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Sample records for archival tumor samples

  1. 3'-end sequencing for expression quantification (3SEQ from archival tumor samples.

    Directory of Open Access Journals (Sweden)

    Andrew H Beck

    Full Text Available Gene expression microarrays are the most widely used technique for genome-wide expression profiling. However, microarrays do not perform well on formalin fixed paraffin embedded tissue (FFPET. Consequently, microarrays cannot be effectively utilized to perform gene expression profiling on the vast majority of archival tumor samples. To address this limitation of gene expression microarrays, we designed a novel procedure (3'-end sequencing for expression quantification (3SEQ for gene expression profiling from FFPET using next-generation sequencing. We performed gene expression profiling by 3SEQ and microarray on both frozen tissue and FFPET from two soft tissue tumors (desmoid type fibromatosis (DTF and solitary fibrous tumor (SFT (total n = 23 samples, which were each profiled by at least one of the four platform-tissue preparation combinations. Analysis of 3SEQ data revealed many genes differentially expressed between the tumor types (FDR<0.01 on both the frozen tissue (approximately 9.6K genes and FFPET (approximately 8.1K genes. Analysis of microarray data from frozen tissue revealed fewer differentially expressed genes (approximately 4.64K, and analysis of microarray data on FFPET revealed very few (69 differentially expressed genes. Functional gene set analysis of 3SEQ data from both frozen tissue and FFPET identified biological pathways known to be important in DTF and SFT pathogenesis and suggested several additional candidate oncogenic pathways in these tumors. These findings demonstrate that 3SEQ is an effective technique for gene expression profiling from archival tumor samples and may facilitate significant advances in translational cancer research.

  2. 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...

  3. miRNA Expression Profiling Enables Risk Stratification in Archived and Fresh Neuroblastoma Tumor Samples

    NARCIS (Netherlands)

    K. de Preter; P. Mestdagh; J. Vermeulen; F. Zeka; A. Naranjo; I. Bray; V. Castel; C. Chen; E. Drozynska; A. Eggert; M.D. Hogarty; E. Izycka-Swieszewska; W.B. London; R. Noguera; M. Piqueras; K. Bryan; B. Schowe; P. van Sluis; J.J. Molenaar; A Schramm; J.H. Schulte; R.L. Stallings; R. Versteeg; G. Laureys; N. van Roy; F. Speleman; J. Vandesompele

    2011-01-01

    Purpose: More accurate assessment of prognosis is important to further improve the choice of risk-related therapy in neuroblastoma (NB) patients. In this study, we aimed to establish and validate a prognostic miRNA signature for children with NB and tested it in both fresh frozen and archived formal

  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_tggates_cell.zip File URL: ftp://ftp.biosciencedbc.jp/archive/open-tggates...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.

    Science.gov (United States)

    Lund, Bendik; Najmi, Laeya A; Wesolowska-Andersen, Agata; Landsem, Veslemøy M; Rasmussen, Kirsten K; Borst, Louise; Gupta, Ramneek; Schmiegelow, Kjeld; Klungland, Helge

    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 genome amplification (WGA), multiple marker analysis including 10 short tandem repeats, and finally a comprehensive genotyping of 33,683 single nucleotide polymorphisms (SNPs) with multiplexed targeted next-generation sequencing. A total of 73 samples from 21 bone marrow smears and 13 bone marrow biopsies from 18 Danish and Norwegian childhood acute lymphoblastic leukemia patients were included and compared with corresponding blood samples. Samples were grouped according to the age of sample and whether WGA was performed or not. We found that measurements of DNA concentration after DNA extraction was dependent on detection method and that spectrophotometry overestimated DNA amount compared with fluorometry. In the short tandem repeat analysis, detection rate dropped slightly with longer fragments. After WGA, this drop was more pronounced. Samples stored for 0 to 3 years showed better results compared 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 analysis seems feasible, but the method has to be further optimized.

  6. 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.

  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. 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.

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

    Directory of Open Access Journals (Sweden)

    Alessandro Tanca

    2016-06-01

    Full Text Available 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 <1%. MS data are available in the PeptideAtlas repository at http://www.peptideatlas.org/PASS/PASS00375.

  10. 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

    2016-01-01

    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 <1%. MS data are available in the PeptideAtlas repository at http://www.peptideatlas.org/PASS/PASS00375. PMID:27054153

  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 <1%. MS data are available in the PeptideAtlas repository at http://www.peptideatlas.org/PASS/PASS00375.

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

    Science.gov (United States)

    Magbanua, Mark Jesus M; Roy, Ritu; Sosa, Eduardo V; Hauranieh, Louai; Kablanian, Andrea; Eisenbud, Lauren E; Ryazantsev, Artem; Au, Alfred; Scott, Janet H; Melisko, Michelle; Park, John W

    2014-12-01

    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. 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.

  14. Major copy proportion analysis of tumor samples using SNP arrays

    Directory of Open Access Journals (Sweden)

    Li Cheng

    2008-04-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are the most common genetic variations in the human genome and are useful as genomic markers. Oligonucleotide SNP microarrays have been developed for high-throughput genotyping of up to 900,000 human SNPs and have been used widely in linkage and cancer genomics studies. We have previously used Hidden Markov Models (HMM to analyze SNP array data for inferring copy numbers and loss-of-heterozygosity (LOH from paired normal and tumor samples and unpaired tumor samples. Results We proposed and implemented major copy proportion (MCP analysis of oligonucleotide SNP array data. A HMM was constructed to infer unobserved MCP states from observed allele-specific signals through emission and transition distributions. We used 10 K, 100 K and 250 K SNP array datasets to compare MCP analysis with LOH and copy number analysis, and showed that MCP performs better than LOH analysis for allelic-imbalanced chromosome regions and normal contaminated samples. The major and minor copy alleles can also be inferred from allelic-imbalanced regions by MCP analysis. Conclusion MCP extends tumor LOH analysis to allelic imbalance analysis and supplies complementary information to total copy numbers. MCP analysis of mixing normal and tumor samples suggests the utility of MCP analysis of normal-contaminated tumor samples. The described analysis and visualization methods are readily available in the user-friendly dChip software.

  15. 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

    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...... 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 BRCA...... samples from non-tumor tissue. Accurate genetic counseling is achievable in families where variant testing would otherwise be impossible.European Journal of Human Genetics advance online publication, 6 January 2016; doi:10.1038/ejhg.2015.268....

  16. Sampling circulating tumor cells for clinical benefits: how frequent?

    Science.gov (United States)

    Leong, Sai Mun; Tan, Karen M L; Chua, Hui Wen; Tan, Doreen; Fareda, Delly; Osmany, Saabry; Li, Mo-Huang; Tucker, Steven; Koay, Evelyn S C

    2015-06-25

    Circulating tumor cells (CTCs) are cells shed from tumors or metastatic sites and are a potential biomarker for cancer diagnosis, management, and prognostication. The majority of current studies use single or infrequent CTC sampling points. This strategy assumes that changes in CTC number, as well as phenotypic and molecular characteristics, are gradual with time. In reality, little is known today about the actual kinetics of CTC dissemination and phenotypic and molecular changes in the blood of cancer patients. Herein, we show, using clinical case studies and hypothetical simulation models, how sub-optimal CTC sampling may result in misleading observations with clinical consequences, by missing out on significant CTC spikes that occur in between sampling times. Initial studies using highly frequent CTC sampling are necessary to understand the dynamics of CTC dissemination and phenotypic and molecular changes in the blood of cancer patients. Such an improved understanding will enable an optimal, study-specific sampling frequency to be assigned to individual research studies and clinical trials and better inform practical clinical decisions on cancer management strategies for patient benefits.

  17. Evaluating Quality of Aged Archival Formalin-Fixed Paraffin-Embedded Samples for RNA-Sequencing

    Science.gov (United States)

    Archival formalin-fixed paraffin-embedded (FFPE) samples offer a vast, untapped source of genomic data for biomarker discovery. However, the quality of FFPE samples is often highly variable, and conventional methods to assess RNA quality for RNA-sequencing (RNA-seq) are not infor...

  18. 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.

  19. 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.

  20. 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...

  1. 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.

  2. 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. ...

  3. Sample (S): SE37_S18 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE37_S18 PSEUDO: Unlabeled and labeled Medicago samples for metabolite annotation u...sing ShiftedIonsFinder This is a pseudo metadata prepared for integrated analyses of multiple datasets. The unlabel...ed Medicago samples and a blank sample (S17), Medicago samples labeled by 13C (S05), 15N (S07), 28O (S10), and 34S (S13) are included. ...

  4. 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.

  5. Sample Preparation (SS): SE51_SS01 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available e Master NEO, BMS, Tokyo, Japan), and the seed powder was extracted with 1 mL of extraction buffer (0.1% HCO...trifugation (4 ℃, 10,000 rpm, 5 min), the sample tubes were subjected to sample preparation (buffer transfer

  6. 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

  7. Sample Preparation (SS): SE45_SS01 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available tration of 15 ng µl-1 for each 1-µl injection. After 5-min centrifugation at 15,1...0 mg/ml in pyridine) was added to the sample. After 24 h of derivatization at room temperature, the sample w...µl of methoxyamine hydrochloride (20 mg ml-1 in pyridine) were added to the sample. After 24 h of derivatiza...f MSTFA at 37°C with shaking. After silylation 30 µl of n-heptane were added. All derivatization steps were

  8. Sample (S): SE37_S07 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available ged daily. The shoot (aerial part) and root were separated with a scalpel and they were immediately frozen using liquid nitrogen. Aft...er lyophilization, the sample was stored at room temperature. ...

  9. Sample (S): SE37_S08 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available ged daily. The shoot (aerial part) and root were separated with a scalpel and they were immediately frozen using liquid nitrogen. Aft...er lyophilization, the sample was stored at room temperature. ...

  10. 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. ...

  11. Sample (S): SE37_S09 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available ged daily. The shoot (aerial part) and root were separated with a scalpel and they were immediately frozen using liquid nitrogen. Aft...er lyophilization, the sample was stored at room temperature. ...

  12. 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. ...

  13. Sample Set (SE): SE5 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available Mitsuo Enomoto, Nozomu Sakurai, Hideyuki Suzuki, Daiskue Shibata, Kazusa DNA Research Institute Direct Submittion version 4 ... ...s subsp. patens metabolites. 4 replicates data are examined for each sample. Norimoto Shimada, Takeshi Ara,

  14. 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. ...

  15. Sample Preparation (SS): SE55_SS01 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available 80℃ until analysis. The frozen tissues were homogenized in five volumes of 80% aqueous methanol containing 0...SE55_SS01 Metabolic profiling Collected sample tissues were weighed and stored at -

  16. 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. ...

  17. Sample Set (SE): SE32 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available camaldulensis leaf metabolites. 3 replicates data are examined for each sample. Yukiko Nakamura, Takeshi Ara..., Takashi Matsuura, Mitsuo Enomoto, Nozomu Sakurai, Hideyuki Suzuki, Daisuke Shibata, Kazusa DNA Research Institute Direct Submittion version 1 ...

  18. Sample Set (SE): SE33 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available leaf metabolites. 3 replicates data are examined for each sample. Yukiko Nakamura, Takeshi Ara, Takashi Mats...uura, Mitsuo Enomoto, Nozomu Sakurai, Hideyuki Suzuki, Daisuke Shibata, Kazusa DNA Research Institute Direct Submittion version 1 ...

  19. Sample Set (SE): SE36 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available metabolites. 3 replicates data are examined for each sample. Yukiko Nakamura, Takeshi Ara, Takashi Matsuura..., Mitsuo Enomoto, Nozomu Sakurai, Hideyuki Suzuki, Daisuke Shibata, Kazusa DNA Research Institute Direct Submittion version 1 ...

  20. Sample Set (SE): SE35 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available s leaf metabolites. 3 replicates data are examined for each sample. Yukiko Nakamura, Takeshi Ara, Takashi Ma...tsuura, Mitsuo Enomoto, Nozomu Sakurai, Hideyuki Suzuki, Daisuke Shibata, Kazusa DNA Research Institute Direct Submittion version 1 ...

  1. Sample Preparation (SS): SE52_SS01 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available Tokyo, Japan) using a mixer mill (MM 300, Retsch) with a zirconia bead for 6 min... at 20 Hz. Next, the samples were centrifuged at 15,000 g for 10 min and filtered (Ultrafree-MC filter, 0.2 μm; Mil...lipore, Bedford, MA, USA). The sample extracts were then applied to an HLB μElution plate (Waters, Mil

  2. 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 performing automated...applied to high-throughput automated analysis of biological samples using TQMS coupled with ultra performanc...ies, and family-specifi c metabolites could be predicted using a batch-learning self organizing map analysis. Thus, the automated

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

    DEFF Research Database (Denmark)

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

    2015-01-01

    was dependent on detection method and that spectrophotometry overestimated DNA amount compared with fluorometry. In the short tandem repeat analysis, detection rate dropped slightly with longer fragments. After WGA, this drop was more pronounced. Samples stored for 0 to 3 years showed better results compared...

  4. 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

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

    Lifescience Database Archive (English)

    Full Text Available SE47 Metabolomic correlation-network modules in Arabidopsis based on a graph-cluste...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 network

  6. Robustness of genome-wide scanning using archived dried blood spot samples as a DNA source

    Directory of Open Access Journals (Sweden)

    Børglum Anders D

    2011-07-01

    Full Text Available Abstract Background The search to identify disease-susceptible genes requires access to biological material from numerous well-characterized subjects. Archived residual dried blood spot (DBS samples, also known as Guthrie cards, from national newborn screening programs may provide a DNA source for entire populations. Combined with clinical information from medical registries, DBS samples could provide a rich source for productive research. However, the amounts of DNA which can be extracted from these precious samples are minute and may be prohibitive for numerous genotypings. Previously, we demonstrated that DBS DNA can be whole-genome amplified and used for reliable genetic analysis on different platforms, including genome-wide scanning arrays. However, it remains unclear whether this approach is workable on a large sample scale. We examined the robustness of using DBS samples for whole-genome amplification following genome-wide scanning, using arrays from Illumina and Affymetrix. Results This study is based on 4,641 DBS samples from the Danish Newborn Screening Biobank, extracted for three separate genome-wide association studies. The amount of amplified DNA was significantly (P Conclusion Our study indicates that archived DBS samples from the Danish Newborn Screening Biobank represent a reliable resource of DNA for whole-genome amplification and subsequent genome-wide association studies. With call-rates equivalent to high quality DNA samples, our results point to new opportunities for using the neonatal biobanks available worldwide in the hunt for genetic components of disease.

  7. A Survey of Mesenchyme-related Tumors of the Rat Kidney in the National Toxicology Program Archives, with Particular Reference to Renal Mesenchymal Tumor.

    Science.gov (United States)

    Hard, Gordon C; Seely, John Curtis; Betz, Laura J

    2016-08-01

    In order to harmonize diagnostic terminology, confirm diagnostic criteria, and describe aspects of tumor biology characteristic of different tumor types, a total of 165 cases of mesenchyme-related tumors and nephroblastomas of the rat kidney were reexamined from the National Toxicology Program (NTP) Archives. This survey demonstrated that renal mesenchymal tumor (RMT) was the most common spontaneous nonepithelial tumor in the rat kidney, also occurring more frequently in the NTP studies than nephroblastoma. Renal sarcoma was a distinct but very rare tumor entity, representing a malignant, monomorphous population of densely crowded, fibroblast-like cells, in which, unlike RMT, preexisting tubules did not persist. Nephroblastoma was characterized by early death of affected animals, suggesting an embryonal origin for this tumor type. Male and female rats were equally disposed to developing RMT, but most of the cases of nephroblastoma occurred in female rats and liposarcoma occurred mostly in male rats. This survey confirmed discrete histopathological and biological differences between the mesenchyme-related renal tumor types and between RMT and nephroblastoma. Statistical analysis also demonstrated a lack of any relationship of these renal tumor types to test article administration in the NTP data bank.

  8. Concordance of ATM (ataxia telangiectasia mutated) immunohistochemistry between biopsy or metastatic tumor samples and primary tumors in gastric cancer patients.

    Science.gov (United States)

    Kim, Hee Sung; Kim, Min A; Hodgson, Darren; Harbron, Christopher; Wellings, Robert; O'Connor, Mark J; Womack, Christopher; Yin, Xiaolu; Bang, Yung-Jue; Im, Seok-Ah; Lee, Byung Lan; Kim, Woo Ho

    2013-01-01

    ATM (ataxia telangiectasia mutated) is one of several DNA repair proteins that are suggested to sensitize tumor cells to the poly(ADP-ribose) polymerase inhibitor olaparib when deficient. The aim of this study was to assess the spatiotemporal concordance of ATM immunohistochemistry (IHC) in gastric cancer in order to determine if measurements made at the level of various sample types and times could be inferred as having the potential to be relevant to treatment decisions made at the patient level. Two independent cohorts composed of 591 gastric cancer patients divided into a gastrectomy cohort (n = 450) and a metastasis cohort (n = 141) were used in this study. A total of 2,705 ATM IHC samples were examined, including 450 whole tissue, 3 sets of 450 tissue microarray (TMA), 301 biopsy, 222 metastatic tumor and 2 additional whole tissue samples of 50 cases from the gastrectomy cohort, and 141 pairs of primary and metastatic tumors from the metastasis cohort. The prevalence of ATM negativity was 13.1% in biopsies, 13.9, 15.1, and 16.0% in TMAs and 15.9% in whole tissue samples of the gastrectomy cohort, and 21.4% in primary tumor and 21.5% in metastatic tumor samples of the metastasis cohort. coefficients were 0.341 for biopsy, 0.572 as the average of 3 TMAs and 0.415 for the largely synchronous metastatic tumors of the gastrectomy cohort, and 0.153 for the largely asynchronous metastatic tumors of the metastasis cohort. Using whole tissue sections from tumor resections or primary tumor, respectively, as the reference standards, specificity and sensitivity were 91.6 and 41.0% for biopsy, 93.9 and 61.9% as the average of 3 TMAs, and 86.6 and 58.8% for metastatic tumors of the gastrectomy cohort and 81.7 and 33.3% for metastatic tumors of the metastasis cohort, respectively. Although we have demonstrated that the IHC assay for ATM was robust and reproducible in gastric tumor samples, we have also found that measurements were subject to significant discordance across

  9. 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.

  10. Immunoelectron microscopic localization of elastic tissue components in archival tissue samples.

    Science.gov (United States)

    Fanning, J C; White, J F; Polewski, R; Cleary, E G

    1991-06-01

    Tissue samples that have been stored for many years, in different media and under a variety of conditions, have been examined by modern techniques of immunoelectron microscopy, using antibodies against elastic tissue components. A range of postembedding restorative procedures has been identified, which will allow reliable immunolocalization of antibodies against the elastic tissue component of such specimens. These methods have been applied successfully to autopsy-derived material, fixed in buffered formaldehyde, to archival material stored frozen at -70 or -20 degrees C, to specimens fixed for electron microscopy and stored for many years in buffer, and even to archival material from formaldehyde-fixed, paraffin-embedded blocks, reprocessed for electron microscopic examination. The successful restorative methods included pre-treatment of the sections with 6 M guanidine hydrochloride, or 1 M Tris/saline, each containing 100 mM dithiothreitol (a reducing agent) followed by alkylation with 220 mM iodoacetamide. The application of these techniques allowed reliable study of elastic tissue antibody distributions in archival tissues that could not be obtained again, as well as comparative studies with tissues processed many years previously.

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

    Science.gov (United States)

    2016-11-21

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-06-01

    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.

  13. Profiling critical cancer gene mutations in clinical tumor samples.

    Directory of Open Access Journals (Sweden)

    Laura E MacConaill

    Full Text Available BACKGROUND: Detection of critical cancer gene mutations in clinical tumor specimens may predict patient outcomes and inform treatment options; however, high-throughput mutation profiling remains underdeveloped as a diagnostic approach. We report the implementation of a genotyping and validation algorithm that enables robust tumor mutation profiling in the clinical setting. METHODOLOGY: We developed and implemented an optimized mutation profiling platform ("OncoMap" to interrogate approximately 400 mutations in 33 known oncogenes and tumor suppressors, many of which are known to predict response or resistance to targeted therapies. The performance of OncoMap was analyzed using DNA derived from both frozen and FFPE clinical material in a diverse set of cancer types. A subsequent in-depth analysis was conducted on histologically and clinically annotated pediatric gliomas. The sensitivity and specificity of OncoMap were 93.8% and 100% in fresh frozen tissue; and 89.3% and 99.4% in FFPE-derived DNA. We detected known mutations at the expected frequencies in common cancers, as well as novel mutations in adult and pediatric cancers that are likely to predict heightened response or resistance to existing or developmental cancer therapies. OncoMap profiles also support a new molecular stratification of pediatric low-grade gliomas based on BRAF mutations that may have immediate clinical impact. CONCLUSIONS: Our results demonstrate the clinical feasibility of high-throughput mutation profiling to query a large panel of "actionable" cancer gene mutations. In the future, this type of approach may be incorporated into both cancer epidemiologic studies and clinical decision making to specify the use of many targeted anticancer agents.

  14. Tumorer

    DEFF Research Database (Denmark)

    Prause, J.U.; Heegaard, S.

    2005-01-01

    oftalmologi, øjenlågstumorer, conjunctivale tumorer, malignt melanom, retinoblastom, orbitale tumorer......oftalmologi, øjenlågstumorer, conjunctivale tumorer, malignt melanom, retinoblastom, orbitale tumorer...

  15. 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.

  16. Dose-Response Analysis of RNA-Seq Profiles in Archival Formalin-Fixed Paraffin-Embedded (FFPE) Samples.

    Science.gov (United States)

    Use of archival resources has been limited to date by inconsistent methods for genomic profiling of degraded RNA from formalin-fixed paraffin-embedded (FFPE) samples. RNA-sequencing offers a promising way to address this problem. Here we evaluated transcriptomic dose responses us...

  17. Coupling meteorology, metal concentrations, and Pb isotopes for source attribution in archived precipitation samples.

    Science.gov (United States)

    Graney, Joseph R; Landis, Matthew S

    2013-03-15

    A technique that couples lead (Pb) isotopes and multi-element concentrations with meteorological analysis was used to assess source contributions to precipitation samples at the Bondville, Illinois USA National Trends Network (NTN) site. Precipitation samples collected over a 16month period (July 1994-October 1995) at Bondville were parsed into six unique meteorological flow regimes using a minimum variance clustering technique on back trajectory endpoints. Pb isotope ratios and multi-element concentrations were measured using high resolution inductively coupled plasma-sector field mass spectrometry (ICP-SFMS) on the archived precipitation samples. Bondville is located in central Illinois, ~250km downwind from smelters in southeast Missouri. The Mississippi Valley Type ore deposits in Missouri provided a unique multi-element and Pb isotope fingerprint for smelter emissions which could be contrasted to industrial emissions from the Chicago and Indianapolis urban areas (~125km north and east, of Bondville respectively) and regional emissions from electric utility facilities. Differences in Pb isotopes and element concentrations in precipitation corresponded to flow regime. Industrial sources from urban areas, and thorogenic Pb from coal use, could be differentiated from smelter emissions from Missouri by coupling Pb isotopes with variations in element ratios and relative mass factors. Using a three endmember mixing model based on Pb isotope ratio differences, industrial processes in urban airsheds contributed 56±19%, smelters in southeast Missouri 26±13%, and coal combustion 18±7%, of the Pb in precipitation collected in Bondville in the mid-1990s.

  18. Terahertz spectroscopy and detection of brain tumor in rat fresh-tissue samples

    Science.gov (United States)

    Yamaguchi, S.; Fukushi, Y.; Kubota, O.; Itsuji, T.; Yamamoto, S.; Ouchi, T.

    2015-03-01

    Terahertz (THz) spectroscopy and imaging of biomedical samples is expected to be an important application of THz analysis techniques. Identification and localization of tumor tissue, imaging of biological samples, and analysis of DNA by THz spectroscopy have been reported. THz time-domain spectroscopy (TDS) is useful for obtaining the refractive index over a broad frequency range. However, THz-TDS spectra of fresh tissue samples are sensitive to procedures such as sample preparation, and a standardized measurement protocol is required. Therefore, in this work, we establish a protocol for measurements of THz spectra of fresh tissue and demonstrate reliable detection of rat brain tumor tissue. We use a reflection THz-TDS system to measure the refractive index spectra of the samples mounted on a quartz plate. The tissue samples were measured immediately after sectioning to avoid sample denaturalization during storage. Special care was taken in THz data processing to eliminate parasitic reflections and reduce noise. The error level in our refractive index measurements was as low as 0.02 in the frequency range 0.8-1.5 THz. With increasing frequency, the refractive index in the tumor and normal regions monotonically decreased, similarly to water, and it was 0.02 higher in the tumor regions. The spectral data suggest that the tumor regions have higher water content. Hematoxylin-eosin stained images showed that increased cell density was also responsible for the observed spectral features. A set of samples from 10 rats showed consistent results. Our results suggest that reliable tumor detection in fresh tissue without pretreatment is possible with THz spectroscopy measurements. THz spectroscopy has the potential to become a real-time in vivo diagnostic method.

  19. Detection of recurrent alternative splicing switches in tumor samples reveals novel signatures of cancer.

    Science.gov (United States)

    Sebestyén, Endre; Zawisza, Michał; Eyras, Eduardo

    2015-02-18

    The determination of the alternative splicing isoforms expressed in cancer is fundamental for the development of tumor-specific molecular targets for prognosis and therapy, but it is hindered by the heterogeneity of tumors and the variability across patients. We developed a new computational method, robust to biological and technical variability, which identifies significant transcript isoform changes across multiple samples. We applied this method to more than 4000 samples from the The Cancer Genome Atlas project to obtain novel splicing signatures that are predictive for nine different cancer types, and find a specific signature for basal-like breast tumors involving the tumor-driver CTNND1. Additionally, our method identifies 244 isoform switches, for which the change occurs in the most abundant transcript. Some of these switches occur in known tumor drivers, including PPARG, CCND3, RALGDS, MITF, PRDM1, ABI1 and MYH11, for which the switch implies a change in the protein product. Moreover, some of the switches cannot be described with simple splicing events. Surprisingly, isoform switches are independent of somatic mutations, except for the tumor-suppressor FBLN2 and the oncogene MYH11. Our method reveals novel signatures of cancer in terms of transcript isoforms specifically expressed in tumors, providing novel potential molecular targets for prognosis and therapy. Data and software are available at: http://dx.doi.org/10.6084/m9.figshare.1061917 and https://bitbucket.org/regulatorygenomicsupf/iso-ktsp.

  20. Museums and disease: using tissue archive and museum samples to study pathogens.

    Science.gov (United States)

    Tsangaras, Kyriakos; Greenwood, Alex D

    2012-01-20

    Molecular studies of archival and fossil samples have traditionally focused on the nucleic acids derived from the host species. However, there has recently been an increase in ancient DNA research on the identification and characterization of infectious agents within the hosts. The study of pathogens from the past provides great opportunities for discovering the causes of historical infection events, characterizing host-microorganism co-evolution and directly investigating the evolution of specific pathogens. Several research teams have been able to isolate and characterize a variety of different bacterial, parasite and viral microorganisms. However, this emerging field is not without obstacles. The diagenetic processes that make ancient DNA research generally difficult are also impediments to ancient pathogen research and perhaps more so given that their DNA may represent an even rarer proportion of the remaining nucleic acids in a fossil sample than host DNA. However, studies performed under controlled conditions and following stringent ancient DNA protocols can and have yielded reliable and often surprising results. This article reviews the advantages, problems, and failures of ancient microbiological research.

