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Sample records for archival tumor samples

  1. Archival bone marrow samples

    DEFF Research Database (Denmark)

    Lund, Bendik; Najmi, Laeya A; Wesolowska-Andersen, Agata;

    2015-01-01

    AB Archival samples represent a significant potential for genetic studies, particularly in severe diseases with risk of lethal outcome, such as in cancer. In this pilot study, we aimed to evaluate the usability of archival bone marrow smears and biopsies for DNA extraction and purification, whole...... with samples stored for 4 to 10 years. Acceptable call rates for SNPs were detected for 7 of 42 archival samples. In conclusion, archival bone marrow samples are suitable for DNA extraction and multiple marker analysis, but WGA was less successful, especially when longer fragments were analyzed. Multiple SNP...

  2. Analysis of changes in DNA sequence copy number by comparative genomic hybridization in archival paraffin-embedded tumor samples.

    OpenAIRE

    Isola, J; DeVries, S; Chu, L; Ghazvini, S.; Waldman, F.

    1994-01-01

    Analysis of previously unknown genetic aberrations in solid tumors has become possible through the use of comparative genomic hybridization (CGH), which is based on competitive binding of tumor and control DNA to normal metaphase chromosomes. CGH allows detection of DNA sequence copy number changes (deletions, gains, and amplifications) on a genome-wide scale in a single hybridization. We describe here an improved CGH technique, which enables reliable detection of copy number changes in archi...

  3. Hot sample archiving. Revision 3

    International Nuclear Information System (INIS)

    This Engineering Study revision evaluated the alternatives to provide tank waste characterization analytical samples for a time period as recommended by the Tank Waste Remediation Systems Program. The recommendation of storing 40 ml segment samples for a period of approximately 18 months (6 months past the approval date of the Tank Characterization Report) and then composite the core segment material in 125 ml containers for a period of five years. The study considers storage at 222-S facility. It was determined that the critical storage problem was in the hot cell area. The 40 ml sample container has enough material for approximately 3 times the required amount for a complete laboratory re-analysis. The final result is that 222-S can meet the sample archive storage requirements. During the 100% capture rate the capacity is exceeded in the hot cell area, but quick, inexpensive options are available to meet the requirements

  4. Cell sample - Open TG-GATEs | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us Open...ase Description Download License Update History of This Database Site Policy | Contact Us Cell sample - Open TG-GATEs | LSDB Archive ...

  5. Archival Bone Marrow Samples: Suitable for Multiple Biomarker Analysis?

    DEFF Research Database (Denmark)

    Lund, Bendik; Najmi, A. Laeya; Wesolowska, Agata;

    2015-01-01

    Archival samples represent a significant potential for genetic studies, particularly in severe diseases with risk of lethal outcome, such as in cancer. In this pilot study, we aimed to evaluate the usability of archival bone marrow smears and biopsies for DNA extraction and purification, whole...... with samples stored for 4 to 10 years. Acceptable call rates for SNPs were detected for 7 of 42 archival samples. In conclusion, archival bone marrow samples are suitable for DNA extraction and multiple marker analysis, but WGA was less successful, especially when longer fragments were analyzed. Multiple SNP...

  6. Gamma spectroscopy analysis of archived Marshall Island soil samples

    International Nuclear Information System (INIS)

    Four samples of archival Marshall Islands soil were subjected to non-destructive, broad energy (17 keV-2.61 MeV) gamma-ray spectrometry analysis using a series of different high-resolution germanium detectors. These archival samples were collected in 1967 from different locations on Bikini Atoll and were contaminated with a range of fission and activation products, and other nuclear material from multiple weapons tests. Unlike samples collected recently, these samples have been stored in sealed containers and have been unaffected by approximately 50 years of weathering. Initial results show that the samples contained measurable but proportionally different concentrations of plutonium, 241Am, and 137Cs, and 60Co. (author)

  7. Rapid surface sampling and archival record system

    Energy Technology Data Exchange (ETDEWEB)

    Barren, E.; Penney, C.M.; Sheldon, R.B. [GE Corporate Research and Development Center, Schenectady, NY (United States)] [and others

    1995-10-01

    A number of contamination sites exist in this country where the area and volume of material to be remediated is very large, approaching or exceeding 10{sup 6} m{sup 2} and 10{sup 6} m{sup 3}. Typically, only a small fraction of this material is actually contaminated. In such cases there is a strong economic motivation to test the material with a sufficient density of measurements to identify which portions are uncontaminated, so extensively they be left in place or be disposed of as uncontaminated waste. Unfortunately, since contamination often varies rapidly from position to position, this procedure can involve upwards of one million measurements per site. The situation is complicated further in many cases by the difficulties of sampling porous surfaces, such as concrete. This report describes a method for sampling concretes in which an immediate distinction can be made between contaminated and uncontaminated surfaces. Sample acquisition and analysis will be automated.

  8. Mutation detection in tumor suppressor genes using archival tissue specimens.

    Science.gov (United States)

    Astrinidis, Aristotelis; Henske, Elizabeth Petri

    2006-01-01

    Tuberous sclerosis complex (TSC) is a neurocutaneous syndrome characterized by seizures, mental retardation, and benign tumors of many organs, including the brain, kidneys, skin, retina, and heart. TSC is caused by mutations in the TSC1 and TSC2 tumor suppressor genes. The genes follow the two-hit model for tumorigenesis, with germline mutations inactivating one allele and somatic mutations inactivating the remaining wild-type allele. Allelic loss (also called loss of heterozygosity [LOH]) in the 9q34 and 16p13 regions has been found in many tumor types from TSC patients. Cardiac rhabdomyomas are frequently found in infants with TSC. Because rhabdomyomas often spontaneously regress, access to fresh tissue is limited. In this chapter, we present methodology for detection of genetic inactivation of TSC1 and TSC2 in paraffin-embedded archival tissues. The template DNA is obtained either by direct scraping of tissue or after laser capture microdissection. LOH analysis is performed after polymerase chain reaction amplification of microsatellite markers in the 9q34 and 16p13 regions and denaturing polyacrylamide gel electrophoresis. Mutation detection is performed using single-strand conformation polymorphisms on mutation detection enhancement gels. Finally, variant bands are amplified and analyzed by direct sequencing. PMID:16930013

  9. Post-mortem testing; germline BRCA1/2 variant detection using archival FFPE non-tumor tissue

    DEFF Research Database (Denmark)

    Petersen, Annabeth Høgh; Jørgensen, Mads Malik Aagaard; Nielsen, Henriette Roed;

    2016-01-01

    Accurate estimation of cancer risk in HBOC families often requires BRCA1/2 testing, but this may be impossible in deceased family members. Previous, testing archival formalin-fixed, paraffin-embedded (FFPE) tissue for germline BRCA1/2 variants was unsuccessful, except for the Jewish founder...... mutations. A high-throughput method to systematically test for variants in all coding regions of BRCA1/2 in archival FFPE samples of non-tumor tissue is described, using HaloPlex target enrichment and next-generation sequencing. In a validation study, correct identification of variants or wild......1, six variants known to affect function and one variant likely to affect function in BRCA2, as well as four variants of unknown significance (VUS) in BRCA1 and three VUS in BRCA2 were discovered. It is now possible to test for germline BRCA1/2 variants in deceased persons, using archival FFPE...

  10. Use of Sequenom sample ID Plus® SNP genotyping in identification of FFPE tumor samples.

    Directory of Open Access Journals (Sweden)

    Jessica K Miller

    Full Text Available Short tandem repeat (STR analysis, such as the AmpFlSTR® Identifiler® Plus kit, is a standard, PCR-based human genotyping method used in the field of forensics. Misidentification of cell line and tissue DNA can be costly if not detected early; therefore it is necessary to have quality control measures such as STR profiling in place. A major issue in large-scale research studies involving archival formalin-fixed paraffin embedded (FFPE tissues is that varying levels of DNA degradation can result in failure to correctly identify samples using STR genotyping. PCR amplification of STRs of several hundred base pairs is not always possible when DNA is degraded. The Sample ID Plus® panel from Sequenom allows for human DNA identification and authentication using SNP genotyping. In comparison to lengthy STR amplicons, this multiplexing PCR assay requires amplification of only 76-139 base pairs, and utilizes 47 SNPs to discriminate between individual samples. In this study, we evaluated both STR and SNP genotyping methods of sample identification, with a focus on paired FFPE tumor/normal DNA samples intended for next-generation sequencing (NGS. The ability to successfully validate the identity of FFPE samples can enable cost savings by reducing rework.

  11. Atypical carcinoid and large cell neuroendocrine carcinoma of the lung: a proteomic dataset from formalin-fixed archival samples.

    Science.gov (United States)

    Tanca, Alessandro; Addis, Maria Filippa; Pisanu, Salvatore; Abbondio, Marcello; Pagnozzi, Daniela; Eccher, Albino; Rindi, Guido; Cossu-Rocca, Paolo; Uzzau, Sergio; Fanciulli, Giuseppe

    2016-06-01

    Here we present a dataset generated using formalin-fixed paraffin-embedded archival samples from two rare lung neuroendocrine tumor subtypes (namely, two atypical carcinoids, ACs, and two large-cell neuroendocrine carcinomas, LCNECs). Samples were subjected to a shotgun proteomics pipeline, comprising full-length protein extraction, SDS removal through spin columns, in solution trypsin digestion, long gradient liquid chromatography peptide separation and LTQ-Orbitrap mass spectrometry analysis. A total of 1260 and 2436 proteins were identified in the AC and LCNEC samples, respectively, with FDR http://www.peptideatlas.org/PASS/PASS00375. PMID:27054153

  12. Genome-wide copy number analysis of cerebrospinal fluid tumor cells and their corresponding archival primary tumors

    Directory of Open Access Journals (Sweden)

    Mark Jesus M. Magbanua

    2014-12-01

    Full Text Available A debilitating complication of breast cancer is the metastatic spread of tumor cells to the leptomeninges or cerebrospinal fluid (CSF. Patients diagnosed with this aggressive clinical syndrome, known as leptomeningeal carcinomatosis, have very poor prognosis. Despite improvements in detecting cerebrospinal fluid tumor cells (CSFTCs, information regarding their molecular biology is extremely limited. In our recent work, we utilized a protocol previously used for circulating tumor cell isolation to purify tumor cells from the CSF. We then performed genomic characterization of CSFTCs as well as archival tumors from the same patient. Here, we describe the microarray data and quality controls associated with our study published in the Cancer Research journal in 2013 [1]. We also provide an R script containing code for quality control of microarray data and assessment of copy number calls. The microarray data has been deposited into Gene Expression Omnibus under accession # GSE46068.

  13. A novel fluorescent in situ hybridization technique for detection of Rickettsia spp. in archival samples

    DEFF Research Database (Denmark)

    Svendsen, Claus Bo; Boye, Mette; Struve, Carsten;

    2009-01-01

    A novel, sensitive and specific method for detecting Rickettsia spp. in archival samples is described. The method involves the use of fluorescently marked oligonucleotide probes for in situ hybridization. Specific hybridization of Ricekttsia was found without problems of cross-reactions with bact......A novel, sensitive and specific method for detecting Rickettsia spp. in archival samples is described. The method involves the use of fluorescently marked oligonucleotide probes for in situ hybridization. Specific hybridization of Ricekttsia was found without problems of cross...

  14. In Vitro Efficient Expansion of Tumor Cells Deriving from Different Types of Human Tumor Samples

    Directory of Open Access Journals (Sweden)

    Ilaria Turin

    2014-03-01

    Full Text Available Obtaining human tumor cell lines from fresh tumors is essential to advance our understanding of antitumor immune surveillance mechanisms and to develop new ex vivo strategies to generate an efficient anti-tumor response. The present study delineates a simple and rapid method for efficiently establishing primary cultures starting from tumor samples of different types, while maintaining the immuno-histochemical characteristics of the original tumor. We compared two different strategies to disaggregate tumor specimens. After short or long term in vitro expansion, cells analyzed for the presence of malignant cells demonstrated their neoplastic origin. Considering that tumor cells may be isolated in a closed system with high efficiency, we propose this methodology for the ex vivo expansion of tumor cells to be used to evaluate suitable new drugs or to generate tumor-specific cytotoxic T lymphocytes or vaccines.

  15. Whole-exome sequencing and clinical interpretation of FFPE tumor samples to guide precision cancer medicine

    Science.gov (United States)

    Allen, Eliezer M. Van; Wagle, Nikhil; Stojanov, Petar; Perrin, Danielle L.; Cibulskis, Kristian; Marlow, Sara; Jane-Valbuena, Judit; Friedrich, Dennis C.; Kryukov, Gregory; Carter, Scott L.; McKenna, Aaron; Sivachenko, Andrey; Rosenberg, Mara; Kiezun, Adam; Voet, Douglas; Lawrence, Michael; Lichtenstein, Lee T.; Gentry, Jeff G.; Huang, Franklin W.; Fostel, Jennifer; Farlow, Deborah; Barbie, David; Gandhi, Leena; Lander, Eric S.; Gray, Stacy W.; Joffe, Steven; Janne, Pasi; Garber, Judy; MacConaill, Laura; Lindeman, Neal; Rollins, Barrett; Kantoff, Philip; Fisher, Sheila A.; Gabriel, Stacey; Getz, Gad; Garraway, Levi A.

    2013-01-01

    Translating whole exome sequencing (WES) for prospective clinical use may impact the care of cancer patients; however, multiple innovations are necessary for clinical implementation. These include: (1) rapid and robust WES from formalin-fixed paraffin embedded (FFPE) tumor tissue, (2) analytical output similar to data from frozen samples, and (3) clinical interpretation of WES data for prospective use. Here, we describe a prospective clinical WES platform for archival FFPE tumor samples. The platform employs computational methods for effective clinical analysis and interpretation of WES data. When applied retrospectively to 511 exomes, the interpretative framework revealed a “long tail” of somatic alterations in clinically important genes. Prospective application of this approach identified clinically relevant alterations in 15/16 patients. In one patient, previously undetected findings guided clinical trial enrollment leading to an objective clinical response. Overall, this methodology may inform the widespread implementation of precision cancer medicine. PMID:24836576

  16. Examination of PACAP-Like Immunoreactivity in Urogenital Tumor Samples.

    Science.gov (United States)

    Tamas, Andrea; Javorhazy, Andras; Reglodi, Dora; Sarlos, Donat Peter; Banyai, Daniel; Semjen, David; Nemeth, Jozsef; Lelesz, Beata; Fulop, Daniel Balazs; Szanto, Zalan

    2016-06-01

    Numerous studies investigated the localization of pituitary adenylate cyclase-activating polypeptide (PACAP) and its receptors in different tumors and described the effects of analogs on tumor growth to show its potential role in oncogenesis. Recently, our research group has found significantly lower levels of PACAP27-like immunorreactivity (LI) and PACAP38-LI in different human samples of primary small cell lung cancer and colon cancer compared to normal healthy tissues. There are only few human studies showing the presence of PACAP and its receptors in urogenital tumors; therefore, the aim of the present study was to compare PACAP-LI in different healthy and pathological human samples from urogenital organs (kidney, urinary bladder, prostate, testis) with radioimmunoassay (RIA) method. Similar to our earlier observations, the PACAP27-LI was significantly lower compared to PACAP38-LI in all samples. We did not find significant alterations in PACAP-LI between healthy and tumoral samples from the urinary bladder and testis. On the other hand, we found significantly lower PACAP38-LI level in kidney tumors compared with healthy tissue samples, and we showed higher PACAP27-LI in prostatic cancer compared to samples from benign prostatic hyperplasia. These data indicate that PACAP levels of different tissue samples are altered under pathological conditions suggesting a potential role of PACAP in the development of different urogenital tumors. PMID:26454744

  17. Sample (S): SE37_S19 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available ing ShiftedIonsFinder This is a pseudo metadata prepared for integrated analyses of multiple datasets. The Medicago samples (S01, S02, and S03) and a blank sample (S16) are included. ...

  18. Preparation of measurement sources of archive xenon samples for HPGe γ spectrometer in radionuclide verification

    International Nuclear Information System (INIS)

    The radionuclide network of the International Monitoring System (IMS) for verification of the comprehensive nuclear-test-ban treaty (CTBT) comprises of 80 particulate stations and 40 co-located noble gas stations, and 16 radionuclide laboratories. The suspicious samples detected by the IMS radionuclide station will be further evaluated at the certified radionuclide laboratories. Therefore, it is expected that they could analyze the archive xenon samples by HPGe γ spectrometry or β-γ coincidence spectrometry. To improve the xenon monitoring ability, the Installation and Certification Group (ICG) of the IMS Division organized the LABS XENON EXERCISE in 2007. ICG distributed archive xenon samples from stations to participated laboratories during the exercise. In the process of detection of the xenon isotopes activity by HPGe γ spectrometer, the xenon sample must be transferred from the archive bottle to a special measurement cell. Based on the principle that xenon was adsorbed by activated charcoal, then desorbed by heating and pumped by diaphragmatic pump, four CTBT archive xenon samples were transferred in 2007. The xenon transfer efficiencies were measured by gas chromatograph. The results show that the transfer efficiencies are all about 80%. (authors)

  19. Sample (S): SE37_S17 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available repared for integrated analyses of multiple datasets. The Medicago samples (S01, S02, and S03) and a blank sample (S16) are included. ... ...etection of reproducible metabolite peaks Medicago truncatula NCBI taxonomy:3880 This is a pseudo metadata p

  20. Sample Set (SE): SE55 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available analyzed phytochemical accumulation during development of the model plant Arabidopsis (Arabidopsis thaliana) using liquid chromatogra...phy-mass spectrometry in samples covering many growth stages and organs. We also ob

  1. Sample (S): SE37_S14 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available oot (aerial part) and root were separated with a scalpel and they were immediately frozen using liquid nitrogen. After lyophilization, the sample was stored at room temperature. ...

  2. Sample (S): SE37_S13 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available oot (aerial part) and root were separated with a scalpel and they were immediately frozen using liquid nitrogen. After lyophilization, the sample was stored at room temperature. ...

  3. Sample (S): SE37_S15 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available oot (aerial part) and root were separated with a scalpel and they were immediately frozen using liquid nitrogen. After lyophilization, the sample was stored at room temperature. ...

  4. Sample (S): SE24_S1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available s into 1-cm squares, the samples were immediately frozen with liquid nitrogen and lyophilized at -55 C. The lyophilized materials were stored at room temperature with silica gel. ...

  5. Sample Preparation (SS): SE58_SS01 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available 1 μL injection. After centrifugation, a 200 μL aliquot of the supernatant (∼0.5 mg of DW of each sample) wa... Each isotope compound was adjusted to a final concentration of 15 ng/μL for each

  6. Sample Set (SE): SE47 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available itions. Although several studies have assessed topologies in metabolomic correlation networks, it remains un...clear whether highly connected metabolites in these networks have specific functions in known tissue- and/or...orrelations in samples of roots and aerial parts. We then applied graph clustering to the constructed correlation networks

  7. Archival policies and collections database for the Woods Hole Science Center's marine sediment samples

    Science.gov (United States)

    Buczkowski, Brian J.; Kelsey, Sarah A.

    2007-01-01

    The Woods Hole Science Center of the U.S. Geological Survey (USGS) has been an active member of the Woods Hole research community, Woods Hole, Massachusetts, for over 40 years. In that time there have been many projects that involved the collection of sediment samples conducted by USGS scientists and technicians for the research and study of seabed environments and processes. These samples were collected at sea or near shore and then brought back to the Woods Hole Science Center (WHSC) for analysis. While at the center, samples are stored in ambient temperature, refrigerated and freezing conditions ranging from +2º Celsius to -18º Celsius, depending on the best mode of preparation for the study being conducted or the duration of storage planned for the samples. Recently, storage methods and available storage space have become a major concern at the WHSC. The core and sediment archive program described herein has been initiated to set standards for the management, methods, and duration of sample storage. A need has arisen to maintain organizational consistency and define storage protocol. This handbook serves as a reference and guide to all parties interested in using and accessing the WHSC's sample archive and also defines all the steps necessary to construct and maintain an organized collection of geological samples. It answers many questions as to the way in which the archive functions.

  8. Molecular strain identification of the Mycobacterium tuberculosis complex in archival tissue samples

    OpenAIRE

    Zink, A. R.; Nerlich, A G

    2004-01-01

    Aims: To investigate the use of different molecular analyses that can identify distinct strains of human pathogenic mycobacteria in formalin fixed and paraffin wax embedded archival tissue samples to see whether it is possible to differentiate between the members of the Mycobacterium tuberculosis complex (M tuberculosis, M bovis, M africanum, M microti, or M canettii) and/or substrains in a high number of samples. This would be of interest for identifying individual infection traits and super...

  9. Impairment of Methotrexate Transport Is Common in Osteosarcoma Tumor Samples

    OpenAIRE

    Richard Gorlick; Levy, Adam S.; John H. Healey; Paul A. Meyers; Wenzel, Bethanne D.; Condon Richardson; Rebecca Sowers

    2010-01-01

    Osteosarcoma does not respond well to conventional dose methotrexate but does respond to high-dose methotrexate. Previous work has indicated that this resistance may be due to impaired transport of methotrexate across the cell membrane. In this study, the PT430 competitive displacement assay was adapted to evaluate methotrexate transport in 69 high-grade osteosarcoma tumor samples. All samples studied were shown to have relatively impaired methotrexate transport by PT430 assay. Ninety-nine pe...

  10. Post-mortem testing; germline BRCA1/2 variant detection using archival FFPE non-tumor tissue. A new paradigm in genetic counseling.

    Science.gov (United States)

    Petersen, Annabeth Høgh; Aagaard, Mads Malik; Nielsen, Henriette Roed; Steffensen, Karina Dahl; Waldstrøm, Marianne; Bojesen, Anders

    2016-08-01

    Accurate estimation of cancer risk in HBOC families often requires BRCA1/2 testing, but this may be impossible in deceased family members. Previous, testing archival formalin-fixed, paraffin-embedded (FFPE) tissue for germline BRCA1/2 variants was unsuccessful, except for the Jewish founder mutations. A high-throughput method to systematically test for variants in all coding regions of BRCA1/2 in archival FFPE samples of non-tumor tissue is described, using HaloPlex target enrichment and next-generation sequencing. In a validation study, correct identification of variants or wild-type was possible in 25 out of 30 (83%) FFPE samples (age range 1-14 years), with a known variant status in BRCA1/2. No false positive was found. Unsuccessful identification was due to highly degraded DNA or presence of large intragenic deletions. In clinical use, a total of 201 FFPE samples (aged 0-43 years) were processed. Thirty-six samples were rejected because of highly degraded DNA or failed library preparation. Fifteen samples were investigated to search for a known variant. In the remaining 150 samples (aged 0-38 years), three variants known to affect function and one variant likely to affect function in BRCA1, six variants known to affect function and one variant likely to affect function in BRCA2, as well as four variants of unknown significance (VUS) in BRCA1 and three VUS in BRCA2 were discovered. It is now possible to test for germline BRCA1/2 variants in deceased persons, using archival FFPE samples from non-tumor tissue. Accurate genetic counseling is achievable in families where variant testing would otherwise be impossible. PMID:26733283

  11. STP K Basin Sludge Sample Archive at the Pacific Northwest National Laboratory FY2014

    Energy Technology Data Exchange (ETDEWEB)

    Fiskum, Sandra K.; Smoot, Margaret R.; Schmidt, Andrew J.

    2014-06-01

    The Pacific Northwest National Laboratory (PNNL) currently houses 88 samples (~10.5 kg) of K Basin sludge (81 wet and seven dry samples) on behalf of the Sludge Treatment Project (STP), which is managed for the U.S. Department of Energy (DOE) by the CH2M Hill Plateau Remediation Company (CHPRC). Selected samples are intended to serve, in part, as sentinels to enhance understanding of sludge properties after long-term storage, and thus enhance understanding of sludge behavior following transfer to sludge transfer and storage containers (STSCs) and storage at the Hanford 200 Area central plateau. In addition, remaining samples serve in contingency for future testing requirements. At PNNL, the samples are tracked and maintained under a prescriptive and disciplined monthly sample-monitoring program implemented by PNNL staff. This report updates the status of the K Basin archive sludge sample inventory to April 2014. The previous inventory status report, PNNL 22245 (Fiskum et al. 2013, limited distribution report), was issued in February of 2013. This update incorporates changes in the inventory related to repackaging of 17 samples under test instructions 52578 TI052, K Basin Sludge Sample Repackaging for Continued Long Term Storage, and 52578 TI053, K Basin Sludge Sample Repackaging Post-2014 Shear Strength Measurements. Note that shear strength measurement results acquired in 2014 are provided separately. Specifically, this report provides the following: • a description of the K Basin sludge sample archive program and the sample inventory • a summary and images of the samples that were repackaged in April 2014 • up-to-date images and plots of the settled density and water loss from all applicable samples in the inventory • updated sample pedigree charts, which provide a roadmap of the genesis and processing history of each sample in the inventory • occurrence and deficiency reports associated with sample storage and repackaging

  12. The SHADOZ Data Base: History, Archive Web Guide, and Sample Climatologies

    Science.gov (United States)

    White, J. C.; Thompson, A. M.; Einaudi, Franco (Technical Monitor)

    2000-01-01

    SHADOZ (Southern Hemisphere Additional Ozonesonde) is a project to augment and archive ozonesonde data from ten tropical and subtropical ozone stations. Started in 1998 by NASA's Goddard Space Flight Center and other US and international co-investigators, SHADOZ is an important tool for tropospheric ozone research in the equatorial region. The rationale for SHADOZ is to: (1) validate and improve remote sensing techniques (e.g., the Total Ozone Mapping Spectrometer (TOMS) satellite) for estimating tropical ozone, (2) contribute to climatology and trend analyses of tropical ozone and (3) provide research topics to scientists and educate students, especially in participating countries. SHADOZ is envisioned as a data service to the global scientific community by providing a central public archive location via the internet: http://code9l6.gsfc.nasa.gov/Data_services/shadoz. While the SHADOZ website maintains a standard data format for the archive, it also informs the data users on the differing stations' preparation techniques and data treatment. The presentation navigates through the SHADOZ website to access each station's sounding data and summarize each station's characteristics. Since the start of the project in 1998, the SHADOZ archive has accumulated over 600 ozonesonde profiles and received over 30,000 outside data requests. Data also includes launches from various SHADOZ supported field campaigns, such as, the Indian Ocean Experiment (INDOEX), Sounding of Ozone and Water in the Equatorial Region (SOWER) and Aerosols99 Atlantic Cruise. Using data from the archive, sample climatologies and profiles from selected stations and campaigns will be shown.

  13. Genome-wide scans using archived neonatal dried blood spot samples

    Directory of Open Access Journals (Sweden)

    Wiuf Carsten

    2009-07-01

    Full Text Available Abstract Background Identification of disease susceptible genes requires access to DNA from numerous well-characterised subjects. Archived residual dried blood spot samples from national newborn screening programs may provide DNA from entire populations and medical registries the corresponding clinical information. The amount of DNA available in these samples is however rarely sufficient for reliable genome-wide scans, and whole-genome amplification may thus be necessary. This study assess the quality of DNA obtained from different amplification protocols by evaluating fidelity and robustness of the genotyping of 610,000 single nucleotide polymorphisms, using the Illumina Infinium HD Human610-Quad BeadChip. Whole-genome amplified DNA from 24 neonatal dried blood spot samples stored between 15 to 25 years was tested, and high-quality genomic DNA from 8 of the same individuals was used as reference. Results Using 3.2 mm disks from dried blood spot samples the optimal DNA-extraction and amplification protocol resulted in call-rates between 99.15% – 99.73% (mean 99.56%, N = 16, and conflicts with reference DNA in only three per 10,000 genotype calls. Conclusion Whole-genome amplified DNA from archived neonatal dried blood spot samples can be used for reliable genome-wide scans and is a cost-efficient alternative to collecting new samples.

  14. Impairment of Methotrexate Transport Is Common in Osteosarcoma Tumor Samples

    Directory of Open Access Journals (Sweden)

    Rebecca Sowers

    2011-01-01

    Full Text Available Osteosarcoma does not respond well to conventional dose methotrexate but does respond to high-dose methotrexate. Previous work has indicated that this resistance may be due to impaired transport of methotrexate across the cell membrane. In this study, the PT430 competitive displacement assay was adapted to evaluate methotrexate transport in 69 high-grade osteosarcoma tumor samples. All samples studied were shown to have relatively impaired methotrexate transport by PT430 assay. Ninety-nine percent of the samples had less than 20% PT430 displacement by methotrexate. Eighty-eight percent exhibited displacement by methotrexate at less than 50% of the displacement by trimetrexate. The high frequency of impaired transport suggests the presence of decreased functionality of the reduced folate carrier protein. The overwhelming presence of impaired transport may explain why methotrexate needs to be given in high doses to be effective in osteosarcoma therapy and suggests that reduced folate carrier-independent antifolates should be explored.

  15. Reanalysis of archived IMPROVE PM2.5 samples previously analyzed over a 15-year period.

    Science.gov (United States)

    Hyslop, Nicole P; Trzepla, Krystyna; White, Warren H

    2012-09-18

    The IMPROVE (Interagency Monitoring of Protected Visual Environments) network has collected airborne particulate matter (PM) samples at locations throughout the United States since 1988. These samples have been analyzed for elemental content using analytical methods that evolved over the years. Changes in analytical methods sometimes introduced shifts in reported concentrations that are evident in the historical record. We sought to illuminate the effects of methodological changes by reanalyzing archived samples with current methods. To test the feasibility of this approach, the 15-year archive of PM samples from Great Smoky Mountains National Park was selected for reanalysis as a single analytical batch using a common protocol and calibration. Comparisons of the reanalyses and original analyses indicate that concentrations of all but one measured element, Br, remained stable on the filters over years of storage. The agreement between the two analyses varied with element and original measurement method. For elements measured well above their contemporary detection limits - S, K, Ca, Fe, and Zn - the reanalysis established that method changes had limited impacts on reported concentrations, generally record, many of which were previously recognized and documented as method-related. PMID:22913377

  16. Rapid Surface Sampling and Archival Record (RSSAR) System. Topical report, October 1, 1993--December 31, 1994

    International Nuclear Information System (INIS)

    This report describes the results of Phase 1 efforts to develop a Rapid Surface Sampling and Archival Record (RSSAR) System for the detection of semivolatile organic contaminants on concrete, transite, and metal surfaces. The characterization of equipment and building surfaces for the presence of contaminants as part of building decontamination and decommissioning activities is an immensely large tacks of concern to both government and industry. Contaminated and clean materials must be clearly identified and segregated so that the clean materials can be recycled or reused, if possible, or disposed of more cheaply as nonhazardous waste. Characterization of building and equipment surfaces will be needed during initial investigations, during cleanup operations, and during the final confirmatory process, increasing the total number of samples well beyond that needed for initial characterization. This multiplicity of information places a premium on the ability to handle and track data as efficiently as possible. Aware of the shortcomings of traditional surface characterization technology, GE, with DOE support has undertaken a 12-month effort to complete Phase 1 of a proposed four-phase program to develop the RSSAR system. The objectives of this work are to provide instrumentation to cost-effectively sample concrete and steel surfaces, provide a quick-look indication for the presence or absence of contaminants, and collect samples for later, more detailed analysis in a readily accessible and addressable form. The Rapid Surface Sampling and Archival Record (RSSAR) System will be a modular instrument made up of several components: (1) sampling heads for concrete surfaces, steel surfaces, and bulk samples; (2) quick-look detectors for photoionization and ultraviolet; (3) multisample trapping module to trap and store vaporized contaminants in a manner suitable for subsequent detailed lab-based analyses

  17. Signal transduction pathway profiling of individual tumor samples

    Directory of Open Access Journals (Sweden)

    Peterson Carsten

    2005-06-01

    Full Text Available Abstract Background Signal transduction pathways convey information from the outside of the cell to transcription factors, which in turn regulate gene expression. Our objective is to analyze tumor gene expression data from microarrays in the context of such pathways. Results We use pathways compiled from the TRANSPATH/TRANSFAC databases and the literature, and three publicly available cancer microarray data sets. Variation in pathway activity, across the samples, is gauged by the degree of correlation between downstream targets of a pathway. Two correlation scores are applied; one considers all pairs of downstream targets, and the other considers only pairs without common transcription factors. Several pathways are found to be differentially active in the data sets using these scores. Moreover, we devise a score for pathway activity in individual samples, based on the average expression value of the downstream targets. Statistical significance is assigned to the scores using permutation of genes as null model. Hence, for individual samples, the status of a pathway is given as a sign, + or -, and a p-value. This approach defines a projection of high-dimensional gene expression data onto low-dimensional pathway activity scores. For each dataset and many pathways we find a much larger number of significant samples than expected by chance. Finally, we find that several sample-wise pathway activities are significantly associated with clinical classifications of the samples. Conclusion This study shows that it is feasible to infer signal transduction pathway activity, in individual samples, from gene expression data. Furthermore, these pathway activities are biologically relevant in the three cancer data sets.

  18. Rapid Surface Sampling and Archival Record (RSSAR) system. Final report, October 1995 - May 1997

    International Nuclear Information System (INIS)

    This report describes the results of Phase 2 efforts to develop a Rapid Surface Sampling and Archival Record (RSSAR) System for the detection of semivolatile organic contaminants on concrete, transite, and metal surfaces. The characterization of equipment and building surfaces for the presence of contaminants as part of building decontamination and decommissioning activities is an immensely large task of concern to both government and industry. Because of the high cost of hazardous waste disposal, old, contaminated buildings cannot simply be demolished and scrapped. Contaminated and clean materials must be clearly identified and segregated so that the clean material can be recycled or reused, if possible, or disposed of more cheaply as nonhazardous waste. DOE has a number of sites requiring surface characterization. These sites are large, contain very heterogeneous patterns of contamination (requiring high sampling density), and will thus necessitate an enormous number of samples to be taken and analyzed. Characterization of building and equipment surfaces will be needed during initial investigations, during cleanup operations, and during the final confirmation process, increasing the total number of samples well beyond that needed for initial characterization. This multiplicity of information places a premium on the ability to handle and track data as efficiently as possible

  19. Rapid Surface Sampling and Archival Record (RSSAR) system. Final report, October 1995--May 1997

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-12-31

    This report describes the results of Phase 2 efforts to develop a Rapid Surface Sampling and Archival Record (RSSAR) System for the detection of semivolatile organic contaminants on concrete, transite, and metal surfaces. The characterization of equipment and building surfaces for the presence of contaminants as part of building decontamination and decommissioning activities is an immensely large task of concern to both government and industry. Because of the high cost of hazardous waste disposal, old, contaminated buildings cannot simply be demolished and scrapped. Contaminated and clean materials must be clearly identified and segregated so that the clean material can be recycled or reused, if possible, or disposed of more cheaply as nonhazardous waste. DOE has a number of sites requiring surface characterization. These sites are large, contain very heterogeneous patterns of contamination (requiring high sampling density), and will thus necessitate an enormous number of samples to be taken and analyzed. Characterization of building and equipment surfaces will be needed during initial investigations, during cleanup operations, and during the final confirmation process, increasing the total number of samples well beyond that needed for initial characterization. This multiplicity of information places a premium on the ability to handle and track data as efficiently as possible.

  20. File list: ALL.Dig.10.AllAg.Gastric_tumor [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  1. File list: Oth.Dig.05.AllAg.Gastric_tumor [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  2. File list: ALL.Dig.50.AllAg.Gastric_tumor [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  3. File list: ALL.Dig.05.AllAg.Gastric_tumor [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  4. File list: Oth.Dig.20.AllAg.Gastric_tumor [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  5. File list: ALL.Dig.20.AllAg.Gastric_tumor [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  6. File list: Oth.Dig.10.AllAg.Gastric_tumor [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  7. File list: Unc.Lng.10.AllAg.Lung_tumors [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  8. File list: InP.Lng.05.AllAg.Lung_tumors [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  9. File list: InP.Lng.10.AllAg.Lung_tumors [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  10. File list: ALL.Lng.05.AllAg.Lung_tumors [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  11. File list: InP.Lng.50.AllAg.Lung_tumors [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  12. File list: ALL.Lng.50.AllAg.Lung_tumors [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  13. File list: ALL.Lng.10.AllAg.Lung_tumors [Chip-atlas[Archive

    Lifescience Database Archive (English)

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    Lifescience Database Archive (English)

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  15. File list: Unc.Lng.50.AllAg.Lung_tumors [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  16. File list: InP.Lng.20.AllAg.Lung_tumors [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  17. File list: ALL.Lng.20.AllAg.Lung_tumors [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  18. File list: DNS.Oth.10.AllAg.Tumor [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  19. Collecting and Storing Blood and Brain Tumor Tissue Samples From Children With Brain Tumors

    Science.gov (United States)

    2016-05-17

    Childhood Atypical Teratoid/Rhabdoid Tumor; Childhood Central Nervous System Germ Cell Tumor; Childhood Choroid Plexus Tumor; Childhood Craniopharyngioma; Childhood Grade I Meningioma; Childhood Grade II Meningioma; Childhood Grade III Meningioma; Childhood High-grade Cerebral Astrocytoma; Childhood Infratentorial Ependymoma; Childhood Low-grade Cerebral Astrocytoma; Childhood Oligodendroglioma; Childhood Supratentorial Ependymoma; Newly Diagnosed Childhood Ependymoma; Recurrent Childhood Cerebellar Astrocytoma; Recurrent Childhood Cerebral Astrocytoma; Recurrent Childhood Ependymoma; Recurrent Childhood Medulloblastoma; Recurrent Childhood Supratentorial Primitive Neuroectodermal Tumor; Recurrent Childhood Visual Pathway and Hypothalamic Glioma; Recurrent Childhood Visual Pathway Glioma

  20. Gene expression, single nucleotide variant and fusion transcript discovery in archival material from breast tumors.

    Directory of Open Access Journals (Sweden)

    Nadine Norton

    Full Text Available Advantages of RNA-Seq over array based platforms are quantitative gene expression and discovery of expressed single nucleotide variants (eSNVs and fusion transcripts from a single platform, but the sensitivity for each of these characteristics is unknown. We measured gene expression in a set of manually degraded RNAs, nine pairs of matched fresh-frozen, and FFPE RNA isolated from breast tumor with the hybridization based, NanoString nCounter (226 gene panel and with whole transcriptome RNA-Seq using RiboZeroGold ScriptSeq V2 library preparation kits. We performed correlation analyses of gene expression between samples and across platforms. We then specifically assessed whole transcriptome expression of lincRNA and discovery of eSNVs and fusion transcripts in the FFPE RNA-Seq data. For gene expression in the manually degraded samples, we observed Pearson correlations of >0.94 and >0.80 with NanoString and ScriptSeq protocols, respectively. Gene expression data for matched fresh-frozen and FFPE samples yielded mean Pearson correlations of 0.874 and 0.783 for NanoString (226 genes and ScriptSeq whole transcriptome protocols respectively, p<2x10(-16. Specifically for lincRNAs, we observed superb Pearson correlation (0.988 between matched fresh-frozen and FFPE pairs. FFPE samples across NanoString and RNA-Seq platforms gave a mean Pearson correlation of 0.838. In FFPE libraries, we detected 53.4% of high confidence SNVs and 24% of high confidence fusion transcripts. Sensitivity of fusion transcript detection was not overcome by an increase in depth of sequencing up to 3-fold (increase from ~56 to ~159 million reads. Both NanoString and ScriptSeq RNA-Seq technologies yield reliable gene expression data for degraded and FFPE material. The high degree of correlation between NanoString and RNA-Seq platforms suggests discovery based whole transcriptome studies from FFPE material will produce reliable expression data. The RiboZeroGold ScriptSeq protocol

  1. Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material

    OpenAIRE

    Nederlof Petra M; van Beers Erik H; Joosse Simon A

    2007-01-01

    Abstract Background Array Comparative Genomic Hybridization (aCGH) is a rapidly evolving technology that still lacks complete standardization. Yet, it is of great importance to obtain robust and reproducible data to enable meaningful multiple hybridization comparisons. Special difficulties arise when aCGH is performed on archival formalin-fixed, paraffin-embedded (FFPE) tissue due to its variable DNA quality. Recently, we have developed an effective DNA quality test that predicts suitability ...

  2. Analytical test results for archived core composite samples from tanks 241-TY-101 and 241-TY-103

    Energy Technology Data Exchange (ETDEWEB)

    Beck, M.A.

    1993-07-16

    This report describes the analytical tests performed on archived core composite samples form a 1.085 sampling of the 241-TY-101 (101-TY) and 241-TY-103 (103-TY) single shell waste tanks. Both tanks are suspected of containing quantities of ferrocyanide compounds, as a result of process activities in the late 1950`s. Although limited quantities of the composite samples remained, attempts were made to obtain as much analytical information as possible, especially regarding the chemical and thermal properties of the material.

