Children With Central Nervous System Atypical Teratoid Rhabdoid Tumors

    Energy Technology Data Exchange (ETDEWEB)

    De Amorim Bernstein, Karen; Sethi, Roshan; Trofimov, Alexei; Zeng, Chuan [Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts (United States); Fullerton, Barbara [Department of Otology and Laryngology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts (United States); Yeap, Beow Y. [Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts (United States); Ebb, David [Department of Pediatric Hematology-Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts (United States); Tarbell, Nancy J.; Yock, Torunn I. [Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts (United States); MacDonald, Shannon M., E-mail: smacdonald@partners.org [Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts (United States)

    2013-05-01

    Purpose: Atypical teratoid/rhabdoid tumor (AT/RT) is an uncommon and aggressive tumor that often affects infants. Irradiation improves survival but has traditionally been avoided in patients under the age of 3 due to the increasing risk of neurocognitive side effects. We report the first cohort of AT/RT patients treated with proton therapy. Methods and Materials: All patients with AT/RT treated at Massachusetts General Hospital (MGH) Frances H. Burr Proton Beam Therapy Benter between July 2004 and November 2011 were included in this study. All patients were treated with 3-dimensional conformal proton therapy (3D-CPT). Results: Ten consecutive patients of a median 2.3 years of age and with a median follow-up of 27.3 months (range, 11.3-99.4 months) were identified. Two patients suffered distant relapse; 1 patient was successfully treated with involved field irradiation and chemotherapy, while the second patient died of disease. At last follow-up, 9 patients were alive without evidence of disease. Proton radiation demonstrated increasing sparing of the cerebrum, temporal lobe, cochlea, and hypothalamus. Conclusions: Initial clinical outcomes with proton therapy are favorable. The advantages of proton therapy are particularly suited to the treatment of AT/RT, a tumor that often requires irradiation treatment at an age when avoiding irradiation to healthy tissues is most desirable.

  17. The development of early pediatric models and their application to radiation absorbed dose calculations

    International Nuclear Information System (INIS)

    Poston, J.W.

    1989-01-01

    This presentation will review and describe the development of pediatric phantoms for use in radiation dose calculations . The development of pediatric models for dose calculations essentially paralleled that of the adult. In fact, Snyder and Fisher at the Oak Ridge National Laboratory reported on a series of phantoms for such calculations in 1966 about two years before the first MIRD publication on the adult human phantom. These phantoms, for a newborn, one-, five-, ten-, and fifteen-year old, were derived from the adult phantom. The ''pediatric'' models were obtained through a series of transformations applied to the major dimensions of the adult, which were specified in a Cartesian coordinate system. These phantoms suffered from the fact that no real consideration was given to the influence of these mathematical transformations on the actual organ sizes in the other models nor to the relation of the resulting organ masses to those in humans of the particular age. Later, an extensive effort was invested in designing ''individual'' pediatric phantoms for each age based upon a careful review of the literature. Unfortunately, the phantoms had limited use and only a small number of calculations were made available to the user community. Examples of the phantoms, their typical dimensions, common weaknesses, etc. will be discussed

  18. 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.

  19. 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.

  20. 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.)

  1. Impact of early dysphagia intervention on swallowing function and quality of life in head and neck cancer patients treated with intensity-modulated radiation therapy or image guided radiation therapy with or without surgery/chemotherapy

    Directory of Open Access Journals (Sweden)

    Rajender Kumar

    2015-01-01

    Conclusion: Results from this study demonstrated that swallowing exercises, if administered from first week of chemo-radiation and continued till 6 months, results in significant improvement in swallowing function and quality of life. Use of FEES helps in detection of silent aspiration at an early stage and reduces aspiration related morbidities.

  2. 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.

  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. Quality of Life Following Stereotactic Ablative Radiation Therapy Versus Surgery for Early-Stage Lung Cancer : Results From the ROSEL Randomized Controlled Trial and a Systematic Review

    NARCIS (Netherlands)

    Louie, A V; Chen, H.; Van Werkhoven, E; Smit, E.; Palma, D A; Paul, M A; Warner, A; Widder, J; Groen, H. J. M.; van Den Borne, B; De Jaeger, K; Rodrigues, G; Slotman, B J; Senan, S

    2016-01-01

    Purpose/Objective(s) One of the purported advantages of stereotactic ablative radiation therapy (SABR) as an alternative treatment option to surgery for early-stage non-small cell lung cancer (ES-NSCLC) is health-related quality of life (HRQOL). The objectives of this study are 1) to assess HRQOL

  5. Reduction of the treated volume to involved node radiation therapy as part of combined modality treatment for early stage aggressive non-Hodgkin's lymphoma.

    NARCIS (Netherlands)

    Verhappen, M.H.; Poortmans, P.M.P.; Raaijmakers, E.; Raemaekers, J.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

  6. 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)

  7. 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)

  8. The potential of translational bioinformatics approaches for pharmacology research.

    Science.gov (United States)

    Li, Lang

    2015-10-01

    The field of bioinformatics has allowed the interpretation of massive amounts of biological data, ushering in the era of 'omics' to biomedical research. Its potential impact on pharmacology research is enormous and it has shown some emerging successes. A full realization of this potential, however, requires standardized data annotation for large health record databases and molecular data resources. Improved standardization will further stimulate the development of system pharmacology models, using translational bioinformatics methods. This new translational bioinformatics paradigm is highly complementary to current pharmacological research fields, such as personalized medicine, pharmacoepidemiology and drug discovery. In this review, I illustrate the application of transformational bioinformatics to research in numerous pharmacology subdisciplines. © 2015 The British Pharmacological Society.

  9. Development of a cloud-based Bioinformatics Training Platform

    Science.gov (United States)

    Revote, Jerico; Watson-Haigh, Nathan S.; Quenette, Steve; Bethwaite, Blair; McGrath, Annette

    2017-01-01

    Abstract 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. PMID:27084333

  10. 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 ...

  11. 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.

  12. 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.

  13. Bioinformatics Analyst | Center for Cancer Research

    Science.gov (United States)

    BASIC QUALIFICATIONS To be considered for this position, you must minimally meet the knowledge, skills, and abilities listed below: Bachelor’s degree in life science/bioinformatics/math/physics/computer related field from an accredited college or university according to the Council for Higher Education Accreditation (CHEA). (Additional qualifying experience may be substituted for the required education). Foreign degrees must be evaluated for U.S. equivalency. In addition to the educational requirements, a minimum of five (5) years of progressively responsible relevant experience. Must be able to obtain and maintain a security clearance. PREFERRED QUALIFICATIONS Candidates with these desired skills will be given preferential consideration: A Masters’ or PhD degree in any quantitative science is preferred. Commitment to solving biological problems and communicating these solutions. Ability to multi-task across projects. Experience in submitting data sets to public repositories. Management of large genomic data sets including integration with data available from public sources. Prior customer-facing role. Record of scientific achievements including journal publications and conference presentations. Expected Competencies: Deep understanding of and experience in processing high throughput biomedical data: data cleaning, normalization, analysis, interpretation and visualization. Ability to understand and analyze data from complex experimental designs. Proficiency in at least two of the following programming languages: Perl, Python, R, Java and C/C++. Experience in at least two of the following areas: metagenomics, ChIPSeq, RNASeq, ExomeSeq, DHS-Seq, microarray analysis. Familiarity with public databases: NCBI, Ensembl, TCGA, cBioPortal, Broad FireHose. Knowledge of working in a cluster environment.

  14. 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

  15. 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.

  16. 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

    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.......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...

  17. Use of BEXA Family Algorithms in Bioinformatics Data Classification

    OpenAIRE

    Gasparoviča-Asīte, M; Aleksejeva, L; Gersons, V

    2012-01-01

    This article studies the possibilities of BEXA family classification algorithms – BEXA, FuzzyBexa and FuzzyBexa II in data, especially bioinformatics data, classification. Three different types of data sets were used in the study – data sets often used in the literature (like Iris data set), UCI data repository real life data sets (like breast cancer data set) and real bioinformatics data sets that have the specific character – a large number of attributes (several thousands) and a small numb...

  18. 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

  19. 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.

  20. 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

  1. 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

  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. Prostate cancer volume adds significantly to prostate specific antigen in the prediction of early biochemical failure after external beam radiation therapy

    International Nuclear Information System (INIS)

    D'Amico, A.V.; Propert, K.J.

    1995-01-01

    Purpose A new clinical pre-treatment quantity that closely approximates the true prostate cancer volume is defined. Materials and Methods The cancer specific prostate specific antigen, PSA density, prostate cancer volume (V Ca ) and the volume fraction of the gland involved with carcinoma (V Ca fx) were calculated for 227 prostate cancer patients managed definitively with external beam radiation therapy. A Cox regression multivariate analysis was employed to test if any of these clinical pre-treatment parameters added significantly to PSA in predicting early post-radiation PSA failure. Cancer specific PSA = PSA - [PSA from benign epithelial tissue] V Ca = Cancer specific/[PSA in serum per cm 3 of cancer] V Ca fx = V Ca /ultrasound prostate gland volume Results The prostate cancer volume (p = .039) and the volume fraction of the gland involved by carcinoma (p = .035) significantly added to the PSA in predicting post-radiation PSA failure on multivariate analysis. Conversely, the PSA density and the cancer specific PSA did not add significantly (p > .05) to PSA in predicting post-radiation PSA failure. Conclusion The volume of cancer (V Ca ) and the resulting volume fraction of cancer both added significantly to PSA in their ability to predict for early post-radiation PSA failure. These new parameters may be used to optimize the selection of patients in prospective randomized trials that examine the efficacy of combining radiation and androgen ablative therapy in patients with clinically localized disease but who are at high risk for early post-radiation PSA failure

  4. 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.

  5. Low dose cisplatin as a radiation sensitizer in management of locally advanced squamous cell carcinoma of the uterine cervix: evaluation of acute toxicity and early response

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Hun Jung; Cho, Young Kap; Kim, Chul Su; Kim, Woo Chul; Lee, Suk Ho; Loh, John J. K. [College of Medicine, Inha Univ., Inchon (Korea, Republic of)

    1999-06-01

    To evluate possible acute toxicity and early response of concurrent radiation therapy and low dose daily cisplatin as a radiosensitizer in patients with locally advanced uterine cervical carcinomas. From December 1996 to January 1999, 38 previously untreated patients with locally advanced squamous cell carcinoma of the uterine cervix (from stage IIB to stage IIIB) were treated at lnha University Hospital. All patients underwent standard pretreatment staging procedures after the initial evaluation by gynecologists and radiation oncologists. Sixteen patients with huge cervical mass (>4 cm) were submitted to the group treated with concurrent radiation therapy and low dose daily cisplatin while the remainder was treated with radiation therapy alone. Radiation therapy consisted of 4500 cGy external beam irradiation to whole pelvis (midline block after 3060 cGy), 900-1000 cGy boost to involved parametrium, and high dose-rate intracavitary brachytherapy (a total dose of 3000-3500 cGy/500 cGy per fraction to point A, twice per week). In the group treated with low dose cisplatin concurrently, 10 mg of daily intravenous cisplatin was given from the 1 st day of radiation therapy to the 20th day of radiation therapy. Acute toxicity was measured according to expanded common toxicity criteria of the NCI (C) Clinical Trials. Early response data were analyzed at minimum 4 weeks' follow-up after completion of the treatment protocol. Hematolgic toxicity was more prominent in patients treated with radiation therapy and cisplatin. Six of 16 patients (37.5%) treated with radiation therapy and cisplatin and one of 22 patients (4.5%) treated with radiation therapy alone experienced grade 3 leukopenia. In Fisher's exact test, there was statistically significant difference between two groups regarding leukopenia (p=0.030). There was no apparent difference in the frequency of gastrointestinal and genitourinary toxicity between two groups (p=0.066). Three of 16 patients (18

  6. Low dose cisplatin as a radiation sensitizer in management of locally advanced squamous cell carcinoma of the uterine cervix: evaluation of acute toxicity and early response

    International Nuclear Information System (INIS)

    Kim, Hun Jung; Cho, Young Kap; Kim, Chul Su; Kim, Woo Chul; Lee, Suk Ho; Loh, John J. K.

    1999-01-01

    To evluate possible acute toxicity and early response of concurrent radiation therapy and low dose daily cisplatin as a radiosensitizer in patients with locally advanced uterine cervical carcinomas. From December 1996 to January 1999, 38 previously untreated patients with locally advanced squamous cell carcinoma of the uterine cervix (from stage IIB to stage IIIB) were treated at lnha University Hospital. All patients underwent standard pretreatment staging procedures after the initial evaluation by gynecologists and radiation oncologists. Sixteen patients with huge cervical mass (>4 cm) were submitted to the group treated with concurrent radiation therapy and low dose daily cisplatin while the remainder was treated with radiation therapy alone. Radiation therapy consisted of 4500 cGy external beam irradiation to whole pelvis (midline block after 3060 cGy), 900-1000 cGy boost to involved parametrium, and high dose-rate intracavitary brachytherapy (a total dose of 3000-3500 cGy/500 cGy per fraction to point A, twice per week). In the group treated with low dose cisplatin concurrently, 10 mg of daily intravenous cisplatin was given from the 1 st day of radiation therapy to the 20th day of radiation therapy. Acute toxicity was measured according to expanded common toxicity criteria of the NCI (C) Clinical Trials. Early response data were analyzed at minimum 4 weeks' follow-up after completion of the treatment protocol. Hematolgic toxicity was more prominent in patients treated with radiation therapy and cisplatin. Six of 16 patients (37.5%) treated with radiation therapy and cisplatin and one of 22 patients (4.5%) treated with radiation therapy alone experienced grade 3 leukopenia. In Fisher's exact test, there was statistically significant difference between two groups regarding leukopenia (p=0.030). There was no apparent difference in the frequency of gastrointestinal and genitourinary toxicity between two groups (p=0.066). Three of 16 patients (18.7%) treated with

  7. Observation of early shell-dopant mix in OMEGA direct-drive implosions and comparisons with radiation-hydrodynamic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Baumgaertel, J. A.; Bradley, P. A.; Hsu, S. C.; Cobble, J. A.; Hakel, P.; Tregillis, I. L.; Krasheninnikova, N. S.; Murphy, T. J.; Schmitt, M. J.; Shah, R. C.; Obrey, K. D.; Batha, S. [Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Johns, H.; Joshi, T.; Mayes, D.; Mancini, R. C.; Nagayama, T. [Physics Department, University of Nevada, Reno, Nevada 89557 (United States)

    2014-05-15

    Temporally, spatially, and spectrally resolved x-ray image data from direct-drive implosions on OMEGA were interpreted with the aid of radiation-hydrodynamic simulations. Neither clean calculations nor those using a turbulent mix model can explain fully the observed migration of shell-dopant material (titanium) into the core. Shell-dopant migration was observed via time-dependent, spatially integrated spectra, and spatially and spectrally resolved x-ray images of capsule implosions and resultant dopant emissions. The titanium emission was centrally peaked in narrowband x-ray images. In post-processed clean simulations, the peak titanium emission forms in a ring in self-emission images as the capsule implodes. Post-processed simulations with mix reproduce trends in time-dependent, spatially integrated spectra, as well having centrally peaked Ti emission in synthetic multiple monochromatic imager. However, mix simulations still do not transport Ti to the core as is observed in the experiment. This suggests that phenomena in addition to the turbulent mix must be responsible for the transport of Ti. Simple diffusion estimates are unable to explain the early Ti mix into the core. Mechanisms suggested for further study are capsule surface roughness, illumination non-uniformity, and shock entrainment.