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

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

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

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  15. File list: ALL.Pan.50.AllAg.Islet_tumor [Chip-atlas[Archive

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  1. File list: ALL.Liv.50.AllAg.Liver_tumor [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  4. File list: ALL.Brs.20.AllAg.Mammary_tumor [Chip-atlas[Archive

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  5. File list: ALL.Brs.50.AllAg.Mammary_tumor [Chip-atlas[Archive

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  6. 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

  7. Validation of whole genome amplification for analysis of the p53 tumor suppressor gene in limited amounts of tumor samples.

    Science.gov (United States)

    Hasmats, Johanna; Green, Henrik; Solnestam, Beata Werne; Zajac, Pawel; Huss, Mikael; Orear, Cedric; Validire, Pierre; Bjursell, Magnus; Lundeberg, Joakim

    2012-08-24

    Personalized cancer treatment requires molecular characterization of individual tumor biopsies. These samples are frequently only available in limited quantities hampering genomic analysis. Several whole genome amplification (WGA) protocols have been developed with reported varying representation of genomic regions post amplification. In this study we investigate region dropout using a φ29 polymerase based WGA approach. DNA from 123 lung cancers specimens and corresponding normal tissue were used and evaluated by Sanger sequencing of the p53 exons 5-8. To enable comparative analysis of this scarce material, WGA samples were compared with unamplified material using a pooling strategy of the 123 samples. In addition, a more detailed analysis of exon 7 amplicons were performed followed by extensive cloning and Sanger sequencing. Interestingly, by comparing data from the pooled samples to the individually sequenced exon 7, we demonstrate that mutations are more easily recovered from WGA pools and this was also supported by simulations of different sequencing coverage. Overall this data indicate a limited random loss of genomic regions supporting the use of whole genome amplification for genomic analysis.

  8. 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.

  9. 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.

  10. Mucosal Incision and Forceps Biopsy for Reliable Tissue Sampling of Gastric Subepithelial Tumors

    Science.gov (United States)

    Shin, Sa Young; Lee, Sang Jin; Jun, Jae Hyuck; Park, Jong Kyu; Seo, Hyun Il; Han, Koon Hee; Kim, Young Don; Jeong, Woo Jin; Cheon, Gab Jin

    2017-01-01

    Background/Aims The diagnostic efficacy of current tissue sampling techniques for gastric subepithelial tumors (SETs) is limited. Better tissue sampling techniques are needed to improve pathological diagnosis. The aim of this study was to evaluate the safety and efficacy of a new technique, mucosal incision and forceps biopsy, for reliable tissue sampling of gastric SETs. Methods This study enrolled 12 consecutive patients who underwent mucosal incision and forceps biopsy of gastric SETs between November 2011 and September 2014 at Gangneung Asan Hospital. The medical records of patients were reviewed retrospectively. The safety and diagnostic yield of this method were evaluated. Results By performing mucosal incision and forceps biopsy, we were able to provide a definitive histological diagnosis for 11 out of 12 cases. The pathological diagnoses were leiomyoma (3/11), gastrointestinal stromal tumor (GIST; 2/11), lipoma (2/11), schwannoma (1/11), and ectopic pancreas (3/11). In cases of leiomyoma (n=3) and GIST (n=2), tissue samples were of sufficient size to allow immunohistochemical staining. In addition, the mitotic index was evaluated in two cases of GIST. There were no procedure-related complications. Conclusions Mucosal incision and forceps biopsy can be used as one of several methods to obtain adequate tissue samples from gastric SETs. PMID:26942580

  11. From the archives of the AFIP. Imaging of musculoskeletal neurogenic tumors: radiologic-pathologic correlation.

    Science.gov (United States)

    Murphey, M D; Smith, W S; Smith, S E; Kransdorf, M J; Temple, H T

    1999-01-01

    Numerous neurogenic tumors can affect the musculoskeletal system, including traumatic neuroma, Morton neuroma, neural fibrolipoma, nerve sheath ganglion, neurilemoma, neurofibroma, and malignant peripheral nerve sheath tumors (PNSTs). The diagnosis of neurogenic tumors can be suggested from their imaging appearances, including lesion shape and intrinsic imaging characteristics. It is also important to establish lesion location along a typical nerve distribution (eg, plantar digital nerve in Morton neuroma, median nerve in neural fibrolipoma, large nerve trunk in benign and malignant PNSTs). Traumatic and Morton neuromas are commonly related to an amputation stump or are located in the intermetatarsal space, respectively. Neural fibrolipomas show fat interspersed between nerve fascicles and are often associated with macrodactyly. Nerve sheath ganglion has a cystic appearance and commonly occurs about the knee. Radiologic characteristics of neurilemoma, neurofibroma, and malignant PNST at computed tomography (CT), ultrasonography, and magnetic resonance imaging include fusiform shape, identification of entering and exiting nerve, low attenuation at CT, target sign, fascicular sign, split-fat sign, and associated muscle atrophy. Although differentiation of neurilemoma from neurofibroma and of benign from malignant PNST is problematic, recognition of the radiologic appearances of neurogenic tumors often allows prospective diagnosis and improves clinical management of patients.

  12. Expression profiling of gastric cancer samples by oligonucleotide microarray analysis reveals low degree of intra-tumor variability

    Institute of Scientific and Technical Information of China (English)

    Karolin Trautmann; Christine Steudel; Dana Grossmann; Daniela Aust; Gerhard Ehninger; Stephan Miehlke; Christian Thiede

    2005-01-01

    AIM: Gene expression profiling provides an unique opportunity to gain insight into the development of different types of gastric cancer. Tumor sample heterogeneity is thought to decrease the sensitivity and tumor specificity of microarray analysis. Thus, microdissection and preamplification of RNA is frequently performed. However, this technique may also induce considerable changes to the expression profile. To assess the effect of gastric tumor heterogeneity on expression profiling results, we measured the variation in gene expression within the same gastric cancer sample by performing a gene chip analysis with two RNA preparations extracted from the same tumor specimen.METHODS: Tumor samples from six intestinal T2 gastric tumors were dissected under liquid nitrogen and RNA was prepared from two separate tumor fragments. Each extraction was individually processed and hybridized to an Affymetrix U133A gene chip covering approximately 18 000 human gene transcripts. Expression profiles were analyzed using Microarray Suite 5.0 (Affymetrix) and GeneSpring 6.0 (Silicon Genetics).RESULTS: All gastric cancers showed little variance in expression profiles between different regions of the same tumor sample. In this case, gene chips displayed mean pair wise correlation coefficients of 0.94±0.02 (mean±SD),compared to values of 0.61±0.1 for different tumor samples. Expression of the variance between the two expression profiles as a percentage of "total change"(Affymetrix) revealed a remarkably low average value of 1.18±0.78 for comparing fragments of the same tumor sample.In contrast, comparison of fragments from different tumors revealed a percentage of 24.4±4.5.CONCLUSION: Our study indicates a low degree of expression profile variability within gastric tumor samples isolated from one patient. These data suggest that tumor tissue heterogeneity is not a dominant source of error for microarray analysis of larger tumor samples, making total RNA extraction an appropriate

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

    Science.gov (United States)

    2016-10-05

    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

  14. A Tumor-stroma Targeted Oncolytic Adenovirus Replicated in Human Ovary Cancer Samples and Inhibited Growth of Disseminated Solid Tumors in Mice

    Science.gov (United States)

    Lopez, M Veronica; Rivera, Angel A; Viale, Diego L; Benedetti, Lorena; Cuneo, Nicasio; Kimball, Kristopher J; Wang, Minghui; Douglas, Joanne T; Zhu, Zeng B; Bravo, Alicia I; Gidekel, Manuel; Alvarez, Ronald D; Curiel, David T; Podhajcer, Osvaldo L

    2012-01-01

    Targeting the tumor stroma in addition to the malignant cell compartment is of paramount importance to achieve complete tumor regression. In this work, we modified a previously designed tumor stroma-targeted conditionally replicative adenovirus (CRAd) based on the SPARC promoter by introducing a mutated E1A unable to bind pRB and pseudotyped with a chimeric Ad5/3 fiber (Ad F512v1), and assessed its replication/lytic capacity in ovary cancer in vitro and in vivo. AdF512v1 was able to replicate in fresh samples obtained from patients: (i) with primary human ovary cancer; (ii) that underwent neoadjuvant treatment; (iii) with metastatic disease. In addition, we show that four intraperitoneal (i.p.) injections of 5 × 1010 v.p. eliminated 50% of xenografted human ovary tumors disseminated in nude mice. Moreover, AdF512v1 replication in tumor models was enhanced 15–40-fold when the tumor contained a mix of malignant and SPARC-expressing stromal cells (fibroblasts and endothelial cells). Contrary to the wild-type virus, AdF512v1 was unable to replicate in normal human ovary samples while the wild-type virus can replicate. This study provides evidence on the lytic capacity of this CRAd and highlights the importance of targeting the stromal tissue in addition to the malignant cell compartment to achieve tumor regression. PMID:22948673

  15. 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...

  16. New in vitro system to predict chemotherapeutic efficacy of drug combinations in fresh tumor samples

    Directory of Open Access Journals (Sweden)

    Frank Christian Kischkel

    2017-03-01

    Full Text Available Background To find the best individual chemotherapy for cancer patients, the efficacy of different chemotherapeutic drugs can be predicted by pretesting tumor samples in vitro via the chemotherapy-resistance (CTR-Test®. Although drug combinations are widely used among cancer therapy, so far only single drugs are tested by this and other tests. However, several first line chemotherapies are combining two or more chemotherapeutics, leading to the necessity of drug combination testing methods. Methods We established a system to measure and predict the efficacy of chemotherapeutic drug combinations with the help of the Loewe additivity concept in combination with the CTR-test. A combination is measured by using half of the monotherapy’s concentration of both drugs simultaneously. With this method, the efficacy of a combination can also be calculated based on single drug measurements. Results The established system was tested on a data set of ovarian carcinoma samples using the combination carboplatin and paclitaxel and confirmed by using other tumor species and chemotherapeutics. Comparing the measured and the calculated values of the combination testings revealed a high correlation. Additionally, in 70% of the cases the measured and the calculated values lead to the same chemotherapeutic resistance category of the tumor. Conclusion Our data suggest that the best drug combination consists of the most efficient single drugs and the worst drug combination of the least efficient single drugs. Our results showed that single measurements are sufficient to predict combinations in specific cases but there are exceptions in which it is necessary to measure combinations, which is possible with the presented system.

  17. New in vitro system to predict chemotherapeutic efficacy of drug combinations in fresh tumor samples

    Science.gov (United States)

    Weidemüller, Paula; Krapfl, Jens; Yassin-Kelepir, Rauaa; Job, Laura; Fraefel, Marius; Braicu, Ioana; Kopp-Schneider, Annette; Sehouli, Jalid; De Wilde, Rudy Leon

    2017-01-01

    Background To find the best individual chemotherapy for cancer patients, the efficacy of different chemotherapeutic drugs can be predicted by pretesting tumor samples in vitro via the chemotherapy-resistance (CTR)-Test®. Although drug combinations are widely used among cancer therapy, so far only single drugs are tested by this and other tests. However, several first line chemotherapies are combining two or more chemotherapeutics, leading to the necessity of drug combination testing methods. Methods We established a system to measure and predict the efficacy of chemotherapeutic drug combinations with the help of the Loewe additivity concept in combination with the CTR-test. A combination is measured by using half of the monotherapy’s concentration of both drugs simultaneously. With this method, the efficacy of a combination can also be calculated based on single drug measurements. Results The established system was tested on a data set of ovarian carcinoma samples using the combination carboplatin and paclitaxel and confirmed by using other tumor species and chemotherapeutics. Comparing the measured and the calculated values of the combination testings revealed a high correlation. Additionally, in 70% of the cases the measured and the calculated values lead to the same chemotherapeutic resistance category of the tumor. Conclusion Our data suggest that the best drug combination consists of the most efficient single drugs and the worst drug combination of the least efficient single drugs. Our results showed that single measurements are sufficient to predict combinations in specific cases but there are exceptions in which it is necessary to measure combinations, which is possible with the presented system.

  18. 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

    2016-05-05

    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.

  19. Kinase genotype analysis of gastric gastrointestinal stromal tumor cytology samples using targeted next-generation sequencing.

    Science.gov (United States)

    Gleeson, Ferga C; Kipp, Benjamin R; Kerr, Sarah E; Voss, Jesse S; Graham, Rondell P; Campion, Michael B; Minot, Douglas M; Tu, Zheng J; Klee, Eric W; Lazaridis, Konstantinos N; Henry, Michael R; Levy, Michael J

    2015-01-01

    Gastric gastrointestinal stromal tumors (GISTs) usually contain the mast/stem cell growth factor receptor Kit gene (KIT) or platelet-derived growth factor receptor A (PDGFRA) mutations that can be targeted by, or mediate resistance to, imatinib. Diagnostic material often is obtained by endoscopic ultrasound-guided fine-needle aspiration, which often is unsuitable for molecular analysis. We investigated whether targeted next-generation sequencing (NGS) can be used in multiplex genotype analysis of cytology samples collected by endoscopic ultrasound-guided fine-needle aspiration. We used the Ion AmpliSeq V2 Cancer Hotspot NGS Panel (Life Technologies, Carlsbad, CA) to identify mutations in more than 2800 exons from 50 cancer-associated genes in GIST samples from 20 patients. We identified KIT mutations in 58% of samples (91% in exon 11 and 9% in exon 17) and PDGFRA mutations in 26% (60% in exon 18 and 40% in exon 12); 16% of samples had no mutations in KIT or PDGFRA. No pathogenic alterations were found in PIK3CA, BRAF, KRAS, NRAS, or FGFR3. We predicted that 32% of patients would have primary resistance to imatinib, based on mutations in exon 17 of KIT, exon 18 of PDGFRA (D842V), or no mutation in either gene. Targeted NGS of cytology samples from GISTs is feasible and provides clinically relevant data about kinase genotypes that can help guide individualized therapy.

  20. The stem cell self-renewal gene, Musashi 1, is highly expressed in tumor and non-tumor samples of human bladder

    Directory of Open Access Journals (Sweden)

    P Nikpour

    2013-01-01

    Full Text Available Context: The stem cell model for cancer assumes that a key event in tumorigenesis is the deregulation of genes involved in the regulation of stem cell self-renewal. The Musashi family is an evolutionarily conserved group of neural RNA-binding proteins. In mammals, the family consists of two individual genes, Musashi 1 (MSI1 and MSI2, encoding the Musashi 1 and Musashi 2 proteins. Musashi 1 is involved in the regulation of self-renewal of stem cells. Recently, its over-expression has also been reported in a variety of human tumors. Aims: To investigate a potential expression of the stem cell self-renewal gene, Musashi 1, in human bladder cancer, we examined its gene expression in a series of tumor and non-tumor tissue samples of bladder. Materials and Methods: Relative expression of MSI1 was determined by the real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR in 70 surgical samples of bladder. Results: Using specific primers for MSI1 and TBP (as an internal control for qRT-PCR technique, we found a relatively high expression level of MSI1 in all examined tumor and non-tumor bladder tissue specimens. However, our data did not show any correlation between the level of gene expression and tumor/non-tumor states of the samples (P>0.05. Conclusions: All together, our data demonstrated that Musashi 1 is highly and un-differentially expressed in both examined tumoral and apparently normal bladder tissues.

  1. Tumor

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    2008479 Preliminary study of MR elastography in brain tumors. XU Lei(徐磊), et al.Neurosci Imaging Center, Beijing Tiantan Hosp, Capital Med Univ, Beijing 100050.Chin J Radiol 2008;42(6):605-608. Objective To investigate the potential values of magnetic resonance elastography (MRE) for evaluating the brain tumor consistency in vivo. Methods Fourteen patients with known solid brain tumor (5 male, 9 female; age range: 16-63 years)

  2. File list: Pol.Kid.50.AllAg.Nephrectomy_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  3. File list: Pol.Kid.05.AllAg.Nephrectomy_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  4. File list: DNS.Kid.05.AllAg.Nephrectomy_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  5. File list: Unc.Kid.20.AllAg.Nephrectomy_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  6. File list: DNS.Kid.20.AllAg.Nephrectomy_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  7. File list: DNS.Kid.50.AllAg.Nephrectomy_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  8. File list: Unc.Kid.50.AllAg.Nephrectomy_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  9. File list: Unc.Kid.10.AllAg.Nephrectomy_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Unc.Kid.10.AllAg.Nephrectomy_sample hg19 Unclassified Kidney Nephrectomy sample htt...p://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Unc.Kid.10.AllAg.Nephrectomy_sample.bed ...

  10. 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...

  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.10.AllAg.Gastric_primary_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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

    Lifescience Database Archive (English)

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  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: 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 prim...ary sample SRX201807,SRX201812 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/DNS.Dig.50.AllAg.Gastric_primary_sample.bed ...

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

    Lifescience Database Archive (English)

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

    Lifescience Database Archive (English)

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

    Lifescience Database Archive (English)

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

    Lifescience Database Archive (English)

    Full Text Available DNS.Dig.20.AllAg.Gastric_primary_sample hg19 DNase-seq Digestive tract Gastric prim...ary sample SRX201807,SRX201812 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/DNS.Dig.20.AllAg.Gastric_primary_sample.bed ...

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

    Lifescience Database Archive (English)

    Full Text Available Oth.Dig.50.AllAg.Gastric_primary_sample hg19 TFs and others Digestive tract Gastric... primary sample http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Oth.Dig.50.AllAg.Gastric_primary_sample.bed ...

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

    Lifescience Database Archive (English)

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

    Lifescience Database Archive (English)

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

    Lifescience Database Archive (English)

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

    Lifescience Database Archive (English)

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

    Lifescience Database Archive (English)

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

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  7. File list: InP.Kid.20.AllAg.Nephrectomy_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  8. File list: His.Kid.20.AllAg.Nephrectomy_sample [Chip-atlas[Archive

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  9. File list: NoD.Kid.20.AllAg.Nephrectomy_sample [Chip-atlas[Archive

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  10. File list: His.Kid.05.AllAg.Nephrectomy_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  11. File list: Oth.Kid.05.AllAg.Nephrectomy_sample [Chip-atlas[Archive

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  12. File list: InP.Kid.10.AllAg.Nephrectomy_sample [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  13. File list: NoD.Kid.10.AllAg.Nephrectomy_sample [Chip-atlas[Archive

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  14. File list: His.Kid.50.AllAg.Nephrectomy_sample [Chip-atlas[Archive

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  15. File list: Oth.Kid.20.AllAg.Nephrectomy_sample [Chip-atlas[Archive

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  16. File list: Oth.Kid.10.AllAg.Nephrectomy_sample [Chip-atlas[Archive

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  17. File list: InP.Kid.50.AllAg.Nephrectomy_sample [Chip-atlas[Archive

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  18. File list: InP.Kid.05.AllAg.Nephrectomy_sample [Chip-atlas[Archive

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  19. File list: His.Kid.10.AllAg.Nephrectomy_sample [Chip-atlas[Archive

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  20. File list: Oth.Kid.50.AllAg.Nephrectomy_sample [Chip-atlas[Archive

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  1. 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

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

    Lifescience Database Archive (English)

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

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

    Lifescience Database Archive (English)

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  5. Test Results for Caustic Demand Measurements on Tank 241-AX-101 and Tank 241-AX-103 Archive Samples

    Energy Technology Data Exchange (ETDEWEB)

    Doll, Stephanie R. [Washington River Protection Solutions, Richland, WA (United States); Bolling, Stacie D. [Washington River Protection Solutions, Richland, WA (United States)

    2016-07-14

    Caustic demand testing is used to determine the necessary amount of caustic required to neutralize species present in the Hanford tank waste and obtain a target molarity of free hydroxide for tank corrosion control. The presence and quantity of hydroxide-consuming analytes are just as important in determining the caustic demand as is the amount of free hydroxide present. No single data point can accurately predict whether a satisfactory hydroxide level is being met, as it is dependent on multiple factors (e.g., free hydroxide, buffers, amphoteric metal hydroxides, bicarbonate, etc.). This enclosure contains the caustic demand, scanning electron microscopy (SEM), polarized light microscopy (PLM), and X-ray diffraction (XRD) analysis for the tank 241-AX-101 (AX-101) and 241-AX-103 (AX-103) samples. The work was completed to fulfill a customer request outlined in the test plan, WRPS-1505529, “Test Plan and Procedure for Caustic Demand Testing on Tank 241-AX-101 and Tank 241-AX-103 Archive Samples.” The work results will provide a baseline to support planned retrieval of AX-101 and AX-103.

  6. Test Results for Caustic Demand Measurements on Tank 241-AX-101 and Tank 241-AX-103 Archive Samples

    Energy Technology Data Exchange (ETDEWEB)

    Doll, Stephanie R. [Washington River Protection Solutions, Richland, WA (United States); Bolling, Stacie D. [Washington River Protection Solutions, Richland, WA (United States)

    2016-07-14

    Caustic demand testing is used to determine the necessary amount of caustic required to neutralize species present in the Hanford tank waste and obtain a target molarity of free hydroxide for tank corrosion control. The presence and quantity of hydroxide-consuming analytes are just as important in determining the caustic demand as is the amount of free hydroxide present. No single data point can accurately predict whether a satisfactory hydroxide level is being met as it is dependent on multiple factors (e.g., free hydroxide, buffers, amphoteric metal hydroxides, bicarbonate, etc.). This enclosure contains the caustic demand, scanning electron microscopy (SEM), polarized light microscopy (PLM), and X-ray diffraction (XRD) analysis for the tank 241-AX-101 (AX-101) and 241-AX-103 (AX-103) samples. The work was completed to fulfill a customer request outlined in the test plan, WRPS-1505529, “Test Plan and Procedure for Caustic Demand Testing on Tank 241-AX-101 and Tank 241-AX-103 Archive Samples.” The work results will provide a baseline to support planned retrieval of AX-101 and AX-103.

  7. Archived neonatal dried blood spot samples can be used for accurate whole genome and exome-targeted next-generation sequencing

    DEFF Research Database (Denmark)

    Hollegaard, Mads Vilhelm; Grauholm, Jonas; Nielsen, Ronni;

    2013-01-01

    Dried blood spot samples (DBSS) have been collected and stored for decades as part of newborn screening programmes worldwide. Representing almost an entire population under a certain age and collected with virtually no bias, the Newborn Screening Biobanks are of immense value in medical studies......, for example, to examine the genetics of various disorders. We have previously demonstrated that DNA extracted from a fraction (2×3.2mm discs) of an archived DBSS can be whole genome amplified (wgaDNA) and used for accurate array genotyping. However, until now, it has been uncertain whether wgaDNA from DBSS...... can be used for accurate whole genome sequencing (WGS) and exome sequencing (WES). This study examined two individuals represented by three different types of samples each: whole-blood (reference samples), 3-year-old DBSS spotted with reference material (refDBSS), and 27- to 29-year-old archived...

  8. A novel SNP analysis method to detect copy number alterations with an unbiased reference signal directly from tumor samples

    Directory of Open Access Journals (Sweden)

    LaFramboise William A

    2011-01-01

    Full Text Available Abstract Background Genomic instability in cancer leads to abnormal genome copy number alterations (CNA as a mechanism underlying tumorigenesis. Using microarrays and other technologies, tumor CNA are detected by comparing tumor sample CN to normal reference sample CN. While advances in microarray technology have improved detection of copy number alterations, the increase in the number of measured signals, noise from array probes, variations in signal-to-noise ratio across batches and disparity across laboratories leads to significant limitations for the accurate identification of CNA regions when comparing tumor and normal samples. Methods To address these limitations, we designed a novel "Virtual Normal" algorithm (VN, which allowed for construction of an unbiased reference signal directly from test samples within an experiment using any publicly available normal reference set as a baseline thus eliminating the need for an in-lab normal reference set. Results The algorithm was tested using an optimal, paired tumor/normal data set as well as previously uncharacterized pediatric malignant gliomas for which a normal reference set was not available. Using Affymetrix 250K Sty microarrays, we demonstrated improved signal-to-noise ratio and detected significant copy number alterations using the VN algorithm that were validated by independent PCR analysis of the target CNA regions. Conclusions We developed and validated an algorithm to provide a virtual normal reference signal directly from tumor samples and minimize noise in the derivation of the raw CN signal. The algorithm reduces the variability of assays performed across different reagent and array batches, methods of sample preservation, multiple personnel, and among different laboratories. This approach may be valuable when matched normal samples are unavailable or the paired normal specimens have been subjected to variations in methods of preservation.

  9. ENO1 Protein Levels in the Tumor Tissues and Circulating Plasma Samples of Non-small Cell Lung Cancer Patients

    Directory of Open Access Journals (Sweden)

    Ying ZHANG

    2010-12-01

    Full Text Available Background and objective Proper tumor markers are useful to diagnosis, prognosis and treatment for lung cancer. The aim of this study is to examine the levels of alpha-enolase (ENO1 protein in the tumor tissues and peripheral plasma samples obtained from non-small cell lung cancer (NSCLC patients, and evaluate its potential clinical significance. Methods The ENO1 protein levels in the tumor tissues and corresponding normal tissues from 16 cases of lung squamous cell carcinoma were analyzed by Western blot. The ENO1 protein levels in the plasma samples from 42 healthy individuals, 34 patients with lung benign disease and 84 patients with NSCLC were measured by double antibody sandwich enzyme-linked immunosorbent assay. Results For 87.5% (14/16 of the patients with lung squamous cell carcinoma, the ENO1 protein level in the tumor tissues was higher than that in the corresponding normal lung tissues. The ENO1 protein level in the plasma of NSCLC patients was significantly higher than that in the plasma of healthy individuals (P=0.031 and patients with lung benign disease (P=0.019. Furthermore, the ENO1 protein level was significantly higher in the plasma of patients with lung adenocarcinoma than that of patients with lung squamous cell carcinoma. Conclusion The elevated levels of ENO1 protein in the tumor tissues and the plasma samples from NSCLC patients indicate ENO1 may be a candidate biomarker of lung cancer.

  10. 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.

  11. Tumor producing fibroblast growth factor 23 localized by two-staged venous sampling.

    NARCIS (Netherlands)

    Boekel, G.A.J van; Ruinemans-Koerts, J.; Joosten, F.; Dijkhuizen, P.; Sorge, A van; Boer, H de

    2008-01-01

    BACKGROUND: Tumor-induced osteomalacia is a rare paraneoplastic syndrome characterized by hypophosphatemia, renal phosphate wasting, suppressed 1,25-dihydroxyvitamin D production, and osteomalacia. It is caused by a usually benign mesenchymal tumor producing fibroblast growth factor 23 (FGF-23). Sur

  12. 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.

  13. 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.

  14. Flexible Lab-Tailored Cut-Offs for Suitability of Formalin-Fixed Tumor Samples for Diagnostic Mutational Analyses

    Science.gov (United States)

    Mariani, Sara; Tondat, Fabrizio; Pacchioni, Donatella; Molinaro, Luca; Barreca, Antonella; Macrì, Luigia; Chiusa, Luigi; di Celle, Paola Francia; Cassoni, Paola; Sapino, Anna

    2015-01-01

    The selection of proper tissues from formalin-fixed and paraffin-embedded tumors before diagnostic molecular testing is responsibility of the pathologist and represents a crucial step to produce reliable test results. The international guidelines suggest two cut-offs, one for the percentage and one for the number of tumor cells, in order to enrich the tumor content before DNA extraction. The aim of the present work was two-fold: to evaluate to what extent a low percentage or absolute number of tumor cells can be qualified for somatic mutation testing; and to determine how assay sensitivities can guide pathologists towards a better definition of morphology-based adequacy cut-offs. We tested 1797 tumor specimens from melanomas, colorectal and lung adenocarcinomas. Respectively, their BRAF, K-RAS and EGFR genes were analyzed at specific exons by mutation-enriched PCR, pyrosequencing, direct sequencing and real-time PCR methods. We demonstrate that poorly cellular specimens do not modify the frequency distribution of either mutated or wild-type DNA samples nor that of specific mutations. This observation suggests that currently recommended cut-offs for adequacy of specimens to be processed for molecular assays seem to be too much stringent in a laboratory context that performs highly sensitive routine analytical methods. In conclusion, new cut-offs are needed based on test sensitivities and documented tumor heterogeneity. PMID:25844806

  15. 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......Background: Testing for mutations of the TP53 gene in tumors is a valuable predictor for disease outcome in certain cancers, but the time and cost of conventional sequencing limit its use. The present study compares traditional sequencing with the much faster microarray sequencing on a commercially...