  3. Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine.

    Science.gov (United States)

    Van Allen, Eliezer M; Wagle, Nikhil; Stojanov, Petar; Perrin, Danielle L; Cibulskis, Kristian; Marlow, Sara; Jane-Valbuena, Judit; Friedrich, Dennis C; Kryukov, Gregory; Carter, Scott L; McKenna, Aaron; Sivachenko, Andrey; Rosenberg, Mara; Kiezun, Adam; Voet, Douglas; Lawrence, Michael; Lichtenstein, Lee T; Gentry, Jeff G; Huang, Franklin W; Fostel, Jennifer; Farlow, Deborah; Barbie, David; Gandhi, Leena; Lander, Eric S; Gray, Stacy W; Joffe, Steven; Janne, Pasi; Garber, Judy; MacConaill, Laura; Lindeman, Neal; Rollins, Barrett; Kantoff, Philip; Fisher, Sheila A; Gabriel, Stacey; Getz, Gad; Garraway, Levi A

    2014-06-01

    Translating whole-exome sequencing (WES) for prospective clinical use may have an impact on the care of patients with cancer; however, multiple innovations are necessary for clinical implementation. These include rapid and robust WES of DNA derived from formalin-fixed, paraffin-embedded tumor tissue, analytical output similar to data from frozen samples and clinical interpretation of WES data for prospective use. Here, we describe a prospective clinical WES platform for archival formalin-fixed, paraffin-embedded tumor samples. The platform employs computational methods for effective clinical analysis and interpretation of WES data. When applied retrospectively to 511 exomes, the interpretative framework revealed a 'long tail' of somatic alterations in clinically important genes. Prospective application of this approach identified clinically relevant alterations in 15 out of 16 patients. In one patient, previously undetected findings guided clinical trial enrollment, leading to an objective clinical response. Overall, this methodology may inform the widespread implementation of precision cancer medicine. PMID:24836576

  4. Use of Sequenom Sample ID Plus® SNP Genotyping in Identification of FFPE Tumor Samples

    OpenAIRE

    Jessica K Miller; Nicholas Buchner; Lee Timms; Shirley Tam; Xuemei Luo; Brown, Andrew M. K.; Danielle Pasternack; Robert G Bristow; Michael Fraser; Boutros, Paul C; McPherson, John D.

    2014-01-01

    Short tandem repeat (STR) analysis, such as the AmpFlSTR® Identifiler® Plus kit, is a standard, PCR-based human genotyping method used in the field of forensics. Misidentification of cell line and tissue DNA can be costly if not detected early; therefore it is necessary to have quality control measures such as STR profiling in place. A major issue in large-scale research studies involving archival formalin-fixed paraffin embedded (FFPE) tissues is that varying levels of DNA degradation can re...

  5. Experimental Approaches to Microarray Analysis of Tumor Samples

    Science.gov (United States)

    Furge, Laura Lowe; Winter, Michael B.; Meyers, Jacob I.; Furge, Kyle A.

    2008-01-01

    Comprehensive measurement of gene expression using high-density nucleic acid arrays (i.e. microarrays) has become an important tool for investigating the molecular differences in clinical and research samples. Consequently, inclusion of discussion in biochemistry, molecular biology, or other appropriate courses of microarray technologies has…

  6. Intraparenchymal mesenchymal chondrosarcoma of the frontal lobe--a case report and molecular detection of specific gene fusions from archival FFPE sample.

    Science.gov (United States)

    Sajjad, Emir Ahmed; Sikora, Katarzyna; Paciejewski, Tomasz; Garbicz, Filip; Paskal, Wiktor; Szacht, Milena; Grajkowska, Wieslawa; Włodarski, Pawel Krzysztof

    2015-01-01

    Mesenchymal chondrosarcoma is a rare tumor of cartilaginous origin characterized by its bimorphic pattern composed of highly undifferentiated small round cells separated by islands of well-differentiated hyaline cartilage. It exhibits higher malignancy and earlier occurrence in comparison to classic chondrosarcomas. Recently identified HEY1-NCOA2 and IRF2BP2-CDX1 gene fusions confirm their distinct molecular origin and pose a promising diagnostic marker. The majority of cases arise from craniofacial bones. In this study, we present a rare case of mesenchymal chondrosarcoma encompassed within the brain parenchyma of the frontal lobe without any dural or bone attachment. We demonstrate histopathological findings and confirm the HEY1-NCOA2 gene fusion in a formalin-fixed paraffin-embedded archival sample using simple reverse transcription polymerase chain reaction (RT-PCR) method. IRF2BP2-CDX1 gene fusion was absent in the analyzed sample. The clinical follow-up is also presented with a review of treatment modalities for this entity. PMID:25907264

  7. Hormone receptor and ERBB2 status in gene expression profiles of human breast tumor samples.

    Directory of Open Access Journals (Sweden)

    Anna Dvorkin-Gheva

    Full Text Available The occurrence of large publically available repositories of human breast tumor gene expression profiles provides an important resource to discover new breast cancer biomarkers and therapeutic targets. For example, knowledge of the expression of the estrogen and progesterone hormone receptors (ER and PR, and that of the ERBB2 in breast tumor samples enables choice of therapies for the breast cancer patients that express these proteins. Identifying new biomarkers and therapeutic agents affecting the activity of signaling pathways regulated by the hormone receptors or ERBB2 might be accelerated by knowledge of their expression levels in large gene expression profiling data sets. Unfortunately, the status of these receptors is not invariably reported in public databases of breast tumor gene expression profiles. Attempts have been made to employ a single probe set to identify ER, PR and ERBB2 status, but the specificity or sensitivity of their prediction is low. We enquired whether estimation of ER, PR and ERBB2 status of profiled tumor samples could be improved by using multiple probe sets representing these three genes and others with related expression.We used 8 independent datasets of human breast tumor samples to define gene expression signatures comprising 24, 51 and 14 genes predictive of ER, PR and ERBB2 status respectively. These signatures, as demonstrated by sensitivity and specificity measures, reliably identified hormone receptor and ERBB2 expression in breast tumors that had been previously determined using protein and DNA based assays. Our findings demonstrate that gene signatures can be identified which reliably predict the expression status of the estrogen and progesterone hormone receptors and that of ERBB2 in publically available gene expression profiles of breast tumor samples. Using these signatures to query transcript profiles of breast tumor specimens may enable discovery of new biomarkers and therapeutic targets for

  8. Malignant Tumors and Forensics – Dilemmas and Proposals

    OpenAIRE

    Budimlija, Zoran; Lu, Connie; Axler-DiPerte, Grace; Seifarth, Jessica; Popiolek, Dorota; Fogt, Franz; Prinz, Mechthild

    2009-01-01

    Aim To evaluate the effect of genetic instability and degradation in archived histology samples from cancerous tumors and to investigate the validity of short tandem repeat (STR) typing of these samples and its potential effect on human identification. Methods Two hundred and twenty eight slides of archival pathology tissues from 13 different types of malignant tumors were compared with healthy tissues from the same individuals. DNA analysis was performed using standar...

  9. The effects of age-in-block on RNA-seq analysis of archival formalin-fixed paraffin-embedded (FFPE) samples

    Science.gov (United States)

    Archival samples represent a vast resource for identification of chemical and pharmaceutical targets. Previous use of formalin-fixed paraffin-embedded (FFPE) samples has been limited due to changes in RNA introduced by fixation and embedding procedures. Recent advances in RNA-seq...

  10. COSMOS: accurate detection of somatic structural variations through asymmetric comparison between tumor and normal samples

    OpenAIRE

    Yamagata, Koichi; Yamanishi, Ayako; Kokubu, Chikara; TAKEDA, Junji; Sese, Jun

    2016-01-01

    An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the mapped read pairs in tumor samples with isogenic normal control samples in a distinct asymmetric manner. COSMOS also prioritizes the candidate SVs using strand-specific read-depth i...

  11. Archive of Geosample Data and Information from the Woods Hole Oceanographic Institution (WHOI) Seafloor Samples Laboratory

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Woods Hole Oceanographic Institution (WHOI) Seafloor Samples Laboratory is a partner in the Index to Marine and Lacustrine Geological Samples (IMLGS) database,...

  12. File list: DNS.Dig.05.AllAg.Gastric_primary_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  13. File list: Pol.Dig.10.AllAg.Gastric_primary_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Dig.10.AllAg.Gastric_primary_sample hg19 RNA polymerase Digestive tract Gastric... primary sample http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Dig.10.AllAg.Gastric_primary_sample.bed ...

  14. File list: Pol.Dig.05.AllAg.Gastric_primary_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Dig.05.AllAg.Gastric_primary_sample hg19 RNA polymerase Digestive tract Gastric... primary sample http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Pol.Dig.05.AllAg.Gastric_primary_sample.bed ...

  15. File list: Unc.Dig.20.AllAg.Gastric_primary_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  16. File list: Oth.Dig.20.AllAg.Gastric_primary_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.Dig.20.AllAg.Gastric_primary_sample hg19 TFs and others Digestive tract Gastric primary... sample http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Oth.Dig.20.AllAg.Gastric_primary_sample.bed ...

  17. File list: DNS.Dig.50.AllAg.Gastric_primary_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available DNS.Dig.50.AllAg.Gastric_primary_sample hg19 DNase-seq Digestive tract Gastric primary... sample SRX201807,SRX201812 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/DNS.Dig.50.AllAg.Gastric_primary_sample.bed ...

  18. File list: Oth.Dig.05.AllAg.Gastric_primary_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.Dig.05.AllAg.Gastric_primary_sample hg19 TFs and others Digestive tract Gastric primary... sample http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Oth.Dig.05.AllAg.Gastric_primary_sample.bed ...

  19. File list: Pol.Dig.50.AllAg.Gastric_primary_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  20. File list: Unc.Dig.50.AllAg.Gastric_primary_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  1. File list: Pol.Dig.20.AllAg.Gastric_primary_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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    Lifescience Database Archive (English)

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  3. File list: Oth.Dig.10.AllAg.Gastric_primary_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  4. File list: Oth.Dig.50.AllAg.Gastric_primary_sample [Chip-atlas[Archive

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  5. File list: DNS.Dig.20.AllAg.Gastric_primary_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  6. File list: Unc.Dig.05.AllAg.Gastric_primary_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Unc.Dig.05.AllAg.Gastric_primary_sample hg19 Unclassified Digestive tract Gastric primary... sample http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Unc.Dig.05.AllAg.Gastric_primary_sample.bed ...

  7. Towards an Understanding of Changing-Look Quasars With a Statistical Sample: An Archival Spectroscopic Search in SDSS

    CERN Document Server

    Ruan, John J; Cales, Sabrina L; Eracleous, Michael; Green, Paul J; Morganson, Eric; Runnoe, Jessie C; Shen, Yue; Wilkinson, Tessa D; Blanton, Michael R; Dwelly, Tom; Georgakakis, Antonis; Greene, Jenny E; LaMassa, Stephanie M; Merloni, Andrea; Schneider, Donald P

    2015-01-01

    The uncertain origin of the recently-discovered 'changing-looking' quasar phenomenon - in which a luminous quasar dims significantly to a quiescent state in repeat spectroscopy over ~10 year timescales - may present unexpected challenges to our understanding of quasar accretion. To better understand this phenomenon, we take a first step to building a statistical sample of changing-look quasars with a systematic but simple archival search for these objects in the Sloan Digital Sky Survey Data Release 12. By leveraging the >10 year baselines for objects with repeat spectroscopy, we uncover two new changing-look quasars. Decomposition of the multi-epoch spectra and analysis of the broad emission lines suggest that the quasar accretion disk emission dims due to rapidly decreasing accretion rates, while disfavoring changes in intrinsic dust extinction. Narrow emission line energetics also support intrinsic dimming of quasar emission as the origin for this phenomenon rather than transient tidal disruption events. A...

  8. Eosinophilia in routine blood samples as a biomarker for solid tumor development

    DEFF Research Database (Denmark)

    Andersen, Christen Bertel L; Siersma, V.D.; Hasselbalch, H.C.;

    2014-01-01

    eosinophilia in routine blood samples as a potential biomarker of solid tumor development in a prospective design. MATERIAL AND METHODS: From the Copenhagen Primary Care Differential Count (CopDiff) Database, we identified 356 196 individuals with at least one differential cell count (DIFF) encompassing the...... tumors within the first three years following the DIFF. Using multivariable logistic regression, odds ratios (OR) were calculated and adjusted for previous eosinophilia, sex, age, year, month, C-reactive protein, previous cancer and Charlson's Comorbidity Index. RESULTS: The risk of bladder cancer was...

  9. Temporal genetic variation as revealed by a microsatellite analysis of European sardine ( Sardina pilchardus) archived samples

    DEFF Research Database (Denmark)

    Ruggeri, Paolo; Splendiani, Andrea; Bonanomi, Sara;

    2012-01-01

    ) that explain the genetic diversity variation, while the same parameters turned out to be more stable in the southern samples. In addition, we detected the presence of a genetic bottleneck and low effective population size ( Ne) values in several northern samples. Even if the northern and southern...

  10. File list: His.Dig.20.AllAg.Gastric_primary_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  11. File list: His.Dig.10.AllAg.Gastric_primary_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  12. File list: His.Dig.05.AllAg.Gastric_primary_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  13. Identification of pyrimethamine- and chloroquine-resistant Plasmodium falciparum in Africa between 1984 and 1998: genotyping of archive blood samples

    Directory of Open Access Journals (Sweden)

    Saito-Nakano Yumiko

    2011-12-01

    Full Text Available Abstract Background Understanding the geographical distribution of drug resistance of Plasmodium falciparum is important for the effective treatment of malaria. Drug resistance has previously been inferred mainly from records of clinical resistance. However, clinical resistance is not always consistent with the parasite's genetic resistance. Thus, molecular identification of the parasite's drug resistance is required. In Africa, clinical resistance to pyrimethamine (Pyr and chloroquine (CQ was evident before 1980 but few studies investigating the genetic resistance to these drugs were conducted before the late 1990s. In this study, genotyping of genes involved in resistance to Pyr and CQ was performed using archive blood samples from Africa between 1984 and 1998. Methods Parasite DNA was extracted from P. falciparum-infected blood smears collected from travellers returning to Japan from Africa between 1984 and 1998. Genotypes of the dihydrofolate reductase gene (dhfr and CQ-resistance transporter gene (pfcrt were determined by polymerase chain reaction amplification and sequencing. Results Genotyping of dhfr and pfcrt was successful in 59 and 80 samples, respectively. One wild-type and seven mutant dhfr genotypes were identified. Three dhfr genotypes lacking the S108N mutation (NRSI, ICSI, IRSI; amino acids at positions 51, 59, 108, and 164 with mutations underlined were highly prevalent before 1994 but reduced after 1995, accompanied by an increase in genotypes with the S108N mutation. The dhfr IRNI genotype was first identified in Nigeria in 1991 in the present samples, and its frequency gradually increased. However, two double mutants (ICNI and NRNI, the latter of which was exclusively found in West Africa, were more frequent than the IRNI genotype. Only two pfcrt genotypes were found, the wild-type and a Southeast Asian type (CVIET; amino acids at positions 72-76 with mutations underlined. The CVIET genotype was already present as early as

  14. Collecting, archiving and processing DNA from wildlife samples using FTA® databasing paper

    OpenAIRE

    Burgoyne LA; Smith LM

    2004-01-01

    Abstract Background Methods involving the analysis of nucleic acids have become widespread in the fields of traditional biology and ecology, however the storage and transport of samples collected in the field to the laboratory in such a manner to allow purification of intact nucleic acids can prove problematical. Results FTA® databasing paper is widely used in human forensic analysis for the storage of biological samples and for purification of nucleic acids. The possible uses of FTA® databas...

  15. Detection of a Hobi-like virus in archival samples suggests circulation of this emerging pestivirus species in Europe prior to 2007

    Science.gov (United States)

    The first reported incidence of Hobi-like viruses in Europe dates to a 2010 outbreak of respiratory disease in cattle in Italy. In this study, a Hobi-like virus was detected in archival samples, collected in 2007 in Italy from a cattle herd displaying respiratory disease, during the validation of a...

  16. Analysis of tumor template from multiple compartments in a blood sample provides complementary access to peripheral tumor biomarkers.

    Science.gov (United States)

    Strauss, William M; Carter, Chris; Simmons, Jill; Klem, Erich; Goodman, Nathan; Vahidi, Behrad; Romero, Juan; Masterman-Smith, Michael; O'Regan, Ruth; Gogineni, Keerthi; Schwartzberg, Lee; Austin, Laura K; Dempsey, Paul W; Cristofanilli, Massimo

    2016-05-01

    Targeted cancer therapeutics are promised to have a major impact on cancer treatment and survival. Successful application of these novel treatments requires a molecular definition of a patient's disease typically achieved through the use of tissue biopsies. Alternatively, allowing longitudinal monitoring, biomarkers derived from blood, isolated either from circulating tumor cell derived DNA (ctcDNA) or circulating cell-free tumor DNA (ccfDNA) may be evaluated. In order to use blood derived templates for mutational profiling in clinical decisions, it is essential to understand the different template qualities and how they compare to biopsy derived template DNA as both blood-based templates are rare and distinct from the gold-standard. Using a next generation re-sequencing strategy, concordance of the mutational spectrum was evaluated in 32 patient-matched ctcDNA and ccfDNA templates with comparison to tissue biopsy derived DNA template. Different CTC antibody capture systems for DNA isolation from patient blood samples were also compared. Significant overlap was observed between ctcDNA, ccfDNA and tissue derived templates. Interestingly, if the results of ctcDNA and ccfDNA template sequencing were combined, productive samples showed similar detection frequency (56% vs 58%), were temporally flexible, and were complementary both to each other and the gold standard. These observations justify the use of a multiple template approach to the liquid biopsy, where germline, ctcDNA, and ccfDNA templates are employed for clinical diagnostic purposes and open a path to comprehensive blood derived biomarker access. PMID:27049831

  17. Characteristics of KE Basin Sludge Samples Archived in the RPL - 2007

    Energy Technology Data Exchange (ETDEWEB)

    Delegard, Calvin H.; Schmidt, Andrew J.; Chenault, Jeffrey W.

    2011-11-22

    Samples of sludge were collected from the K East fuel storage basin (KE Basin) floor, contiguous pits (Weasel Pit, North Load Out Pit, Dummy Elevator Pit, and Tech View Pit), and fuel storage canisters between 1995 and 2003 for chemical and radionuclide concentration analysis, physical property determination, and chemical process testing work. Because of the value of the sludge in this testing and because of the cost of obtaining additional fresh samples, an ongoing program of sludge preservation has taken place with the goals to track the sludge identities and preserve, as well as possible, the sludge composition by keeping the sludge in sealed jars and maintaining water coverage on the sludge consistent with the controlling Fluor Hanford (FH) Sampling and Analysis plans and FH contracts with the Pacific Northwest National Laboratory (PNNL). This work was originally initiated to provide material for planned hydrothermal treatment testing in accordance with the test plan for the Sludge Treatment Project (STP) corrosion process chemistry follow on testing (Delegard et al. 2007). Although most of the planned hydrothermal testing was canceled in July 2007 (as described in the forward of Delegard et al. 2007), sample consolidation and characterization was continued to identify a set of well-characterized sludge samples that are suited to support evolving STP initiatives. The work described in the letter was performed by the PNNL under the direction of the Sludge Treatment Project, managed by Fluor Hanford.

  18. Matrix Metalloproteinase-9/Neutrophil Gelatinase-Associated Lipocalin Complex Activity in Human Glioma Samples Predicts Tumor Presence and Clinical Prognosis

    Directory of Open Access Journals (Sweden)

    Ming-Fa Liu

    2015-01-01

    Full Text Available Matrix metalloproteinase-9/neutrophil gelatinase-associated lipocalin (MMP-9/NGAL complex activity is elevated in brain tumors and may serve as a molecular marker for brain tumors. However, the relationship between MMP-9/NGAL activity in brain tumors and patient prognosis and treatment response remains unclear. Here, we compared the clinical characteristics of glioma patients with the MMP-9/NGAL activity measured in their respective tumor and urine samples. Using gelatin zymography assays, we found that MMP-9/NGAL activity was significantly increased in tumor tissues (TT and preoperative urine samples (Preop-1d urine. Activity was reduced by seven days after surgery (Postop-1w urine and elevated again in cases of tumor recurrence. The MMP-9/NGAL status correlated well with MRI-based tumor assessments. These findings suggest that MMP-9/NGAL activity could be a novel marker to detect gliomas and predict the clinical outcome of patients.

  19. Optimizing 4-Dimensional Magnetic Resonance Imaging Data Sampling for Respiratory Motion Analysis of Pancreatic Tumors

    Energy Technology Data Exchange (ETDEWEB)

    Stemkens, Bjorn, E-mail: b.stemkens@umcutrecht.nl [Department of Radiotherapy, University Medical Center Utrecht, Utrecht (Netherlands); Tijssen, Rob H.N. [Department of Radiotherapy, University Medical Center Utrecht, Utrecht (Netherlands); Senneville, Baudouin D. de [Imaging Division, University Medical Center Utrecht, Utrecht (Netherlands); L' Institut de Mathématiques de Bordeaux, Unité Mixte de Recherche 5251, Centre National de la Recherche Scientifique/University of Bordeaux, Bordeaux (France); Heerkens, Hanne D.; Vulpen, Marco van; Lagendijk, Jan J.W.; Berg, Cornelis A.T. van den [Department of Radiotherapy, University Medical Center Utrecht, Utrecht (Netherlands)

    2015-03-01

    Purpose: To determine the optimum sampling strategy for retrospective reconstruction of 4-dimensional (4D) MR data for nonrigid motion characterization of tumor and organs at risk for radiation therapy purposes. Methods and Materials: For optimization, we compared 2 surrogate signals (external respiratory bellows and internal MRI navigators) and 2 MR sampling strategies (Cartesian and radial) in terms of image quality and robustness. Using the optimized protocol, 6 pancreatic cancer patients were scanned to calculate the 4D motion. Region of interest analysis was performed to characterize the respiratory-induced motion of the tumor and organs at risk simultaneously. Results: The MRI navigator was found to be a more reliable surrogate for pancreatic motion than the respiratory bellows signal. Radial sampling is most benign for undersampling artifacts and intraview motion. Motion characterization revealed interorgan and interpatient variation, as well as heterogeneity within the tumor. Conclusions: A robust 4D-MRI method, based on clinically available protocols, is presented and successfully applied to characterize the abdominal motion in a small number of pancreatic cancer patients.

  20. Optimizing 4-Dimensional Magnetic Resonance Imaging Data Sampling for Respiratory Motion Analysis of Pancreatic Tumors

    International Nuclear Information System (INIS)

    Purpose: To determine the optimum sampling strategy for retrospective reconstruction of 4-dimensional (4D) MR data for nonrigid motion characterization of tumor and organs at risk for radiation therapy purposes. Methods and Materials: For optimization, we compared 2 surrogate signals (external respiratory bellows and internal MRI navigators) and 2 MR sampling strategies (Cartesian and radial) in terms of image quality and robustness. Using the optimized protocol, 6 pancreatic cancer patients were scanned to calculate the 4D motion. Region of interest analysis was performed to characterize the respiratory-induced motion of the tumor and organs at risk simultaneously. Results: The MRI navigator was found to be a more reliable surrogate for pancreatic motion than the respiratory bellows signal. Radial sampling is most benign for undersampling artifacts and intraview motion. Motion characterization revealed interorgan and interpatient variation, as well as heterogeneity within the tumor. Conclusions: A robust 4D-MRI method, based on clinically available protocols, is presented and successfully applied to characterize the abdominal motion in a small number of pancreatic cancer patients

  1. Use of Raman Spectroscopy in Characterizing Formalin-Fixed, Paraffin-Embedded Breast Tumor Samples (abstract)

    Science.gov (United States)

    Downey, Frances; Cade, Nicholas; Cook, Richard; Springall, Robert; Gillet, Cheryl; Richards, David; Festy, Frederic

    2009-04-01

    Formalin-fixed, paraffin-embedded (FFPE) sections of breast tissue are used by pathologists to correctly type and grade the primary tumor and to assess the extent of a patient's disease. The cut sections represent a reproducible likeness of the morphology of the tissue when viewed through a microscope, although the fixation technique creates some artifacts. What is not known is how the sections differ chemically from how the tumor would look or behave within the breast. Raman spectroscopy is, like many other optical techniques, fast, noninvasive, and generally inexpensive. The advantage Raman has over other techniques is its powerful ability to identify specific chemicals, molecules, and bonds within a sample. Using Raman spectroscopy the chemicals present in both fresh tissue and FFPE sections can be identified and compared, allowing any differences between them to be identified. This information may be useful to the pathologist as an aid to further treatment regimes or novel molecular techniques, and as an aid to patient management. If these sections are found to be chemically similar to fresh tissue, they could be used to further characterize breast tumors, particularly rare tumors, using Raman spectroscopy.

  2. Global distribution of polymorphisms associated with delayed Plasmodium falciparum parasite clearance following artemisinin treatment: genotyping of archive blood samples.

    Science.gov (United States)

    Murai, Kenji; Culleton, Richard; Hisaoka, Teruhiko; Endo, Hiroyoshi; Mita, Toshihiro

    2015-06-01

    The recent emergence and spread of artemisinin-resistant Plasmodium falciparum isolates is a growing concern for global malaria-control efforts. A recent genome-wide analysis study identified two SNPs at genomic positions MAL10-688956 and MAL13-1718319, which are linked to delayed clearance of parasites following artemisinin combination therapy (ACT). It is expected that continuous artemisinin pressure will affect the distribution of these SNPs. Here, we investigate the worldwide distribution of these SNPs using a large number of archived samples in order to generate baseline data from the period before the emergence of ACT resistance. The presence of SNPs in MAL10-688956 and MAL13-1718319 was assessed by nested PCR RFLP and direct DNA sequencing using 653 global P. falciparum samples obtained before the reported emergence of ACT resistance. SNPs at MAL10-688956 and MAL13-1718319 associated with delayed parasite clearance following ACT administration were observed in 8% and 3% of parasites, respectively, mostly in Cambodia and Thailand. Parasites harbouring both SNPs were found in only eight (1%) isolates, all of which were from Cambodia and Thailand. Linkage disequilibrium was detected between MAL10-688956 and MAL13-1718319, suggesting that this SNP combination may have been selected by ACT drug pressure. Neither of the SNPs associated with delayed parasite clearance were observed in samples from Africa or South America. Baseline information of the geographical difference of MAL10-688956 and MAL13-1718319 SNPs provides a solid basis for assessing whether these SNPs are selected by artemisinin-based combination therapies. PMID:25449286

  3. DNA Analysis in Samples From Younger Patients With Germ Cell Tumors and Their Parents or Siblings

    Science.gov (United States)

    2016-04-07

    Childhood Malignant Ovarian Germ Cell Tumor; Childhood Malignant Testicular Germ Cell Tumor; Ovarian Choriocarcinoma; Ovarian Embryonal Carcinoma; Ovarian Mixed Germ Cell Tumor; Ovarian Teratoma; Ovarian Yolk Sac Tumor; Testicular Choriocarcinoma; Testicular Embryonal Carcinoma; Testicular Seminoma; Testicular Teratoma; Testicular Yolk Sac Tumor

  4. COSMOS: accurate detection of somatic structural variations through asymmetric comparison between tumor and normal samples.

    Science.gov (United States)

    Yamagata, Koichi; Yamanishi, Ayako; Kokubu, Chikara; Takeda, Junji; Sese, Jun

    2016-05-01

    An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the mapped read pairs in tumor samples with isogenic normal control samples in a distinct asymmetric manner. COSMOS also prioritizes the candidate SVs using strand-specific read-depth information. Performance tests on modeled tumor genomes revealed that COSMOS outperformed existing methods in terms of F-measure. We also applied COSMOS to an experimental mouse cell-based model, in which SVs were induced by genome engineering and gamma-ray irradiation, followed by polymerase chain reaction-based confirmation. The precision of COSMOS was 84.5%, while the next best existing method was 70.4%. Moreover, the sensitivity of COSMOS was the highest, indicating that COSMOS has great potential for cancer genome analysis. PMID:26833260

  5. COSMOS: accurate detection of somatic structural variations through asymmetric comparison between tumor and normal samples

    Science.gov (United States)

    Yamagata, Koichi; Yamanishi, Ayako; Kokubu, Chikara; Takeda, Junji; Sese, Jun

    2016-01-01

    An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the mapped read pairs in tumor samples with isogenic normal control samples in a distinct asymmetric manner. COSMOS also prioritizes the candidate SVs using strand-specific read-depth information. Performance tests on modeled tumor genomes revealed that COSMOS outperformed existing methods in terms of F-measure. We also applied COSMOS to an experimental mouse cell-based model, in which SVs were induced by genome engineering and gamma-ray irradiation, followed by polymerase chain reaction-based confirmation. The precision of COSMOS was 84.5%, while the next best existing method was 70.4%. Moreover, the sensitivity of COSMOS was the highest, indicating that COSMOS has great potential for cancer genome analysis. PMID:26833260

  6. Mutational profile of KIT and PDGFRA genes in gastrointestinal stromal tumors in Peruvian samples

    Directory of Open Access Journals (Sweden)

    José Buleje

    2015-02-01

    Full Text Available Introduction: Gastrointestinal stromal tumors (GISTs are mesenchymal neoplasms usually caused by somatic mutations in the genes KIT (c-KIT or PDGFRA. Mutation characterization has become an important exam for GIST patients because it is useful in predicting the response to the inhibitors of receptor tyrosine kinase (RTK. Objectives: The aim of this study was to determine the frequency of KIT and PDGFRA mutations in 25 GIST samples collected over two years at two national reference hospitals in Peru. There were 21 samples collected from the Instituto Nacional de Enfermedades Neoplásicas (INEN, national cancer center and 4 samples collected from Hospital A. Loayza. Methods and materials: In this retrospective study, we performed polymerase chain reaction (PCR amplification and deoxyribonucleic acid (DNA sequencing of KIT (exons 9, 11, 13, and 17 and PDGFRA (exons 12 and 18 genes in 20 FFPE (formalin-fixed, paraffin-embedded and 5 frozen GIST samples. Results: We report 21 mutations, including deletions, duplications, and missense, no mutations in 2 samples, and 2 samples with no useful DNA for further analysis. Eighty-six percent of these mutations were located in exon 11 of KIT, and 14 % were located in exon 18 of PDGFRA. Conclusions: Our study identified mutations in 21 out of 25 GIST samples from 2 referential national hospitals in Peru, and the mutation proportion follows a global tendency observed from previous studies (i.e., the majority of samples presented KIT mutations followed by a minor percentage of PDGFRA mutations. This study presents the first mutation data of the KIT and PDGFRA genes from Peruvian individuals with GIST.

  7. Development of an inventory/archive program for the retention, management, and disposition of tank characterization samples at the 222-S laboratory

    Energy Technology Data Exchange (ETDEWEB)

    Seidel, C.M.

    1998-04-29

    The Hanford Tank Waste Remediation Systems (TWRS) Characterization Program is responsible for coordinating the sampling and analysis of the 177 large underground storage tanks at the Hanford site. The 222-S laboratory has been the primary laboratory for chemical analysis of this highly-radioactive material and has been accumulating these samples for many years. As part of the Fiscal Year 1998 laboratory work scope, the 222-S laboratory has performed a formal physical inventory of all tank characterization samples which are currently being stored. In addition, an updated inventory/archive program has been designed. This program defines sample storage, retention, consolidation, maintenance, and disposition activities which will ensure that the sample integrity is preserved to the greatest practical extent. In addition, the new program provides for continued availability of waste material in a form which will be useful for future bench-scale studies. Finally, when the samples have exceeded their useful lifetime, the program provides for sample disposition from,the laboratory in a controlled, safe and environmentally compliant manner. The 222-S laboratory maintains custody over samples of tank waste material which have been shipped to the laboratory for chemical analysis. The storage of these samples currently requires an entire hotcell, fully dedicated to sample archive storage, and is rapidly encroaching on additional hotcell space. As additional samples are received, they are beginning to limit the 222-S laboratory hotcell utility for other activities such as sample extrusion and subsampling. The 222-S laboratory tracks the number of sample containers and the mass of each sample through an internal database which has recently been verified and updated via a physical inventory.

  8. Development of an inventory/archive program for the retention, management, and disposition of tank characterization samples at the 222-S laboratory

    International Nuclear Information System (INIS)

    The Hanford Tank Waste Remediation Systems (TWRS) Characterization Program is responsible for coordinating the sampling and analysis of the 177 large underground storage tanks at the Hanford site. The 222-S laboratory has been the primary laboratory for chemical analysis of this highly-radioactive material and has been accumulating these samples for many years. As part of the Fiscal Year 1998 laboratory work scope, the 222-S laboratory has performed a formal physical inventory of all tank characterization samples which are currently being stored. In addition, an updated inventory/archive program has been designed. This program defines sample storage, retention, consolidation, maintenance, and disposition activities which will ensure that the sample integrity is preserved to the greatest practical extent. In addition, the new program provides for continued availability of waste material in a form which will be useful for future bench-scale studies. Finally, when the samples have exceeded their useful lifetime, the program provides for sample disposition from,the laboratory in a controlled, safe and environmentally compliant manner. The 222-S laboratory maintains custody over samples of tank waste material which have been shipped to the laboratory for chemical analysis. The storage of these samples currently requires an entire hotcell, fully dedicated to sample archive storage, and is rapidly encroaching on additional hotcell space. As additional samples are received, they are beginning to limit the 222-S laboratory hotcell utility for other activities such as sample extrusion and subsampling. The 222-S laboratory tracks the number of sample containers and the mass of each sample through an internal database which has recently been verified and updated via a physical inventory

  9. Characteristics of STP Pre-2004 Archived KE Basin Sludge Samples Before and After Re-Jarring in the RPL - April 2012

    Energy Technology Data Exchange (ETDEWEB)

    Sinkov, Sergey I.; Delegard, Calvin H.; Schmidt, Andrew J.; Chenault, Jeffrey W.

    2012-09-28

    This report describes results of work performed in the Shielded Analytical Laboratory (SAL) at the Pacific Northwest National Laboratory’s (PNNL) Radiochemical Processing Laboratory (RPL) with archive K East (KE) Basin sludge samples obtained before the year 2004, with some of them composited and initially characterized five years ago (Delegard et al. 2011). The previously performed testing included the physical properties determinations for selected samples (settled and particle densities, water and solids concentrations), the pH, as well as identification of crystalline phases by X-ray diffractometry (XRD) for selected samples. Another objective of the previous characterization and testing campaign was to transfer some sludge composites and individual samples into new storage containers to overcome the embrittlement effect which develops in original glass containers as a result of extended exposure to high radiation fields and which increases probability of sample loss.

  10. Discriminating somatic and germline mutations in tumor DNA samples without matching normals.

    Science.gov (United States)

    Hiltemann, Saskia; Jenster, Guido; Trapman, Jan; van der Spek, Peter; Stubbs, Andrew

    2015-09-01

    Tumor analyses commonly employ a correction with a matched normal (MN), a sample from healthy tissue of the same individual, in order to distinguish germline mutations from somatic mutations. Since the majority of variants found in an individual are thought to be common within the population, we constructed a set of 931 samples from healthy, unrelated individuals, originating from two different sequencing platforms, to serve as a virtual normal (VN) in the absence of such an associated normal sample. Our approach removed (1) >96% of the germline variants also removed by the MN sample and (2) a large number (2%-8%) of additional variants not corrected for by the associated normal. The combination of the VN with the MN improved the correction for polymorphisms significantly, with up to ∼30% compared with MN and ∼15% compared with VN only. We determined the number of unrelated genomes needed in order to correct at least as efficiently as the MN is about 200 for structural variations (SVs) and about 400 for single-nucleotide variants (SNVs) and indels. In addition, we propose that the removal of common variants with purely position-based methods is inaccurate and incurs additional false-positive somatic variants, and more sophisticated algorithms, which are capable of leveraging information about the area surrounding variants, are needed for optimal accuracy. Our VN correction method can be used to analyze any list of variants, regardless of sequencing platform of origin. This VN methodology is available for use on our public Galaxy server. PMID:26209359

  11. A molecular analysis by gene expression profiling reveals Bik/NBK overexpression in sporadic breast tumor samples of Mexican females

    International Nuclear Information System (INIS)

    Breast cancer is one of the most frequent causes of death in Mexican women over 35 years of age. At molecular level, changes in many genetic networks have been reported as associated with this neoplasia. To analyze these changes, we determined gene expression profiles of tumors from Mexican women with breast cancer at different stages and compared these with those of normal breast tissue samples. 32P-radiolabeled cDNA was synthesized by reverse transcription of mRNA from fresh sporadic breast tumor biopsies, as well as normal breast tissue. cDNA probes were hybridized to microarrays and expression levels registered using a phosphorimager. Expression levels of some genes were validated by real time RT-PCR and immunohistochemical assays. We identified two subgroups of tumors according to their expression profiles, probably related with cancer progression. Ten genes, unexpressed in normal tissue, were turned on in some tumors. We found consistent high expression of Bik gene in 14/15 tumors with predominant cytoplasmic distribution. Recently, the product of the Bik gene has been associated with tumoral reversion in different neoplasic cell lines, and was proposed as therapy to induce apoptosis in cancers, including breast tumors. Even though a relationship among genes, for example those from a particular pathway, can be observed through microarrays, this relationship might not be sufficient to assign a definitive role to Bik in development and progression of the neoplasia. The findings herein reported deserve further investigation

  12. Long time storage (archiving of peptide, protein and tryptic digest samples on disposable nano-coated polymer targets for MALDI MS

    Directory of Open Access Journals (Sweden)

    Stefan Bugovsky

    2015-09-01

    Full Text Available Archiving of biological specimens is important due to the importance of reanalysis of already prepared MALDI MS samples or simultaneuous analysis of a sample series. Proteins/peptides and digests were prepared for measurement on a polymer-based metal nano-coated MALDI target and subjected to various storage conditions (−80 °C to RT in a vacuum-sealed pouch and at atmosphere for 6 months. The MS data gathered from these preparations illustrate trends in the aging of different samples and to find optimal storage conditions (−20 or −80 °C in low oxygen environment. The disposable/low cost target proved to be a suitable platform for storage and MALDI MS.

  13. Archiving challenges

    OpenAIRE

    Ringersma, J.

    2010-01-01

    Teaching slides on: What is a digital archive? Parties involved in digital archiving Archiving challenges organization of data coherence and persistency access and safety Language archiving software Different users, different needs For: Saami Language Documentation and Revitalization. Winter school, Bodø, Norway

  14. Multimodal Raman-fluorescence spectroscopy of formalin fixed samples is able to discriminate brain tumors from dysplastic tissue

    Science.gov (United States)

    Anand, Suresh; Cicchi, Riccardo; Giordano, Flavio; Buccoliero, Anna Maria; Pavone, Francesco Saverio

    2014-05-01

    In the recent years, there has been a considerable surge in the application of spectroscopy for disease diagnosis. Raman and fluorescence spectra provide characteristic spectral profile related to biochemical and morphological changes when tissues progress from normal state towards malignancy. Spectroscopic techniques offer the advantage of being minimally invasive compared to traditional histopathology, real time and quantitative. In biomedical optical diagnostics, freshly excised specimens are preferred for making ex-vivo spectroscopic measurements. With regard to fresh tissues, if the lab is located far away from the clinic it could pose a problem as spectral measurements have to be performed immediately after dissection. Tissue samples are usually placed in a fixative agent such as 4% formaldehyde to preserve the samples before processing them for routine histopathological studies. Fixation prevents the tissues from decomposition by arresting autolysis. In the present study, we intend to investigate the possibility of using formalin fixed samples for discrimination of brain tumours from dysplastic tissue using Raman and fluorescence spectroscopy. Formalin fixed samples were washed with phosphate buffered saline for about 5 minutes in order to remove the effects of formalin during spectroscopic measurements. In case of fluorescence spectroscopy, changes in spectral profile have been observed in the region between 550-670 nm between dysplastic and tumor samples. For Raman measurements, we found significant differences in the spectral profiles between dysplasia and tumor. In conclusion, formalin fixed samples can be potentially used for the spectroscopic discrimination of tumor against dysplastic tissue in brain samples.