  8. 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

  9. The bioinformatics of psychosocial genomics in alternative and complementary medicine.

    Science.gov (United States)

    Rossi, E

    2003-06-01

    The bioinformatics of alternative and complementary medicine is outlined in 3 hypotheses that extend the molecular-genomic revolution initiated by Watson and Crick 50 years ago to include psychology in the new discipline of psychosocial and cultural genomics. Stress-induced changes in the alternative splicing of genes demonstrate how psychosomatic stress in humans modulates activity-dependent gene expression, protein formation, physiological function, and psychological experience. The molecular messengers generated by stress, injury, and disease can activate immediate early genes within stem cells so that they then signal the target genes required to synthesize the proteins that will transform (differentiate) stem cells into mature well-functioning tissues. Such activity-dependent gene expression and its consequent activity-dependent neurogenesis and stem cell healing is proposed as the molecular-genomic-cellular basis of rehabilitative medicine, physical, and occupational therapy as well as the many alternative and complementary approaches to mind-body healing. The therapeutic replaying of enriching life experiences that evoke the novelty-numinosum-neurogenesis effect during creative moments of art, music, dance, drama, humor, literature, poetry, and spirituality, as well as cultural rituals of life transitions (birth, puberty, marriage, illness, healing, and death) can optimize consciousness, personal relationships, and healing in a manner that has much in common with the psychogenomic foundations of naturalistic and complementary medicine. The entire history of alternative and complementary approaches to healing is consistent with this new neuroscience world view about the role of psychological arousal and fascination in modulating gene expression, neurogenesis, and healing via the psychosocial and cultural rites of human societies. Copyright 2003 S. Karger GmbH, Freiburg

  10. Bioinformatics analysis of circulating cell-free DNA sequencing data.

    Science.gov (United States)

    Chan, Landon L; Jiang, Peiyong

    2015-10-01

    The discovery of cell-free DNA molecules in plasma has opened up numerous opportunities in noninvasive diagnosis. Cell-free DNA molecules have become increasingly recognized as promising biomarkers for detection and management of many diseases. The advent of next generation sequencing has provided unprecedented opportunities to scrutinize the characteristics of cell-free DNA molecules in plasma in a genome-wide fashion and at single-base resolution. Consequently, clinical applications of circulating cell-free DNA analysis have not only revolutionized noninvasive prenatal diagnosis but also facilitated cancer detection and monitoring toward an era of blood-based personalized medicine. With the remarkably increasing throughput and lowering cost of next generation sequencing, bioinformatics analysis becomes increasingly demanding to understand the large amount of data generated by these sequencing platforms. In this Review, we highlight the major bioinformatics algorithms involved in the analysis of cell-free DNA sequencing data. Firstly, we briefly describe the biological properties of these molecules and provide an overview of the general bioinformatics approach for the analysis of cell-free DNA. Then, we discuss the specific upstream bioinformatics considerations concerning the analysis of sequencing data of circulating cell-free DNA, followed by further detailed elaboration on each key clinical situation in noninvasive prenatal diagnosis and cancer management where downstream bioinformatics analysis is heavily involved. We also discuss bioinformatics analysis as well as clinical applications of the newly developed massively parallel bisulfite sequencing of cell-free DNA. Finally, we offer our perspectives on the future development of bioinformatics in noninvasive diagnosis. Copyright © 2015 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  11. 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

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. The transition from late G sub 1 to early S phase is most vulnerable to the coclastogenic effect of ultraviolet radiation plus arsenite

    Energy Technology Data Exchange (ETDEWEB)

    Huang, H.; Huang, C.F. (National Tsing-Hua Univ., Hsinchu (Taiwan). Inst. of Radiation Biology); Huang, J.S. (Tung-Hai Univ., Taichung (Taiwan). Dept. of Biology); Wang, T.C.; Jan, K.Y. (Academia Sinica, Tapei (China). Inst. of Zoology)

    1992-01-01

    It has previously been reported that chromosome aberrations induced by ultraviolet (UV) radiation can be enhanced by treatment with sodium arsenite for 24h post-irradiation. Using synchronized CHO-K1 cells, it has now been established that cells in the transitional stage from late G{sub 1} to early S phase are most vulnerable to the coclastogenic effect of treatment with UV radiation and arsenite. This result cannot be explained by the special vulnerability of cells in the late G{sub 1} to early S transition to UV clastogenicity, as the coclastogenic effects of UV and caffeine or UV and arabinofuranosylcytosine were detected when treating the mid-S but not late-G{sub 1} or G{sub 2} phase cells. (author).

  17. Survey of MapReduce frame operation in bioinformatics.

    Science.gov (United States)

    Zou, Quan; Li, Xu-Bin; Jiang, Wen-Rui; Lin, Zi-Yu; Li, Gui-Lin; Chen, Ke

    2014-07-01

    Bioinformatics is challenged by the fact that traditional analysis tools have difficulty in processing large-scale data from high-throughput sequencing. The open source Apache Hadoop project, which adopts the MapReduce framework and a distributed file system, has recently given bioinformatics researchers an opportunity to achieve scalable, efficient and reliable computing performance on Linux clusters and on cloud computing services. In this article, we present MapReduce frame-based applications that can be employed in the next-generation sequencing and other biological domains. In addition, we discuss the challenges faced by this field as well as the future works on parallel computing in bioinformatics. © The Author 2013. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  18. Developing expertise in bioinformatics for biomedical research in Africa.

    Science.gov (United States)

    Karikari, Thomas K; Quansah, Emmanuel; Mohamed, Wael M Y

    2015-09-01

    Research in bioinformatics has a central role in helping to advance biomedical research. However, its introduction to Africa has been met with some challenges (such as inadequate infrastructure, training opportunities, research funding, human resources, biorepositories and databases) that have contributed to the slow pace of development in this field across the continent. Fortunately, recent improvements in areas such as research funding, infrastructural support and capacity building are helping to develop bioinformatics into an important discipline in Africa. These contributions are leading to the establishment of world-class research facilities, biorepositories, training programmes, scientific networks and funding schemes to improve studies into disease and health in Africa. With increased contribution from all stakeholders, these developments could be further enhanced. Here, we discuss how the recent developments are contributing to the advancement of bioinformatics in Africa.

  19. Developing expertise in bioinformatics for biomedical research in Africa

    Directory of Open Access Journals (Sweden)

    Thomas K. Karikari

    2015-09-01

    Full Text Available Research in bioinformatics has a central role in helping to advance biomedical research. However, its introduction to Africa has been met with some challenges (such as inadequate infrastructure, training opportunities, research funding, human resources, biorepositories and databases that have contributed to the slow pace of development in this field across the continent. Fortunately, recent improvements in areas such as research funding, infrastructural support and capacity building are helping to develop bioinformatics into an important discipline in Africa. These contributions are leading to the establishment of world-class research facilities, biorepositories, training programmes, scientific networks and funding schemes to improve studies into disease and health in Africa. With increased contribution from all stakeholders, these developments could be further enhanced. Here, we discuss how the recent developments are contributing to the advancement of bioinformatics in Africa.

  20. 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.

  1. 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.

  2. Absence of toxicity with hypofractionated 3-dimensional radiation therapy for inoperable, early stage non-small cell lung cancer

    Directory of Open Access Journals (Sweden)

    Vuong Te

    2006-11-01

    Full Text Available Abstract Purpose Hypofractionated radiotherapy may overcome repopulation in rapidly proliferating tumors such as lung cancer. It is more convenient for the patients and reduces health care costs. This study reports our results on patients with medically inoperable, early stage, non-small cell lung cancer (NSCLC treated with hypofractionation. Materials and methods Stage T1-2N0 NSCLC patients were treated with hypofractionation alone, 52.5 Gy/15 fractions, in 3 weeks, with 3-dimensional conformal planning. T1-2N1 patients with the hilar lymphnode close to the primary tumor were also eligible for this treatment. We did not use any approach to reduce respiratory motion, but it was monitored in all patients. Elective nodal radiotherapy was not performed. Routine follow up included assessment for acute and late toxicity and radiological tumor response. Median follow up time was 29 months for the surviving patients. Results Thirty-two patients with a median age of 76 years, T1 = 15 and T2 = 17, were treated. Median planning target volume (PTV volume was 150cc and median V16 of both lungs was 13%. The most important finding of this study is that toxicity was minimal. Two patients had grade ≤ 2 acute pneumonitis and 3 had mild (grade 1 acute esophagitis. There was no late toxicity. Actuarial 1 and 2-year overall survival rates are 78% and 56%, cancer specific survival rates (CSS are 90% and 74%, and local relapse free survival rates are 93% and 76% respectively. Conclusion 3-D planning, involved field hypofractionation at a dose of 52.5 Gy in 15 daily fractions is safe, well tolerated and easy radiation treatment for medically inoperable lung cancer patients. It shortens by half the traditional treatment. Results compare favorably with previously published studies. Further studies are needed to compare similar technique with other treatments such as surgery and stereotactic radiotherapy.

  3. 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.

  4. The role of extended field radiation therapy in early stage cervical carcinoma with para-aortic metastases - a study of survival impact and complication rates

    International Nuclear Information System (INIS)

    Chang, John H.C.; Cunningham, Mary J.; Morgan, Mark A.; King, Stephanie A.; Benjamin, Ivor; Rubin, Stephen C.; Mikuta, John; Stevens, Craig

    1997-01-01

    Purpose/Objective: Para-aortic lymph node metastases are found pathologically in ten to thirteen percent of all early stage cervical cancer patients at the time of radical hysterectomy. The treatment of these patients, technically with stage IVB disease, has been controversial. Since para-aortic nodal metastases preclude the need for radical hysterectomy, definitive radiation therapy is usually pursued. Extended field radiation therapy has improved survival in our previously reported series of patients with early stage cervical cancer and para-aortic metastases. In this report, we describe the results of additional follow up and included additional patients in order to study long term outcome, and complications associated with extended field radiation therapy. Materials and Methods: From January 1, 1960 to Nov 31, 1996, six hundred and forty-eight patients with clinically early stage carcinoma of the cervix were surgically explored at the Hospital of the University of Pennsylvania with the purpose of performing a radical hysterectomy. Approximately six percent of these patients were found to have histological documentation of para-aortic nodal metastases. Over ninety percent received extended field external beam radiation therapy with curative intent. This study describes the results in this treated population. Results: Approximately forty percent of those treated have survived greater than five years. Seven have been followed for more than ten years. Long term complications of treatment include radiation enteritis, cystitis, vesico-vaginal fistulae, enteric fistulae, and bowel obstruction. One treatment related death (multiple fistulas and sepsis) was documented at ten months after diagnosis and 6 months after radiation treatments. The major morbidity rate was approximately twenty percent. However, the majority of these patients underwent transperitoneal lymph node dissections and/or relatively high (>55Gy) doses to the PA nodes. Conclusions: Carcinoma of the

  5. Bioinformatic training needs at a health sciences campus.

    Science.gov (United States)

    Oliver, Jeffrey C

    2017-01-01

    Health sciences research is increasingly focusing on big data applications, such as genomic technologies and precision medicine, to address key issues in human health. These approaches rely on biological data repositories and bioinformatic analyses, both of which are growing rapidly in size and scope. Libraries play a key role in supporting researchers in navigating these and other information resources. With the goal of supporting bioinformatics research in the health sciences, the University of Arizona Health Sciences Library established a Bioinformation program. To shape the support provided by the library, I developed and administered a needs assessment survey to the University of Arizona Health Sciences campus in Tucson, Arizona. The survey was designed to identify the training topics of interest to health sciences researchers and the preferred modes of training. Survey respondents expressed an interest in a broad array of potential training topics, including "traditional" information seeking as well as interest in analytical training. Of particular interest were training in transcriptomic tools and the use of databases linking genotypes and phenotypes. Staff were most interested in bioinformatics training topics, while faculty were the least interested. Hands-on workshops were significantly preferred over any other mode of training. The University of Arizona Health Sciences Library is meeting those needs through internal programming and external partnerships. The results of the survey demonstrate a keen interest in a variety of bioinformatic resources; the challenge to the library is how to address those training needs. The mode of support depends largely on library staff expertise in the numerous subject-specific databases and tools. Librarian-led bioinformatic training sessions provide opportunities for engagement with researchers at multiple points of the research life cycle. When training needs exceed library capacity, partnering with intramural and

  6. Information Visualization Techniques in Bioinformatics during the Postgenomic Era

    Science.gov (United States)

    Tao, Ying; Liu, Yang; Friedman, Carol

    2010-01-01

    Information visualization techniques, which take advantage of the bandwidth of human vision, are powerful tools for organizing and analyzing a large amount of data. In the postgenomic era, information visualization tools are indispensable for biomedical research. This paper aims to present an overview of current applications of information visualization techniques in bioinformatics for visualizing different types of biological data, such as from genomics, proteomics, expression profiling and structural studies. Finally, we discuss the challenges of information visualization in bioinformatics related to dealing with more complex biological information in the emerging fields of systems biology and systems medicine. PMID:20976032

  7. Bioinformatic scaling of allosteric interactions in biomedical isozymes

    Science.gov (United States)

    Phillips, J. C.

    2016-09-01

    Allosteric (long-range) interactions can be surprisingly strong in proteins of biomedical interest. Here we use bioinformatic scaling to connect prior results on nonsteroidal anti-inflammatory drugs to promising new drugs that inhibit cancer cell metabolism. Many parallel features are apparent, which explain how even one amino acid mutation, remote from active sites, can alter medical results. The enzyme twins involved are cyclooxygenase (aspirin) and isocitrate dehydrogenase (IDH). The IDH results are accurate to 1% and are overdetermined by adjusting a single bioinformatic scaling parameter. It appears that the final stage in optimizing protein functionality may involve leveling of the hydrophobic limits of the arms of conformational hydrophilic hinges.

  8. Bioinformatics Tools for the Discovery of New Nonribosomal Peptides

    DEFF Research Database (Denmark)

    Leclère, Valérie; Weber, Tilmann; Jacques, Philippe

    2016-01-01

    This chapter helps in the use of bioinformatics tools relevant to the discovery of new nonribosomal peptides (NRPs) produced by microorganisms. The strategy described can be applied to draft or fully assembled genome sequences. It relies on the identification of the synthetase genes and the decip......This chapter helps in the use of bioinformatics tools relevant to the discovery of new nonribosomal peptides (NRPs) produced by microorganisms. The strategy described can be applied to draft or fully assembled genome sequences. It relies on the identification of the synthetase genes...

  9. 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

  10. 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

  11. 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.

  12. 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

  13. 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

  14. 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...

  15. Probabilistic models and machine learning in structural bioinformatics.

    Science.gov (United States)

    Hamelryck, Thomas

    2009-10-01

    Structural bioinformatics is concerned with the molecular structure of biomacromolecules on a genomic scale, using computational methods. Classic problems in structural bioinformatics include the prediction of protein and RNA structure from sequence, the design of artificial proteins or enzymes, and the automated analysis and comparison of biomacromolecules in atomic detail. The determination of macromolecular structure from experimental data (for example coming from nuclear magnetic resonance, X-ray crystallography or small angle X-ray scattering) has close ties with the field of structural bioinformatics. Recently, probabilistic models and machine learning methods based on Bayesian principles are providing efficient and rigorous solutions to challenging problems that were long regarded as intractable. In this review, I will highlight some important recent developments in the prediction, analysis and experimental determination of macromolecular structure that are based on such methods. These developments include generative models of protein structure, the estimation of the parameters of energy functions that are used in structure prediction, the superposition of macromolecules and structure determination methods that are based on inference. Although this review is not exhaustive, I believe the selected topics give a good impression of the exciting new, probabilistic road the field of structural bioinformatics is taking.

  16. 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.

  17. Science Academies' Refresher Course on Bioinformatics in Modern ...

    Indian Academy of Sciences (India)

    IAS Admin

    A Refresher Course on 'Bioinformatics in Modern Biology' for graduate and postgraduate college/university teachers will be held at School of Life Sciences, Manipal University, Manipal for two weeks from 5 to 17 May 2014. The objective of this Course is to improvise on teaching methodologies incorporating online teaching ...

  18. 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

  19. 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

    2015-02-01

    "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).

  20. 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

  1. 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 ...

  2. 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...