  16. 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.

  17. 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.

  18. A high incidence of polymorphic CYP2C19 variants in archival blood samples from Papua New Guinea

    Directory of Open Access Journals (Sweden)

    Hsu Huai-Ling

    2008-09-01

    Full Text Available Abstract There is considerable inter-ethnic variability in the incidence of CYP2C19 genetic poor metabolisers (var/var. About 3 per cent of Caucasians are CYP2C19 var/var. By contrast, an extremely high incidence (70 per cent is observed in the Melanesian island of Vanuatu. The colonisation of the Pacific Islands is believed to have involved migration through Papua New Guinea (PNG, and hence a high incidence may also be expected in this population. The reported incidence in PNG was only 36 per cent, however. PNG is a country of extensive ethnic diversity, and the incidence of the CYP2C19 var/var in other regional populations of PNG is currently not established. In this study, restriction fragment length polymorphism-polymerase chain reaction analysis of archival blood serum samples was used to determine the prevalence of the CYP2C19*2 and *3 variant alleles in three different ethnic and geographically isolated populations of PNG. In the largest population studied (Iruna, the frequency of both variant CYP2C19 alleles was high (0.37 and 0.34, respectively. Specifically, the frequency of the CYP2C19*3 allele was significantly higher than in the PNG (East Sepik population reported previously (0.34 vs 0.16; p 0.0001. In the Iruna population, 48.9 per cent of the samples were homozygous variants for CYP2C19*2 or *3, which although higher was not statistically different from the East Sepik population (36 per cent. The results of this study indicated that other regional populations of PNG also have a relatively high incidence of the CYP2C19 genetic polymorphism compared with Caucasian populations. The high incidence reported in Vanuatu, however, may be due to genetic drift rather than a PNG founder population, as the Vanuatu population is dominated by the CYP2C19*2 allele, with a lower contribution from the *3 allelic variant.

  19. 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.

  20. 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.

  1. Rapid Changes in Circulating Tumor DNA in Serially Sampled Plasma During Treatment of Breast Cancer: A Case Report

    Science.gov (United States)

    Nakagomi, Hiroshi; Hirotsu, Yosuke; Amemiya, Kenji; Nakada, Haruka; Inoue, Masayuki; Mochizuki, Hitoshi; Oyama, Toshio; Omata, Masao

    2017-01-01

    Patient: Female, 45 Final Diagnosis: Breast cancer Symptoms: Breast tumor Medication: — Clinical Procedure: Analysis of circulating tumor DNA Specialty: Oncology Objective: Unusual setting of medical care Background: The analysis of circulating tumor DNA (ctDNA) is expected to be a modality to determine the status of cancer in real time. This case indicated utilities and issues in measuring the ctDNA in cancer patients. Case Report: A 45-year-old woman with metastatic breast cancer was treated with bevacizumab and paclitaxel. The lung metastases were decreased but the meningitis carcinoma developed rapidly and she died. During the treatment with bevacizumab and paclitaxel, blood samples were taken serially and ctDNA was analyzed using a next-generation sequencer. TP53 frameshift mutation (TP53; p.Arg158fs with 7 nucleotides deletion) was identified in the tumor, and dynamic change in this mutation in ctDNA was observed in serially sampled plasma in this patient. We observed a rapid decrease of TP53 mutation at the beginning of treatment, then it increased as a sign of relapse. However, the high allelic fraction value of TP53 mutation was not consistent during the progression of cancer, suggesting that several factors affected the value of ctDNA. Conclusions: Although this is a single-case experience, it strongly suggests ctDNA could be a modality to determine the cancer status in real time. However, we found that several factors affected the value of ctDNA. Further investigations are needed to reveal the significance of these very high-sensitivity changes. PMID:28065930

  2. Feasibility of collecting tumor samples of breast cancer patients diagnosed up to 50 years ago in the Child Health and Development Studies.

    Science.gov (United States)

    Krigbaum, N Y; Rubin, R A; Cirillo, P M; Terry, M B; Habel, L A; Morris, C; Cohn, B A

    2017-03-06

    Environmental exposures during pregnancy may increase breast cancer risk for mothers and female offspring. Tumor tissue assays may provide insight regarding the mechanisms. This study assessed the feasibility of obtaining tumor samples and pathology reports from mothers (F0) who were enrolled in the Child Health and Development Studies during pregnancy from 1959 to 1967 and their daughters (F1) who developed breast cancer over more than 50 years of follow-up. Breast cancer cases were identified through linkage to the California Cancer Registry and self-report. Written consent was obtained from 116 F0 and 95 F1 breast cancer survivors to access their pathology reports and tumor blocks. Of those contacted, 62% consented, 13% refused and 24% did not respond. We obtained tissue samples for 57% and pathology reports for 75%, and if diagnosis was made ⩽10 years we obtained tissue samples and pathology reports for 91% and 79%, respectively. Obtaining pathology reports and tumor tissues of two generations is feasible and will support investigation of the relationship between early-life exposures and molecular tumor markers. However, we found that more recent diagnosis increased the accessibility of tumor tissue. We recommend that cohorts request consent for obtaining future tumor tissues at study enrollment and implement real-time tissue collection to enhance success of collecting tumor samples and data.

  3. Deparaffinization with mineral oil: a simple procedure for extraction of high-quality DNA from archival formalin-fixed paraffin-embedded samples.

    Science.gov (United States)

    Heikal, Nahla; Nussenzveig, Roberto H; Agarwal, Archana M

    2014-09-01

    Extracting DNA from formalin-fixed paraffin-embedded (FFPE) archival samples remains difficult. Successful polymerase chain reactions (PCR) with DNA extracted from FFPE samples is still very low. We extracted DNA from 12 recent and old archival FFPE bone marrow trephine biopsies by use of a simple protocol on the basis of deparaffinization with molecular biology-grade mineral oil followed by DNA extraction with the Qiagen FFPE kit. Comparison of this deparaffinization method with standard protocols, for example, xylene or Hemo-D with subsequent rehydration using graded ethanols, was investigated. The quality and quantity of extracted DNA were tested by a combination of ultraviolet spectroscopy, analysis on a Caliper LabChip GX, and real-time PCR combined with high-resolution melt analysis. Highest quality PCR-amplifiable DNA was obtained by deparaffinization with mineral oil, whereas more variable results were obtained for the other 2 deparaffinization procedures. This result was confirmed by real-time PCR and high-resolution melt analysis. Besides improvements in the quality of extracted DNA, use of mineral oil for deparaffinization has the added benefit of decreased time (20 vs. 75 min) and a significant reduction of hands-on labor (1 step vs. multiple hands-on centrifugation and decanting steps).

  4. [A Large Number of Circulating Tumor Cells(CTCs)Can Be Isolated from Samples Obtained by Using Leukapheresis Procedures].

    Science.gov (United States)

    Soya, Ryoko; Taguchi, Jyunichi; Nagakawa, Yuichi; Takahashi, Osamu; Sandoh, Norimasa; Hosokawa, Yuichi; Kasuya, Kazuhiko; Umeda, Naoki; Okamoto, Masato; Tsujitani, Shunichi; Tsuchida, Akihiko

    2015-09-01

    We hypothesized that a large number of circulating tumor cells(CTCs)may be isolated from samples obtained by using the leukapheresis procedures that are utilized to collect peripheral blood mononuclear cells for dendritic cell vaccine therapy. We utilized the CellSearch System to determine the number of CTCs in samples obtained by using leukapheresis in 7 patients with colorectal cancer, 5 patients with breast cancer, and 3 patients with gastric cancer. In all patients, a large number of CTCs were isolated. The mean number of CTCs per tumor was 17.1(range 10-34)in colorectal cancer, 10.0(range 2-27)in breast cancer, and 24.0(range 2-42)in gastric cancer. We succeeded in culturing the isolated CTCs from 7 patients with colorectal cancer, 5 patients with breast cancer, and 3 patients with gastric cancer. In conclusion, compared to conventional methods, a large number of CTCs can be obtained by using leukapheresis procedures. The molecular analyses of the CTCs isolated by using this method should be promising in the development of personalized cancer treatments.

  5. 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.

  6. Detection of EGFR gene mutations in non-small cell lung cancer: lessons from a single-institution routine analysis of 1,403 tumor samples.

    Science.gov (United States)

    Vallee, Audrey; Sagan, Christine; Le Loupp, Anne-Gaelle; Bach, Kalyane; Dejoie, Thomas; Denis, Marc G

    2013-10-01

    Activating mutations of the epidermal growth factor receptor (EGFR) in lung tumors are associated with a dramatic response to tyrosine kinase inhibitors. Therefore, routine analysis of pathological specimens is mandatory in clinical practice. We have prospectively tested tumors from Caucasian lung tumor patients between January 2010 and June 2012. DNA was extracted from formalin-fixed paraffin-embedded tissues following macrodissection. The p.L858R substitution was assessed by allele-specific PCR and exon 19 deletions by PCR and DNA fragment analysis. Using a robust process from patient sampling to screening methods, we analyzed samples from 1,403 patients. The EGFR status could be successfully determined for 1,322 patients. EGFR mutations were detected in 179 (13.5%) patients, with female and adenocarcinoma histology predominance. Mutated patients were significantly older than non-mutated patients. Similar mutation rates were obtained with primary tumors and metastases, and with surgical resection, bronchial biopsies, CT-guided needle biopsies and transbronchial needle aspiration. The sensitivity of our assays allowed us to detect EGFR mutations in samples poor (<10%) in tumor cells. Finally, the mutation rate was much higher in tumors expressing the TTF-1 antigen (145/820; 17.7%) than in TTF-1 negative tumors (3/218; 1.4%). The results obtained through routine analysis of more than 1,300 samples indicated that all types of specimen can be analyzed without any significant bias. TTF-1 immunostaining may be used to predict negative EGFR mutation status.

  7. Recognition of serous ovarian tumors in human samples by multimodal nonlinear optical microscopy

    Science.gov (United States)

    Adur, Javier; Pelegati, Vitor B.; Costa, Leverson F. L.; Pietro, Luciana; de Thomaz, Andre A.; Almeida, Diogo B.; Bottcher-Luiz, Fatima; Andrade, Liliana A. L. A.; Cesar, Carlos L.

    2011-09-01

    We used a multimodal nonlinear optics microscopy, specifically two-photon excited fluorescence (TPEF), second and third harmonic generation (SHG/THG) microscopies, to observe pathological conditions of ovarian tissues obtained from human samples. We show that strong TPEF + SHG + THG signals can be obtained in fixed samples stained with hematoxylin and eosin (H&E) stored for a very long time, and that H&E staining enhanced the THG signal. We then used the multimodal TPEF-SHG-THG microscopies in a stored file of H&E stained samples of human ovarian cancer to obtain complementary information about the epithelium/stromal interface, such as the transformation of epithelium surface (THG) and the overall fibrillary tissue architecture (SHG). This multicontrast nonlinear optics microscopy is able to not only differentiate between cancerous and healthy tissue, but can also distinguish between normal, benign, borderline, and malignant specimens according to their collagen disposition and compression levels within the extracellular matrix. The dimensions of the layers of epithelia can also be measured precisely and automatically. Our data demonstrate that optical techniques can detect pathological changes associated with ovarian cancer.

  8. 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.

  9. 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 (ppopulation 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 health status of the Czech population.

  10. Development of an Automated and Sensitive Microfluidic Device for Capturing and Characterizing Circulating Tumor Cells (CTCs from Clinical Blood Samples.

    Directory of Open Access Journals (Sweden)

    Priya Gogoi

    Full Text Available Current analysis of circulating tumor cells (CTCs is hindered by sub-optimal sensitivity and specificity of devices or assays as well as lack of capability of characterization of CTCs with clinical biomarkers. Here, we validate a novel technology to enrich and characterize CTCs from blood samples of patients with metastatic breast, prostate and colorectal cancers using a microfluidic chip which is processed by using an automated staining and scanning system from sample preparation to image processing. The Celsee system allowed for the detection of CTCs with apparent high sensitivity and specificity (94% sensitivity and 100% specificity. Moreover, the system facilitated rapid capture of CTCs from blood samples and also allowed for downstream characterization of the captured cells by immunohistochemistry, DNA and mRNA fluorescence in-situ hybridization (FISH. In a subset of patients with prostate cancer we compared the technology with a FDA-approved CTC device, CellSearch and found a higher degree of sensitivity with the Celsee instrument. In conclusion, the integrated Celsee system represents a promising CTC technology for enumeration and molecular characterization.

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

    Science.gov (United States)

    Caboux, Elodie; Paciencia, Maria; Durand, Geoffroy; Robinot, Nivonirina; Wozniak, Magdalena B; Galateau-Salle, Françoise; Byrnes, Graham; Hainaut, Pierre; Le Calvez-Kelm, Florence

    2013-01-01

    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.

  12. 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.

  13. Doing more with less: fluorescence in situ hybridization and gene sequencing assays can be reliably performed on archival stained tumor tissue sections.

    Science.gov (United States)

    Pelosi, Giuseppe; Perrone, Federica; Tamborini, Elena; Fabbri, Alessandra; Testi, Maria Adele; Busico, Adele; Settanni, Giulio; Picciani, Benedetta; Bovio, Enrica; Sonzogni, Angelica; Valeri, Barbara; Garassino, Marina; De Braud, Filippo; Pastorino, Ugo

    2016-04-01

    Little is known about molecular testing on tumor tissue retrieved from stained sections, for which there may be a clinical need. We retrospectively analyzed 112 sections from 56 tumor patients using either fluorescence in situ hybridization (FISH) with different probes (19 sections from 17 patients) or Sanger or targeted next generation sequencing for detection of BRAF, EGFR, KRAS, C-KIT, and TP53 mutations (93 sections from 39 patients). Tumor tissue sections had been stained by hematoxylin and eosin (H&E) (42 sections) or by immunohistochemistry for cytoplasmic or nuclear/nuclear-cytoplasmic markers (70 sections) with a peroxidase (P-IHC, with 3,3'-diaminobenzidine as chromogen) or alkaline phosphatase label (AP-IHC, with Warp Red™ as chromogen). For FISH analysis, the concordance rate between the original diagnosis and that obtained on H&E- or P-IHC-stained tissue sections (AP-IHC was not on record for this set of patients) was 95% (18 out of 19 tumor sections). Only one tumor sample, diffusely positive for MLH1, did not yield any nuclear hybridization signal. For sequencing analysis, the concordance rate was 100% on negative P-IHC and positive AP-IHC-stained sections, regardless of the subcellular localization of the reaction product. Mutations were detected in only 52% of cases expressing nuclear/nuclear-cytoplasmic markers, regardless of the sequencing technology used (p = 0.0002). In conclusion, stained sections may be a valuable resource for FISH or sequencing analysis, but on cases expressing nuclear markers sequencing results need to be interpreted cautiously.

  14. 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.

  15. Sampling

    CERN Document Server

    Thompson, Steven K

    2012-01-01

    Praise for the Second Edition "This book has never had a competitor. It is the only book that takes a broad approach to sampling . . . any good personal statistics library should include a copy of this book." —Technometrics "Well-written . . . an excellent book on an important subject. Highly recommended." —Choice "An ideal reference for scientific researchers and other professionals who use sampling." —Zentralblatt Math Features new developments in the field combined with all aspects of obtaining, interpreting, and using sample data Sampling provides an up-to-date treat

  16. HaloPlex Targeted Resequencing for Mutation Detection in Clinical Formalin-Fixed, Paraffin-Embedded Tumor Samples.

    Science.gov (United States)

    Moens, Lotte N J; Falk-Sörqvist, Elin; Ljungström, Viktor; Mattsson, Johanna; Sundström, Magnus; La Fleur, Linnéa; Mathot, Lucy; Micke, Patrick; Nilsson, Mats; Botling, Johan

    2015-11-01

    In recent years, the advent of massively parallel next-generation sequencing technologies has enabled substantial advances in the study of human diseases. Combined with targeted DNA enrichment methods, high sequence coverage can be obtained for different genes simultaneously at a reduced cost per sample, creating unique opportunities for clinical cancer diagnostics. However, the formalin-fixed, paraffin-embedded (FFPE) process of tissue samples, routinely used in pathology departments, results in DNA fragmentation and nucleotide modifications that introduce a number of technical challenges for downstream biomolecular analyses. We evaluated the HaloPlex target enrichment system for somatic mutation detection in 80 tissue fractions derived from 20 clinical cancer cases with paired tumor and normal tissue available in both FFPE and fresh-frozen format. Several modifications to the standard method were introduced, including a reduced target fragment length and two strand capturing. We found that FFPE material can be used for HaloPlex-based target enrichment and next-generation sequencing, even when starting from small amounts of DNA. By specifically capturing both strands for each target fragment, we were able to reduce the number of false-positive errors caused by FFPE-induced artifacts and lower the detection limit for somatic mutations. We believe that the HaloPlex method presented here will be broadly applicable as a tool for somatic mutation detection in clinical cancer settings.

  17. 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....

  18. 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

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

    Lifescience Database Archive (English)

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

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

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  7. 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...

  8. A COMPARATIVE ANALYSIS OF METHYLATION STATUS OF TUMOR SUPPRESSOR GENES IN PAIRED BIOPSY AND SERUM SAMPLES FROM CERVICAL CANCER PATIENTS AMONG NORTH INDIAN POPULATION.

    Science.gov (United States)

    Jha, A K; Sharma, V; Nikbakht, M; Jain, V; Sehgal, A; Capalash, N; Kaur, J

    2016-02-01

    Tumor-specific genetic or epigenetic alterations have been detected in serum DNA in case of various types of cancers. In breast cancer, the detection of tumor suppressor gene hypermethylation has been reported in several body fluids. Promoter hypermethylation of some genes like MYOD1, CALCA, hTERT etc. has also been detected in serum samples from cervical cancer. The present study is the first report on the comparison of promoter hypermethylation of tumor suppressor genes likep14, p15, p16, p21, p27, p57, p53, p73, RARβ2, FHIT, DAPK, STAT1 and-RB1 genes in paired biopsy and serum samples from cervical cancer patients among north Indian population. This is also the first report on the hypermethylation of these genes in serum samples from cervical cancer patients among north Indian population. According to the results of the present study, promoter hypermethylation of these genes can also be detected in serum samples of cervical cancer patients. The sensitivity of detection of promoter hypermethylation in serum samples of cervical cancer patients as compared to paired biopsy samples was found to be around 83.3%. It was observed that promoter hypermethylation was mainly observed in the serum samples in the higher stages and very rarely in the lower stages. The present study clearly showed that serum of patients with cervical cancer can also be used to study methylated genes as biomarkers.

  9. 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)

    Decaro, Nicola; Mari, Viviana; Lucente, Maria Stella; Sciarretta, Rossana; Elia, Gabriella; Ridpath, Julia F; Buonavoglia, Canio

    2013-12-27

    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 nested PCR protocol for rapid characterization of bovine pestiviruses. Phylogeny conducted with full-length pestivirus genomes and three informative genomic sequences, placed the strain detected in the samples, Italy-129/07, into the Hobi-like virus branch. Italy-129/07, similar to other Hobi-like viruses isolated in Italy, was more closely related to viruses of South American origin, than Hobi-like viruses of Southeast Asian origin. This suggests a possible introduction of this emerging group of pestiviruses into Italy as a consequence of using contaminated biological products such as fetal bovine serum originating in South America. This report of a Hobi-like virus associated with respiratory disease along with the full-genomic characterization of the virus detected provides new data that contributes to the body of knowledge regarding the epidemiology, pathobiology and genetic diversity of this emerging group of pestiviruses. Importantly, it dates the circulation of Hobi-like viruses in Italy to 2007, at least three years before previous reports.

  10. 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.

  11. Ultra-fast local-haplotype variant calling using paired-end DNA-sequencing data reveals somatic mosaicism in tumor and normal blood samples.

    Science.gov (United States)

    Sengupta, Subhajit; Gulukota, Kamalakar; Zhu, Yitan; Ober, Carole; Naughton, Katherine; Wentworth-Sheilds, William; Ji, Yuan

    2016-02-18

    Somatic mosaicism refers to the existence of somatic mutations in a fraction of somatic cells in a single biological sample. Its importance has mainly been discussed in theory although experimental work has started to emerge linking somatic mosaicism to disease diagnosis. Through novel statistical modeling of paired-end DNA-sequencing data using blood-derived DNA from healthy donors as well as DNA from tumor samples, we present an ultra-fast computational pipeline, LocHap that searches for multiple single nucleotide variants (SNVs) that are scaffolded by the same reads. We refer to scaffolded SNVs as local haplotypes (LH). When an LH exhibits more than two genotypes, we call it a local haplotype variant (LHV). The presence of LHVs is considered evidence of somatic mosaicism because a genetically homogeneous cell population will not harbor LHVs. Applying LocHap to whole-genome and whole-exome sequence data in DNA from normal blood and tumor samples, we find wide-spread LHVs across the genome. Importantly, we find more LHVs in tumor samples than in normal samples, and more in older adults than in younger ones. We confirm the existence of LHVs and somatic mosaicism by validation studies in normal blood samples. LocHap is publicly available at http://www.compgenome.org/lochap.

  12. PTEN loss and chromosome 8 alterations in Gleason grade 3 prostate cancer cores predicts the presence of un-sampled grade 4 tumor: implications for active surveillance.

    Science.gov (United States)

    Trock, Bruce J; Fedor, Helen; Gurel, Bora; Jenkins, Robert B; Knudsen, B S; Fine, Samson W; Said, Jonathan W; Carter, H Ballentine; Lotan, Tamara L; De Marzo, Angelo M

    2016-07-01

    Men who enter active surveillance because their biopsy exhibits only Gleason grade 3 (G3) frequently have higher grade tumor missed by biopsy. Thus, biomarkers are needed that, when measured on G3 tissue, can predict the presence of higher grade tumor in the whole prostate. We evaluated whether PTEN loss, chromosome 8q gain (MYC) and/or 8p loss (LPL) measured only on G3 cores is associated with un-sampled G4 tumor. A tissue microarray was constructed of prostatectomy tissue from patients whose prostates exhibited only Gleason score 3+3, only 3+4 or only 4+3 tumor (n=50 per group). Cores sampled only from areas of G3 were evaluated for PTEN loss by immunohistochemistry, and PTEN deletion, LPL/8p loss and MYC/8q gain by fluorescence in situ hybridization. Biomarker results were compared between Gleason score 6 vs 7 tumors using conditional logistic regression. PTEN protein loss, odds ratio=4.99, P=0.033; MYC/8q gain, odds ratio=5.36, P=0.010; and LPL/8p loss, odds ratio=3.96, P=0.003 were significantly more common in G3 cores derived from Gleason 7 vs Gleason 6 tumors. PTEN gene deletion was not statistically significant. Associations were stronger comparing Gleason 4+3 vs 6 than for Gleason 3+4 vs 6. MYC/8q gain, LPL/8p loss and PTEN protein loss measured in G3 tissue microarray cores strongly differentiate whether the core comes from a Gleason 6 or Gleason 7 tumor. If validated to predict upgrading from G3 biopsy to prostatectomy these biomarkers could reduce the likelihood of enrolling high-risk men and facilitate safe patient selection for active surveillance.

  13. 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.

  14. Pre-Analytical Considerations for Successful Next-Generation Sequencing (NGS: Challenges and Opportunities for Formalin-Fixed and Paraffin-Embedded Tumor Tissue (FFPE Samples

    Directory of Open Access Journals (Sweden)

    Gladys Arreaza

    2016-09-01

    Full Text Available In cancer drug discovery, it is important to investigate the genetic determinants of response or resistance to cancer therapy as well as factors that contribute to adverse events in the course of clinical trials. Despite the emergence of new technologies and the ability to measure more diverse analytes (e.g., circulating tumor cell (CTC, circulating tumor DNA (ctDNA, etc., tumor tissue is still the most common and reliable source for biomarker investigation. Because of its worldwide use and ability to preserve samples for many decades at ambient temperature, formalin-fixed, paraffin-embedded tumor tissue (FFPE is likely to be the preferred choice for tissue preservation in clinical practice for the foreseeable future. Multiple analyses are routinely performed on the same FFPE samples (such as Immunohistochemistry (IHC, in situ hybridization, RNAseq, DNAseq, TILseq, Methyl-Seq, etc.. Thus, specimen prioritization and optimization of the isolation of analytes is critical to ensure successful completion of each assay. FFPE is notorious for producing suboptimal DNA quality and low DNA yield. However, commercial vendors tend to request higher DNA sample mass than what is actually required for downstream assays, which restricts the breadth of biomarker work that can be performed. We evaluated multiple genomics service laboratories to assess the current state of NGS pre-analytical processing of FFPE. Significant differences in pre-analytical capabilities were observed. Key aspects are highlighted and recommendations are made to improve the current practice in translational research.

  15. A predictive factor of the quality of microarray comparative genomic hybridization analysis for formalin-fixed paraffin-embedded archival tissue.

    Science.gov (United States)

    Nakao, Kenjiro; Oikawa, Masahiro; Arai, Junichi; Mussazhanova, Zhanna; Kondo, Hisayoshi; Shichijo, Kazuko; Nakashima, Masahiro; Hayashi, Tomayoshi; Yoshiura, Koh-Ichiro; Hatachi, Toshiko; Nagayasu, Takeshi

    2013-09-01

    Utilizing formalin-fixed paraffin-embedded (FFPE) archival tissue, the most common form of tissue preservation in routine practice, for cytogenetic analysis using microarray comparative genomic hybridization (aCGH) remains challenging. We searched for a predictive factor of the performance of FFPE DNA in aCGH analysis. DNA was extracted from 63 FFPE archival tissue samples of various tissue types (31 breast cancers, 24 lung cancers, and 8 thyroid tumors), followed by aCGH analysis using high-density oligonucleotide microarrays. Tumor DNA from matched frozen samples and from FFPE samples after whole-genome amplification were also analyzed in 2 and 4 case, respectively. The derivative log ratio spread (DLRSpread) was used to assess the overall quality of each aCGH result. The DLRSpread correlated significantly with the double-stranded DNA ratio of tumor DNA, storage time, and the degree of labeling with Cy5 (Parchival tissue samples can be utilized for aCGH analysis.

  16. Preoperative tumor localization of primary hyperparathyroidism. Comprehensive study of ultrasonography (US), scintigraphy (RI), arteriography (AG) and venous sampling (VS)

    Energy Technology Data Exchange (ETDEWEB)

    Morita, Yutaka; Shinohara, Masahiro; Ito, Kazuo; Imamura, Fumimoto; Kasai, Yoichi (Hokkaido Univ., Sapporo (Japan). School of Medicine); Ishizuka, Reiki

    1983-02-01

    The diagnostic rate of each methods were discussed in thirty six cases and the following conclusions were made. (1.) The diagnostic rate of US, RI, AG and VS was 64.7%, 50%, 57.9%, 60.7% respectively. (2.) Ultrasonography and subtruction-scintigraphy were useful for screening examination for localization of parathyroid tumor. (3.) The reasonable diagnostic procedures were as follows: (1) In the cases of palpable, reno-uretrolithiasic type, and biochemical type: US ..-->.. RI ..-->.. VS. (2) In the cases of nonpalpable osteolytic type, and previous neck surgery: US ..-->.. RI ..-->.. AG ..-->.. VS. These results indicate that the systemic diagnoses are useful to predict localization of parathyroid tumors.