  15. Normalization of gene expression measurement of tissue samples obtained by transurethral resection of bladder tumors

    Directory of Open Access Journals (Sweden)

    Pop LA

    2016-06-01

    Full Text Available Laura A Pop,1,* Valentina Pileczki,1,2,* Roxana M Cojocneanu-Petric,1 Bogdan Petrut,3,4 Cornelia Braicu,1 Ancuta M Jurj,1 Rares Buiga,5 Patriciu Achimas-Cadariu,6,7 Ioana Berindan-Neagoe1,8 1The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania; 2Department of Analytical Chemistry, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania; 3Department of Surgery II – Urology, The Oncology Institute “Prof Dr Ion Chiricuţă”, Cluj-Napoca, Cluj, Romania; 4Department of Urology, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania; 5Department of Pathology, The Oncology Institute “Prof. Dr Ion Chiricuţă”, Cluj-Napoca, Cluj, Romania; 6Department of Surgery, The Oncology Institute “Prof Dr Ion Chiricuţă”, Cluj-Napoca, Cluj, Romania; 7Department of Surgical Oncology and Gynecological Oncology, Iuliu Haţieganu University of Medicine and Pharmacy, 8Department of Functional Genomics and Experimental Pathology, The Oncology Institute “Prof Dr Ion Chiricuţă”, Cluj-Napoca, Cluj, Romania *These authors contributed equally to this work Background: Sample processing is a crucial step for all types of genomic studies. A major challenge for researchers is to understand and predict how RNA quality affects the identification of transcriptional differences (by introducing either false-positive or false-negative errors. Nanotechnologies help improve the quality and quantity control for gene expression studies. Patients and methods: The study was performed on 14 tumor and matched normal pairs of tissue from patients with bladder urothelial carcinomas. We assessed the RNA quantity by using the NanoDrop spectrophotometer and the quality by nano-microfluidic capillary electrophoresis technology provided by Agilent 2100 Bioanalyzer. We evaluated the amplification status of three

  16. Evaluation of the performance of a p53 sequencing microarray chip using 140 previously sequenced bladder tumor samples

    DEFF Research Database (Denmark)

    Wikman, Friedrik; Lu, Ming-Lan; Andersen, Thomas Thykjær;

    2000-01-01

    available chip and describes a method to increase the specificity of the chip. Methods: DNA from 140 human bladder tumors was extracted and subjected to a multiplex-PCR before loading onto the p53 GeneChip from Affymetrix. The same samples were previously sequenced by manual dideoxy sequencing. In addition...

  17. Evaluation of Picture Archiving and Communication System (Pacs As A Process Improvement Sample (Sivas Numune Hospital Application

    Directory of Open Access Journals (Sweden)

    Ali Rıza İnce

    2013-09-01

    Full Text Available It is a realitythatthefirmsproducinggoods or services frequentlybenefited process improvementand similartechniques toachieve their objectives In today'scompetitive environment.Beingprocess-orientedmeans to give weight to the creation of quality but not to the control of quality. In this sense, process improvement is seen as an approach of Total Quality Management targeted. Hospital informationsystems are computer systems that collect andarchive all orthe majority of the hospitaldatafor use inthe assessment.It isa major problem that storage of visualdatawithout lossanddamage and also the being availableof these data as soon as possiblein this system.System that calledPACShas been developedto overcome this problem.PACS is an archiving system that archive the visual dataobtained fromimaging systems in different unitsin a spaceand, allows the transfer of these data to usersat different points when needed.In this study,efficiency of PACS asa process improvementtechniquewas examined by the application ofahospital.It is concluded that the system providea positive contributionto customers and hospitalas an example ofan importantprocess improvement at the evaluationof the results and implementation of the system.

  18. Chromogenic in situ hybridization (CISH): a novel alternative in screening archival breast cancer tissue samples for HER-2/neu status

    International Nuclear Information System (INIS)

    Chromogenic in situ hybridization (CISH) is emerging as a practical, cost-effective, and valid alternative to fluorescent in situ hybridization in testing for gene alteration, especially in centers primarily working with immunohistochemistry (IHC). We assessed Her-2/neu alteration using CISH on formalin-fixed paraffin-embedded primary invasive ductal carcinoma tumors in which IHC (CB11 antibody) had previously been performed, and we compared the results with IHC. The 160 selected cases were equally stratified randomly into the four IHC categories (scores of 0, 1+, 2+, and 3+). We also compared age at diagnosis and tumor histologic grade with IHC and CISH Her-2/neu. We were able to perform and evaluate CISH successfully on all cases. The agreement between 3+ IHC and CISH-amplified cases as well as between all IHC and CISH Her-2/neu negative cases was 100%, and the concordance on all positive cases was 72.50%, with an overall agreement of 86.25%. All the discordant cases had 2+ IHC scores. Although we noted Her-2/neu positivity more in premenopausal women, the age at diagnosis was not significantly associated with IHC or CISH results. Similarly, although the small group of well-differentiated tumors was apparently Her-2/neu negative in both tests, no significant association was noted between any tumor histologic grade and either IHC or CISH results. CISH is easily integrated into routine testing in our laboratory. It is a necessary adjunct in determining the subset of non-amplified IHC-positive invasive tumors that will not benefit from trastuzumab therapy. Those cases with 2+ IHC results will be triaged and subjected to CISH. Her-2/neu testing should be done on all breast cancer cases regardless of age at presentation and tumor histologic grade

  19. A jackknife-like method for classification and uncertainty assessment of multi-category tumor samples using gene expression information

    Directory of Open Access Journals (Sweden)

    Bertrand Keith

    2010-04-01

    Full Text Available Abstract Background The use of gene expression profiling for the classification of human cancer tumors has been widely investigated. Previous studies were successful in distinguishing several tumor types in binary problems. As there are over a hundred types of cancers, and potentially even more subtypes, it is essential to develop multi-category methodologies for molecular classification for any meaningful practical application. Results A jackknife-based supervised learning method called paired-samples test algorithm (PST, coupled with a binary classification model based on linear regression, was proposed and applied to two well known and challenging datasets consisting of 14 (GCM dataset and 9 (NC160 dataset tumor types. The results showed that the proposed method improved the prediction accuracy of the test samples for the GCM dataset, especially when t-statistic was used in the primary feature selection. For the NCI60 dataset, the application of PST improved prediction accuracy when the numbers of used genes were relatively small (100 or 200. These improvements made the binary classification method more robust to the gene selection mechanism and the size of genes to be used. The overall prediction accuracies were competitive in comparison to the most accurate results obtained by several previous studies on the same datasets and with other methods. Furthermore, the relative confidence R(T provided a unique insight into the sources of the uncertainty shown in the statistical classification and the potential variants within the same tumor type. Conclusion We proposed a novel bagging method for the classification and uncertainty assessment of multi-category tumor samples using gene expression information. The strengths were demonstrated in the application to two bench datasets.

  20. Gaia archive

    CERN Document Server

    Hypki, Arkadiusz

    2016-01-01

    The Gaia archive is being designed and implemented by the DPAC Consortium. The purpose of the archive is to maximize the scientific exploitation of the Gaia data by the astronomical community. Thus, it is crucial to gather and discuss with the community the features of the Gaia archive as much as possible. It is especially important from the point of view of the GENIUS project to gather the feedback and potential use cases for the archive. This paper presents very briefly the general ideas behind the Gaia archive and presents which tools are already provided to the community.

  1. Dose-Response Analysis of RNA-Seq Profiles in Archival Formalin-fixed paraffin-embedded (FFPE) Samples

    Science.gov (United States)

    Formalin-fixed paraffin-embedded (FFPE) samples provide a vast untapped resource for chemical safety and translational science. To date, genomic profiling of FFPE samples has been limited by poor RNA quality and inconsistent results with limited utility in dose-response assessmen...

  2. File list: InP.Dig.10.AllAg.Gastric_primary_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available InP.Dig.10.AllAg.Gastric_primary_sample hg19 Input control Digestive tract Gastric primary...369082 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/InP.Dig.10.AllAg.Gastric_primary_sample.bed ...

  3. File list: NoD.Dig.20.AllAg.Gastric_primary_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  4. File list: NoD.Dig.10.AllAg.Gastric_primary_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  5. File list: InP.Dig.50.AllAg.Gastric_primary_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  6. File list: InP.Dig.20.AllAg.Gastric_primary_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  7. File list: InP.Dig.05.AllAg.Gastric_primary_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  8. File list: NoD.Dig.05.AllAg.Gastric_primary_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  9. File list: NoD.Dig.50.AllAg.Gastric_primary_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  10. Epo receptors are not detectable in primary human tumor tissue samples.

    Directory of Open Access Journals (Sweden)

    Steve Elliott

    Full Text Available Erythropoietin (Epo is a cytokine that binds and activates an Epo receptor (EpoR expressed on the surface of erythroid progenitor cells to promote erythropoiesis. While early studies suggested EpoR transcripts were expressed exclusively in the erythroid compartment, low-level EpoR transcripts were detected in nonhematopoietic tissues and tumor cell lines using sensitive RT-PCR methods. However due to the widespread use of nonspecific anti-EpoR antibodies there are conflicting data on EpoR protein expression. In tumor cell lines and normal human tissues examined with a specific and sensitive monoclonal antibody to human EpoR (A82, little/no EpoR protein was detected and it was not functional. In contrast, EpoR protein was reportedly detectable in a breast tumor cell line (MCF-7 and breast cancer tissues with an anti-EpoR polyclonal antibody (M-20, and functional responses to rHuEpo were reported with MCF-7 cells. In another study, a functional response was reported with the lung tumor cell line (NCI-H838 at physiological levels of rHuEpo. However, the specificity of M-20 is in question and the absence of appropriate negative controls raise questions about possible false-positive effects. Here we show that with A82, no EpoR protein was detectable in normal human and matching cancer tissues from breast, lung, colon, ovary and skin with little/no EpoR in MCF-7 and most other breast and lung tumor cell lines. We show further that M-20 provides false positive staining with tissues and it binds to a non-EpoR protein that migrates at the same size as EpoR with MCF-7 lysates. EpoR protein was detectable with NCI-H838 cells, but no rHuEpo-induced phosphorylation of AKT, STAT3, pS6RP or STAT5 was observed suggesting the EpoR was not functional. Taken together these results raise questions about the hypothesis that most tumors express high levels of functional EpoR protein.

  11. Archiving Websites

    DEFF Research Database (Denmark)

    Brügger, Niels

    This book treats the micro archiving of websites, i.e. archiving by researchers, students or others without special technical knowledge who, using a standard computer, wish to save a website for further study. The phenomenon is discussed from the standpoint that Internet research must be able...... is reached. Firstly, unlike other well-known media, the Internet does not simply exist in a form suited to being archived, but rather is first formed as an object of study in the archiving, and it is formed differently depending on who does the archiving, when, and for what purpose. Secondly, this means...... that there is an element of subjective creation in the archived material, so that methodical deliberations are necessary — in other words, the answers to why and how the archived material has been created. These conclusions form the starting point for the last section of the book, which, based on comprehensive tests...

  12. Application of a global proteomic approach to archival precursor lesions: deleted in malignant brain tumors 1 and tissue transglutaminase 2 are upregulated in pancreatic cancer precursors

    DEFF Research Database (Denmark)

    Cheung, Wang; Darfler, Marlene M; Alvarez, Hector;

    2008-01-01

    of invasive cancer. Biomarker discovery in precursor lesions has been hampered by the ready availability of fresh specimens, and limited yields of proteins suitable for large scale screening. METHODS: We utilized Liquid Tissue, a novel technique for protein extraction from archival formalin-fixed material...... their overexpression in IPMNs. CONCLUSION: Global proteomics analysis using the Liquid Tissue workflow is a feasible approach for unbiased biomarker discovery in limited archival material, particularly applicable to precursor lesions of cancer....

  13. Identification of recently described porcine parvoviruses in archived North American samples from 1996 and association with porcine circovirus associated disease.

    Science.gov (United States)

    Opriessnig, Tanja; Xiao, Chao-Ting; Gerber, Priscilla F; Halbur, Patrick G

    2014-09-17

    The association of porcine circovirus (PCV) type 2 and porcine parvovirus (PPV) type 1 as a cause of porcine circovirus associated disease (PCVAD) is well established. The objective of this study was to investigate the prevalence rates of classical PPV1 and recently recognized PPV2-5 in serum and lung samples from pigs and farms with known PCV2 status. A total of 586 serum samples and 164 lung homogenates collected from 1996 to 2013 in the USA and Canada were utilized. All samples were tested for PPV1-5 and PCV2. PCV2 was detected in 27.7% (162/586) and PPV in 48.8% (286/586) of the serum samples, whereas 78.7% (129/164) of the lung tissues were positive for PCV2 and 56.7% (93/164) were positive for PPV. Overall, PPV2 had the highest prevalence rates in sera (35.2%) and tissues (42.7%). Concurrent infection of PCV2 and PPV occurred in 14.3% (84/586) of the serum samples and in 49.4% (81/164) of the tissue samples. Moreover, the prevalence of PPV1 or PPV2 DNA was significantly higher in tissues containing high amounts of PCV2 DNA compared to non-PCVAD cases. The frequency of concurrent PPV/PCV2 infection was higher for PCVAD herds compared to negative or subclinically infected herds. PPV2, PPV3 and PPV4 were all identified in samples collected in 1998 and PPV5 was first identified in 2006. The obtained findings indicate that similar to PCV2, PPVs are widespread in North American pigs. Nevertheless, diagnostic investigations into PCVAD cases should give more consideration to the role of PPV1 and PPV2 as contributing cofactors. PMID:25081955

  14. Archival Descriptions from the National Archives Catalog

    Data.gov (United States)

    National Archives and Records Administration — Archival Descriptions from the National Archives Catalog data set provides archival descriptions of the permanent holdings of the federal government in the custody...

  15. Examination of Gene Fusion Status in Archival Samples of Alveolar Rhabdomyosarcoma Entered on the Intergroup Rhabdomyosarcoma Study-III Trial : A Report from the Children’s Oncology Group

    OpenAIRE

    Barr, Frederic G.; Smith, Lynette M.; Lynch, James C.; Strzelecki, Donna; Parham, David M.; Qualman, Stephen J.; Breitfeld, Philip P.

    2006-01-01

    Alveolar rhabdomyosarcoma (ARMS) is a soft tissue cancer in which chromosomal translocations generate PAX3-FKHR and PAX7-FKHR gene fusions. To improve the approach for fusion detection in archival samples, we developed a real-time reverse transcriptase-polymerase chain reaction assay for these fusion transcripts. By incorporating consensus primers and gene-specific probes, both presence and subtype of the fusion were determined in one assay. We applied this approach to a convenience sample of...

  16. A divide-and-conquer strategy in tumor sampling enhances detection of intratumor heterogeneity in routine pathology: A modeling approach in clear cell renal cell carcinoma

    Science.gov (United States)

    Lopez, José I.; Cortes, Jesús M.

    2016-01-01

    Intratumor heterogeneity (ITH) is an inherent process in cancer development which follows for most of the cases a branched pattern of evolution, with different cell clones evolving independently in space and time across different areas of the same tumor. The determination of ITH (in both spatial and temporal domains) is nowadays critical to enhance patient treatment and prognosis. Clear cell renal cell carcinoma (CCRCC) provides a good example of ITH. Sometimes the tumor is too big to be totally analyzed for ITH detection and pathologists decide which parts must be sampled for the analysis. For such a purpose, pathologists follow internationally accepted protocols. In light of the latest findings, however, current sampling protocols seem to be insufficient for detecting ITH with significant reliability. The arrival of new targeted therapies, some of them providing promising alternatives to improve patient survival, pushes the pathologist to obtain a truly representative sampling of tumor diversity in routine practice. How large this sampling must be and how this must be performed are unanswered questions so far.  Here we present a very simple method for tumor sampling that enhances ITH detection without increasing costs. This method follows a divide-and-conquer (DAC) strategy, that is, rather than sampling a small number of large-size tumor-pieces as the routine protocol (RP) advises, we suggest sampling many small-size pieces along the tumor. We performed a computational modeling approach to show that the usefulness of the DAC strategy is twofold: first, we show that DAC outperforms RP with similar laboratory costs, and second, DAC is capable of performing similar to total tumor sampling (TTS) but, very remarkably, at a much lower cost. We thus provide new light to push forward a shift in the paradigm about how pathologists should sample tumors for achieving efficient ITH detection. PMID:27127618

  17. ANALYSES OF HTF-48-12-20/24 (FEBRUARY, 2012) AND ARCHIVED HTF-E-05-021 TANK 48H SLURRY SAMPLES

    Energy Technology Data Exchange (ETDEWEB)

    Nash, C.; Peters, T.

    2012-08-02

    Personnel characterized a Savannah River National Laboratory (SRNL) archived sample of Tank 48H slurry (HTF-E-05-021) in addition to the composite of samples HTF-48-12-20 and HTF-48-12-24, which were both retrieved in February 2012. The combined February 2012 sample is referred to as HTF-48-12-20/24 in this report. The results from these analyses are compared with Tank 48H samples analyzed in 2003, 2004, and 2005. This work supports the effort to demonstrate copper-catalyzed peroxide oxidation (CCPO) of organic content in this material. The principal findings with respect to the chemical and physical characteristics of the most recent sample are: (1) The measured potassium tetraphenylborate (KTPB) solid concentration is 1.76 wt %; (2) Titanium was in line with 2004 and 2005 slurry measurements at 897 mg/L, it represents 0.1535 {+-} 0.0012 wt % monosodium titanate (MST); (3) The measured insoluble solids content was 1.467 wt %; (4) The free hydroxide concentration in the Tank 48H filtrate sample (1.02 {+-} 0.02 M) is close to the Tank 48H limit (1.0 M); (5) Carbonate reported by total inorganic carbon (TIC, 1.39 {+-} 0.03 M) is more than double the concentrations measured in past (2003-2005) samples; (6) The soluble potassium content (measured at 286 {+-} 23 mg/L) in the filtrate is in line with all past measurements; and (7) The measured {sup 137}Cs concentration is 7.81E + 08 {+-} 3.9E + 07 dpm/mL of slurry (1.33 {+-} 5% Ci/gallon or 3.18E + 05 {+-} 5% curies of {sup 137}Cs in the tank) in the slurry which is in agreement with the 2005 report of 3.14E + 05 {+-} 1.5% curies of {sup 137}Cs in the tank. The filtrate {sup 137}Cs concentration is 2.57E + 07 {+-} 2.6E + 05 dpm/mL. This result is consistent with previous results. Significant analytical data are summarized in Table 1.

  18. Biodistribution Analysis of Oncolytic Adenoviruses in Patient Autopsy Samples Reveals Vascular Transduction of Noninjected Tumors and Tissues.

    Science.gov (United States)

    Koski, Anniina; Bramante, Simona; Kipar, Anja; Oksanen, Minna; Juhila, Juuso; Vassilev, Lotta; Joensuu, Timo; Kanerva, Anna; Hemminki, Akseli

    2015-10-01

    In clinical trials with oncolytic adenoviruses, there has been no mortality associated with treatment vectors. Likewise, in the Advanced Therapy Access Program (ATAP), where 290 patients were treated with 10 different viruses, no vector-related mortality was observed. However, as the patient population who received adenovirus treatments in ATAP represented heavily pretreated patients, often with very advanced disease, some patients died relatively soon after receiving their virus treatment mandating autopsy to investigate cause of death. Eleven such autopsies were performed and confirmed disease progression as the cause of death in each case. The regulatory requirement for investigating the safety of advanced therapy medical products presented a unique opportunity to study tissue samples collected as a routine part of the autopsies. Oncolytic adenoviral DNA was recovered in a wide range of tissues, including injected and noninjected tumors and various normal tissues, demonstrating the ability of the vector to disseminate through the vascular route. Furthermore, we recovered and cultured viable virus from samples of noninjected brain metastases of an intravenously treated patient, confirming that oncolytic adenovirus can reach tumors through the intravascular route. Data presented here give mechanistic insight into mode of action and biodistribution of oncolytic adenoviruses in cancer patients. PMID:26156245

  19. Exposure and risk assessment of the Czech population to chlorinated pesticides and polychlorinated biphenyls using archived serum samples from the period 1970 to 1990.

    Science.gov (United States)

    Černá, Milena; Krsková, Andrea; Šmíd, Jiří; Malý, Marek

    2016-07-01

    The serum samples from the years 1970-1990 archived at the temperature of -20°C in the biobank primarily intended for serological survey performed in the CR since 1960 were pooled and analyzed for DDT, its metabolites, HCB, HCHs, and indicator PCB congeners using up-to-date GC/MS/MS methods to retrospectively assess health risks according to current health guidelines. Samples were pooled based on the decade of sampling, age, gender, and three geographical areas; in adults, one pooled samples consisted of ten and in children of twenty individual samples. Altogether 233 pooled samples were analyzed. For all organochlorine pesticides (OCPs), significant downward trends were observed in the period 1970-1990 (p<0.001). The levels of HCB exceeded the Biomonitoring Equivalent (BE) value. The hazard quotient (HQ) in Prague and Ostrava during the 1970s and 1980s was about 40 and in the 1990s it had dropped to about five. In Uherské Hradiště, the HQ in 1975 was one order of magnitude higher (about 170), and had decreased to approximately 12 by 1987. For both HCB and the DDT sum, the BE-related carcinogenic risk of actual concentrations in the past exceeded significantly the individually accepted cancer risk level of 10(-4). The levels of the main PCB congeners in the 1970s through 1990s revealed an upward time trend in all analyzed strata. The highest concentrations were found in the serum of residents from the hot-spot area Uherské Hradiště. Critical PCB sum concentration levels (700ng/g lipid for vulnerable population groups and 1800ng/g lipid for other population groups) were substantially exceeded with an increasing time trend. PCB sum had exceeded HBM II values of 7μg/L of serum since 1980 in all age strata. In conclusion, the body burden of the Czech general population relative to persistent organic pollutants (POPs) in the period 1970 through 1990 significantly exceeded currently existing health based limit values. The past exposure might adversely affect the

  20. Does the pretreatment tumor sampling location correspond with metabolic activity on 18F-FDG PET/CT in breast cancer patients scheduled for neoadjuvant chemotherapy?

    Energy Technology Data Exchange (ETDEWEB)

    Koolen, Bas B., E-mail: b.koolen@nki.nl [Department of Nuclear Medicine, Netherlands Cancer Institute – Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands); Department of Surgical Oncology, Netherlands Cancer Institute – Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands); Elshof, Lotte E. [Department of Nuclear Medicine, Netherlands Cancer Institute – Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands); Department of Surgical Oncology, Netherlands Cancer Institute – Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands); Loo, Claudette E. [Department of Radiology, Netherlands Cancer Institute – Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands); Wesseling, Jelle [Department of Pathology, Netherlands Cancer Institute – Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands); Vrancken Peeters, Marie-Jeanne T.F.D. [Department of Surgical Oncology, Netherlands Cancer Institute – Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands); Vogel, Wouter V. [Department of Nuclear Medicine, Netherlands Cancer Institute – Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands); Rutgers, Emiel J.Th. [Department of Surgical Oncology, Netherlands Cancer Institute – Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands); Valdés Olmos, Renato A. [Department of Nuclear Medicine, Netherlands Cancer Institute – Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands)

    2013-12-01

    Purpose: To define the correlation between the core biopsy location and the area with highest metabolic activity on 18F-FDG PET/CT in stage II–III breast cancer patients before neoadjuvant chemotherapy. Also, we would like to select a subgroup of patients in which PET/CT information may optimize tumor sampling. Methods: A PET/CT in prone position was acquired in 199 patients with 203 tumors. The distance and relative difference in standardized uptake value (SUV) between core biopsy localization (indicated by a marker) and area with highest degree of FDG uptake were evaluated. A distance ≥2 cm and a relative difference in SUV ≥25% were considered clinically relevant and a combination of both was defined as non-correspondence. Non-correspondence for different tumor characteristics (TNM stage, lesion morphology on MRI and PET/CT, histology, subtype, grade, and Ki-67) was assessed. Results: Non-correspondence was found in 28 (14%) of 203 tumors. Non-correspondence was significantly associated with T-stage, lesion morphology on MRI and PET/CT, tumor diameter, and histologic type. It was more often seen in tumors with a higher T-stage (p = 0.028), diffuse (non-mass) and multifocal tumors on MRI (p = 0.001), diffuse and multifocal tumors on PET/CT (p < 0.001), tumors >3 cm (p < 0.001), and lobular carcinomas (p < 0.001). No association was found with other features. Conclusion: Non-correspondence between the core biopsy location and area with highest FDG uptake is regularly seen in stage II–III breast cancer patients. PET/CT information and possibly FDG-guided biopsies are most likely to improve pretreatment tumor sampling in tumors >3 cm, lobular carcinomas, and diffuse and multifocal tumors.

  1. Does the pretreatment tumor sampling location correspond with metabolic activity on 18F-FDG PET/CT in breast cancer patients scheduled for neoadjuvant chemotherapy?

    International Nuclear Information System (INIS)

    Purpose: To define the correlation between the core biopsy location and the area with highest metabolic activity on 18F-FDG PET/CT in stage II–III breast cancer patients before neoadjuvant chemotherapy. Also, we would like to select a subgroup of patients in which PET/CT information may optimize tumor sampling. Methods: A PET/CT in prone position was acquired in 199 patients with 203 tumors. The distance and relative difference in standardized uptake value (SUV) between core biopsy localization (indicated by a marker) and area with highest degree of FDG uptake were evaluated. A distance ≥2 cm and a relative difference in SUV ≥25% were considered clinically relevant and a combination of both was defined as non-correspondence. Non-correspondence for different tumor characteristics (TNM stage, lesion morphology on MRI and PET/CT, histology, subtype, grade, and Ki-67) was assessed. Results: Non-correspondence was found in 28 (14%) of 203 tumors. Non-correspondence was significantly associated with T-stage, lesion morphology on MRI and PET/CT, tumor diameter, and histologic type. It was more often seen in tumors with a higher T-stage (p = 0.028), diffuse (non-mass) and multifocal tumors on MRI (p = 0.001), diffuse and multifocal tumors on PET/CT (p < 0.001), tumors >3 cm (p < 0.001), and lobular carcinomas (p < 0.001). No association was found with other features. Conclusion: Non-correspondence between the core biopsy location and area with highest FDG uptake is regularly seen in stage II–III breast cancer patients. PET/CT information and possibly FDG-guided biopsies are most likely to improve pretreatment tumor sampling in tumors >3 cm, lobular carcinomas, and diffuse and multifocal tumors

  2. Impact of delay to cryopreservation on RNA integrity and genome-wide expression profiles in resected tumor samples.

    Directory of Open Access Journals (Sweden)

    Elodie Caboux

    Full Text Available The quality of tissue samples and extracted mRNA is a major source of variability in tumor transcriptome analysis using genome-wide expression microarrays. During and immediately after surgical tumor resection, tissues are exposed to metabolic, biochemical and physical stresses characterized as "warm ischemia". Current practice advocates cryopreservation of biosamples within 30 minutes of resection, but this recommendation has not been systematically validated by measurements of mRNA decay over time. Using Illumina HumanHT-12 v3 Expression BeadChips, providing a genome-wide coverage of over 24,000 genes, we have analyzed gene expression variation in samples of 3 hepatocellular carcinomas (HCC and 3 lung carcinomas (LC cryopreserved at times up to 2 hours after resection. RNA Integrity Numbers (RIN revealed no significant deterioration of mRNA up to 2 hours after resection. Genome-wide transcriptome analysis detected non-significant gene expression variations of -3.5%/hr (95% CI: -7.0%/hr to 0.1%/hr; p = 0.054. In LC, no consistent gene expression pattern was detected in relation with warm ischemia. In HCC, a signature of 6 up-regulated genes (CYP2E1, IGLL1, CABYR, CLDN2, NQO1, SCL13A5 and 6 down-regulated genes (MT1G, MT1H, MT1E, MT1F, HABP2, SPINK1 was identified (FDR <0.05. Overall, our observations support current recommendation of time to cryopreservation of up to 30 minutes and emphasize the need for identifying tissue-specific genes deregulated following resection to avoid misinterpreting expression changes induced by warm ischemia as pathologically significant changes.

  3. MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data.

    Science.gov (United States)

    Fan, Yu; Xi, Liu; Hughes, Daniel S T; Zhang, Jianjun; Zhang, Jianhua; Futreal, P Andrew; Wheeler, David A; Wang, Wenyi

    2016-01-01

    Subclonal mutations reveal important features of the genetic architecture of tumors. However, accurate detection of mutations in genetically heterogeneous tumor cell populations using next-generation sequencing remains challenging. We develop MuSE ( http://bioinformatics.mdanderson.org/main/MuSE ), Mutation calling using a Markov Substitution model for Evolution, a novel approach for modeling the evolution of the allelic composition of the tumor and normal tissue at each reference base. MuSE adopts a sample-specific error model that reflects the underlying tumor heterogeneity to greatly improve the overall accuracy. We demonstrate the accuracy of MuSE in calling subclonal mutations in the context of large-scale tumor sequencing projects using whole exome and whole genome sequencing. PMID:27557938

  4. Visualizing archives: Spanish archives map

    OpenAIRE

    Colmenero-Ruiz, María-Jesús

    2016-01-01

    The 2014/2015 academic year was the first to be taught the Master in Archives, Records Management and Digital Continuity at the University Carlos III Madrid, based on a blended learning model of attendance. This article describes the implementation of a visualization project based on geolocation of Spanish archives and its justification. The project arose from an optional practice proposed to the students of the subject “Re-use of data and documents” of this master course. This subject is opt...

  5. High-resolution copy number analysis of paired normal-tumor samples from diffuse large B cell lymphoma.

    Science.gov (United States)

    Sebastián, Elena; Alcoceba, Miguel; Martín-García, David; Blanco, Óscar; Sanchez-Barba, Mercedes; Balanzategui, Ana; Marín, Luis; Montes-Moreno, Santiago; González-Barca, Eva; Pardal, Emilia; Jiménez, Cristina; García-Álvarez, María; Clot, Guillem; Carracedo, Ángel; Gutiérrez, Norma C; Sarasquete, M Eugenia; Chillón, Carmen; Corral, Rocío; Prieto-Conde, M Isabel; Caballero, M Dolores; Salaverria, Itziar; García-Sanz, Ramón; González, Marcos

    2016-01-01

    Copy number analysis can be useful for assessing prognosis in diffuse large B cell lymphoma (DLBCL). We analyzed copy number data from tumor samples of 60 patients diagnosed with DLBCL de novo and their matched normal samples. We detected 63 recurrent copy number alterations (CNAs), including 33 gains, 30 losses, and nine recurrent acquired copy number neutral loss of heterozygosity (CNN-LOH). Interestingly, 20 % of cases acquired CNN-LOH of 6p21 locus, which involves the HLA region. In normal cells, there were no CNAs but we observed CNN-LOH involving some key lymphoma regions such as 6p21 and 9p24.1 (5 %) and 17p13.1 (2.5 %) in DLBCL patients. Furthermore, a model with some specific CNA was able to predict the subtype of DLBCL, 1p36.32 and 10q23.31 losses being restricted to germinal center B cell-like (GCB) DLBCL. In contrast, 8p23.3 losses and 11q24.3 gains were strongly associated with the non-GCB subtype. A poor prognosis was associated with biallelic inactivation of TP53 or 18p11.32 losses, while prognosis was better in cases carrying 11q24.3 gains. In summary, CNA abnormalities identify specific DLBCL groups, and we describe CNN-LOH in germline cells from DLBCL patients that are associated with genes that probably play a key role in DLBCL development. PMID:26573278

  6. Archival Research Catalog (ARC) Archival Descriptions

    Data.gov (United States)

    National Archives and Records Administration — The Archival Research Catalog (ARC) data set provides archival descriptions of the permanent holdings of the federal government in the custody of the National...

  7. PTCH 1 staining of pancreatic neuroendocrine tumor (PNET) samples from patients with and without multiple endocrine neoplasia (MEN-1) syndrome reveals a potential therapeutic target

    Science.gov (United States)

    Gurung, Buddha; Hua, Xianxin; Runske, Melissa; Bennett, Bonita; LiVolsi, Virginia; Roses, Robert; Fraker, Douglas A; Metz, David C

    2015-01-01

    Pancreatic neuroendocrine tumors (PNETs) are rare, indolent tumors that may occur sporadically or develop in association with well-recognized hereditary syndromes, particularly multiple endocrine neoplasia type 1 (MEN-1). We previously demonstrated that the hedgehog (HH) signaling pathway was aberrantly up-regulated in a mouse model that phenocopies the human MEN-1 syndrome, Men1l/l;RipCre, and that inhibition of this pathway suppresses MEN-1 tumor cell proliferation. We hypothesized that the HH signaling pathway is similarly upregulated in human PNETs. We performed immunohistochemical (IHC) staining for PTCH1 in human fresh and archival PNET specimens to examine whether human sporadic and MEN-1-associated PNETs revealed similar abnormalities as in our mouse model and correlated the results with clinical and demographic factors of the study cohort. PTCH1 staining was positive in 12 of 22 PNET patients (55%). Four of 5 MEN-1 patients stained for PTCH1 (p = 0.32 as compared with sporadic disease patients). Nine of 16 patients with metastatic disease stained for PTCH1 as compared with zero of 3 with localized disease only (p = 0.21). No demographic or clinical features appeared to be predictive of PTCH 1 positivity and PTCH 1 positivity per se was not predictive of clinical outcome. PTCH1, a marker of HH pathway up regulation, is detectable in both primary and metastatic tumors in more than 50% of PNET patients. Although no clinical or demographic factors predict PTCH1 positivity and PTCH1 positivity does not predict clinical outcome, the frequency of expression alone indicates that perturbation of this pathway with agents such as Vismodegib, an inhibitor of Smoothened (SMO), should be examined in future clinical trials. PMID:25482929

  8. Molecular cytogenetic analysis of formalin-fixed, paraffin-embedded solid tumors by comparative genomic hybridization after universal DNA-amplification.

    Science.gov (United States)

    Speicher, M R; du Manoir, S; Schröck, E; Holtgreve-Grez, H; Schoell, B; Lengauer, C; Cremer, T; Ried, T

    1993-11-01

    We present a technique which allows the detection and chromosomal localization of DNA sequence copy number changes in solid tumor genomes from frozen sections and paraffin embedded, formalin fixed specimens. Based on comparative genomic hybridization and on universal DNA amplification procedures this technique is possible even if only a few tumor cells are available. We demonstrate the feasibility of this method to visualize complete and partial chromosome gains and losses and gene amplifications in archived solid tumor samples. PMID:8281155

  9. A novel method for sample preparation of fresh lung cancer tissue for proteomics analysis by tumor cell enrichment and removal of blood contaminants

    Directory of Open Access Journals (Sweden)

    Orre Lotta

    2010-02-01

    Full Text Available Abstract Background In-depth proteomics analyses of tumors are frequently biased by the presence of blood components and stromal contamination, which leads to large experimental variation and decreases the proteome coverage. We have established a reproducible method to prepare freshly collected lung tumors for proteomics analysis, aiming at tumor cell enrichment and reduction of plasma protein contamination. We obtained enriched tumor-cell suspensions (ETS from six lung cancer cases (two adenocarcinomas, two squamous-cell carcinomas, two large-cell carcinomas and from two normal lung samples. The cell content of resulting ETS was evaluated with immunocytological stainings and compared with the histologic pattern of the original specimens. By means of a quantitative mass spectrometry-based method we evaluated the reproducibility of the sample preparation protocol and we assessed the proteome coverage by comparing lysates from ETS samples with the direct lysate of corresponding fresh-frozen samples. Results Cytological analyses on cytospin specimens showed that the percentage of tumoral cells in the ETS samples ranged from 20% to 70%. In the normal lung samples the percentage of epithelial cells was less then 10%. The reproducibility of the sample preparation protocol was very good, with coefficient of variation at the peptide level and at the protein level of 13% and 7%, respectively. Proteomics analysis led to the identification of a significantly higher number of proteins in the ETS samples than in the FF samples (244 vs 109, respectively. Albumin and hemoglobin were among the top 5 most abundant proteins identified in the FF samples, showing a high contamination with blood and plasma proteins, whereas ubiquitin and the mitochondrial ATP synthase 5A1 where among the top 5 most abundant proteins in the ETS samples. Conclusion The method is feasible and reproducible. We could obtain a fair enrichment of cells but the major benefit of the method

  10. Digital PCR analysis of plasma cell-free DNA for non-invasive detection of drug resistance mechanisms in EGFR mutant NSCLC: Correlation with paired tumor samples

    Science.gov (United States)

    Ishii, Hidenobu; Azuma, Koichi; Sakai, Kazuko; Kawahara, Akihiko; Yamada, Kazuhiko; Tokito, Takaaki; Okamoto, Isamu; Nishio, Kazuto; Hoshino, Tomoaki

    2015-01-01

    As the development of resistance to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) has become an issue of concern, identification of the mechanisms responsible has become an urgent priority. However, for research purposes, it is not easy to obtain tumor samples from patients with EGFR mutation-positive non-small-cell lung cancer (NSCLC) that has relapsed after treatment with EGFR-TKIs. Here, using digital PCR assay as an alternative and noninvasive method, we examined plasma and tumor samples from patients with relapsed NSCLC to establish the inter-relationships existing among T790M mutation, activating EGFR mutations, HER2 amplification, and MET amplification. Paired samples of tumor and blood were obtained from a total of 18 patients with NSCLC after they had developed resistance to EGFR-TKI treatment, and the mechanisms of resistance were analyzed by digital PCR. Digital PCR analysis of T790M mutation in plasma had a sensitivity of 81.8% and specificity of 85.7%, the overall concordance between plasma and tissue samples being 83.3%. MET gene copy number gain in tumor DNA was observed by digital PCR in three patients, of whom one exhibited positivity for MET amplification by FISH, whereas no patient demonstrated MET and HER2 copy number gain in plasma DNA. Digital PCR analysis of plasma is feasible and accurate for detection of T790M mutation in NSCLC that becomes resistant to treatment with EGFR-TKIs. PMID:26334838

  11. Intra-tumoral Heterogeneity of KRAS and BRAF Mutation Status in Patients with Advanced Colorectal Cancer (aCRC and Cost-Effectiveness of Multiple Sample Testing

    Directory of Open Access Journals (Sweden)

    Susan D. Richman

    2011-01-01

    Full Text Available KRAS mutation status is established as a predictive biomarker of benefit from anti-EGFr therapies. Mutations are normally assessed using DNA extracted from one formalin-fixed, paraffin-embedded (FFPE tumor block. We assessed heterogeneity of KRAS and BRAF mutation status intra-tumorally (multiple blocks from the same primary tumor. We also investigated the utility and efficiency of genotyping a ‘DNA cocktail’ prepared from multiple blocks. We studied 68 consenting patients in two randomized clinical trials. DNA was extracted, from ≥2 primary tumor FFPE blocks per patient. DNA was genotyped by pyrosequencing for KRAS codons 12, 13 and 61 and BRAF codon 600. In patients with heterogeneous mutation status, DNA cocktails were prepared and genotyped. Among 69 primary tumors in 68 patients, 7 (10.1% showed intratumoral heterogeneity; 5 (7.2% at KRAS codons 12, 13 and 2 (2.9% at BRAF codon 600. In patients displaying heterogeneity, the relevant KRAS or BRAF mutation was also identified in ‘DNA cocktail’ samples when including DNA from mutant and wild-type blocks. Heterogeneity is uncommon but not insignificant. Testing DNA from a single block will wrongly assign wild-type status to 10% patients. Testing more than one block, or preferably preparation of a ‘DNA cocktail’ from two or more tumor blocks, improves mutation detection at minimal extra cost.

  12. BPA uptake does not correlate with LAT1 and Ki67 expressions in tumor samples (results of EORTC trial 11001)

    International Nuclear Information System (INIS)

    The system L-amino acid transporter (LAT1) imports p-boronophenylalanine (BPA) mainly into proliferating cells. This study investigates in three tumor entities whether the proportion of tumor cells expressing LAT1 and/or Ki67 correlates with BPA uptake. Tumors were analyzed for 10B concentration with prompt gamma-ray spectroscopy and for Ki67 and LAT1 expressions with immunohistochemical methods. The proportion of LAT1-expressing cells was much higher (5–90%) than that of Ki67-expressing cells (0–20%) and cells expressing both Ki67 and LAT1 (0–5%). Neither LAT1 nor Ki67 expression predicted BPA uptake.

  13. Pituitary Tumors

    Science.gov (United States)

    ... Tumors Oligoastrocytoma Oligodendroglioma Pineal Tumor Pituitary Tumor PNET Schwannoma Risk Factors Brain Tumor Facts Brain Tumor Dictionary ... Tumors Oligoastrocytoma Oligodendroglioma Pineal Tumor Pituitary Tumor PNET Schwannoma Risk Factors Brain Tumor Facts Brain Tumor Dictionary ...