  3. Robust enzyme design: bioinformatic tools for improved protein stability.

    Science.gov (United States)

    Suplatov, Dmitry; Voevodin, Vladimir; Švedas, Vytas

    2015-03-01

    The ability of proteins and enzymes to maintain a functionally active conformation under adverse environmental conditions is an important feature of biocatalysts, vaccines, and biopharmaceutical proteins. From an evolutionary perspective, robust stability of proteins improves their biological fitness and allows for further optimization. Viewed from an industrial perspective, enzyme stability is crucial for the practical application of enzymes under the required reaction conditions. In this review, we analyze bioinformatic-driven strategies that are used to predict structural changes that can be applied to wild type proteins in order to produce more stable variants. The most commonly employed techniques can be classified into stochastic approaches, empirical or systematic rational design strategies, and design of chimeric proteins. We conclude that bioinformatic analysis can be efficiently used to study large protein superfamilies systematically as well as to predict particular structural changes which increase enzyme stability. Evolution has created a diversity of protein properties that are encoded in genomic sequences and structural data. Bioinformatics has the power to uncover this evolutionary code and provide a reproducible selection of hotspots - key residues to be mutated in order to produce more stable and functionally diverse proteins and enzymes. Further development of systematic bioinformatic procedures is needed to organize and analyze sequences and structures of proteins within large superfamilies and to link them to function, as well as to provide knowledge-based predictions for experimental evaluation. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Science Academies' Refresher Course on Bioinformatics in Modern ...

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 19; Issue 2. Science Academies' Refresher Course on Bioinformatics in Modern Biology. Information and Announcements Volume 19 Issue 2 February 2014 pp 192-192. Fulltext. Click here to view fulltext PDF. Permanent link:

  5. 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

  6. Bioinformatics Analysis of Envelope Glycoprotein E epitopes of ...

    African Journals Online (AJOL)

    User

    2011-05-02

    May 2, 2011 ... A virus-neutralizing antibody by a virus-specific synthetic peptide. J. Virol. 55(3): 836-839. Geourjon C, Deléage G (1995). SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Bioinformatics, 11(6): 681-684. Guex N, Peitsch MC ...

  7. 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...

  8. 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…

  9. 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…

  10. Bioinformatic analyses of kappa casein gene in mammalian ...

    African Journals Online (AJOL)

    Kappa casein (CSN3) gene is a variant of the milk protein highly conserved in mammalian species. Genetic variations in CSN3 gene of six mammalian livestock species were investigated using bioinformatics approach. A total of twenty-seven CSN3 gene sequences with corresponding amino acids belonging to the six ...

  11. 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…

  12. Bioinformatics and phylogenetic analysis of human Tp73 gene

    African Journals Online (AJOL)

    Imtiaz

    2013-06-26

    Jun 26, 2013 ... 2Bioinformatics and Biotechnology, DES, FBAS International Islamic University, Islamabad, Pakistan. Accepted 26 April, 2013. The Tp73 ... New discoveries about the control and function of p73 are still in progress and it is ..... modern research for diagnostics and evolutionary history of p73. REFERENCES.

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. Bioinformatics training: selecting an appropriate learning content management system--an example from the European Bioinformatics Institute.

    Science.gov (United States)

    Wright, Victoria Ann; Vaughan, Brendan W; Laurent, Thomas; Lopez, Rodrigo; Brooksbank, Cath; Schneider, Maria Victoria

    2010-11-01

    Today's molecular life scientists are well educated in the emerging experimental tools of their trade, but when it comes to training on the myriad of resources and tools for dealing with biological data, a less ideal situation emerges. Often bioinformatics users receive no formal training on how to make the most of the bioinformatics resources and tools available in the public domain. The European Bioinformatics Institute, which is part of the European Molecular Biology Laboratory (EMBL-EBI), holds the world's most comprehensive collection of molecular data, and training the research community to exploit this information is embedded in the EBI's mission. We have evaluated eLearning, in parallel with face-to-face courses, as a means of training users of our data resources and tools. We anticipate that eLearning will become an increasingly important vehicle for delivering training to our growing user base, so we have undertaken an extensive review of Learning Content Management Systems (LCMSs). Here, we describe the process that we used, which considered the requirements of trainees, trainers and systems administrators, as well as taking into account our organizational values and needs. This review describes the literature survey, user discussions and scripted platform testing that we performed to narrow down our choice of platform from 36 to a single platform. We hope that it will serve as guidance for others who are seeking to incorporate eLearning into their bioinformatics training programmes.

  1. 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 …

  2. 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

  3. Reduction of the treated volume to involved node radiation therapy as part of combined modality treatment for early stage aggressive non-Hodgkin's lymphoma.

    Science.gov (United States)

    Verhappen, Marieke H; Poortmans, Philip M P; Raaijmakers, Esther; Raemaekers, John M M

    2013-10-01

    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. 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. 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. 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. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  4. Evaluation of lactate as a 1H nuclear magnetic resonance spectroscopy index for noninvasive prediction and early detection of tumor response to radiation therapy in EMT6 tumors.

    Science.gov (United States)

    Aboagye, E O; Bhujwalla, Z M; He, Q; Glickson, J D

    1998-07-01

    lactate levels may serve as sensitive early indices of tumor response to gamma radiation at doses of the order of 2 to 4 Gy.

  5. 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

  6. 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

  7. 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.

  8. 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'…

  9. 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.…

  10. 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…

  11. 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…

  12. 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

  13. 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.

  14. 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.].

  15. 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 climate system and an important driver of the west African monsoon across a range of timescales of variability. The physical mechanisms driving the variability in the SHL remain uncertain, although water vapour has been implicated as of primary importance. Here, we quantify the independent effects of variability in dust and water vapour on the radiation budget and atmospheric heating of the region using a radiative transfer model configured with observational input data from the Fennec field campaign at the location of Bordj Badji Mokhtar (BBM) in southern Algeria (21.4° N, 0.9° E), close to the SHL core for June 2011. Overall, we find dust aerosol and water vapour to be of similar importance in driving variability in the top-of-atmosphere (TOA) radiation budget and therefore the column-integrated heating over the SHL (˜ 7 W m-2 per standard deviation of dust aerosol optical depth - AOD). As such, we infer that SHL intensity is likely to be similarly enhanced by the effects of dust and water vapour surge events. However, the details of the processes differ. Dust generates substantial radiative cooling at the surface (˜ 11 W m-2 per standard deviation of dust AOD), presumably leading to reduced sensible heat flux in the boundary layer, which is more than compensated by direct radiative heating from shortwave (SW) absorption by dust in the dusty boundary layer. In contrast, water vapour invokes a radiative warming at the surface of ˜ 6 W m-2 per standard deviation of column-integrated water vapour in kg m-2. Net effects involve a pronounced net atmospheric radiative convergence with heating rates on average of 0.5 K day-1 and up to 6 K day-1 during synoptic/mesoscale dust events from monsoon surges and convective cold-pool outflows (haboobs). On this basis, we make inferences on the processes driving variability in the SHL associated with radiative and advective heating/cooling. Depending on the

  16. 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.

  17. 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...

  18. Data Mining for Grammatical Inference with Bioinformatics Criteria

    Science.gov (United States)

    López, Vivian F.; Aguilar, Ramiro; Alonso, Luis; Moreno, María N.; Corchado, Juan M.

    In this paper we describe both theoretical and practical results of a novel data mining process that combines hybrid techniques of association analysis and classical sequentiation algorithms of genomics to generate grammatical structures of a specific language. We used an application of a compilers generator system that allows the development of a practical application within the area of grammarware, where the concepts of the language analysis are applied to other disciplines, such as Bioinformatic. The tool allows the complexity of the obtained grammar to be measured automatically from textual data. A technique of incremental discovery of sequential patterns is presented to obtain simplified production rules, and compacted with bioinformatics criteria to make up a grammar.

  19. 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.  .

  20. Bioinformatics data distribution and integration via Web Services and XML.

    Science.gov (United States)

    Li, Xiao; Zhang, Yizheng

    2003-11-01

    It is widely recognized that exchange, distribution, and integration of biological data are the keys to improve bioinformatics and genome biology in post-genomic era. However, the problem of exchanging and integrating biology data is not solved satisfactorily. The eXtensible Markup Language (XML) is rapidly spreading as an emerging standard for structuring documents to exchange and integrate data on the World Wide Web (WWW). Web service is the next generation of WWW and is founded upon the open standards of W3C (World Wide Web Consortium) and IETF (Internet Engineering Task Force). This paper presents XML and Web Services technologies and their use for an appropriate solution to the problem of bioinformatics data exchange and integration.

  1. 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.

  2. 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.

  3. The effect of a Chinese herb (Saireito) therapy for edema and inflamation in early radiation injury; A case series

    Energy Technology Data Exchange (ETDEWEB)

    Kishi, Kazushi (Saiseikai Wakayama Hospital (Japan)); Shirai, Shintaro; Suwa, Kazuhiro; Tanaka, Kayo; Tsuji, Ko; Yamada, Ryusaku

    1991-11-01

    During a course of radiotherapy, inflamation and edema in limbs and in the local skin, occures frequently due to acute radiation injury. Seventeen cases with radiation induced edema and relavant symptoms, are treated with four weeks of oral administration of Saireito, a Chinese herb of diuretic and antiinflamatory effects. Radiotherapies could be carried out without interruption. After four weeks, the edema decreased in 7 of 15 patients, circumference measure of swoolen limbs decreased than 2 cm in 3 of 11, local skin hardness relaxed in 3 of 9, local skin redness decreased in 2 of 11, disturbed limb mobility improved in 4 of 8. In all, at least one symptomatic improvement was obtained in relevant to the radiation induced edema in 11 of 17 patients (63%). No conspicuous side effect was recorded. (author).

  4. Human radiation studies: Remembering the early years. Oral history of physiologist Nello Pace, Ph.D., August 16, 1994

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-06-01

    Dr. Nello Pace was interviewed by representatives of the US DOE Office of Human Radiation Experiments (OHRE). Dr. Pace was selected fro the interview because of the positions he held with the US Navy, at the University of California, Berkeley, and as Director of the White Mountain Research Station near Bishop, California. Following a brief biographical sketch, Dr. Pace related his remembrances concerning tritium injections experiments in animals and humans during World War II, the development of Medical Physics Degree Programs at UC Berkeley, conducting the first radiation survey at Nagasaki after the bomb, and the establishment of a research laboratory at White Mountain. He also offers reflections on Shields Warren and comments on the public`s attitudes towards radiation both then and now.

  5. Human radiation studies: Remembering the early years. Oral history of physiologist Nello Pace, Ph.D., August 16, 1994

    International Nuclear Information System (INIS)

    1995-06-01

    Dr. Nello Pace was interviewed by representatives of the US DOE Office of Human Radiation Experiments (OHRE). Dr. Pace was selected fro the interview because of the positions he held with the US Navy, at the University of California, Berkeley, and as Director of the White Mountain Research Station near Bishop, California. Following a brief biographical sketch, Dr. Pace related his remembrances concerning tritium injections experiments in animals and humans during World War II, the development of Medical Physics Degree Programs at UC Berkeley, conducting the first radiation survey at Nagasaki after the bomb, and the establishment of a research laboratory at White Mountain. He also offers reflections on Shields Warren and comments on the public's attitudes towards radiation both then and now

  6. Human radiation studies: Remembering the early years. Oral history of Oncologist Helen Vodopick, M.D., December 28, 1994

    International Nuclear Information System (INIS)

    1995-08-01

    This report is a transcript of an interview with Dr. Helen Vodopick by representatives of the US DOE Office of Human Radiation Experiments. Dr. Vodopick was chosen for this interview because of her involvement with the Oak Ridge Institute of Nuclear Studies (ORINS) and Oak Ridge Associated Universities (ORAU) experimental cancer-therapy program involving total-body irradiation. After a short biographical sketch Dr. Vodopick relates her remembrances of the Medium-Exposure-Rate Total Body Irradiator (METBI), ORINS radioisotope tracer studies, treatment of cancer patients with the METBI, radiation treatment for leukemia patients, bone marrow treatment of leukemia, the Low-Exposure-Rate Total Body Irradiation (LETBI), treatment of radiation accident victims at ORAU, research with radioactive phosphorus and sulfur, and public opinion issues

  7. A quick guide for building a successful bioinformatics community.

    Directory of Open Access Journals (Sweden)

    Aidan Budd

    2015-02-01

    Full Text Available "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.

  8. 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.

  9. BIRCH: a user-oriented, locally-customizable, bioinformatics system.

    Science.gov (United States)

    Fristensky, Brian

    2007-02-09

    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. 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. 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.

  10. 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

  11. Implication of MMP and TIMP in the matrice remodeling: early and delayed radiation effects of the digestive tractus

    International Nuclear Information System (INIS)

    Strup-Perrot, C.

    2004-12-01

    irradiation induces a marked acute remodeling of the gut wall and may lead to late fibrosis. Combining morphological, biochemical and molecular approach, we studied the expression of MMP and TIMP in the ileum and colon of rats one to seven days after irradiation and in ileum of patients with radiation enteritis. In both studies expression and activity of MMP and TIMP were increased, their balance being in favor of extra-cellular matrix degradation in the acute phase while in favor of matrix accumulation in radiation enteritis. (author)

  12. 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.

  13. Update in research and methods in proteomics and bioinformatics.

    Science.gov (United States)

    Bencharit, Sompop; Border, Michael B; Edelmann, Alex; Byrd, Warren C

    2013-10-01

    The 3rd International Conference on Proteomics & Bioinformatics (Proteomics 2013) Philadelphia, PA, USA, 15-17 July 2013 The Third International Conference on Proteomics & Bioinformatics (Proteomics 2013) was sponsored by the OMICS group and was organized in order to strengthen the future of proteomics science by bringing together professionals, researchers and scholars from leading universities across the globe. The main topics of this conference included the integration of novel platforms in data analysis, the use of a systems biology approach, different novel mass spectrometry platforms and biomarker discovery methods. The conference was divided into proteomic methods and research interests. Among these two categories, interactions between methods in proteomics and bioinformatics, as well as other research methodologies, were discussed. Exceptional topics from the keynote forum, oral presentations and the poster session have been highlighted. The topics range from new techniques for analyzing proteomics data, to new models designed to help better understand genetic variations to the differences in the salivary proteomes of HIV-infected patients.

  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 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.

  18. OWN EXPERIENCE OF LASER THERAPY FOR THE PREVENTION AND TREATMENT OF EARLY AND LATE RADIATION-INDUCED SKIN INJURIES IN PATIENTS WITH BREAST CANCER AFTER SIMULTANEOUS RECONSTRUCTIVE PLASTIC SURGERY

    Directory of Open Access Journals (Sweden)

    S. I. Tkachev

    2017-01-01

    Full Text Available Low-energy laser radiation has a good anti-inflammatory and stimulating effect on the damaged tissues; therefore, it can be used for the prevention and treatment of both early and late radiation-induced skin injuries in patients receiving radiotherapy. So far, the effect of low-energy laser radiation in the prevention of radiation-induced skin damage remains poorly understood. This article presents a brief overview of the results obtained in the latest foreign studies as well as own experience of laser therapy for the prevention and treatment of both early and late radiation-induced skin injuries in patients with breast cancer after simultaneous reconstructive plastic surgery.

  19. Prognostic Importance of the Presence of Early Metabolic Response and Absence of Extrahepatic Metastasis After Selective Internal Radiation Therapy in Colorectal Cancer Liver Metastasis.