  17. 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.

  18. 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...

  19. Quantification of HER expression and dimerization in patients' tumor samples using time-resolved Forster resonance energy transfer.

    Directory of Open Access Journals (Sweden)

    Alexandre Ho-Pun-Cheung

    Full Text Available Following the development of targeted therapies against EGFR and HER2, two members of the human epidermal receptor (HER family of receptor tyrosine kinases, much interest has been focused on their expression in tumors. However, knowing the expression levels of individual receptors may not be sufficient to predict drug response. Here, we describe the development of antibody-based time-resolved Förster resonance energy transfer (TR-FRET assays for the comprehensive analysis not only of EGFR and HER2 expression in tumor cryosections, but also of their activation through quantification of HER homo- or heterodimers. First, EGFR and HER2 expression levels were quantified in 18 breast tumors and the results were compared with those obtained by using reference methods. The EGFR number per cell determined by TR-FRET was significantly correlated with EGFR mRNA copy number (P<0.0001. Moreover, our method detected HER2 overexpression with 100% specificity and sensibility, as confirmed by the standard IHC, FISH and qPCR analyses. EGFR and HER2 dimerization was then assessed, using as controls xenograft tumors from cell lines with known dimer expression profiles. Our results show that quantification of HER dimerization provides information about receptor activation that cannot be obtained by quantification of single receptors. Quantifying HER expression and dimerization by TR-FRET assays might help identifying novel clinical markers for optimizing patients' treatment in oncology.

  20. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Fayad, Laura M.; Mugera, Charles; Grande, Filippo del [Johns Hopkins Medical Institutions, Russell H. Morgan Department of Radiology and Radiological Sciences, Baltimore, MD (United States); Soldatos, Theodoros [Johns Hopkins Medical Institutions, Musculoskeletal Imaging Section, Baltimore, MD (United States); University of Athens, Research Unit of Radiology and Medical Imaging, Evgenidion Hospital, Athens (Greece); Flammang, Aaron [Siemens Corporate Research, Center for Applied Medical Imaging, Baltimore, MD (United States)

    2013-07-15

    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 cm{sup 2}). Images were reviewed by two observers in consensus who recorded image quality (1 = diagnostic, no significant artifacts, 2 = diagnostic, <25 % artifacts, 3 = nondiagnostic) and contrast enhancement characteristics by static MRI (presence/absence of contrast enhancement, percentage of enhancement) and DCE-MRI (presence/absence of arterial enhancement with time-intensity curves). Results were compared with histological response (defined as <5 % viable tumor [soft tissue sarcoma] or <10 % [bone sarcoma] following resection). Diagnostic quality for all conventional and DCE-MRI sequences was rated as 1. In 2 of the 3 sarcomas, there was good histological response ({<=}5 % viable tumor); in 1 there was poor response (50 % viable tumor). By static post-contrast T1-weighted sequences, there was enhancement in all sarcomas, regardless of response (up to >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.)

  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. 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...

  4. 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...

  5. Eosinophilia in routine blood samples as a biomarker for solid tumor development - A study based on the Copenhagen Primary Care Differential Count (CopDiff) Database

    DEFF Research Database (Denmark)

    Andersen, Christen Lykkegaard; Siersma, Volkert Dirk; Hasselbalch, Hans Carl;

    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 eosinophil count during 2000-2007. From these, one DIFF was randomly chosen and categorized according to no (... was increased with mild eosinophilia [OR 1.93 (CI 1.29-2.89), p = 0.0013]. No associations with eosinophilia were observed for the remaining solid cancers. CONCLUSION: We demonstrate that eosinophilia in routine blood samples associates with an increased risk of bladder cancer. Our data emphasize...

  6. 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.

  7. 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.

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

    Science.gov (United States)

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

    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- 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.

  9. [Use of archival formalin-fixed, paraffin-embedded (FFPE) tissue samples for molecular genetic analysis in diffuse large B-cell lymphoma (DLBCL)].

    Science.gov (United States)

    Jarošová, Marie; Kučerová, Jana; Flodr, Patrik; Mikešová, Michaela; Procházka, Vít; Papajík, Tomáš

    2014-04-01

    The currently valid molecular genetic subclassification of patients with diffuse large B-cell lymphoma (DLBCL) into three prognostic subgroups based on expression profiling has been the objective of numerous genetic studies. In routine clinical practice, however, expression profiling technology remains unavailable for the most of centers. Apart from the technology, in some cases molecular genetic laboratories have problems obtaining high-quality material, i.e. fresh tissues, for RNA isolation to determine gene expression. One possibility is to determine the gene expression from RNA obtained by isolation from formalin-fixed, paraffin-embedded (FFPE) tissue. This pilot study aimed at isolating RNA from FFPE in patients diagnosed with DLBCL and verifying the potential use of such RNA for the expression analysis of 7 selected genes. Although the study showed that it is possible to isolate RNA and determine the expression of the selected genes from archival material, the values of relative expression of some genes in the set were too variable to be used for unambiguous prognostic classification. It was confirmed that retrospective analyses of selected genes may be performed with sufficient material obtained, and that properly archived blocks may be used for molecular biology analyses even after 8 years.

  10. 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.

  11. Optimization of methods to assess mitochondrial DNA in archival paraffin-embedded tissues from mammary canine tumors Otimização dos métodos para avaliar o DNA mitocondrial obtido a partir de tumores mamários caninos incluídos em parafina

    Directory of Open Access Journals (Sweden)

    Angélica C. Bertagnolli

    2008-08-01

    Full Text Available In this study we describe the alterations used to extract and amplify mitochondrial desoxyribonucleic acid (DNA from formalin-fixed paraffin-embedded samples of canine mammary tumors. The epithelial and mesenchymal components (chondromyxoid and chondroid of each tumor, as well as the normal mammary gland tissues, were manually microdissected from 19 mixed canine mammary tumors (10 benign mixed tumors and nine carcinomas arising in mixed tumors. DNA was extracted by Invisorb® Spin Tissue Mini Kit, with protocol changes proposed by the manufacturer. A 273-bp fragment was amplified by polymerase chain reaction (PCR and submitted to automatic sequence analysis. The fragment was successfully analyzed in 100% of the samples. However, an additional lysis step, the reduction of volume in buffer solutions and PCR, a higher annealing temperature and an increase in the number of PCR cycles were required. The initial PCR products were diluted and re-amplified in six samples so that they could be successfully analyzed.A presente comunicação descreve as modificações usadas para extrair e amplificar o DNA mitocondrial obtido de amostras de tumores mamários caninos fixados em formol tamponado a 10% e incluídos em parafina. Os componentes epiteliais e mesenquimais (condromixóide e condróide, bem como a mama normal adjacente, foram microdissectados manualmente de 19 tumores mamários (10 tumores mistos benignos e nove carcinomas em tumores mistos. O DNA foi extraído utilizando-se o Invisorb® Spin Tissue Mini Kit com modificações do protocolo proposto pelo fabricante. Um fragmento de 273-pb foi amplificado por reação em cadeia da polimerase (PCR e seqüenciado em seqüenciador automático. O fragmento foi analisado em 100% das amostras, entretanto modificações como lise adicional, redução do volume das soluções de extração e PCR, aumento da temperatura de anelamento e do número de ciclos de amplificação foram necessárias. Em seis

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

    OpenAIRE

    Orre Lotta; Bergman Per; Elmberger Göran; Pernemalm Maria; De Petris Luigi; Lewensohn Rolf; Lehtiö Janne

    2010-01-01

    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 ade...

  13. Antibody-supervised deep learning for quantification of tumor-infiltrating immune cells in hematoxylin and eosin stained breast cancer samples

    Directory of Open Access Journals (Sweden)

    Riku Turkki

    2016-01-01

    Full Text Available Background: Immune cell infiltration in tumor is an emerging prognostic biomarker in breast cancer. The gold standard for quantification of immune cells in tissue sections is visual assessment through a microscope, which is subjective and semi-quantitative. In this study, we propose and evaluate an approach based on antibody-guided annotation and deep learning to quantify immune cell-rich areas in hematoxylin and eosin (H&E stained samples. Methods: Consecutive sections of formalin-fixed parafin-embedded samples obtained from the primary tumor of twenty breast cancer patients were cut and stained with H&E and the pan-leukocyte CD45 antibody. The stained slides were digitally scanned, and a training set of immune cell-rich and cell-poor tissue regions was annotated in H&E whole-slide images using the CD45-expression as a guide. In analysis, the images were divided into small homogenous regions, superpixels, from which features were extracted using a pretrained convolutional neural network (CNN and classified with a support of vector machine. The CNN approach was compared to texture-based classification and to visual assessments performed by two pathologists. Results: In a set of 123,442 labeled superpixels, the CNN approach achieved an F-score of 0.94 (range: 0.92-0.94 in discrimination of immune cell-rich and cell-poor regions, as compared to an F-score of 0.88 (range: 0.87-0.89 obtained with the texture-based classification. When compared to visual assessment of 200 images, an agreement of 90% (k = 0.79 to quantify immune infiltration with the CNN approach was achieved while the inter-observer agreement between pathologists was 90% (k = 0.78. Conclusions: Our findings indicate that deep learning can be applied to quantify immune cell infiltration in breast cancer samples using a basic morphology staining only. A good discrimination of immune cell-rich areas was achieved, well in concordance with both leukocyte antigen expression and

  14. 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.

  15. Bone tumor

    Science.gov (United States)

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

  16. Clinical Application of Picodroplet Digital PCR Technology for Rapid Detection of EGFR T790M in Next-Generation Sequencing Libraries and DNA from Limited Tumor Samples.

    Science.gov (United States)

    Borsu, Laetitia; Intrieri, Julie; Thampi, Linta; Yu, Helena; Riely, Gregory; Nafa, Khedoudja; Chandramohan, Raghu; Ladanyi, Marc; Arcila, Maria E

    2016-11-01

    Although next-generation sequencing (NGS) is a robust technology for comprehensive assessment of EGFR-mutant lung adenocarcinomas with acquired resistance to tyrosine kinase inhibitors, it may not provide sufficiently rapid and sensitive detection of the EGFR T790M mutation, the most clinically relevant resistance biomarker. Here, we describe a digital PCR (dPCR) assay for rapid T790M detection on aliquots of NGS libraries prepared for comprehensive profiling, fully maximizing broad genomic analysis on limited samples. Tumor DNAs from patients with EGFR-mutant lung adenocarcinomas and acquired resistance to epidermal growth factor receptor inhibitors were prepared for Memorial Sloan-Kettering-Integrated Mutation Profiling of Actionable Cancer Targets sequencing, a hybrid capture-based assay interrogating 410 cancer-related genes. Precapture library aliquots were used for rapid EGFR T790M testing by dPCR, and results were compared with NGS and locked nucleic acid-PCR Sanger sequencing (reference high sensitivity method). Seventy resistance samples showed 99% concordance with the reference high sensitivity method in accuracy studies. Input as low as 2.5 ng provided a sensitivity of 1% and improved further with increasing DNA input. dPCR on libraries required less DNA and showed better performance than direct genomic DNA. dPCR on NGS libraries is a robust and rapid approach to EGFR T790M testing, allowing most economical utilization of limited material for comprehensive assessment. The same assay can also be performed directly on any limited DNA source and cell-free DNA.

  17. Flow cytometric DNA ploidy analysis of ovarian granulosa cell tumors

    NARCIS (Netherlands)

    D. Chadha; C.J. Cornelisse; A. Schabert (A.)

    1990-01-01

    textabstractAbstract The nuclear DNA content of 50 ovarian tumors initially diagnosed as granulosa cell tumors was measured by flow cytometry using paraffin-embedded archival material. The follow-up period of the patients ranged from 4 months to 19 years. Thirty-eight tumors were diploid or near-dip

  18. 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.

  19. 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.

  20. Detection of microRNAs in archival cytology urine smears.

    Science.gov (United States)

    Simonato, Francesca; Ventura, Laura; Sartori, Nicola; Cappellesso, Rocco; Fassan, Matteo; Busund, Lill-Tove; Fassina, Ambrogio

    2013-01-01

    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.

  1. 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 o...... as discussions of specific art works, performances, and archives......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...

  2. Constructing an Archive

    DEFF Research Database (Denmark)

    Carbone, Claudia; Wieczorek, Izabela; Francis, Alice;

    2016-01-01

    "Constructing an Archive" contains a collection of student works conducted during the Fall semester of 2015 at the Aarhus School of Architecture, at the master studio Constructing an Archive......."Constructing an Archive" contains a collection of student works conducted during the Fall semester of 2015 at the Aarhus School of Architecture, at the master studio Constructing an Archive....

  3. ATRX mRNA expression combined with IDH1/2 mutational status and Ki-67 expression refines the molecular classification of astrocytic tumors: evidence from the whole transcriptome sequencing of 169 samples samples.

    Science.gov (United States)

    Cai, Jinquan; Yang, Pei; Zhang, Chuanbao; Zhang, Wei; Liu, Yanwei; Bao, Zhaoshi; Liu, Xing; Du, Wenzhong; Wang, Hongjun; Jiang, Tao; Jiang, Chuanlu

    2014-05-15

    Astrocytic tumors are the most common primary brain tumors in adults. ATRX mutations have been identified in gliomas and are correlated with its loss of expression, which causes alternative lengthening of telomeres (ALT) leading to genomic instability. In this study, we aimed to explore the role of ATRX mRNA expression alteration in the progression and subclassification of astrocytic tumors and examine its impact on clinical outcome. We investigated ATRX mRNA expression and its association with IDH1 and IDH2 mutations in 169 adult astrocytic tumors using whole transcriptome sequencing. In our cohort, low ATRX mRNA expression was detected in 68% of astrocytomas, 50% of anaplastic astrocytomas and 41.6% of glioblastomas. Low ATRX expression closely overlapped with mutations in IDH1/2 (PATRX expression and longer overall survival was identified in our cohort (PATRX combined with IDH1/2 and Ki-67 was used to re-classify patients with astrocytic tumors: group A1 containing IDH1/2 mutations and low ATRX expression predicted a better prognostic outcome, whereas group A3 carrying wild-type IDH1/2 and high Ki-67 expression had the shortest overall survival; IDH-mutant tumors with low ATRX expression and IDH-wild-type tumors with high Ki-67 expression were grouped into group A2. In summary, our results showed that ATRX in cooperation with IDH1/2 and Ki-67 defines three subgroups of astrocytic tumors regardless of the conventional WHO grades consensus. The molecular stratification in astrocytic tumors may aid in treatment strategy selection, therapeutic trial design, and clinical prognosis evaluation.

  4. 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

  5. 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

  6. 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...

  7. 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

  8. Online Archives

    Directory of Open Access Journals (Sweden)

    Julian D. Richards

    2004-01-01

    Full Text Available Online archives are of increasing importance in Archaeological Informatics, but like any new genre they prompt a number of questions. What is their relationship to publication? What should go in them? How should they be delivered and indexed? Can they be preserved? Whilst their delivery requires technology, we must also consider how that technology should best be employed in the service of our discipline. This article attempts to address some of these questions but it need not be read from start to finish. The links from this summary provide one fairly linear route through the text but each section is self-contained and can also be accessed directly from the Contents page. The problems posed by effective publication of archaeological fieldwork have exercised the profession for many decades. The issues raised go to the core of discussion of whether preservation by record is a valid concept, and indeed whether archaeological data exist. There are different schools of thought about the relationship between publication and archiving, but hopefully we can accept that data are recorded observations but still agree that they have a re-use value for re-examination and re-interpretation. Since the 1960s archaeology has experienced a publication crisis point. The scenario is familiar. Excavation is destruction; it is an unrepeatable experiment and the archaeologist has a professional obligation to make a full and accessible record of his/her observations. Yet full publication is increasingly expensive and difficult, and excavation monographs are read by few people, and bought by even fewer. In England the development of post-PPG16 fieldwork has exacerbated the problem by creating a mountain of unpublished grey literature and making the work of synthesis even harder; a similar situation exists in other countries. Meanwhile museum archives are also reaching breaking point; most are running out of storage space, few can provide facilities for access, and

  9. 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.

  10. Update History of This Database - tRNADB-CE | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available nce site, URL of the original website and Whole data download are changed. 2012/07/23 - Data Updated The data is up...[ Credits ] BLAST Search Image Search Home About Archive Update History Contact us tRNADB-CE Up...date History of This Database Date Update contents 2014/08/25 Contact address, Database maintena... sample (ENV) from GenBank: 134 Environmental sample (ENV) from Sequence Read Archive: 87 2011/08/25 License is up... This Database Database Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - tRNADB-CE | LSDB Archive ...

  11. An evaluation of multiplex bead-based analysis of cytokines and soluble proteins in archived lithium heparin plasma, EDTA plasma and serum samples

    DEFF Research Database (Denmark)

    Brøndum, Line; Sørensen, Brita Singers; Eriksen, Jesper Grau

    2016-01-01

    in plasma and serum from 86 head and neck cancer patients and 33 controls were evaluated: EGFR, leptin, OPN, VEGFR-1, VEGFR-2, IL-2, IL-13, PDGF-bb, TNF, PAI-1, SDF-1a, IL-4, IL-6, IL-8, eotaxin, G-CSF, VEGF, GRO-a, and HGF. RESULTS: The correlation between measurements of the same samples analyzed...

  12. Radio archive

    OpenAIRE

    Street, Sean

    2008-01-01

    The Centre for Broadcasting History Research, in association with the\\ud British Universities Film and Video Council, is developing an online\\ud audio archive of UK commercial radio, from 1973 to 1992. Work produced\\ud before the Broadcasting Act 1990 represents a different ethos to the role\\ud commercial radio played, and subsequently,continues to play, in the UK.\\ud The change in commercial radio since this period is extraordinary. It is\\ud impossible for the young student of radio, born si...

  13. 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...

  14. 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.

  15. Prevalence of human papillomavirus in archival samples obtained from patients with cervical pre-malignant and malignant lesions from Northeast Brazil

    Directory of Open Access Journals (Sweden)

    Prado José CM

    2010-04-01

    Full Text Available Abstract Background Human Papillomavirus (HPV is considered as a necessary, but not sufficient, cause of cervical cancer. In this study, we aimed to assess the prevalence of HPV in a series of pre-malignant and malignant cervical lesion cases, to identify the virus genotypes, and to assess their distribution pattern according to lesion type, age range, and other considered variables. The samples were submitted to histopathological revision examination and analysed by polymerase chain reaction (PCR for the presence of HPV DNA, followed by HPV typing by dot blot hybridisation. Findings Of the analysed samples, 53.7% showed pre-malignant cervical lesions, and 46.3% presented with cervical cancer. Most cancer samples (84.1% were classified as invasive carcinoma. The mean age of these cancer patients was 47.3 years. The overall HPV prevalence was 82.4% in patients with pre-malignant lesions and 92.0% in the cancer patients. HPV 16 was the most prevalent type, followed by HPV 18 and 58, including both single and double infections. Double infection was detected in 11.6% of the samples, and the most common combination was HPV 16+18. Conclusions Cervical cancer appears to occur in women in a lower age range in the studied area, compared to the situation in other Brazilian regions. Furthermore, among the patients with CIN 3 and those with cancer, we observed a higher proportion of married women, women with more than one sexual partner, smokers, and individuals with less than an elementary education, relative to their counterparts. Findings The overall HPV prevalence was 82.4% in patients with pre-malignant lesions and 92.0% in the cervical cancer patients from Northeast Brazil. HPV 16 was the most prevalent type, followed by HPV 18 and 58. The most common double infection was HPV 16+18. Cervical cancer appears to occur in women in a lower age range in the Northeast Brazil. Among the patients with CIN 3 and those with cancer, we observed a higher

  16. 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…

  17. Expression profiling of 519 kinase genes in matched malignant peripheral nerve sheath tumor/plexiform neurofibroma samples is discriminatory and identifies mitotic regulators BUB1B, PBK and NEK2 as overexpressed with transformation.

    Science.gov (United States)

    Stricker, Thomas P; Henriksen, Kammi J; Tonsgard, James H; Montag, Anthony G; Krausz, Thomas N; Pytel, Peter

    2013-07-01

    About 50% of all malignant peripheral nerve sheath tumors (MPNSTs) arise as neurofibromatosis type 1 associated lesions. In those patients malignant peripheral nerve sheath tumors are thought to arise through malignant transformation of a preexisting plexiform neurofibroma. The molecular changes associated with this transformation are still poorly understood. We sought to test the hypothesis that dysregulation of expression of kinases contributes to this malignant transformation. We analyzed expression of all 519 kinase genes in the human genome using the nanostring nCounter system. Twelve cases of malignant peripheral nerve sheath tumor arising in a background of preexisting plexiform neurofibroma were included. Both components were separately sampled. Statistical analysis compared global changes in expression levels as well as changes observed in the pairwise comparison of samples taken from the same surgical specimen. Immunohistochemical studies were performed on tissue array slides to confirm expression of selected proteins. The expression pattern of kinase genes can separate malignant peripheral nerve sheath tumors and preexisting plexiform neurofibromas. The majority of kinase genes is downregulated rather than overexpressed with malignant transformation. The patterns of expression changes are complex without simple recurring alteration. Pathway analysis demonstrates that differentially expressed kinases are enriched for kinases involved in the direct regulation of mitosis, and several of these show increased expression in malignant peripheral nerve sheath tumors. Immunohistochemical studies for the mitotic regulators BUB1B, PBK and NEK2 confirm higher expression levels at the protein level. These results suggest that the malignant transformation of plexiform neurofibroma is associated with distinct changes in the expression of kinase genes. The patterns of these changes are complex and heterogeneous. There is no single unifying alteration. Kinases involved

  18. PHOTOPROBER® Biotin: An Alternative Method for Labeling Archival DNA for Comparative Genomic Hybridization

    Directory of Open Access Journals (Sweden)

    Dirk Korinth

    2004-01-01

    Full Text Available Comparative genomic hybridization (CGH represents a powerful method for screening the entire genome of solid tumors for chromosomal imbalances. Particularly it enabled the molecular cytogenetic analysis of archival, formalin‐fixed, paraffin‐embedded (FFPE tissue. A well‐known dilemma, however, is the poor DNA quality of this material with fragment sizes below 1000 bp. Nick translation, the conventionally used enzymatic DNA labeling method in CGH, leads to even shorter fragments often below a critical limit for successful analysis. In this study we report the alternative application of non‐enzymatic, PHOTOPROBE® biotin labeling for conjugation of the hapten to the DNA prior to in situ hybridization and fluorescence detection. We analyzed 51 FFPE tumor samples mainly from the upper respiratory tract by both labeling methods. In 19 cases, both approaches were successful. The comparison of hybridized metaphases showed a distinct higher fluorescence signal of the PHOTOPROBE® samples sometimes with a discrete cytoplasm background which however did not interfere with specificity and sensitivity of the detected chromosomal imbalances. For further 32 cases characterized by an average DNA fragment size below 1000 bp, PHOTOPROBE® biotin was the only successful labeling technique thus offering a new option for CGH analysis of highly degraded DNA from archival material.

  19. 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.

  20. Establishment and Management of Multicentral Collection Bio-sample Banks of Malignant Tumors from Digestive System%消化系统恶性肿瘤多中心标本库的建立及管理

    Institute of Scientific and Technical Information of China (English)

    沈思; 沈君炜; 朱樑; 吴超群; 李东良; 余宏宇; 邱媛媛; 周薏; 姚定康

    2015-01-01

    为探讨建立及管理消化道恶性肿瘤多中心标本库的有效策略,该文设计了多中心标本库管理系统并制定标准化操作流程(SOPs)。牵头全国十家医院合作收集标本。建库半年收集消化道恶性肿瘤患者标本共695份。标本临床资料全面完整,统一编号,分类管理。以标本库为基础进行了临床及分子生物学研究,取得了一定成果,为多地区、多种类消化系统恶性肿瘤的研究提供了平台。%To establish and manage of multicentral colection bio-sample banks of malignant tumors from digestive system, the paper designed a multicentral management system, established the standard operation procedures (SOPs) and leaded ten hospitals nationwide to colect tumor samples. The biobank has been established for half a year, and has colected 695 samples from patients with digestive system malignant tumor. The clinical data is ful and complete, labeled in a unified way and classified to be managed. The clinical and molecular biology researches were based on the biobank, and obtained achievements. The biobank provides a research platform for malignant tumor of digestive system from different regions and of different types.

  1. Your Laptop to the Rescue: Using the Child Language Data Exchange System Archive and CLAN Utilities to Improve Child Language Sample Analysis.

    Science.gov (United States)

    Ratner, Nan Bernstein; MacWhinney, Brian

    2016-05-01

    In this article, we review the advantages of language sample analysis (LSA) and explain how clinicians can make the process of LSA faster, easier, more accurate, and more insightful than LSA done "by hand" by using free, available software programs such as Computerized Language Analysis (CLAN). We demonstrate the utility of CLAN analysis in studying the expressive language of a very large cohort of 24-month-old toddlers tracked in a recent longitudinal study; toddlers in particular are the most likely group to receive LSA by clinicians, but existing reference "norms" for this population are based on fairly small cohorts of children. Finally, we demonstrate how a CLAN utility such as KidEval can now extract potential normative data from the very large number of corpora now available for English and other languages at the Child Language Data Exchange System project site. Most of the LSA measures that we studied appear to show developmental profiles suggesting that they may be of specifically higher value for children at certain ages, because they do not show an even developmental trajectory from 2 to 7 years of age.

  2. UNESCO Archive Portal

    Directory of Open Access Journals (Sweden)

    2004-06-01

    Full Text Available A review to the web site of UNESCO Archive Portal which work as a directory for archive and documents web sites , also offer a news and events on archive , the review showing the categories of the site , it's services , and the classification of the web sites in the directories.

  3. Prenatal polychlorinated biphenyl exposure is associated with decreased gestational length but not birth weight: archived samples from the Child Health and Development Studies pregnancy cohort

    Directory of Open Access Journals (Sweden)

    Kezios Katrina L

    2012-07-01

    Full Text Available Abstract Background Polychlorinated biphenyls (PCBs, known endocrine disruptors, were banned in 1979 but persist in the environment. Previous studies are inconsistent regarding prenatal exposure to PCBs and pregnancy outcomes. We investigated associations between prenatal exposure to PCBs and gestational length and birth weight. Methods In a sample of 600 infants (born between 1960 and 1963 randomly selected from Child Health and Development Studies participants followed through adolescence we measured 11 PCB congeners in maternal post partum sera (within three days of delivery. Length of gestation was computed from the reported first day of the last menstrual period (LMP and delivery date. Linear regression was used to estimate associations between PCB exposure and gestational age and birth weight, adjusting for potential confounders. PCBs were grouped according to hypothesized biological action (1b (sum of weak phenobarbital inducers, 2b (sum of limited dioxin activity, and 3 (sum of CYP1A and CYP2b inducers or degree of ortho- substitution (mono, di, tri. Secondary analyses examined associations between total PCB exposure and exposure to individual congeners. Results Each unit increase in mono-ortho substituted PCBs was associated with a 0.30 week decrease (95% confidence interval (CI -0.59, -0.016, corresponding to a 2.1 (95% CI −4.13, -0.11 day decrease in length of gestation. Similar associations were estimated for di-ortho substituted PCBs, (1.4 day decrease; (95% CI −2.9, 0.1 and group 3 PCBs (0.84 day decrease; (95% CI −1.8, 0.11. We found similar associations in congener specific analyses and for the sum of congeners. Conclusions Our study provides new evidence that PCB exposure shortens length of gestation in humans. This may have public health implications for population exposures.