  14. Performing Archives/Archives of Performance

    DEFF Research Database (Denmark)

    Performing Archives/Archives of Performance contributes to the ongoing critical discussions of performance and its disappearance, of the ephemeral and its reproduction, of archives and mediatized recordings of liveness. The many contributions by excellent scholars and artists from a broad range...... of interdisciplinary fields as well as from various locations in research geographies demonstrate that despite the extensive discourse on the relationship between performance and the archive, inquiry into the productive tensions between ephemerality and permanence is by no means outdated or exhausted. New ways...... of understanding archives, history, and memory emerge and address theories of enactment and intervention, while concepts of performance constantly proliferate and enable a critical focus on archival residue. The contributions in Performing Archives/Archives of Performance cover philosophical inquiries as well...

  15. Digital PCR analysis of plasma cell-free DNA for non-invasive detection of drug resistance mechanisms in EGFR mutant NSCLC: Correlation with paired tumor samples

    OpenAIRE

    Ishii, Hidenobu; Azuma, Koichi; Sakai, Kazuko; KAWAHARA, AKIHIKO; Yamada, Kazuhiko; Tokito, Takaaki; Okamoto, Isamu; Nishio, Kazuto; Hoshino, Tomoaki

    2015-01-01

    As the development of resistance to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) has become an issue of concern, identification of the mechanisms responsible has become an urgent priority. However, for research purposes, it is not easy to obtain tumor samples from patients with EGFR mutation-positive non-small-cell lung cancer (NSCLC) that has relapsed after treatment with EGFR-TKIs. Here, using digital PCR assay as an alternative and noninvasive method, we examin...

  16. Quantification analysis of the expression of tumor-associated proteins in serum samples from patients with ovarian cancer and those with other tumor location. Possibilities of their use in the diagnosis and estimation of the extent of a tumorous process

    Directory of Open Access Journals (Sweden)

    T. S. Bobrova

    2012-01-01

    Full Text Available The specific features of the expression of tumor-associated proteins (TAP were immunologically studied in the sera of patients with ovarian cancer (OC and other tumor location by means of immune sera (As or monoclonal antibodies (MAb to find out whether they could be used to diagnose and estimate the extent of a tumorous process.MAb 1 (to HEp-2 cell membrane proteins, larynx cancer, Ac4 (to a pool of two ovarian cystadenocarcinomas, and MAb 3 (to affinity-pu- rified proteins of the apparently intact human gastric mucosa were used to examine the sera of patients with OC and other tumor location and positive responsiveness was detected in 82, ~100, and 77 % of cases, respectively. The differences in the expression of TAP in the patients versus healthy donors were shown to be statistically significant (p = 0.0001; p = 0.015; p = 0.01, respectively.The sensitivity of quantifying ELISA in detecting TAP was 78 and 85 % in patients with Stages I–II and III–IV OC, respectively; ~100 and 89 % in patients with breast cancer and in those with gastrointestinal tract cancer, respectively; and 60 and 14 % in patients with lymphopro- liferative diseases and healthy donors, respectively. Comparison of TAP detection rates in the authors’ test systems with multiplex testing with a biochip array of 12 tumor markers has shown that these test systems are at the world standard level.

  17. A New Method For Robust High-Precision Time-Series Photometry From Well-Sampled Images: Application to Archival MMT/Megacam Observations of the Open Cluster M37

    CERN Document Server

    Chang, S -W; Hartman, J D

    2015-01-01

    We introduce new methods for robust high-precision photometry from well-sampled images of a non-crowded field with a strongly varying point-spread function. For this work, we used archival imaging data of the open cluster M37 taken by MMT 6.5m telescope. We find that the archival light curves from the original image subtraction procedure exhibit many unusual outliers, and more than 20% of data get rejected by the simple filtering algorithm adopted by early analysis. In order to achieve better photometric precisions and also to utilize all available data, the entire imaging database was re-analyzed with our time-series photometry technique (Multi-aperture Indexing Photometry) and a set of sophisticated calibration procedures. The merit of this approach is as follows: we find an optimal aperture for each star with a maximum signal-to-noise ratio, and also treat peculiar situations where photometry returns misleading information with more optimal photometric index. We also adopt photometric de-trending based on ...

  18. Reference Services in Archives.

    Science.gov (United States)

    Whalen, Lucille; And Others

    1986-01-01

    This 16-article issue focuses on history, policy, services, users, organization, evaluation, and automation of the archival reference process. Collections at academic research libraries, a technical university, Board of Education, business archives, a bank, labor and urban archives, a manuscript repository, religious archives, and regional history…

  19. Archives and the computer

    CERN Document Server

    Cook, Michael Garnet

    1980-01-01

    Archives and the Computer deals with the use of the computer and its systems and programs in archiving data and other related materials. The book covers topics such as the scope of automated systems in archives; systems for records management, archival description, and retrieval; and machine-readable archives. The book also features examples of systems for records management from different institutions such as theTyne and Wear Archive Department, Dyfed Record Office, and the University of Liverpool. Included in the last part are appendices. Appendix A is a directory of archival systems, Appen

  20. Archives and the computer

    CERN Document Server

    Cook, Michael Garnet

    1986-01-01

    Archives and the Computer deals with the use of the computer and its systems and programs in archiving data and other related materials. The book covers topics such as the scope of automated systems in archives; systems for records management, archival description, and retrieval; and machine-readable archives. The selection also features examples of archives from different institutions such as the University of Liverpool, Berkshire County Record Office, and the National Maritime Museum.The text is recommended for archivists who would like to know more about the use of computers in archiving of

  1. Genetic Sample Inventory - NRDA

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This database archives genetic tissue samples from marine mammals collected in the North-Central Gulf of Mexico from 2010-2015. The collection includes samples from...

  2. Genetic Sample Inventory

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This database archives genetic tissue samples from marine mammals collected primarily from the U.S. east coast. The collection includes samples from field programs,...

  3. HEASARC Software Archive

    Science.gov (United States)

    White, Nicholas (Technical Monitor); Murray, Stephen S.

    2003-01-01

    's HEADCC meeting was to make the ds9 image display program the primary vehicle for displaying line graphics (as well as images). The first step required to make this possible was to enhance the line graphics capabilities of ds9. SAO therefore spent considerable effort upgrading ds9 to use Tcl 8.4 so that the BLT line graphics package could be built and imported into ds9 from source code, rather than from a pre-built (and generally outdated) shared library. This task, which is nearly complete, allows us to extend BLT as needed for the HEAD community. Following HEADCC discussion concerning archiving and the display of archived data, we extended ds9 to support full access to many astronomical Web-based archives sites, including HEASARC, MAST, CHANDRA, SKYVIEW, ADS, NED, SIMBAD, IRAS, NVRO, SAO TDC, and FIRST. Using ds9's new internal Web access capabilities, these archives can be accessed via their Web page. FITS images, plots, spectra, and journal abstracts can be referenced, down-loaded, and displayed directly and easily in ds9. For more information, see: http://hea-www.harvard.edu/saord/ds9. Also after the HEADCC discussion concerning region filtering, we extended the Funtools sample implementation of region filtering as described in: http://hea-www.harvard.edu/saord/funtools/regions.html. In particular, we added several new composite regions for event and image filtering, including elliptical and box annuli. We also extended the panda (Pie AND Annulus) region support to include box pandas and elliptical pandas. These new composite regions are especially useful in programs that need to count photons in each separate region using only a single pass through the data. Support for these new regions was added to ds9. In the same vein, we developed new region support for filtering images using simple FITS image masks, i.e. 8-bit or 16-bit FITS images where the value of a pixel is the region id number for that pixel. Other important enhancements to DS9 this year, include supporor

  4. Analytical Validation of AmpliChip p53 Research Test for Archival Human Ovarian FFPE Sections.

    Directory of Open Access Journals (Sweden)

    Matthew J Marton

    Full Text Available The p53 tumor suppressor gene (TP53 is reported to be mutated in nearly half of all tumors and plays a central role in genome integrity. Detection of mutations in p53 can be accomplished by many assays, including the AmpliChip p53 Research Test. The AmpliChip p53 Research Test has been successfully used to determine p53 status in hematologic malignancies and fresh frozen solid tissues but there are few reports of using the assay with formalin fixed, paraffin-embedded (FFPE tissue. The objective of this study was to describe analytical performance characterization of the AmpliChip p53 Research Test to detect p53 mutations in genomic DNA isolated from archival FFPE human ovarian tumor tissues. Method correlation with sequencing showed 96% mutation-wise agreement and 99% chip-wise agreement. We furthermore observed 100% agreement (113/113 of the most prevalent TP53 mutations. Workflow reproducibility was 96.8% across 8 samples, with 2 operators, 2 reagent lots and 2 instruments. Section-to-section reproducibility was 100% for each sample across a 60 μm region of the FFPE block from ovarian tumors. These data indicate that the AmpliChip p53 Research Test is an accurate and reproducible method for detecting mutations in TP53 from archival FFPE human ovarian specimens.

  5. National Archives Catalog and API

    Data.gov (United States)

    National Archives and Records Administration — The National Archives Catalog is the online catalog of NARA's nationwide holdings in the Washington, DC area, Regional Archives, and Presidential Libraries.

  6. The Dora Lange Archive

    DEFF Research Database (Denmark)

    Holm, Isak Winkel; Bjering, Jens Christian Borrebye

    2016-01-01

    The first season of Nic Pizzolatto's True Detective (2014) is not only a show about a murder, but also a show about how to gather and organize information in an archive. Having identified two archival problems—its temporal and topical extension—the article turns to Jacques Derrida's Archive Fever......: a Freudian Impression in order to explain how the archiving problems of the crime investigation are, in fact, intrinsic to any archiving practice. Lastly, the article addresses the political significance of the show's archiving problems by help of Derrida's text on the American Constitution and of Hardt...

  7. Archive of Geosample Data and Information from the University of Rhode Island (URI) Graduate School of Oceanography (GSO), Marine Geological Samples Laboratory (MGSL)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Marine Geological Samples Laboratory (MGSL) of the Graduate School of Oceanography (GSO), University of Rhode Island is a partner in the Index to Marine and...

  8. The NEON Soil Archive - A community resource

    Science.gov (United States)

    Ayres, E.

    2013-12-01

    The National Ecological Observatory Network (NEON) is a 30-year National Science Foundation-funded facility for understanding and forecasting the impacts of climate change, land use change, and invasive species on aspects of continental-scale ecology such as biodiversity, biogeochemistry, infectious diseases, and ecohydrology. NEON will measure a wide range of properties at 60 terrestrial and 36 aquatic sites throughout the US using in situ sensors, sample collection/lab analysis, and remote sensing, and all data will be made freely available. The Observatory is currently under construction and will be fully operational by 2017, however, limited data collection and release will begin in 2013. In addition, NEON is archiving large numbers of samples, including surface soils (top ~30 cm) collected from locations across each site, and soils collected by horizon to 2 m deep from a single soil pit at each site. Here I present information about the latter, focusing on sampling and processing, metadata, and currently available samples. At each terrestrial site the soil pit is dug in the locally dominant soil type and soil is collected by horizon, mixed, and ~4-8 liters soil is sent for processing. Soil samples are air-dried and sieved (mineral soil) or air-dried (organic soil) and 1.2 kg is split between 4 glass jars for archiving (protocol available upon request). To date 15 soil pits have been sampled, representing 7 soil orders, and soils from 110 horizons have been archived or are being processed. Metadata associated with each archive sample include a soil profile description, photos, and soil properties (total C, N, S, Al, Ca, Fe, K, Mg, Mn, Na, P, Si, Sr, Ti, Zr, bulk density, pH, and texture). The procedure for requesting samples from the archive is under development and I encourage scientists to use the archive in their future research. Collecting and processing samples for the NEON Soil Archive

  9. Technical innovation in dynamic contrast-enhanced magnetic resonance imaging of musculoskeletal tumors: an MR angiographic sequence using a sparse k-space sampling strategy

    International Nuclear Information System (INIS)

    We demonstrate the clinical use of an MR angiography sequence performed with sparse k-space sampling (MRA), as a method for dynamic contrast-enhanced (DCE)-MRI, and apply it to the assessment of sarcomas for treatment response. Three subjects with sarcomas (2 with osteosarcoma, 1 with high-grade soft tissue sarcomas) underwent MRI after neoadjuvant therapy/prior to surgery, with conventional MRI (T1-weighted, fluid-sensitive, static post-contrast T1-weighted sequences) and DCE-MRI (MRA, time resolution = 7-10 s, TR/TE 2.4/0.9 ms, FOV 40 cm2). Images were reviewed by two observers in consensus who recorded image quality (1 = diagnostic, no significant artifacts, 2 = diagnostic, 75 % with good response, >75 % with poor response). DCE-MRI findings were concordant with histological response (arterial enhancement with poor response, no arterial enhancement with good response). Unlike conventional DCE-MRI sequences, an MRA sequence with sparse k-space sampling is easily integrated into a routine musculoskeletal tumor MRI protocol, with high diagnostic quality. In this preliminary work, tumor enhancement characteristics by DCE-MRI were used to assess treatment response. (orig.)

  10. Rationale and Methods for Archival Sampling and Analysis of Atmospheric Trace Chemical Contaminants On Board Mir and Recommendations for the International Space Station

    Science.gov (United States)

    Perry, J. L.; James, J. T.; Cole, H. E.; Limero, T. F.; Beck, S. W.

    1997-01-01

    Collection and analysis of spacecraft cabin air samples are necessary to assess the cabin air quality with respect to crew health. Both toxicology and engineering disciplines work together to achieve an acceptably clean cabin atmosphere. Toxicology is concerned with limiting the risk to crew health from chemical sources, setting exposure limits, and analyzing air samples to determine how well these limits are met. Engineering provides the means for minimizing the contribution of the various contaminant generating sources by providing active contamination control equipment on board spacecraft and adhering to a rigorous material selection and control program during the design and construction of the spacecraft. A review of the rationale and objectives for sampling spacecraft cabin atmospheres is provided. The presently-available sampling equipment and methods are reviewed along with the analytical chemistry methods employed to determine trace contaminant concentrations. These methods are compared and assessed with respect to actual cabin air quality monitoring needs. Recommendations are presented with respect to the basic sampling program necessary to ensure an acceptably clean spacecraft cabin atmosphere. Also, rationale and recommendations for expanding the scope of the basic monitoring program are discussed.

  11. Detection of microRNAs in archival cytology urine smears.

    Directory of Open Access Journals (Sweden)

    Francesca Simonato

    Full Text Available MicroRNAs' dysregulation and profiling have been demonstrated to be clinically relevant in urothelial carcinoma (UC. Urine cytology is commonly used as the mainstay non-invasive test for secondary prevention and follow-up of UC patients. Ancillary tools are needed to support cytopathologists in the diagnosis of low-grade UC. The feasibility and reliability of microRNAs profiling by qRT-PCR analysis (miR-145 and miR-205 in archival routine urine cytology smears (affected by fixation/staining [Papanicolau] and room temperature storage was tested in a series of 15 non-neoplastic and 10 UC urine specimens. Only samples with >5,000 urothelial cells and with <50% of inflammatory cells/red blood cells clusters were considered. Overall, a satisfactory amount of total RNA was obtained from all the considered samples (mean 1.27±1.43 µg, range 0.06-4.60 µg. Twenty nanograms of total RNA have been calculated to be the minimal total RNA concentration for reliable and reproducible miRNAs expression profiling analysis of archival cytological smears (slope= -3.4084; R-squared=0.99; efficiency=1.94. miR-145 and miR-205 were significantly downregulated in UC samples in comparison to non-tumor controls. These findings demonstrate that urine archival cytology smears are suitable for obtaining high-quality RNA to be used in microRNAs expression profiling. Further studies should investigate if miRNAs profiling can be successfully translated into clinical practice as diagnostic or prognostic markers.

  12. Archives Library Information Center

    Data.gov (United States)

    National Archives and Records Administration — ALIC is an online library catalog of books, periodicals, and other materials contained in Archives I and II and book collections located in other facilities.

  13. Retrospective analysis of oral peripheral nerve sheath tumors in Brazilians

    Directory of Open Access Journals (Sweden)

    Juliana Tito Salla

    2009-03-01

    Full Text Available Traumatic neuroma, neurofibroma, neurilemmoma, palisaded encapsulated neuroma and malignant peripheral nerve sheath tumor (MPNST are peripheral nerve sheath tumors and present neural origin. The goal of this study was to describe the epidemiological data of oral peripheral nerve sheath tumors in a sample of the Brazilian population. Biopsies requested from the Oral Pathology Service, School of Dentistry, Federal University of Minas Gerais (MG, Brazil, between 1966 and 2006 were evaluated. Lesions diagnosed as peripheral nerve sheath tumors were submitted to morphologic and to immunohistochemical analyses. All cases were immunopositive to the S-100 protein. Thirty-five oral peripheral nerve sheath tumors were found, representing 0.16% of all lesions archived in the Oral Pathology Service. Traumatic neuroma (15 cases most frequently affected the mental foramen. Solitary neurofibroma (10 cases was more frequently observed in the palate. Neurofibroma associated with neurofibromatosis type I (2 cases was observed in the gingival and alveolar mucosa. Neurilemmoma (4 cases was more commonly observed in the buccal mucosa. Malignant peripheral nerve sheath tumors (3 cases occurred in the mandible, palate, and tongue. Palisaded encapsulated neuroma (1 case occurred in the buccal mucosa. The data confirmed that oral peripheral nerve sheath tumors are uncommon in the oral region, with some lesions presenting a predilection for a specific gender or site. This study may be useful in clinical dentistry and oral pathology practice and may be used as baseline data regarding oral peripheral nerve sheath tumors in other populations.

  14. MOUSE SKIN TUMOR INITIATION-PROMOTION AND COMPLETE CARCINOGENESIS BIOASSAYS: MECHANISMS AND BIOLOGICAL ACTIVITIES OF EMISSION SAMPLES

    Science.gov (United States)

    Extracts of soots obtained from various sources were applied to the skin of mice in an effort to identify carcinogens in these mixtures and to link these materials to the etiology of human cancer. Samples of coal chimney soot, coke oven materials, industrial carbon black, oil sha...

  15. My Dream Archive

    Science.gov (United States)

    Phelps, Christopher

    2007-01-01

    In this article, the author shares his experience as he traveled from island to island with a single objective--to reach the archives. He found out that not all archives are the same. In recent months, his daydreaming in various facilities has yielded a recurrent question on what would constitute the Ideal Archive. What follows, in no particular…

  16. Calorimeter Process Variable Archiving

    Energy Technology Data Exchange (ETDEWEB)

    Huffman, David; /Fermilab

    2002-01-14

    These steps were taken to maintain weekly archives: (1) Friday morning you stop the archiver and wait for it to finish writing data (the lock file will be removed from the directory); (2) move the current archive information to a PC via FTP; (3) remove all previous archive information in the previous directory; (4) move the current archive into the previous directory; (5) start a new archive; (6) burn a CDROM of the archive; and (7) copy the current archive to a specific directory. There are 2 ways to check if the Calorimeter Archiver is running, either through the WEB based front end or directly from a command line. Once the archiver is running it can be monitored from a WEB page. This only works with a browser launched from the online machine running the archiver. Each time the browser is reloaded there should be an update reported in the last write check field. You might have to wait a few minutes to see the update. Calorimetry currently takes readings every (300 sec.) 5 minutes. The second method to verify the archiver is running is to issue a command from a Linux cluster machine.

  17. Mouse skin tumor initiation-promotion and complete carcinogenesis bioassays: mechanisms and biological activities of emission samples.

    OpenAIRE

    Nesnow, S; Triplett, L L; Slaga, T J

    1983-01-01

    Extracts of soots obtained from various sources were applied to the skin of mice in an effort to identify carcinogens in these mixtures and to link these materials to the etiology of human cancer. Samples of coal chimney soot, coke oven materials, industrial carbon black, oil shale soot, and gasoline vehicle exhaust materials have been examined by this method. The studies reported here have been constructed to compare the carcinogenic and tumorigenic potency of extracts from various particula...

  18. Genotype Data (Phase III) - D-HaploDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us D-HaploDB Gen ... Essentially the same as described in Kukita et al. paper ... (2010), except that two additional samples (CHM010 ...

  19. The Brightest Galaxies at Cosmic Dawn: Securing the Largest Samples of z=9-11 galaxies for JWST by leveraging the HST archive with Spitzer/IRAC.

    Science.gov (United States)

    Bouwens, Rychard; Trenti, Michele; Calvi, Valentina; Bernard, Stephanie; Labbe, Ivo; Oesch, Pascal; Coe, Dan; Holwerda, Benne; Bradley, Larry; Mason, Charlotte; Schmidt, Kasper; Illingworth, Garth

    2015-10-01

    Hubble's WFC3 has been a game changer for studying early galaxy formation in the first 700 Myr after the Big Bang. Reliable samples of sources up to z~10, which can be discovered only from space, are now constraining the evolution of the galaxy luminosity function into the epoch of reionization. Despite these efforts, the size of the highest redshift galaxy samples (z >9 and especially z > 10) is still very small, particularly at high luminosities (L > L*). To deliver transformational results, much larger numbers of bright z > 9 galaxies are needed both to map out the bright end of the luminosity/mass function and for spectroscopic follow-up (with JWST and otherwise). One especially efficient way of expanding current samples is (1) to leverage the huge amounts of pure-parallel data available with HST to identify large numbers of candidate z ~ 9 - 11 galaxies and (2) to follow up each candidate with shallow Spitzer/IRAC observations to distinguish the bona- fide z ~ 9 - 11 galaxies from z ~ 2 old, dusty galaxies. For this program we are requesting shallow Spitzer/IRAC follow-up of 20 candidate z ~ 9 - 11 galaxies we have identified from 130 WFC3/IR pointings obtained from more than 4 separate HST programs with no existing IRAC coverage. Based on our previous CANDELS/GOODS searches, we expect to confirm 5 to 10 sources as L > L* galaxies at z >= 9. Our results will be used to constrain the bright end of the LF at z >= 9, to provide targets for Keck spectroscopy to constrain the ionization state of the z > 8 universe, and to furnish JWST with bright targets for spectroscopic follow-up studies.

  20. Introduction: Consider the Archive.

    Science.gov (United States)

    Yale, Elizabeth

    2016-03-01

    In recent years, historians of archives have paid increasingly careful attention to the development of state, colonial, religious, and corporate archives in the early modern period, arguing that power (of various kinds) was mediated and extended through material writing practices in and around archives. The history of early modern science, likewise, has tracked the production of scientific knowledge through the inscription and circulation of written records within and between laboratories, libraries, homes, and public spaces, such as coffeehouses and bookshops. This Focus section interrogates these two bodies of scholarship against each other. The contributors ask how archival digitization is transforming historical practice; how awareness of archival histories can help us to reconceptualize our work as historians of science; how an archive's layered purposes, built up over centuries of record keeping, can shape the historical narratives we write; and how scientific knowledge emerging from archives gained authority and authenticity. PMID:27197412

  1. Development and evaluation of loop-mediated isothermal amplification (LAMP) for the rapid diagnosis of Penicillium marneffei in archived tissue samples.

    Science.gov (United States)

    Sun, Jiufeng; Li, Xiqing; Zeng, Hanxiang; Xie, Zhi; Lu, Changming; Xi, Liyan; de Hoog, Gert S

    2010-04-01

    Penicillium marneffei is the etiologic agent of a severe systemic disease in immunocompromised hosts in Southeast Asia. In the present study, a novel method, known as loop-mediated isothermal amplification (LAMP), is described for the rapid and specific detection of the species, using a primer set derived from the internal transcribed spacer (ITS) region of the rRNA gene. Amplification products can be detected macroscopically by visual inspection in vials using SYBR Green I as well as by electrophoresis on agarose gel. The LAMP assay resulted in specific amplification of P. marneffei ITS using pure cultures after a 1-h reaction at 65 degrees C in a water bath; no cross-reactivity with other fungi including other biverticillate penicillia was observed. The detectable DNA limit was two copies. In addition, specific amplification was achieved using paraffin wax-embedded tissue samples from patients with penicilliosis marneffei and tissue samples from bamboo rats. The method provides a powerful tool for rapid diagnostics in the clinical lab, and has potential for use in ecological studies. PMID:20113352

  2. A high-performance liquid chromatographic assay for determination of cisplatin in plasma, cancer cell, and tumor samples.

    Science.gov (United States)

    Lopez-Flores, A; Jurado, R; Garcia-Lopez, P

    2005-01-01

    A method for determination of cis-diaminedichloroplatinum (II) (cisplatin) in ultrafiltered plasma, cell, and tumour samples is described. Cisplatin separation was carried out on a reversed-phase column using methanol-acetonitrile-water as the mobile phase. The flow rate was maintained constant at 1.6 mL/min and analysis was performed at 23 degrees C. Detection was carried out by absorbance at 254 nm. The method was linear in the range of 0.2-10 microg/mL, and the coefficients of variation were accumulation of cisplatin in cancer cells and in tumours of mice receiving treatment with cisplatin and evaluated the pharmacokinetics of cisplatin in nu/nu mice after intraperitoneal (i.p.) administration. The method proved to be adequate for measuring cisplatin both in vitro and in vivo and could be suitable for studies of cisplatin pharmacokinetics in animal models. PMID:16112590

  3. Automated solid-phase extraction for the determination of polybrominated diphenyl ethers and polychlorinated biphenyls in serum--application on archived Norwegian samples from 1977 to 2003.

    Science.gov (United States)

    Thomsen, Cathrine; Liane, Veronica Horpestad; Becher, Georg

    2007-02-01

    An analytical method comprised of automated solid-phase extraction and determination using gas chromatography mass spectrometry (single quadrupole) has been developed for the determination of 12 polybrominated diphenyl ethers (PBDEs), 26 polychlorinated biphenyls (PCBs), two organochlorine compounds (OCs) (hexachlorobenzene and octachlorostyrene) and two brominated phenols (pentabromophenol, and tetrabromobisphenol-A (TBBP-A)). The analytes were extracted using a sorbent of polystyrene-divinylbenzene and an additional clean-up was performed on a sulphuric acid-silica column to remove lipids. The method has been validated by spiking horse serum at five levels. The mean accuracy given as recovery relative to internal standards was 95%, 99%, 93% and 109% for the PBDEs PCBs, OCs and brominated phenols, respectively. The mean repeatability given as RSDs was respectively 6.9%, 8.7%, 7.5% and 15%. Estimated limits of detection (S/N=3) were in the range 0.2-1.8 pg/g serum for the PBDEs and phenols, and from 0.1 pg/g to 56 pg/g serum for the PCBs and OCs. The validated method has been used to investigate the levels of PBDEs and PCBs in 21 pooled serum samples from the general Norwegian population. In serum from men (age 40-50 years) the sum of seven PBDE congeners (IUPAC No. 28, 47, 99, 100, 153, 154 and 183) increased from 1977 (0.5 ng/g lipids) to 1998 (4.8 ng/g lipids). From 1999 to 2003 the concentration of PBDEs seems to have stabilised. On the other hand, the sum of five PCBs (IUPAC No. 101, 118, 138, 153 and 180) in these samples decreased steadily from 1977 (666 ng/g lipids) to 2003 (176 ng/g lipids). Tetrabromobisphenol-A and BDE-209 were detected in almost all samples, but no similar temporal trends to that seen for the PBDEs were observed for these compounds, which might be due to the short half-lives of these brominated flame retardants (FR) in humans. PMID:17023223

  4. Numerical and structural genomic aberrations are reliably detectable in tissue microarrays of formalin-fixed paraffin-embedded tumor samples by fluorescence in-situ hybridization.

    Directory of Open Access Journals (Sweden)

    Heike Horn

    Full Text Available Few data are available regarding the reliability of fluorescence in-situ hybridization (FISH, especially for chromosomal deletions, in high-throughput settings using tissue microarrays (TMAs. We performed a comprehensive FISH study for the detection of chromosomal translocations and deletions in formalin-fixed and paraffin-embedded (FFPE tumor specimens arranged in TMA format. We analyzed 46 B-cell lymphoma (B-NHL specimens with known karyotypes for translocations of IGH-, BCL2-, BCL6- and MYC-genes. Locus-specific DNA probes were used for the detection of deletions in chromosome bands 6q21 and 9p21 in 62 follicular lymphomas (FL and six malignant mesothelioma (MM samples, respectively. To test for aberrant signals generated by truncation of nuclei following sectioning of FFPE tissue samples, cell line dilutions with 9p21-deletions were embedded into paraffin blocks. The overall TMA hybridization efficiency was 94%. FISH results regarding translocations matched karyotyping data in 93%. As for chromosomal deletions, sectioning artefacts occurred in 17% to 25% of cells, suggesting that the proportion of cells showing deletions should exceed 25% to be reliably detectable. In conclusion, FISH represents a robust tool for the detection of structural as well as numerical aberrations in FFPE tissue samples in a TMA-based high-throughput setting, when rigorous cut-off values and appropriate controls are maintained, and, of note, was superior to quantitative PCR approaches.

  5. Opening the archives for state of the art tumour genetic research: sample processing for array-CGH using decalcified, formalin-fixed, paraffin-embedded tissue-derived DNA samples

    OpenAIRE

    Bovee Judith VMG; Hogendoorn Pancras CW; Meijer Danielle; Verbeke Sofie LJ; de Jong Danielle; Szuhai Károly

    2011-01-01

    Abstract Background Molecular genetic studies on rare tumour entities, such as bone tumours, often require the use of decalcified, formalin-fixed, paraffin-embedded tissue (dFFPE) samples. Regardless of which decalcification procedure is used, this introduces a vast breakdown of DNA that precludes the possibility of further molecular genetic testing. We set out to establish a robust protocol that would overcome these intrinsic hurdles for bone tumour research. Findings The goal of our study w...

  6. Effects of TGF-beta signalling inhibition with galunisertib (LY2157299) in hepatocellular carcinoma models and in ex vivo whole tumor tissue samples from patients.

    Science.gov (United States)

    Serova, Maria; Tijeras-Raballand, Annemilaï; Dos Santos, Célia; Albuquerque, Miguel; Paradis, Valerie; Neuzillet, Cindy; Benhadji, Karim A; Raymond, Eric; Faivre, Sandrine; de Gramont, Armand

    2015-08-28

    Galunisertib (LY2157299) is a selective ATP-mimetic inhibitor of TGF-β receptor (TβR)-I activation currently under clinical investigation in hepatocellular carcinoma (HCC) patients. Our study explored the effects of galunisertib in vitro in HCC cell lines and ex vivo on patient samples. Galunisertib was evaluated in HepG2, Hep3B, Huh7, JHH6 and SK-HEP1 cells as well as in SK-HEP1-derived cells tolerant to sorafenib (SK-Sora) and sunitinib (SK-Suni). Exogenous stimulation of all HCC cell lines with TGF-β yielded downstream activation of p-Smad2 and p-Smad3 that was potently inhibited with galunisertib treatment at micromolar concentrations. Despite limited antiproliferative effects, galunisertib yielded potent anti-invasive properties. Tumor slices from 13 patients with HCC surgically resected were exposed ex vivo to 1 µM and 10 µM galunisertib, 5 µM sorafenib or a combination of both drugs for 48 hours. Galunisertib but not sorafenib decreased p-Smad2/3 downstream TGF-β signaling. Immunohistochemistry analysis of galunisertib and sorafenib-exposed samples showed a significant decrease of the proliferative marker Ki67 and increase of the apoptotic marker caspase-3. In combination, galunisertib potentiated the effect of sorafenib efficiently by inhibiting proliferation and increasing apoptosis. Our data suggest that galunisertib may be active in patients with HCC and could potentiate the effects of sorafenib. PMID:26057634

  7. AFP mRNA level in enriched circulating tumor cells from hepatocellular carcinoma patient blood samples is a pivotal predictive marker for metastasis.

    Science.gov (United States)

    Jin, Junhua; Niu, Xiaojuan; Zou, Lihui; Li, Lin; Li, Shugang; Han, Jingli; Zhang, Peiying; Song, Jinghai; Xiao, Fei

    2016-08-01

    Circulating tumor cells (CTCs) quantification may be helpful for evaluating cancer dissemination, predicting prognosis and assessing therapeutic effectiveness and safety. In the present study, CTCs from blood samples of 72 patients with hepatocellular carcinoma (HCC) were enriched with anti-EpCAM nanoparticles. AFP mRNA level was detected by nested polymerase chain reaction (PCR) after enrichment of CTCs from HCC blood samples at 0, 3, 6, 9 and 12 months after hepatectomy, respectively. AFP mRNA expression in CTCs was positive in 43 patients (59.7%) and negative in 29 patients (40.3%) before hepatectomy. Among 43 patients with positive AFP mRNA expression in CTCs before hepatectomy, 10 and 11 were diagnosed as intrahepatic/extrahepatic metastasis before and after hepatectomy, respectively. In addition, these 21 patients with metastasis had persisting positive AFP mRNA of CTCs during the whole tested year. Specifically, 3 patients with AFP mRNA negative in CTCs before hepatectomy changed to be positive at 6 and 9 months, and 2 of them were diagnosed as metastasis 12 months after hepatectomy. We conclude that the positive AFP mRNA of CTCs can be a pivotal predictor for HCC metastasis before and after hepatectomy. The release of AFP expression from hepatocellular carcinoma cells into circulation must be a major source of HCC metastasis. PMID:27160647

  8. Data Archive Project

    OpenAIRE

    Kemppainen, Timo-Pekka

    2015-01-01

    In the modern world, digital data archiving and accessing is an issue that needs tailored solutions. This thesis gives one example of designing and implementing a data archiving solution using time tested technologies. Helsinki Metropolia University of Applied Sciences had a need to archive their contracts in digital format instead of using old file cabinets. Specifications were created together with the customer at the start of the project. The project was to produce a complete product fo...

  9. Nearline Web Archiving

    OpenAIRE

    Xie, Zhiwu; Nayyar, Krati; Fox, Edward A

    2016-01-01

    In this paper, we propose a modified approach to real­time transactional web archiving. It leverages the web caching infrastructure that is already prevalent on web servers. Instead of archiving web content at HTTP transaction time, in our approach the archiving happens when the cached copy expires and is about to be expunged. Before the deletion, all expired cache copies are combined and then sent to the web archive in small batches. Since the cache is purged at much lower frequency than HTT...

  10. The GTC Public Archive

    Science.gov (United States)

    Alacid, J. Manuel; Solano, Enrique

    2015-12-01

    The Gran Telescopio Canarias (GTC) archive is operational since November 2011. The archive, maintained by the Data Archive Unit at CAB in the framework of the Spanish Virtual Observatory project, provides access to both raw and science ready data and has been designed in compliance with the standards defined by the International Virtual Observatory Alliance (IVOA) to guarantee a high level of data accessibility and handling. In this presentation I will describe the main capabilities the GTC archive offers to the community, in terms of functionalities and data collections, to carry out an efficient scientific exploitation of GTC data.

  11. Inventing the Archive

    DEFF Research Database (Denmark)

    Eskildsen, Kasper Risbjerg

    2013-01-01

    This article investigates the emergence of the archive as the primary venue for the production of historical knowledge in the 19th century. The turn to archival research, the article argues, may be considered as a response to the discussions about the problems of testimony that dominated 18th......- and early 19th-century German writings on the methodology and epistemology of historical research. These discussions, especially regarding the epistemic virtues of witnesses, also helped create the particular culture of knowledge-making within German historical scholarship that enabled the archival turn...... of the 19th-century archival turn....

  12. Meteorological Archival Facility

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: The Bergen Data Center (BDC) provides data archival capability for meteorological and oceanographic data. DESCRIPTION: The BDC operates as a resource for...

  13. DCC Briefing Paper: Database archiving

    OpenAIRE

    Müller, Heiko

    2009-01-01

    In a computational context, data archiving refers to the storage of electronic documents, data sets, multimedia files, and so on, for a defined period of time. Database archiving is usually seen as a subset of data archiving. Database archiving focuses on archiving data that are maintained under the control of a database management system and structured under a database schema, e.g., a relational database. The primary goal of database archiving is to maintain access to data in case it is late...

  14. Unit 20 - GIS as Archives

    OpenAIRE

    Unit 03, CC in GIS; National Center for Geographic Information and Analysis (UC Santa Barbara, SUNY at Buffalo, University of Maine)

    1990-01-01

    This unit introduces the idea of a GIS database serving as a project or archive database, contrasting it with the traditional geographic archive, the map library. It discusses issues of data currency, justifying the need for digital geographic archives, suitability of data for archiving, platforms, distribution, user interface and costs vs. benefits of digital archives. It illustrates these issues with several examples of spatial data archive systems.

  15. Subject Access Points in the MARC Record and Archival Finding Aid: Enough or Too Many?

    Science.gov (United States)

    Cox, Elizabeth; Czechowski, Leslie

    2007-01-01

    In this research project, the authors set out to discover the current practice in both the archival and cataloging worlds for usage of access points in descriptive records and to learn how archival descriptive practices fit into long-established library cataloging procedures and practices. A sample of archival finding aids and MARC records at 123…

  16. PTCH 1 staining of pancreatic neuroendocrine tumor (PNET) samples from patients with and without multiple endocrine neoplasia (MEN-1) syndrome reveals a potential therapeutic target

    OpenAIRE

    Gurung, Buddha; Hua, Xianxin; Runske, Melissa; Bennett, Bonita; LiVolsi, Virginia; Roses, Robert; Fraker, Douglas A; Metz, David C.

    2014-01-01

    Pancreatic neuroendocrine tumors (PNETs) are rare, indolent tumors that may occur sporadically or develop in association with well-recognized hereditary syndromes, particularly multiple endocrine neoplasia type 1 (MEN-1). We previously demonstrated that the hedgehog (HH) signaling pathway was aberrantly up-regulated in a mouse model that phenocopies the human MEN-1 syndrome, Men1l/l;RipCre, and that inhibition of this pathway suppresses MEN-1 tumor cell proliferation. We hypothesized that the...

  17. Online archives of Science

    CERN Multimedia

    GS Department

    2009-01-01

    CERN Library has enabled till 26th June 2009 a trial access to the online archives of Science, starting in 1880. You are welcome to test this resource at http://www.sciencemag.org/archive/ Please contact mailto:Anne.Gentil-Beccot@cern.ch, for any feedback to share.

  18. Central nervous system tumors: a histopathological study

    OpenAIRE

    Kailash Chand Jat; S. P. Vyas; Naseem A. Bihari; Kuldeep Mehra

    2016-01-01

    Background: Brain tumors can originate in almost any type of tissue, cell or mixture of cell types in the brain or spinal cord. Tumors in different areas of the central nervous system may be treated differently and have a different prognosis. Methods: In the period between 2011-2015, we studied on 59 patients diagnosed with CNS tumors according to the World Health Organization's diagnostic criteria. Patient data were retrieved from the archives of the department of Pathology, Sardar Patel...

  19. Archiving the Relaxed Consistency Web

    OpenAIRE

    Xie, Zhiwu; Van de Sompel, Herbert; Liu, Jinyang; Van Reenen, Johann; Jordan, Ramiro

    2013-01-01

    The historical, cultural, and intellectual importance of archiving the web has been widely recognized. Today, all countries with high Internet penetration rate have established high-profile archiving initiatives to crawl and archive the fast-disappearing web content for long-term use. As web technologies evolve, established web archiving techniques face challenges. This paper focuses on the potential impact of the relaxed consistency web design on crawler driven web archiving. Relaxed consist...

  20. The Cancer Digital Slide Archive - TCGA

    Science.gov (United States)

    Dr. David Gutman and Dr. Lee Cooper developed The Cancer Digital Slide Archive (CDSA), a web platform for accessing pathology slide images of TCGA samples. Find out how they did it and how to use the CDSA website in this Case Study.