    Science.gov (United States)

    Soydal, Cigdem; Kucuk, Nuriye Ozlem; Balci, Deniz; Gecim, Ethem; Bilgic, Sadik; Elhan, Atilla Halil

    2016-11-01

    In this study, the authors aimed to identify prognostic factors after selective internal radiation therapy (SIRT) for colorectal cancer (CRC) liver metastasis. Forty-nine (28 male, 21 female; mean age: 64.6 ± 10.8) patients who received SIRT for CRC liver metastasis were studied. Effects of number (<5 vs. ≥5), maximum dimension, and standardized uptake value (SUV) of liver metastases, liver tumor load (<25% vs. 26%-50% vs. 51%-75%), presence of extrahepatic disease, and metabolic early response on overall survival were analyzed. Mean follow-up time was 44.1 ± 27.5 months. Overall survival time was calculated as 10.03 ± 1.61 (95% CI; 6.86-13.20) months. SUV (0.004) of liver metastases, early metabolic response (p = 0.015), and presence of extrahepatic metastasis (p = 0.001) were identified as significant factors influencing overall survival. The hazard ratio was 1:2.3 for the presence of extrahepatic metastasis and 1:2.7 for the absence of early metabolic response. These findings suggest that patients with CRC liver metastasis who have lower SUV at presentation and early metabolic response have better outcomes after SIRT.

  20. The effects of simulated solar UVB radiation on early developmental stages of the Northwestern Salamander (Ambystoma gracile) from three lakes

    Science.gov (United States)

    Calfee, Robin D.; Little, Edward E.; Pearl, Christopher A.; Hoffman, Robert L.

    2010-01-01

    Solar ultraviolet radiation (UV) has received much attention as a factor that could play a role in amphibian population declines. UV can be hazardous to some amphibians, but the resultant effects depend on a variety of environmental and behavioral factors. In this study, the potential effects of UV on the Northwestern Salamander, Ambystoma gracile, from three lakes were assessed in the laboratory using a solar simulator. We measured the survival of embryos and the survival and growth of larvae exposed to four UV treatments in controlled laboratory studies, the UV absorbance of egg jelly, oviposition depths in the lakes, and UV absorbance in water samples from the three lakes. Hatching success of embryos decreased in the higher UV treatments as compared to the control treatments, and growth of surviving larvae was significantly reduced in the higher UVB irradiance treatments. The egg jelly exhibited a small peak of absorbance within the UVB range (290–320 nm). The magnitude of UV absorbance differed among egg jellies from the three lakes. Oviposition depths at the three sites averaged 1.10 m below the water surface. Approximately 66% of surface UVB radiation was attenuated at 10-cm depth in all three lakes. Results of this study indicate that larvae may be sensitive to UVB exposure under laboratory conditions; however, in field conditions the depths of egg deposition in the lakes, absorbance of UV radiation by the water column, and the potential for behavioral adjustments may mitigate severe effects of UV radiation.

  1. Human radiation studies: Remembering the early years. Oral history of Biochemist Waldo E. Cohn, Ph.D

    International Nuclear Information System (INIS)

    1995-01-01

    In September 1994, the Department of Energy began an oral history project as part of the Openess initiative on the documentation of the human radiation experiments. This paper presents the oral history of Waldo E Cohn, Ph.D., a Biochemist who worked for the Oak Ridge National Laboratory and the Manhattan Project

  2. Early growth rates and their relationships to mortalities of five breeds of chickens following exposure to acute gamma radiation stress

    International Nuclear Information System (INIS)

    Latimer, B.E.; Brisbin, I.L. Jr.

    1987-01-01

    Growth and mortality responses were recorded for 541 chicks, representing five different breeds of chickens, following acute exposures to gamma radiation stress at two days of age. Although there were no statistically significant differences in the LD50/30 of the five breeds studied, Cobb broilers showed the highest (1580R) and White Leghorn bantams the lowest (980R) levels, respectively. Other breeds studied included the standard White Leghorn, Athens Randombreds and a strain of feral bantam. Growth rates of body weights were proportionately more depressed by radiation stress than were body sizes, as measured by the lengths of the culmen, tarsus, middle toe and longest primary wing feather of all 32 day-old survivors. Among these structures, the length of the culmen seemed to be the least affected by radiation stress in all of the breeds studied. Feral bantams were able to tolerate the greatest depression in weight gain before exhibiting mortality at exposures below their LD50/30' while Cobb broilers tolerated the greatest depression of weight gain at higher exposure levels. There was a suggestion that those characteristics which were strongly selected for in the course of a particular breed's development were those which experienced the greatest proportional depressions following exposure to gamma radiation stress

  3. Cisplatin and radiation in the treatment of tumors of the central nervous system: Pharmacological considerations and results of early studies

    International Nuclear Information System (INIS)

    Stewart, D.J.; Molepo, J.M.; Eapen, L.; Montpetit, V.A.J.; Goel, R.; Wong, P.T.T.; Popovic, P.; Taylor, K.D.; Raaphorst, G.P.

    1994-01-01

    The purpose of this study was to review the human central nervous system pharmacology of cisplatin, factors that affect cisplatin uptake in tumors, and use alone and with radiation for the treatment of primary brain tumors. The authors review their own prior published and unpublished experience and data published by other groups on the above issues. Cisplatin is one of the most active chemotherapy drugs available for the treatment of solid tumors. It is synergistic with several other agents, including radiation. While it attains only low concentrations in the normal central nervous system, concentrations and plasma-tissue transfer constants for human intracerebral tumors are comparable to those in extracerebral tumors. Tumor type appears to be a more important determinant of platinum concentration than is tumor location, and gliomas do achieve lower concentrations than do other intracerebral or extracerebral tumors. Several other factors have also been identified that correlate with concentrations of cisplatin achieved in human tumors. While cisplatin alone and in combination with other drugs does have some degree of efficacy against primary brain tumors, combining it with cranial irradiation has generally not resulted in any substantial improvement in outcome to date, although some individual studies have been somewhat encouraging. New approaches are currently under investigation. Human pharmacology studies provide a rationale for use of cisplatin in the treatment of human brain tumors, and human and in vitro studies suggest some manipulations that might potentially further augment tumor platinum concentrations. While clinical studies suggest that cisplatin combinations may be of some value vs. human primary brain tumors and brain metastases, and while in vitro studies suggest that cisplatin potentiates radiation efficacy, no combination of cisplatin plus radiation yet tested has appeared to be superior to radiation alone. 123 refs., 5 tabs

  4. Pathological changes (developmental/growth disturbances) of the spine after radiation therapy of nephroblastomas during early childhood

    International Nuclear Information System (INIS)

    Willich, E.; Kuttig, H.; Pfeil, G.; Scheibel, P.; Heidelberg Univ.; Heidelberg Univ.

    1990-01-01

    82 children with nephroblastomas, who had therapy between 1960 and 1983, underwent continuous follow-up examinations until 1988. 79 children who survived had been treated with nephrectomy followed by radiation therapy (n=72) and chemotherapy (n=72). 64 of these patients had a combination of both post-surgical treatments. Radiotherapy was performed with cobalt-60 until 1977, followed by high-energy photon and electron beam therapy since 1978. In the beginning the dose applied in each patient within five to seven weeks was 46.5 Gy. Since 1972 it was reduced to 42.8 Gy and after 1978 to 32.3 Gy. The overall survival rate between 1960 and 1988 was 65% and rising to 91% since 1980. 47 children had spinal X-ray examinations at regular intervals for more than two years and 28 of these patients could be followed up to 20 years after radiotherapy. 39 children who had been irradiated before the age of 2 1/2 years developed a more pronounced degree of scoliosis and lumbar kyphosis with a higher incidence. 1500 spinal radiograms were evaluated. Measurements of the second lumbar vertebra, which was constantly situated within the target volume, were compared with those of the eight thoracic vertebral body outside the radiation field, and the curvature of the spine was analysed. Late radiation injuries of the spine could be reduced by involving the whole vertebral diameter into the radiation beam, by the use of high-energy radiation techniques and by excluding children under the age of one year from radiotherapy. However, disturbances of spinal growth cannot always be prevented. (orig.) [de

  5. Pretreatment prognostic factors in patients with early-stage (I/II) non-small-cell lung cancer treated with hyperfractionated radiation therapy alone

    International Nuclear Information System (INIS)

    Jeremic, Branislav; Milicic, Biljana; Dagovic, Aleksandar; Acimovic, Ljubisa; Milisavljevic, Slobodan

    2006-01-01

    Purpose: To investigate influence of various pretreatment prognostic factors in patients with early stage (I/II) non-small-cell lung cancer (NSCLC) treated with hyperfractionated radiation therapy alone. Patients and Methods: One hundred and sixteen patients were treated with tumor doses of 69.6 Gy, 1.2-Gy, twice-daily fractionation. There were 49 patients with Stage I and 67 patients with Stage II. Eighty patients had Karnofsky performance status (KPS) 90-100 and 95 patients had <5% weight loss. Peripheral tumors were observed in 57 patients. Squamous histology was observed in 70 patients and the majority of patients had concomitant disease (n = 72). Results: The median survival time for all patients was 29 months; 5-year survival was 29%. The median time to local progression and the distant metastasis were not achieved, whereas 5-year local progression-free and distant metastasis-free survivals were 50% and 72%, respectively. Multivariate analysis identified KPS, weight loss, location, histology, and the reason for not undergoing surgery as prognostic factors for survival. KPS, location, and histology influenced local progression-free survival, whereas only KPS and weight loss influenced distant metastasis-free survival. Conclusions: This retrospective analysis identified KPS and weight loss as the most important prognostic factors of outcome in patients with early-stage NSCLC treated with hyperfractionation radiation therapy

  6. Comparing the impact of melatonin and captopril on early effects of radiation on the heart tissue by studying glutathione, malondialdehyde, and lactate dehydrogenase enzyme activity in rats

    International Nuclear Information System (INIS)

    Shirazi, Alireza; Tabatabaie, Farnaz; Ghazi-Khansari, Mahmoud; Mirzaei, Hamidreza

    2015-01-01

    Prevention of secondary malignancy while the patient is receiving radiotherapy for the management of primary cancer has been an enormous challenge for biological and medical safety. The aim of the study is to compare protective effects of melatonin and captopril on early effects of radiation on the heart tissue of rats. Forty-eight adult male Wistar rats weighing 180-220 g were used. The rats were divided into six groups and the rats were exposed to 8 Gy whole body dose from Cobalt-60 sources. Thirty minutes prior to irradiation, six animals received melatonin (100 mg/kg body weight), and six animals received captopril (50 mg/kg body weight). All groups were sacrificed 10 days post-irradiation, and hearts were collected. Malondialdehyde (MDA), lactate dehydrogenase (LDH), and glutathione (GSH) were measured to evaluate cellular oxidative stress-induced injury. The biochemical data are presented as mean ± standard error of the mean, and the difference between the groups was analyzed using a two-way variance analysis. Treatment with captopril resulted in a significant increase in LDH and MDA, although the level of GSH was decreased (P < 0.01). MDA and LDH levels were decreased after melatonin treatment while GSH level was increased (P < 0.001). Melatonin has protective effects following radiation, while treatment with captopril post-irradiation seems to be radiosensitizing and does not have protective effects against radiation exposure. (author)

  7. A new basal hadrosauroid dinosaur from the Late Cretaceous of Uzbekistan and the early radiation of duck-billed dinosaurs

    Science.gov (United States)

    Sues, Hans-Dieter; Averianov, Alexander

    2009-01-01

    Levnesovia transoxiana gen. et sp. nov., from the Late Cretaceous (Middle–Late Turonian) of Uzbekistan, is the oldest well-documented taxon referable to Hadrosauroidea sensu Godefroit et al. It differs from a somewhat younger and closely related Bactrosaurus from Inner Mongolia (China) by a tall sagittal crest on the parietals and the absence of club-shaped dorsal neural spines in adult specimens. Levnesovia, Bactrosaurus and possibly Gilmoreosaurus represent the earliest radiation of Hadrosauroidea, which took place during the Cenomanian–Turonian and possibly in North America. The second, Santonian-age radiation of Hadrosauroidea included Aralosaurus, Hadrosauridae and lineages leading to Tanius (Campanian) and Telmatosaurus (Maastrichtian). Hadrosauridae appears to be monophyletic, but Hadrosaurinae and Lambeosaurinae originated in North America and Asia, respectively. PMID:19386651

  8. A new basal hadrosauroid dinosaur from the Late Cretaceous of Uzbekistan and the early radiation of duck-billed dinosaurs.

    Science.gov (United States)

    Sues, Hans-Dieter; Averianov, Alexander

    2009-07-22

    Levnesovia transoxiana gen. et sp. nov., from the Late Cretaceous (Middle-Late Turonian) of Uzbekistan, is the oldest well-documented taxon referable to Hadrosauroidea sensu Godefroit et al. It differs from a somewhat younger and closely related Bactrosaurus from Inner Mongolia (China) by a tall sagittal crest on the parietals and the absence of club-shaped dorsal neural spines in adult specimens. Levnesovia, Bactrosaurus and possibly Gilmoreosaurus represent the earliest radiation of Hadrosauroidea, which took place during the Cenomanian-Turonian and possibly in North America. The second, Santonian-age radiation of Hadrosauroidea included Aralosaurus, Hadrosauridae and lineages leading to Tanius (Campanian) and Telmatosaurus (Maastrichtian). Hadrosauridae appears to be monophyletic, but Hadrosaurinae and Lambeosaurinae originated in North America and Asia, respectively.

  9. Effects of simulated solar UVB radiation on early developmental stages of the northwestern salamander (Ambystoma gracile) from three lakes

    Science.gov (United States)

    Calfee, R.D.; Little, E.E.; Pearl, C.A.; Hoffman, R.L.

    2010-01-01

    Solar ultraviolet radiation (UV) has received much attention as a factor that could play a role in amphibian population declines. UV can be hazardous to some amphibians, but the resultant effects depend on a variety of environmental and behavioral factors. In this study, the potential effects of UV on the Northwestern Salamander, Ambystoma gracile, from three lakes were assessed in the laboratory using a solar simulator. We measured the survival of embryos and the survival and growth of larvae exposed to four UV treatments in controlled laboratory studies, the UV absorbance of egg jelly, oviposition depths in the lakes, and UV absorbance in water samples from the three lakes. Hatching success of embryos decreased in the higher UV treatments as compared to the control treatments, and growth of surviving larvae was significantly reduced in the higher UVB irradiance treatments. The egg jelly exhibited a small peak of absorbance within the UVB range (290-320 nm). The magnitude of UV absorbance differed among egg jellies from the three lakes. Oviposition depths at the three sites averaged 1.10 m below the water surface. Approximately 66 of surface UVB radiation was attenuated at 10-cm depth in all three lakes. Results of this study indicate that larvae may be sensitive to UVB exposure under laboratory conditions; however, in field conditions the depths of egg deposition in the lakes, absorbance of UV radiation by the water column, and the potential for behavioral adjustments may mitigate severe effects of UV radiation. Copyright 2010 Society for the Study of Amphibians and Reptiles.

  10. Human radiation studies: Remembering the early years. Oral history of biophysicist Robert Edmund Rowland, Ph.D., January 27, 1995

    International Nuclear Information System (INIS)

    1995-06-01

    This report provides a transcript of an oral interview with Dr. Robert Edmund Rowland by representatives of the US DOE Office of Human Radiation Research on January 27, 1995. Dr. Rowland was involved with the study of radium in the human body since 1950 and relates his knowledge of over 40 years of study of radium in the human body including dial painters, inmates of Elgin State Hospital, and other treated therapeutically with radium

  11. Early Effect of High Dose of Ionizing Radiation Exposure on Plasma Lipids Profile and Liver Fatty Acids Composition in Rats

    International Nuclear Information System (INIS)

    Noaman, E.; Mansour, S.Z.; Ibrahim, N.K.