  4. Secular trends and geographical variations in the dietary intake of polybrominated diphenyl ethers (PBDEs) using archived samples from the early 1980s and mid 1990s in Japan.

    Science.gov (United States)

    Wada, Yasuhiko; Koizumi, Akio; Yoshinaga, Takeo; Harada, Kouji; Inoue, Kayoko; Morikawa, Akiko; Muroi, Junko; Inoue, Sumiko; Eslami, Bita; Hirosawa, Iwao; Hirosawa, Akitsu; Fujii, Shigeo; Fujimine, Yoshinori; Hachiya, Noriyuki; Koda, Shigeki; Kusaka, Yukinori; Murata, Katsuyuki; Nakatsuka, Haruo; Omae, Kazuyuki; Saito, Norimitsu; Shimbo, Shinichiro; Takenaka, Katsunobu; Takeshita, Tatsuya; Todoriki, Hidemi; Watanabe, Takao; Ikeda, Masayuki

    2005-05-01

    A retrospective exposure assessment among the general population for polybrominated diphenyl ethers (PBDEs) was conducted using dietary surveys. We analyzed samples of food duplicate portions collected in the early 1980s (1980 survey: N=40) and the mid 1990s (1995 survey: N=39) from female subjects (5 participants from each of 8 sites per survey except for one site) living throughout Japan, from the north (Hokkaido) to the south (Okinawa). The study populations in the 1980 and 1995 surveys were different, but lived in the same communities. We measured four PBDE congeners [2,2',4,4'-tetrabrominated diphenyl ether (tetraBDE): #47; 2,2',4,4',5-pentaBDE: #99; 2,2',4,4',6-pentaBDE: #100; and 2,2',4,4',5,5'-hexaBDE: #153] in the diet. #99 was the most abundant congener in the diet (49% of the total PBDEs), followed by #47 (33%), #100 (12%) and #153 (6%). Regional variations found in the 1980 survey decreased in the 1995 survey. The total daily intake of PBDEs (ng/d) [GM (GSD)] in the 1980 survey [91.4 (4.1)] was not significantly different from that in the 1995 survey [93.8 (3.4)] for the total population, nor did it differ among the sites including Shimane, in which a 20-fold increase in serum concentrations was observed in the same population1). In consideration of the significant increases in the serum concentration, inhalation may be more important than food ingestion as the route of human exposure to PBDEs.

  5. Assessment of human exposure to polychlorinated biphenyls and polybrominated diphenyl ethers in Japan using archived samples from the early 1980s and mid-1990s.

    Science.gov (United States)

    Koizumi, Akio; Yoshinaga, Takeo; Harada, Kouji; Inoue, Kayoko; Morikawa, Akiko; Muroi, Junko; Inoue, Sumiko; Eslami, Bita; Fujii, Shigeo; Fujimine, Yoshinori; Hachiya, Noriyuki; Koda, Shigeki; Kusaka, Yukinori; Murata, Katsuyuki; Nakatsuka, Haruo; Omae, Kazuyuki; Saito, Norimitsu; Shimbo, Shinichiro; Takenaka, Katsunobu; Takeshita, Tatsuya; Todoriki, Hidemi; Wada, Yasuhiko; Watanabe, Takao; Ikeda, Masayuki

    2005-09-01

    Persistent organic pollutants have been linked to various adverse effects on human health. We conducted a retrospective exposure assessment for 11polychlorinated biphenyl (PCB) congeners and 4 polybrominated diphenyl ether (PBDE) congeners. We analyzed paired samples of blood and food duplicate portions collected in the 1980s (1980 survey, N=40) and the mid-1990s (1995 survey, N=40) from females (five participants from each of eight sites per survey) living throughout Japan, from Hokkaido to Okinawa. The study populations in the 1980 and 1995 surveys were different but had lived in the same community. We measured PCBs and PBDEs in serum and PCBs in diet. Total serum PCBs (ng/g lipid) [geometric mean (geometric standard deviation)] were similar in the 1980 [163.0 (1.7)] and the 1995 [142.6 (2.0)] surveys. In contrast, dietary intake (ng/day) between 1980 and 1995 decreased significantly, from 522.8 (2.5) to 165.9 (3.3), respectively, (P<0.05). We classified the participants by birth year-before 1941 (older generation) and equal to or after 1941 (younger generation). Serum PCB levels decreased significantly in the younger generation, from 179.1 (1.8) in the 1980 survey to 115.4 (2.0) in the 1995 survey (P<0.05). However, in the older generation, serum levels (ng/g lipid) did not change: 150.4 (1.6) in the 1980 survey and 180 (1.8) in the 1995 survey. Total PBDE serum levels (ng/g lipid) increased significantly during the 15 years, from 0.5 (3.5) to 1.8 (3.7) (P<0.05). At the Shimane site, PBDE serum levels (ng/g lipid) increased 20-fold, from 1.3 (4.8) to 26.0 (5.0). The serum levels of PCBs decreased in the younger generation but not in the older, although levels in daily intakes decreased significantly. Exposure levels of PBDEs appear to be increasing in an area-specific manner.

  6. 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

  7. Glucocorticoid receptor expression in 20 solid tumor types using immunohistochemistry assay

    Science.gov (United States)

    Block, Thaddeus S; Murphy, Tiffany I; Munster, Pamela N; Nguyen, Dat P; Lynch, Frank J

    2017-01-01

    Background Glucocorticoid receptor (GR) activity plays a role in many aspects of human physiology and may play a crucial role in chemotherapy resistance in a wide variety of solid tumors. A novel immunohistochemistry (IHC) based assay has been previously developed and validated in order to assess GR immunoreactivity in triple-negative breast cancer. The current study investigates the standardized use of this validated assay to assess GR expression in a broad range of solid tumor malignancies. Methods Archived formalin-fixed paraffin-embedded tumor bank samples (n=236) from 20 different solid tumor types were analyzed immunohistochemically. Nuclear staining was reported based on the H-score method using differential intensity scores (0, 1+, 2+, or 3+) with the percent stained (out of at least 100 carcinoma cells) recorded at each intensity. Results GR was expressed in all tumor types that had been evaluated. Renal cell carcinoma, sarcoma, cervical cancer, and melanoma were those with the highest mean H-scores, indicating high levels of GR expression. Colon, endometrial, and gastric cancers had lower GR staining percentages and intensities, resulting in the lowest mean H-scores. Conclusion A validated IHC assay revealed GR immunoreactivity in all solid tumor types studied and allowed for standardized comparison of reactivity among the different malignancies. Impact Baseline expression levels of GR may be a useful biomarker when pharmaceutically targeting GR in research or clinical setting. PMID:28293120

  8. Home | 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 even true for databases with high-quality datasets. The Life Science Database Archiv...te as national public goods. The Archive makes it easier for many people to search datasets by metadata (des...s with clear terms of use (see here for detailed descriptions). In addition, the Archive provides datasets i...r contribution of each research to life science. Lifescience Database Archive Archiv

  9. NOAO Science Archive

    Science.gov (United States)

    Seaman, Robert L.; De La Pena, Michele; Zarate, Nelson; Lauer, Tod R.

    2002-12-01

    The NOAO Science Archive (NSA) is a step toward building a comprehensive scientific archive of the optical and infrared data holdings of the National Optical Astronomy Observatory. Earlier efforts included the NOAO Save the Bits archive (more properly a data store) with current raw data holdings from telescopes at both Kitt Peak National Observatory and Cerro Tololo Inter-American Observatory of more than 3 million images, totaling in excess of 20 terabytes. The NOAO Science Archive builds on the foundation provided by the NOAO Deep-Wide Field Survey (NDWFS) Archive that offers sophisticated analysis tools -- as well as the coherent and extensive NDWFS data set. NSA is an initiative of the NOAO Data Products Program aimed at identifying scientifically useful datasets from the large and growing NOAO holdings and making these data available to the astronomical community, while providing tools for data discovery, mining and exploration. The goals for the NSA are: to immediately create a scientifically useful archive of NOAO Survey data, to develop in-house expertise in the relevant technologies, to identify and document requirements for NOAO's future comprehensive archive by providing a design study, and to create a high level of visibility and utility for both the NOAO Archive and NOAO Surveys (for example, with web services available at http://archive.noao.edu). The archive and associated NOAO assets are expected to grow into a resource of the National Virtual Observatory.

  10. Random DNA fragmentation allows detection of single-copy, single-exon alterations of copy number by oligonucleotide array CGH in clinical FFPE samples.

    Science.gov (United States)

    Hostetter, Galen; Kim, Su Young; Savage, Stephanie; Gooden, Gerald C; Barrett, Michael; Zhang, Jian; Alla, Lalitamba; Watanabe, April; Einspahr, Janine; Prasad, Anil; Nickoloff, Brian J; Carpten, John; Trent, Jeffrey; Alberts, David; Bittner, Michael

    2010-01-01

    Genomic technologies, such as array comparative genomic hybridization (aCGH), increasingly offer definitive gene dosage profiles in clinical samples. Historically, copy number profiling was limited to large fresh-frozen tumors where intact DNA could be readily extracted. Genomic analyses of pre-neoplastic tumors and diagnostic biopsies are often limited to DNA processed by formalin-fixation and paraffin-embedding (FFPE). We present specialized protocols for DNA extraction and processing from FFPE tissues utilizing DNase processing to generate randomly fragmented DNA. The protocols are applied to FFPE clinical samples of varied tumor types, from multiple institutions and of varied block age. Direct comparative analyses with regression coefficient were calculated on split-sample (portion fresh/portion FFPE) of colorectal tumor samples. We show equal detection of a homozygous loss of SMAD4 at the exon-level in the SW480 cell line and gene-specific alterations in the split tumor samples. aCGH application to a set of archival FFPE samples of skin squamous cell carcinomas detected a novel hemizygous deletion in INPP5A on 10q26.3. Finally we present data on derivative of log ratio, a particular sensitive detector of measurement variance, for 216 sequential hybridizations to assess protocol reliability over a wide range of FFPE samples.

  11. Parallel evolution of tumor subclones mimics diversity between tumors

    DEFF Research Database (Denmark)

    Martinez, Pierre; Birkbak, Nicolai Juul; Gerlinger, Marco;

    2013-01-01

    obtained 48 biopsies from eight stage III and IV clear cell renal cell carcinomas (ccRCC) and used DNA copy-number analyses to compare biopsies from the same tumor with 440 singletumor biopsies from The Cancer Genome Atlas (TCGA). Unsupervised hierarchical clustering of TCGA and multi-region ccRCC samples...... revealed segregation of samples from the same tumor into unrelated clusters. 25% of multi-region samples appeared more similar to unrelated samples than to any other sample originating from the same tumor. We find that the majority of recurrent DNA copy number driver aberrations in single biopsies...

  12. Hypothalamic tumor

    Science.gov (United States)

    Complications of brain surgery may include: Bleeding Brain damage Death (rarely) Infection Seizures can result from the tumor or from any surgical procedure on the brain. Hydrocephalus can occur with some tumors and ...

  13. Wilms Tumor

    Science.gov (United States)

    ... Wilms tumor is 1 pound at diagnosis. Some children also may have nausea, stomach pain, high blood pressure (hypertension), blood in the urine, loss of appetite, or fever. Even though Wilms tumors often are ...

  14. 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.

  15. 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.

  16. 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 ...

  17. 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...

  18. 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

  19. Detection of N-Glycolyl GM3 Ganglioside in Neuroectodermal Tumors by Immunohistochemistry: An Attractive Vaccine Target for Aggressive Pediatric Cancer

    Directory of Open Access Journals (Sweden)

    Alejandra M. Scursoni

    2011-01-01

    Full Text Available The N-glycolylated ganglioside NeuGc-GM3 has been described in solid tumors such as breast carcinoma, nonsmall cell lung cancer, and melanoma, but is usually not detected in normal human cells. Our aim was to evaluate the presence of NeuGc-GM3 in pediatric neuroectodermal tumors by immunohistochemistry. Twenty-seven archival cases of neuroblastoma and Ewing sarcoma family of tumors (ESFT were analyzed. Formalin-fixed, paraffin-embedded tumor samples were cut into 5 μm sections. The monoclonal antibody 14F7, a mouse IgG1 that specifically recognizes NeuGc-GM3, and a peroxidase-labeled polymer conjugated to secondary antibodies were used. Presence of NeuGc-GM3 was evident in 23 of 27 cases (85%, with an average of about 70% of positive tumors cells. Immunoreactivity was moderate to intense in most tumors, showing a diffuse cytoplasmic and membranous staining, although cases of ESFT demonstrated a fine granular cytoplasmic pattern. No significant differences were observed between neuroblastoma with and without NMYC oncogene amplification, suggesting that expression of NeuGc-GM3 is preserved in more aggressive cancers. Until now, the expression of N-glycolylated gangliosides in pediatric neuroectodermal tumors has not been investigated. The present study evidenced the expression of NeuGc-GM3 in a high proportion of neuroectodermal tumors, suggesting its potential utility as a specific target of immunotherapy.

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

    Science.gov (United States)

    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 fresh-frozen and formalin-fixed/paraffin-embedded tumor samples with similar efficiency. The distortion in gene dosage representation in the amplified DNA was nonrandom and reproducibly involved distinct genomic loci. Regional amplification efficiency was significantly linked to regional GC content of the template genome. The biased gene representation in amplified tumor DNA could be effectively normalized by using amplified reference DNA. Our data suggest that genome-wide gene dosage alterations in clinical tumor samples can be reliably assessed from a few hundred tumor cells. Therefore, this amplification method should lend itself to high-throughput genetic analyses of limited sources of tumor, such as fine-needle biopsies, laser-microdissected tissue, and small paraffin-embedded specimens. PMID:15858140

  2. The INTEGRAL-OMC Scientific Archive

    CERN Document Server

    Domingo, A; Risquez, D; Caballero-Garcia, M D; Mas-Hesse, J M; Solano, E

    2008-01-01

    The Optical Monitoring Camera (OMC) on-board the INTEGRAL satellite has, as one of its scientific goals, the observation of a large number of variable sources previously selected. After almost 6 years of operations, OMC has monitored more than 100 000 sources of scientific interest. In this contribution we present the OMC Scientific Archive (http://sdc.laeff.inta.es/omc/) which has been developed to provide the astronomical community with a quick access to the light curves generated by this instrument.We describe the main characteristics of this archive, as well as important aspects for the users: object types, temporal sampling of light curves and photometric accuracy.

  3. Chromatin immunoprecipitation from fixed clinical tissues reveals tumor-specific enhancer profiles.

    Science.gov (United States)

    Cejas, Paloma; Li, Lewyn; O'Neill, Nicholas K; Duarte, Melissa; Rao, Prakash; Bowden, Michaela; Zhou, Chensheng W; Mendiola, Marta; Burgos, Emilio; Feliu, Jaime; Moreno-Rubio, Juan; Guadalajara, Héctor; Moreno, Víctor; García-Olmo, Damián; Bellmunt, Joaquim; Mullane, Stephanie; Hirsch, Michelle; Sweeney, Christopher J; Richardson, Andrea; Liu, X Shirley; Brown, Myles; Shivdasani, Ramesh A; Long, Henry W

    2016-06-01

    Extensive cross-linking introduced during routine tissue fixation of clinical pathology specimens severely hampers chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) analysis from archived tissue samples. This limits the ability to study the epigenomes of valuable, clinically annotated tissue resources. Here we describe fixed-tissue chromatin immunoprecipitation sequencing (FiT-seq), a method that enables reliable extraction of soluble chromatin from formalin-fixed paraffin-embedded (FFPE) tissue samples for accurate detection of histone marks. We demonstrate that FiT-seq data from FFPE specimens are concordant with ChIP-seq data from fresh-frozen samples of the same tumors. By using multiple histone marks, we generate chromatin-state maps and identify cis-regulatory elements in clinical samples from various tumor types that can readily allow us to distinguish between cancers by the tissue of origin. Tumor-specific enhancers and superenhancers that are elucidated by FiT-seq analysis correlate with known oncogenic drivers in different tissues and can assist in the understanding of how chromatin states affect gene regulation.

  4. Immunohistochemical expression of SALL4 in hepatocellular carcinoma, a potential pitfall in the differential diagnosis of yolk sac tumors.

    Science.gov (United States)

    Gonzalez-Roibon, Nilda; Katz, Betina; Chaux, Alcides; Sharma, Rajni; Munari, Enrico; Faraj, Sheila F; Illei, Peter B; Torbenson, Michael; Netto, George J

    2013-07-01

    SALL4 is a transcription factor that serves as a marker of yolk sac tumor. Yolk sac tumor and hepatocellular carcinoma share histologic, serologic, and immunohistochemical features. Previous studies have shown lack of SALL4 expression in hepatocellular carcinoma, suggesting utility in this differential diagnosis. Sixty-nine samples of hepatocellular carcinoma were retrieved from surgical pathology archives and used to construct 9 tissue microarrays. A germ cell tumor tissue microarray containing 10 yolk sac tumors was used for comparison. Extent, intensity, and pattern of nuclear SALL4 expression were assessed in each spot. Mean percentage of expression was calculated for each tumor and used during analysis. Optimal discriminatory extent of expression cutoff was determined by receiver operating characteristic curve analysis. Other potential discriminatory markers including Hep Par1 were also evaluated. Forty-six percent (32/69) of hepatocellular carcinoma and all yolk sac tumors revealed at least focal expression of SALL4. A unique punctuate/clumped pattern of nuclear staining was present in 94% (30/32) of hepatocellular carcinoma, whereas all yolk sac tumors displayed a diffuse finely granular nuclear staining pattern. A 25% extent of SALL4 expression cutoff was found to be optimal for the distinction of yolk sac tumor from hepatocellular carcinoma yielding a sensitivity of 100%, specificity of 92.8%, and a positive predictive value of 66.6% for yolk sac tumor diagnosis. The addition of Hep Par1 increased the specificity (99%) and positive predictive value (90%). This is the first report of SALL4 expression in hepatocellular carcinoma. Our finding should be taken into consideration in the differential diagnosis of hepatocellular carcinoma and yolk sac tumor. The unique punctuate/clumped pattern seen in hepatocellular carcinoma cases could be of further discriminatory value.

  5. 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- an...

  6. 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.

  7. 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...

  8. The Pervasiveness of Archives

    Directory of Open Access Journals (Sweden)

    Gabriella Ivacs

    2013-03-01

    Full Text Available Regardless of the widely spread use in historiography, anthropology, cultural studies, information sciences, archives is a heavily inflated word. Beginning with the ancient Greek administrative role of Archeion, the emergence of archival institution as a symbolic mean to strengthen national identity in the age of nation states, through referencing social construction and parallel stories of postmodern historiography, there is a need for a new archival theory to connect high level theories with new archival practices embedded in the dig- ital society. The essay tries to remove some interpretative layers from the non-discoursive practices of archives and it yields the generative nature of its architecture by referencing media archeology as method. The analysis of Eastern and Central European historical examples add nuance to our understanding of archival complexities: the fate of secret police files in the Post-Communist societies, how to serve the collective memory of traumatized nations with new approaches to collection management, and finally, referencing Pan-European efforts to cooperate or to compete with huge private technology providers in the digital age. The essay is part of a growing body of research on resituating “the archival identity” and suggesting to examine both static and dynamic archives in the light of technology developments to understand digital forgetting, digital remembering and controlling data for the whole society.

  9. LSDB Archive - 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 ...o help medical professionals and people in society to better understand the scientific basis of diseases and drugs. (This archiv...cription Download License Update History of This Database Site Policy | Contact Us LSDB Archive - KEGG MEDICUS | LSDB Archive ...

  10. Revealing the Molecular Portrait of Triple Negative Breast Tumors in an Understudied Population through Omics Analysis of Formalin-Fixed and Paraffin-Embedded Tissues

    Science.gov (United States)

    Vaca-Paniagua, Felipe; Alvarez-Gomez, Rosa María; Maldonado-Martínez, Hector Aquiles; Pérez-Plasencia, Carlos; Fragoso-Ontiveros, Veronica; Lasa-Gonsebatt, Federico; Herrera, Luis Alonso; Cantú, David; Bargallo-Rocha, Enrique; Mohar, Alejandro; Durand, Geoffroy; Forey, Nathalie; Voegele, Catherine; Vallée, Maxime; Le Calvez-Kelm, Florence; McKay, James; Ardin, Maude; Villar, Stéphanie; Zavadil, Jiri; Olivier, Magali

    2015-01-01

    Triple negative breast cancer (TNBC), defined by the lack of expression of the estrogen receptor, progesterone receptor and human epidermal receptor 2, is an aggressive form of breast cancer that is more prevalent in certain populations, in particular in low- and middle-income regions. The detailed molecular features of TNBC in these regions remain unexplored as samples are mostly accessible as formalin-fixed paraffin embedded (FFPE) archived tissues, a challenging material for advanced genomic and transcriptomic studies. Using dedicated reagents and analysis pipelines, we performed whole exome sequencing and miRNA and mRNA profiling of 12 FFPE tumor tissues collected from pathological archives in Mexico. Sequencing analyses of the tumor tissues and their blood pairs identified TP53 and RB1 genes as the most frequently mutated genes, with a somatic mutation load of 1.7 mutations/exome Mb on average. Transcriptional analyses revealed an overexpression of growth-promoting signals (EGFR, PDGFR, VEGF, PIK3CA, FOXM1), a repression of cell cycle control pathways (TP53, RB1), a deregulation of DNA-repair pathways, and alterations in epigenetic modifiers through miRNA:mRNA network de-regulation. The molecular programs identified were typical of those described in basal-like tumors in other populations. This work demonstrates the feasibility of using archived clinical samples for advanced integrated genomics analyses. It thus opens up opportunities for investigating molecular features of tumors from regions where only FFPE tissues are available, allowing retrospective studies on the search for treatment strategies or on the exploration of the geographic diversity of breast cancer. PMID:25961742

  11. Revealing the Molecular Portrait of Triple Negative Breast Tumors in an Understudied Population through Omics Analysis of Formalin-Fixed and Paraffin-Embedded Tissues.

    Directory of Open Access Journals (Sweden)

    Felipe Vaca-Paniagua

    Full Text Available Triple negative breast cancer (TNBC, defined by the lack of expression of the estrogen receptor, progesterone receptor and human epidermal receptor 2, is an aggressive form of breast cancer that is more prevalent in certain populations, in particular in low- and middle-income regions. The detailed molecular features of TNBC in these regions remain unexplored as samples are mostly accessible as formalin-fixed paraffin embedded (FFPE archived tissues, a challenging material for advanced genomic and transcriptomic studies. Using dedicated reagents and analysis pipelines, we performed whole exome sequencing and miRNA and mRNA profiling of 12 FFPE tumor tissues collected from pathological archives in Mexico. Sequencing analyses of the tumor tissues and their blood pairs identified TP53 and RB1 genes as the most frequently mutated genes, with a somatic mutation load of 1.7 mutations/exome Mb on average. Transcriptional analyses revealed an overexpression of growth-promoting signals (EGFR, PDGFR, VEGF, PIK3CA, FOXM1, a repression of cell cycle control pathways (TP53, RB1, a deregulation of DNA-repair pathways, and alterations in epigenetic modifiers through miRNA:mRNA network de-regulation. The molecular programs identified were typical of those described in basal-like tumors in other populations. This work demonstrates the feasibility of using archived clinical samples for advanced integrated genomics analyses. It thus opens up opportunities for investigating molecular features of tumors from regions where only FFPE tissues are available, allowing retrospective studies on the search for treatment strategies or on the exploration of the geographic diversity of breast cancer.

  12. 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.

  13. Characterization of the Tumor Secretome from Tumor Interstitial Fluid (TIF).

    Science.gov (United States)

    Gromov, Pavel; Gromova, Irina

    2016-01-01

    Tumor interstitial fluid (TIF) surrounds and perfuses bodily tumorigenic tissues and cells, and can accumulate by-products of tumors and stromal cells in a relatively local space. Interstitial fluid offers several important advantages for biomarker and therapeutic target discovery, especially for cancer. Here, we describe the most currently accepted method for recovering TIF from tumor and nonmalignant tissues that was initially performed using breast cancer tissue. TIF recovery is achieved by passive extraction of fluid from small, surgically dissected tissue specimens in phosphate-buffered saline. We also present protocols for hematoxylin and eosin (H&E) staining of snap-frozen and formalin-fixed, paraffin-embedded (FFPE) tumor sections and for proteomic profiling of TIF and matched tumor samples by high-resolution two-dimensional gel electrophoresis (2D-PAGE) to enable comparative analysis of tumor secretome and paired tumor tissue.

  14. Pindborg tumor

    Science.gov (United States)

    Caliaperoumal, Santhosh Kumar; Gowri, S.; Dinakar, J.

    2016-01-01

    Calcifying epithelial odontogenic tumor (CEOT), also known as Pindborg tumor, is a rare odontogenic epithelial neoplasm. So far, nearly 200 cases have been reported in the literature. We are reporting a case of CEOT in a 42-year-old male patient with painless bony swelling in the mandible. The clinical, radiographic, and histopathologic features are discussed with relevant references. PMID:27041911

  15. Pindborg tumor

    Directory of Open Access Journals (Sweden)

    Santhosh Kumar Caliaperoumal

    2016-01-01

    Full Text Available Calcifying epithelial odontogenic tumor (CEOT, also known as Pindborg tumor, is a rare odontogenic epithelial neoplasm. So far, nearly 200 cases have been reported in the literature. We are reporting a case of CEOT in a 42-year-old male patient with painless bony swelling in the mandible. The clinical, radiographic, and histopathologic features are discussed with relevant references.

  16. Methylation Status of Vitamin D Receptor Gene Promoter in Benign and Malignant Adrenal Tumors

    Directory of Open Access Journals (Sweden)

    Catia Pilon

    2015-01-01

    Full Text Available We previously showed a decreased expression of vitamin D receptor (VDR mRNA/protein in a small group of adrenocortical carcinoma (ACC tissues, suggesting the loss of a protective role of VDR against malignant cell growth in this cancer type. Downregulation of VDR gene expression may result from epigenetics events, that is, methylation of cytosine nucleotide of CpG islands in VDR gene promoter. We analyzed methylation of CpG sites in the VDR gene promoter in normal adrenals and adrenocortical tumor samples. Methylation of CpG-rich 5′ regions was assessed by bisulfite sequencing PCR using bisulfite-treated DNA from archival microdissected paraffin-embedded adrenocortical tissues. Three normal adrenals and 23 various adrenocortical tumor samples (15 adenomas and 8 carcinomas were studied. Methylation in the promoter region of VDR gene was found in 3/8 ACCs, while no VDR gene methylation was observed in normal adrenals and adrenocortical adenomas. VDR mRNA and protein levels were lower in ACCs than in benign tumors, and VDR immunostaining was weak or negative in ACCs, including all 3 methylated tissue samples. The association between VDR gene promoter methylation and reduced VDR gene expression is not a rare event in ACC, suggesting that VDR epigenetic inactivation may have a role in adrenocortical carcinogenesis.