  1. DNA Ploidy Measured on Archived Pretreatment Biopsy Material May Correlate With Prostate-Specific Antigen Recurrence After Prostate Brachytherapy

    Energy Technology Data Exchange (ETDEWEB)

    Keyes, Mira, E-mail: mkeyes@bccancer.bc.ca [Radiation Oncology, Provincial Prostate Brachytherapy Program, Vancouver Cancer Centre, British Columbia Cancer Agency, Vancouver, British Columbia (Canada); MacAulay, Calum [Department of Integrative Oncology, British Columbia Cancer Research Centre, British Columbia Cancer Agency, Vancouver, British Columbia (Canada); Hayes, Malcolm [Department of Pathology, Vancouver Cancer Centre, British Columbia Cancer Agency, Vancouver, British Columbia (Canada); Korbelik, Jagoda [Department of Integrative Oncology, British Columbia Cancer Research Centre, British Columbia Cancer Agency, Vancouver, British Columbia (Canada); Morris, W. James [Radiation Oncology, Provincial Prostate Brachytherapy Program, Vancouver Cancer Centre, British Columbia Cancer Agency, Vancouver, British Columbia (Canada); Palcic, Branko [Department of Integrative Oncology, British Columbia Cancer Research Centre, British Columbia Cancer Agency, Vancouver, British Columbia (Canada)

    2013-08-01

    Purpose: To explore whether DNA ploidy of prostate cancer cells determined from archived transrectal ultrasound-guided biopsy specimens correlates with disease-free survival. Methods and Materials: Forty-seven failures and 47 controls were selected from 1006 consecutive low- and intermediate-risk patients treated with prostate {sup 125}I brachytherapy (July 1998-October 2003). Median follow-up was 7.5 years. Ten-year actuarial disease-free survival was 94.1%. Controls were matched using age, initial prostate-specific antigen level, clinical stage, Gleason score, use of hormone therapy, and follow-up (all P nonsignificant). Seventy-eight specimens were successfully processed; 27 control and 20 failure specimens contained more than 100 tumor cells were used for the final analysis. The Feulgen-Thionin stained cytology samples from archived paraffin blocks were used to determine the DNA ploidy of each tumor by measuring integrated optical densities. Results: The samples were divided into diploid and aneuploid tumors. Aneuploid tumors were found in 16 of 20 of the failures (80%) and 8 of 27 controls (30%). Diploid DNA patients had a significantly lower rate of disease recurrence (P=.0086) (hazard ratio [HR] 0.256). On multivariable analysis, patients with aneuploid tumors had a higher prostate-specific antigen failure rate (HR 5.13). Additionally, those with “excellent” dosimetry (V100 >90%; D90 >144 Gy) had a significantly lower recurrence rate (HR 0.25). All patients with aneuploid tumors and dosimetry classified as “nonexcellent” (V100 <90%; D90 <144 Gy) (5 of 5) had disease recurrence, compared with 40% of patients with aneuploid tumors and “excellent” dosimetry (8 of 15). In contrast, dosimetry did not affect the outcome for diploid patients. Conclusions: Using core biopsy material from archived paraffin blocks, DNA ploidy correctly classified the majority of failures and nonfailures in this study. The results suggest that DNA ploidy can be used as a

  2. DNA Ploidy Measured on Archived Pretreatment Biopsy Material May Correlate With Prostate-Specific Antigen Recurrence After Prostate Brachytherapy

    International Nuclear Information System (INIS)

    Purpose: To explore whether DNA ploidy of prostate cancer cells determined from archived transrectal ultrasound-guided biopsy specimens correlates with disease-free survival. Methods and Materials: Forty-seven failures and 47 controls were selected from 1006 consecutive low- and intermediate-risk patients treated with prostate 125I brachytherapy (July 1998-October 2003). Median follow-up was 7.5 years. Ten-year actuarial disease-free survival was 94.1%. Controls were matched using age, initial prostate-specific antigen level, clinical stage, Gleason score, use of hormone therapy, and follow-up (all P nonsignificant). Seventy-eight specimens were successfully processed; 27 control and 20 failure specimens contained more than 100 tumor cells were used for the final analysis. The Feulgen-Thionin stained cytology samples from archived paraffin blocks were used to determine the DNA ploidy of each tumor by measuring integrated optical densities. Results: The samples were divided into diploid and aneuploid tumors. Aneuploid tumors were found in 16 of 20 of the failures (80%) and 8 of 27 controls (30%). Diploid DNA patients had a significantly lower rate of disease recurrence (P=.0086) (hazard ratio [HR] 0.256). On multivariable analysis, patients with aneuploid tumors had a higher prostate-specific antigen failure rate (HR 5.13). Additionally, those with “excellent” dosimetry (V100 >90%; D90 >144 Gy) had a significantly lower recurrence rate (HR 0.25). All patients with aneuploid tumors and dosimetry classified as “nonexcellent” (V100 <90%; D90 <144 Gy) (5 of 5) had disease recurrence, compared with 40% of patients with aneuploid tumors and “excellent” dosimetry (8 of 15). In contrast, dosimetry did not affect the outcome for diploid patients. Conclusions: Using core biopsy material from archived paraffin blocks, DNA ploidy correctly classified the majority of failures and nonfailures in this study. The results suggest that DNA ploidy can be used as a useful

  3. Bone tumor

    Science.gov (United States)

    Tumor - bone; Bone cancer; Primary bone tumor; Secondary bone tumor ... The cause of bone tumors is unknown. They often occur in areas of the bone that grow rapidly. Possible causes include: Genetic defects ...

  4. Mariner 10 Image Archive

    Data.gov (United States)

    National Aeronautics and Space Administration — The Mariner 10 Image Archive includes tools to view shaded relief maps of the surface of Mercury, a 3D globe, and all images acquired by NASA's Mariner 10 mission.

  5. Emergency_RDS_ARCHIVE

    Data.gov (United States)

    Vermont Center for Geographic Information — Archive of past 9-1-1 data releases at rough yearly intervals chosen from availbable datasets from 1999 to present. For a historical overview on the genesis of this...

  6. The Digital Archive Experience

    DEFF Research Database (Denmark)

    Søndergaard, Morten

    2009-01-01

    This article, as well as the book, investigates the ways in which new digital media may enhance the experience of the art-archive. Taken as a whole, the new media is a vital component of a 'transdisciplinary' and transformative field, a cultural landscape that is changing rapidly the conditions...... and domains of the archive and the (art)museum. How, then, should the functions and strengths of both archive and museum be shaped to meet those cultural and technological changes? When the Internet and world wide web became 'the place to be' commercially, museums followed suit and established their own sites....... The book discusses the challenges of the archive and the (art)museum in the age of digital media. It is based upon documentation from a research project, MAP - Media Art Platform, that drew upon the talents and collaboration of many institutions, artists, programmers, art historians, designers and others...

  7. Sequence Read Archive (SRA)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome...

  8. Novel Molecular Tumor Cell Markers in Regional Lymph Nodes and Blood Samples from Patients Undergoing Surgery for Non-Small Cell Lung Cancer

    OpenAIRE

    Oddmund Nordgård; Gurpartap Singh; Steinar Solberg; Lars Jørgensen; Ann Rita Halvorsen; Rune Smaaland; Odd Terje Brustugun; Åslaug Helland

    2013-01-01

    INTRODUCTION: Recent evidence suggests that microscopic lymph node metastases and circulating tumor cells may have clinical importance in lung cancer. The purpose of this study was to identify new molecular markers for tumor cells in regional lymph nodes (LNs) and peripheral blood (PB) from patients with non-small cell lung cancer (NSCLC). METHODS: Candidate markers were selected based on digital transcript profiling and previous literature. KRT19, CEACAM5, EPCAM, DSG3, SFTPA, SFTPC and SFTPB...

  9. The Herschel Science Archive

    OpenAIRE

    Verdugo, Eva

    2015-01-01

    The Herschel mission required a Science Archive able to serve data to very different users: The own Data Analysis Software (both Pipeline and Interactive Analysis), the consortia of the different instruments and the scientific community. At the same time, the KP consortia were committed to deliver to the Herschel Science Centre,  the processed products corresponding to the data obtained as part of their Science Demonstration Phase and the Herschel Archive should include the capability to...

  10. Correlation of tumor-infiltrating lymphocytes to histopathological features and molecular phenotypes in canine mammary carcinoma: A morphologic and immunohistochemical morphometric study

    OpenAIRE

    Kim, Jong-Hyuk; Chon, Seung-Ki; Im, Keum-Soon; Kim, Na-Hyun; Sur, Jung-Hyang

    2013-01-01

    Abundant lymphocyte infiltration is frequently found in canine malignant mammary tumors, but the pathological features and immunophenotypes associated with the infiltration remain to be elucidated. The aim of the present study was to evaluate the relationship between lymphocyte infiltration, histopathological features, and molecular phenotype in canine mammary carcinoma (MC). The study was done with archived formalin-fixed, paraffin-embedded samples (n = 47) by histologic and immunohistochemi...

  11. FTP archives for physics

    International Nuclear Information System (INIS)

    We have established archives for programs, data, papers etc. in physics (mainly for plasma physics). The archives are located at computer ftp.muni.cz in the directory pub/muni.cz/physics. These archives can be reached by anonymous FTP or by gopher server gopher.muni.cz (147.251.4.33). At the present time, programs for PC, cross sections for electrons, swarm parameters and rate constants stored are in the archives. We would like to collect the programs for calculations in physics (mainly for PC). We suppose that each program should have a testing example and some description. We would also like to collect physical constants and experimental or theoretical data (e.g. cross sections, swarm parameters and rate constants), which are important for other calculation or for comparison with the results of others studies. Interested scholars are invited to sent us their programs, data, preprints and reports for these archives. All files in the archives are in public domain and can be obtained using computer network Internet

  12. Variation of the prognostic significance of HER-2 expression in breast cancer according to tumor size.

    Science.gov (United States)

    Swede, Helen; Moysich, Kirsten B; Winston, Janet S; Hurd, Thelma C; Edge, Stephen B; Romero-Gutierrez, Maritza; Brooks, John S J; Michalek, Arthur M

    2003-01-01

    The prognostic importance of HER-2 status in breast cancer has been investigated extensively, but findings have not been uniform across immunohistochemical studies using fixed, paraffin-embedded specimens. We speculate that studies with an overrepresentation of large tumors might not produce evidence for an independent effect of a single marker because breast tumors of larger size tend to exhibit multiple adverse attributes as the malignancy advances through the metastatic cascade. Further, it has been posited that results from certain studies of biologic markers might be generalizable only to larger tumors because tumor repositories tend to house a disproportionate number of larger tumors. To test our hypothesis that the prognostic effect of HER-2 status might be modified by the size of the tumor, we conducted a survival analysis of a nested case-case sample of 156 women diagnosed with primary breast cancer from 1983 to 1995. Relative risks (RRs) and confidence intervals (CIs) for recurrence in relation to HER-2 status were estimated using a multivariate Cox proportional hazards model. Immunohistochemistry of archival tissue was used to detect HER-2 expression. Positive HER-2 status was associated with recurrence (RR = 4.24, 95% CI 1.30-13.78) among patients with axillary lymph node-positive involvement. This analysis identified an interaction (p < 0.01) between tumor size and overexpression. Stratification by tumor size revealed an increased risk of recurrence associated with HER-2-positive tumors that were tumors larger than 2 cm. Eligible patients without available tumor tissue tended to have smaller tumors compared to study participants. Our results might partly explain the variation in evidence across HER-2 prognostic studies using fixed tissue and might apply to other putative markers of prognosis in breast cancer. PMID:12603382

  13. Expression of Cathepsin L in tumor cells and tumor-associated macrophages in patients with Ewing sarcoma family of tumors: A pilot study

    Directory of Open Access Journals (Sweden)

    Bivas Biswas

    2015-01-01

    Full Text Available Background: Cysteine protease Cathepsin L is involved in bone remodeling and expressed in activated macrophages. It is highly expressed in metastatic tumor tissue, especially with bone metastases. Aims: We evaluated immunohistochemical expression of Cathepsin L in tumor cells and tumor-associated macrophages (TAMs in chemo-naive Ewing sarcoma. Settings and Design: Retrospective evaluation of archived specimens of Ewing sarcoma. Materials and Methods: Immunohistochemical staining was performed on archived blocks of chemo-naive patients with Ewing sarcoma treated with uniform chemotherapy at our institute between January 2009 and November 2011. Statistical Analysis: Immunohistochemical expression was co-related with baseline demographics and survival. Results: During the study period, we had evaluable baseline samples from 62 patients with median age 15 years (range: 2-40; 26 (42% had metastases. Cathepsin L expression in tumor cells was observed in 8/62 (13% specimens. None of the baseline clinical characteristics correlated with Cathepsin L expression. Cathepsin L positivity was associated with poor response to neoadjuvant chemotherapy (NACT (P = 0.05, but did not influence either event-free-survival (EFS or overall survival. Cathepsin L was expressed in TAMs in all specimens. Grade 3 TAMs (>10 TAMs/high power field was associated with better response to NACT (P = 0.05. On univariate analysis Grade 3 TAMs predicted superior EFS (median EFS 28.5 months in those with Grade 3 TAMs versus 14.8 months in those with grade ½ TAMs [P = 0.04]. Conclusions: Cathepsin L expression by immunohistochemistry was low in our patient cohort, and it did not affect the outcome. In addition, Grade 3 TAMs with Cathepsin L expression was associated with improved EFS.

  14. Transnational archives: the Canadian case

    Directory of Open Access Journals (Sweden)

    Julia Creet

    2011-05-01

    Full Text Available This paper is a brief overview of the concept of the transnational archive as a counterpoint to the idea that a national archive is necessarily a locus of a static idea of nation. The Canadian national archives is used as a case study of an archives that was transnational in its inception, and one that has continued to change in its mandate and materials as a response to patterns in migration and changing notions of multiculturalism as a Canadian federal policy. It introduces the most recent formation of the transnational archive and its denizens: the genealogical archive inhabited by family historians.

  15. Endocrine tumors other than thyroid tumors

    International Nuclear Information System (INIS)

    This paper discusses the tendency for the occurrence of tumors in the endocrine glands, other than the thyroid gland, in A-bomb survivors using both autopsy and clinical data. ABCC-RERF sample data using 4136 autopsy cases (1961-1977) revealed parathyroid tumors in 13 A-bomb survivors, including 3 with the associated hyperparathyroidism, with the suggestion of dose-dependent increase in the occurrence of tumors. Based on clinical data from Hiroshima University, 7 (46.7%) of 15 parathyroid tumors cases were A-bomb survivors. Data (1974-1987) from the Tumor Registry Committee (TRC) in Hiroshima Prefecture revealed that a relative risk of parathyroid tumors was 5.6 times higher in the entire group of A-bomb survivors and 16.2 times higher in the group of heavily exposed A-bomb survivors, suggesting the dose-dependent increase in their occurrence. Adrenal tumors were detected in 47 of 123 cases from the TRC data, and 15 (31.5%) of these 47 were A-bomb survivors. Particularly, 11 cases of adrenal tumors associated with Cushing syndrome included 6 A-bomb survivors (54.5%). The incidence of multiple endocrine gonadial tumors (MEGT) tended to be higher with increasing exposure doses; and the 1-9 rad group, the 10-99 rad group, and the 100 or more rad group had a risk of developing MEGT of 4.1, 5.7, and 7.1, respectively, relative to both the not-in the city group and the 0 rad group. These findings suggested that there is a correlation between A-bomb radiation and the occurrence of parathyroid tumors (including hyperparathyroidism), adrenal tumors associated with Cushing syndrome and MEGT (especially, the combined thyroid and ovarian tumors and the combined thyroid and parathyroid tumors). (N.K.)

  16. Whole transcriptome sequencing enables discovery and analysis of viruses in archived primary central nervous system lymphomas.

    Directory of Open Access Journals (Sweden)

    Christopher DeBoever

    Full Text Available Primary central nervous system lymphomas (PCNSL have a dramatically increased prevalence among persons living with AIDS and are known to be associated with human Epstein Barr virus (EBV infection. Previous work suggests that in some cases, co-infection with other viruses may be important for PCNSL pathogenesis. Viral transcription in tumor samples can be measured using next generation transcriptome sequencing. We demonstrate the ability of transcriptome sequencing to identify viruses, characterize viral expression, and identify viral variants by sequencing four archived AIDS-related PCNSL tissue samples and analyzing raw sequencing reads. EBV was detected in all four PCNSL samples and cytomegalovirus (CMV, JC polyomavirus (JCV, and HIV were also discovered, consistent with clinical diagnoses. CMV was found to express three long non-coding RNAs recently reported as expressed during active infection. Single nucleotide variants were observed in each of the viruses observed and three indels were found in CMV. No viruses were found in several control tumor types including 32 diffuse large B-cell lymphoma samples. This study demonstrates the ability of next generation transcriptome sequencing to accurately identify viruses, including DNA viruses, in solid human cancer tissue samples.

  17. Download - KEGG MEDICUS | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...F URLs by Artio About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - KEGG MEDICUS | LSDB Archive ...

  18. Download - TP Atlas | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...Ls by Artio About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - TP Atlas | LSDB Archive ...

  19. Protein - AT Atlas | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...base Description Download License Update History of This Database Site Policy | Contact Us Protein - AT Atlas | LSDB Archive ...

  20. Download - RGP caps | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...atabase Description Download License Update History of This Database Site Policy | Contact Us Download - RGP caps | LSDB Archive ...

  1. Main - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ... Download License Update History of This Database Site Policy | Contact Us Main - KOME | LSDB Archive ...

  2. Download - PLACE | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ... About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - PLACE | LSDB Archive ...

  3. Nucleotide Sequence - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...rtio About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Nucleotide Sequence - KOME | LSDB Archive ...

  4. Reference - PLACE | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ... Artio About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Reference - PLACE | LSDB Archive ...

  5. Download - AT Atlas | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...base Description Download License Update History of This Database Site Policy | Contact Us Download - AT Atlas | LSDB Archive ...

  6. Trimming information - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...SEF URLs by Artio About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Trimming information - KOME | LSDB Archive ...

  7. Download - GETDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...io About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - GETDB | LSDB Archive ...

  8. Main data - RMG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...Description Download License Update History of This Database Site Policy | Contact Us Main data - RMG | LSDB Archive ...

  9. Experiments list - DGBY | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...This Database Database Description Download License Update History of This Database Site Policy | Contact Us Experiments list - DGBY | LSDB Archive ...

  10. Download - Plabrain DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us Plabrain...escription Download License Update History of This Database Site Policy | Contact Us Download - Plabrain DB | LSDB Archive ...

  11. How Are Wilms Tumors Diagnosed?

    Science.gov (United States)

    ... at under a microscope. The cells in Wilms tumors have a distinct appearance when looked at this way. Doctors also look at the sample to determine the histology of the Wilms tumor (favorable or unfavorable), as was described in the ...

  12. Main - RPSD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ... File URL: ftp://ftp.biosciencedbc.jp/archive/rpsd/LATEST/rpsd_main_sjis.zip File... size: 120 KB File name: rpsd_main_utf8.zip File URL: ftp://ftp.biosciencedbc.jp/archive/rpsd/LATEST/rpsd_ma...icense Update History of This Database Site Policy | Contact Us Main - RPSD | LSDB Archive ...

  13. Whipple Made Simple For Surgical Pathologists: Orientation, Dissection, and Sampling of Pancreaticoduodenectomy Specimens For a More Practical and Accurate Evaluation of Pancreatic, Distal Common Bile Duct, and Ampullary Tumors

    OpenAIRE

    Adsay, N. Volkan; Basturk, Olca; Saka, Burcu; Bagci, Pelin; Ozdemir, Denizhan; Balci, Serdar; Sarmiento, Juan M; Kooby, David A; Staley, Charles; Maithel, Shishir K; Everett, Rhonda; Cheng, Jeanette D.; Thirabanjasak, Duangpeng; Weaver, Donald W.

    2014-01-01

    Pancreaticoduodenectomy (PD) specimens present a challenge for surgical pathologists because of the relative rarity of these specimens, combined with the anatomic complexity. Here, we describe our experience on the orientation, dissection, and sampling of PD specimens for a more practical and accurate evaluation of pancreatic, distal common bile duct (CBD), and ampullary tumors. For orientation of PDs, identification of the “trapezoid,” created by the vascular bed at the center, the pancreati...

  14. Main - PLACE | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...URL: ftp://ftp.biosciencedbc.jp/archive/place/LATEST/place_main.zip File size: 48...97) Joomla SEF URLs by Artio About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Main - PLACE | LSDB Archive ...

  15. Entire Sequence - RMG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...us RAP-DB genome browser. Data file File name: rmg_seq.zip File URL: ftp://ftp.biosciencedbc.jp/archive/rmg/...n Download License Update History of This Database Site Policy | Contact Us Entire Sequence - RMG | LSDB Archive ...

  16. ORF information - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...e longest ORFs Data file File name: kome_orf_infomation.zip File URL: ftp://ftp.biosciencedbc.jp/archive/kom...e Description Download License Update History of This Database Site Policy | Contact Us ORF information - KOME | LSDB Archive ...

  17. Product annotations - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...ile name: kome_product_annotation.zip File URL: ftp://ftp.biosciencedbc.jp/archiv...ate History of This Database Site Policy | Contact Us Product annotations - KOME | LSDB Archive ...

  18. Envirion - KEGG MEDICUS | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ... file File name: kegg_medicus_environ_en.zip File URL: ftp://ftp.biosciencedbc.jp/archive/kegg-medicus/LATES...oomla SEF URLs by Artio About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Envirion - KEGG MEDICUS | LSDB Archive ...

  19. Basical information - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...ation about full-length cDNA clones Data file File name: kome_basical_information.zip File URL: ftp://ftp.biosciencedbc.jp/archiv...base Database Description Download License Update History of This Database Site Policy | Contact Us Basical information - KOME | LSDB Archive ...

  20. Training in the Archives: Archival Research as Professional Development

    Science.gov (United States)

    Buehl, Jonathan; Chute, Tamar; Fields, Anne

    2012-01-01

    This article describes the rationale and efficacy of a graduate-level teaching module providing loosely structured practice with real archives. Introducing early career scholars to archival methods changed their beliefs about knowledge, research, teaching, and their discipline(s). This case study suggests that archives can be productive training…

  1. Life Sciences Data Archive (LSDA)

    Data.gov (United States)

    National Aeronautics and Space Administration — NASA's Life Sciences Data Archive (LSDA) is an active archive that provides information and data from 1961 (Mercury Project) through current flight and flight...

  2. Ten years of archival science

    NARCIS (Netherlands)

    E. Ketelaar

    2010-01-01

    This article reviews how the journal Archival Science--International Journal on Recorded Information in the first 10 years has endeavoured to be integrated, interdisciplinary, and intercultural in promoting the development of archival science as an autonomous scientific discipline.

  3. 20 Years of Archive Fever

    OpenAIRE

    Atkins, Guy; Bulley, James

    2014-01-01

    "It is what is happening, right here, when a house, the Freuds' last house, becomes a museum: the passage from one institution to another." (Jacques Derrida, 'Archive Fever') Presented as a gift to the Freud Museum, Jacques Derrida's 1994 lecture 'Archive Fever' remains a compelling work for scholars and artists interested in the relationship between archives, memory, and technology. Originally titled 'The Concept of the Archive: A Freudian Impression', Derrida's deconstruction of the...

  4. Queering archives: A roundtable discussion

    OpenAIRE

    Arondekar, A; Cvetkovich, A; Hanhardt, CB; Kunzel, R; Nyong O, T; Rodríguez, JM; Stryker, S.

    2015-01-01

    © 2015 by MARHO: The Radical Historians’ Organization, Inc. “Queering Archives: A Roundtable Discussion” provides a reflection on histories of queer archives studies, while marking out some key directions for the field's future development. As a broad conversation about the career of the queer archival, as both intellectual project and political practice, this discussion focuses on developments and limits within North American queer studies of the archive, which emerges as a central object of...

  5. Old and New Archives

    Directory of Open Access Journals (Sweden)

    Ioana Vasiloiu

    2015-01-01

    Full Text Available Library and museum archives are real testimony of collective memory. Old or new, their "universe" is fascinating. They are the path to an almost forgotten world with all its cultural and intellectual problems or allow us to reconsider the social, historical, political and cultural present. The inestimable value of their manuscripts, books and periodicals made medieval Romanian library archives to be famous in that age. Its content figured out the Romanian humanist's vast intellectual activity and their connection to European values. Their remains, which can be found today especially at Romanian Academy Library, depict some aspects of Romanian medieval cultural life. Particularly, with its huge number of manuscripts, books and periodicals, the National Romanian Literature Museum archives contribute to Romanian history reconstruction from the commencement to present.

  6. In through the Archive

    DEFF Research Database (Denmark)

    Breinbjerg, Morten; Fritsch, Jonas; Bertelsen, Olav W.

    In this paper we will present a project in which we have orchestrated a collective listening process framed around the notion of the echo - and the interactive listening machine Ekkomaten – to build a participatory sound archive that reflects people’s perceptions and imaginations of a local...... community in the city of Aarhus Denmark. The archive is seen as indicative to the rhythm and nature of the place revealing not only aspects of the lives that unfold, but also how people sense and interpret the local community through their auditory sensibility. During the project we have asked people of all...... in the area for many years. The sound material has been organized in an archive, whichis handled by custom build software (API), and accessible through a physical, designfictional machine called Ekkomaten. In the paper, we would like to discuss the project in relation to the following subjects: 1) Methodology...

  7. Cultivating archives: meanings and identities

    NARCIS (Netherlands)

    E. Ketelaar

    2012-01-01

    By cultivating archives through successive activations, people and communities define their identities. In these activations, the meanings of archives are constructed and reconstructed. Archives are not a static artifact imbued with the record creator’s voice alone, but a dynamic process involving a

  8. The Ethics of Archival Research

    Science.gov (United States)

    McKee, Heidi A.; Porter, James E.

    2012-01-01

    What are the key ethical issues involved in conducting archival research? Based on examination of cases and interviews with leading archival researchers in composition, this article discusses several ethical questions and offers a heuristic to guide ethical decision making. Key to this process is recognizing the person-ness of archival materials.…

  9. Digital audiovisual archives

    CERN Document Server

    Stockinger, Peter

    2013-01-01

    Today, huge quantities of digital audiovisual resources are already available - everywhere and at any time - through Web portals, online archives and libraries, and video blogs. One central question with respect to this huge amount of audiovisual data is how they can be used in specific (social, pedagogical, etc.) contexts and what are their potential interest for target groups (communities, professionals, students, researchers, etc.).This book examines the question of the (creative) exploitation of digital audiovisual archives from a theoretical, methodological, technical and practical

  10. Costs of Archival Storage

    DEFF Research Database (Denmark)

    Nielsen, Anders Bo; Thirifays, Alex; Kejser, Ulla Bøgvad

    2012-01-01

    This paper presents an analysis of the cost of archival storage. The study is part of a project conducted by The Danish National Archives, The Royal Library, and The State and University Library to develop a generic cost model for digital preservation (CMDP). The purposes of the study were to...... determine the costs of establishing and maintaining a preservation solution destined for long-term preservation of digital materials and to develop a tool capable of doing this operation. In order to fulfill the purposes, the project employed a combination of own and external experience as well as the OAIS...

  11. Medullary thyroid cancer: RET testing of an archival material

    DEFF Research Database (Denmark)

    Godballe, Christian; Jørgensen, Gita; Gerdes, Anne-Marie Axø;

    2010-01-01

    might be missed? Today mutation analysis of the RET proto-oncogene is routinely performed on DNA. Departments of pathology often store tissue specimens from performed surgical procedures. The purpose of this study was to examine if analysis of DNA extracted from formalin fixed archival tissue might...... by testing of non-tumor tissue from patients with known hereditary MTC. This study shows that genetic testing of archival MTC material is technically possible and might be a way of identifying patients with previously not recognized hereditary MTC....

  12. Medullary thyroid cancer: RET testing of an archival material

    DEFF Research Database (Denmark)

    Godballe, Christian; Jørgensen, Gita; Gerdes, Anne-Marie;

    2009-01-01

    might be missed? Today mutation analysis of the RET proto-oncogene is routinely performed on DNA. Departments of pathology often store tissue specimens from performed surgical procedures. The purpose of this study was to examine if analysis of DNA extracted from formalin fixed archival tissue might...... by testing of non-tumor tissue from patients with known hereditary MTC. This study shows that genetic testing of archival MTC material is technically possible and might be a way of identifying patients with previously not recognized hereditary MTC....

  13. Numerical and Structural Genomic Aberrations Are Reliably Detectable in Tissue Microarrays of Formalin-Fixed Paraffin-Embedded Tumor Samples by Fluorescence In-Situ Hybridization

    OpenAIRE

    Heike Horn; Julia Bausinger; Staiger, Annette M.; Maximilian Sohn; Christopher Schmelter; Kim Gruber; Claudia Kalla; M Michaela Ott; Andreas Rosenwald; German Ott

    2014-01-01

    Few data are available regarding the reliability of fluorescence in-situ hybridization (FISH), especially for chromosomal deletions, in high-throughput settings using tissue microarrays (TMAs). We performed a comprehensive FISH study for the detection of chromosomal translocations and deletions in formalin-fixed and paraffin-embedded (FFPE) tumor specimens arranged in TMA format. We analyzed 46 B-cell lymphoma (B-NHL) specimens with known karyotypes for translocations of IGH-, BCL2-, BCL6- an...

  14. NASA Data Archive Evaluation

    Science.gov (United States)

    Holley, Daniel C.; Haight, Kyle G.; Lindstrom, Ted

    1997-01-01

    The purpose of this study was to expose a range of naive individuals to the NASA Data Archive and to obtain feedback from them, with the goal of learning how useful people with varied backgrounds would find the Archive for research and other purposes. We processed 36 subjects in four experimental categories, designated in this report as C+R+, C+R-, C-R+ and C-R-, for computer experienced researchers, computer experienced non-researchers, non-computer experienced researchers, and non-computer experienced non-researchers, respectively. This report includes an assessment of general patterns of subject responses to the various aspects of the NASA Data Archive. Some of the aspects examined were interface-oriented, addressing such issues as whether the subject was able to locate information, figure out how to perform desired information retrieval tasks, etc. Other aspects were content-related. In doing these assessments, answers given to different questions were sometimes combined. This practice reflects the tendency of the subjects to provide answers expressing their experiences across question boundaries. Patterns of response are cross-examined by subject category in order to bring out deeper understandings of why subjects reacted the way they did to the archive. After the general assessment, there will be a more extensive summary of the replies received from the test subjects.

  15. Software Archive Related Issues

    Science.gov (United States)

    Angelini, Lorella

    2008-01-01

    With the archive opening of the major X-ray and Gamma ray missions, the school is intended to provide information on the resource available in the data archive and the public software. This talk reviews the archive content, the data format for the major active missions Chandra, XMM-Newton, Swift, RXTE, Integral and Suzaku and the available software for each of these missions. It will explain the FITS format in general and the specific layout for the most popular mission, explaining the role of keywords and how they fit in the multimission standard approach embrace by the High Energy Community. Specifically, it reviews : the difference data levels and the difference software applicable; the popular/standard method of analysis for high level products such as spectra, timing and images; the role of calibration in the multi mission approach; how to navigate the archive query databases. It will present also how the school is organized and how the information provided will be relevant to each of the afternoon science projects that will be proposed to the students and led by a project leader

  16. Open Archives Initiative

    OpenAIRE

    McMillan, Gail

    2004-01-01

    This presentation, which was given at the annual meeting of the Society of Scholarly Publishing on June 1, 2000, describes the Open Archives Initiative (OAI), a protocol for exchanging content between digital repositories. The presentation outlines OAI's history, core components, key stakeholders, and ongoing developments. Presented at the Society for Scholarly Publishing: June 1, 2000

  17. CLASSIFICATION OF TUMOR HISTOPATHOLOGY VIA SPARSE FEATURE LEARNING.

    Science.gov (United States)

    Nayak, Nandita; Chang, Hang; Borowsky, Alexander; Spellman, Paul; Parvin, Bahram

    2013-04-01

    Our goal is to decompose whole slide images (WSI) of histology sections into distinct patches (e.g., viable tumor, necrosis) so that statistics of distinct histopathology can be linked with the outcome. Such an analysis requires a large cohort of histology sections that may originate from different laboratories, which may not use the same protocol in sample preparation. We have evaluated a method based on a variation of the restricted Boltzmann machine (RBM) that learns intrinsic features of the image signature in an unsupervised fashion. Computed code, from the learned representation, is then utilized to classify patches from a curated library of images. The system has been evaluated against a dataset of small image blocks of 1k-by-1k that have been extracted from glioblastoma multiforme (GBM) and clear cell kidney carcinoma (KIRC) from the cancer genome atlas (TCGA) archive. The learned model is then projected on each whole slide image (e.g., of size 20k-by-20k pixels or larger) for characterizing and visualizing tumor architecture. In the case of GBM, each WSI is decomposed into necrotic, transition into necrosis, and viable. In the case of the KIRC, each WSI is decomposed into tumor types, stroma, normal, and others. Evaluation of 1400 and 2500 samples of GBM and KIRC indicates a performance of 84% and 81%, respectively. PMID:24319533

  18. The Materiality of Method: The Case of the Mass Observation Archive

    OpenAIRE

    Liz Moor; Emma Uprichard

    2014-01-01

    The Mass Observation Archive presents numerous methodological issues for social researchers. The data are idiosyncratic, difficult to analyze, and the sample design is nonsystematic. Such issues seriously challenge conventional social research protocols. This article highlights a further characteristic of the archive: its unwieldy materiality. Focusing on the sensory experiences of the archive and its particular type of data, the article shows how the experience of getting ‘dirty with dataâ...

  19. HyperArchiver: an EPICS archiver prototype based on Hypertable

    International Nuclear Information System (INIS)

    This work started in the context of NSLS2 project at Brookhaven National Laboratory. The NSLS2 control system foresees a very high number of PV variables and has strict requirements in terms of archiving/retrieving rate: our goal was to store 10 K PV/sec and retrieve 4 K PV/sec for a group of 4 signals. The HyperArchiver is an EPICS Archiver implementation engined by Hypertable, an open source database whose internal architecture is derived from Google's Big Table. We discuss the performance of HyperArchiver and present the results of some comparative tests. (authors)

  20. Archives, Education, and Access: Learning at Interference Archive

    Directory of Open Access Journals (Sweden)

    Bonnie Gordon

    2016-07-01

    Full Text Available Archives are a tool for education and the access policy of an archive affects what kind of education takes place in its space. In this paper, we describe how Interference Archive (IA, a community archive in Brooklyn, New York, provides access through an open stacks policy and experiential learning, which allows for unique educational opportunities. These methods of providing access are intended to subvert representational power, allowing visitors, donors, and volunteers to take part in deciding how histories are told, how materials are accessed, and how the collection is re-used as a resource for learning about contemporary and historical social movements.

  1. Les archives des bagnes

    Directory of Open Access Journals (Sweden)

    Archives Nationales d’Outre-Mer

    2008-01-01

    Full Text Available Les établissements pénitentiaires coloniaux étaient administrés par le ministère de la Marine et des Colonies, puis par le ministère des Colonies (1881, en liaison avec les ministères de la Justice et de l’Intérieur. Les archives ont par conséquent été versées aux Archives nationales d’outre-mer avec le fonds du ministère des Colonies.Le fonds représente environ 760 ml (5358 articles. Il concerne presque exclusivement les bagnes de Guyane et de Nouvelle-Calédonie et couvre la période 1852-1...

  2. Tumor vaccines

    International Nuclear Information System (INIS)

    Tumor vaccines have several potential advantages over standard anticancer regiments. They represent highly specific anticancer therapy. Inducing tumor-specific memory T-lymphocytes, they have potential for long-lived antitumor effects. However, clinical trials, in which cancer patients were vaccinated with tumor vaccines, have been so far mainly disappointing. There are many reasons for the inefficiency of tumor vaccines. Most cancer antigens are normal self-molecules to which immune tolerance exists. That is why the population of tumor-specific lymphocytes is represented by a small number of low-affinity T-lymphocytes that induce weak antitumor immune response. Simultaneously, tumors evolve many mechanisms to actively evade immune system, what makes them poorly immunogenic or even tolerogenic. Novel immunotherapeutic strategies are directed toward breaking immune tolerance to tumor antigens, enhancing immunogenicity of tumor vaccines and overcoming mechanisms of tumor escape. There are several approaches, unfortunately, all of them still far away from an ideal tumor vaccine that would reject a tumor. Difficulties in the activation of antitumor immune response by tumor vaccines have led to the development of alternative immunotherapeutic strategies that directly focus on effector mechanisms of immune system (adoptive tumor- specific T-lymphocyte transfer and tumor specific monoclonal antibodies). (author)

  3. Archiving tools for EOS

    Science.gov (United States)

    Sindrilaru, Elvin-Alin; Peters, Andreas-Joachim; Duellmann, Dirk

    2015-12-01

    Archiving data to tape is a critical operation for any storage system, especially for the EOS system at CERN which holds production data for all major LHC experiments. Each collaboration has an allocated quota it can use at any given time therefore, a mechanism for archiving "stale" data is needed so that storage space is reclaimed for online analysis operations. The archiving tool that we propose for EOS aims to provide a robust client interface for moving data between EOS and CASTOR (tape backed storage system) while enforcing best practices when it comes to data integrity and verification. All data transfers are done using a third-party copy mechanism which ensures point-to- point communication between the source and destination, thus providing maximum aggregate throughput. Using ZMQ message-passing paradigm and a process-based approach enabled us to achieve optimal utilisation of the resources and a stateless architecture which can easily be tuned during operation. The modular design and the implementation done in a high-level language like Python, has enabled us to easily extended the code base to address new demands like offering full and incremental backup capabilities.

  4. Critical experiment data archiving

    International Nuclear Information System (INIS)

    Critical experiment facilities produced a large number of important data during the past 45 years; however, many useful data remain unpublished. The unpublished material exists in the form of experimenters' logbooks, notes, photographs, material descriptions, etc., This data could be important for computer code validation, understanding the physics of criticality, facility design, or for setting process limits. In the past, criticality specialists have been able to obtain unpublished details by direct contact with the experimenters. Obviously, this will not be possible indefinitely. Most of the US critical experiment facilities are now closed, and the experimenters are moving to other jobs, retiring, or otherwise becoming unavailable for this informal assistance. Also, the records are in danger of being discarded or lost during facility closures, cleanup activities, or in storage. A project was begun in 1989 to ensure that important unpublished data from critical experiment facilities in the United States are archived and made available as a resource of the US Department of Energy's (DOE's) Nuclear Criticality Information System (NCIS). The objective of this paper is to summarize the project accomplishments to date and bring these activities to the attention of those who might be aware of the location of source information needed for archiving and could assist in getting the materials included in the archive

  5. Critical experiment data archiving

    International Nuclear Information System (INIS)

    Critical experiment facilities produced a large amount of important data during the past forty-five years. However, much useful data remains unpublished. The unpublished material exists in the form of experimenters' logbooks, notes, photographs, material descriptions, etc. This data could be important for computer code validation, understanding the physics of criticality, facility design, or for setting process limits. In the past, criticality specialists have been able to obtain unpublished details by direct contact with the experimenters. Obviously, this will not be possible indefinitely. Most of the US critical experiment facilities are now closed and the experimenters are moving to other jobs, retiring, or otherwise becoming unavailable for this informal assistance. Also, the records are in danger of being discarded or lost during facility closures, cleanup activities, or in storage. A project was begun in 1989 to ensure that important unpublished data from critical experiment facilities in the United States are archived and made available as a resource of the US Department of Energy's Nuclear Criticality Information System. The objective of this paper is to summarize the project accomplishments to date and bring these activities to the attention of those who might be aware of the location of source information needed for archiving, and could assist us in getting the materials included in the archive

  6. The Yohkoh Legacy Archive

    Science.gov (United States)

    Acton, L. W.; Takeda, A.; McKenzie, D. E.

    2008-12-01

    Yohkoh was a Japan/US/UK mission for the study of high energy processes on the sun. Scientific operation extended from September 1991 until 14 December 2001, nearly an entire solar activity cycle. Observations included full-disk soft and hard x-ray imaging, hard x-ray spectroscopy, and high resolution flare spectroscopy in S XV, Ca XIX, Fe XXV and Fe XXVI from the Bent Crystal Spectrometer (BCS). The Yohkoh Legacy Archive (YLA) brings together all Yohkoh observational data along with extensive documentation required for a full understanding of instrumentation, mission operations, and data reduction and correction. Extensive meta-data aid the user in efficiently accessing the data base. Creation of the YLA has been the work of 8 years; the top objective has been to present the extensive Yohkoh database in a form fully usable for scientists or students who are unfamiliar with Yohkoh instrumentation. The YLA may be accessed at http://solar.physics.montana.edu/ylegacy or through the Virtual Solar Observatory (VSO), although the VSO capability is still under development. Data from the Yohkoh hard x-ray instruments and BCS are presented in flare list formats. The Soft X-ray Telescope (SXT) images are available in quantitative and movie formats. This long, uniform, archive of SXT images is especially useful for solar cycle studies as well as high resolution soft x-ray flare studies. Examples of YLA data products and research enabled by the archive will be presented.

  7. Data Quality in Web Archiving

    OpenAIRE

    Spaniol, Marc; Denev, Dimitar; Mazeika, Arturas; Weikum, Gerhard

    2009-01-01

    Web archives preserve the history of Web sites and have high long-term value for media and business analysts. Such archives are maintained by periodically re-crawling entire Web sites of interest. From an archivist's point of view, the ideal case to ensure highest possible data quality of the archive would be to ``freeze'' the complete contents of an entire Web site during the time span of crawling and capturing the site. Of course, this is practically infea...