    2005-01-01

    The present study was conducted to analyze the effect of acute gamma-irradiation on rats at supralethal doses of 20 Gy to determine the synthesis and amounts of free fatty acids, neutral lipids and phospholipids of plasma and liver after 24 and 48 h of gamma-irradiation. Male Wistar rats weighing 120+- 20 g were exposed to 20 Gy of gamma radiation (dose rate of 0.59 Gy/min). Exposure of rats to ionizing radiation resulted in significant alterations in the assayed parameters indicating lipid metabolism disturbance. Plasma cholesterol and phospholipid levels increased up to 71.3 and 71.5 %, respectively, after 24 h from radiation exposure and then returned to 28 and 27 % change in-compare with control values after 48 h post-irradiation. Plasma triacylglycerol concentrations increased concomitantly with irradiation, but their values are less high than cholesterol and phospholipid levels recording significant changes at 19 and 9 % comparing with control rats. Lipid peroxidation measured as MDA recorded significant elevation after 24 and 48 h post irradiation. It was shown that the synthesis of free fatty acids, cholesterol, cholesterol ethers and phospholipids was activated 48 h after irradiation at 20 Gy. The amount of free fatty acids of the rat liver decreased at 20 Gy exposures. This is assumed to be a result of the radioresistance to some degree in the system of free fatty acid synthesis of the rat to the gamma-irradiation in the lethal doses

  12. Fractionated stereotactic radiation therapy and single high-dose radiosurgery for acoustic neuroma: early results of a prospective clinical study

    International Nuclear Information System (INIS)

    Meijer, O.W.M.; Wolbers, J.G.; Baayen, J.C.; Slotman, B.J.

    2000-01-01

    Purpose: To prospectively assess the local control and toxicity rate in acoustic neuroma patients treated with linear accelerator-based radiosurgery and fractionated stereotactic radiation therapy. Methods and Materials: We evaluated 37 consecutive patients treated with stereotactic radiation therapy for acoustic neuroma. All patients had progressive tumors, progressive symptoms, or both. Mean tumor diameter was 2.3 cm (range 0.8-3.3) on magnetic resonance (MR) scan. Dentate patients were given a dose of 5 x 4 Gy or 5 x 5 Gy and edentate patients were given a dose of 1 x 10 Gy or 1 x 12.50 Gy prescribed to the 80% isodose. All patients were treated with a single isocenter. Results: With a mean follow-up period of 25 months (range 12-61), the actuarial local control rate at 5 years was 91% (only 1 patient failed). The actuarial rate of hearing preservation at 5 years was 66% in previously-hearing patients. The actuarial rate of freedom from trigeminal nerve toxicity was 97% at 5 years. No patient developed facial nerve toxicity or other complications. Conclusion: In this unselected series, fractionated stereotactic radiation therapy and linear accelerator-based radiosurgery give excellent local control in acoustic neuroma. It combines a high rate of preservation of hearing with a very low rate of other toxicity, although follow-up is relatively short

  13. Prostate cancer volume adds significantly to prostate-specific antigen in the prediction of early biochemical failure after external beam radiation therapy

    International Nuclear Information System (INIS)

    D'Amico, Anthony V.; Propert, Kathleen J.

    1996-01-01

    Purpose: A new clinical pretreatment quantity that closely approximates the true prostate cancer volume is defined. Methods and Materials: The cancer-specific prostate-specific antigen (PSA), PSA density, prostate cancer volume (V Ca ), and the volume fraction of the gland involved with carcinoma (V Ca fx) were calculated for 227 prostate cancer patients managed definitively with external beam radiation therapy. 1. PSA density PSA/ultrasound prostate gland volume 2. Cancer-specific PSA = PSA - [PSA from benign epithelial tissue] 3. V Ca = Cancer-specific PSA/[PSA in serum per cm 3 of cancer] 4. V Ca fx = V Ca /ultrasound prostate gland volume A Cox multiple regression analysis was used to test whether any of these-clinical pretreatment parameters added significantly to PSA in predicting early postradiation PSA failure. Results: The prostate cancer volume (p = 0.039) and the volume fraction of the gland involved by carcinoma (p = 0.035) significantly added to the PSA in predicting postradiation PSA failure. Conversely, the PSA density and the cancer-specific PSA did not add significantly (p > 0.05) to PSA in predicting postradiation PSA failure. The 20-month actuarial PSA failure-free rates for patients with calculated tumor volumes of ≤0.5 cm 3 , 0.5-4.0 cm 3 , and >4.0 cm 3 were 92, 80, and 47%, respectively (p = 0.00004). Conclusion: The volume of prostate cancer (V Ca ) and the resulting volume fraction of cancer both added significantly to PSA in their ability to predict for early postradiation PSA failure. These new parameters may be used to select patients in prospective randomized trials that examine the efficacy of combining radiation and androgen ablative therapy in patients with clinically localized disease, who are at high risk for early postradiation PSA failure

  14. Early Graphical Appearance of Radiation Pneumonitis Correlates With the Severity of Radiation Pneumonitis After Stereotactic Body Radiotherapy (SBRT) in Patients With Lung Tumors

    International Nuclear Information System (INIS)

    Takeda, Atsuya; Ohashi, Toshio; Kunieda, Etsuo

    2010-01-01

    Purpose: To investigate factors associated with Grade ≥3 radiation pneumonitis (RP) in patients with lung tumors treated with stereotactic body radiotherapy (SBRT). Methods and Materials: We retrospectively analyzed 128 patients with 133 lung tumors treated with SBRT. RP was graded according to the Common Terminology Criteria for Adverse Events version 3.0. Univariate analyses were used to identify predictive factors for RP. Results: The median follow-up period after SBRT was 12 months (range, 5-45 months). Incidences of Grades 0, 1, 2, and 3 RP were 27%, 52%, 16%, and 5%, respectively. No patients suffered Grade 4 or 5 RP. For all patients with Grade 2 or 3, symptoms occurred either simultaneously with or subsequent to graphical appearances. The latent period was the only significant factor associated with Grade ≥3 RP (p < 0.01). A latent period of 1 or 2 months indicated a 40% (6/15) risk for Grade 3. However, the risk for Grade 3 was 1.2% (1/82) 3 months after SBRT. No pretreatment clinical or dosimetric factors were significantly associated with Grade ≥3 RP. However, 4 of 7 patients with Grade 3 RP had severe pulmonary comorbidities. Conclusion: Only the latency period was a significant factor in the development of RP. No pretreatment clinical or dosimetric factors were significantly associated with Grade ≥3 RP. Patients, especially those with severe pulmonary comorbidities, should be carefully observed for the graphical appearance of RP within a few months during the follow-up period after SBRT.

  15. Bioinformatics in microbial biotechnology – a mini review

    Directory of Open Access Journals (Sweden)

    Bansal Arvind K

    2005-06-01

    Full Text Available Abstract The revolutionary growth in the computation speed and memory storage capability has fueled a new era in the analysis of biological data. Hundreds of microbial genomes and many eukaryotic genomes including a cleaner draft of human genome have been sequenced raising the expectation of better control of microorganisms. The goals are as lofty as the development of rational drugs and antimicrobial agents, development of new enhanced bacterial strains for bioremediation and pollution control, development of better and easy to administer vaccines, the development of protein biomarkers for various bacterial diseases, and better understanding of host-bacteria interaction to prevent bacterial infections. In the last decade the development of many new bioinformatics techniques and integrated databases has facilitated the realization of these goals. Current research in bioinformatics can be classified into: (i genomics – sequencing and comparative study of genomes to identify gene and genome functionality, (ii proteomics – identification and characterization of protein related properties and reconstruction of metabolic and regulatory pathways, (iii cell visualization and simulation to study and model cell behavior, and (iv application to the development of drugs and anti-microbial agents. In this article, we will focus on the techniques and their limitations in genomics and proteomics. Bioinformatics research can be classified under three major approaches: (1 analysis based upon the available experimental wet-lab data, (2 the use of mathematical modeling to derive new information, and (3 an integrated approach that integrates search techniques with mathematical modeling. The major impact of bioinformatics research has been to automate the genome sequencing, automated development of integrated genomics and proteomics databases, automated genome comparisons to identify the genome function, automated derivation of metabolic pathways, gene

  16. Video Bioinformatics Analysis of Human Embryonic Stem Cell Colony Growth

    Science.gov (United States)

    Lin, Sabrina; Fonteno, Shawn; Satish, Shruthi; Bhanu, Bir; Talbot, Prue

    2010-01-01

    Because video data are complex and are comprised of many images, mining information from video material is difficult to do without the aid of computer software. Video bioinformatics is a powerful quantitative approach for extracting spatio-temporal data from video images using computer software to perform dating mining and analysis. In this article, we introduce a video bioinformatics method for quantifying the growth of human embryonic stem cells (hESC) by analyzing time-lapse videos collected in a Nikon BioStation CT incubator equipped with a camera for video imaging. In our experiments, hESC colonies that were attached to Matrigel were filmed for 48 hours in the BioStation CT. To determine the rate of growth of these colonies, recipes were developed using CL-Quant software which enables users to extract various types of data from video images. To accurately evaluate colony growth, three recipes were created. The first segmented the image into the colony and background, the second enhanced the image to define colonies throughout the video sequence accurately, and the third measured the number of pixels in the colony over time. The three recipes were run in sequence on video data collected in a BioStation CT to analyze the rate of growth of individual hESC colonies over 48 hours. To verify the truthfulness of the CL-Quant recipes, the same data were analyzed manually using Adobe Photoshop software. When the data obtained using the CL-Quant recipes and Photoshop were compared, results were virtually identical, indicating the CL-Quant recipes were truthful. The method described here could be applied to any video data to measure growth rates of hESC or other cells that grow in colonies. In addition, other video bioinformatics recipes can be developed in the future for other cell processes such as migration, apoptosis, and cell adhesion. PMID:20495527

  17. WU-Blast2 server at the European Bioinformatics Institute

    Science.gov (United States)

    Lopez, Rodrigo; Silventoinen, Ville; Robinson, Stephen; Kibria, Asif; Gish, Warren

    2003-01-01

    Since 1995, the WU-BLAST programs (http://blast.wustl.edu) have provided a fast, flexible and reliable method for similarity searching of biological sequence databases. The software is in use at many locales and web sites. The European Bioinformatics Institute's WU-Blast2 (http://www.ebi.ac.uk/blast2/) server has been providing free access to these search services since 1997 and today supports many features that both enhance the usability and expand on the scope of the software. PMID:12824421

  18. MicroRNA from tuberculosis RNA: A bioinformatics study

    OpenAIRE

    Wiwanitkit, Somsri; Wiwanitkit, Viroj

    2012-01-01

    The role of microRNA in the pathogenesis of pulmonary tuberculosis is the interesting topic in chest medicine at present. Recently, it was proposed that the microRNA can be a useful biomarker for monitoring of pulmonary tuberculosis and might be the important part in pathogenesis of disease. Here, the authors perform a bioinformatics study to assess the microRNA within known tuberculosis RNA. The microRNA part can be detected and this can be important key information in further study of the p...

  19. Multilevel Cellular Automata as a Tool for Studying Bioinformatic Processes

    Science.gov (United States)

    Hogeweg, Paulien

    The signature feature of Cellular Automata is the realization that "simple rules can give rise to complex behavior". In particular how fixed "rock-bottom" simple rules can give rise to multiple levels of organization. Here we describe Multilevel Cellular Automata, in which the microscopic entities (states) and their transition rules themselves are adjusted by the mesoscale patterns that they themselves generate. Thus we study the feedback of higher levels of organization on the lower levels. Such an approach is preeminently important for studying bioinformatic systems. We will here focus on an evolutionary approach to formalize such Multilevel Cellular Automata, and review examples of studies that use them.

  20. [Pharmacogenetics II. Research molecular methods, bioinformatics and ethical concerns].

    Science.gov (United States)

    Daudén, E

    2007-01-01

    Pharmacogenetics refers to the study of the individual pharmacological response based on the genotype. Its objective is to optimize treatment in an individual basis, thereby creating a more efficient and safe personalized therapy. In the second part of this review, the molecular methods of study in pharmacogenetics, including microarray technology or DNA chips, are discussed. Among them we highlight the microarrays used to determine the gene expression that detect specific RNA sequences, and the microarrays employed to determine the genotype that detect specific DNA sequences, including polymorphisms, particularly single nucleotide polymorphisms (SNPs). The relationship between pharmacogenetics, bioinformatics and ethical concerns is reviewed.

  1. Application of bioinformatics on the detection of pathogens by Pcr

    International Nuclear Information System (INIS)

    Rezig, Slim; Sakhri, Saber

    2007-01-01

    Salmonellas are the main responsible agent for the frequent food-borne gastrointestinal diseases. Their detection using classical methods are laborious and their results take a lot of time to be revealed. In this context, we tried to set up a revealing technique of the invA virulence gene, found in the majority of Salmonella species. After amplification with PCR using specific primers created and verified by bioinformatics programs, two couples of primers were set up and they appeared to be very specific and sensitive for the detection of invA gene. (Author)

  2. Quantification of regional early stage gas exchange changes using hyperpolarized {sup 129}Xe MRI in a rat model of radiation-induced lung injury

    Energy Technology Data Exchange (ETDEWEB)

    Doganay, Ozkan, E-mail: ozkan.doganay@oncology.ox.ac.uk [Department of Medical Biophysics, Western University, London, Ontario N6A5C1 (Canada); Imaging Research Laboratories, Robarts Research Institute, London, Ontario N6A5C1 (Canada); Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ (United Kingdom); Stirrat, Elaine [Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G1X8 (Canada); McKenzie, Charles [Department of Medical Biophysics, Western University, London, Ontario N6A5C1 (Canada); Imaging Research Laboratories, Robarts Research Institute, London, Ontario N6A5C1 (Canada); Schulte, Rolf F. [General Electric Global Research, Munich 85748 (Germany); Santyr, Giles E. [Department of Medical Biophysics, Western University, London, Ontario N6A5C1 (Canada); Imaging Research Laboratories, Robarts Research Institute, London, Ontario N6A5C1 (Canada); Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G1X8 (Canada); Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G1L7 (Canada)

    2016-05-15

    Purpose: To assess the feasibility of hyperpolarized (HP) {sup 129}Xe MRI for detection of early stage radiation-induced lung injury (RILI) in a rat model involving unilateral irradiation by assessing differences in gas exchange dynamics between irradiated and unirradiated lungs. Methods: The dynamics of gas exchange between alveolar air space and pulmonary tissue (PT), PT and red blood cells (RBCs) was measured using single-shot spiral iterative decomposition of water and fat with echo asymmetry and least-squares estimation images of the right and left lungs of two age-matched cohorts of Sprague Dawley rats. The first cohort (n = 5) received 18 Gy irradiation to the right lung using a {sup 60}Co source and the second cohort (n = 5) was not irradiated and served as the healthy control. Both groups were imaged two weeks following irradiation when radiation pneumonitis (RP) was expected to be present. The gas exchange data were fit to a theoretical gas exchange model to extract measurements of pulmonary tissue thickness (L{sub PT}) and relative blood volume (V{sub RBC}) from each of the right and left lungs of both cohorts. Following imaging, lung specimens were retrieved and percent tissue area (PTA) was assessed histologically to confirm RP and correlate with MRI measurements. Results: Statistically significant differences in L{sub PT} and V{sub RBC} were observed between the irradiated and non-irradiated cohorts. In particular, L{sub PT} of the right and left lungs was increased approximately 8.2% and 5.0% respectively in the irradiated cohort. Additionally, V{sub RBC} of the right and left lungs was decreased approximately 36.1% and 11.7% respectively for the irradiated cohort compared to the non-irradiated cohort. PTA measurements in both right and left lungs were increased in the irradiated group compared to the non-irradiated cohort for both the left (P < 0.05) and right lungs (P < 0.01) confirming the presence of RP. PTA measurements also correlated with the

  3. Results of Roshydromet agencies activities on radiation monitoring of the territories affected the Chernobyl accident (on early stage)

    International Nuclear Information System (INIS)

    Vakulovskij, S.M.