  17. The Planetary Archive

    Science.gov (United States)

    Penteado, Paulo F.; Trilling, David; Szalay, Alexander; Budavári, Tamás; Fuentes, César

    2014-11-01

    We are building the first system that will allow efficient data mining in the astronomical archives for observations of Solar System Bodies. While the Virtual Observatory has enabled data-intensive research making use of large collections of observations across multiple archives, Planetary Science has largely been denied this opportunity: most astronomical data services are built based on sky positions, and moving objects are often filtered out.To identify serendipitous observations of Solar System objects, we ingest the archive metadata. The coverage of each image in an archive is a volume in a 3D space (RA,Dec,time), which we can represent efficiently through a hierarchical triangular mesh (HTM) for the spatial dimensions, plus a contiguous time interval. In this space, an asteroid occupies a curve, which we determine integrating its orbit into the past. Thus when an asteroid trajectory intercepts the volume of an archived image, we have a possible observation of that body. Our pipeline then looks in the archive's catalog for a source with the corresponding coordinates, to retrieve its photometry. All these matches are stored into a database, which can be queried by object identifier.This database consists of archived observations of known Solar System objects. This means that it grows not only from the ingestion of new images, but also from the growth in the number of known objects. As new bodies are discovered, our pipeline can find archived observations where they could have been recorded, providing colors for these newly-found objects. This growth becomes more relevant with the new generation of wide-field surveys, particularly LSST.We also present one use case of our prototype archive: after ingesting the metadata for SDSS, 2MASS and GALEX, we were able to identify serendipitous observations of Solar System bodies in these 3 archives. Cross-matching these occurrences provided us with colors from the UV to the IR, a much wider spectral range than that

  18. 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.

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    Lifescience Database Archive (English)

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

  11. License - 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 Database Description Download License Update History of This Database Site Policy | Contact Us License - RGP physicalmap | LSDB Archive ...

  12. Mapping data - 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 ...bout This Database Database Description Download License Update History of This Database Site Policy | Contact Us Mapping data - KOME | LSDB Archive ...

  13. 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 ...

  14. 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...

  15. 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.

  16. 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...

  17. NASA's Astrophysics Data Archives

    Science.gov (United States)

    Hasan, H.; Hanisch, R.; Bredekamp, J.

    2000-09-01

    The NASA Office of Space Science has established a series of archival centers where science data acquired through its space science missions is deposited. The availability of high quality data to the general public through these open archives enables the maximization of science return of the flight missions. The Astrophysics Data Centers Coordinating Council, an informal collaboration of archival centers, coordinates data from five archival centers distiguished primarily by the wavelength range of the data deposited there. Data are available in FITS format. An overview of NASA's data centers and services is presented in this paper. A standard front-end modifyer called `Astrowbrowse' is described. Other catalog browsers and tools include WISARD and AMASE supported by the National Space Scince Data Center, as well as ISAIA, a follow on to Astrobrowse.

  18. Police Incident Blotter (Archive)

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — The Police Blotter Archive contains crime incident data after it has been validated and processed to meet Uniform Crime Reporting (UCR) standards, published on a...

  19. [The Montalenti archive].

    Science.gov (United States)

    Valente, Nicoletta

    2006-01-01

    The archival fund by Giuseppe Montalenti, the distinguished Italian genetist and biologist, comprehends correspondence--both personal and scientific--, papers on his activity as a collaborator to the Enciclopedia Treccani, documentation on Montalenti's engagement in the politics of science in Italy and abroad in the 1950s-60s, a collection of offprints and books. A large part of the archive refers to the activities of the IUSB (International Union of Biological Sciences).

  20. 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 ..._db.zip File URL: ftp://ftp.biosciencedbc.jp/archive/kome/LATEST/kome_ine_full_se...quence_db.zip File size: 19 MB File name: FASTA: kome_ine_full_sequence_db.fasta.zip File URL: ftp://ftp.biosciencedbc.jp/archiv...rtio About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Nucleotide Sequence - KOME | LSDB Archive ...

  1. 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 ...

  2. 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 ... this page, are not included in the Taxonomy Icon archive, and therefore under different terms of use. First...that the following data #4 and #5 are not included in the Taxonomy Icon archive, and therefore under differe...Joomla SEF URLs by Artio About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - Taxonomy Icon | LSDB Archive ...

  3. Pituitary Tumors

    Science.gov (United States)

    ... impairment, and behavioral changes. Tumors can also either produce excessive amounts of hormone or limit how much hormone is produced. The hormones most commonly affected include: growth hormone (regulates body height and structure), prolactin (controls ...

  4. Ear Tumors

    Science.gov (United States)

    ... Japanese Espaniol Find information on medical topics, symptoms, drugs, procedures, news and more, written in everyday language. * This is ... the Ears, Nose, and Throat Additional Content Medical News Ear Tumors ... NOTE: This is the Consumer Version. DOCTORS: Click ...

  5. Tumor Grade

    Science.gov (United States)

    ... Other Funding Find NCI funding for small business innovation, technology transfer, and contracts Training Cancer Training at ... much of the tumor tissue has normal breast (milk) duct structures Nuclear grade : an evaluation of the ...

  6. Pituitary tumor

    Science.gov (United States)

    ... enough of its hormones. This condition is called hypopituitarism . The causes of pituitary tumors are unknown. Some ... Cyst Endocrine glands Gigantism Growth hormone test Hyperthyroidism Hypopituitarism Multiple endocrine neoplasia (MEN) I Prolactin blood test ...

  7. Wilms' Tumor

    Science.gov (United States)

    ... team and have training in child development, recreation, psychology or social work. If your child must remain ... conditions/wilms-tumor/basics/definition/CON-20043492 . Mayo Clinic Footer Legal Conditions and Terms Any use of ...

  8. Reading Robin Kelsey's "Archive Style" across the Archival Divide

    Science.gov (United States)

    Schwartz, Joan M.

    2008-01-01

    This article presents the author's comments on Robin Kelsey's "Archive Style: Photographs and Illustrations for U.S. Surveys, 1850-1890," a book about government documents that happen to be visual materials. The word "archive" now has intellectual cache in the academic world, but its currency has little to do with the "real world of archives" as…

  9. 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 ...

  10. 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 ... File URL: ftp://ftp.biosciencedbc.jp/archive/place/LATEST/place_reference.zip Fi... Artio About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Reference - PLACE | LSDB Archive ...

  11. Drug - 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 ...ftp://ftp.biosciencedbc.jp/archive/kegg-medicus/LATEST/kegg_medicus_drug_en.zip File size: 5.2 MB Simple sea...bout This Database Database Description Download License Update History of This Database Site Policy | Contact Us Drug - KEGG MEDICUS | LSDB Archive ...

  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 ...p File URL: ftp://ftp.biosciencedbc.jp/archive/taxonomy-icon/LATEST/taxonomy_icon... Database Database Description Download License Update History of This Database Site Policy | Contact Us Comment - Taxonomy Icon | LSDB Archive ...

  13. 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 ...

  14. 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 ...to the public. Data file File name: rmg_main.zip File URL: ftp://ftp.biosciencedbc.jp/archive/rmg/LATEST/rmg...Description Download License Update History of This Database Site Policy | Contact Us Main data - RMG | LSDB Archive ...

  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 ...ile URL: ftp://ftp.biosciencedbc.jp/archive/kome/LATEST/kome_ops_index.zip File s...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. Genomic Dynamism - 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 ...le name: rmg_genomic_dynamism.zip File URL: ftp://ftp.biosciencedbc.jp/archive/rmg/LATEST/rmg_genomic_dynami...abase Database Description Download License Update History of This Database Site Policy | Contact Us Genomic Dynamism - RMG | LSDB Archive ...

  17. Images - 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 ...//ftp.biosciencedbc.jp/archive/rpsd/LATEST/rpsd_images.zip File size: 18.3 MB Sim...a SEF URLs by Artio About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Images - RPSD | LSDB Archive ...

  18. Genome 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 ....zip File URL: ftp://ftp.biosciencedbc.jp/archive/kome/LATEST/kome_genome_annotat...e Update History of This Database Site Policy | Contact Us Genome annotations - KOME | LSDB Archive ...

  19. 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 ...ation.zip File URL: ftp://ftp.biosciencedbc.jp/archive/kome/LATEST/kome_trimming_information.zip File size: ...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 ...

  20. 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 ...

  1. 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 ...

  2. 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 ...

  3. 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 ..._main.zip File URL: ftp://ftp.biosciencedbc.jp/archive/kome/LATEST/kome_main.zip File size: 1.3 KB Simple se... Download License Update History of This Database Site Policy | Contact Us Main - KOME | LSDB Archive ...

  4. 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 ...

  5. 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…

  6. INTERNATIONAL DATA ARCHIVE AND ANALYSIS CENTER. INTERNATIONAL RELATIONS ARCHIVE

    Science.gov (United States)

    The International Relations Archive undertakes as its primary goal the acquisition, management and dissemination of international affairs data. This...goal necessitates direct interaction between the International Relations Archive staff and the academic community to ensure more adequate standards...contains two documents. The first document is the latest version of the memorandum, ’Data Holdings and Servicing Policies, International Relations Archive

  7. 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 analog...

  8. 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.

  9. Ependymal tumors.

    Science.gov (United States)

    Moynihan, Timothy J

    2003-12-01

    Ependymal tumors are rare malignancies that arise from the cells that line the ventricles and central canal of the spinal cord. Although they are more common in children, adults may also be effected by ependymal tumors. Prognosis is dependent on tumor location, histology, especially for myxopapillary tumors that tend to occur in the lumbar spine, extent of surgical resection, and stage of disease. Standard therapy consists of complete resection when feasible. The exact role of adjuvant radiotherapy in patients with radiographically confirmed complete resection is poorly defined. Patients with known residual disease may benefit from local radiation therapy, but the extent of radiation field and total dose are controversial. Even in patients treated with involved field radiotherapy, most relapses occur within the original tumor bed, thus local control remains the biggest obstacle to effective therapy. Chemotherapy has little impact against this tumor and has no role in the adjuvant setting, outside of a well designed clinical trial, with the possible exception of children younger than 5 years in an effort to delay radiation. A minority of patients may respond to one of several chemotherapy regimens at the time of recurrence, but the impact of this therapy is limited. Newer treatment strategies are needed.

  10. 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

  11. 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.…

  12. Archiving a Software Development Project

    Science.gov (United States)

    2013-04-01

    24 H.4.3 Info on National Archives digital preservation software...a copy of a disposal authority? • Can I have more information on the National Archives digital preservation software? • Can I use the training...General Disposal Authority or under Normal Administrative Practice. H.4.3 Info on National Archives digital preservation software Information on National

  13. Tumor Types: Understanding Brain Tumors

    Science.gov (United States)

    ... Classification of Tumors of the Central Nervous System Purchase WHO Blue Book NBTS Official Statement Questions and ... Privacy Copyright Site Search Search term Submit Submit Facebook Twitter YouTube Flickr

  14. TUMOR CONTAMINATION IN THE BIOPSY PATH OF PRIMARY MALIGNANT BONE TUMORS

    OpenAIRE

    Oliveira,Marcelo Parente; Lima, Pablo Moura de Andrade; Mello,Roberto José Vieira de

    2015-01-01

    Objective: To study factors possibly associated with tumor contamination in the biopsy path of primary malignant bone tumors. Method: Thirty-five patients who underwent surgical treatment with diagnoses of osteosarcoma, Ewing's tumor and chondrosarcoma were studied retrospectively. The sample was analyzed to characterize the biopsy technique used, histological type of the tumor, neoadjuvant chemotherapy used, local recurrences and tumor contamination in the biopsy path. Results: Among the 35 ...

  15. Epidemiologic Study of Human Epidermal Growth Factor Receptor 2 Expression in Advanced/Metastatic Gastric Cancer: an Assessment of Human Epidermal Growth Factor Receptor 2 Status in Tumor Tissue Samples of Gastric and Gastro-Esophageal Junction Cancer

    Science.gov (United States)

    Seo, Kyung Won; Jeon, Taeyong; Kim, Sewon; Kim, Sung Soo; Kim, Kwanghee; Suh, Byoung-Jo; Hwang, Sunhwi; Choi, SeongHee; Ryu, Seungwan; Min, Jae Seok; Lee, Young-Joon; Jee, Ye Seob; Chae, Hyeondong

    2017-01-01

    Purpose The Trastuzumab for gastric cancer (GC) trial identified human epidermal growth factor receptor 2 (HER2) as a predictor of successful treatment with trastuzumab (HER2 receptor targeting agent) among patients with advanced/metastatic GC. To date, the prevalence of HER2 overexpression in the Korean population is unknown. The present study aimed to assess the incidence of HER2 positivity among GC and gastroesophageal (GE) junction cancer samples and the relationship between HER2 overexpression and clinicopathological characteristics in Korean patients. Materials and Methods Tumor samples collected from 1,695 patients with histologically proven GC or GE junction enrolled at 14 different hospitals in Korea were examined. After gathering clinicopathological data of all patients, HER2 status was assessed by immunohistochemistry (IHC) at each hospital, and IHC 2+ cases were subjected to silver-enhanced in situ hybridization at 3 central laboratories. Results A total of 182 specimens tested positive for HER2, whereas 1,505 tested negative. Therefore, the overall HER2-positive rate in this study was 10.8% (95% confidence interval=9.3%–12.3%). The HER2-positive rate was higher among intestinal-type cases (17.6%) than among other types, and was higher among patients older than 70 years and 50 years of age, compared to other age groups. Conclusions Our evaluation of the HER2 positivity rate (10.8%) among Korean patients with GC and GE junction indicated the necessity of epidemiological data when conducting studies related to HER2 expression in GC and GE junction.

  16. 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.

  17. Radio data archiving system

    Science.gov (United States)

    Knapic, C.; Zanichelli, A.; Dovgan, E.; Nanni, M.; Stagni, M.; Righini, S.; Sponza, M.; Bedosti, F.; Orlati, A.; Smareglia, R.

    2016-07-01

    Radio Astronomical Data models are becoming very complex since the huge possible range of instrumental configurations available with the modern Radio Telescopes. What in the past was the last frontiers of data formats in terms of efficiency and flexibility is now evolving with new strategies and methodologies enabling the persistence of a very complex, hierarchical and multi-purpose information. Such an evolution of data models and data formats require new data archiving techniques in order to guarantee data preservation following the directives of Open Archival Information System and the International Virtual Observatory Alliance for data sharing and publication. Currently, various formats (FITS, MBFITS, VLBI's XML description files and ancillary files) of data acquired with the Medicina and Noto Radio Telescopes can be stored and handled by a common Radio Archive, that is planned to be released to the (inter)national community by the end of 2016. This state-of-the-art archiving system for radio astronomical data aims at delegating as much as possible to the software setting how and where the descriptors (metadata) are saved, while the users perform user-friendly queries translated by the web interface into complex interrogations on the database to retrieve data. In such a way, the Archive is ready to be Virtual Observatory compliant and as much as possible user-friendly.

  18. Testicular tumors

    Directory of Open Access Journals (Sweden)

    Giovanni Rosti

    2011-12-01

    Full Text Available Germ cell tumors of the testes represent a unique paradigm of diseases which can be cured even in extremely advanced phase. Unfortunately, this makes them unique among adult solid tumors. Seminoma and non seminoma are relatively rare with approximatively 25,000 patients in Europe per year, but numbers are increasing world wide. Different strategies are needed depending on stage and prognostic scores. Seminoma is extremely sensitive to radiation therapy and chemotherapy, while all germ cell tumors show a very good response to chemotherapy. Clinical stage I seminoma is currently treated with radiation, single course carboplatin or surveillance policy. Clinical stage I non seminoma can also be approached with different strategies such as retroperitoneal lymph node dissection, observation or one-two courses of standard chemotherapy. Stage II seminoma may be treated with either radiation or chemotherapy, while for all advanced stages chemotherapy is mandatory. Since the mid-eighties PEB (Cisplatin, Etoposide and Bleomycin is the regimen of choice and no other schedule has proved superior in terms of efficacy. Surgery on the residual disease is crucial to the whole strategy and should be performed or attempted in all cases. Consequently, the correct treatment strategy for these tumors does not depend only on the ability of a single physician, but on a skilled team specialized in this particular tumor. Second line therapies (VeIP, PEI, TIP can cure 25%–40% of patients, but improved strategies for resistant tumors are desperately needed. High-dose chemotherapy has shown very good results in some studies while being less impressive in others. In any case, it should remain an option for relapsing patients and could be used in some cases of upfront chemotherapy in patients with slow marker decline, but this should only be considered in referring centers.

  19. Superior sulcus tumors (Pancoast tumors).

    Science.gov (United States)

    Marulli, Giuseppe; Battistella, Lucia; Mammana, Marco; Calabrese, Francesca; Rea, Federico

    2016-06-01

    Superior Sulcus Tumors, frequently termed as Pancoast tumors, are a wide range of tumors invading the apical chest wall. Due to its localization in the apex of the lung, with the potential invasion of the lower part of the brachial plexus, first ribs, vertebrae, subclavian vessels or stellate ganglion, the superior sulcus tumors cause characteristic symptoms, like arm or shoulder pain or Horner's syndrome. The management of superior sulcus tumors has dramatically evolved over the past 50 years. Originally deemed universally fatal, in 1956, Shaw and Paulson introduced a new treatment paradigm with combined radiotherapy and surgery ensuring 5-year survival of approximately 30%. During the 1990s, following the need to improve systemic as well as local control, a trimodality approach including induction concurrent chemoradiotherapy followed by surgical resection was introduced, reaching 5-year survival rates up to 44% and becoming the standard of care. Many efforts have been persecuted, also, to obtain higher complete resection rates using appropriate surgical approaches and involving multidisciplinary team including spine surgeon or vascular surgeon. Other potential treatment options are under consideration like prophylactic cranial irradiation or the addition of other chemotherapy agents or biologic agents to the trimodality approach.

  20. The NASA Exoplanet Archive

    Science.gov (United States)

    Akeson, Rachel L.; Christiansen, Jessie; Ciardi, David R.; Ramirez, Solange; Schlieder, Joshua; Van Eyken, Julian C.; NASA Exoplanet Archive Team

    2017-01-01

    The NASA Exoplanet Archive supports research and mission planning by the exoplanet community by operating a service providing confirmed and candidate planets, numerous project and contributed data sets and integrated analysis tools. We present the current data contents and functionality of the archive including: interactive tables of confirmed and candidate planetary and stellar properties; Kepler planet candidates, threshold-crossing events, data validation and occurrence rate products; light curves from Kepler, CoRoT, SuperWASP, KELT and other ground-based projects; and spectra and radial velocity data from the literature. Tools provided include a transit ephemeris predictor, light curve viewing utilities, a periodogram service and user-configurable interactive tables. The NASA Exoplanet Archive is funded by NASA’s Exoplanet Exploration Program.

  1. 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

  2. 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

  3. Analyzing Archival Intelligence: A Collaboration Between Library Instruction and Archives

    Directory of Open Access Journals (Sweden)

    Merinda Kaye Hensley

    2014-07-01

    Full Text Available 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 well to collaborate with and learn from their experience. This study examines lessons learned from one such collaboration between an instructional services librarian and archivist to evaluate and enhance archival instruction in the University Archives’ Student Life and Culture Archival Program (SLC Archives at the University of Illinois at Urbana-Champaign Library. Based on evaluative data from a student survey and in-depth interviews, the authors offer strategies for meeting and exceeding learning outcomes for archival intelligence more successfully.

  4. 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...

  5. Tumor thrombus

    DEFF Research Database (Denmark)

    Ravina, Mudalsha; Hess, Søren; Chauhan, Mahesh Singh;

    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......), but most other major branches of the venous vasculature was represented, and some patients had thrombi in several vessels. FDG uptake was linear in 7 patients, linear with a dilated vessel in 6 patients, and focal in 7 patients. The mean SUVmax of the primary tumors was 10.3 (range, 2.6-31.2; median, 6...

  6. Hydrolysis Profiles of Formalin Fixed Paraffin-Embedded Tumors Based on IOD (Integrated Optical Density and Nuclear Texture Feature Measurements

    Directory of Open Access Journals (Sweden)

    Margareta Fležar

    1999-01-01

    Full Text Available The aim of the study was to determine optimal hydrolysis time for the Feulgen DNA staining of archival formalin fixed paraffin‐embedded surgical samples, prepared as single cell suspensions for image cytometric measurements. The nuclear texture features along with the IOD (integrated optical density of the tumor nuclei were analysed by an automated high resolution image cytometer as a function of duration of hydrolysis treatment (in 5 N HCl at room temperature. Tissue blocks of breast carcinoma, ovarian serous carcinoma, ovarian serous tumor of borderline malignancy and leiomyosarcoma were included in the study. IOD hydrolysis profiles showed plateau between 30 and 60 min in the breast carcinoma and leiomyosarcoma, and between 40 and 60 min in the ovarian serous carcinoma and ovarian serous tumor of borderline malignancy. Most of the nuclear texture features remained stable after 20 min of hydrolysis treatment. Our results indicate that the optimal hydrolysis time for IOD and for nuclear texture feature measurements, was between 40 and 60 min in the cell preparations from tissue blocks of three epithelial and one soft tissue tumor.

  7. Archiver ailleurs, archiver autrement ? Archiving Elsewhere, Archiving Differently? : The Arab Image Foundation

    Directory of Open Access Journals (Sweden)

    Stefanie Baumann

    2012-05-01

    Full Text Available La « Fondation arabe pour l’image » est un projet archivistique dont le siège est à Beyrouth, et qui est dédié à la collection de photographies du Moyen-Orient prises par des photographes arabes entre 1860 et 1960. Elle a été lancée par un groupe d’artistes en vue d’instaurer une sorte d’histoire alternative de la photographie — qui contrerait les manuels d’histoire de la photographie européens ou américains dans lesquels les représentations photographiques du monde arabe sont souvent construites à partir d’un point de vue orientaliste. La structure et le fonctionnement de ce centre d’archives suivent des logiques hétérogènes remettant en question non seulement le concept d’archive et ses pratiques institutionnelles, mais aussi l’image photographique dans différents contextes, et selon ses différentes propriétés et connotations.The “Arab Image Foundation” is an archival project based in Beirut, dedicated to collecting photographs of the Middle East taken by Arab photographers between 1860 and 1960. It was founded by a group of artists who wanted to establish a kind of alternative history of photography—which would counter European and American textbooks on the history of photography, in which photographic representations of the Arab world are often constructed from an orientalist point of view. The structure and operation of this archive centre follow heterogeneous rationales, calling into question not only the concept of archives and their institutional practices, but also that of the photographic image in different contexts, and according to its different properties and connotations.

  8. 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 ...

  9. Adrenal Gland Tumors: Statistics

    Science.gov (United States)

    ... Gland Tumor: Statistics Request Permissions Adrenal Gland Tumor: Statistics Approved by the Cancer.Net Editorial Board , 03/ ... primary adrenal gland tumor is very uncommon. Exact statistics are not available for this type of tumor ...

  10. Understanding Brain Tumors

    Science.gov (United States)

    ... to Know About Brain Tumors . What is a Brain Tumor? A brain tumor is an abnormal growth
 ... Tumors” from Frankly Speaking Frankly Speaking About Cancer: Brain Tumors Download the full book Questions to ask ...

  11. 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, ...

  12. 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

  13. Treasures in Archived Histopathology Collections: Preserving the Past for Future Understanding (IMCC09)

    Science.gov (United States)

    Extensive collections of histopathology materials from studies of marine and freshwater fish, mollusks, crustaceans, echinoderms, and other organisms are archived in the Registry of Tumors in Lower Animals (RTLA), the U.S. Environmental Protection Agency, NOAA’s National Marine...

  14. Treasures in Archived Histopathology Collections: Preserving the Past for Future Understanding.(SETAC)

    Science.gov (United States)

    Extensive collections of histopathology materials from studies of marine and freshwater mollusks, crustaceans, echinoderms, and other organisms are archived in the Registry of Tumors in Lower Animals (RTLA), the U.S. Environmental Protection Agency, NOAA’s National Marine Fisheri...

  15. Treasures in Archived Histopathology Collections: Preserving the Past for Future Understanding (NACSETAC)

    Science.gov (United States)

    Extensive collections of histopathology materials from studies of marine and freshwater mollusks, crustaceans, echinoderms, and other organisms are archived in the Registry of Tumors in Lower Animals (RTLA), the U.S. Environmental Protection Agency, NOAA’s National Marine Fishe...

  16. Treasures in Archived Histopathology Collections: Preserving the Past for Future Understanding (Histologic)

    Science.gov (United States)

    Extensive collections of histopathology materials from studies of marine and freshwater fish, mollusks, crustaceans, echinoderms, and other organisms are archived at the Registry of Tumors in Lower Animals (RTLA), the U.S. Environmental Protection Agency (EPA), NOAA’s National Ma...

  17. Treasures in Archived Histolopathology Collections: Preserving the Past for Future Understanding

    Science.gov (United States)

    Extensive collections of histopathology materials from studies of marine and freshwater mollusks, crustaceans, echinoderms, and other organisms are archived in the Registry of Tumors in Lower Animals (RTLA), the U.S. Environmental Protection Agency, NOAA’s National Marine Fishe...

  18. Treasures in Archived Histopathology Collections: Preserving the Past for Future Understanding (ISAAH-6)

    Science.gov (United States)

    Extensive collections of histopathology materials from studies of marine and freshwater fish, mollusks, crustaceans, echinoderms, and other organisms are archived in the Registry of Tumors in Lower Animals (RTLA), the U.S. Environmental Protection Agency, NOAA’s National Marine F...

  19. Selected Declassified Chinese Diplomatic Archives

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Since the gradual declassification of China’s diplomatic archives beginning in January 2004, a great number of confidential historical archives have been unveiled to the public, providing experts and scholars with first-hand information of great value, thus facilitating the deepening of international studies on a solid base. For the benefit of our readers, China International Studies will print on a selective basis valuable declassified archives at irregular intervals.

  20. 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.)

  1. 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 the...

  2. 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...

  3. 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...

  4. The utopian Darcy Ribeiro archive.

    Science.gov (United States)

    Heymann, Luciana Quillet

    2012-03-01

    The project in memory of anthropologist, writer and politician Darcy Ribeiro is analyzed, with emphasis on the relationship he had with his personal archives and the creation of the Darcy Ribeiro Foundation, established to give continuity to his 'legacy.' It highlights the influences present in the formation of his archive and presents an ethnography that seeks to restore the historicity of the archive. It reveals the significance attributed to it by the creator himself, and after his death, by those responsible for his memory. From this study, an attempt is made to evaluate the analytical return from socio-historical approaches to the archives.

  5. SODA: Smart Objects, Dumb Archives

    Science.gov (United States)

    Nelson, Michael L.; Maly, Kurt; Zubair, Mohammad; Shen, Stewart N. T.

    2004-01-01

    We present the Smart Object, Dumb Archive (SODA) model for digital libraries (DLs). The SODA model transfers functionality traditionally associated with archives to the archived objects themselves. We are exploiting this shift of responsibility to facilitate other DL goals, such as interoperability, object intelligence and mobility, and heterogeneity. Objects in a SODA DL negotiate presentation of content and handle their own terms and conditions. In this paper we present implementations of our smart objects, buckets, and our dumb archive (DA). We discuss the status of buckets and DA and how they are used in a variety of DL projects.

  6. 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.

  7. Letter to the editor: Microbial diversity in archived soils

    NARCIS (Netherlands)

    Dolfing, J.; Vos, A.; Bloem, J.; Ehlert, P.A.I.; Naumova, N.B.; Kuikman, P.J.

    2004-01-01

    A topic not covered in the recent special Section on Soils: The Final Frontier (11 June, pp. 1613-1637) is the possibility of using modern DNA-based molecular techniques to study microbial diversity in archived soil samples. Like other soil research institutes in countries such as the United Kingdom

  8. 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.

  9. Natural sound archives: past, present and future

    Directory of Open Access Journals (Sweden)

    Ranft Richard

    2004-01-01

    Full Text Available 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 theworld'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 inMexico, Colombia and Brazil are given in individually authored sections in an Appendix.