  8. Archived film analysis and restoration

    OpenAIRE

    Rares, A.

    2004-01-01

    The progressive degradation of current film archives poses a serious threat to the preservation of our cultural and technical heritage. Digitization and digital restoration are currently the most viable solutions for the long term preservation and high quality restoration of filmed material. They also open the path for more effective search, reuse and distribution of the archived content. This thesis covers various aspects of digital restoration applied to archived film. The main focus here l...

  9. High-risk human papilloma virus in archival tissues of oral pathosis and normal oral mucosa

    Directory of Open Access Journals (Sweden)

    Raghu Dhanapal

    2015-01-01

    Full Text Available Objectives: Oral cancer ranks third among all cancers in the Indian population. Human papilloma virus (HPV plays a significant role in oral carcinogenesis. Population-based subtype variations are present in the HPV prevalence. This study gives an emphasis on the parameters to be considered in formalin fixed paraffin embedded tissues for polymerase chain reaction (PCR-based research work. Materials and Methods: Cross-sectional study on archival paraffin-embedded tissue samples of oral squamous cell carcinoma (OSCC, epithelial dysplasia, and normal oral mucosa surrounding impacted tooth was amplified by PCR for the E6 gene of HPV type 16 and E1 gene of HPV type 18. Results: HPV 18 was positive in three OSCC cases. There was no statistically significant association of the positivity of HPV with the age, gender or habit. The HPV positive patients had a tobacco habit and were of a younger age group. Conclusion: The presence of HPV in carcinomatous tissue highlights the possible role of HPV in carcinogenesis and archival paraffin embedded tissue specimen can be used for this analysis. Recent studies on genomic analyses have highlighted that the HPV positive tumors are a separate subgroup based on genomic sequencing. The results of a larger retrospective study will help further in our understanding of the role of HPV in carcinogenesis, this study could form the baseline for such follow-up studies.

  10. Volatile aldehydes in libraries and archives

    Science.gov (United States)

    Fenech, Ann; Strlič, Matija; Kralj Cigić, Irena; Levart, Alenka; Gibson, Lorraine T.; de Bruin, Gerrit; Ntanos, Konstantinos; Kolar, Jana; Cassar, May

    2010-06-01

    Volatile aldehydes are produced during degradation of paper-based materials. This may result in their accumulation in archival and library repositories. However, no systematic study has been performed so far. In the frame of this study, passive sampling was carried out at ten locations in four libraries and archives. Despite the very variable sampling locations, no major differences were found, although air-filtered repositories were found to have lower concentrations while a non-ventilated newspaper repository exhibited the highest concentrations of volatile aldehydes (formaldehyde, acetaldehyde, furfural and hexanal). Five employees in one institution were also provided with personal passive samplers to investigate employees' exposure to volatile aldehydes. All values were lower than the presently valid exposure limits. The concentration of volatile aldehydes, acetic acid, and volatile organic compounds (VOCs) in general was also compared with that of outdoor-generated pollutants. It was evident that inside the repository and particularly inside archival boxes, the concentration of VOCs and acetic acid was much higher than the concentration of outdoor-generated pollutants, which are otherwise more routinely studied in connection with heritage materials. This indicates that further work on the pro-degradative effect of VOCs on heritage materials is necessary and that monitoring of VOCs in heritage institutions should become more widespread.

  11. Mammary tumors

    International Nuclear Information System (INIS)

    Mammary neoplasia is one of the more common malignancies affecting domestic species. Despite their importance, they are often over- diagnosed, undertreated and subject to several misconceptions propagated by veterinarians and pet owners alike. Mammary neoplasia is the most frequent tumor type encountered in the female accounting for almost half of all malignancies reported. The canine has the highest incidence of mammary tumors of all domestic species. In the dog, about 65 percent of mammary tumors are benign mixed tumors, and 25 percent are carcinomas. The rest are adenomas, myoepitheliomas, and malignant mixed tumors. The age distribution of mammary tumors closely follows the age distribution of most tumors in the dog. Mammary tumors are rare in dogs 2 years old, but incidence begins to increase sharply at approximately 6 years of age. Median age at diagnosis is about 10 years. No breed predilection has been consistently reported

  12. The Scent of the Digital Archive. Dilemmas with Archive Digitisation

    NARCIS (Netherlands)

    C. Jeurgens

    2013-01-01

    Archival infrastructure is changing at a rapid pace as a consequence of digitisation. The effort to digitise analogue collections seems to have benefits only for researchers. Still, only a fraction of analogue archive material is currently available in digital form. This article raises some of the p

  13. Analyzing Archival Intelligence: A Collaboration between Library Instruction and Archives

    Science.gov (United States)

    Hensley, Merinda Kaye; Murphy, Benjamin P.; Swain, Ellen D.

    2014-01-01

    Although recent archival scholarship promotes the use of primary sources for developing students' analytical research skills, few studies focus on standards or protocols for teaching or assessing archival instruction. Librarians have designed and tested standards and learning assessment strategies for library instruction, and archivists would do…

  14. Social Media and Archives: A Survey of Archive Users

    Science.gov (United States)

    Washburn, Bruce; Eckert, Ellen; Proffitt, Merrilee

    2013-01-01

    In April and May of 2012, the Online Computer Library Center (OCLC) Research conducted a survey of users of archives to learn more about their habits and preferences. In particular, they focused on the roles that social media, recommendations, reviews, and other forms of user-contributed annotation play in archival research. OCLC surveyed faculty,…

  15. OPS index - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...la SEF URLs by Artio About This Database Database Description Download License Update History of This Database Site Policy | Contact Us OPS index - KOME | LSDB Archive ...

  16. High Energy Astrophysics Science Archive Research Center

    Data.gov (United States)

    National Aeronautics and Space Administration — The High Energy Astrophysics Science Archive Research Center (HEASARC) is the primary archive for NASA missions dealing with extremely energetic phenomena, from...

  17. Brain Tumors

    Science.gov (United States)

    A brain tumor is a growth of abnormal cells in the tissues of the brain. Brain tumors can be benign, with no cancer cells, or ... cancer cells that grow quickly. Some are primary brain tumors, which start in the brain. Others are metastatic, ...

  18. Odontogenic Tumors

    OpenAIRE

    TAHSİNOĞLU, Melih

    2013-01-01

    DefinitionThe neoplasms that consist of the cells considered specialized for odontogenesis, and their product (dentin, enamel, cementum) are called odontogenic tumors.ClassificationTo initiate odontogenesis, epithelium is a must. Same rule holds for the odontogenic tumors: without odontogenic epithelium, odontogenic tumors cannot be, without the induction of odontogenic epithelium odontogenic mesenchyme cannot develop.

  19. Brain Tumors

    Science.gov (United States)

    A brain tumor is a growth of abnormal cells in the tissues of the brain. Brain tumors can be benign, with no cancer cells, ... cancer cells that grow quickly. Some are primary brain tumors, which start in the brain. Others are ...

  20. Tumor Markers

    Science.gov (United States)

    ... guidelines on a variety of topics, including tumor markers for breast cancer, colorectal cancer, lung cancer, and others. The ... of recurrence 70-Gene signature (Mammaprint®) Cancer type: Breast ... Can tumor markers be used in cancer screening? Because tumor markers ...

  1. Urogenital tumors

    Energy Technology Data Exchange (ETDEWEB)

    Weller, R.E.

    1994-03-01

    An overview is provided for veterinary care of urogenital tumors in companion animals, especially the dog. Neoplasms discussed include tumors of the kidney, urinary bladder, prostate, testis, ovary, vagina, vulva and the canine transmissible venereal tumor. Topics addressed include description, diagnosis and treatment.

  2. Wilms Tumor

    Science.gov (United States)

    ... Kids Up for Sports Pregnant? Your Baby's Growth Cerebral Palsy: Caring for Your Child All About Food Allergies Wilms Tumor KidsHealth > For Parents > Wilms Tumor Print A A A Text Size What's in this article? Signs and Symptoms Diagnosis Treatment Caring for Your Child en español Tumor ...

  3. Iatrogenic Tumor Implantation

    Institute of Scientific and Technical Information of China (English)

    Ying Ma; Ping Bai

    2008-01-01

    Iatrogenic tumor implantation is a condition that results from various medical procedures used during diagnosis or treatment of a malignancy. It involves desquamation and dissemination of tumor cells that develop into a local recurrence or distant metastasis from the tumor under treatment. The main clinical feature of the condition is nodules at the operation's porous channel or incision, which is easily diagnosed in accordance with the case history. Final diagnosis can be made based on pathological examination. Tumor implantation may occur in various puncturing porous channels, including a laparoscopic port, abdominal wall incision, and perineal incision, etc. Besides a malignant tumor,implantation potential exists with diseases, such as a borderline tumor and endometriosis etc. Once a tumor implantation is diagnosed, or suspected, surgical resection is usually conducted.During the diagnosis and treatment of diseases, avoiding and reducing iatrogenic implantation and dissemination has been regarded as an important principle for surgical treatment of tumors. In a clinical practice setting, if possible, excisional biopsy should be employed, if a biopsy is needed. Repeated puncturing should be avoided during a paracentesis. In a laparoscopic procedure, the tissue is first put into a sample bag and then is taken out from the point of incision. After a laparoscopic procedure, the peritoneum, abdominal muscular fasciae, and skin should be carefully closed, and/or the punctured porous channel be excised. In addition, the sample/tissue should be rinsed with distilled water before surgical closure of the abdominal cavity,allowing the exfoliated tumor cells to swell and rupture in the hypo-osmolar solution. Then surgical closure can be conducted following a change of gloves and equipment. The extent of hysteromyomectomy should as far as possible be away from the uterine cavity. The purpose of this study is to make clinicians aware of the possibility of tumor implantation

  4. Granulosa cell tumor of testis: Clinicopathological correlation of a rare tumor

    Directory of Open Access Journals (Sweden)

    Swapnil Ulhas Rane

    2014-01-01

    Full Text Available Background: Granulosa cell tumor of testis is a rare tumor accounting for less than 4% of adult testicular tumors though they account for nearly 30% of childhood testicular tumors. Due to the rarity of these tumors, exact etiology, pathogenesis, prognostic factors and best treatment approach are not well known. The molecular events in pathogenesis of these stromal tumors have begun to unravel and these developments put forth a reasonable and scientific explanation for the association of these tumors with developmental anomalies like undescended testis. However, many questions remain unanswered. Materials and Methods: We performed a retrospective analysis of clinicopathological features of all Granulosa Cell Tumors of testis from our archives in addition to an extensive literature search using PUBMED with the key words "Granulosa Cell Tumor, testis". Results: We found six cases in our archives, two of which were of juvenile type and four of adult type. One out of these six cases presented with metastases. All cases underwent radical orchidectomy. Morphology and immunohistochemistry were classical in all cases and there was no diagnostic dilemma. Literature search revealed 63 cases of testicular Granulosa Cell Tumor in addition to highlighting the similarities in the biology and the dissimilarities in the clinical behavior as compared to ovarian Granulosa Cell Tumor. Conclusion: Testicular Granulosa Cell Tumor is a rare tumor, which although histologically similar to its ovarian counterpart, differs in clinical behavior. Further detailed investigations are needed to reveal the mystery behind the differing clinical behavior despite histological and immunohistochemical similarity between the testicular and ovarian Granulosa Cell Tumors.

  5. Long term e-archiving

    OpenAIRE

    Dobratz, Susanne

    2002-01-01

    Conclusions of the breakout session "Long term e-archiving". Looking at the motto of this workshop “Gaining independence with e-Print archives and OAI” it suggests first of all that using e-Print publishing methods especially in the sense of a scholarly non-profit publishing independently from any commercial publishing house offers a unique chance to scientists.

  6. EPRINT ARCHIVE USER SURVEY

    CERN Multimedia

    2001-01-01

    University of Southampton invites the CERN community to participate in a survey Professor Stevan Harnad is conducting on current users and non-users of Eprint Archives. http://www.eprints.org/survey/ The findings will be used to suggest potential enhancements of the services as well as to get a deeper understanding of the very rapid developments in the on-line dissemination and use of scientific and scholarly research. (The survey is anonymous. Revealing your identity is optional and it will be kept confidential.)

  7. Pediatric Intracerebral Tumors

    Directory of Open Access Journals (Sweden)

    Ersin Haciyakupoglu

    2014-06-01

    Full Text Available Histopathology, appearance, biological behaviour, cytogenesis, molecular biology, physiology and effects on the brain development of the pediatric intracerebral tumors are completely different from the tumours in adults. In adults, glioblastoma multiforme and meningiomas are seen mostly, but in children pilocytic astrocytoma, medulloblastoma and germ cell tumours are more common. When pediatric intracerebral tumours are detected, families should be supported and the physcosocial trauma affecting the family should be reduced. As pediatric intracranial tumours are located mostly in the midline, neurological symptoms of them are quite faint. As cerebrospinal fluid paths are obstructed, increased intracranial pressure symptoms appear. Special anesthetic and surgical techniques should be performed for children. Stereotactic surgery, neuroendoscopy, functional and intraoperative magnetic resonance imaging and neuromonitoring could be used. Radiotherapy (in patients aged 3 and more years old, stereotactic radiosurgery, chemotherapy and gene therapies could be performed as the other treatment modalities. [Archives Medical Review Journal 2014; 23(3.000: 367-386

  8. Proteomic profiles of white sucker (Catostomus commersonii) sampled from within the Thunder Bay Area of Concern reveal up-regulation of proteins associated with tumor formation and exposure to environmental estrogens.

    Science.gov (United States)

    Simmons, Denina B D; Bols, Niels C; Duncker, Bernard P; McMaster, Mark; Miller, Jason; Sherry, James P

    2012-02-01

    White sucker (Catostomus commersonii) sampled from the Thunder Bay Area of Concern were assessed for health using a shotgun approach to compile proteomic profiles. Plasma proteins were sampled from male and female fish from a reference location, an area in recovery within Thunder Bay Harbour, and a site at the mouth of the Kaministiquia River where water and sediment quality has been degraded by industrial activities. The proteins were characterized using reverse-phase liquid chromatography tandem to a quadrupole-time-of-flight (LC-Q-TOF) mass spectrometer and were identified by searching in peptide databases. In total, 1086 unique proteins were identified. The identified proteins were then examined by means of a bioinformatics pathway analysis to gain insight into the biological functions and disease pathways that were represented and to assess whether there were any significant changes in protein expression due to sampling location. Female white sucker exhibited significant (p = 0.00183) site-specific changes in the number of plasma proteins that were related to tumor formation, reproductive system disease, and neurological disease. Male fish plasma had a significantly different (p < 0.0001) number of proteins related to neurological disease and tumor formation. Plasma concentrations of vitellogenin were significantly elevated in females from the Kaministiquia River compared to the Thunder Bay Harbour and reference sites. The protein expression profiles indicate that white sucker health has benefited from the remediation of the Thunder Bay Harbour site, whereas white sucker from the Kaministiquia River site are impacted by ongoing contaminant discharges. PMID:22260729

  9. Internet Art and the Archive

    Directory of Open Access Journals (Sweden)

    Karin Wagner

    2007-07-01

    Full Text Available Internet art is ephemeral by nature and several initiatives have been taken to preserve it for the future. Apart from formal archives holding art of this kind, there are also artworks which exist outside these web based institutions. In what way can they be regarded as archived? In the article, criteria are suggested which can be used to judge whether an artwork is active or archived and these criteria are applied in the analysis of twelve different artworks. Different kinds of dating are important for how the status of a work is perceived by the visitor. The concepts of explicit and implicit archiving are used to characterize archiving of Internet art, where works can be "dead" and "alive" at the same time.

  10. Community archiving of imaging studies

    Science.gov (United States)

    Fritz, Steven L.; Roys, Steven R.; Munjal, Sunita

    1996-05-01

    The quantity of image data created in a large radiology practice has long been a challenge for available archiving technology. Traditional methods ofarchiving the large quantity of films generated in radiology have relied on warehousing in remote sites, with courier delivery of film files for historical comparisons. A digital community archive, accessible via a wide area network, represents a feasible solution to the problem of archiving digital images from a busy practice. In addition, it affords a physician caring for a patient access to imaging studies performed at a variety ofhealthcare institutions without the need to repeat studies. Security problems include both network security issues in the WAN environment and access control for patient, physician and imaging center. The key obstacle to developing a community archive is currently political. Reluctance to participate in a community archive can be reduced by appropriate design of the access mechanisms.

  11. Archiving: The Overlooked Spreadsheet Risk

    CERN Document Server

    Lemieux, Victoria

    2008-01-01

    This paper maintains that archiving has been overlooked as a key spreadsheet internal control. The case of failed Jamaican commercial banks demonstrates how poor archiving can lead to weaknesses in spreadsheet control that contribute to operational risk. In addition, the Sarbanes-0xley Act contains a number of provisions that require tighter control over the archiving of spreadsheets. To mitigate operational risks and achieve compliance with the records-related provisions of Sarbanes-Oxley, the author argues that organisations should introduce records management programmes that provide control over the archiving of spreadsheets. At a minimum, spreadsheet archiving controls should identify and ensure compliance with retention requirements, support document production in the event of regulatory inquiries or litigation, and prevent unauthorised destruction of records.

  12. Experiment list: SRX695777 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available SRX695777 mm9 Histone H3K27me3 Lung Lung tumors NA 44077215,97.2,10.6,646 GSM149921...0: ChIP sample rep2; Mus musculus; ChIP-Seq source_name=lung tumors || tissue=NSCLC orthotopic tumor || geno

  13. Experiment list: SRX695776 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available SRX695776 mm9 Histone H3K27me3 Lung Lung tumors NA 35138178,95.7,9.0,371 GSM1499209...: ChIP sample rep1; Mus musculus; ChIP-Seq source_name=lung tumors || tissue=NSCLC orthotopic tumor || genot

  14. Effects of TGF-beta signalling inhibition with galunisertib (LY2157299) in hepatocellular carcinoma models and in ex vivo whole tumor tissue samples from patients

    OpenAIRE

    Serova, Maria; Tijeras-Raballand, Annemilaï; Santos, Célia Dos; Albuquerque, Miguel; Paradis, Valerie; Neuzillet, Cindy; Benhadji, Karim A; Raymond, Eric; Faivre, Sandrine; De Gramont, Armand

    2015-01-01

    Galunisertib (LY2157299) is a selective ATP-mimetic inhibitor of TGF-β receptor (TβR)-I activation currently under clinical investigation in hepatocellular carcinoma (HCC) patients. Our study explored the effects of galunisertib in vitro in HCC cell lines and ex vivo on patient samples. Galunisertib was evaluated in HepG2, Hep3B, Huh7, JHH6 and SK-HEP1 cells as well as in SK-HEP1-derived cells tolerant to sorafenib (SK-Sora) and sunitinib (SK-Suni). Exogenous stimulation of all HCC cell lines...

  15. Natural sound archives: past, present and future.

    Science.gov (United States)

    Ranft, Richard

    2004-06-01

    Recordings of wild animals were first made in the Palearctic in 1900, in the Nearctic in 1929, in Antarctica in 1934, in Asia in 1937, and in the Neotropics in the 1940s. However, systematic collecting did not begin until the 1950s. Collections of animal sound recordings serve many uses in education, entertainment, science and nature conservation. In recent years, technological developments have transformed the ways in which sounds can be sampled, stored and accessed. Now the largest collections between them hold altogether around 0.5 million recordings with their associated data. The functioning of a major archive will be described with reference to the British Library Sound Archive. Preserving large collections for the long term is a primary concern in the digital age. While digitization and digital preservation has many advantages over analogue methods, the rate of technology change and lack of standardization are a serious problem for the world's major audio archives. Another challenge is to make collections more easily and widely accessible via electronic networks. On-line catalogues and access to the actual sounds via the internet are already available for some collections. Case studies describing the establishment and functioning of sound libraries in Mexico, Colombia and Brazil are given in individually authored sections in an Appendix. PMID:15258666

  16. Introducing the PRIDE Archive RESTful web services.

    Science.gov (United States)

    Reisinger, Florian; del-Toro, Noemi; Ternent, Tobias; Hermjakob, Henning; Vizcaíno, Juan Antonio

    2015-07-01

    The PRIDE (PRoteomics IDEntifications) database is one of the world-leading public repositories of mass spectrometry (MS)-based proteomics data and it is a founding member of the ProteomeXchange Consortium of proteomics resources. In the original PRIDE database system, users could access data programmatically by accessing the web services provided by the PRIDE BioMart interface. New REST (REpresentational State Transfer) web services have been developed to serve the most popular functionality provided by BioMart (now discontinued due to data scalability issues) and address the data access requirements of the newly developed PRIDE Archive. Using the API (Application Programming Interface) it is now possible to programmatically query for and retrieve peptide and protein identifications, project and assay metadata and the originally submitted files. Searching and filtering is also possible by metadata information, such as sample details (e.g. species and tissues), instrumentation (mass spectrometer), keywords and other provided annotations. The PRIDE Archive web services were first made available in April 2014. The API has already been adopted by a few applications and standalone tools such as PeptideShaker, PRIDE Inspector, the Unipept web application and the Python-based BioServices package. This application is free and open to all users with no login requirement and can be accessed at http://www.ebi.ac.uk/pride/ws/archive/. PMID:25904633

  17. Multimedia medical archiving system

    Science.gov (United States)

    Sood, Arun K.; Atallah, George C.; Rao, Amar; Perez-Lopez, Kathleen G.; Freedman, Matthew T.

    1995-11-01

    The demand for digital radiological imaging and archiving applications has been increasingly rapidly. These digital applications offer significant advantages to the physician over the traditional film-based technique. They result in faster and better quality services, support remote access and conferencing capabilities, provide on demand service availability, eliminate film processing costs, and most significantly, they are suitable services for the evolving global information super highway. Several existing medical multimedia systems incorporate and utilize those advanced technical features. However, radiologists are seeking an order of magnitude improvement in the overall current system design and performance indices (such as transactions response times, system utilization and throughput). One of the main technical concern radiologists are raising is the miss-filing occurrence. This even will decrease the radiologist productivity; introduce unnecessarily workload; and will result in total customer dissatisfaction. This paper presents Multimedia Medical Archiving System, which can be used in hospitals and medical centers for storing and retrieving radiological images. Furthermore, this paper emphasizes a viable solution for the miss-filing problem. The results obtained demonstrate and quantify the improvement in the overall radiological operations. Specifically this paper demonstrates an order of 80% improvement in the response time for retrieving images. This enhancement in system performance directly translates to a tremendous improvement in the radiologist's productivity.

  18. Archive of Geosample Data and Information from the U.S. Geological Survey (USGS) Coastal and Marine Geology Program (CMGP) St. Petersburg Coastal and Marine Science Center (SPCMSC) Samples Repository

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The U.S. Geological Survey Coastal and Marine Geology Program (CMGP) St. Petersburg Coastal and Marine Science Center (SPCMSC) Samples Repository is a partner in...

  19. Archive of Geosample Data and Information from the U.S. Geological Survey (USGS) Coastal and Marine Geology Program (CMGP) Woods Hole Coastal and Marine Science Center (WHCMSC) Samples Repository

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The U.S. Geological Survey Coastal and Marine Geology Program (CMGP) Woods Hole Coastal and Marine Science Center (WHCMSC) Samples Repository is a partner in the...

  20. Archive of Geosample Data and Information from the U.S. Geological Survey (USGS) Coastal and Marine Geology Program (CMGP) Pacific Coastal and Marine Science Center (PCMSC) Samples Repository

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The U.S. Geological Survey Coastal and Marine Geology Program (CMGP) Pacific Coastal and Marine Science Center (PCMSC) Samples Repository is a partner in the Index...

  1. Doublecortin-like kinase 1 is elevated serologically in pancreatic ductal adenocarcinoma and widely expressed on circulating tumor cells.

    Directory of Open Access Journals (Sweden)

    Dongfeng Qu

    Full Text Available Doublecortin-like kinase 1 (DCLK1 is a putative pancreatic stem cell marker and is upregulated in pancreatic cancer, colorectal cancer, and many other solid tumors. It marks tumor stem cells in mouse models of intestinal neoplasia. Here we sought to determine whether DCLK1 protein can be detected in the bloodstream and if its levels in archived serum samples could be quantitatively assessed in pancreatic cancer patients. DCLK1 specific ELISA, western blotting, and immunohistochemical analyses were used to determine expression levels in the serum and staining intensity in archived tumor tissues of pancreatic ductal adenocarcinoma (PDAC patients and in pancreatic cancer mouse models. DCLK1 levels in the serum were elevated in early stages of PDAC (stages I and II compared to healthy volunteers (normal controls. No differences were observed between stages III/IV and normal controls. In resected surgical tissues, DCLK1 expression intensity in the stromal cells was significantly higher than that observed in tumor epithelial cells. Circulating tumor cells were isolated from KPCY mice and approximately 52% of these cells were positive for Dclk1 staining. Dclk1 levels in the serum of KPC mice were also elevated. We have previously demonstrated that DCLK1 plays a potential role in regulating epithelial mesenchymal transition (EMT. Given the increasingly recognized role of EMT derived stem cells in cancer progression and metastasis, we hypothesize that DCLK1 may contribute to the metastatic process. Taken together, our results suggest that DCLK1 serum levels and DCLK1 positive circulating tumor cells should be further assessed for their potential diagnostic and prognostic significance.

  2. (Per)Forming Archival Research Methodologies

    Science.gov (United States)

    Gaillet, Lynee Lewis

    2012-01-01

    This article raises multiple issues associated with archival research methodologies and methods. Based on a survey of recent scholarship and interviews with experienced archival researchers, this overview of the current status of archival research both complicates traditional conceptions of archival investigation and encourages scholars to adopt…

  3. Ethics and Truth in Archival Research

    Science.gov (United States)

    Tesar, Marek

    2015-01-01

    The complexities of the ethics and truth in archival research are often unrecognised or invisible in educational research. This paper complicates the process of collecting data in the archives, as it problematises notions of ethics and truth in the archives. The archival research took place in the former Czechoslovakia and its turbulent political…

  4. Profiling of adrenocorticotropic hormone and arginine vasopressin in human pituitary gland and tumor thin tissue sections using droplet-based liquid-microjunction surface-sampling-HPLC-ESI-MS-MS.

    Science.gov (United States)

    Kertesz, Vilmos; Calligaris, David; Feldman, Daniel R; Changelian, Armen; Laws, Edward R; Santagata, Sandro; Agar, Nathalie Y R; Van Berkel, Gary J

    2015-08-01

    Described here are the results from the profiling of the proteins arginine vasopressin (AVP) and adrenocorticotropic hormone (ACTH) from normal human pituitary gland and pituitary adenoma tissue sections, using a fully automated droplet-based liquid-microjunction surface-sampling-HPLC-ESI-MS-MS system for spatially resolved sampling, HPLC separation, and mass spectrometric detection. Excellent correlation was found between the protein distribution data obtained with this method and data obtained with matrix-assisted laser desorption/ionization (MALDI) chemical imaging analyses of serial sections of the same tissue. The protein distributions correlated with the visible anatomic pattern of the pituitary gland. AVP was most abundant in the posterior pituitary gland region (neurohypophysis), and ATCH was dominant in the anterior pituitary gland region (adenohypophysis). The relative amounts of AVP and ACTH sampled from a series of ACTH-secreting and non-secreting pituitary adenomas correlated with histopathological evaluation. ACTH was readily detected at significantly higher levels in regions of ACTH-secreting adenomas and in normal anterior adenohypophysis compared with non-secreting adenoma and neurohypophysis. AVP was mostly detected in normal neurohypophysis, as expected. This work reveals that a fully automated droplet-based liquid-microjunction surface-sampling system coupled to HPLC-ESI-MS-MS can be readily used for spatially resolved sampling, separation, detection, and semi-quantitation of physiologically-relevant peptide and protein hormones, including AVP and ACTH, directly from human tissue. In addition, the relative simplicity, rapidity, and specificity of this method support the potential of this basic technology, with further advancement, for assisting surgical decision-making. Graphical Abstract Mass spectrometry based profiling of hormones in human pituitary gland and tumor thin tissue sections. PMID:26084546

  5. Tumor classification: molecular analysis meets Aristotle

    OpenAIRE

    Berman Jules J

    2004-01-01

    Abstract Background Traditionally, tumors have been classified by their morphologic appearances. Unfortunately, tumors with similar histologic features often follow different clinical courses or respond differently to chemotherapy. Limitations in the clinical utility of morphology-based tumor classifications have prompted a search for a new tumor classification based on molecular analysis. Gene expression array data and proteomic data from tumor samples will provide complex data that is unobt...

  6. Correlation of tumor-infiltrating lymphocytes to histopathological features and molecular phenotypes in canine mammary carcinoma: A morphologic and immunohistochemical morphometric study.

    Science.gov (United States)

    Kim, Jong-Hyuk; Chon, Seung-Ki; Im, Keum-Soon; Kim, Na-Hyun; Sur, Jung-Hyang

    2013-04-01

    Abundant lymphocyte infiltration is frequently found in canine malignant mammary tumors, but the pathological features and immunophenotypes associated with the infiltration remain to be elucidated. The aim of the present study was to evaluate the relationship between lymphocyte infiltration, histopathological features, and molecular phenotype in canine mammary carcinoma (MC). The study was done with archived formalin-fixed, paraffin-embedded samples (n = 47) by histologic and immunohistochemical methods. The degree of lymphocyte infiltration was evaluated by morphologic analysis, and the T- and B-cell populations as well as the T/B-cell ratio were evaluated by morphometric analysis; results were compared with the histologic features and molecular phenotypes. The degree of lymphocyte infiltration was significantly higher in MCs with lymphatic invasion than in those without lymphatic invasion (P aggressive histologic features, lymphocytes may be important for tumor aggressiveness and greater malignant behavior in the tumor microenvironment. PMID:24082407

  7. Newspaper archives : a knowledge asset

    OpenAIRE

    Pujari, Anita; Pai, Priya

    2005-01-01

    This paper deals with Newspaper Content as a source of knowledge and how Times Archives of the Times Group has converted the 166-year span of socio-political content of “The Times of India” and the 43 year economic and business barometer “The Economic Times” into an easily accessible Archive. The value of this Archive as a Knowledge Asset lies in its potential of being recalled, researched, reused and re-expressed by the various ventures of the Group. This paper describes the process of Micro...

  8. Download - Society Catalog | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...ip (41.9 KB) - Downlaod via FTP Joomla SEF URLs by Artio About This Database Database Description Download License Update History

  9. Download - Trypanosomes Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...earch and download Downlaod via FTP Joomla SEF URLs by Artio About This Database Database Description Download License Update History

  10. Download - RGP gmap | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available FTP Joomla SEF URLs by Artio About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - RGP gmap | LSDB Archive ...

  11. Open archive solutions to traditional archive/library cooperation

    Directory of Open Access Journals (Sweden)

    Donatella Castelli

    2003-09-01

    Full Text Available The diffusion of Internet is changing the role of archives and libraries and it is opening a wide range of new possibilities. The new vision is that in few years it will be possible to cross-access multiple libraries, archives, museums, and data repositories. The implementation of this revolutionary vision requires the solution of a number of technical, organizational, sociological, and economical issues. Recently, the proposal of a new, low cost technical solution for open repositories of pre-print material, the Open Archives Initiative Protocol for Metadata Harvesting ( OAI-PMH, has greatly stimulated the discussion about these issues in many application frameworks. This paper overviews the status of this discussion in the library and conventional archives frameworks.

  12. License - Plabrain DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us Plabrain... . If you use data from this database, please be sure attribute this database as follows: Plabrain DB © 2010...me and URL of this database (http://dbarchive.lifesciencedb.jp/english/en/plabrain-db/desc.html) in the arti...se Database Description Download License Update History of This Database Site Policy | Contact Us License - Plabrain DB | LSDB Archive ...

  13. Small Data Archives and Libraries

    Science.gov (United States)

    Holl, A.

    2010-10-01

    Preservation is important for documenting original observations, and existing data are an important resource which can be re-used. Observatories should set up electronic data archives and formulate archiving policies. VO (Virtual Observatory) compliance is desirable; even if this is not possible, at least some VO ideas should be applied. Data archives should be visible and their data kept on-line. Metadata should be plentiful, and as standard as possible, just like file formats. Literature and data should be cross-linked. Libraries can play an important role in this process. In this paper, we discuss data archiving for small projects and observatories. We review the questions of digitization, cost factors, manpower, organizational structure and more.

  14. NCEI Marine Geology Data Archive

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Marine Geologic data compilations and reports in the NCEI archive are from academic and government sources around the world. Over ten terabytes of analyses,...

  15. Archiving in the networked world

    OpenAIRE

    Seadle, Michael

    2011-01-01

    Purpose – This paper aims to focus on how long-term digital archiving systems are tested and what benchmarks and other metrics are necessary for that testing to produce data that the community can use to make decisions. Design/methodology/approach – The article reviews recent literature about digital archiving systems involving public and semi-public tests. It then looks specifically at the rules and metrics needed for doing public or semi-public testing for three specific issues: triggeri...

  16. Applied Archival Downloading with Wget

    OpenAIRE

    Kellen Kurschinski

    2013-01-01

    Archival websites offer a wealth of resources to historians, but increased accessibility does not always translate into increased utility. In other words, while online collections often allow historians to access hitherto unavailable or cost-prohibitive materials, they can also be limited by the manner in which content is presented and organized. Take for example the Indian Affairs Annual Reports database hosted on the Library and Archives Canada [LAC] website. Say you wanted to download an e...

  17. Tumor de Krukenberg Krunkenberg's tumor

    Directory of Open Access Journals (Sweden)

    Daisy Hernández Durán

    2011-09-01

    Full Text Available El tumor de Krukenberg supone el 30-40 % de los cánceres metastásicos al ovario y el 1-2 % de todos los tumores malignos de ovario. En la actualidad, y pese a que el concepto de tumor de Krukenberg ha sido usado para referirse a todos los tumores metastásicos del ovario, se consideran como tal a los que tienen un origen digestivo. Su pronóstico es malo con raras supervivencias más allá del año. Se presenta un caso de una paciente femenina de 38 años de edad, que ingresa por ascitis moderada, anorexia y pérdida de peso, a la cual se le realizó una laparotomía con el posible diagnóstico de un proceso oncoproliferativo del ovario y el diagnóstico histopatológico arrojó un tumor de Krukenberg.Krukenberg's tumor accounts for 30-40 % of ovarian metastatic cancer and for the 1-2 % of all ovarian malignant tumors. Nowadays and in spite of the fact that the concept of Krukenberg' tumor has been used to refer to all ovarian metastatic tumors those with a digestive origin, its prognosis if bad with only a few survivals beyond one year. This is the case of a female patient aged 38 admitted due to a moderate ascites, anorexia and lose weight undergoes laparotomy with the possible diagnosis of a oncoproliferous ovarian process and the histopathological diagnosis showed a Krukenberg's tumor.

  18. Brain tumor

    International Nuclear Information System (INIS)

    BNCT in the past was not widely accepted because of poor usability of a nuclear reactor as a neutron source. Recently, technical advancements in the accelerator field have made accelerator-based BNCT feasible. Consequently, clinical trials of intractable brain tumors have started using it since 2012. In this review, our clinical results obtained from conventional reactor-based BNCT for treatment of brain tumors are introduced. It is strong hope that accelerator-based BNCT becomes a standard therapy for current intractable brain tumors. (author)

  19. Amplification of Whole Tumor Genomes and Gene-by-Gene Mapping of Genomic Aberrations from Limited Sources of Fresh-Frozen and Paraffin-Embedded DNA

    OpenAIRE

    Bredel, Markus; Bredel, Claudia; Juric, Dejan; Kim, Young; Vogel, Hannes; Harsh, Griffith R.; Recht, Lawrence D.; Pollack, Jonathan R.; Sikic, Branimir I.

    2005-01-01

    Sufficient quantity of genomic DNA can be a bottleneck in genome-wide analysis of clinical tissue samples. DNA polymerase Phi29 can be used for the random-primed amplification of whole genomes, although the amplification may introduce bias in gene dosage. We have performed a detailed investigation of this technique in archival fresh-frozen and formalin-fixed/paraffin-embedded tumor DNA by using cDNA microarray-based comparative genomic hybridization. Phi29 amplified DNA from matched pairs of ...

  20. Optimisation and validation of methods to assess single nucleotide polymorphisms (SNPs) in archival histological material

    DEFF Research Database (Denmark)

    Andreassen, C N; Sørensen, Flemming Brandt; Overgaard, J;

    2004-01-01

    only archival specimens are available. This study was conducted to validate protocols optimised for assessment of SNPs based on paraffin embedded, formalin fixed tissue samples. PATIENTS AND METHODS: In 137 breast cancer patients, three TGFB1 SNPs were assessed based on archival histological specimens....... In 37 of these patients, the SNPs were also assessed using cultured fibroblasts and the assays were validated by direct comparison of the results. From the remaining 100 patients, only archival material was available. In these patients, the existence of a genetic linkage pattern between the assessed...... precipitation). RESULTS: Assessment of SNPs based on archival histological material is encumbered by a number of obstacles and pitfalls. However, these can be widely overcome by careful optimisation of the methods used for sample selection, DNA extraction and PCR. Within 130 samples that fulfil the criteria...

  1. Bone Tumor

    Science.gov (United States)

    ... the knee in either the femur (thigh) or tibia (shinbone). Other common locations include the hip and ... bone that is weakened by a tumor to fracture, or break. This may be severely painful. Occasionally, ...

  2. The Planck Legacy Archive

    Science.gov (United States)

    Dupac, X.; Arviset, C.; Fernandez Barreiro, M.; Lopez-Caniego, M.; Tauber, J.

    2015-12-01

    The Planck Collaboration has released in 2015 their second major dataset through the Planck Legacy Archive (PLA). It includes cosmological, Extragalactic and Galactic science data in temperature (intensity) and polarization. Full-sky maps are provided with unprecedented angular resolution and sensitivity, together with a large number of ancillary maps, catalogues (generic, SZ clusters and Galactic cold clumps), time-ordered data and other information. The extensive cosmological likelihood package allows cosmologists to fully explore the plausible parameters of the Universe. A new web-based PLA user interface is made public since Dec. 2014, allowing easier and faster access to all Planck data, and replacing the previous Java-based software. Numerous additional improvements to the PLA are also being developed through the so-called PLA Added-Value Interface, making use of an external contract with the Planetek Hellas and Expert Analytics software companies. This will allow users to process time-ordered data into sky maps, separate astrophysical components in existing maps, simulate the microwave and infrared sky through the Planck Sky Model, and use a number of other functionalities.

  3. Archival storage solutions for PACS

    Science.gov (United States)

    Chunn, Timothy

    1997-05-01

    While they are many, one of the inhibitors to the wide spread diffusion of PACS systems has been robust, cost effective digital archive storage solutions. Moreover, an automated Nearline solution is key to a central, sharable data repository, enabling many applications such as PACS, telemedicine and teleradiology, and information warehousing and data mining for research such as patient outcome analysis. Selecting the right solution depends on a number of factors: capacity requirements, write and retrieval performance requirements, scaleability in capacity and performance, configuration architecture and flexibility, subsystem availability and reliability, security requirements, system cost, achievable benefits and cost savings, investment protection, strategic fit and more.This paper addresses many of these issues. It compares and positions optical disk and magnetic tape technologies, which are the predominant archive mediums today. Price and performance comparisons will be made at different archive capacities, plus the effect of file size on storage system throughput will be analyzed. The concept of automated migration of images from high performance, high cost storage devices to high capacity, low cost storage devices will be introduced as a viable way to minimize overall storage costs for an archive. The concept of access density will also be introduced and applied to the selection of the most cost effective archive solution.

  4. Vendor neutral archive in PACS

    Directory of Open Access Journals (Sweden)

    Tapesh Kumar Agarwal

    2012-01-01

    Full Text Available An archive is a location containing a collection of records, documents, or other materials of historical importance. An integral part of Picture Archiving and Communication System (PACS is archiving. When a hospital needs to migrate a PACS vendor, the complete earlier data need to be migrated in the format of the newly procured PACS. It is both time and money consuming. To address this issue, the new concept of vendor neutral archive (VNA has emerged. A VNA simply decouples the PACS and workstations at the archival layer. This is achieved by developing an application engine that receives, integrates, and transmits the data using the different syntax of a Digital Imaging and Communication in Medicine (DICOM format. Transferring the data belonging to the old PACS to a new one is performed by a process called migration of data. In VNA, a number of different data migration techniques are available to facilitate transfer from the old PACS to the new one, the choice depending on the speed of migration and the importance of data. The techniques include simple DICOM migration, prefetch-based DICOM migration, medium migration, and the expensive non-DICOM migration. "Vendor neutral" may not be a suitable term, and "architecture neutral," "PACS neutral," "content neutral," or "third-party neutral" are probably better and preferred terms. Notwithstanding this, the VNA acronym has come to stay in both the medical IT user terminology and in vendor nomenclature, and radiologists need to be aware of its impact in PACS across the globe.