    2016-01-01

    The work of the radiometric divisions of Hydrometeorological service on the USSR territory, first aero- and surface radiation surveys just after the Chernobyl accident are described. As a result of these works the map of contamination of the nearest zone of the emergency reactor, map-scheme of soil contamination of Kaluga and Tula Regions with the areas of increased contamination, have been constructed. The first estimations of radioactive contamination of surface waters, possibilities of the territory decontamination have been given. The organization of mass gamma-spectroscopic analysis of soil samples in Kiev, Obninsk, Minsk have been considerated [ru

  4. Human radiation studies: Remembering the early years. Oral history of biophysicist Cornelius A. Tobias, Ph.D., January 16, 1995

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-07-01

    Dr. Cornelius A. Tobias was interviewed by representatives of US DOE Office of Human Radiation Experiments (OHRE). He was chosen for this interview because of his extensive biophysics and medical physics research activities while he was employed by the University of California, Berkeley and San Francisco and at the Donner Laboratory. He discusses his involvement in wartime studies of effects of high altitude on aviators, carbon monoxide with radioactive tracers, blood studies with radioactive iron, human use committees, heavy-ion research with the Bevatron, boron isotope research, classified research involving human subjects, heavy-particle radiography, heavy- particle beams and medical research, and pituitary irradiation studies,.

  5. Human radiation studies: Remembering the early years. Oral history of Donner Lab Administrator Baird G. Whaley, August 15, 1994

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-09-01

    Baird G. Whaley, Donner Lab Administrator, was interviewed by representatives of US DOE Office of Human Radiation Experiments (OHRE). The purpose of the interview was to capture the remembrances of Mr. Whaley concerning what he could relate on activities at the Donner Lab that pertain to the OHRE responsibilities. Following a brief biographical sketch, Mr. Whaley relates his experiences in administration at the LAB including funding activities, staffing concerns, intralaboraory politics, and remembrances of John Lawrence, John Gofman, Cornelius Tobias, Jim Born, Alex Margolis, B.V.A. Low- Beer, and Ed Alpen. Further patient care procedures for Donner Clinic Research Programs were discussed.

  6. Human radiation studies: Remembering the early years. Oral history of Donner Lab Administrator Baird G. Whaley, August 15, 1994

    International Nuclear Information System (INIS)

    1995-09-01

    Baird G. Whaley, Donner Lab Administrator, was interviewed by representatives of US DOE Office of Human Radiation Experiments (OHRE). The purpose of the interview was to capture the remembrances of Mr. Whaley concerning what he could relate on activities at the Donner Lab that pertain to the OHRE responsibilities. Following a brief biographical sketch, Mr. Whaley relates his experiences in administration at the LAB including funding activities, staffing concerns, intralaboraory politics, and remembrances of John Lawrence, John Gofman, Cornelius Tobias, Jim Born, Alex Margolis, B.V.A. Low- Beer, and Ed Alpen. Further patient care procedures for Donner Clinic Research Programs were discussed

  7. Human radiation studies: Remembering the early years. Oral history of Dr. Nadine Foreman, M.D., August 19, 1994

    International Nuclear Information System (INIS)

    1995-07-01

    Dr. Nadine Foreman was interviewed by representatives of the US DOE Office of Human Radiation Experiments (OHRE). Dr. Foreman was selected for interview because of the position she held at the University of California, San Francisco. Following a brief biographical sketch, Dr. Foreman describes her work with Dr. Mayo Soley using I-131 in treatment of hyperthyroidism, selection criteria for patients in the radioiodine project, work with Dr. Earl Miller, work at Highland Hospital, radioiodine treatment of diffuse toxic goiter (myxedema), the radiophosphorus and radioiodine programs with Dr. Bert Low-Beer, and treatment of polycythemia vera

  8. Human radiation studies: Remembering the early years. Oral history of biophysicist Cornelius A. Tobias, Ph.D., January 16, 1995

    International Nuclear Information System (INIS)

    1995-07-01

    Dr. Cornelius A. Tobias was interviewed by representatives of US DOE Office of Human Radiation Experiments (OHRE). He was chosen for this interview because of his extensive biophysics and medical physics research activities while he was employed by the University of California, Berkeley and San Francisco and at the Donner Laboratory. He discusses his involvement in wartime studies of effects of high altitude on aviators, carbon monoxide with radioactive tracers, blood studies with radioactive iron, human use committees, heavy-ion research with the Bevatron, boron isotope research, classified research involving human subjects, heavy-particle radiography, heavy- particle beams and medical research, and pituitary irradiation studies,

  9. Bioinformatics Methods and Tools to Advance Clinical Care. Findings from the Yearbook 2015 Section on Bioinformatics and Translational Informatics.

    Science.gov (United States)

    Soualmia, L F; Lecroq, T

    2015-08-13

    To summarize excellent current research in the field of Bioinformatics and Translational Informatics with application in the health domain and clinical care. We provide a synopsis of the articles selected for the IMIA Yearbook 2015, from which we attempt to derive a synthetic overview of current and future activities in the field. As last year, a first step of selection was performed by querying MEDLINE with a list of MeSH descriptors completed by a list of terms adapted to the section. Each section editor has evaluated separately the set of 1,594 articles and the evaluation results were merged for retaining 15 articles for peer-review. The selection and evaluation process of this Yearbook's section on Bioinformatics and Translational Informatics yielded four excellent articles regarding data management and genome medicine that are mainly tool-based papers. In the first article, the authors present PPISURV a tool for uncovering the role of specific genes in cancer survival outcome. The second article describes the classifier PredictSNP which combines six performing tools for predicting disease-related mutations. In the third article, by presenting a high-coverage map of the human proteome using high resolution mass spectrometry, the authors highlight the need for using mass spectrometry to complement genome annotation. The fourth article is also related to patient survival and decision support. The authors present datamining methods of large-scale datasets of past transplants. The objective is to identify chances of survival. The current research activities still attest the continuous convergence of Bioinformatics and Medical Informatics, with a focus this year on dedicated tools and methods to advance clinical care. Indeed, there is a need for powerful tools for managing and interpreting complex, large-scale genomic and biological datasets, but also a need for user-friendly tools developed for the clinicians in their daily practice. All the recent research and

  10. Human radiation studies: Remembering the early years: Oral history of cell biologist Don Francis Petersen, Ph.D., conducted November 29, 1994

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-08-01

    This report is a transcript of an interview of Dr. Don Francis Petersen by representatives of the US DOE Office of Human Radiation Experiments. Dr. Petersen was selected for this interview because of his long research career at Los Alamos and his knowledge of the Atomic Energy Commission`s biomedical program. Dr. Petersen did not personally conduct research on human subjects. After a brief biographical sketch Dr. Petersen discusses his remembrances of the early use of radionuclides as biological tracers, aspects of nuclear weapons testing in the 1940`s and 1950`s including fallout studies, the means by which research projects were approved, use of humans in the whole-body counter, and the Health Division Biomedical responsibilities.

  11. Human radiation studies: Remembering the early years: Oral history of cell biologist Don Francis Petersen, Ph.D., conducted November 29, 1994

    International Nuclear Information System (INIS)

    1995-08-01

    This report is a transcript of an interview of Dr. Don Francis Petersen by representatives of the US DOE Office of Human Radiation Experiments. Dr. Petersen was selected for this interview because of his long research career at Los Alamos and his knowledge of the Atomic Energy Commission's biomedical program. Dr. Petersen did not personally conduct research on human subjects. After a brief biographical sketch Dr. Petersen discusses his remembrances of the early use of radionuclides as biological tracers, aspects of nuclear weapons testing in the 1940's and 1950's including fallout studies, the means by which research projects were approved, use of humans in the whole-body counter, and the Health Division Biomedical responsibilities

  12. Are the American Society for Radiation Oncology Guidelines Accurate Predictors of Recurrence in Early Stage Breast Cancer Patients Treated with Balloon-Based Brachytherapy?

    Directory of Open Access Journals (Sweden)

    Moira K. Christoudias

    2013-01-01

    Full Text Available The American Society for Radiation Oncology (ASTRO consensus statement (CS provides guidelines for patient selection for accelerated partial breast irradiation (APBI following breast conserving surgery. The purpose of this study was to evaluate recurrence rates based on ASTRO CS groupings. A single institution review of 238 early stage breast cancer patients treated with balloon-based APBI via balloon based brachytherapy demonstrated a 4-year actuarial ipsilateral breast tumor recurrence (IBTR rate of 5.1%. There were no significant differences in the 4-year actuarial IBTR rates between the “suitable,” “cautionary,” and “unsuitable” ASTRO categories (0%, 7.2%, and 4.3%, resp., P=0.28. ER negative tumors had higher rates of IBTR than ER positive tumors. The ASTRO groupings are poor predictors of patient outcomes. Further studies evaluating individual clinicopathologic features are needed to determine the safety of APBI in higher risk patients.

  13. Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders

    Directory of Open Access Journals (Sweden)

    Martin Hofmann-Apitius

    2015-12-01

    Full Text Available Since the decoding of the Human Genome, techniques from bioinformatics, statistics, and machine learning have been instrumental in uncovering patterns in increasing amounts and types of different data produced by technical profiling technologies applied to clinical samples, animal models, and cellular systems. Yet, progress on unravelling biological mechanisms, causally driving diseases, has been limited, in part due to the inherent complexity of biological systems. Whereas we have witnessed progress in the areas of cancer, cardiovascular and metabolic diseases, the area of neurodegenerative diseases has proved to be very challenging. This is in part because the aetiology of neurodegenerative diseases such as Alzheimer´s disease or Parkinson´s disease is unknown, rendering it very difficult to discern early causal events. Here we describe a panel of bioinformatics and modeling approaches that have recently been developed to identify candidate mechanisms of neurodegenerative diseases based on publicly available data and knowledge. We identify two complementary strategies—data mining techniques using genetic data as a starting point to be further enriched using other data-types, or alternatively to encode prior knowledge about disease mechanisms in a model based framework supporting reasoning and enrichment analysis. Our review illustrates the challenges entailed in integrating heterogeneous, multiscale and multimodal information in the area of neurology in general and neurodegeneration in particular. We conclude, that progress would be accelerated by increasing efforts on performing systematic collection of multiple data-types over time from each individual suffering from neurodegenerative disease. The work presented here has been driven by project AETIONOMY; a project funded in the course of the Innovative Medicines Initiative (IMI; which is a public-private partnership of the European Federation of Pharmaceutical Industry Associations

  14. Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders.

    Science.gov (United States)

    Hofmann-Apitius, Martin; Ball, Gordon; Gebel, Stephan; Bagewadi, Shweta; de Bono, Bernard; Schneider, Reinhard; Page, Matt; Kodamullil, Alpha Tom; Younesi, Erfan; Ebeling, Christian; Tegnér, Jesper; Canard, Luc

    2015-12-07

    Since the decoding of the Human Genome, techniques from bioinformatics, statistics, and machine learning have been instrumental in uncovering patterns in increasing amounts and types of different data produced by technical profiling technologies applied to clinical samples, animal models, and cellular systems. Yet, progress on unravelling biological mechanisms, causally driving diseases, has been limited, in part due to the inherent complexity of biological systems. Whereas we have witnessed progress in the areas of cancer, cardiovascular and metabolic diseases, the area of neurodegenerative diseases has proved to be very challenging. This is in part because the aetiology of neurodegenerative diseases such as Alzheimer´s disease or Parkinson´s disease is unknown, rendering it very difficult to discern early causal events. Here we describe a panel of bioinformatics and modeling approaches that have recently been developed to identify candidate mechanisms of neurodegenerative diseases based on publicly available data and knowledge. We identify two complementary strategies-data mining techniques using genetic data as a starting point to be further enriched using other data-types, or alternatively to encode prior knowledge about disease mechanisms in a model based framework supporting reasoning and enrichment analysis. Our review illustrates the challenges entailed in integrating heterogeneous, multiscale and multimodal information in the area of neurology in general and neurodegeneration in particular. We conclude, that progress would be accelerated by increasing efforts on performing systematic collection of multiple data-types over time from each individual suffering from neurodegenerative disease. The work presented here has been driven by project AETIONOMY; a project funded in the course of the Innovative Medicines Initiative (IMI); which is a public-private partnership of the European Federation of Pharmaceutical Industry Associations (EFPIA) and the European

  15. Emerging role of bioinformatics tools and software in evolution of clinical research

    Directory of Open Access Journals (Sweden)

    Supreet Kaur Gill

    2016-01-01

    Full Text Available Clinical research is making toiling efforts for promotion and wellbeing of the health status of the people. There is a rapid increase in number and severity of diseases like cancer, hepatitis, HIV etc, resulting in high morbidity and mortality. Clinical research involves drug discovery and development whereas clinical trials are performed to establish safety and efficacy of drugs. Drug discovery is a long process starting with the target identification, validation and lead optimization. This is followed by the preclinical trials, intensive clinical trials and eventually post marketing vigilance for drug safety. Softwares and the bioinformatics tools play a great role not only in the drug discovery but also in drug development. It involves the use of informatics in the development of new knowledge pertaining to health and disease, data management during clinical trials and to use clinical data for secondary research. In addition, new technology likes molecular docking, molecular dynamics simulation, proteomics and quantitative structure activity relationship in clinical research results in faster and easier drug discovery process. During the preclinical trials, the software is used for randomization to remove bias and to plan study design. In clinical trials software like electronic data capture, Remote data capture and electronic case report form (eCRF is used to store the data. eClinical, Oracle clinical are software used for clinical data management and for statistical analysis of the data. After the drug is marketed the safety of a drug could be monitored by drug safety software like Oracle Argus or ARISg. Therefore, softwares are used from the very early stages of drug designing, to drug development, clinical trials and during pharmacovigilance. This review describes different aspects related to application of computers and bioinformatics in drug designing, discovery and development, formulation designing and clinical research.

  16. Identification of the intestinal type gastric adenocarcinoma transcriptomic markers using bioinformatic and gene expression analysis

    Directory of Open Access Journals (Sweden)

    V. V. Volkomorov

    2017-01-01

    Full Text Available Introduction. Searching for specific and sensitive molecular tumor markers is one of the important tasks of modern oncology. These markers can be used for early tumor diagnosis and prognosis as well as for prediction of therapeutic response, estimation of tumor volume or to assess disease recurrence through monitoring. Gene expression data base mining followed by experimental validation of results obtained is one of the promising approaches for searching of that kind.Objective: to identify several membrane proteins which can be used for serum diagnosis of intestinal type of gastric adenocarcinoma.Materials and methods. We used bioinformatic-driven search using Gene Ontology and The Cancer Genome Atlas (TCGA data to identify mRNA up-regulated in gastric cancer (GC. Then, the expression levels of the mRNAs in 55 pare clinical specimens were investigated using reverse transcription polymerase chain reaction.Results. Comparative analysis of the mRNA levels in normal and tumor tissues using a new bioinformatics algorithm allowed to identify 3 high-copy transcripts (SULF1, PMEPA1 and SPARC, intracellular content of which markedly increased in GC. Expression analysis of these genes in clinical specimens showed significantly higher mRNA levels of PMEPA1 and SPARC in tumor as compared to normal gastric tissue. Interestingly more than twofold increase in expression level of these genes was observed in 75 % of intestinal-type GC. The same results were found only in 25 and 38 % of diffuse-type GC respectively.Conclusions. As a result of original bioinforamtic analysis using TCGA data base two genes (PMEPA1 and SPARC were shown to be significantly upregulated in intestinal-type gastric adenocarcinoma. The findings show the importance of further investigation to clarify the clinical value of their expression level in stomach tumors as well as their role in carcinogenesis.

  17. Protecting innovation in bioinformatics and in-silico biology.

    Science.gov (United States)

    Harrison, Robert

    2003-01-01

    Commercial success or failure of innovation in bioinformatics and in-silico biology requires the appropriate use of legal tools for protecting and exploiting intellectual property. These tools include patents, copyrights, trademarks, design rights, and limiting information in the form of 'trade secrets'. Potentially patentable components of bioinformatics programmes include lines of code, algorithms, data content, data structure and user interfaces. In both the US and the European Union, copyright protection is granted for software as a literary work, and most other major industrial countries have adopted similar rules. Nonetheless, the grant of software patents remains controversial and is being challenged in some countries. Current debate extends to aspects such as whether patents can claim not only the apparatus and methods but also the data signals and/or products, such as a CD-ROM, on which the programme is stored. The patentability of substances discovered using in-silico methods is a separate debate that is unlikely to be resolved in the near future.