  10. Draft Genome Sequences of Mycobacterium bovis BZ 31150 and Mycobacterium bovis B2 7505, Pathogenic Bacteria Isolated from Archived Captive Animal Bronchial Washes and Human Sputum Samples in Uganda.

    Science.gov (United States)

    Wanzala, Sylvia I; Nakavuma, Jesca; Travis, Dominic A; Kia, Praiscillia; Ogwang, Sam; Sreevatsan, Srinand

    2015-10-08

    Bovine tuberculosis (BTB), a zoonotic infection of cattle caused by Mycobacterium bovis, results in losses of $3 billion to the global agricultural industry and represents the fourth most important livestock disease worldwide. M. bovis as a source of human infection is likely underreported due to the culture medium conditions used to isolate the organism from sputum or other sample sources. We report here the draft genome sequences of M. bovis BZ 31150, isolated from a bronchial washing from a captive chimpanzee, and M. bovis B2 7505, isolated from a human sputum sample in Uganda.

  11. 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 DGBY Experiments... list Data detail Data name Experiments list Description of data contents Published experime...This Database Database Description Download License Update History of This Database Site Policy | Contact Us Experiments list - DGBY | LSDB Archive ...

  12. Download - RGP gmap | 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 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 ...

  13. 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 ...oomla SEF URLs by Artio About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - Gclust Server | LSDB Archive ...

  14. 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 ...od via FTP Joomla SEF URLs by Artio About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - DGBY | LSDB Archive ...

  15. 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 ...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 ...

  16. 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…

  17. 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,…

  18. The Self-Organized Archive: SPASE, PDS and Archive Cooperatives

    Science.gov (United States)

    King, T. A.; Hughes, J. S.; Roberts, D. A.; Walker, R. J.; Joy, S. P.

    2005-05-01

    Information systems with high quality metadata enable uses and services which often go beyond the original purpose. There are two types of metadata: annotations which are items that comment on or describe the content of a resource and identification attributes which describe the external properties of the resource itself. For example, annotations may indicate which columns are present in a table of data, whereas an identification attribute would indicate source of the table, such as the observatory, instrument, organization, and data type. When the identification attributes are collected and used as the basis of a search engine, a user can constrain on an attribute, the archive can then self-organize around the constraint, presenting the user with a particular view of the archive. In an archive cooperative where each participating data system or archive may have its own metadata standards, providing a multi-system search engine requires that individual archive metadata be mapped to a broad based standard. To explore how cooperative archives can form a larger self-organized archive we will show how the Space Physics Archive Search and Extract (SPASE) data model will allow different systems to create a cooperative and will use Planetary Data System (PDS) plus existing space physics activities as a demonstration.

  19. Patient-Derived Tumor Xenografts Are Susceptible to Formation of Human Lymphocytic Tumors

    Directory of Open Access Journals (Sweden)

    Gennadiy Bondarenko

    2015-09-01

    Full Text Available Patient-derived xenograft (PDX tumor models have emerged as a new approach to evaluate the effects of cancer drugs on patients’ personalized tumor grafts enabling to select the best treatment for the cancer patient and providing a new tool for oncology drug developers. Here, we report that human tumors engrafted in immunodeficient mice are susceptible to formation of B-and T-cell PDX tumors. We xenografted human primary and metastatic tumor samples into immunodeficient mice and found that a fraction of PDX tumors generated from patients’ samples of breast, colon, pancreatic, bladder and renal cancer were histologically similar to lymphocytic neoplasms. Moreover, we found that the first passage of breast and pancreatic cancer PDX tumors after initial transplantation of the tumor pieces from the same human tumor graft could grow as a lymphocytic tumor in one mouse and as an adenocarcinoma in another mouse. Whereas subcutaneous PDX tumors resembling human adenocarcinoma histology were slow growing and non-metastatic, we found that subcutaneous PDX lymphocytic tumors were fast growing and formed large metastatic lesions in mouse lymph nodes, liver, lungs, and spleen. PDX lymphocytic tumors were comprised of B-cells which were Epstein-Barr virus positive and expressed CD45 and CD20. Because B-cells are typically present in malignant solid tumors, formation of B-cell tumor may evolve in a wide range of PDX tumor models. Although PDX tumor models show great promise in the development of personalized therapy for cancer patients, our results suggest that confidence in any given PDX tumor model requires careful screening of lymphocytic markers.

  20. (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…

  1. 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…

  2. Venous Sampling

    Science.gov (United States)

    ... Physician Resources Professions Site Index A-Z Venous sampling Venous sampling is a diagnostic procedure that uses ... the limitations of venous sampling? What is venous sampling? Venous sampling is a diagnostic procedure that involves ...

  3. The Digital Archive Experience

    DEFF Research Database (Denmark)

    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....... These can be coarsely divided into two categories: purely utilitarian websites with information about admission, hours of operation, directions, and the current show. The other - more ambitious - type of website tried to expand the exhibition area of the museum into virtual reality. The idea sounds great....... 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...

  4. 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.

  5. Cholecystokinin expression in tumors

    DEFF Research Database (Denmark)

    Rehfeld, Jens F

    2016-01-01

    in different neuroendocrine tumors; cerebral gliomas and astrocytomas and specific pediatric tumors. Tumor hypersecretion of CCK was recently reported in a patient with a metastatic islet cell tumor and hypercholecystokininemia resulting in a novel tumor syndrome, the cholecystokininoma syndrome. This review...... presents an overview of the cell-specific biogenesis of CCK peptides, and a description of the CCK expression in tumors and of the cholecystokininoma syndrome. Finally, assays for the diagnosis of CCK-producing tumors are reviewed....

  6. THE LA PALMA DATA ARCHIVE

    NARCIS (Netherlands)

    ZUIDERWIJK, EJ; MARTIN, R; RAIMOND, E; VANDIEPEN, GNJ

    1994-01-01

    The operation of the La Palma Data Archive is described in detail. The archive contains data taken since early 1986 with the Isaac Newton Group; 74% of the 260,000 entries are of astronomical sources. Several hundreds of queries are made on the catalog each year, resulting in approximately one reque

  7. Characterisation of particulate matter in different types of archives

    Science.gov (United States)

    Mašková, Ludmila; Smolík, Jiří; Vodička, Petr

    2015-04-01

    To determine the composition of particulate matter (PM) in the indoor environments of four different types of archives (three naturally ventilated and one filtered), intensive size-resolved sampling was performed for four seasons of the year. For reconstituting indoor PM, nine aerosol components were considered. Organic matter was the dominant component of both fine and coarse fractions and represented approximately 50-80% of the PM. In the fine fraction, the next most abundant components were elemental carbon and sulphate, and in the coarse fraction the next most abundant were crustal matter, sulphate and nitrate. The resulting mass closure explained 95(±13)% and 115(±38)% of the gravimetric indoor PM in the fine and coarse size fractions, respectively. The results revealed that all the particles found indoors can be considered to be potentially threatening to the stored materials. The results also showed that the most important source of indoor PM in the naturally ventilated archives was penetration from the outdoor air, whereas in the filtered archive, the concentrations of particles were strongly reduced. In naturally ventilated archives the influence of domestic heating, road traffic and local sources (industrial pollution, camp fires) was observed. Furthermore, activities of the staff were identified as an indoor source of coarse particles in all archives.

  8. Isolation of Plasmodium falciparum by flow-cytometry: implications for single-trophozoite genotyping and parasite DNA purification for whole-genome high-throughput sequencing of archival samples

    Directory of Open Access Journals (Sweden)

    Boissière Anne

    2012-05-01

    Full Text Available Abstract Background Flow cytometry and cell sorting are powerful tools enabling the selection of particular cell types within heterogeneous cell mixtures. These techniques, combined with whole genome amplification that non-specifically amplify small amounts of starting DNA, offer exciting new opportunities for the study of malaria genetics. Among them, two are tested in this paper: (1 single cell genotyping and (2 parasite DNA purification for subsequent whole genome sequencing using shotgun technologies. Methods The method described allows isolation of Plasmodium falciparum trophozoites, genotyping and whole genome sequencing from the blood of infected patients. For trophozoite isolation, parasite and host nuclei are stained using propidium iodide (PI followed by flow cytometry and cell sorting to separate trophozoites from host cells. Before genotyping or sequencing, whole genome amplification is used to increase the amount of DNA within sorted samples. The method has been specifically designed to deal with frozen blood samples. Results and conclusion The results demonstrate that single trophozoite genotyping is possible and that cell sorting can be successfully applied to reduce the contaminating host DNA for subsequent whole genome sequencing of parasites extracted from infected blood samples.

  9. 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.

  10. Planetary Data Archiving Activities of ISRO

    Science.gov (United States)

    Gopala Krishna, Barla; D, Rao J.; Thakkar, Navita; Prashar, Ajay; Manthira Moorthi, S.

    ISRO has launched its first planetary mission to moon viz., Chandrayaan-1 on October 22, 2008. This mission carried eleven instruments; a wealth of science data has been collected during its mission life (November 2008 to August 2009), which is archived at Indian Space Science Data Centre (ISSDC). The data centre ISSDC is responsible for the Ingest, storage, processing, Archive, and dissemination of the payload and related ancillary data in addition to real-time spacecraft operations support. ISSDC is designed to provide high computation power, large storage and hosting a variety of applications necessary to support all the planetary and space science missions of ISRO. State-of-the-art architecture of ISSDC provides the facility to ingest the raw payload data of all the science payloads of the science satellites in automatic manner, processes raw data and generates payload specific processed outputs, generate higher level products and disseminates the data sets to principal investigators, guest observers, payload operations centres (POC) and to general public. The data archive makes use of the well-proven archive standards of the Planetary Data System (PDS). The long term Archive for five payloads of Chandrayaan-1 data viz., TMC, HySI, SARA, M3 and MiniSAR is released from ISSDC on19th April 2013 (http://www.issdc.gov.in) to the users. Additionally DEMs generated from possible passes of Chandrayaan-1 TMC stereo data and sample map sheets of Lunar Atlas are also archived and released from ISSDC along with the LTA. Mars Orbiter Mission (MOM) is the recent planetary mission launched on October 22, 2013; currently enroute to MARS, carrying five instruments (http://www.isro.org) viz., Mars Color Camera (MCC) to map various morphological features on Mars with varying resolution and scales using the unique elliptical orbit, Methane Sensor for Mars (MSM) to measure total column of methane in the Martian atmosphere, Thermal Infrared Imaging Spectrometer (TIS) to map surface

  11. Molecular detection of EWS-Ets fusion transcripts and their clinicopathologic significance in Ewing's sarcoma/peripheral primitive neuroectodermal tumor

    Institute of Scientific and Technical Information of China (English)

    WANG Hua; ZHENG Jie; WANG Yu-ping; YANG Yu; YOU Jiang-feng

    2005-01-01

    Background Ewing's sarcoma/peripheral primitive neuroectodermal tumor (ES/pPNET) is often difficult to distinguish from other small round cell tumors. The EWS-Ets gene fusions that result from chromosomal translocations in this tumor provide potential molecular diagnostic markers. To apply these molecular markers to commonly available archival materials, we evaluated the feasibility of detecting EWS-Ets including EWS-Fli1 and EWS-ERG fusion transcripts in paraffin-embedded tissues and its diagnostic value for detecting ES/pPNET.Methods Thirteen paraffin-embedded samples of ES/pPNETs were retrieved from archives. Thirteen cases of other tumors with small round cell features (including rhabdomyosarcoma, neuroblastoma, lymphoma, small cell carcinoma, and desmoplastic small round cell tumor) were used as negative controls. Β-actin and β2-microglobulin were used as internal controls. A nested reverse transcriptase-polymerase chain reaction (RT-PCR)-based assay was performed to detect the EWS-Fli1 and EWS-ERG fusion transcripts.Results β-actin and β2-microglobulin were detected in 10/13 and 13/13 ES/pPNETs, respectively. EWS-Fli1 fusion transcripts were detected in 11 of 13 (85%) ES/pPNETs. Three chimeric transcripts, all EWS-Fli1, were detected in ES/pPNET samples. Among 11 EWS-Fli1-positive cases, 7 cases had a typeⅠfusion transcript involving fusion of EWS exon 7 with Fli1 exon 6, 2 cases had a typeⅡfusion transcript involving EWS exon 7 with Fli1 exon 5, and 2 cases expressed fusion transcripts involving EWS exon 7 and Fli1 exon 8. Type Ⅰ EWS-Fli1 fusion predominated over other types. Fusion types could not be distinguished in the remaining 2 cases. Thirteen negative controls did not show detectable chimeric messages. There was a significant relationship between EWS-Fli1 fusion transcripts and CD99 expression. Conclusions Molecular detection of EWS-Fli1 fusion transcripts in formalin-fixed paraffin-embedded material by nested RT-PCR is feasible and is

  12. BRAF mutation analysis in circulating free tumor DNA of melanoma patients treated with BRAF inhibitors.

    Science.gov (United States)

    Gonzalez-Cao, Maria; Mayo-de-Las-Casas, Clara; Molina-Vila, Miguel A; De Mattos-Arruda, Leticia; Muñoz-Couselo, Eva; Manzano, Jose L; Cortes, Javier; Berros, Jose P; Drozdowskyj, Ana; Sanmamed, Miguel; Gonzalez, Alvaro; Alvarez, Carlos; Viteri, Santiago; Karachaliou, Niki; Martin Algarra, Salvador; Bertran-Alamillo, Jordi; Jordana-Ariza, Nuria; Rosell, Rafael

    2015-12-01

    BRAFV600E is a unique molecular marker for metastatic melanoma, being the most frequent somatic point mutation in this malignancy. Detection of BRAFV600E in blood could have prognostic and predictive value and could be useful for monitoring response to BRAF-targeted therapy. We developed a rapid, sensitive method for the detection and quantification of BRAFV600E in circulating free DNA (cfDNA) isolated from plasma and serum on the basis of a quantitative 5'-nuclease PCR (Taqman) in the presence of a peptide-nucleic acid. We validated the assay in 92 lung, colon, and melanoma archival serum and plasma samples with paired tumor tissue (40 wild-type and 52 BRAFV600E). The correlation of cfDNA BRAFV600E with clinical parameters was further explored in 22 metastatic melanoma patients treated with BRAF inhibitors. Our assay could detect and quantify BRAFV600E in mixed samples with as little as 0.005% mutant DNA (copy number ratio 1 : 20 000), with a specificity of 100% and a sensitivity of 57.7% in archival serum and plasma samples. In 22 melanoma patients treated with BRAF inhibitors, the median progression-free survival was 3.6 months for those showing BRAFV600E in pretreatment cfDNA compared with 13.4 months for those in whom the mutation was not detected (P=0.021). Moreover, the median overall survival for positive versus negative BRAFV600E tests in pretreatment cfDNA differed significantly (7 vs. 21.8 months, P=0.017). This finding indicates that the sensitive detection and accurate quantification of low-abundance BRAFV600E alleles in cfDNA using our assay can be useful for predicting treatment outcome.

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

    Directory of Open Access Journals (Sweden)

    Firas M. Abed

    2016-05-01

    Full Text Available 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.

  14. Lung Carcinoid Tumor: Surgery

    Science.gov (United States)

    ... Disease Lung Carcinoid Tumor Treating Lung Carcinoid Tumors Surgery to Treat Lung Carcinoid Tumors Surgery is the ... be cured by surgery alone. Types of lung surgery Different operations can be used to treat (and ...

  15. Tumors and Pregnancy

    Science.gov (United States)

    Tumors during pregnancy are rare, but they can happen. Tumors can be either benign or malignant. Benign tumors aren't cancer. Malignant ones are. The most common cancers in pregnancy are breast cancer, cervical cancer, lymphoma, and melanoma. ...

  16. Neuroendocrine Tumor: Statistics

    Science.gov (United States)

    ... Tumor > Neuroendocrine Tumor: Statistics Request Permissions Neuroendocrine Tumor: Statistics Approved by the Cancer.Net Editorial Board , 11/ ... the body. It is important to remember that statistics on how many people survive this type of ...

  17. Brain Tumors (For Parents)

    Science.gov (United States)

    ... Old Feeding Your 1- to 2-Year-Old Brain Tumors KidsHealth > For Parents > Brain Tumors Print A ... radiation therapy or chemotherapy, or both. Types of Brain Tumors There are many different types of brain ...

  18. Childhood Brain Tumors

    Science.gov (United States)

    Brain tumors are abnormal growths inside the skull. They are among the most common types of childhood ... still be serious. Malignant tumors are cancerous. Childhood brain and spinal cord tumors can cause headaches and ...

  19. Valproic acid reduces the tolerability of temsirolimus in children and adolescents with solid tumors.

    Science.gov (United States)

    Coulter, Don W; Walko, Christine; Patel, Jai; Moats-Staats, Billie M; McFadden, Andrew; Smith, Scott V; Khan, Wasiuddin A; Bridges, Arlene S; Deal, Allison M; Oesterheld, Javier; Davis, Ian J; Blatt, Julie

    2013-04-01

    A pediatric study has established a maximum tolerated dose (MTD) for temsirolimus (Tem) of more than 150 mg/m intravenously/week. A phase I trial was conducted to establish the MTD for Tem in combination with valproic acid (VPA) in children and adolescents with refractory solid tumors. The secondary aims included expression of mammalian target of rapamycin (mTOR) markers on archival tumor tissue; Tem pharmacokinetics; assessment of histone acetylation (HA); and tumor response. Patients were treated with VPA (5 mg/kg orally three times daily) with a target serum level of 75-100 mcg/ml. Tem was started at an initial dose of 60 mg/m/week. Pharmacokinetics and HA measurements were performed during weeks 1 and 5. Two of the first three patients experienced dose-limiting toxicity (grade 3 mucositis). Tem at 35 mg/m/week was found to be tolerable. Peak Tem concentrations were higher in all patients compared with those in previously published reports of single agent Tem. Increases in HA are correlated with VPA levels. All tumor samples expressed mTORC1 and mTORC2. An objective response was observed in one patient (melanoma), whereas transient stable disease was observed in four other patients (spinal cord ependymoma, alveolar soft part sarcoma, medullary thyroid carcinoma, and hepatocellular carcinoma). The MTD of Tem when administered with VPA is considerably lower than when used as a single agent, with mucositis the major dose-limiting toxicity. The combination merits further study and may have activity in melanoma. Attention to drug-drug interactions will be important in future multiagent trials including Tem.

  20. Necessity of Microdissecting Different Tumor Components in Pulmonary Tumor Pyrosequencing

    Directory of Open Access Journals (Sweden)

    Dahui Qin

    2016-01-01

    Full Text Available Microdissection is a useful method in tissue sampling prior to molecular testing. Tumor heterogeneity imposes new challenges for tissue sampling. Different microdissecting methods have been employed in face of such challenge. We improved our microdissection method by separately microdissecting the morphologically different tumor components. This improvement helped the pyrosequencing data analysis of two specimens. One specimen consisted of both adenocarcinoma and neuroendocrine components. When both tumor components were sequenced together for KRAS (Kirsten rat sarcoma viral oncogene homolog gene mutations, the resulting pyrogram indicated that it was not a wild type, suggesting that it contained KRAS mutation. However, the pyrogram did not match any KRAS mutations and a conclusion could not be reached. After microdissecting and testing the adenocarcinoma and neuroendocrine components separately, it was found that the adenocarcinoma was positive for KRAS G12C mutation and the neuroendocrine component was positive for KRAS G12D mutation. The second specimen consisted of two morphologically different tumor nodules. When microdissected and sequenced separately, one nodule was positive for BRAF (v-raf murine sarcoma viral oncogene homolog B1 V600E and the other nodule was wild type at the BRAF codon 600. These examples demonstrate that it is necessary to microdissect morphologically different tumor components for pyrosequencing.

  1. A Comparison of Fresh Frozen vs. Formalin-Fixed, Paraffin-Embedded Specimens of Canine Mammary Tumors via Branched-DNA Assay

    Directory of Open Access Journals (Sweden)

    Florenza Lüder Ripoli

    2016-05-01

    Full Text Available Mammary neoplasms are the tumors most affecting female dogs and women. Formalin-fixed, paraffin-embedded (FFPE tissues are an invaluable source of archived biological material. Fresh frozen (FF tissue is considered ideal for gene expression analysis. However, strategies based on FFPE material offer several advantages. Branched-DNA assays permit a reliable and fast workflow when analyzing gene expression. The aim of this study was to assess the comparability of the branched-DNA assay when analyzing certain gene expression patterns between FF and FFPE samples in canine mammary tumors. RNA was isolated from 109 FFPE samples and from 93 FF samples of different canine mammary tissues. Sixteen (16 target genes (Tp53; Myc; HMGA1; Pik3ca; Mcl1; MAPK3; FOXO3; PTEN; GATA4; PFDN5; HMGB1; MAPK1; BRCA2; BRCA1; HMGA2; and Her2 were analyzed via branched-DNA assay (b-DNA. ACTB, GAPDH, and HPRT1 were used as data normalizers. Overall, the relative gene expression of the two different origins of samples showed an agreement of 63%. Still, care should be taken, as FFPE specimens showed lower expression of the analyzed targets when compared to FF samples. The fact that the gene expression in FFPE proved to be lower than in FF specimens is likely to have been caused by the effect of storage time. ACTB had the best performance as a data normalizer.

  2. EPRINT ARCHIVE USER SURVEY

    CERN Document Server

    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.)

  3. Detection of EWS-FLI1 fusion transcripts in paraffin embedded tissues of peripheral primitive neuroectodermal tumors by nested reverse transcription polymerase chain reaction

    Institute of Scientific and Technical Information of China (English)

    Qixing Gong; Qinhe Fan; Zhihong Zhang; Weiming Zhang

    2005-01-01

    Objective: To assess the feasibility and significance of detecting EWS-FLIlfusion transcripts in paraffin embedded tissues of peripheral primitive neuroectodermal tumors (PNETs) by nested reverse transcription polymerase chain reaction (RT-PCR).Methods: Twelve formalin-fixed and paraffin-embedded (FFPE) samples of PNET were retrieved from archive and consultation materials,together with eight cases of controlled tumor. EWS-FLI1 fusion transcripts were detected by nested RT-PCR. Home-keeping gene β-actin was used to detect the quality of mRNA. Results: β-actin mRNA was detected in 9 of the 12 tumor cases. EWS-FLI1 fusion transcripts were detected in 6 cases, among which 4 had a "type 1" fusion transcript and 2 had a "type 2" fusion transcript. None of the controlled tumor was detected the fusion gene. Conclusion: RT-PCR is a feasible method for the detection of EWS-FLI1 fusion transcripts in FFPE tissues in PNET and the result is meaningful in differential diagnosis and prognostic evaluation.

  4. 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.

  5. Download - DMPD | 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 ...MB) - Downlaod via FTP Joomla SEF URLs by Artio About This Database Database Description Download License Update History

  6. 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

  7. 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.

  8. Prognostic impact of tumor MET expression among patients with stage IV gastric cancer

    DEFF Research Database (Denmark)

    Erichsen, Rune; Kelsh, Michael A; Oliner, Kelly S;

    2016-01-01

    PURPOSE: We aimed to investigate the prevalence and prognostic impact of tumor mesenchymal epithelial transition factor (MET) expression in stage IV gastric cancers in a real-world clinical setting because existing evidence is sparse. METHODS: The study included archived cancer specimens from 103...

  9. SACS: Spitzer Archival Cluster Survey

    Science.gov (United States)

    Stern, Daniel

    Emerging from the cosmic web, galaxy clusters are the most massive gravitationally bound structures in the universe. Thought to have begun their assembly at z > 2, clusters provide insights into the growth of large-scale structure as well as the physics that drives galaxy evolution. Understanding how and when the most massive galaxies assemble their stellar mass, stop forming stars, and acquire their observed morphologies in these environments remain outstanding questions. The redshift range 1.3 galaxies start to become the dominant population in cluster cores, and star formation in spiral galaxies is being quenched. Until recently, however, this redshift range was essentially unreachable with available instrumentation, with clusters at these redshifts exceedingly challenging to identify from either ground-based optical/nearinfrared imaging or from X-ray surveys. Mid-infrared (MIR) imaging with the IRAC camera on board of the Spitzer Space Telescope has changed the landscape. High-redshift clusters are easily identified in the MIR due to a combination of the unique colors of distant galaxies and a negative k-correction in the 3-5 μm range which makes such galaxies bright. Even 90-sec observations with Spitzer/IRAC, a depth which essentially all extragalactic observations in the archive achieve, is sufficient to robustly detect overdensities of L* galaxies out to z~2. Here we request funding to embark on a ambitious scientific program, the “SACS: Spitzer Archival Cluster Survey”, a comprehensive search for the most distant galaxy clusters in all Spitzer/IRAC extragalactic pointings available in the archive. With the SACS we aim to discover ~2000 of 1.3 star formation and AGN activity out to z~2, and to study the effect of star-forming galaxies and AGNs on cosmological results from ongoing Sunyaev-Zel'dovich (SZ) and X-ray cluster surveys. The identified clusters will be valuable for both astrophysics and cosmology. In terms of astrophysics, the redshift probed

  10. The VISTA Science Archive

    CERN Document Server

    Cross, Nicholas J G; Mann, Robert G; Read, Mike A; Sutorius, Eckhard T W; Blake, Robert P; Holliman, Mark S; Hambly, Nigel C; Emerson, Jim P; Lawrence, Andrew; Noddle, Keith T

    2012-01-01

    We describe the VISTA Science Archive (VSA) and its first public release of data from five of the six VISTA Public Surveys. The VSA exists to support the VISTA Surveys through their lifecycle: the VISTA Public Survey consortia can use it during their quality control assessment of survey data products before submission to the ESO Science Archive Facility (ESO SAF); it supports their exploitation of survey data prior to its publication through the ESO SAF; and, subsequently, it provides the wider community with survey science exploitation tools that complement the data product repository functionality of the ESO SAF. This paper has been written in conjunction with the first public release of public survey data through the VSA and is designed to help its users understand the data products available and how the functionality of the VSA supports their varied science goals. We describe the design of the database and outline the database-driven curation processes that take data from nightly pipeline-processed and ca...

  11. Evaluation of continued storage of samples at the 325 Laboratory

    Energy Technology Data Exchange (ETDEWEB)

    McVey, C.B.

    1996-01-01

    This report provides identification of potential Program users for samples that are archived at Pacific Northwest National Laboratory (PNNL) facilities, establishes cost releated to packaging and transportation of these samples to 222-S, for continued storage at 325 facilities, disposal and transfer costs. The report provides a recommendation to dispose of 20 samples, transfer 99 samples to PNNL and to continue storage of the remaining samples at PNNL`s 325 facility.

  12. 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,...

  13. Updates in Orbital Tumors

    Institute of Scientific and Technical Information of China (English)

    Nila; F.Moeloek

    1993-01-01

    Orbital anatomy, the clinical features of orbital tumors, the recent development of the diagnosis and management of orbital tumors were described. The incidence of orbital tumors in Dr. Cipto Mangunkusumo Hospital in the past years were introduced. The principle of management of orbital tumors and their prognosis were discussed.

  14. Epidemiology of Brain Tumors.

    Science.gov (United States)

    McNeill, Katharine A

    2016-11-01

    Brain tumors are the commonest solid tumor in children, leading to significant cancer-related mortality. Several hereditary syndromes associated with brain tumors are nonfamilial. Ionizing radiation is a well-recognized risk factor for brain tumors. Several industrial exposures have been evaluated for a causal association with brain tumor formation but the results are inconclusive. A casual association between the common mutagens of tobacco, alcohol, or dietary factors has not yet been established. There is no clear evidence that the incidence of brain tumors has changed over time. This article presents the descriptive epidemiology of the commonest brain tumors of children and adults.