  5. The ``One Archive'' for JWST

    Science.gov (United States)

    Greene, G.; Kyprianou, M.; Levay, K.; Sienkewicz, M.; Donaldson, T.; Dower, T.; Swam, M.; Bushouse, H.; Greenfield, P.; Kidwell, R.; Wolfe, D.; Gardner, L.; Nieto-Santisteban, M.; Swade, D.; McLean, B.; Abney, F.; Alexov, A.; Binegar, S.; Aloisi, A.; Slowinski, S.; Gousoulin, J.

    2015-09-01

    The next generation for the Space Telescope Science Institute data management system is gearing up to provide a suite of archive system services supporting the operation of the James Webb Space Telescope. We are now completing the initial stage of integration and testing for the preliminary ground system builds of the JWST Science Operations Center which includes multiple components of the Data Management Subsystem (DMS). The vision for astronomical science and research with the JWST archive introduces both solutions to formal mission requirements and innovation derived from our existing mission systems along with the collective shared experience of our global user community. We are building upon the success of the Hubble Space Telescope archive systems, standards developed by the International Virtual Observatory Alliance, and collaborations with our archive data center partners. In proceeding forward, the “one archive” architectural model presented here is designed to balance the objectives for this new and exciting mission. The STScI JWST archive will deliver high quality calibrated science data products, support multi-mission data discovery and analysis, and provide an infrastructure which supports bridges to highly valued community tools and services.

  6. The new European Hubble archive

    Science.gov (United States)

    De Marchi, Guido; Arevalo, Maria; Merin, Bruno

    2016-01-01

    The European Hubble Archive (hereafter eHST), hosted at ESA's European Space Astronomy Centre, has been released for public use in October 2015. The eHST is now fully integrated with the other ESA science archives to ensure long-term preservation of the Hubble data, consisting of more than 1 million observations from 10 different scientific instruments. The public HST data, the Hubble Legacy Archive, and the high-level science data products are now all available to scientists through a single, carefully designed and user friendly web interface. In this talk, I will show how the the eHST can help boost archival research, including how to search on sources in the field of view thanks to precise footprints projected onto the sky, how to obtain enhanced previews of imaging data and interactive spectral plots, and how to directly link observations with already published papers. To maximise the scientific exploitation of Hubble's data, the eHST offers connectivity to virtual observatory tools, easily integrates with the recently released Hubble Source Catalog, and is fully accessible through ESA's archives multi-mission interface.

  7. Download - RGP physicalmap | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us RGP physical...e File Simple search and download 1 README README_e.html - 2 YAC contig information rgp_physicalmap_yac_cont...igs.zip (1 KB) Simple search and download 3 YAC clone information rgp_physicalmap_yac_clones.zip (18.7 KB) S...imple search and download 4 Insert size of YAC clones rgp_physicalmap_insert_size...ase Description Download License Update History of This Database Site Policy | Contact Us Download - RGP physicalmap | LSDB Archive ...

  8. The Need to Ethics on Archive Profession

    OpenAIRE

    Hind Ulwy

    2007-01-01

    An article about ethics in archive profession, it states the concept of the profession and professional ethics, then the relation between the ethical responsibility and legal responsibility. Finally, it discuss the need for ethical rules in archive profession

  9. IMAGES: An IMage Archive Generated for Exoplanet Surveys

    Science.gov (United States)

    Tanner, A.

    2014-03-01

    Over the past few years the advent of adaptive optics and central star suppression has resulted in multiple low-mass companion surveys of both main sequence and young star systems. The goal of these surveys is to directly detect sub-stellar companions such as brown dwarfs (10 AU from their host stars. To date, direct imaging studies have produced a sample of directly imaged, very low mass objects (3-22 MJ, Schneider 2013). This small sample of very low-mass companions results from observations of over one thousand mature and young stars. Since many AO observing programs are quick to publish interesting common proper motion companions but slow to publish the results of the entire survey, there is a surplus of unpublished images that can be utilized for both future high contrast imaging programs and, when combined into a ~3000 star survey, provide further constraints on the companion fraction as a function of age, spectral type, and planet formation environment. Therefore, it is the goal of the IMAGES program to complete a high contrast imaging archive. Our database will help scientists use their telescope time more efficiently and would increase the discovery rate. This archive will also serve as a testbed for the development of a user-friendly, user contributor archive in which astronomers can upload new archival high contrast images in addition to downloading.

  10. Renal Tumor Biopsy Technique

    Institute of Scientific and Technical Information of China (English)

    Lei Zhang; Xue-Song Li; Li-Qun Zhou

    2016-01-01

    Objective:To review hot issues and future direction of renal tumor biopsy (RTB) technique.Data Sources:The literature concerning or including RTB technique in English was collected from PubMed published from 1990 to 2015.Study Selection:We included all the relevant articles on RTB technique in English,with no limitation of study design.Results:Computed tomography and ultrasound were usually used for guiding RTB with respective advantages.Core biopsy is more preferred over fine needle aspiration because of superior accuracy.A minimum of two good-quality cores for a single renal tumor is generally accepted.The use of coaxial guide is recommended.For biopsy location,sampling different regions including central and peripheral biopsies are recommended.Conclusion:In spite of some limitations,RTB technique is relatively mature to help optimize the treatment of renal tumors.

  11. The Archive of the Hero City Novorossiysk

    OpenAIRE

    Sergey A. Saneev

    2015-01-01

    The article considers the history and current state of the archive of the city Novorossiysk. The conversions of the Novorossiysk archive were closely connected with the milestones of the city’s history. The author analyzes the changes in the system of completion of funds, material resources and staffing of the archive. The most commonly used funds and the possibilities of using archival documents by researchers are characterized.

  12. Models and methods for web archive crawling

    OpenAIRE

    Denev, Dimitar

    2012-01-01

    Web archives offer a rich and plentiful source of information to researchers, analysts, and legal experts. For this purpose, they gather Web sites as the sites change over time. In order to keep up to high standards of data quality, Web archives have to collect all versions of the Web sites. Due to limited resuources and technical constraints this is not possible. Therefore, Web archives consist of versions archived at various time points without guarantee for mutual consistency. This thes...

  13. Imaging of brain tumors

    International Nuclear Information System (INIS)

    The contents are diagnostic approaches, general features of tumors -hydrocephalus, edema, attenuation and/or intensity value, hemorrhage, fat, contrast enhancement, intra-axial supratentorial tumors - tumors of glial origin, oligodendrogliomas, ependymomas, subependymomas, subependymal giant cell astrocytomas, choroid plexus papilloma; midline tumors - colloid cysts, craniopharyngiomas; pineal region tumors and miscellaneous tumors i.e. primary intracerebral lymphoma, primitive neuroectodermal tumors, hemangioblastomas; extraaxial tumors - meningiomas; nerve sheath tumors -schwannomas, epidermoids, dermoids, lipomas, arachnoid cysts; metastatic tumors (8 refs.)

  14. The mycobiota associated with paper archives and their potential control

    Directory of Open Access Journals (Sweden)

    SAIFELDIN A. F. EL-NAGERABI

    2014-07-01

    Full Text Available El-Nagerabi SAF, Elshafie AE, Al-Hinai UA. 2014. The mycobiota associated with paper archives and their potential control. Nusantara Bioscience 6: 19-25. Historical collections kept in archives and libraries represent a cultural and artistic heritage of innumerable value. Recently in Oman, more than seventy thousand documents were collected from different countries and displayed as archives showed evident sign of mold contamination. The objectives of the present study were to screen these archives for mold invasion and a test for the effective control measure. For this, 102 samples were collected from documents of different sources and incubated on potato dextrose agar (PDA at ambient temperature (25○C±2. The isolated fungi were identified microscopically and confirmed with DNA extraction, PCR and DNA sequencing. Twenty-two fungal species belonging to 11 genera were recovered. The genus Penicillium (46.8% was the most prevalent, followed by Aspergillus (30.7%, Cladosporium (7%, Rhizopus (4%, and Chaetomium (3.5% whereas the remaining 6 genera represent only 8%. Eleven species were previously reported from similar substrates, whereas 11 species and one genus are new records for the mycoflora of archives. Sodium hypochlorite at 0.3-5.2% completely inhibited the fungal growth of the 10 tested fungal isolates with minimum inhibition concentration at 0.7%. Fumigation of books with 0.7-5.2% sodium hypochlorite completely inhibited all fungi without evident damage of the documents or ink discoloration. Therefore, sodium hypochlorite can be recommended as effective and eco-friendly disinfectant for archives comparable to other hazardous chemicals.

  15. Physical Review Online Archives (PROLA)

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, T.; Davies, J.; Kilman, D.; Laroche, F. [and others

    1997-05-01

    In cooperation with the American Physical Society, the Computer Research and Applications Group (CIC-3 -- see Section 13 for an acronym glossary) at Los Alamos National Laboratory has developed and deployed a journal archive system called, The Physical Review OnLine Archive (PROLA). It is intended to be a complete, full service on-line archive of the existing issues of the journal Physical Review from its inception to the advent of a full-service electronic version. The fundamental goals of PROLA are to provide screen-viewable and printable images of every article, full-text and fielded search capability, good browsing features, direct article retrieval tools, and hyperlinking to all references, errata, and comments. The research focus is on transitioning large volumes of paper journals to a modern electronic environment.

  16. BPA and BSH accumulation in experimental tumors

    International Nuclear Information System (INIS)

    The accumulation of boronated compounds into tumors is a critical component to the success of BNCT. To date, great variability has been demonstrated in the tumor:blood ratio achieved in samples both from different patients and within samples taken from the same patient. The factors that probably influence the level of uptake include the vascular perfusion within the tumor, the permeability of these vessels and the viability of the tumor cells themselves. These experiments were designed to measure these various factors in different experimental tumor models and to relate these measurements to the uptake of both BPA (Boronophenylalanine) and BSH (Sodiumborocaptate). They demonstrate that within different tumors there can be wide variations in the vascular parameters. In addition, the viability of the tumor cells may also be an important determinant of tumor uptake. (author)

  17. Encoded Archival Description as a Halfway Technology

    Science.gov (United States)

    Dow, Elizabeth H.

    2009-01-01

    In the mid 1990s, Encoded Archival Description (EAD) appeared as a revolutionary technology for publishing archival finding aids on the Web. The author explores whether or not, given the advent of Web 2.0, the archival community should abandon EAD and look for something to replace it. (Contains 18 notes.)

  18. 50 CFR 635.33 - Archival tags.

    Science.gov (United States)

    2010-10-01

    ... 50 Wildlife and Fisheries 8 2010-10-01 2010-10-01 false Archival tags. 635.33 Section 635.33..., DEPARTMENT OF COMMERCE ATLANTIC HIGHLY MIGRATORY SPECIES Management Measures § 635.33 Archival tags. (a) Implantation report. Any person affixing or implanting an archival tag into a regulated species must...

  19. 36 CFR 1275.24 - Archival processing.

    Science.gov (United States)

    2010-07-01

    ... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Archival processing. 1275.24... THE NIXON ADMINISTRATION Preservation and Protection § 1275.24 Archival processing. When authorized by the Archivist and until the commencement of archival processing in accordance with subpart D of...

  20. Lung tumors

    International Nuclear Information System (INIS)

    This volume 17 in the series of clinicoradiological seminars deals with malignant lung tumors. Twenty-four authors contributed to this comprehensive survey of current knowledge and methods, with about half of the contributions in the monography being concerned with aetiology and epidemiology of the lung, anatomy of the lung and anatomy of lung tumors, as well as with the current diagnostic methods. The latter are discussed in great detail and include CT, differential diagnosis of pulmonary nodules, angiography for lung tumor diagnostics, and nuclear medical diagnostics. The main issue of the other contributions is a new approach in oncology that works towards interdisciplinary exchange of information among experts in search for improved therapies. (orig./MG) With 44 tabs., 111 figs

  1. Download - Open TG-GATEs | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us Open TG-GATEs Down...load First of all, please read the license of this database. Data names and data descriptions are about the down...File Simple search and download 1 README README_e.html - 2 Compound list open_tggates_main.zip (6.4 KB) Simple search and down...te.zip (199 KB) Simple search and download 5 Cell sample open_tggates_cell.zip (54 KB) Simple search and down...load 6 Cell viability open_tggates_cell_viability.zip (51 KB) Simple search and download 7 Individual list

  2. Gene expression data (CEL files) - Open TG-GATEs | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us Open TG-GATEs Gene expres...sion data (CEL files) Data detail Data name Gene expression data (CEL files) Descri...Tab Separated Value (TSV) format is included. CEL is one of the file formats that expresses gene expression ...data (raw data) generated from Affymetrix GeneChip®. Data file File name: Gene expression data from rat samp...ze: 12.0GB total File name: Gene expression data from human samples File URL: ftp://ftp.biosciencedbc.jp/arc

  3. Archiving in the networked world

    OpenAIRE

    Seadle, Michael

    2011-01-01

    Purpose – The purpose of this paper is to investigate how extensively LOCKSS/CLOCKSS, Portico, and e-Depot provide long-term digital archiving for the journals listed in the Directory of Open Access Journals (DOAJ). Design/methodology/approach – The paper uses publicly available online data, which are processed in a set of PERL programs to measure the number of DOAJ articles in the three archiving systems. Findings – The findings show that only 8 per cent of the DOAJ titles are in LOCKS...

  4. MESA: Mercator scheduler and archive system

    Science.gov (United States)

    Merges, Florian; Prins, Saskia; Pessemier, Wim; Raskin, Gert; Perez Padilla, Jesus; Van Winckel, Hans; Aerts, Conny

    2012-09-01

    We have developed an observing scheduling and archive system for the 1.2 meter Mercator Telescope. The goal was to optimize the specific niche of this modern small telescope in observational astrophysics: the building-up of long-term time series of photometric or high-resolution spectroscopic data with appropriate sampling for any given scientific program. This system allows PIs to easily submit their technical requirements and keep track of the progress of the observing programmes. The scheduling system provides the observer with an optimal schedule for the night which takes into account the current observing conditions as well as the priorities and requirements of the programmes in the queue. The observer can conveniently plan an observing night but also quickly adapt it to changing conditions. The archiving system automatically processes new files as they are created, including reduced data. It extracts the metadata and performs the normalization. A user can query, inspect and retrieve observing data. The progress of individual programmes, including timeline and reduced data plots can be seen at any time. Our MESA project is based on free and open source software (FOSS) using the Python programming language. The system is fully integrated with the Mercator Observing Control System1 (MOCS).

  5. Brain tumors

    International Nuclear Information System (INIS)

    Magnetic Resonance Tomography (MRT) is the method of choice for the diagnostics of cerebral gliomas, but the differentiation of tumour tissue from unspecific tissue changes is limited. Positron emission tomography (PET) and Single-Photon-Emission-Computed Tomography (SPECT) may offer relevant additional information which allows for a more accurate diagnostics in unclear situations. Especially, radiolabeled amino acids offer a better delineation of cerebral gliomas which allows an improved guidance of biopsy, planning of surgery and radiation therapy. Furthermore, amino acid imaging appears to be useful to differentiate tumor recurrence from unspecific posttherapeutic tissue, to predict the prognosis especially in low grade gliomas and to monitor the metabolic response during tumor therapy. (orig.)

  6. Determining the utility of veterinary tissue archives for retrospective DNA analysis.

    Science.gov (United States)

    Abed, Firas M; Dark, Michael J

    2016-01-01

    Histopathology tissue archives can be an important source of specimens for retrospective studies, as these include samples covering a large number of diseases. In veterinary medicine, archives also contain samples from a large variety of species and may represent naturally-occurring models of human disease. The formalin-fixed, paraffin-embedded (FFPE) tissues comprising these archives are rich resources for retrospective molecular biology studies and pilot studies for biomarkers, as evidenced by a number of recent publications highlighting FFPE tissues as a resource for analysis of specific diseases. However, DNA extracted from FFPE specimens are modified and fragmented, making utilization challenging. The current study examines the utility of FFPE tissue samples from a veterinary diagnostic laboratory archive in five year intervals from 1977 to 2013, with 2015 as a control year, to determine how standard processing and storage conditions has affected their utility for future studies. There was a significant difference in our ability to obtain large amplicons from samples from 2015 than from the remaining years, as well as an inverse correlation between the age of the samples and product size obtainable. However, usable DNA samples were obtained in at least some of the samples from all years tested, despite variable storage, fixation, and processing conditions. This study will help make veterinary diagnostic laboratory archives more useful in future studies of human and veterinary disease. PMID:27168995

  7. Determining the utility of veterinary tissue archives for retrospective DNA analysis

    Science.gov (United States)

    Abed, Firas M.

    2016-01-01

    Histopathology tissue archives can be an important source of specimens for retrospective studies, as these include samples covering a large number of diseases. In veterinary medicine, archives also contain samples from a large variety of species and may represent naturally-occurring models of human disease. The formalin-fixed, paraffin-embedded (FFPE) tissues comprising these archives are rich resources for retrospective molecular biology studies and pilot studies for biomarkers, as evidenced by a number of recent publications highlighting FFPE tissues as a resource for analysis of specific diseases. However, DNA extracted from FFPE specimens are modified and fragmented, making utilization challenging. The current study examines the utility of FFPE tissue samples from a veterinary diagnostic laboratory archive in five year intervals from 1977 to 2013, with 2015 as a control year, to determine how standard processing and storage conditions has affected their utility for future studies. There was a significant difference in our ability to obtain large amplicons from samples from 2015 than from the remaining years, as well as an inverse correlation between the age of the samples and product size obtainable. However, usable DNA samples were obtained in at least some of the samples from all years tested, despite variable storage, fixation, and processing conditions. This study will help make veterinary diagnostic laboratory archives more useful in future studies of human and veterinary disease. PMID:27168995

  8. Protein - TP Atlas | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available otein information on other websites. Data file File name: tp_atlas_protein.zip Fi...le URL: ftp://ftp.biosciencedbc.jp/archive/tp_atlas/LATEST/tp_atlas_protein.zip File size: 49.8 KB Simple se...arch URL http://togodb.biosciencedbc.jp/togodb/view/tp_atlas_protein#en Data acquisition method - Data analy

  9. Encoded Archival Context (EAC) and Archival Description: Rationale and Background

    Science.gov (United States)

    Szary, Richard V.

    2005-01-01

    The use of contextual information about the creators and users of archival and manuscript resources has always been a critical method for discovering and providing access to them. Traditionally, this information has been unstructured and ephemeral, being part of the knowledge that experienced staff bring to reference queries. The development of…

  10. Images - RPSD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available ures of the proteins of plant seven kinds, such as rice. Data file File name: rpsd_images.zip File URL: ftp:...//ftp.biosciencedbc.jp/archive/rpsd/LATEST/rpsd_images.zip File size: 18.3 MB Sim

  11. Expression of Hyaluronan in human tumor progression

    Directory of Open Access Journals (Sweden)

    Boregowda Rajeev K

    2006-01-01

    Full Text Available Abstract Background The development and progression of human tumors is accompanied by various cellular, biochemical and genetic alterations. These events include tumor cells interaction with extracellular matrix molecules including hyaluronan (HA. Hyaluronan is a large polysaccharide associated with pericellular matrix of proliferating, migrating cells. Its implication in malignant transformation, tumor progression and with the degree of differentiation in various invasive tumors has well accepted. It has been well known the role HA receptors in tumor growth and metastasis in various cancer tissues. Previously we have observed the unified over expression of Hyaluronic Acid Binding Protein (HABP, H11B2C2 antigen by the tumor cells in various types progressing tumor tissues with different grades. However, the poor understanding of relation between HA and HA-binding protein expression on tumor cells during tumor progression as well as the asymmetric observations of the role of HA expression in tumor progression prompted us to examine the degree of HA expression on tumor cells vs. stroma in various types of human tumors with different grades. Methods In the present study clinically diagnosed tumor tissue samples of different grades were used to screen the histopathological expression of hyaluronan by using b-PG (biotinylated proteoglycan as a probe and we compared the relative HA expression on tumor cells vs. stroma in well differentiated and poorly differentiated tumors. Specificity of the reaction was confirmed either by pre-digesting the tissue sections with hyaluronidase enzyme or by staining the sections with pre-absorbed complex of the probe and HA-oligomers. Results We show here the down regulation of HA expression in tumor cells is associated with progression of tumor from well differentiated through poorly differentiated stage, despite the constant HA expression in the tumor associated stroma. Conclusion The present finding enlighten the

  12. An Open Dataset for Research on Audio Field Recording Archives: freefield1010

    OpenAIRE

    Stowell, D; Plumbley, MD

    2014-01-01

    We introduce a free and open dataset of 7690 audio clips sampled from the field-recording tag in the Freesound audio archive. The dataset is designed for use in research related to data mining in audio archives of field recordings / soundscapes. Audio is standardised, and audio and metadata are Creative Commons licensed. We describe the data preparation process, characterise the dataset descriptively, and illustrate its use through an auto-tagging experiment.

  13. Central versus institutional self-archiving

    OpenAIRE

    Harnad, Stevan

    2006-01-01

    NIH's, PLoS's, the Wellcome Trust's and now the UK MRC's unreflective support for PubMed Central (PMC), a Central Repository (CR), as the locus for direct self-archiving by authors is very unfortunate for Institutional Repositories (IRs), for self-archiving, and for Open Access (OA) progress in general. Alma Swan has published key papers on both OA self-archiving policy and institutional versus central self-archiving (IRs vs. CRs) analysing the reasons. (a) Institutional self-archiving and ce...

  14. Archiving Reproducible Research with R and Dataverse

    DEFF Research Database (Denmark)

    Leeper, Thomas

    2014-01-01

    Reproducible research and data archiving are increasingly important issues in research involving statistical analyses of quantitative data. This article introduces the dvn package, which allows R users to publicly archive datasets, analysis files, codebooks, and associated metadata in Dataverse...... Network online repositories, an open-source data archiving project sponsored by Harvard University. In this article I review the importance of data archiving in the context of reproducible research, introduce the Dataverse Network, explain the implementation of the dvn package, and provide example code...... for archiving and releasing data using the package....

  15. Experiment list: SRX1528656 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available SRX1528656 mm9 Unclassified Unclassified Lung Lung tumors NA 30926044,96.2,8.5,340 ...GSM2037953: 2249 8 61-K27me3 ChIP sample rep4; Mus musculus; ChIP-Seq source_name=lung tumors || genotype=Kr

  16. Experiment list: SRX1528655 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available SRX1528655 mm9 Unclassified Unclassified Lung Lung tumors NA 36031976,94.2,15.3,603... GSM2037952: 2249 6 59-K27me3 ChIP sample rep3; Mus musculus; ChIP-Seq source_name=lung tumors || genotype=K

  17. Experiment list: SRX1528654 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available SRX1528654 mm9 Input control Input control Lung Lung tumors NA 28857200,98.0,9.8,50...6 GSM2037951: 2249 9 I58 Input sample rep2; Mus musculus; ChIP-Seq source_name=lung tumors || genotype=KrasG

  18. Experiment list: SRX695775 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available SRX695775 mm9 Input control Input control Lung Lung tumors NA 23147669,97.0,15.5,54...3 GSM1499208: Input sample rep1; Mus musculus; ChIP-Seq source_name=lung tumors || tissue=NSCLC orthotopic t

  19. Natural Learning Case Study Archives

    Science.gov (United States)

    Lawler, Robert W.

    2015-01-01

    Natural Learning Case Study Archives (NLCSA) is a research facility for those interested in using case study analysis to deepen their understanding of common sense knowledge and natural learning (how the mind interacts with everyday experiences to develop common sense knowledge). The database comprises three case study corpora based on experiences…

  20. Archived film analysis and restoration

    NARCIS (Netherlands)

    Rares, A.

    2004-01-01

    The progressive degradation of current film archives poses a serious threat to the preservation of our cultural and technical heritage. Digitization and digital restoration are currently the most viable solutions for the long term preservation and high quality restoration of filmed material. They al

  1. Teacher Evaluation: Archiving Teaching Effectiveness

    Science.gov (United States)

    Nielsen, Lance D.

    2014-01-01

    Teacher evaluation is a current hot topic within music education. This article offers strategies for K-12 music educators on how to promote their effectiveness as teachers through archival documentation in a teacher portfolio. Using the Danielson evaluation model (based on four domains of effective teaching practices), examples of music teaching…

  2. Preservation and Archives in Vietnam.

    Science.gov (United States)

    Henchy, Judith

    This report, based on visits to Vietnamese libraries and archives between 1987 and 1997, examines the largely unexplored corpus of Vietnamese textual resources in research institutions and libraries there and elsewhere, the associated problems of bibliographic control, and issues of preservation. The following topics are addressed: the history of…

  3. Analysis of aberrant methylation on promoter sequences of tumor suppressor genes and total DNA in sputum samples: a promising tool for early detection of COPD and lung cancer in smokers

    Directory of Open Access Journals (Sweden)

    Guzmán Leda

    2012-07-01

    Full Text Available Abstract Background Chronic obstructive pulmonary disease (COPD is a disorder associated to cigarette smoke and lung cancer (LC. Since epigenetic changes in oncogenes and tumor suppressor genes (TSGs are clearly important in the development of LC. In this study, we hypothesize that tobacco smokers are susceptible for methylation in the promoter region of TSGs in airway epithelial cells when compared with non-smoker subjects. The purpose of this study was to investigate the usefulness of detection of genes promoter methylation in sputum specimens, as a complementary tool to identify LC biomarkers among smokers with early COPD. Methods We determined the amount of DNA in induced sputum from patients with COPD (n = 23, LC (n = 26, as well as in healthy subjects (CTR (n = 33, using a commercial kit for DNA purification, followed by absorbance measurement at 260 nm. The frequency of CDKN2A, CDH1 and MGMT promoter methylation in the same groups was determined by methylation-specific polymerase chain reaction (MSP. The Fisher’s exact test was employed to compare frequency of results between different groups. Results DNA concentration was 7.4 and 5.8 times higher in LC and COPD compared to the (CTR (p  Conclusions We provide evidence that aberrant methylation of TSGs in samples of induced sputum is a useful tool for early diagnostic of lung diseases (LC and COPD in smoker subjects. Virtual slides The abstract MUST finish with the following text: Virtual Slides The virtual slide(s for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1127865005664160

  4. Frequency of Odontogenic Tumors in Zahedan-Iran from 2000 to 2010

    OpenAIRE

    Hamideh Kadeh; Shirin Saravani; Tahereh Nosratzehi; Feizorrahman Rasulizadeh

    2012-01-01

    Introduction: Odontogenic tumors constitute an important aspect of oral and maxillofacial pathology. Frequency of odontogenic tumors varies in different societies but no study has been done in Zahedan so far. The purpose of this study was to achieve the sex, location and age distribution of odontogenic tumors and frequency of each one in a period of ten years.Materials & Methods: In this study, documents in archive of maxillofacial pathology department of Zahedan dental school, Khatamolanbia,...

  5. Sample (S): SE25_S02 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE25_S02 Brassica oleracea var. capitata Satsuki Jouou Leaf Brassica oleracea var. ...capitata NCBI taxonomy:3716 Brassica oleracea var. capitata are grown at agricultural field in natural conditions. ...

  6. Sample (S): SE25_S06 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE25_S06 Brassica oleracea var. capitata K7-705 Leaf Brassica oleracea var. capitata NCBI taxonomy:3716 Brassica oleracea var. capitata are grown at agricultural field in natural conditions. ...

  7. Sample (S): SE10_S02 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE10_S02 Brassica oleracea var. capitata Hatukoi Leaf Brassica oleracea var. capitata NCBI taxonomy:3716 Bra...ssica oleracea var. capitata plants are grown in the open field with low phosphorus condition (25kg/10a). ...

  8. Sample (S): SE25_S07 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE25_S07 Brassica oleracea var. capitata T-767 Leaf Brassica oleracea var. capitata NCBI taxonomy:3716 Brass...ica oleracea var. capitata are grown at agricultural field in natural conditions. ...

  9. Sample (S): SE25_S03 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE25_S03 Brassica oleracea var. capitata Satsukiou Leaf Brassica oleracea var. capi...tata NCBI taxonomy:3716 Brassica oleracea var. capitata are grown at agricultural field in natural conditions. ...

  10. Sample (S): SE27_S02 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE27_S02 Brassica oleracea var. capitata YR Tenkuu Leaf Brassica oleracea var. capitata NCBI taxonomy:3716 Brassica oleracea var. capitata plants are grown at agricultural field under normal film. ...

  11. Sample (S): SE25_S05 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE25_S05 Brassica oleracea var. capitata Hatukoi Leaf Brassica oleracea var. capitata NCBI taxonomy:3716 Bra...ssica oleracea var. capitata are grown at agricultural field in natural conditions. ...

  12. Sample (S): SE25_S10 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE25_S10 Brassica oleracea var. capitata Kanpachi Leaf Brassica oleracea var. capit...ata NCBI taxonomy:3716 Brassica oleracea var. capitata are grown at agricultural field in natural conditions. ...

  13. Sample (S): SE10_S03 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE10_S03 Brassica oleracea var. capitata Hatukoi Leaf Brassica oleracea var. capitata NCBI taxonomy:3716 Bra...ssica oleracea var. capitata plants are grown in the open field with no phosphorus condition (0kg/10a). ...

  14. Sample (S): SE25_S01 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE25_S01 Brassica oleracea var. capitata Kanroku Leaf Brassica oleracea var. capitata NCBI taxonomy:3716 Bra...ssica oleracea var. capitata plants are grown at agricultural field. ...

  15. Sample (S): SE10_S01 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE10_S01 Brassica oleracea var. capitata Hatukoi Leaf Brassica oleracea var. capitata NCBI taxonomy:3716 Bra...ssica oleracea var. capitata plants are grown in the open field with high phosphorus condition (273.4kg/10a). ...

  16. Sample (S): SE27_S01 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE27_S01 Brassica oleracea var. capitata YR Tenkuu Leaf Brassica oleracea var. capi...tata NCBI taxonomy:3716 Brassica oleracea var. capitata plants are grown at agricultural field. ...

  17. Sample (S): SE25_S09 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE25_S09 Brassica oleracea var. capitata Teruyoshi Leaf Brassica oleracea var. capi...tata NCBI taxonomy:3716 Brassica oleracea var. capitata are grown at agricultural field in natural conditions. ...

  18. Sample (S): SE27_S03 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE27_S03 Brassica oleracea var. capitata YR Tenkuu Leaf Brassica oleracea var. capi...tata NCBI taxonomy:3716 Brassica oleracea var. capitata plants are grown at agricultural field under UV film. ...

  19. Sample (S): SE25_S08 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE25_S08 Brassica oleracea var. capitata YR Tenkuu Leaf Brassica oleracea var. capi...tata NCBI taxonomy:3716 Brassica oleracea var. capitata are grown at agricultural field in natural conditions. ...

  20. Sample (S): SE26_S01 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE26_S01 Brassica oleracea var. capitata YR Seisyun Leaf Brassica oleracea var. capitata NCBI taxonomy:3716 Brassica oleracea var. capitata are grown at agricultural field in natural conditions with 0t compost treatment. ...

  1. Sample (S): SE25_S04 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE25_S04 Brassica oleracea var. capitata Kinkei201gou Leaf Brassica oleracea var. c...apitata NCBI taxonomy:3716 Brassica oleracea var. capitata are grown at agricultural field in natural conditions. ...

  2. Sample (S): SE26_S02 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE26_S02 Brassica oleracea var. capitata YR Seisyun Leaf Brassica oleracea var. cap...itata NCBI taxonomy:3716 Brassica oleracea var. capitata are grown at agricultural field in natural conditions with 6t compost treatment. ...

  3. Sample Set (SE): SE20 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE20 Arabidopsis thaliana leaf metabolite analysis for a software test Investigatio...es that were investigated to optimize the parameters of PowerGet software for better metabolite annotation i

  4. Sample Set (SE): SE12 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE12 Effect of agricultural films for spinach leaf metabolites Investigation of Spi...nacia oleracea leaf metabolites. 2 cultivars (Nihon and Wasesaradaakari), 2 growth conditions (normal film and UV film

  5. Sample Set (SE): SE41 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available 1, Daisuke Shibata 1, 2, 1:Graduate School of Agriculture, Kyoto University, Japan, 2:Kazusa DNA Research Institute, Japan, 3:KAGOME CO., LTD., Japan Direct Submittion version 1 ...

  6. Sample Set (SE): SE57 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available etabolite accumulation patterns in plants We optimized the MRM conditions for specifi c compounds by perform...nds, the MRM conditions of 497 compounds were successfully optimized. These were

  7. Sample Set (SE): SE53 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available pplication of our multi-platform approach that assesses the substantial equivalen...coCyc database. Following a proof-of-safety approach, we show that w92% had an ac...signature. We conclude that multi-platform metabolomics is an approach that is both sensitive and robust and

  8. Sample Set (SE): SE52 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available e data to explore phytochemical diversity A novel framework for automated elucidation of metabolite structures in liquid chromatograp...hy窶杜ass spectrometer metabolome data was constructed by integrating databases. High

  9. Sample Set (SE): SE27 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE27 Effect of agricultural films for cabbage leaf metabolites Investigation of Bra...ssica oleracea var. capitata YR Tenkuu leaf metabolites. 3 growth conditions (covered with normal or UV cut agricultural... film or no agricultural film), 3 replicates data are examined. Takeshi Ara 1, Naoki Yamamoto 1,

  10. Sample Set (SE): SE14 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE14 Effect of agricultural films for tomato fruit metabolites Investigation of Sol...anum lycopersicum fruit metabolites. 3 growth conditions (covered with normal or UV cut agricultural film or no agricultural

  11. Sample Set (SE): SE16 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE16 Effect of agricultural films for spinach leaf metabolites 2 Investigation of S...pinacia oleracea leaf metabolites. 3 growth conditions (covered with normal or UV cut agricultural film or no agricultural

  12. Sample (S): SE59_S01 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE59_S01 Arabidopsis Arabidopsis thaliana NCBI taxonomy:3702 Arabidopsis (Col-0) pl...ants were used in this study. All plates were placed in a growth chamber at 22 °C with a relative humidity o

  13. Sample Set (SE): SE10 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE10 Effect of phosphorus nutrition for cabbage metabolites Investigation of Brassi...ca oleracea var. capitata Hatukoi leaf metabolites. 3 growth conditions (high, low and no phosphorus nutrition

  14. Sample Set (SE): SE58 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE58 Exploring matrix effects and quantification performance in metabolomics experiments using artificial...ificial biological gradients is a general and inexpensive tool for calibration that... the peaks but also highlights cases with strong background-dependent signal interference. Analysis of art

  15. Sample Set (SE): SE24 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available We provide a chemical assignment strategy for S-metabolites using 12C- and 13C-based MS and tandem mass spectrometry... (MS/MS) spectra recorded by Fourier transform ion cyclotron resonance-mass spectrometry

  16. Sample (S): SE22_S07 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available Ind., Tokyo, Japan, and Kanto Hiryou Ind., Saitama, Japan) and kept in the contro...awn in the pot (500 ml) filled with mixture of vermiculite and Powersoil (mix ratio 1 to 1, Kureha Chemical

  17. Sample (S): SE22_S03 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available Ind., Tokyo, Japan, and Kanto Hiryou Ind., Saitama, Japan) and kept in the contro...awn in the pot (500 ml) filled with mixture of vermiculite and Powersoil (mix ratio 1 to 1, Kureha Chemical

  18. Sample (S): SE22_S06 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available Ind., Tokyo, Japan, and Kanto Hiryou Ind., Saitama, Japan) and kept in the contro...awn in the pot (500 ml) filled with mixture of vermiculite and Powersoil (mix ratio 1 to 1, Kureha Chemical

  19. Sample (S): SE22_S02 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available Ind., Tokyo, Japan, and Kanto Hiryou Ind., Saitama, Japan) and kept in the contro...awn in the pot (500 ml) filled with mixture of vermiculite and Powersoil (mix ratio 1 to 1, Kureha Chemical

  20. Sample (S): SE22_S04 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available Ind., Tokyo, Japan, and Kanto Hiryou Ind., Saitama, Japan) and kept in the contro...awn in the pot (500 ml) filled with mixture of vermiculite and Powersoil (mix ratio 1 to 1, Kureha Chemical

  1. Sample (S): SE22_S01 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available Ind., Tokyo, Japan, and Kanto Hiryou Ind., Saitama, Japan) and kept in the contro...awn in the pot (500 ml) filled with mixture of vermiculite and Powersoil (mix ratio 1 to 1, Kureha Chemical

  2. Sample (S): SE22_S08 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available Ind., Tokyo, Japan, and Kanto Hiryou Ind., Saitama, Japan) and kept in the contro...awn in the pot (500 ml) filled with mixture of vermiculite and Powersoil (mix ratio 1 to 1, Kureha Chemical

  3. Sample (S): SE22_S05 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available Ind., Tokyo, Japan, and Kanto Hiryou Ind., Saitama, Japan) and kept in the contro...awn in the pot (500 ml) filled with mixture of vermiculite and Powersoil (mix ratio 1 to 1, Kureha Chemical

  4. Sample Set (SE): SE45 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available aphy-mass spectrometry. To make the data set available as an efficient public functional genomics tool for h... for genes of interest and for improving gene annotation. MeKO is publicly available at http://prime.psc.rik

  5. Sample (S): SE56_S01 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available ings of Arabidopsis thaliana (Col-0) were grown in pots containing soil at 20℃ with a 16 h daily photoperiod...e half-strength MS medium plates at 20℃ with a 16 h daily photoperiod. Two weeks after germination, whole tissues of 20 seedlings were collected, weighed, and stored at 80℃. ...

  6. Sample (S): SE58_S01 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available ely (Otsuka Chemical, Osaka, Japan), in a growth chamber at 25 ℃/20 ℃ (light/dark) and 900 ppm CO2 concent...ration with a light/dark cycle of 16 h/8 h at Chiba University, Matsudo, Japan. Pho

  7. Sample Set (SE): SE60 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available cies produces more diverse phytochemicals than previously expected, and plants still contain many useful compounds for human applicat...ions. Fumio Matsuda, Ryo Nakabayashi, Zhigang Yang, Yozo

  8. Sample (S): SE54_S01 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available er natural light at 22℃ with application of 2,000-fold-diluted Hyponex until flowering finished. Then seeds ... were grown for 3 weeks under a 16-h light/8-h dark cycle at 22℃, transferred to soil and grown under the same conditions with applic...ation of 2,000-fold diluted Hyponex (Hyponex Japan Co Ltd., Osaka, Japan) until see

  9. Sample Set (SE): SE54 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available ic profiling of large-scale bioresources We established a novel methodology, termed widely targeted metabolo...ucted a targeted metabolite analysis of large-scale Arabidopsis bioresources, nam

  10. Sample (S): SE40_S27 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE40_S27 Solanum lycopersicum Carol7 (Karin) fruit Solanum lycopersicum NCBI taxono...my:4081 Solanum lycopersicum Carol7 (Karin) were purchased at a local market of Kyoto city, (Kyoto, Japan) (November, 2015). Aichi-san. ...

  11. Sample (S): SE19_S2 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE19_S2 Mouse white adipose tissue (WAT) Mus musculus NCBI taxonomy:10090 Mice (C57...BL/6) were purchased from SLC, Shizuoka, Japan. White adipose tissue was extracted and used. ...

  12. Sample (S): SE11_S01 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available ng was done at May 31 and fix planting was done at June 28 in the pots with synthet...1 Solanum lycopersicum Furikoma were grown in a greenhouse located in Chiba, Japan. Seeds were sown at May 11, 2011. Temporary planti

  13. Sample Set (SE): SE18 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available spholipid molecular species was established with negative ion mode analyses by high accuracy MS and auto mat... were applied to the comprehensive analyses and differences in molecular species were detected. Taguchi R an

  14. Sample Set (SE): SE37 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE37 Medicago truncatula shoot metabolite analysis using stable isotopes Metabolite...formed to estimate the elemental composition with high reliability using the number of stable isotopes incor

  15. Sample (S): SE50_S01 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available iting both Basta and kanamycin tolerance in the F2 and F3 generations, were obtained and named WOX1-1 and WO...respectively. Progenies that exhibited both Basta and kanamycin tolerance (F2 and F3 generations) were obt...ained. Sterilized seeds were kept for 2 days at 4°C in the dark and were sown on pl

  16. Sample Set (SE): SE56 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE56 MS/MS spectral tag-based annotation of non-targeted profile of plant secondary...sis, resulting in clarification of the functions of reported genes involved in glycosylation of flavonoids. Thus, non-target

  17. Sample (S): SE45_S01 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o quench enzymatic activity. The all raw data are also available in MetaboLights (Salek et al., 2013) (accession no. MTBLS47), and The MetabolomeExpress (Carroll et al., 2010). ...