  18. A review of bioinformatic methods for forensic DNA analyses.

    Science.gov (United States)

    Liu, Yao-Yuan; Harbison, SallyAnn

    2018-03-01

    Short tandem repeats, single nucleotide polymorphisms, and whole mitochondrial analyses are three classes of markers which will play an important role in the future of forensic DNA typing. The arrival of massively parallel sequencing platforms in forensic science reveals new information such as insights into the complexity and variability of the markers that were previously unseen, along with amounts of data too immense for analyses by manual means. Along with the sequencing chemistries employed, bioinformatic methods are required to process and interpret this new and extensive data. As more is learnt about the use of these new technologies for forensic applications, development and standardization of efficient, favourable tools for each stage of data processing is being carried out, and faster, more accurate methods that improve on the original approaches have been developed. As forensic laboratories search for the optimal pipeline of tools, sequencer manufacturers have incorporated pipelines into sequencer software to make analyses convenient. This review explores the current state of bioinformatic methods and tools used for the analyses of forensic markers sequenced on the massively parallel sequencing (MPS) platforms currently most widely used. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. MOWServ: a web client for integration of bioinformatic resources

    Science.gov (United States)

    Ramírez, Sergio; Muñoz-Mérida, Antonio; Karlsson, Johan; García, Maximiliano; Pérez-Pulido, Antonio J.; Claros, M. Gonzalo; Trelles, Oswaldo

    2010-01-01

    The productivity of any scientist is affected by cumbersome, tedious and time-consuming tasks that try to make the heterogeneous web services compatible so that they can be useful in their research. MOWServ, the bioinformatic platform offered by the Spanish National Institute of Bioinformatics, was released to provide integrated access to databases and analytical tools. Since its release, the number of available services has grown dramatically, and it has become one of the main contributors of registered services in the EMBRACE Biocatalogue. The ontology that enables most of the web-service compatibility has been curated, improved and extended. The service discovery has been greatly enhanced by Magallanes software and biodataSF. User data are securely stored on the main server by an authentication protocol that enables the monitoring of current or already-finished user’s tasks, as well as the pipelining of successive data processing services. The BioMoby standard has been greatly extended with the new features included in the MOWServ, such as management of additional information (metadata such as extended descriptions, keywords and datafile examples), a qualified registry, error handling, asynchronous services and service replication. All of them have increased the MOWServ service quality, usability and robustness. MOWServ is available at http://www.inab.org/MOWServ/ and has a mirror at http://www.bitlab-es.com/MOWServ/. PMID:20525794

  20. Agonist Binding to Chemosensory Receptors: A Systematic Bioinformatics Analysis

    Directory of Open Access Journals (Sweden)

    Fabrizio Fierro

    2017-09-01

    Full Text Available Human G-protein coupled receptors (hGPCRs constitute a large and highly pharmaceutically relevant membrane receptor superfamily. About half of the hGPCRs' family members are chemosensory receptors, involved in bitter taste and olfaction, along with a variety of other physiological processes. Hence these receptors constitute promising targets for pharmaceutical intervention. Molecular modeling has been so far the most important tool to get insights on agonist binding and receptor activation. Here we investigate both aspects by bioinformatics-based predictions across all bitter taste and odorant receptors for which site-directed mutagenesis data are available. First, we observe that state-of-the-art homology modeling combined with previously used docking procedures turned out to reproduce only a limited fraction of ligand/receptor interactions inferred by experiments. This is most probably caused by the low sequence identity with available structural templates, which limits the accuracy of the protein model and in particular of the side-chains' orientations. Methods which transcend the limited sampling of the conformational space of docking may improve the predictions. As an example corroborating this, we review here multi-scale simulations from our lab and show that, for the three complexes studied so far, they significantly enhance the predictive power of the computational approach. Second, our bioinformatics analysis provides support to previous claims that several residues, including those at positions 1.50, 2.50, and 7.52, are involved in receptor activation.

  1. Bioinformatic prediction and functional characterization of human KIAA0100 gene

    Directory of Open Access Journals (Sweden)

    He Cui

    2017-02-01

    Full Text Available Our previous study demonstrated that human KIAA0100 gene was a novel acute monocytic leukemia-associated antigen (MLAA gene. But the functional characterization of human KIAA0100 gene has remained unknown to date. Here, firstly, bioinformatic prediction of human KIAA0100 gene was carried out using online softwares; Secondly, Human KIAA0100 gene expression was downregulated by the clustered regularly interspaced short palindromic repeats (CRISPR/CRISPR-associated (Cas 9 system in U937 cells. Cell proliferation and apoptosis were next evaluated in KIAA0100-knockdown U937 cells. The bioinformatic prediction showed that human KIAA0100 gene was located on 17q11.2, and human KIAA0100 protein was located in the secretory pathway. Besides, human KIAA0100 protein contained a signalpeptide, a transmembrane region, three types of secondary structures (alpha helix, extended strand, and random coil , and four domains from mitochondrial protein 27 (FMP27. The observation on functional characterization of human KIAA0100 gene revealed that its downregulation inhibited cell proliferation, and promoted cell apoptosis in U937 cells. To summarize, these results suggest human KIAA0100 gene possibly comes within mitochondrial genome; moreover, it is a novel anti-apoptotic factor related to carcinogenesis or progression in acute monocytic leukemia, and may be a potential target for immunotherapy against acute monocytic leukemia.

  2. Targeting folate metabolism for therapeutic option: A bioinformatics approach.

    Science.gov (United States)

    Hande, Sneha; Goswami, Kalyan; Sharma, Richa; Bhoj, Priyanka; Jena, Lingaraj; Reddy, Maryada Venkata Rami

    2015-11-01

    Lymphatic filariasis, commonly called elephantiasis, poses a burden of estimated level of 5.09 million disability adjusted life year. Limitations of its sole drug, diethylcarbamazine (DEC) drive exploration of effective filarial target. A few plant extracts having polyphenolic ingredients and some synthetic compounds possess potential dihydrofolate reductase (DHFR) inhibitory effect. Here, we postulated a plausible link between folates and polyphenolics based on their common precursor in shikimate metabolism. Considering its implication in structural resemblance based antagonism, we have attempted to validate parasitic DHFR protein as a target. The bioinformatics approach, in the absence of crystal structure of the proposed target, used to authenticate and for virtual docking with suitable tested compounds, showed remarkably lower thermodynamic parameters as opposed to the positive control. A comparative docking analysis between human and Brugia malayi DHFR also showed effective binding parameters with lower inhibition constants of these ligands with parasitic target, but not with human counterpart highlighting safety and efficacy. This study suggests that DHFR could be a valid drug target for lymphatic filariasis, and further reveal that bioinformatics may be an effective tool in reverse pharmacological approach for drug design.

  3. MAPI: towards the integrated exploitation of bioinformatics Web Services

    Directory of Open Access Journals (Sweden)

    Karlsson Johan

    2011-10-01

    Full Text Available Abstract Background Bioinformatics is commonly featured as a well assorted list of available web resources. Although diversity of services is positive in general, the proliferation of tools, their dispersion and heterogeneity complicate the integrated exploitation of such data processing capacity. Results To facilitate the construction of software clients and make integrated use of this variety of tools, we present a modular programmatic application interface (MAPI that provides the necessary functionality for uniform representation of Web Services metadata descriptors including their management and invocation protocols of the services which they represent. This document describes the main functionality of the framework and how it can be used to facilitate the deployment of new software under a unified structure of bioinformatics Web Services. A notable feature of MAPI is the modular organization of the functionality into different modules associated with specific tasks. This means that only the modules needed for the client have to be installed, and that the module functionality can be extended without the need for re-writing the software client. Conclusions The potential utility and versatility of the software library has been demonstrated by the implementation of several currently available clients that cover different aspects of integrated data processing, ranging from service discovery to service invocation with advanced features such as workflows composition and asynchronous services calls to multiple types of Web Services including those registered in repositories (e.g. GRID-based, SOAP, BioMOBY, R-bioconductor, and others.

  4. Computational Lipidomics and Lipid Bioinformatics: Filling In the Blanks.

    Science.gov (United States)

    Pauling, Josch; Klipp, Edda

    2016-12-22

    Lipids are highly diverse metabolites of pronounced importance in health and disease. While metabolomics is a broad field under the omics umbrella that may also relate to lipids, lipidomics is an emerging field which specializes in the identification, quantification and functional interpretation of complex lipidomes. Today, it is possible to identify and distinguish lipids in a high-resolution, high-throughput manner and simultaneously with a lot of structural detail. However, doing so may produce thousands of mass spectra in a single experiment which has created a high demand for specialized computational support to analyze these spectral libraries. The computational biology and bioinformatics community has so far established methodology in genomics, transcriptomics and proteomics but there are many (combinatorial) challenges when it comes to structural diversity of lipids and their identification, quantification and interpretation. This review gives an overview and outlook on lipidomics research and illustrates ongoing computational and bioinformatics efforts. These efforts are important and necessary steps to advance the lipidomics field alongside analytic, biochemistry, biomedical and biology communities and to close the gap in available computational methodology between lipidomics and other omics sub-branches.

  5. No Clinically Significant Changes in Pulmonary Function Following Stereotactic Body Radiation Therapy for Early- Stage Peripheral Non-Small Cell Lung Cancer: An Analysis of RTOG 0236

    Energy Technology Data Exchange (ETDEWEB)

    Stanic, Sinisa, E-mail: sinisa.stanic@carle.com [Carle Cancer Center and University of Illinois College of Medicine, Urbana, Illinois (United States); Paulus, Rebecca [Radiation Therapy Oncology Group Statistical Center, Philadelphia, Pennsylvania (United States); Timmerman, Robert D. [University of Texas Southwestern, Dallas, Texas (United States); Michalski, Jeff M. [Washington University, St. Louis, Missouri (United States); Barriger, Robert B. [Indiana University, Indianapolis, Indiana (United States); Bezjak, Andrea [Princess Margaret Cancer Center, Toronto, Ontario (Canada); Videtic, Gregory M.M. [Cleveland Clinic Foundation, Cleveland, Ohio (United States); Bradley, Jeffrey [Washington University, St. Louis, Missouri (United States)

    2014-04-01

    Purpose: To investigate pulmonary function test (PFT) results and arterial blood gas changes (complete PFT) following stereotactic body radiation therapy (SBRT) and to see whether baseline PFT correlates with lung toxicity and overall survival in medically inoperable patients receiving SBRT for early stage, peripheral, non-small cell lung cancer (NSCLC). Methods and Materials: During the 2-year follow-up, PFT data were collected for patients with T1-T2N0M0 peripheral NSCLC who received effectively 18 Gy × 3 in a phase 2 North American multicenter study (Radiation Therapy Oncology Group [RTOG] protocol 0236). Pulmonary toxicity was graded by using the RTOG SBRT pulmonary toxicity scale. Paired Wilcoxon signed rank test, logistic regression model, and Kaplan-Meier method were used for statistical analysis. Results: At 2 years, mean percentage predicted forced expiratory volume in the first second and diffusing capacity for carbon monoxide declines were 5.8% and 6.3%, respectively, with minimal changes in arterial blood gases and no significant decline in oxygen saturation. Baseline PFT was not predictive of any pulmonary toxicity following SBRT. Whole-lung V5 (the percentage of normal lung tissue receiving 5 Gy), V10, V20, and mean dose to the whole lung were almost identical between patients who developed pneumonitis and patients who were pneumonitis-free. Poor baseline PFT did not predict decreased overall survival. Patients with poor baseline PFT as the reason for medical inoperability had higher median and overall survival rates than patients with normal baseline PFT values but with cardiac morbidity. Conclusions: Poor baseline PFT did not appear to predict pulmonary toxicity or decreased overall survival after SBRT in this medically inoperable population. Poor baseline PFT alone should not be used to exclude patients with early stage lung cancer from treatment with SBRT.

  6. Utility of Deep Inspiration Breath Hold for Left-Sided Breast Radiation Therapy in Preventing Early Cardiac Perfusion Defects: A Prospective Study

    Energy Technology Data Exchange (ETDEWEB)

    Zagar, Timothy M., E-mail: zagar@med.unc.edu [Department of Radiation Oncology, University of North Carolina, Chapel Hill, North Carolina (United States); Kaidar-Person, Orit [Department of Radiation Oncology, University of North Carolina, Chapel Hill, North Carolina (United States); Tang, Xiaoli [Memorial Sloan Kettering Cancer Center, West Harrison, New York (United States); Jones, Ellen E.; Matney, Jason; Das, Shiva K.; Green, Rebecca L. [Department of Radiation Oncology, University of North Carolina, Chapel Hill, North Carolina (United States); Sheikh, Arif [Department of Radiology, Columbia University, New York, New York (United States); Khandani, Amir H.; McCartney, William H.; Oldan, Jorge Daniel; Wong, Terence Z. [Department of Radiology, University of North Carolina, Chapel Hill, North Carolina (United States); Marks, Lawrence B. [Department of Radiation Oncology, University of North Carolina, Chapel Hill, North Carolina (United States)

    2017-04-01

    Purpose: To evaluate early cardiac single photon computed tomography (SPECT) findings after left breast/chest wall postoperative radiation therapy (RT) in the setting of deep inspiration breath hold (DIBH). Methods and Materials: We performed a prospective single-institution single-arm study of patients who were planned for tangential RT with DIBH to the left breast/chest wall (± internal mammary nodes). The DIBH was done by use of a controlled surface monitoring technique (AlignRT, Vision RT Ltd, London, UK). The RT was given with tangential fields and a heart block. Radiation-induced cardiac perfusion and wall motion changes were assessed by pre-RT and 6-month post-RT SPECT scans. A cumulative SPECT summed-rest score was used to quantify perfusion in predefined left ventricle segments. The incidence of wall motion abnormalities was assessed in each of these same segments. Results: A total of 20 patients with normal pre-RT scans were studied; their median age was 56 years (range, 39-72 years). Seven (35%) patients also received irradiation to the left internal mammary chain, and 5 (25%) received an additional RT field to supraclavicular nodes. The median heart dose was 94 cGy (range, 56-200 cGy), and the median V25{sub Gy} was zero (range, 0-0.1). None of the patients had post-RT perfusion or wall motion abnormalities. Conclusions: Our results suggest that DIBH and conformal cardiac blocking for patients receiving tangential RT for left-sided breast cancer is an effective means to avoid early RT-associated cardiac perfusion defects.

  7. Human radiation studies: Remembering the early years: Oral history of biochemist William D. Moss, conducted November 30, 1994

    International Nuclear Information System (INIS)

    1995-09-01

    This report is a transcript of an interview with William D. Moss by representatives of the US DOE Office of Human Radiation Experiments. Mr. Moss was selected for this interview because of his work at Los Alamos National Laboratory concerning analytical methods in the chemical determination of plutonium in biological materials. After a brief biographical sketch, Mr. Moss relates his understanding of how occupational exposure limits were determined for the Manhattan Project, how data from those workers who were exposed to plutonium was collected and analyzed, how the experiments were planned and data was gathered from plutonium or polonium injections in man, how problems with analytical procedures compounded health physics aspects of the project, and problems remaining in the interpretation of these data

  8. The effect of ultraviolet radiation on early stages of activation of human lymphocytes: inhibition is independent of effects on DNA

    DEFF Research Database (Denmark)

    Castellanos, G; Owens, T; Rudd, C

    1982-01-01

    Low doses (30-84 ergs/mm2, 1 erg = 10(7) J) of ultraviolet radiation (UV) caused severe inhibition of the proliferation of human lymphocytes in vitro. Greatest inhibition was produced when resting cells were irradiated immediately prior to stimulation with concanavalin A (Con A); this was true...... whether activation was measured by the incorporation of labelled leucine, uridine, or thymidine. If UV was applied at 44 h after culture in presence of Con A, the incorporation of [3H]thymidine measured 4 h later was seen to be inhibited but transcription and translation were scarcely affected. UV...... lymphocytes, when this was measured by means of 86Rb uptake after 2-4 h culture. The mitogen-stimulated activation of cation pump function has previously been shown to be unaffected by concentrations of cycloheximide and actinomycin D which produce virtually complete inhibition of protein and RNA synthesis...