  15. Supratentorial tumors; Supratentorielle Tumoren

    Energy Technology Data Exchange (ETDEWEB)

    Grunwald, I.; Dillmann, K.; Roth, C.; Backens, M.; Reith, W. [Universitaetsklinikum Saarland, Homburg (Germany). Klinik fuer Diagnostische und Interventionelle Neuroradiologie

    2007-06-15

    Magnetic resonance imaging is a routine diagnostic measure for a suspected intracerebral mass. Computed tomography is usually also indicated. Further diagnostic procedures as well as the interpretation of the findings vary depending on the tumor location. This contribution discusses the symptoms and diagnostics for supratentorial tumors separated in relation to their intra- or extracranial location. Supratentorial tumors include astrocytoma, differentiated by their circumscribed and diffuse growth, ganglioglioma, ependyoma, neurocytoma, primitive neuroectodermal tumors (PNET), oligodendroglioma, dysembryoplastic neuroepithelial tumors (DNET), meningoangiomatosis, pineal tumors, hamartoma, lymphoma, craniopharyngeoma and metastases. The supratentorial extracranial tumors include the choroid plexus, colloid cysts, meningeoma, infantile myofibromatosis and lipoma. The most common subforms, especially of astrocytoma, will also be presented. (orig.)

  16. Cardiac Tumors; Tumeurs cardiaques

    Energy Technology Data Exchange (ETDEWEB)

    Laissy, J.P.; Fernandez, P. [Centre Hospitalier Universitaire Bichat Claude Bernard, Service d' Imagerie, 76 - Rouen (France); Mousseaux, E. [Hopital Europeen Georges Pompidou (HEGP), Service de Radiologie Cardio Vasculaire et Interventionnelle, 75 - Paris (France); Dacher, J.N. [Centre Hospitalier Universitaire Charles Nicolle, 75 - Rouen (France); Crochet, D. [Centre Hospitalier Universitaire, Hopital Laennec, Centre Hemodynamique, Radiologie Thoracique et Vasculaire, 44 - Nantes (France)

    2004-04-01

    Metastases are the most frequent tumors of the heart even though they seldom are recognized. Most primary cardiac tumors are benign. The main role of imaging is to differentiate a cardiac tumor from thrombus and rare pseudo-tumors: tuberculoma, hydatid cyst. Echocardiography is the fist line imaging technique to detect cardiac tumors, but CT and MRl arc useful for further characterization and differential diagnosis. Myxoma of the left atrium is the most frequent benign cardiac tumor. It usually is pedunculated and sometimes calcified. Sarcoma is the most frequent primary malignant tumor and usually presents as a sessile infiltrative tumor. Lymphoma and metastases are usually recognized by the presence of known tumor elsewhere of by characteristic direct contiguous involvement. Diagnosing primary and secondary pericardial tumors often is difficult. Imaging is valuable for diagnosis, characterization, pre-surgical evaluation and follow-up. (author)

  17. Sample Design.

    Science.gov (United States)

    Ross, Kenneth N.

    1987-01-01

    This article considers various kinds of probability and non-probability samples in both experimental and survey studies. Throughout, how a sample is chosen is stressed. Size alone is not the determining consideration in sample selection. Good samples do not occur by accident; they are the result of a careful design. (Author/JAZ)

  18. Balanced sampling

    NARCIS (Netherlands)

    Brus, D.J.

    2015-01-01

    In balanced sampling a linear relation between the soil property of interest and one or more covariates with known means is exploited in selecting the sampling locations. Recent developments make this sampling design attractive for statistical soil surveys. This paper introduces balanced sampling

  19. National Archives and Records Administration Employee Locator

    Data.gov (United States)

    National Archives and Records Administration — The National Archives and Records Administration Employee Locator is an online system that provides the name, office symbol, location, room, telephone number, and...

  20. 50 CFR 635.33 - Archival tags.

    Science.gov (United States)

    2010-10-01

    ...) Implantation report. Any person affixing or implanting an archival tag into a regulated species must obtain... catch, possess, retain, and land an Atlantic HMS in which an archival tag has been implanted or...

  1. Slice Sampling

    CERN Document Server

    Neal, R M

    2000-01-01

    Markov chain sampling methods that automatically adapt to characteristics of the distribution being sampled can be constructed by exploiting the principle that one can sample from a distribution by sampling uniformly from the region under the plot of its density function. A Markov chain that converges to this uniform distribution can be constructed by alternating uniform sampling in the vertical direction with uniform sampling from the horizontal `slice' defined by the current vertical position, or more generally, with some update that leaves the uniform distribution over this slice invariant. Variations on such `slice sampling' methods are easily implemented for univariate distributions, and can be used to sample from a multivariate distribution by updating each variable in turn. This approach is often easier to implement than Gibbs sampling, and more efficient than simple Metropolis updates, due to the ability of slice sampling to adaptively choose the magnitude of changes made. It is therefore attractive f...

  2. Metabolomic profiling from formalin-fixed, paraffin-embedded tumor tissue using targeted LC/MS/MS: application in sarcoma.

    Directory of Open Access Journals (Sweden)

    Andrew D Kelly

    Full Text Available The relatively new field of onco-metabolomics attempts to identify relationships between various cancer phenotypes and global metabolite content. Previous metabolomics studies utilized either nuclear magnetic resonance spectroscopy or gas chromatography/mass spectrometry, and analyzed metabolites present in urine and serum. However, direct metabolomic assessment of tumor tissues is important for determining altered metabolism in cancers. In this respect, the ability to obtain reliable data from archival specimens is desirable and has not been reported to date. In this feasibility study, we demonstrate the analysis of polar metabolites extracted directly from ten formalin-fixed, paraffin-embedded (FFPE specimens, including five soft tissue sarcomas and five paired normal samples. Using targeted liquid chromatography-tandem mass spectrometry (LC/MS/MS via selected reaction monitoring (SRM, we detect an average of 106 metabolites across the samples with excellent reproducibility and correlation between different sections of the same specimen. Unsupervised hierarchical clustering and principal components analysis reliably recovers a priori known tumor and normal tissue phenotypes, and supervised analysis identifies candidate metabolic markers supported by the literature. In addition, we find that diverse biochemical processes are well-represented in the list of detected metabolites. Our study supports the notion that reliable and broadly informative metabolomic data may be acquired from FFPE soft tissue sarcoma specimens, a finding that is likely to be extended to other malignancies.

  3. Researchers’ Attitudes and Behaviour to Data Archiving Policies and Practice is Typified by Low Awareness and Little Planning. A Review of: Perry, Carol Marie. “Archiving of Publicly Funded Research Data: A Survey of Canadian Researchers.” Government Information Quarterly 25 (2008: 133-48.

    Directory of Open Access Journals (Sweden)

    Gaby Haddow

    2008-12-01

    Full Text Available Objective – To assess researchers’ attitudes and behaviours in relation to archiving research data and to determine researchers’views about policies relating to data archiving.Design – Survey.Setting – Canadian universities.Subjects – Social sciences and humanities researchers from universities across Canada.Methods – A questionnaire comprising 15 questions was mailed to 175 researchers randomly sampled from a publicly available list of 5,821 individuals who had received grants and awards from the Social Sciences and Humanities Research Council of Canada (SSHRC. From this sample, 75 (43.4% responded within the five week time-frame stipulated. The questionnaire was constructed using four existing surveys and asked researchers for information about: geographical location, years of research experience, research funding sources, current plans to archive research data, awareness of archiving policies, attitude to mandated research data archiving, effect of mandatory data archiving policies on grant-seeking, attitude to making archived research data accessible, and use of research data collected by others. The questionnaire also included space for respondents to make comments. Responses to each question were analyzed, followed by a series of cross-analyses to investigate associations between findings. These cross-analyses include: whether attitudes to making data accessible differed according to length of experience, support for a national archive initiative, or agreement with a mandatory policy; and whether plans to archive research data were associated with awareness of policy, agreement with mandatory policy, or funding from government agencies other than SSHRC. Some cross-analyses were conducted between responses to questions and the comments provided by respondents. Most of the questionnaire responses were analyzed as percentages in two categories only. For example, length of service responses were presented as “up to 20years

  4. 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.

  5. Archival analyses of eyewitness identification test outcomes: what can they tell us about eyewitness memory?

    Science.gov (United States)

    Horry, Ruth; Halford, Paul; Brewer, Neil; Milne, Rebecca; Bull, Ray

    2014-02-01

    Several archival studies of eyewitness identification have been conducted, but the results have been inconsistent and contradictory. We identify some avoidable pitfalls that have been present in previous analyses and present new data that address these pitfalls. We explored associations among various estimator variables and lineup outcomes for 833 "real life" lineups, including 588 lineups in which corroborating evidence of the suspect's guilt existed. Suspect identifications were associated with exposure duration, viewing distance, and the age of the witness. Nonidentifications were associated with the number of perpetrators. We also consider some of the inherent, unavoidable limitations with archival studies and consider what such studies can really tell researchers. We conclude that differences in sampling prohibit sensible comparisons between the results of laboratory and archival studies, and that the informational value of archival studies is actually rather limited.

  6. Multimodality Imaging of Tumor Response to Doxil

    Directory of Open Access Journals (Sweden)

    Fan Zhang, Lei Zhu, Gang Liu, Naoki Hida, Guangming Lu, Henry S. Eden, Gang Niu, Xiaoyuan Chen

    2011-01-01

    Full Text Available Purpose: Early assessment of tumor responses to chemotherapy could enhance treatment outcomes by ensuring that, from the beginning, treatments meet the individualized needs of patients. In this study, we applied multiple modality molecular imaging techniques to pre-clinical monitoring of early tumor responses to Doxil, focusing on imaging of apoptosis.Methods: Mice bearing UM-SCC-22B human head and neck squamous cancer tumors received either PBS or 1 to 2 doses of Doxil® (doxorubicin HCl liposome injection (10 mg/kg/dose. Bioluminescence signals from an apoptosis-responsive reporter gene were captured for apoptosis evaluation. Tumor metabolism and proliferation were assessed by 18F-FDG and 3'-18F-fluoro-3'-deoxythymidine (18F-FLT positron emission tomography. Diffusion-weighted magnetic resonance imaging (DW-MRI was performed to calculate averaged apparent diffusion coefficients (ADCs for the whole tumor volume. After imaging, tumor samples were collected for histological evaluation, including terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL, anti-CD31, and Ki-67 immunostaining.Results: Two doses of Doxil significantly inhibited tumor growth. Bioluminescence imaging (BLI indicated apoptosis of tumor cells after just 1 dose of Doxil treatment, before apparent tumor shrinkage. 18F-FDG and 18F-FLT PET imaging identified decreased tumor metabolism and proliferation at later time points than those at which BLI indicated apoptosis. MRI measurements of ADC altered in response to Doxil, but only after tumors were treated with 2 doses. Decreased tumor proliferation and increased apoptotic cells were confirmed by changes of Ki-67 index and apoptotic ratio.Conclusion: Our study of tumor responses to different doses of Doxil demonstrated that it is essential to combine apoptosis imaging strategies with imaging of other critical biological or pathological pathways, such as metabolism and proliferation, to improve clinical decision making

  7. Gastrointestinal Neuroendocrine Tumors: Pancreatic Endocrine Tumors

    OpenAIRE

    2008-01-01

    Pancreatic endocrine tumors (PETs) have long fascinated clinicians and investigators despite their relative rarity. Their clinical presentation varies depending upon whether the tumor is functional or not and also according to the specific hormonal syndrome produced. Tumors may be sporadic or inherited but little is known about their molecular pathology, especially the sporadic forms. Chromogranin A appears to be the most useful serum marker for diagnosis, staging and monitoring. Initially, t...

  8. In through the Archive

    DEFF Research Database (Denmark)

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

    2014-01-01

    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...... of different qualities i.e. sounds they like or dislike, sounds they find intimidating or pleasing, sounds that evoke imaginations, good or bad connotations, or sounds that represent their home, their favourite place etc. Additionally, we have collected several lengthy interviews with people who have lived...... ages including children in the local youth club to collect sounds and stories from their neighbourhood by handing out a range of sound probes, containing small portable sound recorders, note books and more. The participants were encouraged to collect and notate sounds from the neighbourhood...

  9. 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...... of different qualities i.e. sounds they like or dislike, sounds they find intimidating or pleasing, sounds that evoke imaginations, good or bad connotations, or sounds that represent their home, their favourite place etc. Additionally, we have collected several lengthy interviews with people who have lived...... ages including children in the local youth club to collect sounds and stories from their neighbourhood by handing out a range of sound probes, containing small portable sound recorders, note books and more. The participants were encouraged to collect and notate sounds from the neighbourhood...

  10. Electric-Magnetic-Waves Resident Archive for Polar (EMWRAP)

    Science.gov (United States)

    Hart, R.; Chi, P. J.; Faden, J.; Granroth, L. J.; Menietti, J. D.; Mozer, F. S.; Russell, C. T.; Vernetti, J.

    2010-12-01

    EMWRAP is a NASA-sponsored resident archive (RA) for the Electric Field Instrument (EFI), Magnetic Field Experiment (MFE), and Plasma Wave Instrument (PWI) data collected by the Polar satellite. The main objective of EMWRAP is to maintain the data availability to the scientific community after Polar ended its operation in April 2008. With more than eleven years of observations, Polar sampled all the regions of the magnetosphere inside a distance of 9 Re, and its dataset continues to be valuable for magnetospheric research through the use of these data either alone or with other joint observations. In this presentation we demonstrate the existing capability of disseminating Polar EFI, MFE, and PWI data, and we also describe the ongoing efforts to construct the RA, such as: (1) Establishing a central web server and two backup servers, each equipped with the entire data archive to safeguard against data loss; (2) Generating documentation for the data sets following widely accepted standards, and archiving the expertise in data interpretation for the use by future researchers; (3) Providing the metadata to fully integrate with the Virtual Magnetospheric Observatory (VMO) and other components of NASA's Heliophysics Data Environment (HPDE). When these essential functions are established, a copy of the data products and documentation will be submitted to NSSDC for permanent archives.

  11. 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.)

  12. 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...

  13. Discussion Forum: Federal Records and Archives.

    Science.gov (United States)

    Bradsher, James Gregory

    1987-01-01

    Introduces various topics relating to federal records and archives, including descriptions of federal records, permanent records, and archives; responsibility for the creation and maintenance of these items; the policy for deciding which records become archives; and legal issues relating to records and access to them. (Author/CLB)

  14. Using polarization-sensitive optical coherence tomography to identify tumor stromal fibrosis and increase tumor biopsy yield (Conference Presentation)

    Science.gov (United States)

    Hariri, Lida P.; Adams, David C.; Miller, Alyssa J.; Mino-Kenudson, Mari; Suter, Melissa J.

    2016-03-01

    Tissue biopsy is the principal method used to diagnose tumors in a variety of organ systems. It is essential to maximize tumor yield in biopsy specimens for both clinical diagnostic and research purposes. This is particularly important in tumors where additional tissue is needed for molecular analysis to identify patients who would benefit from mutation-specific targeted therapy, such as in lung carcinomas. Inadvertent sampling of fibrotic stroma within tumor nodules contaminates biopsies, decreases tumor yield, and can impede diagnosis. The ability to assess tumor composition and guide biopsy site selection in real time is likely to improve diagnostic yield. Polarization sensitive OCT (PS-OCT) measures birefringence in organized tissues, such as collagen, and could be used to distinguish tumor from fibrosis. In this study, PS-OCT was obtained in 65 lung nodule samples from surgical resection specimens containing varying ratios of tumor and fibrosis. PS-OCT was obtained with either a custom-built helical scanning catheter (0.8 or 1.6mm in diameter) or a dual-axis bench top scanner. Strong birefringence was observed in nodules containing dense fibrosis, with no birefringence in adjacent regions of tumor. Tumors admixed with early, loosely-organized collagen demonstrated mild-to-moderate birefringence, and tumors with little collagen content showed little to no birefringent signal. PS-OCT provides significant insights into tumor nodule composition, and has potential to differentiate tumor from stromal fibrosis during biopsy site selection to increase diagnostic tumor yield.

  15. Childhood Fibroblastic and Myofibroblastic Tumors: A Multicenter Documentation and Review of the Literature

    Directory of Open Access Journals (Sweden)

    Ayper KAÇAR

    2012-01-01

    Full Text Available Objective: In this study, we aimed to give a documentation of 37 cases of childhood fibroblastic/myofibroblastic tumors retrieved from the archives of 6 reference centers in Ankara along with a comprehensive review on the subject.Material and Method: A retrospective archive search was carried out for the period between 2006-2010 in 6 reference centers in Ankara covering patients with ages ranging between 0-18 years. All the tumors categorized under fibroblastic and myofibroblastic group according to World Health Organization criteria were collected.Results: The study comprised 407 soft tissue tumors in total. Fibroblastic/myofibroblastic tumors constituted 9,1 % (37 cases of these tumors. According to histopathology; 16 cases were categorized as fibromatosis, 8 cases as inflammatory myofibroblastic tumor, 6 cases as infantile fibrous hamartoma, 3 cases as nodular fasciitis and 2 cases as infantile myofibroblastic tumor/myofibromatosis and 1 case as cranial fasciitis. The only malignant case was an infantile fibrosarcoma.Conclusion: Infantile fibrosarcoma was lower than reported series and a male predominance was noted. The low incidence of newly described entities as well suggests that these tumors may have been unrecognized.

  16. Expressions of matrix metalloproteinase-9 and tissue inhibitor of metalloproteinase-1 in malignant peripheral nerve sheath tumor

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    BACKGROUND: Matrix metalloproteinase-9 (MMP-9) can degrade collagen Ⅳ (the main structural ingredient of basilar membrane), and it also plays an important role in tumor vascularization, tumor cell progression, formation of metastatic focus, etc. Tissue inhibitor of metalloproteinase-1 (TIMP-1) can bind with MMP-9 to form 1∶1 compound and inhibit its activity, and can negatively regulate the tumor progression and metastasis.OBJECTIVE: To analyze the relationship of MMP-9 and TIMP-1 expressions with the pathological grade,metastasis and prognosis of malignant peripheral nerve sheath tumor (MPNST).DESIGN: An observational comparative experiment.SETTING: Heze Medical College.PARTICIPANTS: Fifty-eight surgical pathological samples, which were clearly diagnosed to be MPNST,were collected from the pathological laboratory archives in the Department of Pathology, Heze Municipal Hospital from January 1988 to December 2003. The MPNST pathological types were common tumor in 53 cases, malignant triton tumor in 2 cases, epithelial MPNST in 2 cases and MPNST with gland differentiation in 1 case. The pathological grade was grade 1 in 11 cases, grade 2 in 24 cases and grade 3 in 23 cases.Besides, the resected tumor samples of 20 patients with benign peripheral nerve tumor (10 cases of nerve sheath tumor and 10 cases of neurofibromatosis) and the normal peripheral nerves (by-products of some surgeries) of 5 patients were also collected. The samples were used with the approval of the patients.Rat-anti-human MMP-9, TIMP-1 monoclonal antibody and S-P kit were purchased from Fuzhou Maixin Biotechnology, Co.,Ltd.METHODS: The documented paraffin blocks were again prepared to sections of 5 μ m. The expressions of MMP-9 and TIMP-1 in the samples were detected with mmunohistochemical S-P method. The relationships of the MPNST severity, recurrence, metastasis and survival rate with the expressions of MMP-9 and TIMP-1 were analyzed.MAIN OUTCOME MEASURES: Relationships of MMP-9 and TIMP-1

  17. 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. ...

  18. 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

  19. 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

  20. 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

  1. 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,

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

    Lifescience Database Archive (English)

    Full Text Available dition. Following peak picking by using PowerFT (S01 to S16), the metabolite list was prepared from unlabele...hetic pathway. The Medicago seedlings were labeled with 13C, 15N, 18O, and 34S, respectively in the same con

  3. Sample (S): SE3_S02 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE3_S02 Solanum lycopersicum House Momotaro fruit Solanum lycopersicum NCBI taxonom...y:4081 Solanum lycopersicum House Momotaro (ref: http://www.e-taneya.com/item/914.html) are grown at agricultural field under normal film in natural conditions. ...

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

    Lifescience Database Archive (English)

    Full Text Available e Chemical Industries) and were incubated for 21 days. After the stress treatment, frozen aerial parts were ...er watering. Three-week-old plants were incubated in 2-ml tubes with 2 ml o...f water for 3 days in the growth chamber to assess drought stress. The detached leaves of the incuba

  5. Sample (S): SE52_S01 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available s were soaked on MS agar plates and then incubated at 22°C under 16 h day and 8 h night conditions. At 18 days after germination, the aerial parts of the seedlings were harvested. ...

  6. Sample Set (SE): SE13 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available ia oleracea leaf metabolites. 4 cultivers (Nihon, Kanaji, Kurohaminstarland and Wasesaradaakari) and 3 repli...1, Hideyuki Suzuki 1, Tatsuya Suzuki 2, Daisuke Shibata 1, 1: Kazusa DNA Research Inst

  7. 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 network...s. We investigated the metabolic network between wild-type and 2 mutant (methionine-over a...o1 were much lower than those of the wild-type and tt4 plants, indicating the loss of overall network stabil...esting an adaptive reconfiguration of the network. Gene-expression correlations p...resumably responsible for these metabolic networks were determined using the metabolite correlations as clue

  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 Set (SE): SE52 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE52 Mass spectra-based framework for automated structural elucidation of metabolom...e data to explore phytochemical diversity A novel framework for automated elucidation of metabolite structur...te ontology system was also introduced to attain putative characterization of the metabolite signals.The automated

  11. Sample Preparation (SS): SE54_SS01 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available tonitrile in H2O with 25 μM hydroxyphenyl–glucosinolate (GSL) and 50 μM norleucine ...s of each independent mutant and accession were homogenized using a mixer mill MM 200 (Retsch) in 80 μL of extraction buffer [40% ace

  12. 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

  13. Sample Set (SE): SE19 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE19 Grobal triacylglycerol analysis in mouse liver and white adipose tissue (WAT) ...rol (TAG) molecular species from complex lipid mixtures of mouse liver and white adipose tissue (WAT) using

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

    Lifescience Database Archive (English)

    Full Text Available SE55 AtMetExpress development: a phytochemical atlas of arabidopsis development We ...or elucidation of metabolite structure. These are part of the AtMetExpress metabolite accumulation atlas. Ba

  15. 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 ...

  16. Sample Set (SE): SE40 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available 2, 1:Graduate School of Agriculture, Kyoto University, Japan, 2:Kazusa DNA Research Institute, Kazusa Kamat...ari 2-6-7, Kisarazu, Chiba 292-0818, Japan, 3:Kagome Co., Ltd., Japan, 4:Experimental Farm of Kyoto University, Japan Direct Submittion version 1 ...

  17. 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.

  18. 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. ...

  19. Sample Preparation (SS): SE48_SS01 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available 5 % formic acid) to afford nine fractions (Fr.1–9). These fractions were purified using semipreparative HPLC...ining 0.1 %v/v formic acid; and flowrate, 3.0 mL/min. The following compounds were obtained: 1 (4.52 mg), 2

  20. 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. ...

  1. Sample Set (SE): SE48 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE48 Toward better annotation in plant metabolomics: isolation and structure elucidation of 36 special... elucidated the structures of specialized metabolites from rice by using MS/MS and NMR. Thirty-six compounds

  2. Sample Preparation (SS): SE59_SS01 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE59_SS01 Drought stress Three-week-old plants vertically grown on GM plates were i...ncubated in 24-well plates (TPP, http://www.tpp.ch/index.php). Each plant was put in a well with 3 ml water. Three

  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 (S): SE3_S01 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE3_S01 Solanum lycopersicum Lovely ai fruit Solanum lycopersicum NCBI taxonomy:408...1 Solanum lycopersicum Lovely ai (ref: http://www.mikadokyowa.com/Seed/034_tomato/034_lovely_ai/034_lovely_a

  5. Sample Set (SE): SE59 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available iana We reported that flavonoids, a class of specialized metabolites, including flavonols and anthocyanins w...metabolites of drought stress, e.g., proline, raffinose, and galactinol. These findings indicate that flavonols and anthocyanins...n of 5 flavonols and 5 anthocyanins was revealed together with changes in marker ...he aerial part of Arabidopsis (wild type, Col-0) during drought stress by LC-QTO F-MS. Thedrastic alternatio

  6. 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

  7. Sample Set (SE): SE30 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE30 Comparison of seed metabolites among soybean varieties Investigation of Glycin...e max. green seed metabolites. 3 varieties (Kamogawashichiri, Koitozairai, Tanbakuro) data are examined. Tak

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

    Lifescience Database Archive (English)

    Full Text Available tz et al., 2000; Mehrtens et al., 2005). Homozygous WOX1-1 and WOX1-2 were prepared by crossing MYB12OX and ...X1-2. The homozygous MYB12OX/tt4 and pap1-D/tt4 lines were prepared by crossing MYB12OX or pap1-D with tt4,

  9. Sample (S): SE40_S24 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE40_S24 Solanum lycopersicum Kyotemari fruit Solanum lycopersicum NCBI taxonomy:40...81 Solanum lycopersicum Kyotemari fruit are grown in greenhouses of the Experimental Farm of Kyoto University (Takatsuki, Osaka, Japan) from winter 2013 to spring 2014. ...

  10. 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

  11. Sample Set (SE): SE22 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available green, orange, red) data are examined. Yoko Iijima 1, Yukiko Nakamura 2, Yoshiyuki Ogata 1, Kenichi Tanaka ...3, Nozomu Sakurai 1, Kunihiro Suda 1, Tatsuya Suzuki 1, Hideyuki Suzuki 1, Koei O

  12. 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

  13. Sample Set (SE): SE17 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available Sakurai 1, Hideyuki Suzuki 1, Tatsuya Suzuki 2, Daisuke Shibata 1, 1: Kazusa DNA Research Institute, 2: Chiba Prefectural Agriculture Research Center Direct Submittion version 1 ...

  14. Sample Set (SE): SE28 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available mined. Yukiko Nakamura, Takeshi Ara, Takashi Matsuura, Mitsuo Enomoto, Nozomu Sakurai, Hideyuki Suzuki, Daisuke Shibata, Kazusa DNA Research Institute Direct Submittion version 1 ...

  15. Sample Set (SE): SE34 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available examined. Yukiko Nakamura, Takeshi Ara, Takashi Matsuura, Mitsuo Enomoto, Nozomu Sakurai, Hideyuki Suzuki, Daisuke Shibata, Kazusa DNA Research Institute Direct Submittion version 1 ...

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

    Lifescience Database Archive (English)

    Full Text Available in by Orbitrap MS and automated search engine Lipid Search A comprehensive and precise identification of pho...ed search engine Lipid Search. Two tissues, liver (S01) and brain (S02) from mice...spholipid molecular species was established with negative ion mode analyses by high accuracy MS and auto mat

  17. Sample (S): SE57_S08 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available SE57_S08 Lotus japonicus (accessions B129 gifu and MG20 miyakojima) Lotus japonicus... NCBI taxonomy:34305 Lotus japonicus accessions were a gift from Dr. Toshio Aoki (Nihon University, Japan). ...

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

    Lifescience Database Archive (English)

    Full Text Available on bulbs. We performed comprehensive peak picking using the theoretical mass difference (1.99579 Da) between...ass spectrometry (FTICR-MS) coupled with liquid chromatography (LC) as a case study of the metabolite of oni

  19. 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

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

    Lifescience Database Archive (English)

    Full Text Available g common fragmentations in MS/MS data. Using this data resource and database, a case study was conducted for...ccessions (Gifu and Miyakojima) of a model legume Lotus japonicus. In the case study, unknown metabolites we