  18. Sample Set (SE): SE51 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o be narrowed down to candidate structures. Therefore, a web-based database of MS/MS data pertaining to phyt...ined from authentic standards. As a main web application of ReSpect, a fragment search was established based...re successfully narrowed down to putative structures in the website. Yuji Sawada,

  19. Sample (S): SE36_S01 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available plants are grown on pots filled by soil under natural conditions. Plants are grown at room temperature with natural light condition in winter. Leaves are harvested at spring of 2008. ...

  20. Sample (S): SE53_S01 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available tted in 1/2000 a Wagner pot containing compost soil (Kureha, Tokyo, Japan) for the soil experiment. Seeds we... pilot and HC experiments) and late summer (the soil experiment) in 2006, 2008, and 2009.

  1. Sample Set (SE): SE46 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available lar processes. The modes of regulation at the metabolome level can be revealed by metabolic networks...resumably responsible for these metabolic networks were determined using the metabolite correlations as clue...s. Two Arabidopsis mutants, mto1 and tt4, exhibited the following changes in entire metabolome networks: the

  2. Sample Preparation (SS): SE50_SS01 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available er watering. > Three-week-old plants were incubated in 2-ml tubes with 2 ml o...eaves of the incubated plants were used for DAB staining (Thordal-Christensen et al., 1997).

  3. Archives of Atmospheric Lead Pollution

    Science.gov (United States)

    Weiss, Dominik; Shotyk, William; Kempf, Oliver

    Environmental archives such as peat bogs, sediments, corals, trees, polar ice, plant material from herbarium collections, and human tissue material have greatly helped to assess both ancient and recent atmospheric lead deposition and its sources on a regional and global scale. In Europe detectable atmospheric lead pollution began as early as 6000years ago due to enhanced soil dust and agricultural activities, as studies of peat bogs reveal. Increased lead emissions during ancient Greek and Roman times have been recorded and identified in many long-term archives such as lake sediments in Sweden, ice cores in Greenland, and peat bogs in Spain, Switzerland, the United Kingdom, and the Netherlands. For the period since the Industrial Revolution, other archives such as corals, trees, and herbarium collections provide similar chronologies of atmospheric lead pollution, with periods of enhanced lead deposition occurring at the turn of the century and since 1950. The main sources have been industry, including coal burning, ferrous and nonferrous smelting, and open waste incineration until c.1950 and leaded gasoline use since 1950. The greatest lead emissions to the atmosphere all over Europe occurred between 1950 and 1980 due to traffic exhaust. A marked drop in atmospheric lead fluxes found in most archives since the 1980s has been attributed to the phasing out of leaded gasoline. The isotope ratios of lead in the various archives show qualitatively similar temporal changes, for example, the immediate response to the introduction and phasing out of leaded gasoline. Isotope studies largely confirm source assessments based on lead emission inventories and allow the contributions of various anthropogenic sources to be calculated.

  4. Auto-choreography: Animating Sentient Archives

    Directory of Open Access Journals (Sweden)

    Kim Satchell

    2010-03-01

    Full Text Available The stories lives tell, the narratives they follow and the spaces they embody are critical to articulating the conditions of everyday life. This resonates in the fraught relations within and between surf cultures, affluent societies and economic development. In the context of Rural Cultural Studies the analysis of coastal place allows for a combination of self-reflexive, critical and transformative modes of inquiry. This pedagogy of the coast offers innovative approaches to contemporary anthropogenic and existential challenges. For the Ecological Humanities, adjusting to living synergistically requires dialogue, ethical frameworks and care. This includes attention to the more-than human world and the non-human inhabitants with whose lives people become entangled in the mutuality of wandering paths and shared haunts. The imaginary-material architectures and geographies of these samples of coastal life, are topographies woven of spatiality and contemporary coastal writing. These contemplations attempt to sketch performative interactions from the auto-choreography animating sentient archives.

  5. Ammonia in Archives.

    Czech Academy of Sciences Publication Activity Database

    Mašková, Ludmila

    -: -, 2016, s. 58-59. ISBN N. [Indoor Air Quality - in Heritage and Historic Environment s. Birmingham (GB), 03.03.2016-04.03.2016] R&D Projects: GA MK DF11P01OVV020 Keywords : ammonia * diffusive sampling * indoor source Subject RIV: CF - Physical ; Theoretical Chemistry

  6. Coming out in the archives: the Hall-Carpenter Archives at the London School of Economics

    OpenAIRE

    Donnelly, Sue

    2008-01-01

    The archive and journal collections of the Hall-Carpenter Archives (HCA) have been housed at the LSE since 1988. The archive, named in honour of novelist Radclyffe Hall and socialist writer, Edward Carpenter, was founded in 1982 to document the development of gay activism in the UK since the publication of the Wolfenden Report in 1958. The archive operated as an independent archive based at the London Lesbian and Gay Centre for several years before being transferred to the Archives of the Lon...

  7. The clinical characteristics and the frequency of metastatic cutaneous tumors among primary skin tumors

    Directory of Open Access Journals (Sweden)

    Güldehan Atış

    2013-09-01

    Full Text Available Background and Design: Our aim was to find out the ratio of cutaneous metastatic tumors among all cutaneous and skin appendage tumors and to establish their clinical characteriaMaterial-methods: We scanned the histopathological diagnoses of all the skin tumors records from the archives between 2006 to 2012 and recorded the age, gender, the diagnosis of internal malignancy, the type of cutenous lesion, the location and the period between the appearance of the primary malignancies and cutaneous metastases.Results: We found that 20 (0,48% out of 4126 skin tumors were diagnosed as cutaneous metastatic tumors. Ten of the patients were men and ten of them were women ( median age of 51,3±18,34. When considered primary internal malignancies of these patients 6 patients with gastroenterologic malignancy, 4 patients with lung cancer, 4 patients with breast cancer, 3 patients with malignant melanoma, 1 patient with Ewing sarcoma, 1 with acute myeloblastic leukemia and 1 with prostatic cancer were diagnosed. The clinical appearance of the tumors were as follows; 14 nodule, 2 eczematized plaque, 2 papule, 1 papulonodule, 1 infitrated plaque. The localizations of the cutaneous metastatic tumors were as follows; 7 lesions on the anterior trunk, 5 lesions on the abdominal wall, 2 lesions on the back, 2 lesions on the thigh, 2 lesions on the scalp, 1 on the anterior arm, 1 on the inguinal site. We found that 3 patients (15 % attended with cutaneous metastatic tumors before the diagnosis of internal malignancies while 17 patients (85 % attended 18,97±24,76 months (1,5 -109 months after the diagnosis of internal malignancies.Conclusion: Cutaneous metastatic tumors are rarely seen skin lesions. We found that cutaneous metastatic tumors are mostly nodular and with trunk localization. It is important to recogniza these tumors, because they address primary internal tumor

  8. Tackling the vascular heterogeneity issue in tumors : identification of novel targets for tumor therapy

    NARCIS (Netherlands)

    Roodink, I.

    2009-01-01

    This thesis focuses on the identification of novel vascular targeting agents directed against tumor endothelium and the expression patterns of their targets in (clinical) tumor samples. Tumors obtain their blood supply by the formation of new vessels and/or by the incorporation, and possibly subsequ

  9. Database Description - RMG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us RMG Database... Description General information of database Database name RMG Alternative name Rice Mitochondri...ational Institute of Agrobiological Sciences E-mail : Database classification Nucleotide Sequence Databases ...Organism Taxonomy Name: Oryza sativa Japonica Group Taxonomy ID: 39947 Database description This database co...e of rice mitochondrial genome and information on the analysis results. Features and manner of utilization of database

  10. Database Description - RPSD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us RPSD Database... Description General information of database Database name RPSD Alternative name Summary inform...n National Institute of Agrobiological Sciences Toshimasa Yamazaki E-mail : Database classification Structure Database...idopsis thaliana Taxonomy ID: 3702 Taxonomy Name: Glycine max Taxonomy ID: 3847 Database description We have...nts such as rice, and have put together the result and related informations. This database contains the basi

  11. Home | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available downloadable, it may not be fully used, cited or rightly acknowledged by the (research) communities. This i...nstitute of Agrobiological Sciences Junichi Yonemaru QTL Rice The database of Rice QTL information extracted from published research...r contribution of each research to life science. Lifescience Database Archive Arc...n forms friendly to different types of users in public and private institutions, and thereby supports furthe

  12. Comment - Taxonomy Icon | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...ame of species Icon File name of the icon (The icon is displayed in Simple Search.) Image File name of the i...mage posted on the icon entry (The image is displayed in Simple Search.) License License of the image posted... on the icon entry (This License information is shown at Image column in Simple Search

  13. Protein - Trypanosomes Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credit s ] BLAST Search Image Search Home About Archive Update History Contact us Trypanosomes ... ail Data name Protein Description of data contents It ... is a summaly table of protein information; such as ... otein. There is also information of candidate inhibit or of the protein. Data file File name: trypanosome ... ciencedbc.jp/togodb/view/trypanosome#en Data acquisit ion method - Data analysis method - Number of data ... entries 17 entries Data it em Description symbol Symbol of the protein name Na ...

  14. Brain tumor - primary - adults

    Science.gov (United States)

    ... Vestibular schwannoma (acoustic neuroma) - adults; Meningioma - adults; Cancer - brain tumor (adults) ... Primary brain tumors include any tumor that starts in the brain. Primary brain tumors can start from brain cells, ...

  15. Brain tumor - children

    Science.gov (United States)

    ... children; Neuroglioma - children; Oligodendroglioma - children; Meningioma - children; Cancer - brain tumor (children) ... The cause of primary brain tumors is unknown. Primary brain tumors may ... (spread to nearby areas) Cancerous (malignant) Brain tumors ...

  16. Brain tumor (image)

    Science.gov (United States)

    Brain tumors are classified depending on the exact site of the tumor, the type of tissue involved, benign ... tendencies of the tumor, and other factors. Primary brain tumors can arise from the brain cells, the meninges ( ...

  17. Brain Tumor Diagnosis

    Science.gov (United States)

    ... Tumors Tumor Grading and Staging Types of Tumors Risk Factors Brain Tumor Statistics Webinars Anytime Learning About Us Our Founders Board of Directors Staff Leadership Strategic Plan Financials News Careers Brain ...

  18. Tumor-associated B cells in cutaneous primary melanoma and improved clinical outcome.

    Science.gov (United States)

    Garg, Kanika; Maurer, Margarita; Griss, Johannes; Brüggen, Marie-Charlotte; Wolf, Ingrid H; Wagner, Christine; Willi, Niels; Mertz, Kirsten D; Wagner, Stephan N

    2016-08-01

    B cells often infiltrate the microenvironment of human tumors. B cells can both positively and negatively regulate antitumor immune responses. In several human cancers, higher numbers of CD20(+) TAB are associated with a favorable prognosis, whereas in human primary melanomas, this association is contentious. In this study, we determined the association of TAB numbers in cutaneous primary melanoma tissue samples and patients' overall survival. The CD20 immunohistochemistry on archival nonmetastasized and metastasized cutaneous primary melanoma tissues from 2 independent patient cohorts was performed. One cohort was used in class comparison for metastasis, the most important prognostic factor for overall survival, and the other cohort for a subsequent survival analysis. Survival association was further validated with RNA data from a third independent cohort. Whole tissue sections were read automatically via quantitative digital imaging and analysis. Survival data were analyzed by Cox proportional hazard modeling. We discovered that cutaneous primary melanomas without metastasis contain significantly more TAB than primary melanomas that had metastasized. At time of first diagnosis, a higher number of TAB is associated with a significantly better overall survival in patients with cutaneous primary melanomas of >1 mm Breslow depth. Also, higher CD20/CD19 tumor mRNA levels are correlated with a significantly better overall survival. Thus, our data support TAB numbers as a prognostic biomarker in cutaneous primary melanoma patients with a tumor of >1 mm Breslow depth. For a survey in larger studies, whole tissue section analysis seems to be key to accurate assessment of TAB numbers. PMID:27107457

  19. Tumor classification: molecular analysis meets Aristotle

    International Nuclear Information System (INIS)

    Traditionally, tumors have been classified by their morphologic appearances. Unfortunately, tumors with similar histologic features often follow different clinical courses or respond differently to chemotherapy. Limitations in the clinical utility of morphology-based tumor classifications have prompted a search for a new tumor classification based on molecular analysis. Gene expression array data and proteomic data from tumor samples will provide complex data that is unobtainable from morphologic examination alone. The growing question facing cancer researchers is, 'How can we successfully integrate the molecular, morphologic and clinical characteristics of human cancer to produce a helpful tumor classification?' Current efforts to classify cancers based on molecular features ignore lessons learned from millennia of experience in biological classification. A tumor classification must include every type of tumor and must provide a unique place for each tumor within the classification. Groups within a classification inherit the properties of their ancestors and impart properties to their descendants. A classification was prepared grouping tumors according to their histogenetic development. The classification is simple (reducing the complexity of information received from the molecular analysis of tumors), comprehensive (providing a place for every tumor of man), and consistent with recent attempts to characterize tumors by cytogenetic and molecular features. The clinical and research value of this historical approach to tumor classification is discussed. This manuscript reviews tumor classification and provides a new and comprehensive classification for neoplasia that preserves traditional nomenclature while incorporating information derived from the molecular analysis of tumors. The classification is provided as an open access XML document that can be used by cancer researchers to relate tumor classes with heterogeneous experimental and clinical tumor

  20. The Gaia Archive at ESAC: a VO-inside archive

    Science.gov (United States)

    Gonzalez-Nunez, J.

    2015-12-01

    The ESDC (ESAC Science Data Center) is one of the active members of the IVOA (International Virtual Observatory Alliance) that have defined a set of standards, libraries and concepts that allows to create flexible,scalable and interoperable architectures on the data archives development. In the case of astronomy science that involves the use of big catalogues, as in Gaia or Euclid, TAP, UWS and VOSpace standards can be used to create an architecture that allows the explotation of this valuable data from the community. Also, new challenges arise like the implementation of the new paradigm "move code close to the data", what can be partially obtained by the extension of the protocols (TAP+, UWS+, etc) or the languages (ADQL). We explain how we have used VO standards and libraries for the Gaia Archive that, not only have producing an open and interoperable archive but, also, minimizing the developement on certain areas. Also we will explain how we have extended these protocols and the future plans.

  1. Pediatric brain tumors

    International Nuclear Information System (INIS)

    Among all causes of death in children from solid tumors, pediatric brain tumors are the most common. This article includes an overview of a subset of infratentorial and supratentorial tumors with a focus on tumor imaging features and molecular advances and treatments of these tumors. Key to understanding the imaging features of brain tumors is a firm grasp of other disease processes that can mimic tumor on imaging. We also review imaging features of a common subset of tumor mimics. (orig.)

  2. Pediatric brain tumors

    Energy Technology Data Exchange (ETDEWEB)

    Poussaint, Tina Y. [Department of Radiology, Boston, MA (United States); Panigrahy, Ashok [Children' s Hospital of Pittsburgh of University of Pittsburgh Medical Center, Department of Radiology, Pittsburgh, PA (United States); Huisman, Thierry A.G.M. [Charlotte R. Bloomberg Children' s Center, Johns Hopkins Hospital, Division of Pediatric Radiology and Pediatric Neuroradiology, Baltimore, MD (United States)

    2015-09-15

    Among all causes of death in children from solid tumors, pediatric brain tumors are the most common. This article includes an overview of a subset of infratentorial and supratentorial tumors with a focus on tumor imaging features and molecular advances and treatments of these tumors. Key to understanding the imaging features of brain tumors is a firm grasp of other disease processes that can mimic tumor on imaging. We also review imaging features of a common subset of tumor mimics. (orig.)

  3. American Brain Tumor Association

    Science.gov (United States)

    ... For Health Care Professionals About Us Our Founders Board of Directors Staff Leadership Strategic Plan Financials News Careers Brain Tumor Information Brain Anatomy Brain Tumor Symptoms Diagnosis Types of Tumors Tumor Grade Risk Factors Brain Tumor Statistics ABTA Publications Brain Tumor ...

  4. Brain Tumor Surgery

    Science.gov (United States)

    ... Pediatric Caregiver Resource Center About Us Our Founders Board of Directors Staff Leadership Strategic Plan Financials News Careers Brain Tumor Information Brain Anatomy Brain Tumor Symptoms Diagnosis Types of Tumors Tumor Grade Risk Factors Brain Tumor Statistics ABTA Publications Brain Tumor ...

  5. The PSA: Planetary Science Archive

    Science.gov (United States)

    Barthelemy, M.; Martinez, S.; Heather, D.; Vazquez, J. L.; Arviset, C.; Osuna, P.; PSA development Team

    2012-04-01

    Scientific and engineering data from ESA's planetary missions are made accessible to the world-wide scientific community via the Planetary Science Archive (PSA). The PSA consists of online services incorporating search, preview, download, notification and delivery basket functionality. Besides data from the GIOTTO spacecraft and several ground-based cometary observations, the PSA contains data from the Mars Express, Venus Express, Rosetta, SMART-1 and Huygens missions. The focus of the PSA activities is on the long-term preservation of data and knowledge from ESA's planetary missions. Scientific users can access the data online using several interfaces: - The Advanced Search Interface allows complex parameter based queries, providing the end user with a facility to complete very specific searches on meta-data and geometrical parameters. By nature, this interface requires careful use and heavy interaction with the end-user to input and control the relevant search parameters. - The Map-based Interface is currently operational only for Mars Express HRCS and OMEGA data. This interface allows an end-user to specify a region-of-interest by dragging a box onto a base map of Mars. From this interface, it is possible to directly visualize query results. The Map-based and Advanced interfaces are linked and cross-compatible. If a user defines a region-of-interest in the Map-based interface, the results can be refined by entering more detailed search parameters in the Advanced interface. - The FTP Browser Interface is designed for more experienced users, and allows for direct browsing and access of the data set content through ftp-tree search. Each dataset contains documentation and calibration information in addition to the scientific or engineering data. All data are prepared by the corresponding instrument teams, mostly located in Europe. PSA supports the instrument teams in the full archiving process, from the definition of the data products, meta-data and product labels

  6. Download - RGP estmap2001 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...e Description Download License Update History of This Database Site Policy | Contact Us Download - RGP estmap2001 | LSDB Archive ...

  7. Image File - AT Atlas | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...io About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Image File - AT Atlas | LSDB Archive ...

  8. Update History of This Database - GETDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us GETDB Update History... Download License Update History of This Database Site Policy | Contact Us Update History of This Database - GETDB | LSDB Archive ...

  9. PIR search result - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ... Download License Update History of This Database Site Policy | Contact Us PIR search result - KOME | LSDB Archive ...

  10. Download - GenLibi | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...ription Download License Update History of This Database Site Policy | Contact Us Download - GenLibi | LSDB Archive ...

  11. Download - ClEST | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...bout This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - ClEST | LSDB Archive ...

  12. Download - RGP gmap2000 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...out This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - RGP gmap2000 | LSDB Archive ...

  13. Download - RGP gmap98 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...tio About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - RGP gmap98 | LSDB Archive ...

  14. Download - tRNADB-CE | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...abase Database Description Download License Update History of This Database Site Policy | Contact Us Download - tRNADB-CE | LSDB Archive ...

  15. Download - Q-TARO | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...s Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - Q-TARO | LSDB Archive ...

  16. Images on Comment (PNG format) - Taxonomy Icon | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...n Download License Update History of This Database Site Policy | Contact Us Images on Comment (PNG format) - Taxonomy Icon | LSDB Archive ...

  17. Organ weight - Open TG-GATEs | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us Open...load License Update History of This Database Site Policy | Contact Us Organ weight - Open TG-GATEs | LSDB Archive ...

  18. Individual list - Open TG-GATEs | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us Open... History of This Database Site Policy | Contact Us Individual list - Open TG-GATEs | LSDB Archive ...

  19. Cell viability - Open TG-GATEs | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us Open... Database Description Download License Update History of This Database Site Policy | Contact Us Cell viability - Open TG-GATEs | LSDB Archive ...

  20. Hematology - Open TG-GATEs | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us Open...base Description Download License Update History of This Database Site Policy | Contact Us Hematology - Open TG-GATEs | LSDB Archive ...

  1. Biochemistry - Open TG-GATEs | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us Open...e Database Description Download License Update History of This Database Site Policy | Contact Us Biochemistry - Open TG-GATEs | LSDB Archive ...

  2. Pathological items - Open TG-GATEs | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us Open... This Database Site Policy | Contact Us Pathological items - Open TG-GATEs | LSDB Archive ...

  3. Body weight - Open TG-GATEs | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us Open...d License Update History of This Database Site Policy | Contact Us Body weight - Open TG-GATEs | LSDB Archive ...

  4. Taxonomy Icon Images (PNG format) - Taxonomy Icon | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...se Database Description Download License Update History of This Database Site Policy | Contact Us Taxonomy Icon Images (PNG format) - Taxonomy Icon | LSDB Archive ...

  5. Download - AcEST | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...t This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - AcEST | LSDB Archive ...

  6. High-resolution genomic analysis suggests the absence of recurrent genomic alterations other than SMARCB1 aberrations in atypical teratoid/rhabdoid tumors.

    Science.gov (United States)

    Hasselblatt, Martin; Isken, Sarah; Linge, Anna; Eikmeier, Kristin; Jeibmann, Astrid; Oyen, Florian; Nagel, Inga; Richter, Julia; Bartelheim, Kerstin; Kordes, Uwe; Schneppenheim, Reinhard; Frühwald, Michael; Siebert, Reiner; Paulus, Werner

    2013-02-01

    Atypical teratoid/rhabdoid tumor (AT/RT) is a rare malignant pediatric brain tumor characterized by genetic alterations affecting the SMARCB1 (hSNF5/INI1) locus in chromosome band 22q11.2. To identify potential additional genetic alterations, high-resolution genome-wide analysis was performed using a molecular inversion probe single-nucleotide polymorphism (MIP SNP) assay (Affymetrix OncoScan formalin-fixed paraffin-embedded express) on DNA isolated from 18 formalin-fixed paraffin-embedded archival samples. Alterations affecting the SMARCB1 locus could be demonstrated by MIP SNP in 15 out of 16 evaluable cases (94%). These comprised five tumors with homozygous deletions, six tumors with heterozygous deletions, and four tumors with copy number neutral loss of heterozygosity (LOH) involving chromosome band 22q11.2. Remarkably, MIB SNP analysis did not yield any further recurrent chromosomal gains, losses, or copy neutral LOH. On MIP SNP screening for somatic mutations, the presence of a SMARCB1 mutation (c.472C>T p.R158X) was confirmed, but no recurrent mutations of other cancer relevant genes could be identified. Results of fluorescence in situ hybridization, multiplex ligation-dependent probe amplification, and SMARCB1 sequencing were highly congruent with that of the MIP SNP assay. In conclusion, these data further suggest the absence of recurrent genomic alterations other than SMARCB1 in AT/RT. PMID:23074045

  7. Archiving Government Documents using DSpace

    OpenAIRE

    Devakos, Rea

    2005-01-01

    Description: A collaborative multi-phased pilot to archive Canadian government documents using DSpace Participants: The Ontario Council of University Libraries (OCUL), a 20 member consortium, is working with municipalities, special and community college libraries. Objectives: To address long standing and widespread concerns about the rapid rate of disappearance of electronic government documents, as well as the desire for greater efficiencies possible through shared catalogu...

  8. Archiving in the networked world

    OpenAIRE

    Seadle, Michael

    2011-01-01

    The purpose is to investigate: 1) how many journal titles are both in LOCKSS and in Portico? 2) what is the relationship of small publishers to LOCKSS/CLOCKSS and Portico? 2) what is the relationship of large publishers to LOCKSS/CLOCKSS and Portico? The article describes describes how data from Portico, LOCKSS, and CLOCKSS was cleaned and analyzed using Perl programs to discover duplications. The findings show a significant overlap among the archiving systems. It also shows that Portico has...

  9. System Architecture for a Hubble Legacy Archive

    Science.gov (United States)

    Miller, W. W., III; Gaffney, N.; Jenkner, H.; Whitmore, B.

    2007-10-01

    The Space Telescope Science Institute (STScI), in collaboration with the European Coordinating Facility (ECF) and the Canadian Astronomy Data Centre (CADC), is studying the development of an enhanced archive for the Hubble Space Telescope (HST). Distinct from (but complimentary to) the existing archive system at the STScI, development of this enhanced archive affords the opportunity to leverage modern architectural and design principles toward meeting project objectives and serving the archive community. To wit, the STScI is designing the entire system as a service-oriented architecture (SOA). Composed of loosely-coupled, highly-interoperable Web services, an SOA embodies a great deal of flexibility in meeting future needs placed on the HST archive while also positioning it well within the emerging Virtual Observatory (VO) framework. A high-level architecture for the enhanced archive at the STScI is presented.

  10. Commercial imagery archive product development

    Science.gov (United States)

    Sakkas, Alysa

    1999-12-01

    The Lockheed Martin (LM) team had garnered over a decade of operational experience in digital imagery management and analysis for the US Government at numerous worldwide sites. Recently, it set out to create a new commercial product to serve the needs of large-scale imagery archiving and analysis markets worldwide. LM decided to provide a turnkey commercial solution to receive, store, retrieve, process, analyze and disseminate in 'push' or 'pull' modes components and adapted and developed its own algorithms to provide added functionality not commercially available elsewhere. The resultant product, Intelligent Library System, satisfies requirements for (a) a potentially unbounded, data archive automated workflow management for increased user productivity; (c) automatic tracking and management of files stored on shelves; (d) ability to ingest, process and disseminate data involves with bandwidths ranging up to multi-gigabit per second; (e) access through a thin client- to-server network environment; (f) multiple interactive users needing retrieval of filters in seconds from both archived images or in real time, and (g) scalability that maintains information throughput performance as the size of the digital library grows.

  11. A Policy-based Institutional Web Archiving System with Adjustable Exposure of Archived Resources

    OpenAIRE

    Hiiragi, Wasuke; Sakaguchi, Tetsuo; Sugimoto, Shigeo

    2009-01-01

    Despite the recognition that Archiving Web content is important and Web archiving systems freely crawl and collect resources on the Web for preservation, they have difficulties in collecting all versions of a single Web page and in preserving a collected resource with policies of use given by its creator. In order to solve the problems, we have proposed an Institutional Web Archiving System, which collects resources with the archiving policy given to the resources by its ...

  12. Teratoid Wilms′ tumor - A rare renal tumor

    Directory of Open Access Journals (Sweden)

    Biswanath Mukhopadhyay

    2011-01-01

    Full Text Available Teratoid Wilms′ tumor is an extremely rare renal tumor. We report a case of unilateral teratoid Wilms′ tumor in a 4-year-old girl. The patient was admitted with a right-sided abdominal mass. The mass was arising from the right kidney. Radical nephrectomy was done and the patient had an uneventful recovery. Histopathology report showed teratoid Wilms′ tumor.

  13. Tumor thrombus

    DEFF Research Database (Denmark)

    Ravina, Mudalsha; Hess, Søren; Chauhan, Mahesh Singh; Jacob, Mattakorottu Joseph; Alavi, Abass

    2014-01-01

    PURPOSE: Thrombosis in cancer may manifest itself as venous thromboembolic disease or tumor thrombosis (TT). We present our experience with incidentally detected TT on FDG PET/CT in 21 oncologic patients. PATIENTS AND METHODS: We retrospectively reviewed all FDG PET/CT examinations during a 5-year......-one patients were included; the most common malignancies were renal cell carcinoma (n=6), hepatocellular carcinoma (n=3), and lung cancer (n=3). Indication for the scan was initial staging (n=15) and suspected recurrence (n=6). Several vessels were affected, the most common was the inferior vena cava (n=14...

  14. Web Archiving and Digital Libraries (WADL)

    OpenAIRE

    Edward A Fox; Xie, Zhiwu

    2015-01-01

    This workshop will explore integration of Web archiving and digital libraries, so the complete life cycle involved is covered: creation/authoring, uploading/publishing in the Web (2.0), (focused) crawling, indexing, exploration (searching, browsing), ..., archiving (of events). It will include particular coverage of current topics of interest:, big data, mobile web archiving, and systems (e.g., Memento, SiteStory, Uninterruptible Web Service).

  15. Update History of This Database - KEGG MEDICUS | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us KEGG MEDICUS Update Histo...io About This Database Database Description Download License Update History of Th...is Database Site Policy | Contact Us Update History of This Database - KEGG MEDICUS | LSDB Archive ... ...ry of This Database Date Update contents 2014/05/09 KEGG MEDICUS English archive si

  16. Organizing archival records a practical method of arrangement and description for small archives

    CERN Document Server

    Carmicheal, David W

    2012-01-01

    Organizing Archival Records equips non-professional archivists with the skills to tackle one of the most challenging tasks of archiving: arranging and describing archival materials. Carmichael brings this third edition into the 21st century with extended discussions about computerizing the process, making descriptions available on the web, and organizing electronic records.

  17. PLACE search result - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...ce_search_result.zip File URL: ftp://ftp.biosciencedbc.jp/archive/kome/LATEST/kom...n Download License Update History of This Database Site Policy | Contact Us PLACE search result - KOME | LSDB Archive ...

  18. Blocks search result - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...://ftp.biosciencedbc.jp/archive/kome/LATEST/kome_blocks_search_result.zip File si...atabase Site Policy | Contact Us Blocks search result - KOME | LSDB Archive ...

  19. Cluster - ClEST | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...including Blastx search results and GO annotations Data file File name: clest_cluster.zip File URL: ftp://ftp.biosciencedbc.jp/archiv...istory of This Database Site Policy | Contact Us Cluster - ClEST | LSDB Archive ...

  20. Cluster Table - KAIKOcDNA | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...dentical cDNA sequences that make up cluster. Data file File name: kaiko_cdna_cluster.zip File URL: ftp://ftp.biosciencedbc.jp/archiv...scription Download License Update History of This Database Site Policy | Contact Us Cluster Table - KAIKOcDNA | LSDB Archive ...

  1. Genotype data - RGP gmap98 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...URL: ftp://ftp.biosciencedbc.jp/archive/rgp-gmap98/LATEST/rgp_gmap98_genotype_dat...his Database Database Description Download License Update History of This Database Site Policy | Contact Us Genotype data - RGP gmap98 | LSDB Archive ...

  2. Mapping data detail - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...ct (IRGSP) Data file File name: kome_mapping_data_detail.zip File URL: ftp://ftp.biosciencedbc.jp/archiv...istory of This Database Site Policy | Contact Us Mapping data detail - KOME | LSDB Archive ...

  3. tRNA - RMG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...genomes of other plants. Data file File name: rmg_trna.zip File URL: ftp://ftp.biosciencedbc.jp/archive/rmg/...cription Download License Update History of This Database Site Policy | Contact Us tRNA - RMG | LSDB Archive ...

  4. Tos17 link result - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...s17 mutant clones Data file File name: kome_tos17_link_result.zip File URL: ftp://ftp.biosciencedbc.jp/archiv...te History of This Database Site Policy | Contact Us Tos17 link result - KOME | LSDB Archive ...

  5. 75 FR 63141 - Information Collection; Research Data Archive Use Tracking

    Science.gov (United States)

    2010-10-14

    ...; ] DEPARTMENT OF AGRICULTURE Forest Service Information Collection; Research Data Archive Use Tracking AGENCY... organizations on the currently approved information collection, Research Data Archive Use Tracking. DATES..., Monday through Friday. SUPPLEMENTARY INFORMATION: Title: Research Data Archive Use Tracking. OMB...

  6. Chronique des Archives 2010-2011

    OpenAIRE

    Eichenlaub, Jean-Luc

    2012-01-01

    La Chronique des Archives rendant compte des activités 2009 est parue dans la Revue d’Alsace no136, 2010, p. 391‑397. Le lecteur a pu avoir un aperçu des activités des Archives départementales (Bas‑Rhin, Haut‑Rhin, Territoire de Belfort) et des archives municipales de Belfort, Colmar, Erstein, Guebwiller, Illkirch, Illzach, Ingersheim, Mulhouse, Munster, Saint-Louis, Turckheim, Strasbourg. Il n’y a pas eu de Chronique des Archives complète dans la Revue d’Alsace no137, 2011, mais une page con...

  7. Seventy Years of the Journal "Medical Archives".

    Science.gov (United States)

    Masic, Izet

    2016-02-01

    This year journal "Medical Archives" celebrates 70th anniversary of its continuing publication. Medical Archives is oldest biomedical journal in Bosnia and Herzegovina and one of the oldest medical journals in Europe, established in the year 1947, as official scientific and professional journal of Association of Physicians of Bosnia and Herzegovina. Until present Medical Archives has published over 5000 articles. Today Medical Archives is internationally recognized medical peer-reviewed indexed journal, visible in more than 30 international on-line databases. PMID:26980925

  8. The AMBRE Project: Parameterisation of FGK-type stars from the ESO:HARPS archived spectra

    CERN Document Server

    De Pascale, Marco; de Laverny, Patrick; Recio-Blanco, Alejandra; Hill, Vanessa; Bijaoui, Albert

    2014-01-01

    The AMBRE project is a collaboration between the European Southern Observatory (ESO) and the Observatoire de la Cote d'Azur (OCA). It has been established to determine the stellar atmospheric parameters (effective temperature, surface gravity, global metallicities and abundance of alpha-elements over iron) of the archived spectra of four ESO spectrographs. The analysis of the ESO:HARPS archived spectra is presented. The sample being analysed (AMBRE:HARPS) covers the period from 2003 to 2010 and is comprised of 126688 scientific spectra corresponding to 17218 different stars. For the analysis of the spectral sample, the automated pipeline developed for the analysis of the AMBRE:FEROS archived spectra has been adapted to the characteristics of the HARPS spectra. Within the pipeline, the stellar parameters are determined by the MATISSE algorithm, developed at OCA for the analysis of large samples of stellar spectra in the framework of galactic archaeology. In the present application, MATISSE uses the AMBRE grid ...

  9. History, Archives and the Internet

    Directory of Open Access Journals (Sweden)

    Robert, Jean-Claude

    2012-03-01

    Full Text Available The relationship between historians and archives is generally taken for granted. But this impression is misleading. Across the world, the building of archival collections involves a complicated process of selection and destruction. Traditionally, historians do not really know how this process is being conducted and very often a good proportion of them believe that all documents should be kept. The evolution of history and the questioning of the archives by philosophers cannot be ignored and these have changed the relationship between historians and archives. However, the construction of tomorrow’s archives is happening right now, and historians should be prepared to find a way to participate in this operation. The role of archivists is central in the whole process. In the past, archivists generally received a basic training as historians, but since the 1950s, they have been more and more involved with other disciplines like library or information sciences. They became professionals in a new discipline. Historians should take notice of this reality and be prepared to work with archivists on an equal footing. They must learn what archivists are doing and join them to help create archival collections for the future. The last part of the paper takes a quick looks at the evolution of the Internet as an addition, or rather than as an extension, of archival holdings.

    La relación de los historiadores con los archivos se considera segura, pero esta impresión confunde. En todo el mundo, la construcción de colecciones de archivo supone un complejo proceso de selección y destrucción. Los historiadores no suelen conocer este proceso, creyendo que todos los documentos se conservan. La evolución de la historiografía y el cuestionamiento de los archivos por los filósofos no se pueden ignorar, pues han cambiado la relación entre historiadores y archivos. Pero la construcción de archivos futuros sucede hoy, y los historiadores deben estar

  10. Web Services interface of SSRF archive data analysis system

    Institute of Scientific and Technical Information of China (English)

    LI Lin; SHEN Liren; ZHU Qing; WAN Tianmin

    2007-01-01

    Accelerator database stores various static parameters and real-time data of accelerator. SSRF (Shanghai Synchrotron Radiation Facility) adopts relational database to save the data. We developed a data retrieval system based on XML Web Services for accessing the archive data. It includes a bottom layer interface and an interface applicable for accelerator physics. Client samples exemplifying how to consume the interface are given. The users can browse, retrieve and plot data by the client samples. Also, we give a method to test its stability. The test result and performance are described.

  11. Web services interface of SSRF archive data analysis system

    International Nuclear Information System (INIS)

    Accelerator database stores various static parameters and real-time data of accelerator. SSRF (Shanghai Synchrotron Radiation Facility) adopts relational database to save the data. We developed a data retrieval system based on XML Web Services for accessing the archive data. It includes a bottom layer interface and an interface applicable for accelerator physics. Client samples exemplifying how to consume the interface are given. The users can browse, retrieve and plot data by the client samples. Also, we give a method to test its stability. The test result and performance are described. (authors)

  12. Classification and grading of canine malignant mammary tumors

    OpenAIRE

    Abbas Tavasoly; Hannaneh Golshahi; Annahita Rezaie; Mohammad Farhadi

    2013-01-01

    Histological grading is a good parameter to stratify tumors according to their biological aggressiveness. The Elston and Ellis grading method in humans, invasive ductal breast carcinomas and other invasive tumors are routinely used. The aims of this study were classification of mammary gland tumors and also application of a human grading method in canine mammary carcinoma. The samples included 37 tumors of mammary glands. Mammary tumors were carcinomas (n = 32) and sarcomas (n = 5). The carci...

  13. Toward a Greater Discourse: Issues in Religious Archives

    Directory of Open Access Journals (Sweden)

    Robert Presutti

    2010-06-01

    Full Text Available The topic of religious archives, a catalyst of much discussion in archival literature, has traditionally been overlooked within the discourse of the American Theological Library Association (ATLA. This essay provides a survey analysis of three pertinent issues in religious archives with the intention of generating a wider discussion on religious archives within ATLA. These issues include the role of graduate archival education, the effects of religious faith on both the archival record and the individual archivist, and the idea of a theology of archives. An extended review of the contributions of James O’Toole to the discussion of religious archives is utilized.

  14. Animation archives: collaboration with archivists, academics, and practitioners

    OpenAIRE

    Taylor, Rebekah

    2015-01-01

    How animation archives can be promoted and made accessible through collaboration - the paper looks at workshops in collaboration with academics, interviews with academics using archives, and infographics.

  15. Download - RMG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us RMG Down...load First of all, please read the license of this database. Data names and data descriptions are about the down...Click the links on Data Name for descriptions of the data. # Data name File Simple search and down...load 1 README README_e.html - 2 Main data rmg_main.zip (1 KB) Simple search and download 3 ...Entire Sequence rmg_seq.zip (142 KB) - 4 Genes (including RNA editing information) rmg_gene.zip (3 KB) Simple search and down

  16. Download - Taxonomy Icon | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us Taxonomy Icon Down...load Please note that the data Commment and Images on Comment, shown in the bottom half of... of all, please read the license of this database. Data names and data descriptions are about the down...atabase. Click the links on Data Name for descriptions of the data. # Data name File Simple search and downl...oad 1 README README_e.html - 2 Taxonomy Icon Data taxonomy_icon_en.zip (14.1 KB) Simple search and down

  17. Download - Gclust Server | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us Gclust Server Down...load First of all, please read the license of this database. Data names and data descriptions are about the down...umber of characters in a cell exceeds the maximum size given in MS Excel. # Data name File Simple search and down...nd their annotation for 95 organism species. gclust_seq.zip (152MB) Simple search and download 3 Cluster bas...ed on sequence comparison of homologous proteins of 95 organism species gclust_cluster.zip (8.72MB) Simple search and down

  18. Download - RPSD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us RPSD Down...load First of all, please read the license of this database. Data names and data descriptions are about the down... Click the links on Data Name for descriptions of the data. # Data name File Simple search and down....zip (120 KB, UTF-8) Simple search and download 3 Images rpsd_images.zip (18.3 MB) - Downlaod via FTP Joomla... SEF URLs by Artio About This Database Database Description Download License Upda

  19. Download - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us KOME Down...load First of all, please read the license of this database. Data names and data descriptions are about the down... Click the links on Data Name for descriptions of the data. # Data name File Simple search and down...load 1 README README_e.html - 2 Main kome_main.zip (1.3 KB) Simple search and download 3 B...asical information kome_basical_information.zip (607 KB) Simple search and download 4 Mapping data kome_mapp

  20. Download - DGBY | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us DGBY Down...load First of all, please read the license of this database. Data names and data descriptions are about the down... Click the links on Data Name for descriptions of the data. # Data name File Simple search and down...load 1 README README_e.html - 2 Experiments List dgby_main_en.zip (1KB) Simple search and down...zip (90KB) Original File(Excel): High-sugar_stress.xls (674KB) Simple search and download 7 Phenome data - F