  9. Human radiation studies: Remembering the early years. Oral history of hematologist Karl F. Hubner, M.D., December 30, 1994

    International Nuclear Information System (INIS)

    1995-09-01

    This report is a transcript of an interview of Dr. Karl F. Hubner by representatives of the US DOE Human Radiation Experiments. Dr. Hubner was selected for this interview because of his participation in the Oak Ridge Institute of Nuclear Studies(ORINS)/Oak Ridge Associated Universities(ORAU) Medical Division cancer therapy research program involving total body irradiation. After a short biographical sketch Dr. Hubner discusses his research in Bone Marrow Transplants, his participation in the development of Nuclear Medicine in Oak Ridge, use of the total body irradiation machine at the University of Tennessee School of Agriculture Animal Research Laboratory (later the Comparative Animal Research Laboratory or CARL) to deliver a high enough dose rate to destroy a patients immune system, the operation of a sterile environment for recovery of patients following bone- marrow transplantation, and the closing of the ORAU Medical Division's Clinical Program following a negative review. Finally, Dr. Hubner describes his later research using PET

  10. Cosmesis and Breast-Related Quality of Life Outcomes After Intraoperative Radiation Therapy for Early Breast Cancer: A Substudy of the TARGIT-A Trial

    Energy Technology Data Exchange (ETDEWEB)

    Corica, Tammy, E-mail: Tammy.Corica@health.wa.gov.au [Radiation Oncology Clinical Trials and Research Unit, Comprehensive Cancer Centre, Sir Charles Gairdner Hospital, Nedlands, Western Australia (Australia); School of Medicine and Pharmacology, University of Western Australia, Crawley, Western Australia (Australia); Nowak, Anna K. [School of Medicine and Pharmacology, University of Western Australia, Crawley, Western Australia (Australia); Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, Western Australia (Australia); Saunders, Christobel M. [School of Surgery, University of Western Australia, Crawley, Western Australia (Australia); Department of Surgery Fiona Stanley Hospital, Western Australia (Australia); Bulsara, Max [Institute for Health Research, University of Notre Dame, Fremantle, Western Australia (Australia); Taylor, Mandy [Radiation Oncology, Comprehensive Cancer Centre, Sir Charles Gairdner Hospital Nedlands, Western Australia (Australia); Vaidya, Jayant S. [Department of Surgery, Royal Free Hospital, London (United Kingdom); Clinical Trials Group, Division of Surgery and Interventional Science, University College, London, London (United Kingdom); Department of Surgery, Whittington Health, London (United Kingdom); Baum, Michael [Clinical Trials Group, Division of Surgery and Interventional Science, University College London, London (United Kingdom); Joseph, David J. [School of Surgery, University of Western Australia, Western Australia (Australia); Genesis Cancer Care, Western Australia (Australia); Radiation Oncology, Comprehensive Cancer Centre, Sir Charles Gairdner Hospital, Western Australia (Australia)

    2016-09-01

    Purpose: To report the first comprehensive investigation of patient-reported cosmesis and breast-related quality of life (QOL) outcomes comparing patients randomized to risk-adapted single-dose intraoperative radiation therapy (TARGIT-IORT) versus external beam radiation therapy (EBRT) on the TARGIT-A trial. Methods and Materials: Longitudinal cosmesis and QOL data were collected from a subset of TARGIT-A participants who received TARGIT-IORT as a separate procedure (postpathology). Patients completed a cosmetic assessment before radiation therapy and annually thereafter for at least 5 years. Patients also completed the combined European Organization for Research and Treatment of Cancer (EORTC) core questionnaire and Breast-Specific Module in addition to the Body Image after Breast Cancer Questionnaire at baseline and annually thereafter. The combined EORTC questionnaires were also collected 3, 6, and 9 months after wide local excision. Results: An Excellent–Good cosmetic result was scored more often than a Fair–Poor result for both treatment groups across all time points. The TARGIT-IORT patients reported better breast-related QOL than EBRT patients. Statistically and clinically significant differences were seen at month 6 and year 1, with EBRT patients having moderately worse breast symptoms (a statistically significant difference of more than 10 in a 100-point scale) than TARGIT-IORT patients at these time points. Conclusion: Patients treated with TARGIT-IORT on the TARGIT-A trial have similar self-reported cosmetic outcome but better breast-related QOL outcomes than patients treated with EBRT. This important evidence can facilitate the treatment decision-making process for patients who have early breast cancer suitable for breast-conserving surgery and inform their clinicians.

  11. Five-year Local Control in a Phase II Study of Hypofractionated Intensity Modulated Radiation Therapy With an Incorporated Boost for Early Stage Breast Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Freedman, Gary M., E-mail: Gary.Freedman@uphs.upenn.edu [Radiation Oncology, University of Pennsylvania, Philadelphia, Pennsylvania (United States); Anderson, Penny R. [Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania (United States); Bleicher, Richard J. [Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania (United States); Litwin, Samuel; Li Tianyu [Department of Biostatistics, Fox Chase Cancer Center, Philadelphia, Pennsylvania (United States); Swaby, Ramona F. [Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania (United States); Ma, Chang-Ming Charlie; Li Jinsheng [Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania (United States); Sigurdson, Elin R. [Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania (United States); Watkins-Bruner, Deborah [School of Nursing, Emory University, Atlanta, Georgia (United States); Morrow, Monica [Department of Surgical Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York (United States); Goldstein, Lori J. [Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania (United States)

    2012-11-15

    Purpose: Conventional radiation fractionation of 1.8-2 Gy per day for early stage breast cancer requires daily treatment for 6-7 weeks. We report the 5-year results of a phase II study of intensity modulated radiation therapy (IMRT), hypofractionation, and incorporated boost that shortened treatment time to 4 weeks. Methods and Materials: The study design was phase II with a planned accrual of 75 patients. Eligibility included patients aged {>=}18 years, Tis-T2, stage 0-II, and breast conservation. Photon IMRT and an incorporated boost was used, and the whole breast received 2.25 Gy per fraction for a total of 45 Gy, and the tumor bed received 2.8 Gy per fraction for a total of 56 Gy in 20 treatments over 4 weeks. Patients were followed every 6 months for 5 years. Results: Seventy-five patients were treated from December 2003 to November 2005. The median follow-up was 69 months. Median age was 52 years (range, 31-81). Median tumor size was 1.4 cm (range, 0.1-3.5). Eighty percent of tumors were node negative; 93% of patients had negative margins, and 7% of patients had close (>0 and <2 mm) margins; 76% of cancers were invasive ductal type: 15% were ductal carcinoma in situ, 5% were lobular, and 4% were other histology types. Twenty-nine percent of patients 29% had grade 3 carcinoma, and 20% of patients had extensive in situ carcinoma; 11% of patients received chemotherapy, 36% received endocrine therapy, 33% received both, and 20% received neither. There were 3 instances of local recurrence for a 5-year actuarial rate of 2.7%. Conclusions: This 4-week course of hypofractionated radiation with incorporated boost was associated with excellent local control, comparable to historical results of 6-7 weeks of conventional whole-breast fractionation with sequential boost.

  12. Identifying early dehydration risk with home-based sensors during radiation treatment: a feasibility study on patients with head and neck cancer.

    Science.gov (United States)

    Peterson, Susan K; Shinn, Eileen H; Basen-Engquist, Karen; Demark-Wahnefried, Wendy; Prokhorov, Alexander V; Baru, Chaitanya; Krueger, Ingolf H; Farcas, Emilia; Rios, Philip; Garden, Adam S; Beadle, Beth M; Lin, Kai; Yan, Yan; Martch, Stephanie L; Patrick, Kevin

    2013-12-01

    Systems that enable remote monitoring of patients' symptoms and other health-related outcomes may optimize cancer care outside of the clinic setting. CYCORE (CYberinfrastructure for COmparative effectiveness REsearch) is a software-based prototype for a user-friendly cyberinfrastructure supporting the comprehensive collection and analyses of data from multiple domains using a suite of home-based and mobile sensors. This study evaluated the feasibility of using CYCORE to address early at-home identification of dehydration risk in head and neck cancer patients undergoing radiation therapy. Head and neck cancer patients used home-based sensors to capture weight, blood pressure, pulse, and patient-reported outcomes for two 5-day periods during radiation therapy. Data were sent to the radiation oncologist of each head and neck cancer patient, who viewed them online via a Web-based interface. Feasibility outcomes included study completion rate, acceptability and perceived usefulness of the intervention, and adherence to the monitoring protocol. We also evaluated whether sensor data could identify dehydration-related events. Fifty patients consented to participate, and 48 (96%) completed the study. More than 90% of patients rated their ease, self-efficacy, and satisfaction regarding use of the sensor suite as extremely favorable, with minimal concerns expressed regarding data privacy issues. Patients highly valued the ability to have immediate access to objective, self-monitoring data related to personal risk for dehydration. Clinician assessments indicated a high degree of satisfaction with the ease of using the CYCORE system and the resulting ability to monitor their patients remotely. Implementing CYCORE in a clinical oncology care setting is feasible and highly acceptable to both patients and providers.

  13. Cosmesis and Breast-Related Quality of Life Outcomes After Intraoperative Radiation Therapy for Early Breast Cancer: A Substudy of the TARGIT-A Trial

    International Nuclear Information System (INIS)

    Corica, Tammy; Nowak, Anna K.; Saunders, Christobel M.; Bulsara, Max; Taylor, Mandy; Vaidya, Jayant S.; Baum, Michael; Joseph, David J.

    2016-01-01

    Purpose: To report the first comprehensive investigation of patient-reported cosmesis and breast-related quality of life (QOL) outcomes comparing patients randomized to risk-adapted single-dose intraoperative radiation therapy (TARGIT-IORT) versus external beam radiation therapy (EBRT) on the TARGIT-A trial. Methods and Materials: Longitudinal cosmesis and QOL data were collected from a subset of TARGIT-A participants who received TARGIT-IORT as a separate procedure (postpathology). Patients completed a cosmetic assessment before radiation therapy and annually thereafter for at least 5 years. Patients also completed the combined European Organization for Research and Treatment of Cancer (EORTC) core questionnaire and Breast-Specific Module in addition to the Body Image after Breast Cancer Questionnaire at baseline and annually thereafter. The combined EORTC questionnaires were also collected 3, 6, and 9 months after wide local excision. Results: An Excellent–Good cosmetic result was scored more often than a Fair–Poor result for both treatment groups across all time points. The TARGIT-IORT patients reported better breast-related QOL than EBRT patients. Statistically and clinically significant differences were seen at month 6 and year 1, with EBRT patients having moderately worse breast symptoms (a statistically significant difference of more than 10 in a 100-point scale) than TARGIT-IORT patients at these time points. Conclusion: Patients treated with TARGIT-IORT on the TARGIT-A trial have similar self-reported cosmetic outcome but better breast-related QOL outcomes than patients treated with EBRT. This important evidence can facilitate the treatment decision-making process for patients who have early breast cancer suitable for breast-conserving surgery and inform their clinicians.

  14. Prospective study of sequential volumetric changes of parotid gland in early oropharyngeal carcinoma patients treated by intensity-modulated radiation therapy: An institutional experience.

    Science.gov (United States)

    Patel, Pooja Nandwani; Goyal, Sumit; Shah, Anand; Gohel, Mehul; Suryanarayana, Unnikrishnan

    2018-01-01

    During course of radiation therapy, anatomical variations occur risking overdose of parotid gland. We tried to quantify volume of parotid gland and mean dose to parotid gland after every 10 fractions (#). We conducted the prospective study from July 2016 to May 2017 in 25 patients of early-stage oropharyngeal carcinoma. Patients had Karnofsy Performance Score of 80-100, median age was 54 years, and 18 patients were males. Patients were planned with intensity-modulated radiation therapy planning with dose as 66 Gy/30# to planning target volume (PTV) including primary and 54 Gy/30# to PTV-nodal including elective neck irradiation. After each 10#, replanning was done, and variations in parotid volume were studied including D mean (mean dose to parotids) and D 50 (the dose delivered to 50% of volume). Other tumor characteristic like PTV of primary was also assessed and minimum PTV volume covered by 95% isodose line was kept as 95%. Average parotid volumes decreased by the mean value of 10% and 6% for the left and right parotids, respectively, and PTV of primary target decreased by mean of 13%. The difference in D mean doses to parotid glands was 32% and 42% and difference in D 50 dose was 30% and 35% on the left and right side, respectively. The parotid volumes differ considerably during adaptive planning done after every ten fractions. These differences in parotid volumes and doses received to parotid glands play a significant role in the risk of xerostomia observed during later follow-up.

  15. Radon migration in soil and its relation to terrestrial gamma radiation in different locations of the Greek early warning system network

    International Nuclear Information System (INIS)

    Clouvas, A.; Leontaris, F.; Xanthos, S.; Alifragis, D.

    2017-01-01

    Radon concentration as function of the soil depth was measured during the years (2011 2015), in a location of the Aristotle University campus. Radium distribution in soil was found constant. On the contrary, as expected, radon concentration increases with soil depth. The experimental distribution was reproduced by solving the general transport equation (diffusion and advection). From the general radon migration (diffusion and advection) equation it was indirectly deduced, from the measured radon profile in the soil, the radon exhalation rate from the soil (26.7 ± 4.5 Bq m -2 h -1 ). In the same location, during 2010 2015, 113 direct radon exhalation measurements were performed and give an average value for the 6 years of 21.1 ± 3 Bq m -2 h -1 . The comparison between the radon exhalation rates deduced by the indirect and direct method indicates the validity of the diffusion advection model predictions concerning the radon exhalation rate from soil. The relation between radon migration in soil and terrestrial gamma radiation was studied. In particular, in the present study was investigated the correlation between gamma radiation 1 m above soil and radon exhalation in six locations of the Greek early warning system network. A positive correlation between gamma dose rate in air and radon exhalation rate from soil was found. (authors)

  16. RESPONSE OF THE GREEK EARLY WARNING SYSTEM REUTER-STOKES IONIZATION CHAMBERS TO TERRESTRIAL AND COSMIC RADIATION EVALUATED IN COMPARISON WITH SPECTROSCOPIC DATA AND TIME SERIES ANALYSIS.

    Science.gov (United States)

    Leontaris, F; Clouvas, A; Xanthos, S; Maltezos, A; Potiriadis, C; Kiriakopoulos, E; Guilhot, J

    2018-02-01

    The Telemetric Early Warning System Network of the Greek Atomic Energy Commission consists mainly of a network of 24 Reuter-Stokes high-pressure ionization chambers (HPIC) for gamma dose rate measurements and covers all Greece. In the present work, the response of the Reuter-Stokes HPIC to terrestrial and cosmic radiation was evaluated in comparison with spectroscopic data obtained by in situ gamma spectrometry measurements with portable hyper pure Germanium detectors (HPGe), near the Reuter-Stokes detectors and time series analysis. For the HPIC detectors, a conversion factor for the measured absorbed dose rate in air (in nGy h-1) to the total ambient dose equivalent rate Ḣ*(10), due to terrestrial and cosmic component, was deduced by the field measurements. Time series analysis of the mean monthly dose rate (measured by the Reuter-Stokes detector in Thessaloniki, northern Greece, from 2001 to 2016) was performed with advanced statistical methods (Fast Fourier Analysis and Zhao Atlas Marks Transform). Fourier analysis reveals several periodicities (periodogram). The periodogram of the absorbed dose rate in air values was compared with the periodogram of the values measured for the same period (2001-16) and in the same location with a NaI (Tl) detector which in